Reactivity of dinuclear copper(II) complexes towards melanoma cells: Correlation with its stability, tyrosinase mimicking and nuclease activity.

PubMed

Nunes, Cléia Justino; Borges, Beatriz Essenfelder; Nakao, Lia Sumie; Peyroux, Eugénie; Hardré, Renaud; Faure, Bruno; Réglier, Marius; Giorgi, Michel; Prieto, Marcela Bach; Oliveira, Carla Columbano; Da Costa Ferreira, Ana M

2015-08-01

In this work, the influence of two new dinuclear copper(II) complexes in the viability of melanoma cells (B16F10 and TM1MNG3) was investigated, with the aim of verifying possible correlations between their cytotoxicity and their structure. One of the complexes had a polydentate dinucleating amine-imine ligand (complex 2), and the other a tridentate imine and a diamine-bridging ligand (complex 4). The analogous mononuclear copper(II) species (complexes 1 and 3, respectively) were also prepared for comparative studies. Crystal structure determination of complex 2 indicated a square-based pyramidal geometry around each copper, coordinated to three N atoms from the ligand and the remaining sites being occupied by either solvent molecules or counter-ions. Complex 4 has a tetragonal geometry. Interactions of these complexes with human albumin protein (HSA) allowed an estimation of their relative stabilities. Complementary studies of their reactivity towards DNA indicated that all of them are able of causing significant oxidative damage, with single and double strand cleavages, in the presence of hydrogen peroxide. However, nuclease activity of the dinuclear species was very similar and much higher than that of the corresponding mononuclear compounds. Although complex 2, with a more flexible structure, exhibits a much higher tyrosinase activity than complex 4, having a more rigid environment around the metal ion, both complexes showed comparable cytotoxicity towards melanoma cells. Corresponding mononuclear complexes showed to be remarkably less reactive as tyrosinase mimics as well as cytotoxic agents. Moreover, the dinuclear complexes showed higher cytotoxicity towards more melanogenic cells. The obtained results indicated that the structure of these species is decisive for its activity towards the malignant tumor cells tested. Copyright © 2015 Elsevier Inc. All rights reserved.

Correlation of ash-flow tuffs.

USGS Publications Warehouse

Hildreth, W.; Mahood, G.

1985-01-01

Discrimination and correlation of ash-flow sheets is important in structurally complex, long-lived volcanic fields where such sheets provide the best keys to the regional stratigraphic framework. Three-dimensional complexities resulting from pulsatory eruptions, sectorial emplacement, mechanical sorting during outflow, thermal and compositional zoning of magmas, the physical zoning of cooling units, and structural and erosional disruption can make such correlation and discrimination difficult. When lithologic, magnetic, petrographic, chemical, and isotopic criteria for correlating ash-flow sheets are critically evaluated, many problems and pitfalls can be identified. Distinctive phenocrysts, pumice clasts, and lithic fragments are among the more reliable criteria, as are high-precision K-Ar ages and thermal remanent magnetization (TRM) directions in unaltered welded tuff. Chemical correlation methods should rely principally upon welded or nonwelded pumice blocks, not upon the ash-flow matrix, which is subject to fractionation, mixing, and contamination during emplacement. Compositional zoning of most large sheets requires that many samples be analyzed before phenocryst, glass or whole-rock chemical trends can be used confidently as correlation criteria.-Authors

Identifying States of a Financial Market

NASA Astrophysics Data System (ADS)

Münnix, Michael C.; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H.; Guhr, Thomas; Stanley, H. Eugene

2012-09-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical ``market states''. Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Identifying states of a financial market.

PubMed

Münnix, Michael C; Shimada, Takashi; Schäfer, Rudi; Leyvraz, Francois; Seligman, Thomas H; Guhr, Thomas; Stanley, H Eugene

2012-01-01

The understanding of complex systems has become a central issue because such systems exist in a wide range of scientific disciplines. We here focus on financial markets as an example of a complex system. In particular we analyze financial data from the S&P 500 stocks in the 19-year period 1992-2010. We propose a definition of state for a financial market and use it to identify points of drastic change in the correlation structure. These points are mapped to occurrences of financial crises. We find that a wide variety of characteristic correlation structure patterns exist in the observation time window, and that these characteristic correlation structure patterns can be classified into several typical "market states". Using this classification we recognize transitions between different market states. A similarity measure we develop thus affords means of understanding changes in states and of recognizing developments not previously seen.

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

PubMed Central

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A.; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E.

2015-01-01

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives. PMID:26510750

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores

DOE PAGES

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; ...

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinelmore » that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. Furthermore, these results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.« less

Opposite correlations between cation disordering and amorphization resistance in spinels versus pyrochlores.

PubMed

Uberuaga, Blas Pedro; Tang, Ming; Jiang, Chao; Valdez, James A; Smith, Roger; Wang, Yongqiang; Sickafus, Kurt E

2015-10-29

Understanding and predicting radiation damage evolution in complex materials is crucial for developing next-generation nuclear energy sources. Here, using a combination of ion beam irradiation, transmission electron microscopy and X-ray diffraction, we show that, contrary to the behaviour observed in pyrochlores, the amorphization resistance of spinel compounds correlates directly with the energy to disorder the structure. Using a combination of atomistic simulation techniques, we ascribe this behaviour to structural defects on the cation sublattice that are present in spinel but not in pyrochlore. Specifically, because of these structural defects, there are kinetic pathways for the relaxation of disorder in spinel that are absent in pyrochlore. This leads to a direct correlation between amorphization resistance and disordering energetics in spinel, the opposite of that observed in pyrochlores. These results provide new insight into the origins of amorphization resistance in complex oxides beyond fluorite derivatives.

Model correlation and damage location for large space truss structures: Secant method development and evaluation

NASA Technical Reports Server (NTRS)

Smith, Suzanne Weaver; Beattie, Christopher A.

1991-01-01

On-orbit testing of a large space structure will be required to complete the certification of any mathematical model for the structure dynamic response. The process of establishing a mathematical model that matches measured structure response is referred to as model correlation. Most model correlation approaches have an identification technique to determine structural characteristics from the measurements of the structure response. This problem is approached with one particular class of identification techniques - matrix adjustment methods - which use measured data to produce an optimal update of the structure property matrix, often the stiffness matrix. New methods were developed for identification to handle problems of the size and complexity expected for large space structures. Further development and refinement of these secant-method identification algorithms were undertaken. Also, evaluation of these techniques is an approach for model correlation and damage location was initiated.

Structure-Activity Relationship in TLR4 Mutations: Atomistic Molecular Dynamics Simulations and Residue Interaction Network Analysis

NASA Astrophysics Data System (ADS)

Anwar, Muhammad Ayaz; Choi, Sangdun

2017-03-01

Toll-like receptor 4 (TLR4), a vital innate immune receptor present on cell surfaces, initiates a signaling cascade during danger and bacterial intrusion. TLR4 needs to form a stable hexamer complex, which is necessary to dimerize the cytoplasmic domain. However, D299G and T399I polymorphism may abrogate the stability of the complex, leading to compromised TLR4 signaling. Crystallography provides valuable insights into the structural aspects of the TLR4 ectodomain; however, the dynamic behavior of polymorphic TLR4 is still unclear. Here, we employed molecular dynamics simulations (MDS), as well as principal component and residue network analyses, to decipher the structural aspects and signaling propagation associated with mutations in TLR4. The mutated complexes were less cohesive, displayed local and global variation in the secondary structure, and anomalous decay in rotational correlation function. Principal component analysis indicated that the mutated complexes also exhibited distinct low-frequency motions, which may be correlated to the differential behaviors of these TLR4 variants. Moreover, residue interaction networks (RIN) revealed that the mutated TLR4/myeloid differentiation factor (MD) 2 complex may perpetuate abnormal signaling pathways. Cumulatively, the MDS and RIN analyses elucidated the mutant-specific conformational alterations, which may help in deciphering the mechanism of loss-of-function mutations.

Sequence co-evolution gives 3D contacts and structures of protein complexes

PubMed Central

Hopf, Thomas A; Schärfe, Charlotta P I; Rodrigues, João P G L M; Green, Anna G; Kohlbacher, Oliver; Sander, Chris; Bonvin, Alexandre M J J; Marks, Debora S

2014-01-01

Protein–protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions, and structural biology has provided detailed functional insight for select 3D protein complexes. An alternative rich source of information about protein interactions is the evolutionary sequence record. Building on earlier work, we show that analysis of correlated evolutionary sequence changes across proteins identifies residues that are close in space with sufficient accuracy to determine the three-dimensional structure of the protein complexes. We evaluate prediction performance in blinded tests on 76 complexes of known 3D structure, predict protein–protein contacts in 32 complexes of unknown structure, and demonstrate how evolutionary couplings can be used to distinguish between interacting and non-interacting protein pairs in a large complex. With the current growth of sequences, we expect that the method can be generalized to genome-wide elucidation of protein–protein interaction networks and used for interaction predictions at residue resolution. DOI: http://dx.doi.org/10.7554/eLife.03430.001 PMID:25255213

The q-dependent detrended cross-correlation analysis of stock market

NASA Astrophysics Data System (ADS)

Zhao, Longfeng; Li, Wei; Fenu, Andrea; Podobnik, Boris; Wang, Yougui; Stanley, H. Eugene

2018-02-01

Properties of the q-dependent cross-correlation matrices of the stock market have been analyzed by using random matrix theory and complex networks. The correlation structures of the fluctuations at different magnitudes have unique properties. The cross-correlations among small fluctuations are much stronger than those among large fluctuations. The large and small fluctuations are dominated by different groups of stocks. We use complex network representation to study these q-dependent matrices and discover some new identities. By utilizing those q-dependent correlation-based networks, we are able to construct some portfolios of those more independent stocks which consistently perform better. The optimal multifractal order for portfolio optimization is around q  =  2 under the mean-variance portfolio framework, and q\\in[2, 6] under the expected shortfall criterion. These results have deepened our understanding regarding the collective behavior of the complex financial system.

The Correlation Entropy as a Measure of the Complexity of High-Lying Single-Particle Modes

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

Stoyanov, Chavdar; Zelevinsky, Vladimir; Department of Physics and Astronomy, Michigan State University, East Lansing, Michigan 48824-1321

Highly-excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phonon-like modes of the core. In the framework of the quasiparticle-phonon model we consider the structure of resulting complex configurations using the 1k17/2 orbital in 209Pb as an example. The eigenstates of the model carry significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the system undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks.

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

DOE PAGES

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.; ...

2017-11-17

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

Influence of Countercation Hydration Enthalpies on the Formation of Molecular Complexes: A Thorium–Nitrate Example

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

Jin, Geng Bang; Lin, Jian; Estes, Shanna L.

Here, the influence of countercations (A n+) in directing the composition of monomeric metal–ligand (ML) complexes that precipitate from solution are often overlooked despite the wide usage of A n+ in materials synthesis. Herein, we describe a correlation between the composition of ML complexes and A + hydration enthalpies found for two related series of thorium (Th)–nitrate molecular compounds obtained by evaporating acidic aqueous Th–nitrate solutions in the presence of A + counterions. Analyses of their chemical composition and solid-state structures demonstrate that A + not only affects the overall solid-state packing of the Th–nitrato complexes but also influences themore » composition of the Th–nitrato monomeric anions themselves. Trends in composition and structure are found to correlate with A + hydration enthalpies, such that the A + with smaller hydration enthalpies associate with less hydrated and more anionic Th–nitrato complexes. This perspective, broader than the general assumption of size and charge as the dominant influence of A n+, opens a new avenue for the design and synthesis of targeted metal–ligand complexes.« less

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

PubMed

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

2016-01-01

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

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

PubMed Central

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

2016-01-01

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

Local shear stress and its correlation with local volume fraction in concentrated non-Brownian suspensions: Lattice Boltzmann simulation

NASA Astrophysics Data System (ADS)

Lee, Young Ki; Ahn, Kyung Hyun; Lee, Seung Jong

2014-12-01

The local shear stress of non-Brownian suspensions was investigated using the lattice Boltzmann method coupled with the smoothed profile method. Previous studies have only focused on the bulk rheology of complex fluids because the local rheology of complex fluids was not accessible due to technical limitations. In this study, the local shear stress of two-dimensional solid particle suspensions in Couette flow was investigated with the method of planes to correlate non-Newtonian fluid behavior with the structural evolution of concentrated particle suspensions. Shear thickening was successfully captured for highly concentrated suspensions at high particle Reynolds number, and both the local rheology and local structure of the suspensions were analyzed. It was also found that the linear correlation between the local particle stress and local particle volume fraction was dramatically reduced during shear thickening. These results clearly show how the change in local structure of suspensions influences the local and bulk rheology of the suspensions.

Cationic liposome/DNA complexes: from structure to interactions with cellular membranes.

PubMed

Caracciolo, Giulio; Amenitsch, Heinz

2012-10-01

Gene-based therapeutic approaches are based upon the concept that, if a disease is caused by a mutation in a gene, then adding back the wild-type gene should restore regular function and attenuate the disease phenotype. To deliver the gene of interest, both viral and nonviral vectors are used. Viruses are efficient, but their application is impeded by detrimental side-effects. Among nonviral vectors, cationic liposomes are the most promising candidates for gene delivery. They form stable complexes with polyanionic DNA (lipoplexes). Despite several advantages over viral vectors, the transfection efficiency (TE) of lipoplexes is too low compared with those of engineered viral vectors. This is due to lack of knowledge about the interactions between complexes and cellular components. Rational design of efficient lipoplexes therefore requires deeper comprehension of the interactions between the vector and the DNA as well as the cellular pathways and mechanisms involved. The importance of the lipoplex structure in biological function is revealed in the application of synchrotron small-angle X-ray scattering in combination with functional TE measurements. According to current understanding, the structure of lipoplexes can change upon interaction with cellular membranes and such changes affect the delivery efficiency. Recently, a correlation between the mechanism of gene release from complexes, the structure, and the physical and chemical parameters of the complexes has been established. Studies aimed at correlating structure and activity of lipoplexes are reviewed herein. This is a fundamental step towards rational design of highly efficient lipid gene vectors.

Inference of Functionally-Relevant N-acetyltransferase Residues Based on Statistical Correlations.

PubMed

Neuwald, Andrew F; Altschul, Stephen F

2016-12-01

Over evolutionary time, members of a superfamily of homologous proteins sharing a common structural core diverge into subgroups filling various functional niches. At the sequence level, such divergence appears as correlations that arise from residue patterns distinct to each subgroup. Such a superfamily may be viewed as a population of sequences corresponding to a complex, high-dimensional probability distribution. Here we model this distribution as hierarchical interrelated hidden Markov models (hiHMMs), which describe these sequence correlations implicitly. By characterizing such correlations one may hope to obtain information regarding functionally-relevant properties that have thus far evaded detection. To do so, we infer a hiHMM distribution from sequence data using Bayes' theorem and Markov chain Monte Carlo (MCMC) sampling, which is widely recognized as the most effective approach for characterizing a complex, high dimensional distribution. Other routines then map correlated residue patterns to available structures with a view to hypothesis generation. When applied to N-acetyltransferases, this reveals sequence and structural features indicative of functionally important, yet generally unknown biochemical properties. Even for sets of proteins for which nothing is known beyond unannotated sequences and structures, this can lead to helpful insights. We describe, for example, a putative coenzyme-A-induced-fit substrate binding mechanism mediated by arginine residue switching between salt bridge and π-π stacking interactions. A suite of programs implementing this approach is available (psed.igs.umaryland.edu).

Temporal Structure of Support Surface Translations Drive the Temporal Structure of Postural Control During Standing

PubMed Central

Rand, Troy J.; Myers, Sara A.; Kyvelidou, Anastasia; Mukherjee, Mukul

2015-01-01

A healthy biological system is characterized by a temporal structure that exhibits fractal properties and is highly complex. Unhealthy systems demonstrate lowered complexity and either greater or less predictability in the temporal structure of a time series. The purpose of this research was to determine if support surface translations with different temporal structures would affect the temporal structure of the center of pressure (COP) signal. Eight healthy young participants stood on a force platform that was translated in the anteroposterior direction for input conditions of varying complexity: white noise, pink noise, brown noise, and sine wave. Detrended fluctuation analysis was used to characterize the long-range correlations of the COP time series in the AP direction. Repeated measures ANOVA revealed differences among conditions (P < .001). The less complex support surface translations resulted in a less complex COP compared to normal standing. A quadratic trend analysis demonstrated an inverted-u shape across an increasing order of predictability of the conditions (P < .001). The ability to influence the complexity of postural control through support surface translations can have important implications for rehabilitation. PMID:25994281

The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

NASA Technical Reports Server (NTRS)

Wolf, David R.

2004-01-01

The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

Structure of amplitude correlations in open chaotic systems

NASA Astrophysics Data System (ADS)

Ericson, Torleif E. O.

2013-02-01

The Verbaarschot-Weidenmüller-Zirnbauer (VWZ) model is believed to correctly represent the correlations of two S-matrix elements for an open quantum chaotic system, but the solution has considerable complexity and is presently only accessed numerically. Here a procedure is developed to deduce its features over the full range of the parameter space in a transparent and simple analytical form preserving accuracy to a considerable degree. The bulk of the VWZ correlations are described by the Gorin-Seligman expression for the two-amplitude correlations of the Ericson-Gorin-Seligman model. The structure of the remaining correction factors for correlation functions is discussed with special emphasis of the rôle of the level correlation hole both for inelastic and elastic correlations.

Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

NASA Technical Reports Server (NTRS)

Alterovitz, Samuel A.; Sekula-Moise, Patricia A.; Sieg, Robert M.; Drotos, Mark N.; Bogner, Nancy A.

1992-01-01

An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

The Dichotomy in Degree Correlation of Biological Networks

PubMed Central

Hao, Dapeng; Li, Chuanxing

2011-01-01

Most complex networks from different areas such as biology, sociology or technology, show a correlation on node degree where the possibility of a link between two nodes depends on their connectivity. It is widely believed that complex networks are either disassortative (links between hubs are systematically suppressed) or assortative (links between hubs are enhanced). In this paper, we analyze a variety of biological networks and find that they generally show a dichotomous degree correlation. We find that many properties of biological networks can be explained by this dichotomy in degree correlation, including the neighborhood connectivity, the sickle-shaped clustering coefficient distribution and the modularity structure. This dichotomy distinguishes biological networks from real disassortative networks or assortative networks such as the Internet and social networks. We suggest that the modular structure of networks accounts for the dichotomy in degree correlation and vice versa, shedding light on the source of modularity in biological networks. We further show that a robust and well connected network necessitates the dichotomy of degree correlation, suggestive of an evolutionary motivation for its existence. Finally, we suggest that a dichotomous degree correlation favors a centrally connected modular network, by which the integrity of network and specificity of modules might be reconciled. PMID:22164269

Characterization of structural and electrostatic complexity in pentacene thin films by scanning probe microscopy

NASA Astrophysics Data System (ADS)

Puntambekar, Kanan Prakash

The advancement of organic electronics for applications in solar energy conversion, printed circuitry, displays, and solid-state lighting depends upon optimization of structure and properties for a variety of organic semiconductor interfaces. Organic semiconductor/insulator (O/I) and organic-metal (O/M) interfaces, in particular, are critical to the operation of organic thin film transistors (OTFTs) currently being developed for printed flexible electronics. Scanning probe microscopy (SPM) is a powerful tool to isolate and characterize the bottlenecks to charge transport at these interfaces. This thesis establishes a direct correlation between the structural disorder and electrical complexity at these interfaces, using various SPM based methods and discusses the implications of such complexity on device performance. To examine the O/M interfaces, surface potentials of operating pentacene TFTs with two different contact geometries (bottom or top) were mapped by Kelvin probe force microscopy (KFM). The surface potential distribution was used to isolate the potential drops at the source and drain contacts. Simultaneously obtained topography and surface potential maps elucidated the correlation between the morphology and contact resistance at the O/M interface; the bottom contact TFTs were observed to be contact limited at large gate voltages, while the top contact TFTs were not contact limited. A direct correlation between structural defects and electric potential variations at the pentacene and silicon dioxide, a common insulator, is demonstrated. Lateral force microscopy (LFM) generates striking images of the polycrystalline microstructure of a monolayer thick pentacene film, allowing clear visualization of the grain boundary network. Further more, surface potential wells localized at the grain boundaries were observed by KFM, suggesting that the grain boundaries may serve as charge carrier (hole) traps. Line dislocations were also revealed in the second monolayer by chemical etching and SPM and produce strong variations in the surface potential that must affect the interfacial charge conductance. Structural disorder at the O/I and O/M interfaces degrades both injection and transport of charge, and therefore needs to be minimized. Thus both visualization and correlation of structural and electrical complexity at these interfaces have important implications for understanding electrical transport in OTFTs and for defining strategies to improve device performance.

Structure determination of a key intermediate of the enantioselective Pd complex catalyzed allylic substitution reaction

PubMed

Junker; Reif; Steinhagen; Junker; Felli; Reggelin; Griesinger

2000-09-01

The structure of a catalytic intermediate with important implications for the interpretation of the stereochemical outcome of the palladium complex catalyzed allylic substitution with phosphino-oxazoline (PHOX) ligands is determined by liquid state NMR. The complex displays a novel structure that is highly distorted compared with other palladium eta2-olefin complexes known so far. The structure has been determined from nuclear overhauser data (NOE), scalar coupling constants, and long range projection angle restraints derived from dipole dipole cross-correlated relaxation of multiple quantum coherence. The latter restraints have been implemented into a distance geometry protocol. The projection angle restraints yield a higher precision in the determination of the relative orientation of the two molecular moieties and are essential to provide an exact structural definition of the olefinic part of the catalytic intermediate with respect to the ligand.

Lipidomics of glycosphingolipids.

PubMed

Farwanah, Hany; Kolter, Thomas

2012-02-02

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed.

Lipidomics of Glycosphingolipids

PubMed Central

Farwanah, Hany; Kolter, Thomas

2012-01-01

Glycosphingolipids (GSLs) contain one or more sugars that are attached to a sphingolipid moiety, usually to a ceramide, but in rare cases also to a sphingoid base. A large structural heterogeneity results from differences in number, identity, linkage, and anomeric configuration of the carbohydrate residues, and also from structural differences within the hydrophobic part. GSLs form complex cell-type specific patterns, which change with the species, the cellular differentiation state, viral transformation, ontogenesis, and oncogenesis. Although GSL structures can be assigned to only a few series with a common carbohydrate core, their structural variety and the complex pattern are challenges for their elucidation and quantification by mass spectrometric techniques. We present a general overview of the application of lipidomics for GSL determination. This includes analytical procedures and instrumentation together with recent correlations of GSL molecular species with human diseases. Difficulties such as the structural complexity and the lack of standard substances for complex GSLs are discussed. PMID:24957371

Small-world bias of correlation networks: From brain to climate

NASA Astrophysics Data System (ADS)

Hlinka, Jaroslav; Hartman, David; Jajcay, Nikola; Tomeček, David; Tintěra, Jaroslav; Paluš, Milan

2017-03-01

Complex systems are commonly characterized by the properties of their graph representation. Dynamical complex systems are then typically represented by a graph of temporal dependencies between time series of state variables of their subunits. It has been shown recently that graphs constructed in this way tend to have relatively clustered structure, potentially leading to spurious detection of small-world properties even in the case of systems with no or randomly distributed true interactions. However, the strength of this bias depends heavily on a range of parameters and its relevance for real-world data has not yet been established. In this work, we assess the relevance of the bias using two examples of multivariate time series recorded in natural complex systems. The first is the time series of local brain activity as measured by functional magnetic resonance imaging in resting healthy human subjects, and the second is the time series of average monthly surface air temperature coming from a large reanalysis of climatological data over the period 1948-2012. In both cases, the clustering in the thresholded correlation graph is substantially higher compared with a realization of a density-matched random graph, while the shortest paths are relatively short, showing thus distinguishing features of small-world structure. However, comparable or even stronger small-world properties were reproduced in correlation graphs of model processes with randomly scrambled interconnections. This suggests that the small-world properties of the correlation matrices of these real-world systems indeed do not reflect genuinely the properties of the underlying interaction structure, but rather result from the inherent properties of correlation matrix.

Small-world bias of correlation networks: From brain to climate.

PubMed

Hlinka, Jaroslav; Hartman, David; Jajcay, Nikola; Tomeček, David; Tintěra, Jaroslav; Paluš, Milan

2017-03-01

Complex systems are commonly characterized by the properties of their graph representation. Dynamical complex systems are then typically represented by a graph of temporal dependencies between time series of state variables of their subunits. It has been shown recently that graphs constructed in this way tend to have relatively clustered structure, potentially leading to spurious detection of small-world properties even in the case of systems with no or randomly distributed true interactions. However, the strength of this bias depends heavily on a range of parameters and its relevance for real-world data has not yet been established. In this work, we assess the relevance of the bias using two examples of multivariate time series recorded in natural complex systems. The first is the time series of local brain activity as measured by functional magnetic resonance imaging in resting healthy human subjects, and the second is the time series of average monthly surface air temperature coming from a large reanalysis of climatological data over the period 1948-2012. In both cases, the clustering in the thresholded correlation graph is substantially higher compared with a realization of a density-matched random graph, while the shortest paths are relatively short, showing thus distinguishing features of small-world structure. However, comparable or even stronger small-world properties were reproduced in correlation graphs of model processes with randomly scrambled interconnections. This suggests that the small-world properties of the correlation matrices of these real-world systems indeed do not reflect genuinely the properties of the underlying interaction structure, but rather result from the inherent properties of correlation matrix.

Genetic Structure of Bluefin Tuna in the Mediterranean Sea Correlates with Environmental Variables

PubMed Central

Riccioni, Giulia; Stagioni, Marco; Landi, Monica; Ferrara, Giorgia; Barbujani, Guido; Tinti, Fausto

2013-01-01

Background Atlantic Bluefin Tuna (ABFT) shows complex demography and ecological variation in the Mediterranean Sea. Genetic surveys have detected significant, although weak, signals of population structuring; catch series analyses and tagging programs identified complex ABFT spatial dynamics and migration patterns. Here, we tested the hypothesis that the genetic structure of the ABFT in the Mediterranean is correlated with mean surface temperature and salinity. Methodology We used six samples collected from Western and Central Mediterranean integrated with a new sample collected from the recently identified easternmost reproductive area of Levantine Sea. To assess population structure in the Mediterranean we used a multidisciplinary framework combining classical population genetics, spatial and Bayesian clustering methods and a multivariate approach based on factor analysis. Conclusions FST analysis and Bayesian clustering methods detected several subpopulations in the Mediterranean, a result also supported by multivariate analyses. In addition, we identified significant correlations of genetic diversity with mean salinity and surface temperature values revealing that ABFT is genetically structured along two environmental gradients. These results suggest that a preference for some spawning habitat conditions could contribute to shape ABFT genetic structuring in the Mediterranean. However, further studies should be performed to assess to what extent ABFT spawning behaviour in the Mediterranean Sea can be affected by environmental variation. PMID:24260341

PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps.

PubMed

Kuzu, Guray; Keskin, Ozlem; Nussinov, Ruth; Gursoy, Attila

2016-10-01

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

World currency exchange rate cross-correlations

NASA Astrophysics Data System (ADS)

Droå¼dż, S.; Górski, A. Z.; Kwapień, J.

2007-08-01

World currency network constitutes one of the most complex structures that is associated with the contemporary civilization. On a way towards quantifying its characteristics we study the cross correlations in changes of the daily foreign exchange rates within the basket of 60 currencies in the period December 1998 May 2005. Such a dynamics turns out to predominantly involve one outstanding eigenvalue of the correlation matrix. The magnitude of this eigenvalue depends however crucially on which currency is used as a base currency for the remaining ones. Most prominent it looks from the perspective of a peripheral currency. This largest eigenvalue is seen to systematically decrease and thus the structure of correlations becomes more heterogeneous, when more significant currencies are used as reference. An extreme case in this later respect is the USD in the period considered. Besides providing further insight into subtle nature of complexity, these observations point to a formal procedure that in general can be used for practical purposes of measuring the relative currencies significance on various time horizons.

Protein-ligand binding free energy estimation using molecular mechanics and continuum electrostatics. Application to HIV-1 protease inhibitors

NASA Astrophysics Data System (ADS)

Zoete, V.; Michielin, O.; Karplus, M.

2003-12-01

A method is proposed for the estimation of absolute binding free energy of interaction between proteins and ligands. Conformational sampling of the protein-ligand complex is performed by molecular dynamics (MD) in vacuo and the solvent effect is calculated a posteriori by solving the Poisson or the Poisson-Boltzmann equation for selected frames of the trajectory. The binding free energy is written as a linear combination of the buried surface upon complexation, SAS bur, the electrostatic interaction energy between the ligand and the protein, Eelec, and the difference of the solvation free energies of the complex and the isolated ligand and protein, ΔGsolv. The method uses the buried surface upon complexation to account for the non-polar contribution to the binding free energy because it is less sensitive to the details of the structure than the van der Waals interaction energy. The parameters of the method are developed for a training set of 16 HIV-1 protease-inhibitor complexes of known 3D structure. A correlation coefficient of 0.91 was obtained with an unsigned mean error of 0.8 kcal/mol. When applied to a set of 25 HIV-1 protease-inhibitor complexes of unknown 3D structures, the method provides a satisfactory correlation between the calculated binding free energy and the experimental pIC 50 without reparametrization.

Evaluating Abstract Art: Relation between Term Usage, Subjective Ratings, Image Properties and Personality Traits.

PubMed

Lyssenko, Nathalie; Redies, Christoph; Hayn-Leichsenring, Gregor U

2016-01-01

One of the major challenges in experimental aesthetics is the uncertainty of the terminology used in experiments. In this study, we recorded terms that are spontaneously used by participants to describe abstract artworks and studied their relation to the second-order statistical image properties of the same artworks (Experiment 1). We found that the usage frequency of some structure-describing terms correlates with statistical image properties, such as PHOG Self-Similarity, Anisotropy and Complexity. Additionally, emotion-associated terms correlate with measured color values. Next, based on the most frequently used terms, we created five different rating scales (Experiment 2) and obtained ratings of participants for the abstract paintings on these scales. We found significant correlations between descriptive score ratings (e.g., between structure and subjective complexity), between evaluative and descriptive score ratings (e.g., between preference and subjective complexity/interest) and between descriptive score ratings and statistical image properties (e.g., between interest and PHOG Self-Similarity, Complexity and Anisotropy). Additionally, we determined the participants' personality traits as described in the 'Big Five Inventory' (Goldberg, 1990; Rammstedt and John, 2005) and correlated them with the ratings and preferences of individual participants. Participants with higher scores for Neuroticism showed preferences for objectively more complex images, as well as a different notion of the term complex when compared with participants with lower scores for Neuroticism. In conclusion, this study demonstrates an association between objectively measured image properties and the subjective terms that participants use to describe or evaluate abstract artworks. Moreover, our results suggest that the description of abstract artworks, their evaluation and the preference of participants for their low-level statistical properties are linked to personality traits.

Evaluating Abstract Art: Relation between Term Usage, Subjective Ratings, Image Properties and Personality Traits

PubMed Central

Lyssenko, Nathalie; Redies, Christoph; Hayn-Leichsenring, Gregor U.

2016-01-01

One of the major challenges in experimental aesthetics is the uncertainty of the terminology used in experiments. In this study, we recorded terms that are spontaneously used by participants to describe abstract artworks and studied their relation to the second-order statistical image properties of the same artworks (Experiment 1). We found that the usage frequency of some structure-describing terms correlates with statistical image properties, such as PHOG Self-Similarity, Anisotropy and Complexity. Additionally, emotion-associated terms correlate with measured color values. Next, based on the most frequently used terms, we created five different rating scales (Experiment 2) and obtained ratings of participants for the abstract paintings on these scales. We found significant correlations between descriptive score ratings (e.g., between structure and subjective complexity), between evaluative and descriptive score ratings (e.g., between preference and subjective complexity/interest) and between descriptive score ratings and statistical image properties (e.g., between interest and PHOG Self-Similarity, Complexity and Anisotropy). Additionally, we determined the participants’ personality traits as described in the ‘Big Five Inventory’ (Goldberg, 1990; Rammstedt and John, 2005) and correlated them with the ratings and preferences of individual participants. Participants with higher scores for Neuroticism showed preferences for objectively more complex images, as well as a different notion of the term complex when compared with participants with lower scores for Neuroticism. In conclusion, this study demonstrates an association between objectively measured image properties and the subjective terms that participants use to describe or evaluate abstract artworks. Moreover, our results suggest that the description of abstract artworks, their evaluation and the preference of participants for their low-level statistical properties are linked to personality traits. PMID:27445933

Density functional studies on the exchange interaction of a dinuclear Gd(iii)-Cu(ii) complex: method assessment, magnetic coupling mechanism and magneto-structural correlations.

PubMed

Rajaraman, Gopalan; Totti, Federico; Bencini, Alessandro; Caneschi, Andrea; Sessoli, Roberta; Gatteschi, Dante

2009-05-07

Density functional calculations have been performed on a [Gd(iii)Cu(ii)] complex [L(1)CuGd(O(2)CCF(3))(3)(C(2)H(5)OH)(2)] () (where L(1) is N,N'-bis(3-ethoxy-salicylidene)-1,2-diamino-2-methylpropanato) with an aim of assessing a suitable functional within the DFT formalism to understand the mechanism of magnetic coupling and also to develop magneto-structural correlations. Encouraging results have been obtained in our studies where the application of B3LYP on the crystal structure of yields a ferromagnetic J value of -5.8 cm(-1) which is in excellent agreement with the experimental value of -4.42 cm(-1) (H = JS(Gd).S(Cu)). After testing varieties of functional for the method assessment we recommend the use of B3LYP with a combination of an effective core potential basis set. For all electron basis sets the relativistic effects should be incorporated either via the Douglas-Kroll-Hess (DKH) or zeroth-order regular approximation (ZORA) methods. A breakdown approach has been adopted where the calculations on several model complexes of have been performed. Their wave functions have been analysed thereafter (MO and NBO analysis) in order to gain some insight into the coupling mechanism. The results suggest, unambiguously, that the empty Gd(iii) 5d orbitals have a prominent role on the magnetic coupling. These 5d orbitals gain partial occupancy via Cu(ii) charge transfer as well as from the Gd(iii) 4f orbitals. A competing 4f-3d interaction associated with the symmetry of the complex has also been observed. The general mechanism hence incorporates both contributions and sets forth rather a prevailing mechanism for the 3d-4f coupling. The magneto-structural correlations reveal that there is no unique parameter which the J values are strongly correlated with, but an exponential relation to the J value found for the O-Cu-O-Gd dihedral angle parameter is the most credible correlation.

Symmetry Groups of the Austenite Lattice and Construction of Self-Accommodation Complexes of Martensite Crystals in Alloys with the Shape-Memory Effect

NASA Astrophysics Data System (ADS)

Khundjua, A. G.; Ptitsin, A. G.; Brovkina, E. A.

2018-01-01

The internal structure of experimentally observed self-accommodation complexes of martensite crystals, which is determined by the system of twinning planes, is studied in this work. The direct correlation of the construction type of the complexes with the subgroups of the austenite lattice symmetry group is shown.

Brain architecture and social complexity in modern and ancient birds.

PubMed

Burish, Mark J; Kueh, Hao Yuan; Wang, Samuel S-H

2004-01-01

Vertebrate brains vary tremendously in size, but differences in form are more subtle. To bring out functional contrasts that are independent of absolute size, we have normalized brain component sizes to whole brain volume. The set of such volume fractions is the cerebrotype of a species. Using this approach in mammals we previously identified specific associations between cerebrotype and behavioral specializations. Among primates, cerebrotypes are linked principally to enlargement of the cerebral cortex and are associated with increases in the complexity of social structure. Here we extend this analysis to include a second major vertebrate group, the birds. In birds the telencephalic volume fraction is strongly correlated with social complexity. This correlation accounts for almost half of the observed variation in telencephalic size, more than any other behavioral specialization examined, including the ability to learn song. A prominent exception to this pattern is owls, which are not social but still have very large forebrains. Interpolating the overall correlation for Archaeopteryx, an ancient bird, suggests that its social complexity was likely to have been on a par with modern domesticated chickens. Telencephalic volume fraction outperforms residuals-based measures of brain size at separating birds by social structure. Telencephalic volume fraction may be an anatomical substrate for social complexity, and perhaps cognitive ability, that can be generalized across a range of vertebrate brains, including dinosaurs. Copyright 2004 S. Karger AG, Basel

Modulation of electronic structures of bases through DNA recognition of protein.

PubMed

Hagiwara, Yohsuke; Kino, Hiori; Tateno, Masaru

2010-04-21

The effects of environmental structures on the electronic states of functional regions in a fully solvated DNA·protein complex were investigated using combined ab initio quantum mechanics/molecular mechanics calculations. A complex of a transcriptional factor, PU.1, and the target DNA was used for the calculations. The effects of solvent on the energies of molecular orbitals (MOs) of some DNA bases strongly correlate with the magnitude of masking of the DNA bases from the solvent by the protein. In the complex, PU.1 causes a variation in the magnitude among DNA bases by means of directly recognizing the DNA bases through hydrogen bonds and inducing structural changes of the DNA structure from the canonical one. Thus, the strong correlation found in this study is the first evidence showing the close quantitative relationship between recognition modes of DNA bases and the energy levels of the corresponding MOs. Thus, it has been revealed that the electronic state of each base is highly regulated and organized by the DNA recognition of the protein. Other biological macromolecular systems can be expected to also possess similar modulation mechanisms, suggesting that this finding provides a novel basis for the understanding for the regulation functions of biological macromolecular systems.

Structure of calmodulin complexed with an olfactory CNG channel fragment and role of the central linker: residual dipolar couplings to evaluate calmodulin binding modes outside the kinase family.

PubMed

Contessa, Gian Marco; Orsale, Maria; Melino, Sonia; Torre, Vincent; Paci, Maurizio; Desideri, Alessandro; Cicero, Daniel O

2005-03-01

The NMR high-resolution structure of calmodulin complexed with a fragment of the olfactory cyclic-nucleotide gated channel is described. This structure shows features that are unique for this complex, including an active role of the linker connecting the N- and C-lobes of calmodulin upon binding of the peptide. Such linker is not only involved in the formation of an hydrophobic pocket to accommodate a bulky peptide residue, but it also provides a positively charged region complementary to a negative charge of the target. This complex of calmodulin with a target not belonging to the kinase family was used to test the residual dipolar coupling (RDC) approach for the determination of calmodulin binding modes to peptides. Although the complex here characterized belongs to the (1--14) family, high Q values were obtained with all the 1:1 complexes for which crystalline structures are available. Reduction of the RDC data set used for the correlation analysis to structured regions of the complex allowed a clear identification of the binding mode. Excluded regions comprise calcium binding loops and loops connecting the EF-hand motifs.

Community structure from spectral properties in complex networks

NASA Astrophysics Data System (ADS)

Servedio, V. D. P.; Colaiori, F.; Capocci, A.; Caldarelli, G.

2005-06-01

We analyze the spectral properties of complex networks focusing on their relation to the community structure, and develop an algorithm based on correlations among components of different eigenvectors. The algorithm applies to general weighted networks, and, in a suitably modified version, to the case of directed networks. Our method allows to correctly detect communities in sharply partitioned graphs, however it is useful to the analysis of more complex networks, without a well defined cluster structure, as social and information networks. As an example, we test the algorithm on a large scale data-set from a psychological experiment of free word association, where it proves to be successful both in clustering words, and in uncovering mental association patterns.

Modeling the pressure-strain correlation of turbulence: An invariant dynamical systems approach

NASA Technical Reports Server (NTRS)

Speziale, Charles G.; Sarkar, Sutanu; Gatski, Thomas B.

1990-01-01

The modeling of the pressure-strain correlation of turbulence is examined from a basic theoretical standpoint with a view toward developing improved second-order closure models. Invariance considerations along with elementary dynamical systems theory are used in the analysis of the standard hierarchy of closure models. In these commonly used models, the pressure-strain correlation is assumed to be a linear function of the mean velocity gradients with coefficients that depend algebraically on the anisotropy tensor. It is proven that for plane homogeneous turbulent flows the equilibrium structure of this hierarchy of models is encapsulated by a relatively simple model which is only quadratically nonlinear in the anisotropy tensor. This new quadratic model - the SSG model - is shown to outperform the Launder, Reece, and Rodi model (as well as more recent models that have a considerably more complex nonlinear structure) in a variety of homogeneous turbulent flows. Some deficiencies still remain for the description of rotating turbulent shear flows that are intrinsic to this general hierarchy of models and, hence, cannot be overcome by the mere introduction of more complex nonlinearities. It is thus argued that the recent trend of adding substantially more complex nonlinear terms containing the anisotropy tensor may be of questionable value in the modeling of the pressure-strain correlation. Possible alternative approaches are discussed briefly.

Modelling the pressure-strain correlation of turbulence - An invariant dynamical systems approach

NASA Technical Reports Server (NTRS)

Speziale, Charles G.; Sarkar, Sutanu; Gatski, Thomas B.

1991-01-01

The modeling of the pressure-strain correlation of turbulence is examined from a basic theoretical standpoint with a view toward developing improved second-order closure models. Invariance considerations along with elementary dynamical systems theory are used in the analysis of the standard hierarchy of closure models. In these commonly used models, the pressure-strain correlation is assumed to be a linear function of the mean velocity gradients with coefficients that depend algebraically on the anisotropy tensor. It is proven that for plane homogeneous turbulent flows the equilibrium structure of this hierarchy of models is encapsulated by a relatively simple model which is only quadratically nonlinear in the anisotropy tensor. This new quadratic model - the SSG model - is shown to outperform the Launder, Reece, and Rodi model (as well as more recent models that have a considerably more complex nonlinear structure) in a variety of homogeneous turbulent flows. Some deficiencies still remain for the description of rotating turbulent shear flows that are intrinsic to this general hierarchy of models and, hence, cannot be overcome by the mere introduction of more complex nonlinearities. It is thus argued that the recent trend of adding substantially more complex nonlinear terms containing the anisotropy tensor may be of questionable value in the modeling of the pressure-strain correlation. Possible alternative approaches are discussed briefly.

Changes in habitat complexity negatively affect diverse gastropod assemblages in coralline algal turf.

PubMed

Kelaher, B P

2003-05-01

The physical structure of a habitat generally has a strong influence on the diversity and abundance of associated organisms. I investigated the role of coralline algal turf structure in determining spatial variation of gastropod assemblages at different tidal heights of a rocky shore near Sydney, Australia. The structural characteristics of algal turf tested were frond density (or structural complexity) and frond length (the vertical scale over which structural complexity was measured). This definition of structural complexity assumes that complexity of the habitat increases with increasing frond density. While frond length was unrelated to gastropod community structure, I found significant correlations between density of fronds and multivariate and univariate measures of gastropod assemblages, indicating the importance of structural complexity. In contrast to previous studies, here there were negative relationships between the density of fronds and the richness and abundance of gastropods. Artificial habitat mimics were used to manipulate the density of fronds to test the hypothesis that increasing algal structural complexity decreases the richness and abundance of gastropods. As predicted, there were significantly more species of gastropods in loosely packed than in tightly packed turf at both low- and mid-shore levels. Despite large differences between gastropod assemblages at different tidal heights, the direction and magnitude of these negative effects were similar at low- and mid-shore levels and, therefore, relatively independent of local environmental conditions. These novel results extend our previous understanding of the ecological effects of habitat structure because they demonstrate possible limitations of commonly used definitions of structural complexity, as well as distinct upper thresholds in the relationship between structural complexity and faunal species richness.

Structure of Ce2RhIn8: an example of complementary use of high-resolution neutron powder diffraction and reciprocal-space mapping to study complex materials.

PubMed

Moshopoulou, E G; Ibberson, R M; Sarrao, J L; Thompson, J D; Fisk, Z

2006-04-01

The room-temperature crystal structure of the heavy fermion antiferromagnet Ce2RhIn8, dicerium rhodium octaindide, has been studied by a combination of high-resolution synchrotron X-ray reciprocal-space mapping of single crystals and high-resolution time-of-flight neutron powder diffraction. The structure is disordered, exhibiting a complex interplay of non-periodic, partially correlated planar defects, coexistence and segregation of polytypic phases (induced by periodic planar ;defects'), mosaicity (i.e. domain misalignment) and non-uniform strain. These effects evolve as a function of temperature in a complicated way, but they remain down to low temperatures. The room-temperature diffraction data are best represented by a complex mixture of two polytypic phases, which are affected by non-periodic, partially correlated planar defects, differ slightly in their tetragonal structures, and exhibit different mosaicities and strain values. Therefore, Ce2RhIn8 approaches the paracrystalline state, rather than the classic crystalline state and thus several of the concepts of conventional single-crystal crystallography are inapplicable. The structural results are discussed in the context of the role of disorder in the heavy-fermion state and in the interplay between superconductivity and magnetism.

Ranking structures and rank-rank correlations of countries: The FIFA and UEFA cases

NASA Astrophysics Data System (ADS)

Ausloos, Marcel; Cloots, Rudi; Gadomski, Adam; Vitanov, Nikolay K.

2014-04-01

Ranking of agents competing with each other in complex systems may lead to paradoxes according to the pre-chosen different measures. A discussion is presented on such rank-rank, similar or not, correlations based on the case of European countries ranked by UEFA and FIFA from different soccer competitions. The first question to be answered is whether an empirical and simple law is obtained for such (self-) organizations of complex sociological systems with such different measuring schemes. It is found that the power law form is not the best description contrary to many modern expectations. The stretched exponential is much more adequate. Moreover, it is found that the measuring rules lead to some inner structures in both cases.

Role of cooperative structural distortions in the metal--insulator transitions of perovskite ferrates

NASA Astrophysics Data System (ADS)

Cammarata, Antonio; Rondinelli, James

2012-02-01

Transition-metal oxides within the perovskite crystal family exhibit strong electron--electron correlation effects that coexist with complex structural distortions, leading to metal-insulator (MI) transitions. Using first-principles density functional calculations, we investigate the effects of cooperative octahedral rotations and dilations/contractions on the charge-ordering MI-transition in CaFeO3. By calculating the evolution in the lattice phonons, which describe the different octahedral distortions present in the low-symmetry monoclinic phase of CaFeO3 with increasing electron correlation, we show that the MI-transition results from a complex interplay between these modes and correlation effects. We combine this study with group theoretical tools to disentangle the electron--lattice interactions by computing the evolution in the low-energy electronic band structure with the lattice phonons, demonstrating the MI-transition in CaFeO3 proceeds through a symmetry-lowering transition driven by a cooperative three-dimensional octahedral dilation/contraction pattern. Finally, we suggest a possible route by which to control the charge ordering by fine-tuning the electron--lattice coupling.

Structural changes of homodimers in the PDB.

PubMed

Koike, Ryotaro; Amemiya, Takayuki; Horii, Tatsuya; Ota, Motonori

2018-04-01

Protein complexes are involved in various biological phenomena. These complexes are intrinsically flexible, and structural changes are essential to their functions. To perform a large-scale automated analysis of the structural changes of complexes, we combined two original methods. An application, SCPC, compares two structures of protein complexes and decides the match of binding mode. Another application, Motion Tree, identifies rigid-body motions in various sizes and magnitude from the two structural complexes with the same binding mode. This approach was applied to all available homodimers in the Protein Data Bank (PDB). We defined two complex-specific motions: interface motion and subunit-spanning motion. In the former, each subunit of a complex constitutes a rigid body, and the relative movement between subunits occurs at the interface. In the latter, structural parts from distinct subunits constitute a rigid body, providing the relative movement spanning subunits. All structural changes were classified and examined. It was revealed that the complex-specific motions were common in the homodimers, detected in around 40% of families. The dimeric interfaces were likely to be small and flat for interface motion, while large and rugged for subunit-spanning motion. Interface motion was accompanied by a drastic change in contacts at the interface, while the change in the subunit-spanning motion was moderate. These results indicate that the interface properties of homodimers correlated with the type of complex-specific motion. The study demonstrates that the pipeline of SCPC and Motion Tree is useful for the massive analysis of structural change of protein complexes. Copyright © 2017 Elsevier Inc. All rights reserved.

Structure and Transport Anomalies in Soft Colloids

NASA Astrophysics Data System (ADS)

Srivastava, Samanvaya; Archer, Lynden A.; Narayanan, Suresh

2013-04-01

Anomalous trends in nanoparticle correlation and motion are reported in soft nanoparticle suspensions using static and dynamic x-ray scattering measurements. Contrary to normal expectations, we find that particle-particle correlations decrease and particle dynamics become faster as volume fraction rises above a critical particle loading associated with overlap. Our observations bear many similarities to the cascade of structural and transport anomalies reported for complex, network forming molecular fluids such as water, and are argued to share similar physical origins.

Predicting the potentials, solubilities and stabilities of metal-acetylacetonates for non-aqueous redox flow batteries using density functional theory calculations

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

Kucharyson, J. F.; Cheng, L.; Tung, S. O.

New active materials are needed to improve the performance and reduce the cost of non-aqueous redox flow batteries (RFBs) for grid-scale energy storage applications. Efforts to develop better performing materials, which have largely been empirical, would benefit from a better understanding of relationships between structural, electronic and RFB-relevant functional properties. This paper focuses on metal-acetylacetonates, a class of metal coordination complexes that has shown promise for use in RFBs, and describes correlations between their experimentally measured standard potentials, solubilities, and stabilities (cycle lifes), and selected chemical, structural and electronic properties determined from Density Functional Theory (DFT) calculations. The training setmore » consisted of 16 complexes including 5 different metals and 11 different substituents on the acetylacetonate ligand. Standard potentials for those compounds were calculated and are in good agreement with experimentally measured results. A predictive equation based on the solvation energies and dipole moments, two easily computed properties, reasonably modeled the experimentally determined solubilities. Importantly, we were able to identify a descriptor for the stability of acetylacetonates. The experimentally determined stability, quantified as the cycle life to a given degree of degradation, correlated with the percentage of the highest occupied (HOMO) or lowest unoccupied molecular orbital (LUMO) on the metal of the complex. This percentage is influenced by the degree of ligand innocence (irreducibility), and complexes with the most innocent ligands yielded the most stable redox reactions. To this end, VO(acetylacetonate)(2) and Fe(acetylacetonate)(3), with nearly 80% of the HOMO and LUMO on the metal, possessed the most stable oxidation and reduction half-reactions, respectively. The structure-function relationships and correlations presented in this paper could be used to predict new, highly soluble and stable complexes for RFB applications.« less

Direct Investigation of Slow Correlated Dynamics in Proteins via Dipolar Interactions

PubMed Central

Fenwick, R. Bryn; Schwieters, Charles D.; Vögeli, Beat

2016-01-01

The synchronization of native state motions as they transition between microstates influences catalysis kinetics, mediates allosteric interactions and reduces the conformational entropy of proteins. However, it has proven difficult to describe native microstates because they are usually minimally frustrated and may interconvert on the μs-ms time scale. Direct observation of concerted equilibrium fluctuations would therefore be an important tool for describing protein native states. Here we propose a strategy that relates NMR cross-correlated relaxation (CCR) rates between dipolar interactions to residual dipolar couplings (RDCs) of individual consecutive HN–N and Hα–Cα bonds, which act as a proxy for the peptide planes and the side chains respectively. Using Xplor-NIH ensemble structure calculations restrained with the RDC and CCR data we observe collective motions on time scales slower than nanoseconds in the backbone for GB3. To directly access the correlations from CCR we develop a structure-free data analysis. The resulting dynamic correlation map is consistent with the ensemble-restrained simulations and reveals a complex network. In general we find that the bond motions are on average slightly correlated, and that the local environment dominates many observations. Despite this, some patterns are typical over entire secondary structure elements. In the β-sheet, nearly all bonds are weakly correlated and there is an approximately binary alternation in correlation intensity corresponding to the solvent exposure/shielding alternation of the side chains. For α-helices there is also a weak correlation in the HN-N bonds and the degree of correlation involving Hα-Cα bonds is directly affected by side-chain fluctuations, while loops show complex and non-uniform behavior. PMID:27331619

Fitting direct covariance structures by the MSTRUCT modeling language of the CALIS procedure.

PubMed

Yung, Yiu-Fai; Browne, Michael W; Zhang, Wei

2015-02-01

This paper demonstrates the usefulness and flexibility of the general structural equation modelling (SEM) approach to fitting direct covariance patterns or structures (as opposed to fitting implied covariance structures from functional relationships among variables). In particular, the MSTRUCT modelling language (or syntax) of the CALIS procedure (SAS/STAT version 9.22 or later: SAS Institute, 2010) is used to illustrate the SEM approach. The MSTRUCT modelling language supports a direct covariance pattern specification of each covariance element. It also supports the input of additional independent and dependent parameters. Model tests, fit statistics, estimates, and their standard errors are then produced under the general SEM framework. By using numerical and computational examples, the following tests of basic covariance patterns are illustrated: sphericity, compound symmetry, and multiple-group covariance patterns. Specification and testing of two complex correlation structures, the circumplex pattern and the composite direct product models with or without composite errors and scales, are also illustrated by the MSTRUCT syntax. It is concluded that the SEM approach offers a general and flexible modelling of direct covariance and correlation patterns. In conjunction with the use of SAS macros, the MSTRUCT syntax provides an easy-to-use interface for specifying and fitting complex covariance and correlation structures, even when the number of variables or parameters becomes large. © 2014 The British Psychological Society.

Topological structures in the equities market network

PubMed Central

Leibon, Gregory; Pauls, Scott; Rockmore, Daniel; Savell, Robert

2008-01-01

We present a new method for articulating scale-dependent topological descriptions of the network structure inherent in many complex systems. The technique is based on “partition decoupled null models,” a new class of null models that incorporate the interaction of clustered partitions into a random model and generalize the Gaussian ensemble. As an application, we analyze a correlation matrix derived from 4 years of close prices of equities in the New York Stock Exchange (NYSE) and National Association of Securities Dealers Automated Quotation (NASDAQ). In this example, we expose (i) a natural structure composed of 2 interacting partitions of the market that both agrees with and generalizes standard notions of scale (e.g., sector and industry) and (ii) structure in the first partition that is a topological manifestation of a well-known pattern of capital flow called “sector rotation.” Our approach gives rise to a natural form of multiresolution analysis of the underlying time series that naturally decomposes the basic data in terms of the effects of the different scales at which it clusters. We support our conclusions and show the robustness of the technique with a successful analysis on a simulated network with an embedded topological structure. The equities market is a prototypical complex system, and we expect that our approach will be of use in understanding a broad class of complex systems in which correlation structures are resident.

Phylogenetic review of tonal sound production in whales in relation to sociality

PubMed Central

May-Collado, Laura J; Agnarsson, Ingi; Wartzok, Douglas

2007-01-01

Background It is widely held that in toothed whales, high frequency tonal sounds called 'whistles' evolved in association with 'sociality' because in delphinids they are used in a social context. Recently, whistles were hypothesized to be an evolutionary innovation of social dolphins (the 'dolphin hypothesis'). However, both 'whistles' and 'sociality' are broad concepts each representing a conglomerate of characters. Many non-delphinids, whether solitary or social, produce tonal sounds that share most of the acoustic characteristics of delphinid whistles. Furthermore, hypotheses of character correlation are best tested in a phylogenetic context, which has hitherto not been done. Here we summarize data from over 300 studies on cetacean tonal sounds and social structure and phylogenetically test existing hypotheses on their co-evolution. Results Whistles are 'complex' tonal sounds of toothed whales that demark a more inclusive clade than the social dolphins. Whistles are also used by some riverine species that live in simple societies, and have been lost twice within the social delphinoids, all observations that are inconsistent with the dolphin hypothesis as stated. However, cetacean tonal sounds and sociality are intertwined: (1) increased tonal sound modulation significantly correlates with group size and social structure; (2) changes in tonal sound complexity are significantly concentrated on social branches. Also, duration and minimum frequency correlate as do group size and mean minimum frequency. Conclusion Studying the evolutionary correlation of broad concepts, rather than that of their component characters, is fraught with difficulty, while limits of available data restrict the detail in which component character correlations can be analyzed in this case. Our results support the hypothesis that sociality influences the evolution of tonal sound complexity. The level of social and whistle complexity are correlated, suggesting that complex tonal sounds play an important role in social communication. Minimum frequency is higher in species with large groups, and correlates negatively with duration, which may reflect the increased distances over which non-social species communicate. Our findings are generally stable across a range of alternative phylogenies. Our study points to key species where future studies would be particularly valuable for enriching our understanding of the interplay of acoustic communication and sociality. PMID:17692128

Fractal structure enables temporal prediction in music.

PubMed

Rankin, Summer K; Fink, Philip W; Large, Edward W

2014-10-01

1/f serial correlations and statistical self-similarity (fractal structure) have been measured in various dimensions of musical compositions. Musical performances also display 1/f properties in expressive tempo fluctuations, and listeners predict tempo changes when synchronizing. Here the authors show that the 1/f structure is sufficient for listeners to predict the onset times of upcoming musical events. These results reveal what information listeners use to anticipate events in complex, non-isochronous acoustic rhythms, and this will entail innovative models of temporal synchronization. This finding could improve therapies for Parkinson's and related disorders and inform deeper understanding of how endogenous neural rhythms anticipate events in complex, temporally structured communication signals.

High-lying single-particle modes, chaos, correlational entropy, and doubling phase transition

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

Stoyanov, Chavdar; Zelevinsky, Vladimir

Highly excited single-particle states in nuclei are coupled with the excitations of a more complex character, first of all with collective phononlike modes of the core. In the framework of the quasiparticle-phonon model, we consider the structure of resulting complex configurations, using the 1k{sub 17/2} orbital in {sup 209}Pb as an example. Although, on the level of one- and two-phonon admixtures, the fully chaotic Gaussian orthogonal ensemble regime is not reached, the eigenstates of the model carry a significant degree of complexity that can be quantified with the aid of correlational invariant entropy. With artificially enhanced particle-core coupling, the systemmore » undergoes the doubling phase transition with the quasiparticle strength concentrated in two repelling peaks. This phase transition is clearly detected by correlational entropy.« less

Complex-network description of thermal quantum states in the Ising spin chain

NASA Astrophysics Data System (ADS)

Sundar, Bhuvanesh; Valdez, Marc Andrew; Carr, Lincoln D.; Hazzard, Kaden R. A.

2018-05-01

We use network analysis to describe and characterize an archetypal quantum system—an Ising spin chain in a transverse magnetic field. We analyze weighted networks for this quantum system, with link weights given by various measures of spin-spin correlations such as the von Neumann and Rényi mutual information, concurrence, and negativity. We analytically calculate the spin-spin correlations in the system at an arbitrary temperature by mapping the Ising spin chain to fermions, as well as numerically calculate the correlations in the ground state using matrix product state methods, and then analyze the resulting networks using a variety of network measures. We demonstrate that the network measures show some traits of complex networks already in this spin chain, arguably the simplest quantum many-body system. The network measures give insight into the phase diagram not easily captured by more typical quantities, such as the order parameter or correlation length. For example, the network structure varies with transverse field and temperature, and the structure in the quantum critical fan is different from the ordered and disordered phases.

Discovering Structure in High-Dimensional Data Through Correlation Explanation

DTIC Science & Technology

2014-12-08

transforming complex data into simpler, more meaningful forms goes under the rubric of representation learning [2] which shares many goals with...Zhivotovsky, and M.W. Feldman. Genetic structure of human populations. Science, 298(5602):2381–2385, 2002. [14] K. Bache and M. Lichman. UCI machine

High-level ab initio studies of the complex formed between CO and O2

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2017-05-01

The explicitly correlated CCSD(T)-F12 method with VXZ-F12 basis sets was used to find the most stable structures of the van der Waals CO-O2 complexes. With geometry optimizations performed up to the quadruple-zeta level and basis set extrapolation, the calculated interaction energies for the triplet complexes are 123 cm-1 for the H complex in Cs symmetry (slipped near-parallel structure), 118 cm-1 for the X complex, also in Cs symmetry (perpendicular alignment) and 116 cm-1 for the CO-O2 T complex in C2v symmetry. The corresponding CCSD(T)-F12 results using the aug-cc-pVXZ basis sets are nearly the same. Similar calculations were performed for the CO-O2 singlet complexes, which are shown to have much higher stabilization energies, the highest being 206 cm-1 for the X complex.

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

PubMed

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

2004-12-01

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

Reduction-resistant and reduction-catalytic double-crown nickel nanoclusters

NASA Astrophysics Data System (ADS)

Zhu, Min; Zhou, Zhou, Shiming; Yao, Chuanhao; Liao, Lingwen; Wu, Zhikun

2014-11-01

In this work, an attempt to synthesize zero-valent Ni nanoclusters using the Brust method resulted in an unexpected material, Ni6(SCH2CH2Ph)12, which is a nanoscale Ni(ii)-phenylethanethiolate complex and a hexameric, double-crown-like structure, as determined by a series of characterizations, including mass spectrometry (MS), thermal gravimetric analysis (TGA), single-crystal X-ray diffraction (XRD), and X-ray photoelectron spectrometry (XPS). An interesting finding is that this complex is resistant to aqueous BH4-. Investigations into other metal-phenylethanethiolate and Ni-thiolate complexes reveal that this property is not universal and appears only in complexes with a double-crown-like structure, indicating the correlation between this interesting property and the complexes' special structure. Another interesting finding is that the reduction-resistant Ni6(SCH2CH2Ph)12 exhibits remarkably higher catalytic activity than a well-known catalyst, Au25(SCH2CH2Ph)18, toward the reduction of 4-nitrophenol at low temperature (e.g., 0 °C). This work will help stimulate more research on the properties and applications of less noble metal nanoclusters.In this work, an attempt to synthesize zero-valent Ni nanoclusters using the Brust method resulted in an unexpected material, Ni6(SCH2CH2Ph)12, which is a nanoscale Ni(ii)-phenylethanethiolate complex and a hexameric, double-crown-like structure, as determined by a series of characterizations, including mass spectrometry (MS), thermal gravimetric analysis (TGA), single-crystal X-ray diffraction (XRD), and X-ray photoelectron spectrometry (XPS). An interesting finding is that this complex is resistant to aqueous BH4-. Investigations into other metal-phenylethanethiolate and Ni-thiolate complexes reveal that this property is not universal and appears only in complexes with a double-crown-like structure, indicating the correlation between this interesting property and the complexes' special structure. Another interesting finding is that the reduction-resistant Ni6(SCH2CH2Ph)12 exhibits remarkably higher catalytic activity than a well-known catalyst, Au25(SCH2CH2Ph)18, toward the reduction of 4-nitrophenol at low temperature (e.g., 0 °C). This work will help stimulate more research on the properties and applications of less noble metal nanoclusters. Electronic supplementary information (ESI) available: Experimental section, detailed structural data, MS analyses of M-SCH2CH2Ph complexes, stability study of Ni6 and TGA analysis of Au25(SCH2CH2Ph)18. See DOI: 10.1039/c4nr04981k

Finding Correlation between Protein Protein Interaction Modules Using Semantic Web Techniques

NASA Astrophysics Data System (ADS)

Kargar, Mehdi; Moaven, Shahrouz; Abolhassani, Hassan

Many complex networks such as social networks and computer show modular structures, where edges between nodes are much denser within modules than between modules. It is strongly believed that cellular networks are also modular, reflecting the relative independence and coherence of different functional units in a cell. In this paper we used a human curated dataset. In this paper we consider each module in the PPI network as ontology. Using techniques in ontology alignment, we compare each pair of modules in the network. We want to see that is there a correlation between the structure of each module or they have totally different structures. Our results show that there is no correlation between proteins in a protein protein interaction network.

The structural, connectomic and network covariance of the human brain.

PubMed

Irimia, Andrei; Van Horn, John D

2013-02-01

Though it is widely appreciated that complex structural, functional and morphological relationships exist between distinct areas of the human cerebral cortex, the extent to which such relationships coincide remains insufficiently appreciated. Here we determine the extent to which correlations between brain regions are modulated by either structural, connectomic or network-theoretic properties using a structural neuroimaging data set of magnetic resonance imaging (MRI) and diffusion tensor imaging (DTI) volumes acquired from N=110 healthy human adults. To identify the linear relationships between all available pairs of regions, we use canonical correlation analysis to test whether a statistically significant correlation exists between each pair of cortical parcels as quantified via structural, connectomic or network-theoretic measures. In addition to this, we investigate (1) how each group of canonical variables (whether structural, connectomic or network-theoretic) contributes to the overall correlation and, additionally, (2) whether each individual variable makes a significant contribution to the test of the omnibus null hypothesis according to which no correlation between regions exists across subjects. We find that, although region-to-region correlations are extensively modulated by structural and connectomic measures, there are appreciable differences in how these two groups of measures drive inter-regional correlation patterns. Additionally, our results indicate that the network-theoretic properties of the cortex are strong modulators of region-to-region covariance. Our findings are useful for understanding the structural and connectomic relationship between various parts of the brain, and can inform theoretical and computational models of cortical information processing. Published by Elsevier Inc.

Histone modifications influence mediator interactions with chromatin

PubMed Central

Zhu, Xuefeng; Zhang, Yongqiang; Bjornsdottir, Gudrun; Liu, Zhongle; Quan, Amy; Costanzo, Michael; Dávila López, Marcela; Westholm, Jakub Orzechowski; Ronne, Hans; Boone, Charles; Gustafsson, Claes M.; Myers, Lawrence C.

2011-01-01

The Mediator complex transmits activation signals from DNA bound transcription factors to the core transcription machinery. Genome wide localization studies have demonstrated that Mediator occupancy not only correlates with high levels of transcription, but that the complex also is present at transcriptionally silenced locations. We provide evidence that Mediator localization is guided by an interaction with histone tails, and that this interaction is regulated by their post-translational modifications. A quantitative, high-density genetic interaction map revealed links between Mediator components and factors affecting chromatin structure, especially histone deacetylases. Peptide binding assays demonstrated that pure wild-type Mediator forms stable complexes with the tails of Histone H3 and H4. These binding assays also showed Mediator—histone H4 peptide interactions are specifically inhibited by acetylation of the histone H4 lysine 16, a residue critical in transcriptional silencing. Finally, these findings were validated by tiling array analysis that revealed a broad correlation between Mediator and nucleosome occupancy in vivo, but a negative correlation between Mediator and nucleosomes acetylated at histone H4 lysine 16. Our studies show that chromatin structure and the acetylation state of histones are intimately connected to Mediator localization. PMID:21742760

A Structural Theory of Pitch1,2,3

PubMed Central

Laudanski, Jonathan; Zheng, Yi

2014-01-01

Abstract Musical notes can be ordered from low to high along a perceptual dimension called “pitch”. A characteristic property of these sounds is their periodic waveform, and periodicity generally correlates with pitch. Thus, pitch is often described as the perceptual correlate of the periodicity of the sound’s waveform. However, the existence and salience of pitch also depends in a complex way on other factors, in particular harmonic content. For example, periodic sounds made of high-order harmonics tend to have a weaker pitch than those made of low-order harmonics. Here we examine the theoretical proposition that pitch is the perceptual correlate of the regularity structure of the vibration pattern of the basilar membrane, across place and time—a generalization of the traditional view on pitch. While this proposition also attributes pitch to periodic sounds, we show that it predicts differences between resolved and unresolved harmonic complexes and a complex domain of existence of pitch, in agreement with psychophysical experiments. We also present a possible neural mechanism for pitch estimation based on coincidence detection, which does not require long delays, in contrast with standard temporal models of pitch. PMID:26464959

Protein complex prediction in large ontology attributed protein-protein interaction networks.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian; Li, Yanpeng; Xu, Bo

2013-01-01

Protein complexes are important for unraveling the secrets of cellular organization and function. Many computational approaches have been developed to predict protein complexes in protein-protein interaction (PPI) networks. However, most existing approaches focus mainly on the topological structure of PPI networks, and largely ignore the gene ontology (GO) annotation information. In this paper, we constructed ontology attributed PPI networks with PPI data and GO resource. After constructing ontology attributed networks, we proposed a novel approach called CSO (clustering based on network structure and ontology attribute similarity). Structural information and GO attribute information are complementary in ontology attributed networks. CSO can effectively take advantage of the correlation between frequent GO annotation sets and the dense subgraph for protein complex prediction. Our proposed CSO approach was applied to four different yeast PPI data sets and predicted many well-known protein complexes. The experimental results showed that CSO was valuable in predicting protein complexes and achieved state-of-the-art performance.

Spectroscopic techniques to study the immune response in human saliva

NASA Astrophysics Data System (ADS)

Nepomnyashchaya, E.; Savchenko, E.; Velichko, E.; Bogomaz, T.; Aksenov, E.

2018-01-01

Studies of the immune response dynamics by means of spectroscopic techniques, i.e., laser correlation spectroscopy and fluorescence spectroscopy, are described. The laser correlation spectroscopy is aimed at measuring sizes of particles in biological fluids. The fluorescence spectroscopy allows studying of the conformational and other structural changings in immune complex. We have developed a new scheme of a laser correlation spectrometer and an original signal processing algorithm. We have suggested a new fluorescence detection scheme based on a prism and an integrating pin diode. The developed system based on the spectroscopic techniques allows studies of complex process in human saliva and opens some prospects for an individual treatment of immune diseases.

Molecular Structure and Sequence in Complex Coacervates

NASA Astrophysics Data System (ADS)

Sing, Charles; Lytle, Tyler; Madinya, Jason; Radhakrishna, Mithun

Oppositely-charged polyelectrolytes in aqueous solution can undergo associative phase separation, in a process known as complex coacervation. This results in a polyelectrolyte-dense phase (coacervate) and polyelectrolyte-dilute phase (supernatant). There remain challenges in understanding this process, despite a long history in polymer physics. We use Monte Carlo simulation to demonstrate that molecular features (charge spacing, size) play a crucial role in governing the equilibrium in coacervates. We show how these molecular features give rise to strong monomer sequence effects, due to a combination of counterion condensation and correlation effects. We distinguish between structural and sequence-based correlations, which can be designed to tune the phase diagram of coacervation. Sequence effects further inform the physical understanding of coacervation, and provide the basis for new coacervation models that take monomer-level features into account.

The Influence of Solvent on the Structural Properties of trans-(NHC)PtI2Py Complex: A Platinum-Based Anticancer Drug

NASA Astrophysics Data System (ADS)

Sadigh Vishkaee, Teherh; Fazaeli, Reza

2018-06-01

Quantum chemical calculations using MPW1PW91 method were applied to analyze the solvent effect on the structural, spectral, and thermochemical parameters for a platinum-based anticancer drug trans-(NHC)PtI2Py complex. The solvent effects were examined by the self-consistent reaction field theory (SCRF) based on Polarizable Continuum Model (PCM). The linear correlations between the solvation energies, HOMO-LUMO gaps, IR-active stretching vibration of Pt-N bonds and N-H of NHC ligand with dielectric constants of solvents were studied. The wave numbers of these IR-active stretching vibrations in different solvents were correlated with the Kirkwood-Bauer-Magat equation (KBM). The thermodynamic activation parameter such free energy of solvation, enthalpy of solvation were also calculated.

Model for an RNA tertiary interaction from the structure of an intermolecular complex between a GAAA tetraloop and an RNA helix.

PubMed

Pley, H W; Flaherty, K M; McKay, D B

1994-11-03

In large structured RNAs, RNA hairpins in which the strands of the duplex stem are connected by a tetraloop of the consensus sequence 5'-GNRA (where N is any nucleotide, and R is either G or A) are unusually frequent. In group I introns there is a covariation in sequence between nucleotides in the third and fourth positions of the loop with specific distant base pairs in putative RNA duplex stems: GNAA loops correlate with successive 5'-C-C.G-C base pairs in stems, whereas GNGA loops correlate with 5'-C-U.G-A. This has led to the suggestion that GNRA tetraloops may be involved in specific long-range tertiary interactions, with each A in position 3 or 4 of the loop interacting with a C-G base pair in the duplex, and G in position 3 interacting with a U-A base pair. This idea is supported experimentally for the GAAA loop of the P5b extension of the group I intron of Tetrahymena thermophila and the L9 GUGA terminal loop of the td intron of bacteriophage T4 (ref. 4). NMR has revealed the overall structure of the tetraloop for 12-nucleotide hairpins with GCAA and GAAA loops and models have been proposed for the interaction of GNRA tetraloops with base pairs in the minor groove of A-form RNA. Here we describe the crystal structure of an intermolecular complex between a GAAA tetraloop and an RNA helix. The interactions we observe correlate with the specificity of GNRA tetraloops inferred from phylogenetic studies, suggesting that this complex is a legitimate model for intramolecular tertiary interactions mediated by GNRA tetraloops in large structured RNAs.

Robust estimation of fractal measures for characterizing the structural complexity of the human brain: optimization and reproducibility

PubMed Central

Goñi, Joaquín; Sporns, Olaf; Cheng, Hu; Aznárez-Sanado, Maite; Wang, Yang; Josa, Santiago; Arrondo, Gonzalo; Mathews, Vincent P; Hummer, Tom A; Kronenberger, William G; Avena-Koenigsberger, Andrea; Saykin, Andrew J.; Pastor, María A.

2013-01-01

High-resolution isotropic three-dimensional reconstructions of human brain gray and white matter structures can be characterized to quantify aspects of their shape, volume and topological complexity. In particular, methods based on fractal analysis have been applied in neuroimaging studies to quantify the structural complexity of the brain in both healthy and impaired conditions. The usefulness of such measures for characterizing individual differences in brain structure critically depends on their within-subject reproducibility in order to allow the robust detection of between-subject differences. This study analyzes key analytic parameters of three fractal-based methods that rely on the box-counting algorithm with the aim to maximize within-subject reproducibility of the fractal characterizations of different brain objects, including the pial surface, the cortical ribbon volume, the white matter volume and the grey matter/white matter boundary. Two separate datasets originating from different imaging centers were analyzed, comprising, 50 subjects with three and 24 subjects with four successive scanning sessions per subject, respectively. The reproducibility of fractal measures was statistically assessed by computing their intra-class correlations. Results reveal differences between different fractal estimators and allow the identification of several parameters that are critical for high reproducibility. Highest reproducibility with intra-class correlations in the range of 0.9–0.95 is achieved with the correlation dimension. Further analyses of the fractal dimensions of parcellated cortical and subcortical gray matter regions suggest robustly estimated and region-specific patterns of individual variability. These results are valuable for defining appropriate parameter configurations when studying changes in fractal descriptors of human brain structure, for instance in studies of neurological diseases that do not allow repeated measurements or for disease-course longitudinal studies. PMID:23831414

Fractal dimension assessment of brain white matter structural complexity post stroke in relation to upper-extremity motor function

PubMed Central

Zhang, Luduan; Butler, Andrew J.; Sun, Chang-Kai; Sahgal, Vinod; Wittenberg, George F.; Yue, Guang H.

2008-01-01

Little is known about the association between brain white matter (WM) structure and motor function in humans. This study investigated complexity of brain WM interior shape as determined by magnetic resonance imaging (MRI) and its relationship with upper-extremity (UE) motor function in patients post stroke. We hypothesized that (1) the WM complexity would decrease following stroke, and (2) higher WM complexity in non-affected cortical areas would be related to greater UE motor function. Thirty-eight stroke patients (16 with left-hemisphere lesions) underwent MRI anatomical brain scans. Fractal dimension (FD), a quantitative shape metric, was applied onto skeletonized brain WM images to evaluate WM internal structural complexity. Wolf Motor Function Test (WMFT) and Fugl-Meyer Motor Assessment (FM) scores were measured to assess motor function of the affected limb. The WM complexity was lower in the stroke-affected hemisphere. The FD was associated with better motor function in two subgroups: with left-subcortical lesions, FD values of the lesion-free areas of the left hemisphere were associated with better FM scores; with right-cortical lesions, FD values of lesion-free regions were robustly associated with better WMFT scores. These findings suggest that greater residual WM complexity is associated with less impaired UE motor function, which is more robust in patients with right-hemisphere lesions. No correlations were found between lesion volume and WMFT or FM scores. This study addressed WM complexity in stroke patients and its relationship with UE motor function. Measurement of brain WM reorganization may be a sensitive correlate of UE function in people recovering from stroke. PMID:18590710

Dynamic Frequency Shifts of Complexed Ligands: An NMR Study of D-[1- 13C,1- 2H]Glucose Complexed to the Escherichia coliPeriplasmic Glucose/Galactose Receptor

NASA Astrophysics Data System (ADS)

Gabel, Scott A.; Luck, Linda A.; Werbelow, Lawrence G.; London, Robert E.

1997-10-01

The13C multiplet structure ofD-[1-13C,1-2H]glucose complexed to theEscherichia coliperiplasmic glucose/galactose receptor has been studied as a function of temperature. Asymmetric multiplet patterns observed are shown to arise from dynamic frequency shifts. Multiplet asymmetry contributions resulting from shift anisotropy-dipolar cross correlations were found to be small, with optimal fits of the data corresponding to small, negative values of the correlation factor, χCD-CSA. Additional broadening at higher temperatures most probably results from ligand exchange between free and complexed states. Effects of internal motion are also considered theoretically, and indicate that the order parameter for the bound glucose is ≥0.9.

Antiplasmodial activities of gold(I) complexes involving functionalized N-heterocyclic carbenes.

PubMed

Hemmert, Catherine; Ramadani, Arba Pramundita; Boselli, Luca; Fernández Álvarez, Álvaro; Paloque, Lucie; Augereau, Jean-Michel; Gornitzka, Heinz; Benoit-Vical, Françoise

2016-07-01

A series of twenty five molecules, including imidazolium salts functionalized by N-, O- or S-containing groups and their corresponding cationic, neutral or anionic gold(I) complexes were evaluated on Plasmodium falciparum in vitro and then on Vero cells to determine their selectivity. Among them, eight new compounds were synthesized and fully characterized by spectroscopic methods. The X-ray structures of three gold(I) complexes are presented. Except one complex (18), all the cationic gold(I) complexes show potent antiplasmodial activity with IC50 in the micro- and submicromolar range, correlated with their lipophilicity. Structure-activity relationships enable to evidence a lead-complex (21) displaying a good activity (IC50=210nM) close to the value obtained with chloroquine (IC50=514nM) and a weak cytotoxicity. Copyright © 2016 Elsevier Ltd. All rights reserved.

Quantum coherence selective 2D Raman–2D electronic spectroscopy

PubMed Central

Spencer, Austin P.; Hutson, William O.; Harel, Elad

2017-01-01

Electronic and vibrational correlations report on the dynamics and structure of molecular species, yet revealing these correlations experimentally has proved extremely challenging. Here, we demonstrate a method that probes correlations between states within the vibrational and electronic manifold with quantum coherence selectivity. Specifically, we measure a fully coherent four-dimensional spectrum which simultaneously encodes vibrational–vibrational, electronic–vibrational and electronic–electronic interactions. By combining near-impulsive resonant and non-resonant excitation, the desired fifth-order signal of a complex organic molecule in solution is measured free of unwanted lower-order contamination. A critical feature of this method is electronic and vibrational frequency resolution, enabling isolation and assignment of individual quantum coherence pathways. The vibronic structure of the system is then revealed within an otherwise broad and featureless 2D electronic spectrum. This method is suited for studying elusive quantum effects in which electronic transitions strongly couple to phonons and vibrations, such as energy transfer in photosynthetic pigment–protein complexes. PMID:28281541

Rescore protein-protein docked ensembles with an interface contact statistics.

PubMed

Mezei, Mihaly

2017-02-01

The recently developed statistical measure for the type of residue-residue contact at protein complex interfaces, based on a parameter-free definition of contact, has been used to define a contact score that is correlated with the likelihood of correctness of a proposed complex structure. Comparing the proposed contact scores on the native structure and on a set of model structures the proposed measure was shown to generally favor the native structure but in itself was not able to reliably score the native structure to be the best. Adjusting the scores of redocking experiments with the contact score showed that the adjusted score was able to move up the ranking of the native-like structure among the proposed complexes when the native-like was not ranked the best by the respective program. Tests on docking of unbound proteins compared the contact scores of the complexes with the contact score of the crystal structure again showing the tendency of the contact score to favor native-like conformations. The possibility of using the contact score to improve the determination of biological dimers in a crystal structure was also explored. Proteins 2017; 85:235-241. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Collagen Organization in Facet Capsular Ligaments Varies With Spinal Region and With Ligament Deformation.

PubMed

Ban, Ehsan; Zhang, Sijia; Zarei, Vahhab; Barocas, Victor H; Winkelstein, Beth A; Picu, Catalin R

2017-07-01

The spinal facet capsular ligament (FCL) is primarily comprised of heterogeneous arrangements of collagen fibers. This complex fibrous structure and its evolution under loading play a critical role in determining the mechanical behavior of the FCL. A lack of analytical tools to characterize the spatial anisotropy and heterogeneity of the FCL's microstructure has limited the current understanding of its structure-function relationships. Here, the collagen organization was characterized using spatial correlation analysis of the FCL's optically obtained fiber orientation field. FCLs from the cervical and lumbar spinal regions were characterized in terms of their structure, as was the reorganization of collagen in stretched cervical FCLs. Higher degrees of intra- and intersample heterogeneity were found in cervical FCLs than in lumbar specimens. In the cervical FCLs, heterogeneity was manifested in the form of curvy patterns formed by collections of collagen fibers or fiber bundles. Tensile stretch, a common injury mechanism for the cervical FCL, significantly increased the spatial correlation length in the stretch direction, indicating an elongation of the observed structural features. Finally, an affine estimation for the change of correlation length under loading was performed which gave predictions very similar to the actual values. These findings provide structural insights for multiscale mechanical analyses of the FCLs from various spinal regions and also suggest methods for quantitative characterization of complex tissue patterns.

Knowledge structures and the acquisition of a complex skill.

PubMed

Day, E A; Arthur, W; Gettman, D

2001-10-01

The purpose of this study was to examine the viability of knowledge structures as an operationalization of learning in the context of a task that required a high degree of skill. Over the course of 3 days, 86 men participated in 9 training sessions and learned a complex video game. At the end of acquisition, participants' knowledge structures were assessed. After a 4-day nonpractice interval, trainees completed tests of skill retention and skill transfer. Findings indicated that the similarity of trainees' knowledge structures to an expert structure was correlated with skill acquisition and was predictive of skill retention and skill transfer. However, the magnitude of these effects was dependent on the method used to derive the expert referent structure. Moreover, knowledge structures mediated the relationship between general cognitive ability and skill-based performance.

Complex network analysis of resting-state fMRI of the brain.

PubMed

Anwar, Abdul Rauf; Hashmy, Muhammad Yousaf; Imran, Bilal; Riaz, Muhammad Hussnain; Mehdi, Sabtain Muhammad Muntazir; Muthalib, Makii; Perrey, Stephane; Deuschl, Gunther; Groppa, Sergiu; Muthuraman, Muthuraman

2016-08-01

Due to the fact that the brain activity hardly ever diminishes in healthy individuals, analysis of resting state functionality of the brain seems pertinent. Various resting state networks are active inside the idle brain at any time. Based on various neuro-imaging studies, it is understood that various structurally distant regions of the brain could be functionally connected. Regions of the brain, that are functionally connected, during rest constitutes to the resting state network. In the present study, we employed the complex network measures to estimate the presence of community structures within a network. Such estimate is named as modularity. Instead of using a traditional correlation matrix, we used a coherence matrix taken from the causality measure between different nodes. Our results show that in prolonged resting state the modularity starts to decrease. This decrease was observed in all the resting state networks and on both sides of the brain. Our study highlights the usage of coherence matrix instead of correlation matrix for complex network analysis.

Self-organization of the reticular structure of polyurethane

NASA Astrophysics Data System (ADS)

Kiselev, M. R.; Roldugin, V. I.

2010-08-01

The morphology of block samples and coatings of reticular polyurethane were studied by transmission electron microscopy. The morphology was correlated with the internal stresses that appeared in the coatings during their formation. A scenario of the self-assembly of complex structures in reticular polymers was suggested. The boundary between the structural elements of the supermolecular level was found to be strained.

Inhibition of nuclear factor kappaB proteins-platinated DNA interactions correlates with cytotoxic effectiveness of the platinum complexes

PubMed Central

Brabec, Viktor; Kasparkova, Jana; Kostrhunova, Hana; Farrell, Nicholas P.

2016-01-01

Nuclear DNA is the target responsible for anticancer activity of platinum anticancer drugs. Their activity is mediated by altered signals related to programmed cell death and the activation of various signaling pathways. An example is activation of nuclear factor kappaB (NF-κB). Binding of NF-κB proteins to their consensus sequences in DNA (κB sites) is the key biochemical activity responsible for the biological functions of NF-κB. Using gel-mobility-shift assays and surface plasmon resonance spectroscopy we examined the interactions of NF-κB proteins with oligodeoxyribonucleotide duplexes containing κB site damaged by DNA adducts of three platinum complexes. These complexes markedly differed in their toxic effects in tumor cells and comprised highly cytotoxic trinuclear platinum(II) complex BBR3464, less cytotoxic conventional cisplatin and ineffective transplatin. The results indicate that structurally different DNA adducts of these platinum complexes exhibit a different efficiency to affect the affinity of the platinated DNA (κB sites) to NF-κB proteins. Our results support the hypothesis that structural perturbations induced in DNA by platinum(II) complexes correlate with their higher efficiency to inhibit binding of NF-κB proteins to their κB sites and cytotoxicity as well. However, the full generalization of this hypothesis will require to evaluate a larger series of platinum(II) complexes. PMID:27574114

Inhibition of nuclear factor kappaB proteins-platinated DNA interactions correlates with cytotoxic effectiveness of the platinum complexes.

PubMed

Brabec, Viktor; Kasparkova, Jana; Kostrhunova, Hana; Farrell, Nicholas P

2016-08-30

Nuclear DNA is the target responsible for anticancer activity of platinum anticancer drugs. Their activity is mediated by altered signals related to programmed cell death and the activation of various signaling pathways. An example is activation of nuclear factor kappaB (NF-κB). Binding of NF-κB proteins to their consensus sequences in DNA (κB sites) is the key biochemical activity responsible for the biological functions of NF-κB. Using gel-mobility-shift assays and surface plasmon resonance spectroscopy we examined the interactions of NF-κB proteins with oligodeoxyribonucleotide duplexes containing κB site damaged by DNA adducts of three platinum complexes. These complexes markedly differed in their toxic effects in tumor cells and comprised highly cytotoxic trinuclear platinum(II) complex BBR3464, less cytotoxic conventional cisplatin and ineffective transplatin. The results indicate that structurally different DNA adducts of these platinum complexes exhibit a different efficiency to affect the affinity of the platinated DNA (κB sites) to NF-κB proteins. Our results support the hypothesis that structural perturbations induced in DNA by platinum(II) complexes correlate with their higher efficiency to inhibit binding of NF-κB proteins to their κB sites and cytotoxicity as well. However, the full generalization of this hypothesis will require to evaluate a larger series of platinum(II) complexes.

Dynamical mechanism in aero-engine gas path system using minimum spanning tree and detrended cross-correlation analysis

NASA Astrophysics Data System (ADS)

Dong, Keqiang; Zhang, Hong; Gao, You

2017-01-01

Identifying the mutual interaction in aero-engine gas path system is a crucial problem that facilitates the understanding of emerging structures in complex system. By employing the multiscale multifractal detrended cross-correlation analysis method to aero-engine gas path system, the cross-correlation characteristics between gas path system parameters are established. Further, we apply multiscale multifractal detrended cross-correlation distance matrix and minimum spanning tree to investigate the mutual interactions of gas path variables. The results can infer that the low-spool rotor speed (N1) and engine pressure ratio (EPR) are main gas path parameters. The application of proposed method contributes to promote our understanding of the internal mechanisms and structures of aero-engine dynamics.

Disentangling Stability, Variability and Adaptability in Human Performance: Focus on the Interplay between Local Variance and Serial Correlation

ERIC Educational Resources Information Center

Torre, Kjerstin; Balasubramaniam, Ramesh

2011-01-01

We address the complex relationship between the stability, variability, and adaptability of psychological systems by decomposing the global variance of serial performance into two independent parts: the local variance (LV) and the serial correlation structure. For two time series with equal LV, the presence of persistent long-range correlations…

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures

PubMed Central

Theobald, Douglas L.; Wuttke, Deborah S.

2008-01-01

Summary THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. PMID:16777907

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

Deisenhofer, J.; Michel, H.

The history and methods of membrane protein crystallization are described. The solution of the structure of the photosynthetic reaction center from the bacterium Rhodopseudomonas viridis is described, and the structure of this membrane protein complex is correlated with its function as a light-driven electron pump across the photosynthetic membrane. Conclusions about the structure of the photosystem II reaction center from plants are drawn, and aspects of membrane protein structure are discussed. 68 refs., 15 figs., 2 tabs.

Analysis of structural dynamic data from Skylab. Volume 1: Technical discussion

NASA Technical Reports Server (NTRS)

Demchak, L.; Harcrow, H.

1976-01-01

A compendium of Skylab structural dynamics analytical and test programs is presented. These programs are assessed to identify lessons learned from the structural dynamic prediction effort and to provide guidelines for future analysts and program managers of complex spacecraft systems. It is a synopsis of the structural dynamic effort performed under the Skylab Integration contract and specifically covers the development, utilization, and correlation of Skylab Dynamic Orbital Models.

Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

PubMed Central

He, Yi-Ming; Ma, Bin-Guang

2016-01-01

Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions. PMID:27220911

Abundance and Temperature Dependency of Protein-Protein Interaction Revealed by Interface Structure Analysis and Stability Evolution

NASA Astrophysics Data System (ADS)

He, Yi-Ming; Ma, Bin-Guang

2016-05-01

Protein complexes are major forms of protein-protein interactions and implement essential biological functions. The subunit interface in a protein complex is related to its thermostability. Though the roles of interface properties in thermal adaptation have been investigated for protein complexes, the relationship between the interface size and the expression level of the subunits remains unknown. In the present work, we studied this relationship and found a positive correlation in thermophiles rather than mesophiles. Moreover, we found that the protein interaction strength in complexes is not only temperature-dependent but also abundance-dependent. The underlying mechanism for the observed correlation was explored by simulating the evolution of protein interface stability, which highlights the avoidance of misinteraction. Our findings make more complete the picture of the mechanisms for protein complex thermal adaptation and provide new insights into the principles of protein-protein interactions.

Near-infrared branding efficiently correlates light and electron microscopy.

PubMed

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

2011-06-05

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

The current status of the Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) species complex

PubMed Central

Souza, Nataly A; Brazil, Reginaldo P; Araki, Alejandra S

2017-01-01

Lutzomyia longipalpis s.l. is a complex of sibling species and is the principal vector of American visceral leishmaniasis. The present review summarises the diversity of efforts that have been undertaken to elucidate the number of unnamed species in this species complex and the phylogenetic relationships among them. A wide variety of evidence, including chemical, behavioral and molecular traits, suggests very recent speciation events and complex population structure in this group. Although significant advances have been achieved to date, differential vector capacity and the correlation between structure of parasite and vector populations have yet to be elucidated. Furthermore, increased knowledge about recent epidemiological changes, such as urbanisation, is essential for pursuing effective strategies for sandfly control in the New World. PMID:28225906

The current status of the Lutzomyia longipalpis (Diptera: Psychodidae: Phlebotominae) species complex.

PubMed

Souza, Nataly A; Brazil, Reginaldo P; Araki, Alejandra S

2017-03-01

Lutzomyia longipalpis s.l. is a complex of sibling species and is the principal vector of American visceral leishmaniasis. The present review summarises the diversity of efforts that have been undertaken to elucidate the number of unnamed species in this species complex and the phylogenetic relationships among them. A wide variety of evidence, including chemical, behavioral and molecular traits, suggests very recent speciation events and complex population structure in this group. Although significant advances have been achieved to date, differential vector capacity and the correlation between structure of parasite and vector populations have yet to be elucidated. Furthermore, increased knowledge about recent epidemiological changes, such as urbanisation, is essential for pursuing effective strategies for sandfly control in the New World.

Singlet-triplet fission of carotenoid excitation in light-harvesting LH2 complexes of purple phototrophic bacteria.

PubMed

Klenina, I B; Makhneva, Z K; Moskalenko, A A; Gudkov, N D; Bolshakov, M A; Pavlova, E A; Proskuryakov, I I

2014-03-01

The current generally accepted structure of light-harvesting LH2 complexes from purple phototrophic bacteria conflicts with the observation of singlet-triplet carotenoid excitation fission in these complexes. In LH2 complexes from the purple bacterium Allochromatium minutissimum, a drop in the efficiency of carotenoid triplet generation is demonstrated, which correlates with the extent of selective photooxidation of bacteriochlorophylls absorbing at ~850 nm. We conclude that singlet-triplet fission of carotenoid excitation proceeds with participation of these excitonically coupled bacteriochlorophylls. In the framework of the proposed mechanism, the contradiction between LH2 structure and photophysical properties of carotenoids is eliminated. The possibility of singlet-triplet excitation fission involving a third mediator molecule was not considered earlier.

The modelling of the flow-induced vibrations of periodic flat and axial-symmetric structures with a wave-based method

NASA Astrophysics Data System (ADS)

Errico, F.; Ichchou, M.; De Rosa, S.; Bareille, O.; Franco, F.

2018-06-01

The stochastic response of periodic flat and axial-symmetric structures, subjected to random and spatially-correlated loads, is here analysed through an approach based on the combination of a wave finite element and a transfer matrix method. Although giving a lower computational cost, the present approach keeps the same accuracy of classic finite element methods. When dealing with homogeneous structures, the accuracy is also extended to higher frequencies, without increasing the time of calculation. Depending on the complexity of the structure and the frequency range, the computational cost can be reduced more than two orders of magnitude. The presented methodology is validated both for simple and complex structural shapes, under deterministic and random loads.

Direct Imaging of Gene-Carrier Complexes in Animal Cells

NASA Astrophysics Data System (ADS)

Lin, Alison J.; Slack, Nelle L.; Ahmad, Ayesha; Matsumoto, Brian; Safinya, Cyrus R.

1998-03-01

Cationic lipids are promising gene carriers for DNA transfection. Establishing the correlations between structures of cationic lipid/DNA complexes (CL-DNA) and pathways of transfection will greatly aid us in achieving the optimal CL-DNA transfections. Our first step is to determine the uptake mechanism of DNA by studying the interactions and structures of DNA and cationic lipids. X-ray diffraction shows that the CL-DNA undergoes structural phase transitions from lamellar( J. Raedler, I. Koltover, T. Salditt, C. R. Safinya, Science 275, 810 (1997).) to inverted hexagonal self-assemblies as we change the lipid composition. X-ray diffraction and optical microscopy techniques are used to directly image the progress of the CL-DNA in mouse L-cells and unravel the complex structure in-situ. Fluorescence and confocal optical microscopy techniques allow us to monitor the interactions between the complexes and different organelles in the cell cytoplasm. Current results indicate that once inside cells, complexes containing DOPE follow a different pathway from those containing DOPC. This research is funded by NSF-DMR-9624091, PRF-31352-AC7, and Los Alamos-STB/UC:96-108.

Lagrangian space consistency relation for large scale structure

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

Horn, Bart; Hui, Lam; Xiao, Xiao

Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias & Riotto and Peloso & Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present.more » Furthermore, the simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.« less

Lagrangian space consistency relation for large scale structure

DOE PAGES

Horn, Bart; Hui, Lam; Xiao, Xiao

2015-09-29

Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias & Riotto and Peloso & Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present.more » Furthermore, the simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.« less

Quantification of structural changes in acute inflammation by fractal dimension, angular second moment and correlation.

PubMed

Stankovic, Marija; Pantic, Igor; De Luka, Silvio R; Puskas, Nela; Zaletel, Ivan; Milutinovic-Smiljanic, Sanja; Pantic, Senka; Trbovich, Alexander M

2016-03-01

The aim of the study was to examine alteration and possible application of fractal dimension, angular second moment, and correlation for quantification of structural changes in acutely inflamed tissue. Acute inflammation was induced by injection of turpentine oil into the right and left hind limb muscles of mice, whereas control animals received intramuscular saline injection. After 12 h, animals were anesthetised and treated muscles collected. The tissue was stained by hematoxylin and eosin, digital micrographs produced, enabling determination of fractal dimension of the cells, angular second moment and correlation of studied tissue. Histopathological analysis showed presence of inflammatory infiltrate and tissue damage in inflammatory group, whereas tissue structure in control group was preserved, devoid of inflammatory infiltrate. Fractal dimension of the cells, angular second moment and correlation of treated tissue in inflammatory group decreased in comparison to the control group. In this study, we were first to observe and report that fractal dimension of the cells, angular second moment, and correlation were reduced in acutely inflamed tissue, indicating loss of overall complexity of the cells in the tissue, the tissue uniformity and structure regularity. Fractal dimension, angular second moment and correlation could be useful methods for quantification of structural changes in acute inflammation. © 2015 The Authors Journal of Microscopy © 2015 Royal Microscopical Society.

Postprocessing of docked protein-ligand complexes using implicit solvation models.

PubMed

Lindström, Anton; Edvinsson, Lotta; Johansson, Andreas; Andersson, C David; Andersson, Ida E; Raubacher, Florian; Linusson, Anna

2011-02-28

Molecular docking plays an important role in drug discovery as a tool for the structure-based design of small organic ligands for macromolecules. Possible applications of docking are identification of the bioactive conformation of a protein-ligand complex and the ranking of different ligands with respect to their strength of binding to a particular target. We have investigated the effect of implicit water on the postprocessing of binding poses generated by molecular docking using MM-PB/GB-SA (molecular mechanics Poisson-Boltzmann and generalized Born surface area) methodology. The investigation was divided into three parts: geometry optimization, pose selection, and estimation of the relative binding energies of docked protein-ligand complexes. Appropriate geometry optimization afforded more accurate binding poses for 20% of the complexes investigated. The time required for this step was greatly reduced by minimizing the energy of the binding site using GB solvation models rather than minimizing the entire complex using the PB model. By optimizing the geometries of docking poses using the GB(HCT+SA) model then calculating their free energies of binding using the PB implicit solvent model, binding poses similar to those observed in crystal structures were obtained. Rescoring of these poses according to their calculated binding energies resulted in improved correlations with experimental binding data. These correlations could be further improved by applying the postprocessing to several of the most highly ranked poses rather than focusing exclusively on the top-scored pose. The postprocessing protocol was successfully applied to the analysis of a set of Factor Xa inhibitors and a set of glycopeptide ligands for the class II major histocompatibility complex (MHC) A(q) protein. These results indicate that the protocol for the postprocessing of docked protein-ligand complexes developed in this paper may be generally useful for structure-based design in drug discovery.

A Statistical Model for Estimation of Fish Density Including Correlation in Size, Space, Time and between Species from Research Survey Data

PubMed Central

Bastardie, Francois

2014-01-01

Trawl survey data with high spatial and seasonal coverage were analysed using a variant of the Log Gaussian Cox Process (LGCP) statistical model to estimate unbiased relative fish densities. The model estimates correlations between observations according to time, space, and fish size and includes zero observations and over-dispersion. The model utilises the fact the correlation between numbers of fish caught increases when the distance in space and time between the fish decreases, and the correlation between size groups in a haul increases when the difference in size decreases. Here the model is extended in two ways. Instead of assuming a natural scale size correlation, the model is further developed to allow for a transformed length scale. Furthermore, in the present application, the spatial- and size-dependent correlation between species was included. For cod (Gadus morhua) and whiting (Merlangius merlangus), a common structured size correlation was fitted, and a separable structure between the time and space-size correlation was found for each species, whereas more complex structures were required to describe the correlation between species (and space-size). The within-species time correlation is strong, whereas the correlations between the species are weaker over time but strong within the year. PMID:24911631

Vulnerability of coral reef fisheries to a loss of structural complexity.

PubMed

Rogers, Alice; Blanchard, Julia L; Mumby, Peter J

2014-05-05

Coral reefs face a diverse array of threats, from eutrophication and overfishing to climate change. As live corals are lost and their skeletons eroded, the structural complexity of reefs declines. This may have important consequences for the survival and growth of reef fish because complex habitats mediate predator-prey interactions [1, 2] and influence competition [3-5] through the provision of prey refugia. A positive correlation exists between structural complexity and reef fish abundance and diversity in both temperate and tropical ecosystems [6-10]. However, it is not clear how the diversity of available refugia interacts with individual predator-prey relationships to explain emergent properties at the community scale. Furthermore, we do not yet have the ability to predict how habitat loss might affect the productivity of whole reef communities and the fisheries they support. Using data from an unfished reserve in The Bahamas, we find that structural complexity is associated not only with increased fish biomass and abundance, but also with nonlinearities in the size spectra of fish, implying disproportionately high abundances of certain size classes. By developing a size spectrum food web model that links the vulnerability of prey to predation with the structural complexity of a reef, we show that these nonlinearities can be explained by size-structured prey refugia that reduce mortality rates and alter growth rates in different parts of the size spectrum. Fitting the model with data from a structurally complex habitat, we predict that a loss of complexity could cause more than a 3-fold reduction in fishery productivity. Copyright © 2014 Elsevier Ltd. All rights reserved.

A key heterogeneous structure of fractal networks based on inverse renormalization scheme

NASA Astrophysics Data System (ADS)

Bai, Yanan; Huang, Ning; Sun, Lina

2018-06-01

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

Visual Complexity and Affect: Ratings Reflect More Than Meets the Eye.

PubMed

Madan, Christopher R; Bayer, Janine; Gamer, Matthias; Lonsdorf, Tina B; Sommer, Tobias

2017-01-01

Pictorial stimuli can vary on many dimensions, several aspects of which are captured by the term 'visual complexity.' Visual complexity can be described as, "a picture of a few objects, colors, or structures would be less complex than a very colorful picture of many objects that is composed of several components." Prior studies have reported a relationship between affect and visual complexity, where complex pictures are rated as more pleasant and arousing. However, a relationship in the opposite direction, an effect of affect on visual complexity, is also possible; emotional arousal and valence are known to influence selective attention and visual processing. In a series of experiments, we found that ratings of visual complexity correlated with affective ratings, and independently also with computational measures of visual complexity. These computational measures did not correlate with affect, suggesting that complexity ratings are separately related to distinct factors. We investigated the relationship between affect and ratings of visual complexity, finding an 'arousal-complexity bias' to be a robust phenomenon. Moreover, we found this bias could be attenuated when explicitly indicated but did not correlate with inter-individual difference measures of affective processing, and was largely unrelated to cognitive and eyetracking measures. Taken together, the arousal-complexity bias seems to be caused by a relationship between arousal and visual processing as it has been described for the greater vividness of arousing pictures. The described arousal-complexity bias is also of relevance from an experimental perspective because visual complexity is often considered a variable to control for when using pictorial stimuli.

Visual Complexity and Affect: Ratings Reflect More Than Meets the Eye

PubMed Central

Madan, Christopher R.; Bayer, Janine; Gamer, Matthias; Lonsdorf, Tina B.; Sommer, Tobias

2018-01-01

Pictorial stimuli can vary on many dimensions, several aspects of which are captured by the term ‘visual complexity.’ Visual complexity can be described as, “a picture of a few objects, colors, or structures would be less complex than a very colorful picture of many objects that is composed of several components.” Prior studies have reported a relationship between affect and visual complexity, where complex pictures are rated as more pleasant and arousing. However, a relationship in the opposite direction, an effect of affect on visual complexity, is also possible; emotional arousal and valence are known to influence selective attention and visual processing. In a series of experiments, we found that ratings of visual complexity correlated with affective ratings, and independently also with computational measures of visual complexity. These computational measures did not correlate with affect, suggesting that complexity ratings are separately related to distinct factors. We investigated the relationship between affect and ratings of visual complexity, finding an ‘arousal-complexity bias’ to be a robust phenomenon. Moreover, we found this bias could be attenuated when explicitly indicated but did not correlate with inter-individual difference measures of affective processing, and was largely unrelated to cognitive and eyetracking measures. Taken together, the arousal-complexity bias seems to be caused by a relationship between arousal and visual processing as it has been described for the greater vividness of arousing pictures. The described arousal-complexity bias is also of relevance from an experimental perspective because visual complexity is often considered a variable to control for when using pictorial stimuli. PMID:29403412

Structural MRI and Cognitive Correlates in Pest-Control Personnel from Gulf War I

DTIC Science & Technology

2010-04-01

Figure (ROCFT; Corwin & Blysma, 1993) Copying a complex geometric design; assess ability to organize and construct Raw Score...workstations at Boston University School of Medicine where they were reconstructed for morphometric analyses by the study imaging expert, Dr. Killiany...conventional structural MRI and morphometric analysis of K. Sullivan, Ph.D

Hierarchical organization of functional connectivity in the mouse brain: a complex network approach.

PubMed

Bardella, Giampiero; Bifone, Angelo; Gabrielli, Andrea; Gozzi, Alessandro; Squartini, Tiziano

2016-08-18

This paper represents a contribution to the study of the brain functional connectivity from the perspective of complex networks theory. More specifically, we apply graph theoretical analyses to provide evidence of the modular structure of the mouse brain and to shed light on its hierarchical organization. We propose a novel percolation analysis and we apply our approach to the analysis of a resting-state functional MRI data set from 41 mice. This approach reveals a robust hierarchical structure of modules persistent across different subjects. Importantly, we test this approach against a statistical benchmark (or null model) which constrains only the distributions of empirical correlations. Our results unambiguously show that the hierarchical character of the mouse brain modular structure is not trivially encoded into this lower-order constraint. Finally, we investigate the modular structure of the mouse brain by computing the Minimal Spanning Forest, a technique that identifies subnetworks characterized by the strongest internal correlations. This approach represents a faster alternative to other community detection methods and provides a means to rank modules on the basis of the strength of their internal edges.

Hierarchical organization of functional connectivity in the mouse brain: a complex network approach

NASA Astrophysics Data System (ADS)

Bardella, Giampiero; Bifone, Angelo; Gabrielli, Andrea; Gozzi, Alessandro; Squartini, Tiziano

2016-08-01

This paper represents a contribution to the study of the brain functional connectivity from the perspective of complex networks theory. More specifically, we apply graph theoretical analyses to provide evidence of the modular structure of the mouse brain and to shed light on its hierarchical organization. We propose a novel percolation analysis and we apply our approach to the analysis of a resting-state functional MRI data set from 41 mice. This approach reveals a robust hierarchical structure of modules persistent across different subjects. Importantly, we test this approach against a statistical benchmark (or null model) which constrains only the distributions of empirical correlations. Our results unambiguously show that the hierarchical character of the mouse brain modular structure is not trivially encoded into this lower-order constraint. Finally, we investigate the modular structure of the mouse brain by computing the Minimal Spanning Forest, a technique that identifies subnetworks characterized by the strongest internal correlations. This approach represents a faster alternative to other community detection methods and provides a means to rank modules on the basis of the strength of their internal edges.

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Di Felice, Rosa

2011-05-01

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.

The chemistry of peroxovanadium compounds relevant to insulin mimesis.

PubMed

Shaver, A; Ng, J B; Hall, D A; Posner, B I

The inorganic coordination chemistry of peroxovanadium compounds relevant to insulin mimesis is reviewed. The structure and kinetic reactivity of solutions of vanadate anion, vanadyl complexes and peroxovanadate complexes are briefly compared. Peroxovanadium compounds contain an oxo group, one or two peroxo ligands (O2(2-)) and an ancillary ligand which is usually bidentate. These compounds approximate a trigonal bipyramidal structure which can be divided conceptually into a polar 'oxo' half and a relatively non-polar organic half. This presents a number of interesting design variations which are discussed with respect to the development of a rudimentary structure-activity correlation of insulin mimetic ability.

Significance tests for functional data with complex dependence structure.

PubMed

Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

2015-01-01

We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

Models of S/π interactions in protein structures: Comparison of the H2S–benzene complex with PDB data

PubMed Central

Ringer, Ashley L.; Senenko, Anastasia; Sherrill, C. David

2007-01-01

S/π interactions are prevalent in biochemistry and play an important role in protein folding and stabilization. Geometries of cysteine/aromatic interactions found in crystal structures from the Brookhaven Protein Data Bank (PDB) are analyzed and compared with the equilibrium configurations predicted by high-level quantum mechanical results for the H2S–benzene complex. A correlation is observed between the energetically favorable configurations on the quantum mechanical potential energy surface of the H2S–benzene model and the cysteine/aromatic configurations most frequently found in crystal structures of the PDB. In contrast to some previous PDB analyses, configurations with the sulfur over the aromatic ring are found to be the most important. Our results suggest that accurate quantum computations on models of noncovalent interactions may be helpful in understanding the structures of proteins and other complex systems. PMID:17766371

Structural brain aging and speech production: a surface-based brain morphometry study.

PubMed

Tremblay, Pascale; Deschamps, Isabelle

2016-07-01

While there has been a growing number of studies examining the neurofunctional correlates of speech production over the past decade, the neurostructural correlates of this immensely important human behaviour remain less well understood, despite the fact that previous studies have established links between brain structure and behaviour, including speech and language. In the present study, we thus examined, for the first time, the relationship between surface-based cortical thickness (CT) and three different behavioural indexes of sublexical speech production: response duration, reaction times and articulatory accuracy, in healthy young and older adults during the production of simple and complex meaningless sequences of syllables (e.g., /pa-pa-pa/ vs. /pa-ta-ka/). The results show that each behavioural speech measure was sensitive to the complexity of the sequences, as indicated by slower reaction times, longer response durations and decreased articulatory accuracy in both groups for the complex sequences. Older adults produced longer speech responses, particularly during the production of complex sequence. Unique age-independent and age-dependent relationships between brain structure and each of these behavioural measures were found in several cortical and subcortical regions known for their involvement in speech production, including the bilateral anterior insula, the left primary motor area, the rostral supramarginal gyrus, the right inferior frontal sulcus, the bilateral putamen and caudate, and in some region less typically associated with speech production, such as the posterior cingulate cortex.

Complexity, Training Paradigm Design, and the Contribution of Memory Subsystems to Grammar Learning

PubMed Central

Ettlinger, Marc; Wong, Patrick C. M.

2016-01-01

Although there is variability in nonnative grammar learning outcomes, the contributions of training paradigm design and memory subsystems are not well understood. To examine this, we presented learners with an artificial grammar that formed words via simple and complex morphophonological rules. Across three experiments, we manipulated training paradigm design and measured subjects' declarative, procedural, and working memory subsystems. Experiment 1 demonstrated that passive, exposure-based training boosted learning of both simple and complex grammatical rules, relative to no training. Additionally, procedural memory correlated with simple rule learning, whereas declarative memory correlated with complex rule learning. Experiment 2 showed that presenting corrective feedback during the test phase did not improve learning. Experiment 3 revealed that structuring the order of training so that subjects are first exposed to the simple rule and then the complex improved learning. The cumulative findings shed light on the contributions of grammatical complexity, training paradigm design, and domain-general memory subsystems in determining grammar learning success. PMID:27391085

Using iMCFA to Perform the CFA, Multilevel CFA, and Maximum Model for Analyzing Complex Survey Data.

PubMed

Wu, Jiun-Yu; Lee, Yuan-Hsuan; Lin, John J H

2018-01-01

To construct CFA, MCFA, and maximum MCFA with LISREL v.8 and below, we provide iMCFA (integrated Multilevel Confirmatory Analysis) to examine the potential multilevel factorial structure in the complex survey data. Modeling multilevel structure for complex survey data is complicated because building a multilevel model is not an infallible statistical strategy unless the hypothesized model is close to the real data structure. Methodologists have suggested using different modeling techniques to investigate potential multilevel structure of survey data. Using iMCFA, researchers can visually set the between- and within-level factorial structure to fit MCFA, CFA and/or MAX MCFA models for complex survey data. iMCFA can then yield between- and within-level variance-covariance matrices, calculate intraclass correlations, perform the analyses and generate the outputs for respective models. The summary of the analytical outputs from LISREL is gathered and tabulated for further model comparison and interpretation. iMCFA also provides LISREL syntax of different models for researchers' future use. An empirical and a simulated multilevel dataset with complex and simple structures in the within or between level was used to illustrate the usability and the effectiveness of the iMCFA procedure on analyzing complex survey data. The analytic results of iMCFA using Muthen's limited information estimator were compared with those of Mplus using Full Information Maximum Likelihood regarding the effectiveness of different estimation methods.

Current understanding of the correlation of lignin structure with biomass recalcitrance

DOE PAGES

Li, Mi; Pu, Yunqiao; Ragauskas, Arthur J.

2016-11-18

Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresources to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure. Advancement inmore » application of biorefinery to production of biofuels, chemicals, and bio-derived materials necessitates a fundamental understanding of the relationship of lignin structure and biomass recalcitrance. In this mini-review, we focus on recent investigations on the influence of lignin chemical properties on bioprocessability—pretreatment and enzymatic hydrolysis of biomass. Furthermore, lignin-enzyme interactions and the effects of lignin compositional units, hydroxycinnamates, and lignin functional groups on biomass recalcitrance have been highlighted, which will be useful not only in addressing biomass recalcitrance but also in deploying renewable lignocelluloses efficiently.« less

Current understanding of the correlation of lignin structure with biomass recalcitrance

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

Li, Mi; Pu, Yunqiao; Ragauskas, Arthur J.

Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresources to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure. Advancement inmore » application of biorefinery to production of biofuels, chemicals, and bio-derived materials necessitates a fundamental understanding of the relationship of lignin structure and biomass recalcitrance. In this mini-review, we focus on recent investigations on the influence of lignin chemical properties on bioprocessability—pretreatment and enzymatic hydrolysis of biomass. Furthermore, lignin-enzyme interactions and the effects of lignin compositional units, hydroxycinnamates, and lignin functional groups on biomass recalcitrance have been highlighted, which will be useful not only in addressing biomass recalcitrance but also in deploying renewable lignocelluloses efficiently.« less

Agent-based model with multi-level herding for complex financial systems

NASA Astrophysics Data System (ADS)

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-02-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level.

Agent-based model with multi-level herding for complex financial systems

PubMed Central

Chen, Jun-Jie; Tan, Lei; Zheng, Bo

2015-01-01

In complex financial systems, the sector structure and volatility clustering are respectively important features of the spatial and temporal correlations. However, the microscopic generation mechanism of the sector structure is not yet understood. Especially, how to produce these two features in one model remains challenging. We introduce a novel interaction mechanism, i.e., the multi-level herding, in constructing an agent-based model to investigate the sector structure combined with volatility clustering. According to the previous market performance, agents trade in groups, and their herding behavior comprises the herding at stock, sector and market levels. Further, we propose methods to determine the key model parameters from historical market data, rather than from statistical fitting of the results. From the simulation, we obtain the sector structure and volatility clustering, as well as the eigenvalue distribution of the cross-correlation matrix, for the New York and Hong Kong stock exchanges. These properties are in agreement with the empirical ones. Our results quantitatively reveal that the multi-level herding is the microscopic generation mechanism of the sector structure, and provide new insight into the spatio-temporal interactions in financial systems at the microscopic level. PMID:25669427

Mini-review: Current Understanding of the Correlation of Lignin Structure with Biomass Recalcitrance

NASA Astrophysics Data System (ADS)

Li, Mi; Pu, Yunqiao; Ragauskas, Arthur

2016-11-01

Lignin, a complex aromatic polymer in terrestrial plants, contributes significantly to biomass recalcitrance to microbial and/or enzymatic deconstruction. To reduce biomass recalcitrance, substantial endeavors have been exerted on pretreatment and lignin engineering in the past few decades. Lignin removal and/or alteration of lignin structure have been shown to result in reduced biomass recalcitrance with improved cell wall digestibility. While high lignin content is usually a barrier to a cost-efficient application of bioresource to biofuels, the direct correlation of lignin structure and its concomitant properties with biomass remains unclear due to the complexity of cell wall and lignin structure. Advancement in application of biorefinery to production of biofuels, chemicals, and biomaterials necessitates a fundamental understanding of the relationship of lignin structure and biomass recalcitrance. In this mini-review, we focus on recent investigations on the influence of lignin chemical properties on bioprocessability— pretreatment and enzymatic hydrolysis of biomass. Specifically, lignin-enzyme interaction and the effects of lignin compositional units, hydroxycinnamates, and lignin functional groups on biomass recalcitrance have been highlighted, which will be useful not only in addressing biomass recalcitrance but also in deploying renewable lignocelluloses efficiently.

Structure and Abundance of Nitrous Oxide Complexes in Earth's Atmosphere.

PubMed

Salmon, Steven R; de Lange, Katrina M; Lane, Joseph R

2016-04-07

We have investigated the lowest energy structures and binding energies of a series of atmospherically relevant nitrous oxide (N2O) complexes using explicitly correlated coupled cluster theory. Specifically, we have considered complexes with nitrogen (N2-N2O), oxygen (O2-N2O), argon (Ar-N2O), and water (H2O-N2O). We have calculated rotational constants and harmonic vibrational frequencies for the complexes and the constituent monomers. Statistical mechanics was used to determine the thermodynamic parameters for complex formation as a function of temperature and pressure. These results, in combination with relevant atmospheric data, were used to estimate the abundance of N2O complexes in Earth's atmosphere as a function of altitude. We find that the abundance of N2O complexes in Earth's atmosphere is small but non-negligible, and we suggest that N2O complexes may contribute to absorption of terrestrial radiation and be relevant for understanding the atmospheric fate of N2O.

Correlations between Community Structure and Link Formation in Complex Networks

PubMed Central

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

2013-01-01

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

Finer parcellation reveals detailed correlational structure of resting-state fMRI signals.

PubMed

Dornas, João V; Braun, Jochen

2018-01-15

Even in resting state, the human brain generates functional signals (fMRI) with complex correlational structure. To simplify this structure, it is common to parcellate a standard brain into coarse chunks. Finer parcellations are considered less reproducible and informative, due to anatomical and functional variability of individual brains. Grouping signals with similar local correlation profiles, restricted to each anatomical region (Tzourio-Mazoyer et al., 2002), we divide a standard brain into 758 'functional clusters' averaging 1.7cm 3 gray matter volume ('MD758' parcellation). We compare 758 'spatial clusters' of similar size ('S758'). 'Functional clusters' are spatially contiguous and cluster quality (integration and segregation of temporal variance) is far superior to 'spatial clusters', comparable to multi-modal parcellations of half the resolution (Craddock et al., 2012; Glasser et al., 2016). Moreover, 'functional clusters' capture many long-range functional correlations, with O(10 5 ) reproducibly correlated cluster pairs in different anatomical regions. The pattern of functional correlations closely mirrors long-range anatomical connectivity established by fibre tracking. MD758 is comparable to coarser parcellations (Craddock et al., 2012; Glasser et al., 2016) in terms of cluster quality, correlational structure (54% relative mutual entropy vs 60% and 61%), and sparseness (35% significant pairwise correlations vs 36% and 44%). We describe and evaluate a simple path to finer functional parcellations of the human brain. Detailed correlational structure is surprisingly consistent between individuals, opening new possibilities for comparing functional correlations between cognitive conditions, states of health, or pharmacological interventions. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

How cell wall complexity influences saccharification efficiency in Miscanthus sinensis

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

De Souza, Amanda P.; Kamei, Claire L. Alvim; Torres, Andres F.

The production of bioenergy from grasses has been developing quickly during the last decade, with Miscanthus being among the most important choices for production of bioethanol. However, one of the key barriers to producing bioethanol is the lack of information about cell wall structure. Cell walls are thought to display compositional differences that lead to emergence of a very high level of complexity, resulting in great diversity in cell wall architectures. In this work, a set of different techniques was used to access the complexity of cell walls of different genotypes of Miscanthus sinensis in order to understand how theymore » interfere with saccharification efficiency. Three genotypes of M. sinensis displaying different patterns of correlation between lignin content and saccharification efficiency were subjected to cell wall analysis by quantitative/qualitative analytical techniques such as monosaccharide composition, oligosaccharide profiling, and glycome profiling. When saccharification efficiency was correlated negatively with lignin, the structural features of arabinoxylan and xyloglucan were found to contribute positively to hydrolysis. In the absence of such correlation, different types of pectins, and some mannans contributed to saccharification efficiency. In conclusion, different genotypes of M. sinensis were shown to display distinct interactions among their cell wall components, which seem to influence cell wall hydrolysis.« less

How cell wall complexity influences saccharification efficiency in Miscanthus sinensis

DOE PAGES

De Souza, Amanda P.; Kamei, Claire L. Alvim; Torres, Andres F.; ...

2015-04-23

The production of bioenergy from grasses has been developing quickly during the last decade, with Miscanthus being among the most important choices for production of bioethanol. However, one of the key barriers to producing bioethanol is the lack of information about cell wall structure. Cell walls are thought to display compositional differences that lead to emergence of a very high level of complexity, resulting in great diversity in cell wall architectures. In this work, a set of different techniques was used to access the complexity of cell walls of different genotypes of Miscanthus sinensis in order to understand how theymore » interfere with saccharification efficiency. Three genotypes of M. sinensis displaying different patterns of correlation between lignin content and saccharification efficiency were subjected to cell wall analysis by quantitative/qualitative analytical techniques such as monosaccharide composition, oligosaccharide profiling, and glycome profiling. When saccharification efficiency was correlated negatively with lignin, the structural features of arabinoxylan and xyloglucan were found to contribute positively to hydrolysis. In the absence of such correlation, different types of pectins, and some mannans contributed to saccharification efficiency. In conclusion, different genotypes of M. sinensis were shown to display distinct interactions among their cell wall components, which seem to influence cell wall hydrolysis.« less

Correlation of ground tests and analyses of a dynamically scaled Space Station model configuration

NASA Technical Reports Server (NTRS)

Javeed, Mehzad; Edighoffer, Harold H.; Mcgowan, Paul E.

1993-01-01

Verification of analytical models through correlation with ground test results of a complex space truss structure is demonstrated. A multi-component, dynamically scaled space station model configuration is the focus structure for this work. Previously established test/analysis correlation procedures are used to develop improved component analytical models. Integrated system analytical models, consisting of updated component analytical models, are compared with modal test results to establish the accuracy of system-level dynamic predictions. Design sensitivity model updating methods are shown to be effective for providing improved component analytical models. Also, the effects of component model accuracy and interface modeling fidelity on the accuracy of integrated model predictions is examined.

Inheritance, Variscan tectonometamorphic evolution and Permian to Mesozoic rejuvenations in the metamorphic basement complexes of the Romanian Carpathians revealed by monazite microprobe geochronology

NASA Astrophysics Data System (ADS)

Săbău, Gavril; Negulescu, Elena

2014-05-01

Monazite U-Th-Pb chemical dating reaches an acceptable compromise between precision and accuracy on one side, and spatial resolution and textural constraints on the other side. Thus it has a powerful potential in testing the coherence of individual metamorphic basement units, and enabling correlations among them. Yet, sensitivity and specificity issues in monazite response to thermotectonic events, especially in the case of superposed effects, remain still unclear. Monazite dating at informative to detailed scale in the main metamorphic basement units of the Carpathians resulted in complex age spectra. In the main, the spectra are dominated by the most pervasive thermal and structural overprint, as checked against independent geochronological data. Post-peak age resetting is mostly present, but statistically subordinate. Resetting in case of superposed events is correlated with the degree of textural and paragenetic overprinting, inheritances being always indicated by more or less well-defined age clusters. The lack of relict ages correlating with prograde structural and porphyroblast zonation patterns is indicative for juvenile formations. Age data distribution in the Carpathians allowed distinction of pre-Variscan events, syn-metamorphic Variscan tectonic stacking of juvenile and reworked basement, post-Variscan differential tectonic uplift, as well as prograde metamorphic units ranging down to Upper Cretaceous ages. In the South Carpathians, the Alpine Danubian domain consists of several Variscan and Alpine thrust sheets containing a metamorphic complex dominated by Upper Proterozoic to Lower Cambrian metamorphic and magmatic ages (Lainici-Păiuş), and several complexes with metamorphic overprints ranging from Carboniferous to Lower Permian. Any correlation among these units, as well as geotectonic models placing a Lower Paleozoic oceanic domain between pre-existing Lainici-Păiuş and Drăgşan terranes are precluded by the age data. Other basement of the South Carpathians contain lower Paleozoic or older units intruded by Ordovician granitoids, imbricated with juvenile Variscan slivers, the structural sequence differing in individual basement complexes. So, in the Leaota Massif the lowermost term of the sequence is prograde Variscan, tectonically overlain by reworked lower Paleozoic gneisses, supporting thrust sheets with very low- to low-grade Variscan schists. In the Făgăraş Massif a lower Paleozoic (Cumpăna) complex bearing a strong Variscan overprint, straddles Variscan juvenile rocks, and the lowermost visible structural level is assumed by upper Carboniferous to Permian juvenile medium-grade metamorphic schists. In the Lotru Metamorphic Suite of the Alpine Getic Nappe, the Variscan stacking is overprinted by post-orogenic differential uplift, documented by the correlation among younging ages, structural and metamorphic low-pressure overprints, recording often higher metamorphic temperatures. The most spectacular structure is Upper Jurassic in age, contains high-grade metamorphic rocks and peraluminous anatectic granitoids, is outlined by a deformed boundary evolving from ductile to brittle regime during cooling, and induces a thermal overprint in the neighbouring rocks. In the basement units thrust over the Getic Nappe, the Sibişel unit yielded Permian prograde peak metamorphic ages and Triassic post-peak overprints, while an adjacent gneissic unit (Laz) delivered an exclusively Cretaceous age pattern. Unexpectedly young metamorphic ages resulted also for the East Carpathians and the Apuseni Mountains. While most of the ages obtained so far correspond to Variscan retrogression of older basement units, the lowermost structural unit of the infra-Bucovinian nappe system in the East Carpathians yielded Upper Cretaceous metamorphic ages in apparently monometamorphic medium-grade schists. In the Apuseni Mountains, schists of the Baia de Arieş Unit display an Upper Jurassic age spectrum, corresponding to a clearly prograde medium-grade event. The ages recorded not only question some of the currently accepted correlations among basement units, but urge to reconsideration of the way in which the basement-cover relationships are interpreted and extrapolated.

Correlation Between Structural, Spectroscopic, and Reactivity Properties Within a Series of Structurally Analogous Metastable Manganese(III)-Alkylperoxo Complexes

PubMed Central

Coggins, Michael K.; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A.

2013-01-01

Manganese–peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)–OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)–OOR compounds extend the number of known end-on Mn(III)–(η1-peroxos) to six. The ligand backbone is shown to alter the metal–ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O–O and Mn⋯Npy,quin distances), spectroscopic (E(πv*(O–O) → Mn CT band), νO–O), and kinetic (ΔH‡ and ΔS‡) parameters for these complexes provide compelling evidence for rate-limiting O–O bond cleavage. Products identified in the final reaction mixtures of Mn(III)–OOR decay are consistent with homolytic O–O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O–O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O–O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O–O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function. PMID:23432090

Correlation between structural, spectroscopic, and reactivity properties within a series of structurally analogous metastable manganese(III)-alkylperoxo complexes.

PubMed

Coggins, Michael K; Martin-Diaconescu, Vlad; DeBeer, Serena; Kovacs, Julie A

2013-03-20

Manganese-peroxos are proposed as key intermediates in a number of important biochemical and synthetic transformations. Our understanding of the structural, spectroscopic, and reactivity properties of these metastable species is limited, however, and correlations between these properties have yet to be established experimentally. Herein we report the crystallographic structures of a series of structurally related metastable Mn(III)-OOR compounds, and examine their spectroscopic and reactivity properties. The four reported Mn(III)-OOR compounds extend the number of known end-on Mn(III)-(η(1)-peroxos) to six. The ligand backbone is shown to alter the metal-ligand distances and modulate the electronic properties key to bonding and activation of the peroxo. The mechanism of thermal decay of these metastable species is examined via variable-temperature kinetics. Strong correlations between structural (O-O and Mn···N(py,quin) distances), spectroscopic (E(πv*(O-O) → Mn CT band), ν(O-O)), and kinetic (ΔH(‡) and ΔS(‡)) parameters for these complexes provide compelling evidence for rate-limiting O-O bond cleavage. Products identified in the final reaction mixtures of Mn(III)-OOR decay are consistent with homolytic O-O bond scission. The N-heterocyclic amines and ligand backbone (Et vs Pr) are found to modulate structural and reactivity properties, and O-O bond activation is shown, both experimentally and theoretically, to track with metal ion Lewis acidity. The peroxo O-O bond is shown to gradually become more activated as the N-heterocyclic amines move closer to the metal ion causing a decrease in π-donation from the peroxo πv*(O-O) orbital. The reported work represents one of very few examples of experimentally verified relationships between structure and function.

Automated batch fiducial-less tilt-series alignment in Appion using Protomo

PubMed Central

Noble, Alex J.; Stagg, Scott M.

2015-01-01

The field of electron tomography has benefited greatly from manual and semi-automated approaches to marker-based tilt-series alignment that have allowed for the structural determination of multitudes of in situ cellular structures as well as macromolecular structures of individual protein complexes. The emergence of complementary metal-oxide semiconductor detectors capable of detecting individual electrons has enabled the collection of low dose, high contrast images, opening the door for reliable correlation-based tilt-series alignment. Here we present a set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy. PMID:26455557

Structural characterization of a new lipid/DNA complex showing a selective transfection efficiency in ovarian cancer cells

NASA Astrophysics Data System (ADS)

Caracciolo, G.; Pozzi, D.; Caminiti, R.; Congiu Castellano, A.

2003-04-01

We investigated, for the first time, by using Energy Dispersive X-ray Diffraction, the structure of a new ternary cationic liposome formulated with dioleoyl trimethylammonium propane (DOTAP), 1,2-dioleoyl-3-phosphatidylethanolamine (DOPE) and cholesterol (Chol) (DDC) which has been recently found to have a selective high gene transfer ability in ovarian cancer cells. Our structural results provide a further experimental support to the widely accepted statement that there is not a simple and direct correlation between structure and transfection efficiency and that the factors controlling cationic lipid/DNA (CL-DNA) complexes-mediated gene transfer depend not only on the formulations of the cationic liposomes and their thermodynamic phase, but also significantly on the cell properties.

The Complex Action Recognition via the Correlated Topic Model

PubMed Central

Tu, Hong-bin; Xia, Li-min; Wang, Zheng-wu

2014-01-01

Human complex action recognition is an important research area of the action recognition. Among various obstacles to human complex action recognition, one of the most challenging is to deal with self-occlusion, where one body part occludes another one. This paper presents a new method of human complex action recognition, which is based on optical flow and correlated topic model (CTM). Firstly, the Markov random field was used to represent the occlusion relationship between human body parts in terms of an occlusion state variable. Secondly, the structure from motion (SFM) is used for reconstructing the missing data of point trajectories. Then, we can extract the key frame based on motion feature from optical flow and the ratios of the width and height are extracted by the human silhouette. Finally, we use the topic model of correlated topic model (CTM) to classify action. Experiments were performed on the KTH, Weizmann, and UIUC action dataset to test and evaluate the proposed method. The compared experiment results showed that the proposed method was more effective than compared methods. PMID:24574920

Medium range order and structural relaxation in As–Se network glasses through FSDP analysis

DOE PAGES

Golovchak, R.; Lucas, P.; Oelgoetz, J.; ...

2015-01-13

We performed synchrotron X-ray diffraction and neutron scattering studies on As-Se glasses in two states: as-prepared (rejuvenated) and aged for similar to 27 years. The first sharp diffraction peak (FSDP) obtained from the structure factor data as a function of composition and temperature indicates that the cooperative processes that are responsible for structural relaxation do not affect FSDP. The results are correlated with the composition dependence of the complex heat capacity of the glasses and concentration of different structural fragments in the glass network. Furthermore, the comparison of structural information shows that density fluctuations, which were thought previously to havemore » a significant contribution to FSDP, have much smaller effect than the cation-cation correlations, presence of ordered structural fragments or cage molecules.« less

Lagrangian space consistency relation for large scale structure

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

Horn, Bart; Hui, Lam; Xiao, Xiao, E-mail: bh2478@columbia.edu, E-mail: lh399@columbia.edu, E-mail: xx2146@columbia.edu

Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias and Riotto and Peloso and Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present.more » The simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.« less

Anisotropy of machine building materials

NASA Technical Reports Server (NTRS)

Ashkenazi, Y. K.

1981-01-01

The results of experimental studies of the anisotropy of elastic and strength characteristics of various structural materials, including pressure worked metals and alloys, laminated fiberglass plastics, and laminated wood plastics, are correlated and classified. Strength criteria under simple and complex stresses are considered as applied to anisotropic materials. Practical application to determining the strength of machine parts and structural materials is discussed.

Phenotypic integration in an extended phenotype: among-individual variation in nest-building traits of the alfalfa leafcutting bee (Megachile rotundata)

USDA-ARS?s Scientific Manuscript database

Structures such as nests and burrows are an essential component of many organisms’ life-cycle and requires a complex sequence of behaviors. Because behaviors can vary consistently among individuals and be correlated with one another, we hypothesized that these structures would 1) show evidence of am...

Reconstructing networks from dynamics with correlated noise

NASA Astrophysics Data System (ADS)

Tam, H. C.; Ching, Emily S. C.; Lai, Pik-Yin

2018-07-01

Reconstructing the structure of complex networks from measurements of the nodes is a challenge in many branches of science. External influences are always present and act as a noise to the networks of interest. In this paper, we present a method for reconstructing networks from measured dynamics of the nodes subjected to correlated noise that cannot be approximated by a white noise. This method can reconstruct the links of both bidirectional and directed networks, the correlation time and strength of the noise, and also the relative coupling strength of the links when the coupling functions have certain properties. Our method is built upon theoretical relations between network structure and measurable quantities from the dynamics that we have derived for systems that have fixed point dynamics in the noise-free limit. Using these theoretical results, we can further explain the shortcomings of two common practices of inferring links for bidirectional networks using the Pearson correlation coefficient and the partial correlation coefficient.

The structural role of weak and strong links in a financial market network

NASA Astrophysics Data System (ADS)

Garas, A.; Argyrakis, P.; Havlin, S.

2008-05-01

We investigate the properties of correlation based networks originating from economic complex systems, such as the network of stocks traded at the New York Stock Exchange (NYSE). The weaker links (low correlation) of the system are found to contribute to the overall connectivity of the network significantly more than the strong links (high correlation). We find that nodes connected through strong links form well defined communities. These communities are clustered together in more complex ways compared to the widely used classification according to the economic activity. We find that some companies, such as General Electric (GE), Coca Cola (KO), and others, can be involved in different communities. The communities are found to be quite stable over time. Similar results were obtained by investigating markets completely different in size and properties, such as the Athens Stock Exchange (ASE). The present method may be also useful for other networks generated through correlations.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

Inherent structure length in metallic glasses: Simplicity behind complexity

DOE PAGES

Wu, Yuan; Wang, Hui; Cheng, Yongqiang; ...

2015-08-06

One of the central themes in materials science is the structure-property relationship. In conventional crystalline metals, their mechanical behaviour is often dictated by well-defined structural defects such as dislocations, impurities, and twins. However, the structure-property relationship in amorphous alloys is far from being understood, due to great difficulties in characterizing and describing the disordered atomic-level structure. Here, we report a universal, yet simple, correlation between the macroscopic mechanical properties (i.e., yield strength and shear modulus) and a unique characteristic structural length in metallic glasses (MGs). Lastly, our analysis indicates that this characteristic length can incorporate effects of both the inter-atomicmore » distance and valence electron density in MGs, and result in the observed universal correlation. The current findings shed lights on the basic understanding of mechanical properties of MGs from their disordered atomic structures.« less

Cliques of Neurons Bound into Cavities Provide a Missing Link between Structure and Function.

PubMed

Reimann, Michael W; Nolte, Max; Scolamiero, Martina; Turner, Katharine; Perin, Rodrigo; Chindemi, Giuseppe; Dłotko, Paweł; Levi, Ran; Hess, Kathryn; Markram, Henry

2017-01-01

The lack of a formal link between neural network structure and its emergent function has hampered our understanding of how the brain processes information. We have now come closer to describing such a link by taking the direction of synaptic transmission into account, constructing graphs of a network that reflect the direction of information flow, and analyzing these directed graphs using algebraic topology. Applying this approach to a local network of neurons in the neocortex revealed a remarkably intricate and previously unseen topology of synaptic connectivity. The synaptic network contains an abundance of cliques of neurons bound into cavities that guide the emergence of correlated activity. In response to stimuli, correlated activity binds synaptically connected neurons into functional cliques and cavities that evolve in a stereotypical sequence toward peak complexity. We propose that the brain processes stimuli by forming increasingly complex functional cliques and cavities.

Sexual selection and the evolution of genital shape and complexity in water striders.

PubMed

Rowe, Locke; Arnqvist, Göran

2012-01-01

Animal genitalia show two striking but incompletely understood evolutionary trends: a great evolutionary divergence in the shape of genitalic structures, and characteristic structural complexity. Both features are thought to result from sexual selection, but explicit comparative tests are hampered by the fact that it is difficult to quantify both morphological complexity and divergence in shape. We undertake a comparative study of multiple nongenitalic and male genital traits in a clade of 15 water strider species to quantify complexity and shape divergence. We show that genital structures are more complex and their shape more divergent among species than nongenital traits. Further, intromittent genital traits are more complex and have evolved more divergently than nonintromittent genital traits. More importantly, shape and complexity of nonintromittent genital traits show correlated evolution with indices of premating sexual selection and intromittent genital traits with postmating sexual selection, suggesting that the evolution of different components of genital morphology are shaped independently by distinct forms of sexual selection. Our quantitative results provide direct comparative support for the hypothesis that sexual selection is associated with morphological complexity in genitalic traits and highlight the importance of quantifying morphological shape and complexity, rather than size in studies of genital evolution. © 2011 The Author(s). Evolution © 2011 The Society for the Study of Evolution.

Recent progress in heteronuclear long-range NMR of complex carbohydrates: 3D H2BC and clean HMBC.

PubMed

Meier, Sebastian; Petersen, Bent O; Duus, Jens Ø; Sørensen, Ole W

2009-11-02

The new NMR experiments 3D H2BC and clean HMBC are explored for challenging applications to a complex carbohydrate at natural abundance of (13)C. The 3D H2BC experiment is crucial for sequential assignment as it yields heteronuclear one- and two-bond together with COSY correlations for the (1)H spins, all in a single spectrum with good resolution and non-informative diagonal-type peaks suppressed. Clean HMBC is a remedy for the ubiquitous problem of strong coupling induced one-bond correlation artifacts in HMBC spectra of carbohydrates. Both experiments work well for one of the largest carbohydrates whose structure has been determined by NMR, not least due to the enhanced resolution offered by the third dimension in 3D H2BC and the improved spectral quality due to artifact suppression in clean HMBC. Hence these new experiments set the scene to take advantage of the sensitivity boost achieved by the latest generation of cold probes for NMR structure determination of even larger and more complex carbohydrates in solution.

Topological Characteristics of the Hong Kong Stock Market: A Test-based P-threshold Approach to Understanding Network Complexity

NASA Astrophysics Data System (ADS)

Xu, Ronghua; Wong, Wing-Keung; Chen, Guanrong; Huang, Shuo

2017-02-01

In this paper, we analyze the relationship among stock networks by focusing on the statistically reliable connectivity between financial time series, which accurately reflects the underlying pure stock structure. To do so, we firstly filter out the effect of market index on the correlations between paired stocks, and then take a t-test based P-threshold approach to lessening the complexity of the stock network based on the P values. We demonstrate the superiority of its performance in understanding network complexity by examining the Hong Kong stock market. By comparing with other filtering methods, we find that the P-threshold approach extracts purely and significantly correlated stock pairs, which reflect the well-defined hierarchical structure of the market. In analyzing the dynamic stock networks with fixed-size moving windows, our results show that three global financial crises, covered by the long-range time series, can be distinguishingly indicated from the network topological and evolutionary perspectives. In addition, we find that the assortativity coefficient can manifest the financial crises and therefore can serve as a good indicator of the financial market development.

Exact exchange and Wilson-Levy correlation: a pragmatic device for studying complex weakly-bonded systems.

PubMed

Walsh, T R

2005-02-07

The Wilson-Levy (WL) correlation functional is used together with Hartree-Fock (HF) theory to evaluate interaction energies at intermediate separations (i.e. around equilibrium separation) for several weakly-bonded systems. The HF+WL approach reproduces binding trends for all complexes studied: selected rare-gas dimers, isomers of the methane dimer, benzene dimer and naphthalene dimer, and base-pair stacking structures for pyrimidine, cytosine, uracil and guanine dimers. These HF+WL data are contrasted against results obtained from some popular functionals (including B3LYP and PBE), as well as two newly-developed functionals, X3LYP and xPBE. The utility of HF+WL, with reference to exact-exchange (EXX) density-functional theory, is discussed in terms of a suggested EXXWL exchange-correlation functional.

To assess the value of satellite photographs in the resource evaluation on a national scale

NASA Technical Reports Server (NTRS)

Hepworth, J. V. (Principal Investigator); Akehurst, S. M.

1973-01-01

The author has identified the following significant results. Some observations have been made on ERTS-1 color imagery and comparison of imagery. Results of geophysical work are correlated with ERTS-1 imagery and new lineaments are postuated in the northern Kalahari Desert. ERTS-1 imagery reveals complex structural trends in the Basement Complex in the Selebi-Pikwe area.

Wing scale microstructures and nanostructures in butterflies--natural photonic crystals.

PubMed

Vértesy, Z; Bálint, Zs; Kertész, K; Vigneron, J P; Lousse, V; Biró, L P

2006-10-01

The aim of our study was to investigate the correlation between structural colour and scale morphology in butterflies. Detailed correlations between blue colour and structure were investigated in three lycaenid subfamilies, which represent a monophylum in the butterfly family Lycaenidae (Lepidoptera): the Coppers (Lycaeninae), the Hairstreaks (Theclinae) and the Blues (Polyommatinae). Complex investigations such as spectral measurements and characterization by means of light microscopy, scanning electron microscopy and transmission electron microscopy enabled us to demonstrate that: (i) a wide array of nanostructures generate blue colours; (ii) monophyletic groups use qualitatively similar structures; and (iii) the hue of the blue colour is characteristic for the microstructure and nanostructure of the body of the scales.

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

NASA Astrophysics Data System (ADS)

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

2015-11-01

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

Boron difluoride dibenzoylmethane derivatives: Electronic structure and luminescence

NASA Astrophysics Data System (ADS)

Tikhonov, Sergey A.; Vovna, Vitaliy I.; Osmushko, Ivan S.; Fedorenko, Elena V.; Mirochnik, Anatoliy G.

2018-01-01

Electronic structure and optical properties of boron difluoride dibenzoylmethanate and four of its derivatives have been studied by X-ray photoelectron spectroscopy, absorption and luminescence spectroscopy and quantum chemistry (DFT, TDDFT). The relative quantum luminescence yields have been revealed to correlate with charge transfers of HOMO-LUMO transitions, energy barriers of aromatic substituents rotation and the lifetime of excited states in the investigated complexes. The bathochromic shift of intensive bands in the optical spectra has been observed to occur when the functional groups are introduced into p-positions of phenyl cycles due to destabilizing HOMO levels. Calculated energy intervals between electronic levels correlate well with XPS spectra structure of valence and core electrons.

Using Dispersed Modes During Model Correlation

NASA Technical Reports Server (NTRS)

Stewart, Eric C.; Hathcock, Megan L.

2017-01-01

The model correlation process for the modal characteristics of a launch vehicle is well established. After a test, parameters within the nominal model are adjusted to reflect structural dynamics revealed during testing. However, a full model correlation process for a complex structure can take months of man-hours and many computational resources. If the analyst only has weeks, or even days, of time in which to correlate the nominal model to the experimental results, then the traditional correlation process is not suitable. This paper describes using model dispersions to assist the model correlation process and decrease the overall cost of the process. The process creates thousands of model dispersions from the nominal model prior to the test and then compares each of them to the test data. Using mode shape and frequency error metrics, one dispersion is selected as the best match to the test data. This dispersion is further improved by using a commercial model correlation software. In the three examples shown in this paper, this dispersion based model correlation process performs well when compared to models correlated using traditional techniques and saves time in the post-test analysis.

Neural correlates of early-closure garden-path processing: Effects of prosody and plausibility.

PubMed

den Ouden, Dirk-Bart; Dickey, Michael Walsh; Anderson, Catherine; Christianson, Kiel

2016-01-01

Functional magnetic resonance imaging (fMRI) was used to investigate neural correlates of early-closure garden-path sentence processing and use of extrasyntactic information to resolve temporary syntactic ambiguities. Sixteen participants performed an auditory picture verification task on sentences presented with natural versus flat intonation. Stimuli included sentences in which the garden-path interpretation was plausible, implausible because of a late pragmatic cue, or implausible because of a semantic mismatch between an optionally transitive verb and the following noun. Natural sentence intonation was correlated with left-hemisphere temporal activation, but also with activation that suggests the allocation of more resources to interpretation when natural prosody is provided. Garden-path processing was associated with upregulation in bilateral inferior parietal and right-hemisphere dorsolateral prefrontal and inferior frontal cortex, while differences between the strength and type of plausibility cues were also reflected in activation patterns. Region of interest (ROI) analyses in regions associated with complex syntactic processing are consistent with a role for posterior temporal cortex supporting access to verb argument structure. Furthermore, ROI analyses within left-hemisphere inferior frontal gyrus suggest a division of labour, with the anterior-ventral part primarily involved in syntactic-semantic mismatch detection, the central part supporting structural reanalysis, and the posterior-dorsal part showing a general structural complexity effect.

Text mining by Tsallis entropy

NASA Astrophysics Data System (ADS)

Jamaati, Maryam; Mehri, Ali

2018-01-01

Long-range correlations between the elements of natural languages enable them to convey very complex information. Complex structure of human language, as a manifestation of natural languages, motivates us to apply nonextensive statistical mechanics in text mining. Tsallis entropy appropriately ranks the terms' relevance to document subject, taking advantage of their spatial correlation length. We apply this statistical concept as a new powerful word ranking metric in order to extract keywords of a single document. We carry out an experimental evaluation, which shows capability of the presented method in keyword extraction. We find that, Tsallis entropy has reliable word ranking performance, at the same level of the best previous ranking methods.

Entangled singularity patterns of photons in Ince-Gauss modes

NASA Astrophysics Data System (ADS)

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

2013-01-01

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

Modulation of Correlated Segment Fluctuations in IDPs upon Complex Formation as an Allosteric Regulatory Mechanism.

PubMed

Beier, Andreas; Schwarz, Thomas C; Kurzbach, Dennis; Platzer, Gerald; Tribuzio, Francesca; Konrat, Robert

2018-05-05

Molecular recognition of and by intrinsically disordered proteins (IDPs) is an intriguing and still largely elusive phenomenon. Typically, protein recognition involving IDPs requires either folding upon binding or, alternatively, the formation of "fuzzy complexes." Here we show via correlation analyses of paramagnetic relaxation enhancement data unprecedented and striking alterations of the concerted fluctuations within the conformational ensemble of IDPs upon ligand binding. We study the binding of α-synuclein to calmodulin, a ubiquitous calcium-binding protein, and the binding of the extracellular matrix IDP osteopontin to heparin, a mimic of the extracellular matrix ligand hyaluronic acid. In both cases, binding leads to reduction of correlated long-range motions in these two IDPs and thus indicates a loosening of structural compaction upon binding. Most importantly, however, the simultaneous presence of correlated and anti-correlated fluctuations in IDPs suggests the prevalence of "energetic frustration" and provides an explanation for the puzzling observation of disordered allostery in IDPs. Copyright © 2018. Published by Elsevier Ltd.

High-level ab initio studies of NO(X2Π)-O2(X3Σg -) van der Waals complexes in quartet states

NASA Astrophysics Data System (ADS)

Grein, Friedrich

2018-05-01

Geometry optimisations were performed on nine different structures of NO(X2Π)-O2(X3Σg-) van der Waals complexes in their quartet states, using the explicitly correlated RCCSD(T)-F12b method with basis sets up to the cc-pVQZ-F12 level. For the most stable configurations, counterpoise-corrected optimisations as well as extrapolations to the complete basis set (CBS) were performed. The X structure in the 4A‧ state was found to be most stable, with a CBS binding energy of -157 cm-1. The slipped tilted structures with N closer to O2 (Slipt-N), as well as the slipped parallel structure with O of NO closer to O2 (Slipp-O) in 4A″ states have binding energies of about -130 cm-1. C2v and linear complexes are less stable. According to calculated harmonic frequencies, the X isomer is bound. Isotropic hyperfine coupling constants of the complex are compared with those of the monomers.

Effects of Mutations on Structure-Function Relationships of Matrix Metalloproteinase-1.

PubMed

Singh, Warispreet; Fields, Gregg B; Christov, Christo Z; Karabencheva-Christova, Tatyana G

2016-10-14

Matrix metalloproteinase-1 (MMP-1) is one of the most widely studied enzymes involved in collagen degradation. Mutations of specific residues in the MMP-1 hemopexin-like (HPX) domain have been shown to modulate activity of the MMP-1 catalytic (CAT) domain. In order to reveal the structural and conformational effects of such mutations, a molecular dynamics (MD) study was performed of in silico mutated residues in the X-ray crystallographic structure of MMP-1 complexed with a collagen-model triple-helical peptide (THP). The results indicate an important role of the mutated residues in MMP-1 interactions with the THP and communication between the CAT and the HPX domains. Each mutation has a distinct impact on the correlated motions in the MMP-1•THP. An increased collagenase activity corresponded to the appearance of a unique anti-correlated motion and decreased correlated motions, while decreased collagenase activity corresponded both to increased and decreased anti-correlated motions.

Metal-organic complexes in geochemical processes: temperature dependence of the standard thermodynamic properties of aqueous complexes between metal cations and dicarboxylate ligands

NASA Astrophysics Data System (ADS)

Prapaipong, Panjai; Shock, Everett L.; Koretsky, Carla M.

1999-10-01

By combining results from regression and correlation methods, standard state thermodynamic properties for aqueous complexes between metal cations and divalent organic acid ligands (oxalate, malonate, succinate, glutarate, and adipate) are evaluated and applied to geochemical processes. Regression of experimental standard-state equilibrium constants with the revised Helgeson-Kirkham-Flowers (HKF) equation of state yields standard partial molal entropies (S¯°) of aqueous metal-organic complexes, which allow determination of thermodynamic properties of the complexes at elevated temperatures. In cases where S¯° is not available from either regression or calorimetric measurement, the values of S¯° can be estimated from a linear correlation between standard partial molal entropies of association (ΔS¯°r) and standard partial molal entropies of aqueous cations (S¯°M). The correlation is independent of cation charge, which makes it possible to predict S¯° for complexes between divalent organic acids and numerous metal cations. Similarly, correlations between standard Gibbs free energies of association of metal-organic complexes (ΔḠ°r) and Gibbs free energies of formation (ΔḠ°f) for divalent metal cations allow estimates of standard-state equilibrium constants where experimental data are not available. These correlations are found to be a function of ligand structure and cation charge. Predicted equilibrium constants for dicarboxylate complexes of numerous cations were included with those for inorganic and other organic complexes to study the effects of dicarboxylate complexes on the speciation of metals and organic acids in oil-field brines. Relatively low concentrations of oxalic and malonic acids affect the speciation of cations more than similar concentrations of succinic, glutaric, and adipic acids. However, the extent to which metal-dicarboxylate complexes contribute to the speciation of dissolved metals depends on the type of dicarboxylic acid ligand; relative concentration of inorganic, mono-, and dicarboxylate ligands; and the type of metal cation. As an example, in the same solution, dicarboxylic acids have a greater influence on the speciation of Fe+2 and Mg+2 than on the speciation of Zn+2 and Mn+2.

Influence of stochastic geometric imperfections on the load-carrying behaviour of thin-walled structures using constrained random fields

NASA Astrophysics Data System (ADS)

Lauterbach, S.; Fina, M.; Wagner, W.

2018-04-01

Since structural engineering requires highly developed and optimized structures, the thickness dependency is one of the most controversially debated topics. This paper deals with stability analysis of lightweight thin structures combined with arbitrary geometrical imperfections. Generally known design guidelines only consider imperfections for simple shapes and loading, whereas for complex structures the lower-bound design philosophy still holds. Herein, uncertainties are considered with an empirical knockdown factor representing a lower bound of existing measurements. To fully understand and predict expected bearable loads, numerical investigations are essential, including geometrical imperfections. These are implemented into a stand-alone program code with a stochastic approach to compute random fields as geometric imperfections that are applied to nodes of the finite element mesh of selected structural examples. The stochastic approach uses the Karhunen-Loève expansion for the random field discretization. For this approach, the so-called correlation length l_c controls the random field in a powerful way. This parameter has a major influence on the buckling shape, and also on the stability load. First, the impact of the correlation length is studied for simple structures. Second, since most structures for engineering devices are more complex and combined structures, these are intensively discussed with the focus on constrained random fields for e.g. flange-web-intersections. Specific constraints for those random fields are pointed out with regard to the finite element model. Further, geometrical imperfections vanish where the structure is supported.

Short-Range Temporal Interactions in Sleep; Hippocampal Spike Avalanches Support a Large Milieu of Sequential Activity Including Replay

PubMed Central

Mahoney, J. Matthew; Titiz, Ali S.; Hernan, Amanda E.; Scott, Rod C.

2016-01-01

Hippocampal neural systems consolidate multiple complex behaviors into memory. However, the temporal structure of neural firing supporting complex memory consolidation is unknown. Replay of hippocampal place cells during sleep supports the view that a simple repetitive behavior modifies sleep firing dynamics, but does not explain how multiple episodes could be integrated into associative networks for recollection during future cognition. Here we decode sequential firing structure within spike avalanches of all pyramidal cells recorded in sleeping rats after running in a circular track. We find that short sequences that combine into multiple long sequences capture the majority of the sequential structure during sleep, including replay of hippocampal place cells. The ensemble, however, is not optimized for maximally producing the behavior-enriched episode. Thus behavioral programming of sequential correlations occurs at the level of short-range interactions, not whole behavioral sequences and these short sequences are assembled into a large and complex milieu that could support complex memory consolidation. PMID:26866597

One pot synthesis of two Mn(II) perchlorate complexes with s-triazine NNN-pincer ligand; molecular structure, Hirshfeld analysis and DFT studies

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; El-Faham, Ayman

2018-07-01

Self assembly of Mn(II) perchlorate and bis(pyrazolo)-s-triazine pincer ligand (L) in methanol-water mixture afforded the homoleptic [MnL2](ClO4)2 complex (1) as plate colorless crystals. Following the crystallization process till the near dryness of the solution, we noted few needle like crystals of the heteroleptic [MnL(H2O)3](ClO4)2·H2O complex (2). Their molecular and supramolecular structures were analyzed using single crystal structure combined with Hirshfeld analysis. The packing of complexes 1 and 2 is dominated by weak Csbnd H⋯O and strong Osbnd H⋯O hydrogen bonds, respectively, as well as anion-π stacking interactions. Using Hirshfeld analysis, the percentages of the O⋯H intermolecular contacts are 32.7% and 36.8% for 1 and 2, respectively. The Mnsbnd N distances correlated well with the atoms in molecules (AIM) topological parameters. The amount of electron density transferred from the ligand units to the manganese centre are nearly the same (0.9 e) in both complexes.

Geographical genetic structuring and phenotypic variation in the Vellozia hirsuta (Velloziaceae) ochlospecies complex.

PubMed

Barbosa, Ariane R; Fiorini, Cecília F; Silva-Pereira, Viviane; Mello-Silva, Renato; Borba, Eduardo L

2012-09-01

Vellozia hirsuta forms a complex presenting wide morphological and anatomical variation, resulting in five specific names and 14 morpho-anatomical patterns occurring in disjunct populations. We carried out a phylogeographical study to investigate the existence of correlation among the genetic and morphological patterns within this complex, and to determine whether it is composed of various species or should be treated as an ochlospecies, a species having widely polymorphic and weakly polytypic complex variation, with morphological characteristics varying independently. We carried out phylogeographical analyses using cpDNA rpl32F-trnL intergenic region. We found 20 haplotypes in 23 populations sampled. The populations are genetically structured (Φ(ST) = 0.818) into four phylogeographical groups demonstrating geographical structuring but with no correlation with morpho-anatomical patterns. Our analyses do not support recognizing any of the species now synonymized under Vellozia hirsuta. The northern populations were the most genetically differentiated and could be considered a distinct taxon, as they are also morphologically different. It is recommended that Vellozia hirsuta be considered a single enormously variable species. The patterns of variation within V. hirsuta probably are related to climatic changes that occurred during the Pleistocene Epoch in tropical Brazil when reductions in forest cover favored the expansion of V. hirsuta populations into extensive lowland areas. The expansion of forest cover at the end of the glaciations would have again restricted the occurrence of campos rupestres vegetation to high elevations, which constitute the current centers of diversity of this species.

Universal size properties of a star-ring polymer structure in disordered environments

NASA Astrophysics Data System (ADS)

Haydukivska, K.; Blavatska, V.

2018-03-01

We consider the complex polymer system, consisting of a ring polymer connected to the f1-branched starlike structure, in a good solvent in the presence of structural inhomogeneities. In particular cases f1=1 and f1=2 , such a system restores the synthesized tadpole-shaped polystyrenes [Doi et al., Macromolecules 46, 1075 (2013), 10.1021/ma302511j]. We assume that structural defects are correlated at large distances x according to a power law x-a. Applying the direct polymer renormalization approach, we evaluate the universal size characteristics such as the ratio of the radii of gyration of star-ring and star topologies, and compare the effective sizes of single arms in complex structures and isolated polymers of the same total molecular weight. The nontrivial impact of disorder on these quantities is analyzed.

A unifying framework for marginalized random intercept models of correlated binary outcomes

PubMed Central

Swihart, Bruce J.; Caffo, Brian S.; Crainiceanu, Ciprian M.

2013-01-01

We demonstrate that many current approaches for marginal modeling of correlated binary outcomes produce likelihoods that are equivalent to the copula-based models herein. These general copula models of underlying latent threshold random variables yield likelihood-based models for marginal fixed effects estimation and interpretation in the analysis of correlated binary data with exchangeable correlation structures. Moreover, we propose a nomenclature and set of model relationships that substantially elucidates the complex area of marginalized random intercept models for binary data. A diverse collection of didactic mathematical and numerical examples are given to illustrate concepts. PMID:25342871

Automated batch fiducial-less tilt-series alignment in Appion using Protomo.

PubMed

Noble, Alex J; Stagg, Scott M

2015-11-01

The field of electron tomography has benefited greatly from manual and semi-automated approaches to marker-based tilt-series alignment that have allowed for the structural determination of multitudes of in situ cellular structures as well as macromolecular structures of individual protein complexes. The emergence of complementary metal-oxide semiconductor detectors capable of detecting individual electrons has enabled the collection of low dose, high contrast images, opening the door for reliable correlation-based tilt-series alignment. Here we present a set of automated, correlation-based tilt-series alignment, contrast transfer function (CTF) correction, and reconstruction workflows for use in conjunction with the Appion/Leginon package that are primarily targeted at automating structure determination with cryogenic electron microscopy. Copyright © 2015 Elsevier Inc. All rights reserved.

Whole-brain analytic measures of network communication reveal increased structure-function correlation in right temporal lobe epilepsy.

PubMed

Wirsich, Jonathan; Perry, Alistair; Ridley, Ben; Proix, Timothée; Golos, Mathieu; Bénar, Christian; Ranjeva, Jean-Philippe; Bartolomei, Fabrice; Breakspear, Michael; Jirsa, Viktor; Guye, Maxime

2016-01-01

The in vivo structure-function relationship is key to understanding brain network reorganization due to pathologies. This relationship is likely to be particularly complex in brain network diseases such as temporal lobe epilepsy, in which disturbed large-scale systems are involved in both transient electrical events and long-lasting functional and structural impairments. Herein, we estimated this relationship by analyzing the correlation between structural connectivity and functional connectivity in terms of analytical network communication parameters. As such, we targeted the gradual topological structure-function reorganization caused by the pathology not only at the whole brain scale but also both in core and peripheral regions of the brain. We acquired diffusion (dMRI) and resting-state fMRI (rsfMRI) data in seven right-lateralized TLE (rTLE) patients and fourteen healthy controls and analyzed the structure-function relationship by using analytical network communication metrics derived from the structural connectome. In rTLE patients, we found a widespread hypercorrelated functional network. Network communication analysis revealed greater unspecific branching of the shortest path (search information) in the structural connectome and a higher global correlation between the structural and functional connectivity for the patient group. We also found evidence for a preserved structural rich-club in the patient group. In sum, global augmentation of structure-function correlation might be linked to a smaller functional repertoire in rTLE patients, while sparing the central core of the brain which may represent a pathway that facilitates the spread of seizures.

Analysis of thermoelectric properties of high-temperature complex alloys of nickel-base, iron-base and cobalt-base groups

NASA Technical Reports Server (NTRS)

Holanda, R.

1984-01-01

The thermoelectric properties alloys of the nickel-base, iron-base, and cobalt-base groups containing from 1% to 25% 106 chromium were compared and correlated with the following material characteristics: atomic percent of the principle alloy constituent; ratio of concentration of two constituents; alloy physical property (electrical resistivity); alloy phase structure (percent precipitate or percent hardener content); alloy electronic structure (electron concentration). For solid-solution-type alloys the most consistent correlation was obtained with electron concentration, for precipitation-hardenable alloys of the nickel-base superalloy group, the thermoelectric potential correlated with hardener content in the alloy structure. For solid-solution-type alloys, no problems were found with thermoelectric stability to 1000; for precipitation-hardenable alloys, thermoelectric stability was dependent on phase stability. The effects of the compositional range of alloy constituents on temperature measurement uncertainty are discussed.

Atomic scale simulations of vapor cooled carbon clusters

NASA Astrophysics Data System (ADS)

Bogana, M. P.; Colombo, L.

2007-03-01

By means of atomistic simulations we observed the formation of many topologically non-equivalent carbon clusters formed by the condensation of liquid droplets, including: (i) standard fullerenes and onion-like structures, (ii) clusters showing extremely complex surfaces with both positive and negative curvatures and (iii) complex endohedral structures. In this work we offer a thorough structural characterization of the above systems, as well as an attempt to correlate the resulting structure to the actual protocol of growth. The IR and Raman responses of some exotic linear carbon structures have been further investigated, finding good agreement with experimental evidence of carbinoid structures in cluster-assembled films. Towards the aim of fully understanding the process of cluster-to-cluster coalescence dynamics, we further simulated an aerosol of amorphous carbon clusters at controlled temperatures. Various annealing temperatures and times have been observed, identifying different pathways for cluster ripening, ranging from simple coalescence to extensive reconstruction.

The neural correlates of morphological complexity processing: Detecting structure in pseudowords.

PubMed

Schuster, Swetlana; Scharinger, Mathias; Brooks, Colin; Lahiri, Aditi; Hartwigsen, Gesa

2018-06-01

Morphological complexity is a highly debated issue in visual word recognition. Previous neuroimaging studies have shown that speakers are sensitive to degrees of morphological complexity. Two-step derived complex words (bridging through bridge N  > bridge V  > bridging) led to more enhanced activation in the left inferior frontal gyrus than their 1-step derived counterparts (running through run V  > running). However, it remains unclear whether sensitivity to degrees of morphological complexity extends to pseudowords. If this were the case, it would indicate that abstract knowledge of morphological structure is independent of lexicality. We addressed this question by investigating the processing of two sets of pseudowords in German. Both sets contained morphologically viable two-step derived pseudowords differing in the number of derivational steps required to access an existing lexical representation and therefore the degree of structural analysis expected during processing. Using a 2 × 2 factorial design, we found lexicality effects to be distinct from processing signatures relating to structural analysis in pseudowords. Semantically-driven processes such as lexical search showed a more frontal distribution while combinatorial processes related to structural analysis engaged more parietal parts of the network. Specifically, more complex pseudowords showed increased activation in parietal regions (right superior parietal lobe and left precuneus) relative to pseudowords that required less structural analysis to arrive at an existing lexical representation. As the two sets were matched on cohort size and surface form, these results highlight the role of internal levels of morphological structure even in forms that do not possess a lexical representation. © 2018 Wiley Periodicals, Inc.

Geologic Map of Baranof Island, southeastern Alaska

USGS Publications Warehouse

Karl, Susan M.; Haeussler, Peter J.; Himmelberg, Glen R.; Zumsteg, Cathy L.; Layer, Paul W.; Friedman, Richard M.; Roeske, Sarah M.; Snee, Lawrence W.

2015-01-01

This map updates the geology of Baranof Island based on fieldwork, petrographic analyses, paleontologic ages, and isotopic ages. These new data provide constraints on depositional and metamorphic ages of lithostratigraphic rock units and the timing of structures that separate them. Kinematic analyses and thermobarometric calculations provide insights on the regional tectonic processes that affected the rocks on Baranof Island. The rocks on Baranof Island are components of a Paleozoic to Early Tertiary oceanic volcanic arc complex, including sedimentary and volcanic rocks that were deposited on and adjacent to the arc complex, deformed, and accreted. The arc complex consists of greenschist to amphibolite facies Paleozoic metavolcanic and metasedimentary rocks overlain by lower-grade Triassic metasedimentary and metavolcanic rocks and intruded by Jurassic calc-alkaline plutons. The Paleozoic rocks correlate well in age and lithology with rocks of the Sicker and Buttle Lake Groups of the Wrangellia terrane on Vancouver Island and differ from rocks of the Skolai Group that constitute basement to type-Wrangellia in the Wrangell Mountains. The Jurassic intrusive rocks are correlative with plutons that intrude the Wrangellia terrane on Vancouver Island but are lacking in the Wrangell Mountains. The rocks accreted beneath the arc complex are referred to as the Baranof Accretionary Complex in this report and are correlated with the Chugach Accretionary Complex of southern and southeastern Alaska and with the Pacific Rim Complex on Vancouver Island. Stratigraphic correlations between upper- and lower-plate rocks on Baranof Island and western Chichagof Island with rocks on Haida Gwaii and Vancouver Island, in addition to correlative ages of intrusive rocks and restorations of the Fairweather-Queen Charlotte, Chatham Strait, and Peril Strait Faults that define the Baranof-Chichagof block, suggest Baranof Island was near Vancouver Island at the time of initiation of arc magmatism in the Early Jurassic. Early Eocene plutons that intruded the accretionary complex outboard of the arc on Baranof Island are attributed to anatectic melting of trench sediments resulting from subduction of a spreading center. Oligocene intrusive rocks on Baranof Island correlate in age and composition with intrusive rocks in the Kano Plutonic Suite on Haida Gwaii, and similar magmatic sources are inferred.

Complex versus Simple Modeling for DIF Detection: When the Intraclass Correlation Coefficient (?) of the Studied Item Is Less Than the ? of the Total Score

ERIC Educational Resources Information Center

Jin, Ying; Myers, Nicholas D.; Ahn, Soyeon

2014-01-01

Previous research has demonstrated that differential item functioning (DIF) methods that do not account for multilevel data structure could result in too frequent rejection of the null hypothesis (i.e., no DIF) when the intraclass correlation coefficient (?) of the studied item was the same as the ? of the total score. The current study extended…

Environmental Constraints Guide Migration of Malaria Parasites during Transmission

PubMed Central

Hellmann, Janina Kristin; Münter, Sylvia; Kudryashev, Mikhail; Schulz, Simon; Heiss, Kirsten; Müller, Ann-Kristin; Matuschewski, Kai; Spatz, Joachim P.; Schwarz, Ulrich S.; Frischknecht, Friedrich

2011-01-01

Migrating cells are guided in complex environments mainly by chemotaxis or structural cues presented by the surrounding tissue. During transmission of malaria, parasite motility in the skin is important for Plasmodium sporozoites to reach the blood circulation. Here we show that sporozoite migration varies in different skin environments the parasite encounters at the arbitrary sites of the mosquito bite. In order to systematically examine how sporozoite migration depends on the structure of the environment, we studied it in micro-fabricated obstacle arrays. The trajectories observed in vivo and in vitro closely resemble each other suggesting that structural constraints can be sufficient to guide Plasmodium sporozoites in complex environments. Sporozoite speed in different environments is optimized for migration and correlates with persistence length and dispersal. However, this correlation breaks down in mutant sporozoites that show adhesion impairment due to the lack of TRAP-like protein (TLP) on their surfaces. This may explain their delay in infecting the host. The flexibility of sporozoite adaption to different environments and a favorable speed for optimal dispersal ensures efficient host switching during malaria transmission. PMID:21698220

Theoretical study of structure, bonding, and electronic behavior of novel sandwich compounds M₃(C6R6)₂ (M = Ni, Pd, Pt; R = H, F).

PubMed

Zhou, Ke

2012-10-01

The correlations between the structural and electronic properties of the monolayer clusters M₃ (where M = Ni, Pd, Pt) and the sandwich complexes M₃(C₆R₆)₂ (where M = Ni, Pd, Pt; R = H, F) were studied by performing quantum-chemical calculations. All of the sandwich complexes are strongly donating and backdonating metal-ligand bonding structures. The influence of the ligand as well as significant variations in the M-C, M-M, and C-C bond lengths and binding energies were examined to obtain a qualitative and quantitative picture of the intramolecular interactions in C₆R₆-M₃. Our theoretical investigations show that the binding energies of these sandwich complexes gradually decrease from Ni to Pt as well as from H to F, which can be explained via the frontier orbitals of the clusters M₃ and C₆R₆.

Molecular and electronic structure of terminal and alkali metal-capped uranium(V) nitride complexes

PubMed Central

King, David M.; Cleaves, Peter A.; Wooles, Ashley J.; Gardner, Benedict M.; Chilton, Nicholas F.; Tuna, Floriana; Lewis, William; McInnes, Eric J. L.; Liddle, Stephen T.

2016-01-01

Determining the electronic structure of actinide complexes is intrinsically challenging because inter-electronic repulsion, crystal field, and spin–orbit coupling effects can be of similar magnitude. Moreover, such efforts have been hampered by the lack of structurally analogous families of complexes to study. Here we report an improved method to U≡N triple bonds, and assemble a family of uranium(V) nitrides. Along with an isoelectronic oxo, we quantify the electronic structure of this 5f1 family by magnetometry, optical and electron paramagnetic resonance (EPR) spectroscopies and modelling. Thus, we define the relative importance of the spin–orbit and crystal field interactions, and explain the experimentally observed different ground states. We find optical absorption linewidths give a potential tool to identify spin–orbit coupled states, and show measurement of UV···UV super-exchange coupling in dimers by EPR. We show that observed slow magnetic relaxation occurs via two-phonon processes, with no obvious correlation to the crystal field. PMID:27996007

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations.

PubMed

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y; Schwegler, Eric

2016-10-21

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. Such simulations are often performed at elevated temperatures to artificially "correct" for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. To address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na + , K + , and Cl - ions. We show that simulations at 390-400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. Our results suggest that an elevated temperature around 390-400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.

The search for Pleiades in trait constellations: functional integration and phenotypic selection in the complex flowers of Morrenia brachystephana (Apocynaceae).

PubMed

Baranzelli, M C; Sérsic, A N; Cocucci, A A

2014-04-01

Pollinator-mediated natural selection on single traits, such as corolla tube or spur length, has been well documented. However, flower phenotypes are usually complex, and selection is expected to act on several traits that functionally interact rather than on a single isolated trait. Despite the fact that selection on complex phenotypes is expectedly widespread, multivariate selection modelling on such phenotypes still remains under-explored in plants. Species of the subfamily Asclepiadoideae (Apocynaceae) provide an opportunity to study such complex flower contrivances integrated by fine-scaled organs from disparate developmental origin. We studied the correlation structure among linear floral traits (i) by testing a priori morphological, functional or developmental hypotheses among traits and (ii) by exploring the organization of flower covariation, considering alternative expectations of modular organization or whole flower integration through conditional dependence analysis (CDA) and integration matrices. The phenotypic selection approach was applied to determine whether floral traits involved in the functioning of the pollination mechanism were affected by natural selection. Floral integration was low, suggesting that flowers are organized in more than just one correlation pleiad; our hypothetical functional correlation matrix was significantly correlated with the empirical matrix, and the CDA revealed three putative modules. Analyses of phenotypic selection showed significant linear and correlational gradients, lending support to expectations of functional interactions between floral traits. Significant correlational selection gradients found involved traits of different floral whorls, providing evidence for the existence of functional integration across developmental domains. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Intrinsic Thermodynamics and Structure Correlation of Benzenesulfonamides with a Pyrimidine Moiety Binding to Carbonic Anhydrases I, II, VII, XII, and XIII

PubMed Central

Kišonaitė, Miglė; Zubrienė, Asta; Čapkauskaitė, Edita; Smirnov, Alexey; Smirnovienė, Joana; Kairys, Visvaldas; Michailovienė, Vilma; Manakova, Elena; Gražulis, Saulius; Matulis, Daumantas

2014-01-01

The early stage of drug discovery is often based on selecting the highest affinity lead compound. To this end the structural and energetic characterization of the binding reaction is important. The binding energetics can be resolved into enthalpic and entropic contributions to the binding Gibbs free energy. Most compound binding reactions are coupled to the absorption or release of protons by the protein or the compound. A distinction between the observed and intrinsic parameters of the binding energetics requires the dissection of the protonation/deprotonation processes. Since only the intrinsic parameters can be correlated with molecular structural perturbations associated with complex formation, it is these parameters that are required for rational drug design. Carbonic anhydrase (CA) isoforms are important therapeutic targets to treat a range of disorders including glaucoma, obesity, epilepsy, and cancer. For effective treatment isoform-specific inhibitors are needed. In this work we investigated the binding and protonation energetics of sixteen [(2-pyrimidinylthio)acetyl]benzenesulfonamide CA inhibitors using isothermal titration calorimetry and fluorescent thermal shift assay. The compounds were built by combining four sulfonamide headgroups with four tailgroups yielding 16 compounds. Their intrinsic binding thermodynamics showed the limitations of the functional group energetic additivity approach used in fragment-based drug design, especially at the level of enthalpies and entropies of binding. Combined with high resolution crystal structural data correlations were drawn between the chemical functional groups on selected inhibitors and intrinsic thermodynamic parameters of CA-inhibitor complex formation. PMID:25493428

Empirical comparison of local structural similarity indices for collaborative-filtering-based recommender systems

NASA Astrophysics Data System (ADS)

Zhang, Qian-Ming; Shang, Ming-Sheng; Zeng, Wei; Chen, Yong; Lü, Linyuan

2010-08-01

Collaborative filtering is one of the most successful recommendation techniques, which can effectively predict the possible future likes of users based on their past preferences. The key problem of this method is how to define the similarity between users. A standard approach is using the correlation between the ratings that two users give to a set of objects, such as Cosine index and Pearson correlation coefficient. However, the costs of computing this kind of indices are relatively high, and thus it is impossible to be applied in the huge-size systems. To solve this problem, in this paper, we introduce six local-structure-based similarity indices and compare their performances with the above two benchmark indices. Experimental results on two data sets demonstrate that the structure-based similarity indices overall outperform the Pearson correlation coefficient. When the data is dense, the structure-based indices can perform competitively good as Cosine index, while with lower computational complexity. Furthermore, when the data is sparse, the structure-based indices give even better results than Cosine index.

Features of the Correlation Structure of Price Indices

PubMed Central

Gao, Xiangyun; An, Haizhong; Zhong, Weiqiong

2013-01-01

What are the features of the correlation structure of price indices? To answer this question, 5 types of price indices, including 195 specific price indices from 2003 to 2011, were selected as sample data. To build a weighted network of price indices each price index is represented by a vertex, and a positive correlation between two price indices is represented by an edge. We studied the features of the weighted network structure by applying economic theory to the analysis of complex network parameters. We found that the frequency of the price indices follows a normal distribution by counting the weighted degrees of the nodes, and we identified the price indices which have an important impact on the network's structure. We found out small groups in the weighted network by the methods of k-core and k-plex. We discovered structure holes in the network by calculating the hierarchy of the nodes. Finally, we found that the price indices weighted network has a small-world effect by calculating the shortest path. These results provide a scientific basis for macroeconomic control policies. PMID:23593399

Shuttle structural dynamics characteristics: The analysis and verification

NASA Technical Reports Server (NTRS)

Modlin, C. T., Jr.; Zupp, G. A., Jr.

1985-01-01

The space shuttle introduced a new dimension in the complexity of the structural dynamics of a space vehicle. The four-body configuration exhibited structural frequencies as low as 2 hertz with a model density on the order of 10 modes per hertz. In the verification process, certain mode shapes and frequencies were identified by the users as more important than others and, as such, the test objectives were oriented toward experimentally extracting those modes and frequencies for analysis and test correlation purposes. To provide the necessary experimental data, a series of ground vibration tests (GVT's) was conducted using test articles ranging from the 1/4-scale structural replica of the space shuttle to the full-scale vehicle. The vibration test and analysis program revealed that the mode shapes and frequency correlations below 10 hertz were good. The quality of correlation of modes between 10 and 20 hertz ranged from good to fair and that of modes above 20 hertz ranged from poor to good. Since the most important modes, based on user preference, were below 10 hertz, it was judged that the shuttle structural dynamic models were adequate for flight certifications.

Theoretical studies of UO(2)(OH)(H(2)O)(n) (+), UO(2)(OH)(2)(H(2)O)(n), NpO(2)(OH)(H(2)O)(n), and PuO(2)(OH)(H(2)O)(n) (+) (n

PubMed

Cao, Zhiji; Balasubramanian, K

2009-10-28

Extensive ab initio calculations have been carried out to study equilibrium structures, vibrational frequencies, and the nature of chemical bonds of hydrated UO(2)(OH)(+), UO(2)(OH)(2), NpO(2)(OH), and PuO(2)(OH)(+) complexes that contain up to 21 water molecules both in first and second hydration spheres in both aqueous solution and the gas phase. The structures have been further optimized by considering long-range solvent effects through a polarizable continuum dielectric model. The hydrolysis reaction Gibbs free energy of UO(2)(H(2)O)(5) (2+) is computed to be 8.11 kcal/mol at the MP2 level in good agreement with experiments. Our results reveal that it is necessary to include water molecules bound to the complex in the first hydration sphere for proper treatment of the hydrated complex and the dielectric cavity although water molecules in the second hydration sphere do not change the coordination complex. Structural reoptimization of the complex in a dielectric cavity seems inevitable to seek subtle structural variations in the solvent and to correlate with the observed spectra and thermodynamic properties in the aqueous environment. Our computations reveal dramatically different equilibrium structures in the gas phase and solution and also confirm the observed facile exchanges between the complex and bulk solvent. Complete active space multiconfiguration self-consistent field followed by multireference singles+doubles CI (MRSDCI) computations on smaller complexes confirm predominantly single-configurational nature of these species and the validity of B3LYP and MP2 techniques for these complexes in their ground states.

Cation and anion dependence of stable geometries and stabilization energies of alkali metal cation complexes with FSA(-), FTA(-), and TFSA(-) anions: relationship with physicochemical properties of molten salts.

PubMed

Tsuzuki, Seiji; Kubota, Keigo; Matsumoto, Hajime

2013-12-19

Stable geometries and stabilization energies (Eform) of the alkali metal complexes with bis(fluorosulfonyl)amide, (fluorosulfonyl)(trifluoromethylslufonyl)amide and bis(trifluoromethylsulfonyl)amide (FSA(-), FTA(-) and TFSA(-)) were studied by ab initio molecular orbital calculations. The FSA(-) complexes prefer the bidentate structures in which two oxygen atoms of two SO2 groups have contact with the metal cation. The FTA(-) and TFSA(-) complexes with Li(+) and Na(+) prefer the bidentate structures, while the FTA(-) and TFSA(-) complexes with Cs(+) prefer tridentate structures in which the metal cation has contact with two oxygen atoms of an SO2 group and one oxygen atom of another SO2 group. The two structures are nearly isoenergetic in the FTA(-) and TFSA(-) complexes with K(+) and Rb(+). The magnitude of Eform depends on the alkali metal cation significantly. The Eform calculated for the most stable TFSA(-) complexes with Li(+), Na(+), K(+), Rb(+) and Cs(+) cations at the MP2/6-311G** level are -137.2, -110.5, -101.1, -89.6, and -84.1 kcal/mol, respectively. The viscosity and ionic conductivity of the alkali TFSA molten salts have strong correlation with the magnitude of the attraction. The viscosity increases and the ionic conductivity decreases with the increase of the attraction. The melting points of the alkali TFSA and alkali BETA molten salts also have correlation with the magnitude of the Eform, which strongly suggests that the magnitude of the attraction play important roles in determining the melting points of these molten salts. The anion dependence of the Eform calculated for the complexes is small (less than 2.9 kcal/mol). This shows that the magnitude of the attraction is not the cause of the low melting points of alkali FTA molten salts compared with those of corresponding alkali TFSA molten salts. The electrostatic interactions are the major source of the attraction in the complexes. The electrostatic energies for the most stable TFSA(-) complexes with the five alkali metal cations are -140.3, -119.4, -104.1, -96.9, and -91.1 kcal/mol, respectively. The induction interactions also contribute to the attraction. In particular, the induction interactions are large in the Li(+) complexes. The induction energies for the five complexes are -46.6, -25.2, -17.5, -13.3, and -10.4 kcal/mol, respectively.

Electroencephalographic and imaging profile in a subacute sclerosing panencephalitis (SSPE) cohort: a correlative study.

PubMed

Praveen-kumar, S; Sinha, S; Taly, A B; Jayasree, S; Ravi, V; Vijayan, J; Ravishankar, S

2007-09-01

There are only a few studies correlating diverse radiological and EEG features of subacute sclerosing panencephalitis (SSPE). The objective of the study was to (a) describe EEG profile and (b) correlate it with the clinical and imaging data of patients with confirmed SSPE. This study was conducted at a University teaching hospital in south India and involved 58 patients (M:F=37:21, age: 12.3, SD 4.8 years) of SSPE. Diagnosis of SSPE was based on the characteristic clinical manifestations, and raised IgG (1:625) anti-measles antibody in cerebrospinal fluid (CSF) by ELISA in all the patients. Scalp EEGs were recorded on 16 channel machines using standard parameters and procedures. The EEG, clinical and imaging data were reviewed. EEGs were frequently abnormal: typical (37) and atypical (21). Diffuse slowing of background activity (BGA) was noted in 46 records being asymmetrical in six. Periodic complexes were periodic (32), quasi-periodic (21) or a-periodic (4). Periodic complexes (PC) (amplitude: 370.7, SD 171.2 microV; duration - 1.7, SD 2.0 s; inter-complex interval: 8.4, SD 9.2s) were symmetrical in 39 and asymmetrical in 19. CT (32) and MRI (23) scans were normal in 16 patients while others had white matter (15), cerebral edema (8), cerebral atrophy (8), basal ganglia (2), and thalamic (2) changes. There was an independent association of frontally dominant slowing of BGA (p=0.04) and typical PCs (p=0.03) with the diffuse cerebral edema on imaging. White matter changes correlated with slowing of BGA (p=0.04), but not with typical PC (p=0.16). This study provides valuable insight into the structural and clinical correlates of EEG changes in SSPE. Irrespective of the incidence of occurrence of SSPE in a community, a clinician should be aware of the wide spectra of EEG findings. This study also discusses the possible underlying structural and clinical correlates.

Knotting fingerprints resolve knot complexity and knotting pathways in ideal knots.

PubMed

Hyde, David A B; Henrich, Joshua; Rawdon, Eric J; Millett, Kenneth C

2015-09-09

We use disk matrices to define knotting fingerprints that provide fine-grained insights into the local knotting structure of ideal knots. These knots have been found to have spatial properties that highly correlate with those of interesting macromolecules. From this fine structure and an analysis of the associated planar graph, one can define a measure of knot complexity using the number of independent unknotting pathways from the global knot type as the knot is trimmed progressively to a short arc unknot. A specialization of the Cheeger constant provides a measure of constraint on these independent unknotting pathways. Furthermore, the structure of the knotting fingerprint supports a comparison of the tight knot pathways to the unconstrained unknotting pathways of comparable length.

Wide-Band Monolithic Acoustoelectric Memory Correlators.

DTIC Science & Technology

1982-11-01

piezoelectric and non- earlier analysis of thin- oxide varactors . The new analysis ex- conducting. Tapped structures which satisfy this criterion are plains...for tapped LiNbO3/metal- oxide - important realization. The logical consequence is that only silicon [26] structures is, in fact, not applicable here. It...Clarke, "The GaAs SAW depletion layer of’ the diode array. A more complex structure, diode storage correlalor," in 1980 Ultrasonics Synp. Proc., pp a GaAs

Enzymes with lid-gated active sites must operate by an induced fit mechanism instead of conformational selection

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

Sullivan, Sarah M.; Holyoak, Todd

2008-09-17

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Enzymes With Lid-Gated Active Sites Must Operate By An Induced Fit Mechanism Instead of Conformational Selection

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

Sullivan, S.M.; Holyoak, T.

2009-05-26

The induced fit and conformational selection/population shift models are two extreme cases of a continuum aimed at understanding the mechanism by which the final key-lock or active enzyme conformation is achieved upon formation of the correctly ligated enzyme. Structures of complexes representing the Michaelis and enolate intermediate complexes of the reaction catalyzed by phosphoenolpyruvate carboxykinase provide direct structural evidence for the encounter complex that is intrinsic to the induced fit model and not required by the conformational selection model. In addition, the structural data demonstrate that the conformational selection model is not sufficient to explain the correlation between dynamics andmore » catalysis in phosphoenolpyruvate carboxykinase and other enzymes in which the transition between the uninduced and the induced conformations occludes the active site from the solvent. The structural data are consistent with a model in that the energy input from substrate association results in changes in the free energy landscape for the protein, allowing for structural transitions along an induced fit pathway.« less

Data mining graphene: Correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects

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

Ziatdinov, Maxim A.; Fujii, Shintaro; Kiguchi, Manabu

The link between changes in the material crystal structure and its mechanical, electronic, magnetic, and optical functionalities known as the structure-property relationship is the cornerstone of the contemporary materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the materials structure property relationships on the single-impurity and atomic-configuration levels. Lacking, however, are the statistics-based approaches for cross-correlation of structure and property variables obtained in different information channels of the STEM and SPM experiments. Here we have designed an approach based on a combination of sliding windowmore » Fast Fourier Transform, Pearson correlation matrix, linear and kernel canonical correlation, to study a relationship between lattice distortions and electron scattering from the SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels which can explain coexistence of several quasiparticle interference patterns in the nanoscale regions of interest. In addition, the application of the kernel functions allowed us extracting a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. Lastly, the outlined approach can be further utilized to analyzing correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and has usually a complex multidimensional nature.« less

Data mining graphene: Correlative analysis of structure and electronic degrees of freedom in graphenic monolayers with defects

DOE PAGES

Ziatdinov, Maxim A.; Fujii, Shintaro; Kiguchi, Manabu; ...

2016-11-09

The link between changes in the material crystal structure and its mechanical, electronic, magnetic, and optical functionalities known as the structure-property relationship is the cornerstone of the contemporary materials science research. The recent advances in scanning transmission electron and scanning probe microscopies (STEM and SPM) have opened an unprecedented path towards examining the materials structure property relationships on the single-impurity and atomic-configuration levels. Lacking, however, are the statistics-based approaches for cross-correlation of structure and property variables obtained in different information channels of the STEM and SPM experiments. Here we have designed an approach based on a combination of sliding windowmore » Fast Fourier Transform, Pearson correlation matrix, linear and kernel canonical correlation, to study a relationship between lattice distortions and electron scattering from the SPM data on graphene with defects. Our analysis revealed that the strength of coupling to strain is altered between different scattering channels which can explain coexistence of several quasiparticle interference patterns in the nanoscale regions of interest. In addition, the application of the kernel functions allowed us extracting a non-linear component of the relationship between the lattice strain and scattering intensity in graphene. Lastly, the outlined approach can be further utilized to analyzing correlations in various multi-modal imaging techniques where the information of interest is spatially distributed and has usually a complex multidimensional nature.« less

Wave Propagation in Non-Stationary Statistical Mantle Models at the Global Scale

NASA Astrophysics Data System (ADS)

Meschede, M.; Romanowicz, B. A.

2014-12-01

We study the effect of statistically distributed heterogeneities that are smaller than the resolution of current tomographic models on seismic waves that propagate through the Earth's mantle at teleseismic distances. Current global tomographic models are missing small-scale structure as evidenced by the failure of even accurate numerical synthetics to explain enhanced coda in observed body and surface waveforms. One way to characterize small scale heterogeneity is to construct random models and confront observed coda waveforms with predictions from these models. Statistical studies of the coda typically rely on models with simplified isotropic and stationary correlation functions in Cartesian geometries. We show how to construct more complex random models for the mantle that can account for arbitrary non-stationary and anisotropic correlation functions as well as for complex geometries. Although this method is computationally heavy, model characteristics such as translational, cylindrical or spherical symmetries can be used to greatly reduce the complexity such that this method becomes practical. With this approach, we can create 3D models of the full spherical Earth that can be radially anisotropic, i.e. with different horizontal and radial correlation functions, and radially non-stationary, i.e. with radially varying model power and correlation functions. Both of these features are crucial for a statistical description of the mantle in which structure depends to first order on the spherical geometry of the Earth. We combine different random model realizations of S velocity with current global tomographic models that are robust at long wavelengths (e.g. Meschede and Romanowicz, 2014, GJI submitted), and compute the effects of these hybrid models on the wavefield with a spectral element code (SPECFEM3D_GLOBE). We finally analyze the resulting coda waves for our model selection and compare our computations with observations. Based on these observations, we make predictions about the strength of unresolved small-scale structure and extrinsic attenuation.

Analysis of the vibrational frequencies of the UO/sup 2 +//sub 2/ ion in complexes containing acido-ligands

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

Kobets, L.V.; Umreiko, D.S.

1986-02-01

This paper presents an analysis of the vibrational frequencies of the UO/sup 2 +//sub 2/ ion in its complexes with acido-ligands that shows that in the series of the compounds indicated the correlation of UO/sup 2 +//sub 2/ with the nature of the anions and in particular with their basicity is limited in nature and may not be considered without taking account of the specific structures. If neutral ligands are present in the complexes, the situation is probably even more complicated.

Dysprosium complexes with mono-/di-carboxylate ligands—From simple dimers to 2D and 3D frameworks

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

Zhang, Yingjie, E-mail: yzx@ansto.gov.au; Bhadbhade, Mohan; Scales, Nicholas

2014-11-15

Four dysprosium (Dy) single carboxylates, a formate, a propionate, a butyrate and an oxalate have been synthesized and structurally characterized. The structure of Dy(HCO{sub 2}){sub 3} (1) contains nine-fold coordinated Dy polyhedra in perfect tricapped trigonal prisms. They are linked through trigonal O atoms forming 1D pillars which are further linked together through tricapped O atoms into a 3D pillared metal organic framework. The network structure is stable up to 360 °C. The structure of [Dy{sub 2}(C{sub 2}O{sub 4}){sub 3}(H{sub 2}O){sub 6}]·2.5H{sub 2}O (2) contains nine-fold coordinated Dy polyhedra linking together through μ{sub 2}-bridging oxalate anions into a 2D hexagonalmore » layered structure. Both [Dy{sub 2}(Pr){sub 6}(H{sub 2}O){sub 4}]·(HPr){sub 0.5} (3) [Pr=(C{sub 2}H{sub 5}CO{sub 2}){sup −1}] and [Dy{sub 2}(Bu){sub 6}(H{sub 2}O){sub 4}] (4) [Bu=(C{sub 3}H{sub 7}CO{sub 2}){sup −1}] have similar di-nuclear structures. The Raman vibration modes of the complexes have been investigated. - Graphical abstract: Four dysprosium (Dy) complexes with formate, propionate, butyrate and oxalate ligands have been synthesized and characterized. The Dy formato complex has a 3D pillared metal organic framework and the structure is stable up to 360 °C whilst the complexes with longer alkyl chained mono-carboxylates possess similar di-nuclear structures. The Dy oxalato complex has a 2D hexagonal (honeycomb-type) structure. Their Raman vibration modes have been investigated. - Highlights: • New Dysprosium complexes with formate, propionate, butyrate and oxalate ligands. • Crystal structures range from dimers to two and three dimensional frameworks. • Vibrational modes have been investigated and correlated to the structures. • The complexes are thermal robust and stable to over 300 °C.« less

Structural basis for the development of SARS 3CL protease inhibitors from a peptide mimic to an aza-decaline scaffold.

PubMed

Teruya, Kenta; Hattori, Yasunao; Shimamoto, Yasuhiro; Kobayashi, Kazuya; Sanjoh, Akira; Nakagawa, Atsushi; Yamashita, Eiki; Akaji, Kenichi

2016-11-04

Design of inhibitors against severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL(pro) ) is a potentially important approach to fight against SARS. We have developed several synthetic inhibitors by structure-based drug design. In this report, we reveal two crystal structures of SARS 3CL(pro) complexed with two new inhibitors based on our previous work. These structures combined with six crystal structures complexed with a series of related ligands reported by us are collectively analyzed. To these eight complexes, the structural basis for inhibitor binding was analyzed by the COMBINE method, which is a chemometrical analysis optimized for the protein-ligand complex. The analysis revealed that the first two latent variables gave a cumulative contribution ratio of r(2)  = 0.971. Interestingly, scores using the second latent variables for each complex were strongly correlated with root mean square deviations (RMSDs) of side-chain heavy atoms of Met(49) from those of the intact crystal structure of SARS-3CL(pro) (r = 0.77) enlarging the S2 pocket. The substantial contribution of this side chain (∼10%) for the explanation of pIC50 s was dependent on stereochemistry and the chemical structure of the ligand adapted to the S2 pocket of the protease. Thus, starting from a substrate mimic inhibitor, a design for a central scaffold for a low molecular weight inhibitor was evaluated to develop a further potent inhibitor. © 2015 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 391-403, 2016. © 2015 Wiley Periodicals, Inc.

Structural effects in the interstitial solid solution system (La,Ce)(Fe,Si)13Cx-H: Correlation with hydrogenation kinetics

NASA Astrophysics Data System (ADS)

Hai, X.; Porcher, F.; Mayer, C.; Miraglia, S.

2018-02-01

Steady state and in-situ neutron powder diffraction on selected compositions of the magneto-caloric (La,Ce)(Fe,Si)13CxHy compounds has been used to locate the sites accommodated by the interstitial species and to reveal the structural modifications (breathing) that occur upon metal substitution and/or interstitial insertion. The latter type of measurement in which the sequential filling of interstitial sites is followed allows one to extract some useful hydrogenation kinetics data. This structural investigation has allowed to precise the deformations undergone by the complex metallic alloys La(Fe,Si)13 when subjected to light interstitial insertion or rare earth substitution at the cation site of the NaZn13-structure type. We attempt to correlate hydrogenation kinetics variations (depression or enhancement of the hydrogen absorption rate) with a particular inhomogeneous cell variation (breathing) and bonding of the NaZn13 structure-type.

THESEUS: maximum likelihood superpositioning and analysis of macromolecular structures.

PubMed

Theobald, Douglas L; Wuttke, Deborah S

2006-09-01

THESEUS is a command line program for performing maximum likelihood (ML) superpositions and analysis of macromolecular structures. While conventional superpositioning methods use ordinary least-squares (LS) as the optimization criterion, ML superpositions provide substantially improved accuracy by down-weighting variable structural regions and by correcting for correlations among atoms. ML superpositioning is robust and insensitive to the specific atoms included in the analysis, and thus it does not require subjective pruning of selected variable atomic coordinates. Output includes both likelihood-based and frequentist statistics for accurate evaluation of the adequacy of a superposition and for reliable analysis of structural similarities and differences. THESEUS performs principal components analysis for analyzing the complex correlations found among atoms within a structural ensemble. ANSI C source code and selected binaries for various computing platforms are available under the GNU open source license from http://monkshood.colorado.edu/theseus/ or http://www.theseus3d.org.

Interaction of curcumin with Al(III) and its complex structures based on experiments and theoretical calculations

NASA Astrophysics Data System (ADS)

Jiang, Teng; Wang, Long; Zhang, Sui; Sun, Ping-Chuan; Ding, Chuan-Fan; Chu, Yan-Qiu; Zhou, Ping

2011-10-01

Curcumin has been recognized as a potential natural drug to treat the Alzheimer's disease (AD) by chelating baleful metal ions, scavenging radicals and preventing the amyloid β (Aβ) peptides from the aggregation. In this paper, Al(III)-curcumin complexes with Al(III) were synthesized and characterized by liquid-state 1H, 13C and 27Al nuclear magnetic resonance (NMR), mass spectroscopy (MS), ultraviolet spectroscopy (UV) and generalized 2D UV-UV correlation spectroscopy. In addition, the density functional theory (DFT)-based UV and chemical shift calculations were also performed to view insight into the structures and properties of curcumin and its complexes. It was revealed that curcumin could interact strongly with Al(III) ion, and form three types of complexes under different molar ratios of [Al(III)]/[curcumin], which would restrain the interaction of Al(III) with the Aβ peptide, reducing the toxicity effect of Al(III) on the peptide.

Jahn-Teller distortion in the phosphorescent excited state of three-coordinate Au(I) phosphine complexes.

PubMed

Barakat, Khaldoon A; Cundari, Thomas R; Omary, Mohammad A

2003-11-26

DFT calculations were used to optimize the phosphorescent excited state of three-coordinate [Au(PR3)3]+ complexes. The results indicate that the complexes rearrange from their singlet ground-state trigonal planar geometry to a T-shape in the lowest triplet luminescent excited state. The optimized structure of the exciton contradicts the structure predicted based on the AuP bonding properties of the ground-state HOMO and LUMO. The rearrangement to T-shape is a Jahn-Teller distortion because an electron is taken from the degenerate e' (5dxy, 5dx2-y2) orbital upon photoexcitation of the ground-state D3h complex. The calculated UV absorption and visible emission energies are consistent with the experimental data and explain the large Stokes' shifts while such correlations are not possible in optimized models that constrained the exciton to the ground-state trigonal geometry.

PLI: a web-based tool for the comparison of protein-ligand interactions observed on PDB structures.

PubMed

Gallina, Anna Maria; Bisignano, Paola; Bergamino, Maurizio; Bordo, Domenico

2013-02-01

A large fraction of the entries contained in the Protein Data Bank describe proteins in complex with low molecular weight molecules such as physiological compounds or synthetic drugs. In many cases, the same molecule is found in distinct protein-ligand complexes. There is an increasing interest in Medicinal Chemistry in comparing protein binding sites to get insight on interactions that modulate the binding specificity, as this structural information can be correlated with other experimental data of biochemical or physiological nature and may help in rational drug design. The web service protein-ligand interaction presented here provides a tool to analyse and compare the binding pockets of homologous proteins in complex with a selected ligand. The information is deduced from protein-ligand complexes present in the Protein Data Bank and stored in the underlying database. Freely accessible at http://bioinformatics.istge.it/pli/.

The building blocks of economic complexity

PubMed Central

Hidalgo, César A.; Hausmann, Ricardo

2009-01-01

For Adam Smith, wealth was related to the division of labor. As people and firms specialize in different activities, economic efficiency increases, suggesting that development is associated with an increase in the number of individual activities and with the complexity that emerges from the interactions between them. Here we develop a view of economic growth and development that gives a central role to the complexity of a country's economy by interpreting trade data as a bipartite network in which countries are connected to the products they export, and show that it is possible to quantify the complexity of a country's economy by characterizing the structure of this network. Furthermore, we show that the measures of complexity we derive are correlated with a country's level of income, and that deviations from this relationship are predictive of future growth. This suggests that countries tend to converge to the level of income dictated by the complexity of their productive structures, indicating that development efforts should focus on generating the conditions that would allow complexity to emerge to generate sustained growth and prosperity. PMID:19549871

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

Wang, Liwei; Yang, Jin Kuk; Kabaleeswaran, Venkataraman

The death-inducing signaling complex (DISC) formed by the death receptor Fas, the adaptor protein FADD and caspase-8 mediates the extrinsic apoptotic program. Mutations in Fas that disrupt the DISC cause autoimmune lymphoproliferative syndrome (ALPS). Here we show that the Fas-FADD death domain (DD) complex forms an asymmetric oligomeric structure composed of 5-7 Fas DD and 5 FADD DD, whose interfaces harbor ALPS-associated mutations. Structure-based mutations disrupt the Fas-FADD interaction in vitro and in living cells; the severity of a mutation correlates with the number of occurrences of a particular interaction in the structure. The highly oligomeric structure explains the requirementmore » for hexameric or membrane-bound FasL in Fas signaling. It also predicts strong dominant negative effects from Fas mutations, which are confirmed by signaling assays. The structure optimally positions the FADD death effector domain (DED) to interact with the caspase-8 DED for caspase recruitment and higher-order aggregation.« less

Dynamics of water around the complex structures formed between the KH domains of far upstream element binding protein and single-stranded DNA molecules

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

Chakraborty, Kaushik; Bandyopadhyay, Sanjoy, E-mail: sanjoy@chem.iitkgp.ernet.in

2015-07-28

Single-stranded DNA (ss-DNA) binding proteins specifically bind to the single-stranded regions of the DNA and protect it from premature annealing, thereby stabilizing the DNA structure. We have carried out atomistic molecular dynamics simulations of the aqueous solutions of two DNA binding K homology (KH) domains (KH3 and KH4) of the far upstream element binding protein complexed with two short ss-DNA segments. Attempts have been made to explore the influence of the formation of such complex structures on the microscopic dynamics and hydrogen bond properties of the interfacial water molecules. It is found that the water molecules involved in bridging themore » ss-DNA segments and the protein domains form a highly constrained thin layer with extremely retarded mobility. These water molecules play important roles in freezing the conformational oscillations of the ss-DNA oligomers and thereby forming rigid complex structures. Further, it is demonstrated that the effect of complexation on the slow long-time relaxations of hydrogen bonds at the interface is correlated with hindered motions of the surrounding water molecules. Importantly, it is observed that the highly restricted motions of the water molecules bridging the protein and the DNA components in the complexed forms originate from more frequent hydrogen bond reformations.« less

Enhanced collective influence: A paradigm to optimize network disruption

NASA Astrophysics Data System (ADS)

Wu, Tao; Chen, Leiting; Zhong, Linfeng; Xian, Xingping

2017-04-01

The function of complex networks typically relies on the integrity of underlying structure. Sometimes, practical applications need to attack networks' function, namely inactivate and fragment networks' underlying structure. To effectively dismantle complex networks and regulate the function of them, a centrality measure, named CI (Morone and Makse, 2015), was proposed for node ranking. We observe that the performance of CI centrality in network disruption problem may deteriorate when it is used in networks with different topology properties. Specifically, the structural features of local network topology are overlooked in CI centrality, even though the local network topology of the nodes with a fixed CI value may have very different organization. To improve the ranking accuracy of CI, this paper proposes a variant ECI to CI by considering loop density and degree diversity of local network topology. And the proposed ECI centrality would degenerate into CI centrality with the reduction of the loop density and the degree diversity level. By comparing ECI with CI and classical centrality measures in both synthetic and real networks, the experimental results suggest that ECI can largely improve the performance of CI for network disruption. Based on the results, we analyze the correlation between the improvement and the properties of the networks. We find that the performance of ECI is positively correlated with assortative coefficient and community modularity and negatively correlated with degree inequality of networks, which can be used as guidance for practical applications.

Improving Density Functionals with Quantum Harmonic Oscillators

NASA Astrophysics Data System (ADS)

Tkatchenko, Alexandre

2013-03-01

Density functional theory (DFT) is the most widely used and successful approach for electronic structure calculations. However, one of the pressing challenges for DFT is developing efficient functionals that can accurately capture the omnipresent long-range electron correlations, which determine the structure and stability of many molecules and materials. Here we show that, under certain conditions, the problem of computing the long-range correlation energy of interacting electrons can be mapped to a system of coupled quantum harmonic oscillators (QHOs). The proposed model allows us to synergistically combine concepts from DFT, quantum chemistry, and the widely discussed random-phase approximation for the correlation energy. In the dipole limit, the interaction energy for a system of coupled QHOs can be calculated exactly, thereby leading to an efficient and accurate model for the many-body dispersion energy of complex molecules and materials. The studied examples include intermolecular binding energies, the conformational hierarchy of DNA structures, the geometry and stability of molecular crystals, and supramolecular host-guest complexes (A. Tkatchenko, R. A. DiStasio Jr., R. Car, M. Scheffler, Phys. Rev. Lett. 108, 236402 (2012); R. A. DiStasio Jr., A. von Lilienfeld, A. Tkatchenko, PNAS 109, 14791 (2012); A. Tkatchenko, D. Alfe, K. S. Kim, J. Chem. Theory and Comp. (2012), doi: 10.1021/ct300711r; A. Tkatchenko, A. Ambrosetti, R. A. DiStasio Jr., arXiv:1210.8343v1).

Hierarchy in directed random networks.

PubMed

Mones, Enys

2013-02-01

In recent years, the theory and application of complex networks have been quickly developing in a markable way due to the increasing amount of data from real systems and the fruitful application of powerful methods used in statistical physics. Many important characteristics of social or biological systems can be described by the study of their underlying structure of interactions. Hierarchy is one of these features that can be formulated in the language of networks. In this paper we present some (qualitative) analytic results on the hierarchical properties of random network models with zero correlations and also investigate, mainly numerically, the effects of different types of correlations. The behavior of the hierarchy is different in the absence and the presence of giant components. We show that the hierarchical structure can be drastically different if there are one-point correlations in the network. We also show numerical results suggesting that the hierarchy does not change monotonically with the correlations and there is an optimal level of nonzero correlations maximizing the level of hierarchy.

Crustal Seismic Structure beneath Portugal (Western Iberia) and the role of Variscan Inheritance

NASA Astrophysics Data System (ADS)

Veludo, Idalina; Afonso Dias, Nuno; Fonseca, Paulo; Matias, Luís; Carrilho, Fernando; Haberland, Christian; Villaseñor, Antonio

2017-04-01

Mainland Portugal comprises most of the Western portion of the Iberian Peninsula, in a geodynamic setting associated with the Africa-Eurasia plate boundary. The crustal structure in Portugal is the result of a complex assemblage history of continental collision and extension with most of the surface is covered by rocks dating to the Variscan orogeny, the coastal ranges dominated by Mesozoic structures and Mesocenozoic basins covering partially the mainland. The impact and extension of this complex tectonic in the structure of the Iberian Lithosphere is still a matter of discussion, especially in its western part beneath Portugal. The existing knowledge relating the observed surface geology and lithospheric structures is sparse and sometimes incoherent, the relation between shallow and deep structures and their lateral extension still widely undetermined. Some questions still pertinent are the role and influence of the several tectonic units and their contacts in the present tectonic regime and in the stress field observed today, and the relation between the anomalous seismicity and associated crustal deformation rates with the inherited structure from past orogenies. In this study we present the results of a local earthquake tomographic study, performed to image this complex crustal structure down to 20 km depth. The relocation of the onshore seismicity recorded in the period 2000-2014 with the new 3D model allows cleansing some of the alignments and their correlation with some of the main active structures in Portugal enabling for the first time to correlate a large number of tectonic features to the small magnitude seismicity pattern. The seismicity distribution also displays a complex pattern, mainly reflecting the interaction between inherited Variscan structures with more recent fault systems created during the rifting stages of the Atlantic and diapir magmatic intrusions. The complex history of the assemblage of the crust beneath Western Iberia is well-marked in the final models. The arcuate shape of the Ibero-Armorican Arc can be perceived over the general pattern of the Vp and Vp/Vs anomalies and the heterogeneity observed on the surface geology are clearly marked in the tomograms. Other significant features are the low Vp values associated with the Mesocenozoic rocks outcropping in the Lusitanian and Algarve basins, and the low Vp and high Vp/Vs values of the sedimentary cover of the Lower-Tagus and Sado Basin. Publication supported by FCT- project UID/GEO/50019/2013 - Instituto Dom Luiz.

Phase-space perspective on the wavelength-dependent electron correlation of strong-field double ionization of Xe

NASA Astrophysics Data System (ADS)

Shao, Yun; Yuan, Zongqiang; Ye, Difa; Fu, Libin; Liu, Ming-Ming; Sun, Xufei; Wu, Chengyin; Liu, Jie; Gong, Qihuang; Liu, Yunquan

2017-12-01

We measure the wavelength-dependent correlated-electron momentum (CEM) spectra of strong-field double ionization of Xe atoms, and observe a significant change from a roughly nonstructured (uncorrelated) pattern at 795 nm to an elongated distribution with V-shaped structure (correlated) at higher wavelengths of 1320 and 1810 nm, pointing to the transition of the ionization dynamics imprinted in the momentum distributions. These observations are well reproduced by a semiclassical model using Green-Sellin-Zachor potential to take into account the screening effect. We show that the momentum distribution of Xe2+ undergoes a bifurcation structure emerging from single-hump to double-hump structure as the laser wavelength increases, which is dramatically different from that of He2+, indicating the complex multi-electron effect. By back analyzing the double ionization trajectories in the phase space (the initial transverse momentum and the laser phase at the tunneling exit) of the first tunneled electrons, we provide deep insight into the physical origin for electron correlation dynamics. We find that a random distribution in phase-space is responsible for a less distinct structured CEM spectrum at shorter wavelength. While increasing the laser wavelength, a topology-invariant pattern in phase-space appears, leading to the clearly visible V-shaped structures.

Structure, energetics and vibrational spectra of dimers, trimers, and tetramers of HX (X = Cl, Br, I)

NASA Astrophysics Data System (ADS)

Latajka, Zdzislaw; Scheiner, Steve

1997-03-01

The title complexes are studied by correlated ab initio methods using a pseudopotential double-ζ basis set, augmented by diffuse sp and two sets of polarization functions. The binding energies of the complexes decrease in the order HCl > HBr > HI. In the mixed HX…HX' dimers, the nature of the proton-donor molecule is more important than is the proton-acceptor with respect to the strength of the interaction. Only one minimum is found on the potential energy surface of the trimers and tetramers, which corresponds to the C nh cyclic structure. Enlargement of the complex leads to progressively greater individual H-bond energy and HX bond stretch, coupled with reduced intermolecular separation and smaller nonlinearity of each H-bond. Electron correlation makes a larger contribution as the atomic number of X increases. The highest degree of cooperativity is noted for oligomers of HCl and HBr, as compared to HI. The nonadditivity is dominated by terms present at the SCF level. The vibrational frequencies exhibit trends that generally parallel the energetics and geometry patterns, particularly the red shifts of the HX stretches and the intermolecular modes.

(3, 2)D 1H, 13C BIRDr,X-HSQC-TOCSY for NMR structure elucidation of mixtures: application to complex carbohydrates.

PubMed

Brodaczewska, Natalia; Košťálová, Zuzana; Uhrín, Dušan

2018-02-01

Overlap of NMR signals is the major cause of difficulties associated with NMR structure elucidation of molecules contained in complex mixtures. A 2D homonuclear correlation spectroscopy in particular suffers from low dispersion of 1 H chemical shifts; larger dispersion of 13 C chemical shifts is often used to reduce this overlap, while still providing the proton-proton correlation information e.g. in the form of a 2D 1 H, 13 C HSQC-TOCSY experiment. For this methodology to work, 13 C chemical shift must be resolved. In case of 13 C chemical shifts overlap, 1 H chemical shifts can be used to achieve the desired resolution. The proposed (3, 2)D 1 H, 13 C BIRD r,X -HSQC-TOCSY experiment achieves this while preserving singlet character of cross peaks in the F 1 dimension. The required high-resolution in the 13 C dimension is thus retained, while the cross peak overlap occurring in a regular HSQC-TOCSY experiment is eliminated. The method is illustrated on the analysis of a complex carbohydrate mixture obtained by depolymerisation of a fucosylated chondroitin sulfate isolated from the body wall of the sea cucumber Holothuria forskali.

Topological Characteristics of the Hong Kong Stock Market: A Test-based P-threshold Approach to Understanding Network Complexity

PubMed Central

Xu, Ronghua; Wong, Wing-Keung; Chen, Guanrong; Huang, Shuo

2017-01-01

In this paper, we analyze the relationship among stock networks by focusing on the statistically reliable connectivity between financial time series, which accurately reflects the underlying pure stock structure. To do so, we firstly filter out the effect of market index on the correlations between paired stocks, and then take a t-test based P-threshold approach to lessening the complexity of the stock network based on the P values. We demonstrate the superiority of its performance in understanding network complexity by examining the Hong Kong stock market. By comparing with other filtering methods, we find that the P-threshold approach extracts purely and significantly correlated stock pairs, which reflect the well-defined hierarchical structure of the market. In analyzing the dynamic stock networks with fixed-size moving windows, our results show that three global financial crises, covered by the long-range time series, can be distinguishingly indicated from the network topological and evolutionary perspectives. In addition, we find that the assortativity coefficient can manifest the financial crises and therefore can serve as a good indicator of the financial market development. PMID:28145494

Density Functional Calculations for Prediction of 57Fe Mössbauer Isomer Shifts and Quadrupole Splittings in β-Diketiminate Complexes

PubMed Central

2017-01-01

The relative ease of Mössbauer spectroscopy and of density functional theory (DFT) calculations encourages the use of Mössbauer parameters as a validation method for calculations, and the use of calculations as a double check on crystallographic structures. A number of studies have proposed correlations between the computationally determined electron density at the iron nucleus and the observed isomer shift, but deviations from these correlations in low-valent iron β-diketiminate complexes encouraged us to determine a new correlation for these compounds. The use of B3LYP/def2-TZVP in the ORCA platform provides an excellent balance of accuracy and speed. We provide here not only this new correlation and a clear guide to its use but also a systematic analysis of the limitations of this approach. We also highlight the impact of crystallographic inaccuracies, DFT model truncation, and spin states, with intent to assist experimentalists to use Mössbauer spectroscopy and calculations together. PMID:28691111

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

NASA Astrophysics Data System (ADS)

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-01

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade.

PubMed

Samanta, Sudipta; Mukherjee, Sanchita

2018-01-28

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

Structured teleconnections reveal the South American monsoon onset: A network approach

NASA Astrophysics Data System (ADS)

Ciemer, Catrin; Ekhtiari, Nikoo; Barbosa, Henrique; Boers, Niklas; Donner, Reik; Kurths, Jürgen; Rammig, Anja; Winkelmann, Ricarda

2017-04-01

The regional onset dates of the global monsoon systems are, to first order, determined by the seasonal shift of the intertropical convergence zone. However, precise onset dates vary substantially from year to year due to the complexity of the involved mechanisms. In this study, we investigate processes determining the onset of the South American monsoon system (SAMS). In recent years, a trend towards later onset dates of the SAMS has been observed. A later onset of the monsoon can have severe impacts on agriculture and infrastructure such as farming, water transport routes, and the stability of the Amazon rainforest in the long term. Possible reasons for this shift involve a multitude of climatic phenomena and variables relevant for the SAMS. To account for the highly interactive nature of the SAMS, we here investigate it with the help of complex networks. By studying the temporal changes of the correlation structure in spatial rainfall networks, we are able to determine coherent areas of similar precipitation patterns, spot teleconnections in terms of strongly correlated areas, detect key regions for precipitation correlations, and finally reveal the monsoon onset by an abrupt shift from an unordered to an ordered correlation structure of the network. To further evaluate the shift in the monsoon onset, we couple our rainfall network to a network of climate networks using sea surface temperature as a second variable. We are thereby able to emphasize oceanic regions that are particularly important for the SAMS and anticipate the influence of future changes of sea-surface temperature on the SAMS.

Magnetic exchange in {Gd(III)-radical} complexes: method assessment, mechanism of coupling and magneto-structural correlations.

PubMed

Gupta, Tulika; Rajeshkumar, Thayalan; Rajaraman, Gopalan

2014-07-28

Density functional studies have been performed on ten different {Gd(III)-radical} complexes exhibiting both ferro and antiferromagnetic exchange interaction with an aim to assess a suitable exchange-correlation functional within DFT formalism. This study has also been extended to probe the mechanism of magnetic coupling and to develop suitable magneto-structural correlations for this pair. Our method assessments reveal the following order of increasing accuracy for the evaluation of J values compared to experimental coupling constants: B(40HF)LYP < BHandHLYP < TPSSH < PW91 < PBE < BP86 < OLYP < BLYP < PBE0 < X3LYP < B3LYP < B2PLYP. Grimme's double-hybrid functional is found to be superior compared to other functionals tested and this is followed very closely by the conventional hybrid B3LYP functional. At the basis set front, our calculations reveal that the incorporation of relativistic effect is important in these calculations and the relativistically corrected effective core potential (ECP) basis set is found to yield better Js compared to other methods. The supposedly empty 5d/6s/6p orbitals of Gd(III) are found to play an important role in the mechanism of magnetic coupling and different contributions to the exchange terms are probed using Molecular Orbital (MO) and Natural Bond Orbital (NBO) analysis. Magneto-structural correlations for Gd-O distances, Gd-O-N angles and Gd-O-N-C dihedral angles are developed where the bond angles as well as dihedral angle parameters are found to dictate the sign and strength of the magnetic coupling in this series.

Ca K-Edge XAS as a Probe of Calcium Centers in Complex Systems

DOE PAGES

Martin-Diaconescu, Vlad; Gennari, Marcello; Gerey, Bertrand; ...

2014-12-10

Calcium K-edge pre-edges coupled with TD-DFT theoretical calculation of spectra provide a powerful approach for the characterization of complex calcium centers in inorganic and bioinorganic chemistry. Herein, Ca K-edge X-ray absorption spectroscopy (XAS) is developed as a means to characterize the local environment of calcium centers. The spectra for six, seven, and eight coordinate inorganic and molecular calcium complexes were analyzed and determined to be primarily influenced by the coordination environment and site symmetry at the calcium center. The experimental results are closely correlated to time-dependent density functional theory (TD-DFT) calculations of the XAS spectra. The applicability of this methodologymore » to complex systems was investigated using structural mimics of the oxygen-evolving complex (OEC) of PSII. It was found that Ca K-edge XAS is a sensitive probe for structural changes occurring in the cubane heterometallic cluster due to Mn oxidation. Future applications to the OEC are discussed.« less

Structural Element Testing in Support of the Design of the NASA Composite Crew Module

NASA Technical Reports Server (NTRS)

Kellas, Sotiris; Jackson, Wade C.; Thesken, John C.; Schleicher, Eric; Wagner, Perry; Kirsch, Michael T.

2012-01-01

In January 2007, the NASA Administrator and Associate Administrator for the Exploration Systems Mission Directorate chartered the NASA Engineering and Safety Center (NESC) to design, build, and test a full-scale Composite Crew Module (CCM). For the design and manufacturing of the CCM, the team adopted the building block approach where design and manufacturing risks were mitigated through manufacturing trials and structural testing at various levels of complexity. Following NASA's Structural Design Verification Requirements, a further objective was the verification of design analysis methods and the provision of design data for critical structural features. Test articles increasing in complexity from basic material characterization coupons through structural feature elements and large structural components, to full-scale structures were evaluated. This paper discusses only four elements tests three of which include joints and one that includes a tapering honeycomb core detail. For each test series included are specimen details, instrumentation, test results, a brief analysis description, test analysis correlation and conclusions.

Computer-aided molecular modeling techniques for predicting the stability of drug cyclodextrin inclusion complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Faucci, Maria Teresa; Melani, Fabrizio; Mura, Paola

2002-06-01

Molecular modeling was used to investigate factors influencing complex formation between cyclodextrins and guest molecules and predict their stability through a theoretical model based on the search for a correlation between experimental stability constants ( Ks) and some theoretical parameters describing complexation (docking energy, host-guest contact surfaces, intermolecular interaction fields) calculated from complex structures at a minimum conformational energy, obtained through stochastic methods based on molecular dynamic simulations. Naproxen, ibuprofen, ketoprofen and ibuproxam were used as model drug molecules. Multiple Regression Analysis allowed identification of the significant factors for the complex stability. A mathematical model ( r=0.897) related log Ks with complex docking energy and lipophilic molecular fields of cyclodextrin and drug.

Ab initio and DFT study of hydrogen bond interactions between ascorbic acid and dimethylsulfoxide based on FT-IR and FT-Raman spectra

NASA Astrophysics Data System (ADS)

Niazazari, Naser; Zatikyan, Ashkhen L.; Markarian, Shiraz A.

2013-06-01

The hydrogen bonding of 1:1 complexes formed between L-ascorbic acid (LAA) and dimethylsulfoxide (DMSO) has been studied by means of ab initio and density functional theory (DFT) calculations. Solutions of L-ascorbic acid (AA) in dimethylsulfoxide (DMSO) have been studied by means of both FT-IR (4000-220 cm-1) and FT-Raman spectroscopy. Ab initio Hartree-Fock (HF) and DFT methods have been used to determine the structure and energies of stable conformers of various types of L-AA/DMSO complexes in gas phase and solution. The basis sets 6-31++G∗∗ and 6-311+G∗ were used to describe the structure, energy, charges and vibrational frequencies of interacting complexes in the gas phase. The optimized geometric parameters and interaction energies for various complexes at different theories have been estimated. Binding energies have been corrected for basis set superposition error (BSSE) and harmonic vibrational frequencies of the structures have been calculated to obtain the stable forms of the complexes. The self-consistent reaction field (SCRF) has been used to calculate the effect of DMSO as the solvent on the geometry, energy and charges of complexes. The solvent effect has been studied using the Onsager models. It is shown that the polarity of the solvent plays an important role on the structures and relative stabilities of different complexes. The results obtained show that there is a satisfactory correlation between experimental and theoretical predictions.

Direct observation of the actin filament by tip-scan atomic force microscopy

PubMed Central

Narita, Akihiro; Usukura, Eiji; Yagi, Akira; Tateyama, Kiyohiko; Akizuki, Shogo; Kikumoto, Mahito; Matsumoto, Tomoharu; Maéda, Yuichiro; Ito, Shuichi; Usukura, Jiro

2016-01-01

Actin filaments, the actin–myosin complex and the actin–tropomyosin complex were observed by a tip-scan atomic force microscope (AFM), which was recently developed by Olympus as the AFM part of a correlative microscope. This newly developed AFM uses cantilevers of similar size as stage-scan AFMs to improve substantially the spatial and temporal resolution. Such an approach has previously never been possible by a tip-scan system, in which a cantilever moves in the x, y and z directions. We evaluated the performance of this developed tip-scan AFM by observing the molecular structure of actin filaments and the actin–tropomyosin complex. In the image of the actin filament, the molecular interval of the actin subunits (∼5.5 nm) was clearly observed as stripes. From the shape of the stripes, the polarity of the actin filament was directly determined and the results were consistent with the polarity determined by myosin binding. In the image of the actin–tropomyosin complex, each tropomyosin molecule (∼2 nm in diameter) on the actin filament was directly observed without averaging images of different molecules. Each tropomyosin molecule on the actin filament has never been directly observed by AFM or electron microscopy. Thus, our developed tip-scan AFM offers significant potential in observing purified proteins and cellular structures at nanometer resolution. Current results represent an important step in the development of a new correlative microscope to observe nm-order structures at an acceptable frame rate (∼10 s/frame) by AFM at the position indicated by the fluorescent dye observed under a light microscope. PMID:27242058

Structure of local interactions in complex financial dynamics

PubMed Central

Jiang, X. F.; Chen, T. T.; Zheng, B.

2014-01-01

With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906

The Structure of Lombricine Kinase

PubMed Central

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.; Davulcu, Omar; Fabiola, Felcy; Xie, Qing; Somasundaram, Thayumanasamy; Ellington, W. Ross; Chapman, Michael S.

2011-01-01

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309–317, which is disordered in substrate-free structures of homologs and is known from the NMR of arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His178. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates. PMID:21212263

Roles of conjugated double bonds in electron-donating capacity of sorghum grains

USDA-ARS?s Scientific Manuscript database

Electron-donating and metal ion complexation ability of tannins play key roles as antioxidants and in mold/bird resistance. In this study, rapid, sensitive, and nondestructive fluorescence excitation-emission (EEM) spectrophotometry was utilized to correlate structural attributes of sorghum tannins...

Magneto-structural correlations in dirhenium(iv) complexes possessing magnetic pathways with even or odd numbers of atoms.

PubMed

Pedersen, Anders H; Julve, Miguel; Martínez-Lillo, José; Cano, Joan; Brechin, Euan K

2017-09-12

The employment of pyrazine (pyz), pyrimidine (pym) and s-triazine (triz) ligands in Re IV chemistry leads to the isolation of a family of complexes of general formula (NBu 4 ) 2 [(ReX 5 ) 2 (μ-L)] (L = pyz, X = Cl (1) or Br (2); L = pym, X = Br (3); L = triz, X = Br (4)). 1-4 are dinuclear compounds where two pentahalorhenium(iv) fragments are connected by bidentate pyz, pym and triz ligands. Variable-temperature magnetic measurements, in combination with detailed theoretical studies, uncover the underlying magneto-structural correlation whereby the nature of the exchange between the metal ions is dictated by the number of intervening atoms. That is, the spin-polarization mechanism present dictates that odd and even numbers of atoms favour ferromagnetic (F) and antiferromagnetic (AF) exchange interactions, respectively. Hence, while the pyz ligand in 1 and 2 mediates AF coupling, the pym and triz ligands in 3 and 4 promote F interactions.

Towards a nondestructive chemical characterization of biofilm matrix by Raman microscopy.

PubMed

Ivleva, Natalia P; Wagner, Michael; Horn, Harald; Niessner, Reinhard; Haisch, Christoph

2009-01-01

In this study, the applicability of Raman microscopy (RM) for nondestructive chemical analysis of biofilm matrix, including microbial constituents and extracellular polymeric substances (EPS), has been assessed. The examination of a wide range of reference samples such as biofilm-specific polysaccharides, proteins, microorganisms, and encapsulated bacteria revealed characteristic frequency regions and specific marker bands for different biofilm constituents. Based on received data, the assignment of Raman bands in spectra of multispecies biofilms was performed. The study of different multispecies biofilms showed that RM can correlate various structural appearances within the biofilm to variations in their chemical composition and provide chemical information about a complex biofilm matrix. The results of RM analysis of biofilms are in good agreement with data obtained by confocal laser scanning microscopy (CLSM). Thus, RM is a promising tool for a label-free chemical characterization of different biofilm constituents. Moreover, the combination of RM with CLSM analysis for the study of biofilms grown under different environmental conditions can provide new insights into the complex structure/function correlations in biofilms.

A novel Arg H52/Tyr H33 conservative motif in antibodies: A correlation between sequence of antibodies and antigen binding.

PubMed

Petrov, Artem; Arzhanik, Vladimir; Makarov, Gennady; Koliasnikov, Oleg

2016-08-01

Antibodies are the family of proteins, which are responsible for antigen recognition. The computational modeling of interaction between an antigen and an antibody is very important when crystallographic structure is unavailable. In this research, we have discovered the correlation between the amino acid sequence of antibody and its specific binding characteristics on the example of the novel conservative binding motif, which consists of four residues: Arg H52, Tyr H33, Thr H59, and Glu H61. These residues are specifically oriented in the binding site and interact with each other in a specific manner. The residues of the binding motif are involved in interaction strictly with negatively charged groups of antigens, and form a binding complex. Mechanism of interaction and characteristics of the complex were also discovered. The results of this research can be used to increase the accuracy of computational antibody-antigen interaction modeling and for post-modeling quality control of the modeled structures.

Solution Structures of 2 : 1 And 1 : 1 DNA Polymerase - DNA Complexes Probed By Ultracentrifugation And Small-Angle X-Ray Scattering

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

Tang, K.H.; /Ohio State U.; Niebuhr, M.

2009-04-30

We report small-angle X-ray scattering (SAXS) and sedimentation velocity (SV) studies on the enzyme-DNA complexes of rat DNA polymerase {beta} (Pol {beta}) and African swine fever virus DNA polymerase X (ASFV Pol X) with one-nucleotide gapped DNA. The results indicated formation of a 2 : 1 Pol {beta}-DNA complex, whereas only 1 : 1 Pol X-DNA complex was observed. Three-dimensional structural models for the 2 : 1 Pol {beta}-DNA and 1 : 1 Pol X-DNA complexes were generated from the SAXS experimental data to correlate with the functions of the DNA polymerases. The former indicates interactions of the 8 kDamore » 5{prime}-dRP lyase domain of the second Pol {beta} molecule with the active site of the 1 : 1 Pol {beta}-DNA complex, while the latter demonstrates how ASFV Pol X binds DNA in the absence of DNA-binding motif(s). As ASFV Pol X has no 5{prime}-dRP lyase domain, it is reasonable not to form a 2 : 1 complex. Based on the enhanced activities of the 2 : 1 complex and the observation that the 8 kDa domain is not in an optimal configuration for the 5{prime}-dRP lyase reaction in the crystal structures of the closed ternary enzyme-DNA-dNTP complexes, we propose that the asymmetric 2 : 1 Pol {beta}-DNA complex enhances the function of Pol {beta}.« less

Structure-affinity relationships for the binding of actinomycin D to DNA

NASA Astrophysics Data System (ADS)

Gallego, José; Ortiz, Angel R.; de Pascual-Teresa, Beatriz; Gago, Federico

1997-03-01

Molecular models of the complexes between actinomycin D and 14 different DNA hexamers were built based on the X-ray crystal structure of the actinomycin-d(GAAGCTTC)2 complex. The DNA sequences included the canonical GpC binding step flanked by different base pairs, nonclassical binding sites such as GpG and GpT, and sites containing 2,6-diamino- purine. A good correlation was found between the intermolecular interaction energies calculated for the refined complexes and the relative preferences of actinomycin binding to standard and modified DNA. A detailed energy decomposition into van der Waals and electrostatic components for the interactions between the DNA base pairs and either the chromophore or the peptidic part of the antibiotic was performed for each complex. The resulting energy matrix was then subjected to principal component analysis, which showed that actinomycin D discriminates among different DNA sequences by an interplay of hydrogen bonding and stacking interactions. The structure-affinity relationships for this important antitumor drug are thus rationalized and may be used to advantage in the design of novel sequence-specific DNA-binding agents.

Building Complex Kondo Impurities by Manipulating Entangled Spin Chains.

PubMed

Choi, Deung-Jang; Robles, Roberto; Yan, Shichao; Burgess, Jacob A J; Rolf-Pissarczyk, Steffen; Gauyacq, Jean-Pierre; Lorente, Nicolás; Ternes, Markus; Loth, Sebastian

2017-10-11

The creation of molecule-like structures in which magnetic atoms interact controllably is full of potential for the study of complex or strongly correlated systems. Here, we create spin chains in which a strongly correlated Kondo state emerges from magnetic coupling of transition-metal atoms. We build chains up to ten atoms in length by placing Fe and Mn atoms on a Cu 2 N surface with a scanning tunneling microscope. The atoms couple antiferromagnetically via superexchange interaction through the nitrogen atom network of the surface. The emergent Kondo resonance is spatially distributed along the chain. Its strength can be controlled by mixing atoms of different transition metal elements and manipulating their spatial distribution. We show that the Kondo screening of the full chain by the electrons of the nonmagnetic substrate depends on the interatomic entanglement of the spins in the chain, demonstrating the prerequisites to build and probe spatially extended strongly correlated nanostructures.

Does human migration affect international trade? A complex-network perspective.

PubMed

Fagiolo, Giorgio; Mastrorillo, Marina

2014-01-01

This paper explores the relationships between international human migration and merchandise trade, using a complex-network approach. We firstly compare the topological structure of worldwide networks of human migration and bilateral trade over the period 1960-2000. Next, we ask whether the position of any pair of countries in the migration network affects their bilateral trade flows. We show that: (i) both weighted and binary versions of the networks of international migration and trade are strongly correlated; (ii) such correlations can be mostly explained by country economic/demographic size and geographical distance; and (iii) pairs of countries that are more central in the international-migration network trade more. Our findings suggest that bilateral trade between any two countries is not only affected by the presence of migrants from either countries but also by their relative embeddedness in the complex web of corridors making up the network of international human migration.

Does Human Migration Affect International Trade? A Complex-Network Perspective

PubMed Central

Fagiolo, Giorgio; Mastrorillo, Marina

2014-01-01

This paper explores the relationships between international human migration and merchandise trade using a complex-network approach. We firstly compare the topological structure of worldwide networks of human migration and bilateral trade over the period 1960–2000. Next, we ask whether pairs of countries that are more central in the migration network trade more. We show that: (i) the networks of international migration and trade are strongly correlated, and such correlation can be mostly explained by country economic/demographic size and geographical distance; (ii) centrality in the international-migration network boosts bilateral trade; (iii) intensive forms of country centrality are more trade enhancing than their extensive counterparts. Our findings suggest that bilateral trade between any two countries is not only affected by the presence of migrants from either countries, but also by their relative embeddedness in the complex web of corridors making up the network of international human migration. PMID:24828376

Foundational Principles for Large-Scale Inference: Illustrations Through Correlation Mining.

PubMed

Hero, Alfred O; Rajaratnam, Bala

2016-01-01

When can reliable inference be drawn in fue "Big Data" context? This paper presents a framework for answering this fundamental question in the context of correlation mining, wifu implications for general large scale inference. In large scale data applications like genomics, connectomics, and eco-informatics fue dataset is often variable-rich but sample-starved: a regime where the number n of acquired samples (statistical replicates) is far fewer than fue number p of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for "Big Data". Sample complexity however has received relatively less attention, especially in the setting when the sample size n is fixed, and the dimension p grows without bound. To address fuis gap, we develop a unified statistical framework that explicitly quantifies the sample complexity of various inferential tasks. Sampling regimes can be divided into several categories: 1) the classical asymptotic regime where fue variable dimension is fixed and fue sample size goes to infinity; 2) the mixed asymptotic regime where both variable dimension and sample size go to infinity at comparable rates; 3) the purely high dimensional asymptotic regime where the variable dimension goes to infinity and the sample size is fixed. Each regime has its niche but only the latter regime applies to exa cale data dimension. We illustrate this high dimensional framework for the problem of correlation mining, where it is the matrix of pairwise and partial correlations among the variables fua t are of interest. Correlation mining arises in numerous applications and subsumes the regression context as a special case. we demonstrate various regimes of correlation mining based on the unifying perspective of high dimensional learning rates and sample complexity for different structured covariance models and different inference tasks.

Effect of correlations on controllability transition in network control

PubMed Central

Nie, Sen; Wang, Xu-Wen; Wang, Bing-Hong; Jiang, Luo-Luo

2016-01-01

The network control problem has recently attracted an increasing amount of attention, owing to concerns including the avoidance of cascading failures of power-grids and the management of ecological networks. It has been proven that numerical control can be achieved if the number of control inputs exceeds a certain transition point. In the present study, we investigate the effect of degree correlation on the numerical controllability in networks whose topological structures are reconstructed from both real and modeling systems, and we find that the transition point of the number of control inputs depends strongly on the degree correlation in both undirected and directed networks with moderately sparse links. More interestingly, the effect of the degree correlation on the transition point cannot be observed in dense networks for numerical controllability, which contrasts with the corresponding result for structural controllability. In particular, for directed random networks and scale-free networks, the influence of the degree correlation is determined by the types of correlations. Our approach provides an understanding of control problems in complex sparse networks. PMID:27063294

Optimizing Water Exchange Rates and Rotational Mobility for High-Relaxivity of a Novel Gd-DO3A Derivative Complex Conjugated to Inulin as Macromolecular Contrast Agents for MRI.

PubMed

Granato, Luigi; Vander Elst, Luce; Henoumont, Celine; Muller, Robert N; Laurent, Sophie

2018-02-01

Thanks to the understanding of the relationships between the residence lifetime τ M of the coordinated water molecules to macrocyclic Gd-complexes and the rotational mobility τ R of these structures, and according to the theory for paramagnetic relaxation, it is now possible to design macromolecular contrast agents with enhanced relaxivities by optimizing these two parameters through ligand structural modification. We succeeded in accelerating the water exchange rate by inducing steric compression around the water binding site, and by removing the amide function from the DOTA-AA ligand [1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid mono(p-aminoanilide)] (L) previously designed. This new ligand 10[2(1-oxo-1-p-propylthioureidophenylpropyl]-1,4,7,10-tetraazacyclodecane-1,4,7-tetraacetic acid (L 1 ) was then covalently conjugated to API [O-(aminopropyl)inulin] to get the complex API-(GdL 1 )x with intent to slow down the rotational correlation time (τ R ) of the macromolecular complex. The evaluation of the longitudinal relaxivity at different magnetic fields and the study of the 17 O-NMR at variable temperature of the low-molecular-weight compound (GdL 1 ) showed a slight decrease of the τ M value (τM310 = 331 ns vs. τM310 = 450 ns for the GdL complex). Consequently to the increase of the size of the API-(GdL 1 )x complex, the rotational correlation time becomes about 360 times longer compared to the monomeric GdL 1 complex (τ R  = 33,700 ps), which results in an enhanced proton relaxivity. © 2018 Wiley-VHCA AG, Zurich, Switzerland.

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

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

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Structure and dynamics of aqueous solutions from PBE-based first-principles molecular dynamics simulations

DOE PAGES

Pham, Tuan Anh; Ogitsu, Tadashi; Lau, Edmond Y.; ...

2016-10-17

Establishing an accurate and predictive computational framework for the description of complex aqueous solutions is an ongoing challenge for density functional theory based first-principles molecular dynamics (FPMD) simulations. In this context, important advances have been made in recent years, including the development of sophisticated exchange-correlation functionals. On the other hand, simulations based on simple generalized gradient approximation (GGA) functionals remain an active field, particularly in the study of complex aqueous solutions due to a good balance between the accuracy, computational expense, and the applicability to a wide range of systems. In such simulations we often perform them at elevated temperaturesmore » to artificially “correct” for GGA inaccuracies in the description of liquid water; however, a detailed understanding of how the choice of temperature affects the structure and dynamics of other components, such as solvated ions, is largely unknown. In order to address this question, we carried out a series of FPMD simulations at temperatures ranging from 300 to 460 K for liquid water and three representative aqueous solutions containing solvated Na +, K +, and Cl - ions. We show that simulations at 390–400 K with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional yield water structure and dynamics in good agreement with experiments at ambient conditions. Simultaneously, this computational setup provides ion solvation structures and ion effects on water dynamics consistent with experiments. These results suggest that an elevated temperature around 390–400 K with the PBE functional can be used for the description of structural and dynamical properties of liquid water and complex solutions with solvated ions at ambient conditions.« less

Predicting landslide vegetation in patches on landscape gradients in Puerto Rico

USGS Publications Warehouse

Myster, R.W.; Thomlinson, J.R.; Larsen, M.C.

1997-01-01

We explored the predictive value of common landscape characteristics for landslide vegetative stages in the Luquillo Experimental Forest of Puerto Rico using four different analyses. Maximum likelihood logistic regression showed that aspect, age, and substrate type could be used to predict vegetative structural stage. In addition it showed that the structural complexity of the vegetation was greater in landslides (1) facing the southeast (away from the dominant wind direction of recent hurricanes), (2) that were older, and (3) that had volcaniclastic rather than dioritic substrate. Multiple regression indicated that both elevation and age could be used to predict the current vegetation, and that vegetation complexity was greater both at lower elevation and in older landslides. Pearson product-moment correlation coefficients showed that (1) the presence of volcaniclastic substrate in landslides was negatively correlated with aspect, age, and elevation, (2) that road association and age were positively correlated, and (3) that slope was negatively correlated with area. Finally, principal components analysis showed that landslides were differentiated on axes defined primarily by age, aspect class, and elevation in the positive direction, and by volcaniclastic substrate in the negative direction. Because several statistical techniques indicated that age, aspect, elevation, and substrate were important in determining vegetation complexity on landslides, we conclude that landslide succession is influenced by variation in these landscape traits. In particular, we would expect to find more successional development on landslides which are older, face away from hurricane winds, are at lower elevation, and are on volcaniclastic substrate. Finally, our results lead into a hierarchical conceptual model of succession on landscapes where the biota respond first to either gradients or disturbance depending on their relative severity, and then to more local biotic mechanisms such as dispersal, predation and competition.

Comparison of diagnostic capability of macular ganglion cell complex and retinal nerve fiber layer among primary open angle glaucoma, ocular hypertension, and normal population using Fourier-domain optical coherence tomography and determining their functional correlation in Indian population

PubMed Central

Barua, Nabanita; Sitaraman, Chitra; Goel, Sonu; Chakraborti, Chandana; Mukherjee, Sonai; Parashar, Hemandra

2016-01-01

Context: Analysis of diagnostic ability of macular ganglionic cell complex and retinal nerve fiber layer (RNFL) in glaucoma. Aim: To correlate functional and structural parameters and comparing predictive value of each of the structural parameters using Fourier-domain (FD) optical coherence tomography (OCT) among primary open angle glaucoma (POAG) and ocular hypertension (OHT) versus normal population. Setting and Design: Single centric, cross-sectional study done in 234 eyes. Materials and Methods: Patients were enrolled in three groups: POAG, ocular hypertensive and normal (40 patients in each group). After comprehensive ophthalmological examination, patients underwent standard automated perimetry and FD-OCT scan in optic nerve head and ganglion cell mode. The relationship was assessed by correlating ganglion cell complex (GCC) parameters with mean deviation. Results were compared with RNFL parameters. Statistical Analysis: Data were analyzed with SPSS, analysis of variance, t-test, Pearson's coefficient, and receiver operating curve. Results: All parameters showed strong correlation with visual field (P < 0.001). Inferior GCC had highest area under curve (AUC) for detecting glaucoma (0.827) in POAG from normal population. However, the difference was not statistically significant (P > 0.5) when compared with other parameters. None of the parameters showed significant diagnostic capability to detect OHT from normal population. In diagnosing early glaucoma from OHT and normal population, only inferior GCC had statistically significant AUC value (0.715). Conclusion: In this study, GCC and RNFL parameters showed equal predictive capability in perimetric versus normal group. In early stage, inferior GCC was the best parameter. In OHT population, single day cross-sectional imaging was not valuable. PMID:27221682

Identifying the Critical Links in Road Transportation Networks: Centrality-based approach utilizing structural properties

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

Chinthavali, Supriya

Surface transportation road networks share structural properties similar to other complex networks (e.g., social networks, information networks, biological networks, and so on). This research investigates the structural properties of road networks for any possible correlation with the traffic characteristics such as link flows those determined independently. Additionally, we define a criticality index for the links of the road network that identifies the relative importance in the network. We tested our hypotheses with two sample road networks. Results show that, correlation exists between the link flows and centrality measures of a link of the road (dual graph approach is followed) andmore » the criticality index is found to be effective for one test network to identify the vulnerable nodes.« less

Nonlinear Analysis of Time Series in Genome-Wide Linkage Disequilibrium Data

NASA Astrophysics Data System (ADS)

Hernández-Lemus, Enrique; Estrada-Gil, Jesús K.; Silva-Zolezzi, Irma; Fernández-López, J. Carlos; Hidalgo-Miranda, Alfredo; Jiménez-Sánchez, Gerardo

2008-02-01

The statistical study of large scale genomic data has turned out to be a very important tool in population genetics. Quantitative methods are essential to understand and implement association studies in the biomedical and health sciences. Nevertheless, the characterization of recently admixed populations has been an elusive problem due to the presence of a number of complex phenomena. For example, linkage disequilibrium structures are thought to be more complex than their non-recently admixed population counterparts, presenting the so-called ancestry blocks, admixed regions that are not yet smoothed by the effect of genetic recombination. In order to distinguish characteristic features for various populations we have implemented several methods, some of them borrowed or adapted from the analysis of nonlinear time series in statistical physics and quantitative physiology. We calculate the main fractal dimensions (Kolmogorov's capacity, information dimension and correlation dimension, usually named, D0, D1 and D2). We also have made detrended fluctuation analysis and information based similarity index calculations for the probability distribution of correlations of linkage disequilibrium coefficient of six recently admixed (mestizo) populations within the Mexican Genome Diversity Project [1] and for the non-recently admixed populations in the International HapMap Project [2]. Nonlinear correlations showed up as a consequence of internal structure within the haplotype distributions. The analysis of these correlations as well as the scope and limitations of these procedures within the biomedical sciences are discussed.

Identification of different coordination geometries by XAFS in copper(II) complexes with trimesic acid

NASA Astrophysics Data System (ADS)

Gaur, A.; Klysubun, W.; Soni, Balram; Shrivastava, B. D.; Prasad, J.; Srivastava, K.

2016-10-01

X-ray absorption spectroscopy (XAS) is very useful in revealing the information about geometric and electronic structure of a transition-metal absorber and thus commonly used for determination of metal-ligand coordination. But XAFS analysis becomes difficult if differently coordinated metal centers are present in a system. In the present investigation, existence of distinct coordination geometries around metal centres have been studied by XAFS in a series of trimesic acid Cu(II) complexes. The complexes studied are: Cu3(tma)2(im)6 8H2O (1), Cu3(tma)2(mim)6 17H2O (2), Cu3(tma)2(tmen)3 8.5H2O (3), Cu3(tma) (pmd)3 6H2O (ClO4)3 (4) and Cu3(tma)2 3H2O (5). These complexes have not only Cu metal centres with different coordination but in complexes 1-3, there are multiple coordination geometries present around Cu centres. Using XANES spectra, different coordination geometries present in these complexes have been identified. The variation observed in the pre-edge features and edge features have been correlated with the distortion of the specific coordination environment around Cu centres in the complexes. XANES spectra have been calculated for the distinct metal centres present in the complexes by employing ab-initio calculations. These individual spectra have been used to resolve the spectral contribution of the Cu centres to the particular XANES features exhibited by the experimental spectra of the multinuclear complexes. Also, the variation in the 4p density of states have been calculated for the different Cu centres and then correlated with the features originated from corresponding coordination of Cu. Thus, these spectral features have been successfully utilized to detect the presence of the discrete metal centres in a system. The inferences about the coordination geometry have been supported by EXAFS analysis which has been used to determine the structural parameters for these complexes.

What Controls the Magnetic Exchange and Anisotropy in a Family of Tetranuclear {Mn2IIMn2III} Single-Molecule Magnets?

PubMed

Vignesh, Kuduva R; Langley, Stuart K; Gartshore, Christopher J; Moubaraki, Boujemaa; Murray, Keith S; Rajaraman, Gopalan

2017-02-20

Twelve heterovalent, tetranuclear manganese(II/III) planar diamond or "butterfly" complexes, 1-12, have been synthesized and structurally characterized, and their magnetic properties have been probed using experimental and theoretical techniques. The 12 structures are divided into two distinct "classes". Compounds 1-8 place the Mn(III), S = 2, ions in the body positions of the butterfly metallic core, while the Mn(II), S = 5/2, ions occupy the outer wing sites and are described as "Class 1". Compounds 9-12 display the reverse arrangement of ions and are described as "Class 2". Direct current susceptibility measurements for 1-12 reveal ground spin states ranging from S = 1 to S = 9, with each complex displaying unique magnetic exchange parameters (J). Alternating current susceptibility measurements found that that slow magnetic relaxation is observed for all complexes, except for 10 and 12, and display differing anisotropy barriers to magnetization reversal. First, we determined the magnitude of the magnetic exchange parameters for all complexes. Three exchange coupling constants (J bb , J wb , and J ww ) were determined by DFT methods which are found to be in good agreement with the experimental fits. It was found that the orientation of the Jahn-Teller axes and the Mn-Mn distances play a pivotal role in determining the sign and strength of the J bb parameter. Extensive magneto-structural correlations have been developed for the two classes of {Mn II 2 Mn III 2 } butterfly complexes by varying the Mn b -O distance, Mn w -O distance, Mn b -O-Mn b angle (α), Mn b -O-Mn b -O dihedral angle (γ), and out-of-plane shift of the Mn w atoms (β). For the magnetic anisotropy the DFT calculations yielded larger negative D value for complexes 2, 3, 4, and 6 compared to the other complexes. This is found to be correlated to the electron-donating/withdrawing substituents attached to the ligand moiety and suggests a possible way to fine tune the magnetic anisotropy in polynuclear Mn ion complexes.

Sample preparation for SFM imaging of DNA, proteins, and DNA-protein complexes.

PubMed

Ristic, Dejan; Sanchez, Humberto; Wyman, Claire

2011-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate, and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nanometer resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA-bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA, and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

On the origin of donor O–H bond weakening in phenol-water complexes

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

Banerjee, Pujarini; Mukhopadhyay, Deb Pratim; Chakraborty, Tapas, E-mail: pctc@iacs.res.in

2015-11-28

Matrix isolation infrared spectroscopy has been used to investigate intermolecular interactions in a series of binary O–H⋯O hydrogen bonded phenol-water complexes where water is the common acceptor. The interaction at the binding site has been tuned by incorporating multiple fluorine substitutions at different aromatic ring sites of the phenol moiety. The spectral effects for the aforesaid chemical changes are manifested in the infrared spectra of the complexes as systematic increase in spectral shift of the phenolic O–H stretching fundamental (Δν{sub O–H}). While ν{sub O–H} bands of the monomers of all the fluorophenols appear within a very narrow frequency range, themore » increase in Δν{sub O–H} of the complexes from phenol to pentafluorophenol is very large, nearly 90%. The observed values of Δν{sub O–H} do not show a linear correlation with the total binding energies (ΔE{sub b}) of the complexes, expected according to Badger-Bauer rule. However, in the same Δν{sub O–H} vs ΔE{sub b} plot, nice linear correlations are revealed if the complexes of ortho-fluorophenols are treated separately from their meta/para-substituted analogues. The observations imply that in spite of having the same binding site (O–H⋯O) and the same chemical identities (phenolic), the complexes of ortho and non-ortho fluorophenols do not belong, from the viewpoint of detailed molecular interactions, to a homologous series. Linear correlations of Δν{sub O–H} are, however, observed with respect to the electrostatic component of ΔE{sub b} as well as the quantum mechanical charge transfer interaction energy (E{sub CT}). From quantitative viewpoint, the latter correlation along with the associated electronic structure parameters appears more satisfactory. It has also been noted that the observed Δν{sub O–H} values of the complexes display a linear relationship with the aqueous phase pK{sub a} values of the respective phenol derivatives.« less

Assessment of Stone Complexity for PCNL: A Systematic Review of the Literature, How Best Can We Record Stone Complexity in PCNL?

PubMed

Withington, John; Armitage, James; Finch, William; Wiseman, Oliver; Glass, Jonathan; Burgess, Neil

2016-01-01

This study aims to systematically review the literature reporting tools for scoring stone complexity and the stratification of outcomes by stone complexity. In doing so, we aim to determine whether the evidence favors uniform adoption of any one scoring system. PubMed and Embase databases were systematically searched for relevant studies from 2004 to 2014. Reports selected according to predetermined inclusion and exclusion criteria were appraised in terms of methodologic quality and their findings summarized in structured tables. After review, 15 studies were considered suitable for inclusion. Four distinct scoring systems were identified and a further five studies that aimed to validate aspects of those scoring systems. Six studies reported the stratification of outcomes by stone complexity, without specifically defining a scoring system. All studies reported some correlation between stone complexity and stone clearance. Correlation with complications was less clearly established, where investigated. This review does not allow us to firmly recommend one scoring system over the other. However, the quality of evidence supporting validation of the Guy's Stone Score is marginally superior, according to the criteria applied in this study. Further evaluation of the interobserver reliability of this scoring system is required.

Theoretical predictions of the spectroscopic parameters in noble-gas molecules: HXeOH and its complex with water.

PubMed

Cukras, Janusz; Sadlej, Joanna

2011-09-14

We employ state-of-the-art methods and basis sets to study the effect of inserting the Xe atom into the water molecule and the water dimer on their NMR parameters. Our aim is to obtain predictions for the future experimental investigation of novel xenon complexes by NMR spectroscopy. Properties such as molecular structure and energetics have been studied by supermolecular approaches using HF, MP2, CCSD, CCSD(T) and MP4 methods. The bonding in HXeOH···H(2)O complexes has been analyzed by Symmetry-Adapted Perturbation Theory to provide the intricate insight into the nature of the interaction. We focus on vibrational spectra, NMR shielding and spin-spin coupling constants-experimental signals that reflect the electronic structures of the compounds. The parameters have been calculated at electron-correlated and Dirac-Hartree-Fock relativistic levels. This study has elucidated that the insertion of the Xe atom greatly modifies the NMR properties, including both the electron correlation and relativistic effects, the (129)Xe shielding constants decrease in HXeOH and HXeOH···H(2)O in comparison to Xe atom; the (17)O, as a neighbour of Xe, is deshielded too. The HXeOH···H(2)O complex in its most stable form is stabilized mainly by induction and dispersion energies. This journal is © the Owner Societies 2011

Structural Characterization of Am(III)- and Pu(III)-DOTA Complexes.

PubMed

Audras, Matthieu; Berthon, Laurence; Berthon, Claude; Guillaumont, Dominique; Dumas, Thomas; Illy, Marie-Claire; Martin, Nicolas; Zilbermann, Israel; Moiseev, Yulia; Ben-Eliyahu, Yeshayahu; Bettelheim, Armand; Cammelli, Sebastiano; Hennig, Christoph; Moisy, Philippe

2017-10-16

The complexation of 1,4,7,10-tetrazacyclodecane-1,4,7,10-tetraacetic acid (DOTA) ligand with two trivalent actinides (Am 3+ and Pu 3+ ) was investigated by UV-visible spectrophotometry, NMR spectroscopy, and extended X-ray absorption fine structure in conjunction with computational methods. The complexation process of these two cations is similar to what has been previously observed with lanthanides(III) of similar ionic radius. The complexation takes place in different steps and ends with the formation of a (1:1) complex [(An(III)DOTA)(H 2 O)] - , where the cation is bonded to the nitrogen atoms of the ring, the four carboxylate arms, and a water molecule to complete the coordination sphere. The formation of An(III)-DOTA complexes is faster than the Ln(III)-DOTA systems of equivalent ionic radius. Furthermore, it is found that An-N distances are slightly shorter than Ln-N distances. Theoretical calculations showed that the slightly higher affinity of DOTA toward Am over Nd is correlated with slightly enhanced ligand-to-metal charge donation arising from oxygen and nitrogen atoms.

Beyond synergies. Comment on "Hand synergies: Integration of robotics and neuroscience for understanding the control of biological and artificial hands" by Marco Santello et al.

NASA Astrophysics Data System (ADS)

Schwartz, Andrew B.

2016-07-01

The target paper by Santello et al. [1] uses the observation that hand shape during grasping can be described by a small set of basic postures, or ;synergies,; to describe the possible neural basis of motor control during this complex behavior. In the literature, the term ;synergy; has been used with a number of different meanings and is still loosely defined, making it difficult to derive concrete analogs of corresponding neural structure. Here, I will define ;synergy; broadly, as a set of parameters bound together by a pattern of correlation. With this definition, it can be argued that behavioral synergies are just one facet of the correlational structuring used by the brain to generate behavior. As pointed out in the target article, the structure found in synergies is driven by the physical constraints of our bodies and our surroundings, combined with the behavioral control imparted by our nervous system. This control itself is based on correlational structure which is likely to be a fundamental property of brain function.

Analysis of evoked deep brain connectivity.

PubMed

Klimeš, Petr; Janeček, Jiři; Jurák, Pavel; Halámek, Josef; Chládek, Han; Brázdil, Milan

2013-01-01

Establishing dependencies and connectivity among different structures in the human brain is an extremely complex issue. Methods that are often used for connectivity analysis are based on correlation mechanisms. Correlation methods can analyze changes in signal shape or instantaneous power level. Although recent studies imply that observation of results from both groups of methods together can disclose some of the basic functions and behavior of the human brain during mental activity and decision-making, there is no technique covering changes in the shape of signals along with changes in their power levels. We present a method using a time evaluation of the correlation along with a comparison of power levels in every available contact pair from intracranial electrodes placed in deep brain structures. Observing shape changes in signals after stimulation together with their power levels provides us with new information about signal character between different structures in the brain during task-related events - visual stimulation with motor response. The results for a subject with 95 intracerebral contacts used in this paper demonstrate a clear methodology capable of spatially analyzing connectivity among deep brain structures.

Structural variation within the potato Ve gene locus and correlation with molecular marker analysis

USDA-ARS?s Scientific Manuscript database

The disconnect between single genotype model systems and plant breeding using wide crosses of diverse germplasm is often too great to affect progress in understanding complex phenotypes. Whole genome sequencing allows researchers and breeders to quickly and inexpensively resequence interesting indiv...

Multiscale Detrended Cross-Correlation Analysis of STOCK Markets

NASA Astrophysics Data System (ADS)

Yin, Yi; Shang, Pengjian

2014-06-01

In this paper, we employ the detrended cross-correlation analysis (DCCA) to investigate the cross-correlations between different stock markets. We report the results of cross-correlated behaviors in US, Chinese and European stock markets in period 1997-2012 by using DCCA method. The DCCA shows the cross-correlated behaviors of intra-regional and inter-regional stock markets in the short and long term which display the similarities and differences of cross-correlated behaviors simply and roughly and the persistence of cross-correlated behaviors of fluctuations. Then, because of the limitation and inapplicability of DCCA method, we propose multiscale detrended cross-correlation analysis (MSDCCA) method to avoid "a priori" selecting the ranges of scales over which two coefficients of the classical DCCA method are identified, and employ MSDCCA to reanalyze these cross-correlations to exhibit some important details such as the existence and position of minimum, maximum and bimodal distribution which are lost if the scale structure is described by two coefficients only and essential differences and similarities in the scale structures of cross-correlation of intra-regional and inter-regional markets. More statistical characteristics of cross-correlation obtained by MSDCCA method help us to understand how two different stock markets influence each other and to analyze the influence from thus two inter-regional markets on the cross-correlation in detail, thus we get a richer and more detailed knowledge of the complex evolutions of dynamics of the cross-correlations between stock markets. The application of MSDCCA is important to promote our understanding of the internal mechanisms and structures of financial markets and helps to forecast the stock indices based on our current results demonstrated the cross-correlations between stock indices. We also discuss the MSDCCA methods of secant rolling window with different sizes and, lastly, provide some relevant implications and issue.

Correlations between Raman frequencies and structures for planar and nonplanar metalloporphyrins

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

Sparks, L.D.; Anderson, K.K.; Medforth, C.J.

1994-05-11

Resonance Raman spectra were obtained for two series of metalloporphyrins, and frequencies of structure-sensitive Raman lines are correlated with structural changes in the porphyrin macrocycle. In the first series, metal derivatives of tetracyclohexenyltetraphenylporphyrin (TC{sub 6}TPP), the porphinato core size is varied by varying the metal (Ni < Co < Cu), causing little change in the planarity of this nonplanar porphyrin. In the second series, nickel complexes of tetracyclopentenyl-, tetracyclohexenyl-, and tetracycloheptenyltertraphenylporphyrin (NiTc{sub x}TPP, where x = 5-7), the size of the alky ring at the {beta}-carbon positions of the pyrrole rings is varied. In the NiTc{sub x}TPP series, the porphyrinmore » macrocycle becomes significantly more nonplanar as the alkyl ring becomes larger and steric crowding increases. As a consequence of the increasing nonplanarity, the porphyrin core contracts. Correlations between Raman frequencies and structural parameters, including core size and C{sub {alpha}}-N-C{sub {alpha}} angle (obtained from molecular mechanics calculations), are found for both series of porphyrins. These new correlative relationships are compared to similar relationships previously observed for metal octaalkylporphyrins, metal tetraphenylporphyrins, and a series of Ni octaalkyltetraphenylporphyrins. Most importantly, by comparing the metal series (Ni, Co, Cu, Zn, etc.) for differing porphyrin ligands, the authors find a trend toward weaker frequency dependence on core size for the more nonplanar porphyrins. Thus, the applicability of this useful structural correlation is extended to both planar and nonplanar porphyrins. Finally, the differences between these correlative relationships are traced to more fundamental (Badger`s rule) relationships between vibrational frequencies and the length of bond contributing to the total potential energy of the vibrational modes corresponding to the structure-sensitive Raman lines.« less

Fractal Characteristics of Continental Shale Pores and its Significance to the Occurrence of Shale Oil in China: a Case Study of Biyang Depression

NASA Astrophysics Data System (ADS)

Li, Jijun; Liu, Zhao; Li, Junqian; Lu, Shuangfang; Zhang, Tongqian; Zhang, Xinwen; Yu, Zhiyuan; Huang, Kaizhan; Shen, Bojian; Ma, Yan; Liu, Jiewen

Samples from seven major exploration wells in Biyang Depression of Henan Oilfield were compared using low-temperature nitrogen adsorption and shale oil adsorption experiments. Comprehensive analysis of pore development, oiliness and shale oil flowability was conducted by combining fractal dimension. The results show that the fractal dimension of shale in Biyang Depression of Henan Oilfield was negatively correlated with the average pore size and positively correlated with the specific surface area. Compared with the large pore, the small pore has great fractal dimension, indicating the pore structure is more complicated. Using S1 and chloroform bitumen A to evaluate the relationship between shale oiliness and pore structure, it was found that the more heterogeneous the shale pore structure, the higher the complexity and the poorer the oiliness. Clay minerals are the main carriers involved in crude oil adsorption, affecting the mobility of shale oil. When the pore complexity of shale was high, the content of micro- and mesopores was high, and the high specific surface area could enhance the adsorption and reduce the mobility of shale oil.

Harnessing the complexity of gene expression data from cancer: from single gene to structural pathway methods

PubMed Central

2012-01-01

High-dimensional gene expression data provide a rich source of information because they capture the expression level of genes in dynamic states that reflect the biological functioning of a cell. For this reason, such data are suitable to reveal systems related properties inside a cell, e.g., in order to elucidate molecular mechanisms of complex diseases like breast or prostate cancer. However, this is not only strongly dependent on the sample size and the correlation structure of a data set, but also on the statistical hypotheses tested. Many different approaches have been developed over the years to analyze gene expression data to (I) identify changes in single genes, (II) identify changes in gene sets or pathways, and (III) identify changes in the correlation structure in pathways. In this paper, we review statistical methods for all three types of approaches, including subtypes, in the context of cancer data and provide links to software implementations and tools and address also the general problem of multiple hypotheses testing. Further, we provide recommendations for the selection of such analysis methods. Reviewers This article was reviewed by Arcady Mushegian, Byung-Soo Kim and Joel Bader. PMID:23227854

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations.

PubMed

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by "communities" of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information.

Synthesis, Structure, and Conformational Dynamics of Rhodium and Iridium Complexes of Dimethylbis(2-pyridyl)borate.

PubMed

Pennington-Boggio, Megan K; Conley, Brian L; Richmond, Michael G; Williams, Travis J

2014-12-14

Rhodium(I) and Iridium(I) borate complexes of the structure [Me 2 B(2-py) 2 ]ML 2 (L 2 = (tBuNC) 2 , (CO) 2 , (C 2 H 4 ) 2 , cod, dppe) were prepared and structurally characterized (cod = 1,5-cyclooctadiene; dppe = 1,2-diphenylphosphinoethane). Each contains a boat-configured chelate ring that participates in a boat-to-boat ring flip. Computational evidence shows that the ring flip proceeds through a transition state that is near planarity about the chelate ring. We observe an empirical, quantitative correlation between the barrier of this ring flip and the π acceptor ability of the ancillary ligand groups on the metal. The ring flip barrier correlates weakly to the Tolman and Lever ligand parameterization schemes, apparently because these combine both σ and π effects while we propose that the ring flip barrier is dominated by π bonding. This observation is consistent with metal-ligand π interactions becoming temporarily available only in the near-planar transition state of the chelate ring flip and not the boat-configured ground state. Thus, this is a first-of-class observation of metal-ligand π bonding governing conformational dynamics.

Synthesis, Structure, and Conformational Dynamics of Rhodium and Iridium Complexes of Dimethylbis(2-pyridyl)borate†

PubMed Central

Pennington-Boggio, Megan K.; Conley, Brian L.; Richmond, Michael G.; Williams, Travis J.

2014-01-01

Rhodium(I) and Iridium(I) borate complexes of the structure [Me2B(2-py)2]ML2 (L2 = (tBuNC)2, (CO)2, (C2H4)2, cod, dppe) were prepared and structurally characterized (cod = 1,5-cyclooctadiene; dppe = 1,2-diphenylphosphinoethane). Each contains a boat-configured chelate ring that participates in a boat-to-boat ring flip. Computational evidence shows that the ring flip proceeds through a transition state that is near planarity about the chelate ring. We observe an empirical, quantitative correlation between the barrier of this ring flip and the π acceptor ability of the ancillary ligand groups on the metal. The ring flip barrier correlates weakly to the Tolman and Lever ligand parameterization schemes, apparently because these combine both σ and π effects while we propose that the ring flip barrier is dominated by π bonding. This observation is consistent with metal-ligand π interactions becoming temporarily available only in the near-planar transition state of the chelate ring flip and not the boat-configured ground state. Thus, this is a first-of-class observation of metal-ligand π bonding governing conformational dynamics. PMID:25435645

Nucleon correlations and the structure of Zn 41 30 71

DOE PAGES

Bottoni, Simone; Zhu, S.; Janssens, R. V. F.; ...

2017-11-06

Here, the structure of 71Zn was investigated by one-neutron transfer and heavy-ion induced complex (deep-inelastic) reactions using the GRETINA-CHICO2 and the Gammasphere setups, respectively. The observed inversion between the 9/2 + and 1/2 – states is explained in terms of the role of neutron pairing correlations. Non-collective sequences of levels were delineated above the 9/2 + isomeric state. These are interpreted as being associated with a modest oblate deformation in the framework of Monte-Carlo shell-model calculations carried out with the A3DA-m Hamiltonian in the pfg 9/2d 5/2 valence space. Similarities with the structure of 68 28Ni 40 were observed andmore » the shape-coexistence mechanism in the N = 40 region of neutron-rich nuclei is discussed in terms of the so-called Type-II shell evolution, with an emphasis on proton–neutron correlations between valence nucleons, especially those involving the shape-driving g 9/2 neutron orbital.« less

Nucleon correlations and the structure of 41 30 71Zn

NASA Astrophysics Data System (ADS)

Bottoni, S.; Zhu, S.; Janssens, R. V. F.; Carpenter, M. P.; Tsunoda, Y.; Otsuka, T.; Macchiavelli, A. O.; Cline, D.; Wu, C. Y.; Ayangeakaa, A. D.; Bucher, B.; Buckner, M. Q.; Campbell, C. M.; Chiara, C. J.; Crawford, H. L.; Cromaz, M.; David, H. M.; Fallon, P.; Gade, A.; Greene, J. P.; Harker, J.; Hayes, A. B.; Hoffman, C. R.; Kay, B. P.; Korichi, A.; Lauritsen, T.; Sethi, J.; Seweryniak, D.; Walters, W. B.; Weisshaar, D.; Wiens, A.

2017-12-01

The structure of 71Zn was investigated by one-neutron transfer and heavy-ion induced complex (deep-inelastic) reactions using the GRETINA-CHICO2 and the Gammasphere setups, respectively. The observed inversion between the 9/2+ and 1/2- states is explained in terms of the role of neutron pairing correlations. Non-collective sequences of levels were delineated above the 9/2+ isomeric state. These are interpreted as being associated with a modest oblate deformation in the framework of Monte-Carlo shell-model calculations carried out with the A3DA-m Hamiltonian in the pfg9/2d5/2 valence space. Similarities with the structure of 40,28,68Ni were observed and the shape-coexistence mechanism in the N = 40 region of neutron-rich nuclei is discussed in terms of the so-called Type-II shell evolution, with an emphasis on proton-neutron correlations between valence nucleons, especially those involving the shape-driving g9/2 neutron orbital.

Dynamic multifactor clustering of financial networks

NASA Astrophysics Data System (ADS)

Ross, Gordon J.

2014-02-01

We investigate the tendency for financial instruments to form clusters when there are multiple factors influencing the correlation structure. Specifically, we consider a stock portfolio which contains companies from different industrial sectors, located in several different countries. Both sector membership and geography combine to create a complex clustering structure where companies seem to first be divided based on sector, with geographical subclusters emerging within each industrial sector. We argue that standard techniques for detecting overlapping clusters and communities are not able to capture this type of structure and show how robust regression techniques can instead be used to remove the influence of both sector and geography from the correlation matrix separately. Our analysis reveals that prior to the 2008 financial crisis, companies did not tend to form clusters based on geography. This changed immediately following the crisis, with geography becoming a more important determinant of clustering structure.

Geometric representation of spin correlations and applications to ultracold systems

NASA Astrophysics Data System (ADS)

Mukherjee, Rick; Mirasola, Anthony E.; Hollingsworth, Jacob; White, Ian G.; Hazzard, Kaden R. A.

2018-04-01

We provide a one-to-one map between the spin correlations and certain three-dimensional shapes, analogous to the map between single spins and Bloch vectors, and demonstrate its utility. Much as one can reason geometrically about dynamics using a Bloch vector—e.g., a magnetic field causes it to precess and dissipation causes it to shrink—one can reason similarly about the shapes we use to visualize correlations. This visualization demonstrates its usefulness by unveiling the hidden structure in the correlations. For example, seemingly complex correlation dynamics can be described as simple motions of the shapes. We demonstrate the simplicity of the dynamics, which is obscured in conventional analyses, by analyzing several physical systems of relevance to cold atoms.

Modeling the chemistry of complex petroleum mixtures.

PubMed Central

Quann, R J

1998-01-01

Determining the complete molecular composition of petroleum and its refined products is not feasible with current analytical techniques because of the astronomical number of molecular components. Modeling the composition and behavior of such complex mixtures in refinery processes has accordingly evolved along a simplifying concept called lumping. Lumping reduces the complexity of the problem to a manageable form by grouping the entire set of molecular components into a handful of lumps. This traditional approach does not have a molecular basis and therefore excludes important aspects of process chemistry and molecular property fundamentals from the model's formulation. A new approach called structure-oriented lumping has been developed to model the composition and chemistry of complex mixtures at a molecular level. The central concept is to represent an individual molecular or a set of closely related isomers as a mathematical construct of certain specific and repeating structural groups. A complex mixture such as petroleum can then be represented as thousands of distinct molecular components, each having a mathematical identity. This enables the automated construction of large complex reaction networks with tens of thousands of specific reactions for simulating the chemistry of complex mixtures. Further, the method provides a convenient framework for incorporating molecular physical property correlations, existing group contribution methods, molecular thermodynamic properties, and the structure--activity relationships of chemical kinetics in the development of models. PMID:9860903

Positive Disintegration as a Process of Symmetry Breaking.

PubMed

Laycraft, Krystyna

2017-04-01

This article presents an analysis of the positive disintegration as a process of symmetry breaking. Symmetry breaking plays a major role in self-organized patterns formation and correlates directly to increasing complexity and function specialization. According to Dabrowski, a creator of the Theory of Positive Disintegration, the change from lower to higher levels of human development requires a major restructuring of an individual's psychological makeup. Each level of human development is a relatively stable and coherent configuration of emotional-cognitive patterns called developmental dynamisms. Their main function is to restructure a mental structure by breaking the symmetry of a low level and bringing differentiation and then integration to higher levels. The positive disintegration is then the process of transitions from a lower level of high symmetry and low complexity to higher levels of low symmetry and high complexity of mental structure.

Different structure of the complexes of two cytochrome P-450 isozymes with acetanilide by 1H-NMR relaxation and spectrophotometry.

PubMed

Woldman YaYu; Weiner, L M; Lyakhovich, V V

1993-05-28

The functional and spectral characteristics of the interaction of acetanilide with phenobarbital- and methylcholanthrene- induced rat liver microsomes, as well as with corresponding major isozymes (cytochromes P-450b and P-450c) have been compared. The magnitude of the reverse 1st type binding spectra proved to be negatively correlated with the acetanilide oxidation on isozymes under study. The data on paramagnetic relaxation of acetanilide protons in the presence of P-450 have shown the structure of the enzyme-substrate complex to be different for two isozymes, acetanilide molecule being closer to Fe ion in the active site in the case of P-450c, which is active towards acetanilide oxidation. For the P-450c-acetanilide complex the group oxidized (phenyl) is the closest to Fe ion.

Cationic lipids: molecular structure/ transfection activity relationships and interactions with biomembranes.

PubMed

Koynova, Rumiana; Tenchov, Boris

2010-01-01

Abstract Synthetic cationic lipids, which form complexes (lipoplexes) with polyanionic DNA, are presently the most widely used constituents of nonviral gene carriers. A large number of cationic amphiphiles have been synthesized and tested in transfection studies. However, due to the complexity of the transfection pathway, no general schemes have emerged for correlating the cationic lipid chemistry with their transfection efficacy and the approaches for optimizing their molecular structures are still largely empirical. Here we summarize data on the relationships between transfection activity and cationic lipid molecular structure and demonstrate that the transfection activity depends in a systematic way on the lipid hydrocarbon chain structure. A number of examples, including a large series of cationic phosphatidylcholine derivatives, show that optimum transfection is displayed by lipids with chain length of approximately 14 carbon atoms and that the transfection efficiency strongly increases with increase of chain unsaturation, specifically upon replacement of saturated with monounsaturated chains.

Similar Neural Correlates for Language and Sequential Learning: Evidence from Event-Related Brain Potentials

PubMed Central

Christiansen, Morten H.; Conway, Christopher M.; Onnis, Luca

2011-01-01

We used event-related potentials (ERPs) to investigate the time course and distribution of brain activity while adults performed (a) a sequential learning task involving complex structured sequences, and (b) a language processing task. The same positive ERP deflection, the P600 effect, typically linked to difficult or ungrammatical syntactic processing, was found for structural incongruencies in both sequential learning as well as natural language, and with similar topographical distributions. Additionally, a left anterior negativity (LAN) was observed for language but not for sequential learning. These results are interpreted as an indication that the P600 provides an index of violations and the cost of integration of expectations for upcoming material when processing complex sequential structure. We conclude that the same neural mechanisms may be recruited for both syntactic processing of linguistic stimuli and sequential learning of structured sequence patterns more generally. PMID:23678205

Dual roles of f electrons in mixing Al 3 p character into d -orbital conduction bands for lanthanide and actinide dialuminides

DOE PAGES

Altman, Alison B.; Pemmaraju, C. D.; Alayoglu, Selim; ...

2018-01-15

Correlated electron phenomena in lanthanide and actinide materials are driven by a complex interplay between the f and d orbitals. Here in this study, aluminum K-edge x-ray absorption spectroscopy and density functional theory calculations are used to evaluate the electronic structure of the dialuminides, MAl 2 (M = Ce, Sm, Eu, Yb, Lu, U, and Pu). The results show how the energy and occupancy of the 4f or 5f orbitals impacts mixing of Al 3p character into the 5d or 6d conduction bands, which has implications for understanding the magnetic and structural properties of correlated electron systems.

1. Catalytic asymmetric hydroformylation. 2. Hydroformylation with polymer-supported platinum complexes. 3. The reaction between dicobalt octacarbonyl and alcohols

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

Bortinger, A.

1977-01-01

Chiral polymer-supported metal complexes were catalytically active in the hydroformylation of prochiral olefins, but they induced only small optical activity. All the optical rotations in 2-phenylpropanal, obtained by the hydroformylation of styrene, were positive. In studies of asymmetric hydroformylation with homogeneous catalysts, no correlation was found between the optical inductions and ligand structure. Polymer-supported platinum catalysts having similar structure to their homogeneous counterparts showed the same high selectivity toward the formation of straight-chain aldehyde (89-95%) as the homogeneous catalysts in the hydroformylation of 1-hexene. Aldehyde yields were low (up to 45%); no reduction to alcohol occurred.

Effect of salt and surfactant concentration on the structure of polyacrylate gel/surfactant complexes.

PubMed

Nilsson, Peter; Unga, Johan; Hansson, Per

2007-09-20

Small-angle X-ray scattering was used to elucidate the structure of crosslinked polyacrylate gel/dodecyltrimethylammonium bromide complexes equilibrated in solutions of varying concentrations of surfactant and sodium bromide (NaBr). Samples were swollen with no ordering (micelle free), or they were collapsed with either several distinct peaks (cubic Pm3n) or one broad correlation peak (disordered micellar). The main factor determining the structure of the collapsed complexes was found to be the NaBr concentration, with the cubic structure existing up to approximately 150 mM NaBr and above which only the disordered micellar structure was found. Increasing the salt concentration decreases the polyion mediated attractive forces holding the micelles together causing swelling of the gel. At sufficiently high salt concentration the micelle-micelle distance in the gel becomes too large for the cubic structure to be retained, and it melts into a disordered micellar structure. As most samples were above the critical micelle concentration, the bulk of the surfactant was in the form of micelles in the solution and the surfactant concentration thereby had only a minor influence on the structure. However, in the region around 150 mM NaBr, increasing the surfactant concentration, at constant NaBr concentration, was found to change the structure from disordered micellar to ordered cubic and back to disordered again.

Teacher Expectations and Student Literacy Engagement and Achievement

ERIC Educational Resources Information Center

Pantaleo, Sylvia

2016-01-01

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

Complexes of Neutralizing and Non-Neutralizing Affinity Matured Fabs with a Mimetic of the Internal Trimeric Coiled-Coil of HIV-1 gp41

PubMed Central

Gustchina, Elena; Li, Mi; Ghirlando, Rodolfo; Schuck, Peter; Louis, John M.; Pierson, Jason; Rao, Prashant; Subramaniam, Sriram; Gustchina, Alla; Clore, G. Marius; Wlodawer, Alexander

2013-01-01

A series of mini-antibodies (monovalent and bivalent Fabs) targeting the conserved internal trimeric coiled-coil of the N-heptad repeat (N-HR) of HIV-1 gp41 has been previously constructed and reported. Crystal structures of two closely related monovalent Fabs, one (Fab 8066) broadly neutralizing across a wide panel of HIV-1 subtype B and C viruses, and the other (Fab 8062) non-neutralizing, representing the extremes of this series, were previously solved as complexes with 5-Helix, a gp41 pre-hairpin intermediate mimetic. Binding of these Fabs to covalently stabilized chimeric trimers of N-peptides of HIV-1 gp41 (named (CCIZN36)3 or 3-H) has now been investigated using X-ray crystallography, cryo-electron microscopy, and a variety of biophysical methods. Crystal structures of the complexes between 3-H and Fab 8066 and Fab 8062 were determined at 2.8 and 3.0 Å resolution, respectively. Although the structures of the complexes with the neutralizing Fab 8066 and its non-neutralizing counterpart Fab 8062 were generally similar, small differences between them could be correlated with the biological properties of these antibodies. The conformations of the corresponding CDRs of each antibody in the complexes with 3-H and 5-Helix are very similar. The adaptation to a different target upon complex formation is predominantly achieved by changes in the structure of the trimer of N-HR helices, as well as by adjustment of the orientation of the Fab molecule relative to the N-HR in the complex, via rigid-body movement. The structural data presented here indicate that binding of three Fabs 8062 with high affinity requires more significant changes in the structure of the N-HR trimer compared to binding of Fab 8066. A comparative analysis of the structures of Fabs complexed to different gp41 intermediate mimetics allows further evaluation of biological relevance for generation of neutralizing antibodies, as well as provides novel structural insights into immunogen design. PMID:24244293

A Method for the Calculation of Lattice Energies of Complex Crystals with Application to the Oxides of Molybdenum

NASA Technical Reports Server (NTRS)

Chaney, William S.

1961-01-01

A theoretical study has been made of molybdenum dioxide and molybdenum trioxide in order to extend the knowledge of factors Involved in the oxidation of molybdenum. New methods were developed for calculating the lattice energies based on electrostatic valence theory, and the coulombic, polarization, Van der Waals, and repulsion energie's were calculated. The crystal structure was examined and structure details were correlated with lattice energy.

Imaging of DNA and Protein by SFM and Combined SFM-TIRF Microscopy.

PubMed

Grosbart, Małgorzata; Ristić, Dejan; Sánchez, Humberto; Wyman, Claire

2018-01-01

Direct imaging is invaluable for understanding the mechanism of complex genome transactions where proteins work together to organize, transcribe, replicate and repair DNA. Scanning (or atomic) force microscopy is an ideal tool for this, providing 3D information on molecular structure at nm resolution from defined components. This is a convenient and practical addition to in vitro studies as readily obtainable amounts of purified proteins and DNA are required. The images reveal structural details on the size and location of DNA bound proteins as well as protein-induced arrangement of the DNA, which are directly correlated in the same complexes. In addition, even from static images, the different forms observed and their relative distributions can be used to deduce the variety and stability of different complexes that are necessarily involved in dynamic processes. Recently available instruments that combine fluorescence with topographic imaging allow the identification of specific molecular components in complex assemblies, which broadens the applications and increases the information obtained from direct imaging of molecular complexes. We describe here basic methods for preparing samples of proteins, DNA and complexes of the two for topographic imaging and quantitative analysis. We also describe special considerations for combined fluorescence and topographic imaging of molecular complexes.

Structural complexes in the squid giant axon membrane sensitive to ionic concentrations and cardiac glycosides

PubMed Central

Villegas, GM; Villegas, J

1976-01-01

Giant nerve fibers of squid Sepioteuthis sepiodea were incubated for 10 min in artificial sea water (ASW) under control conditions, in the absence of various ions, and in the presence of cardiac glycosides. The nerve fibers were fixed in OsO(4) and embedded in Epon, and structural complexes along the axolemma were studied. These complexes consist of a portion of axolemma exhibiting a three-layered substructure, an undercoating of a dense material (approximately 0.1μm in length and approximately 70-170 A in thickness), and a narrowing to disappearance of the axon-Schwann cell interspace. In the controls, the incidence of complexes per 1,000μm of axon perimeter was about 137. This number decreased to 10-25 percent when magnesium was not present in the incubating media, whatever the calcium concentration (88, 44, or 0 mM). In the presence of magnesium, the number and structural features of the complexes were preserved, though the number decreased to 65 percent when high calcium was simultaneously present. The complexes were also modified and decreased to 26-32 percent by incubating the nerves in solutions having low concentrations of sodium and potassium. The adding of 10(-5) M ouabain or strophanthoside to normal ASW incubating solution decreased them to 20-40 percent. Due to their sensitivity to changes in external ionic concentrations and to the presence of cardiac glycosides, the complexes are proposed to represent the structural correlate of specialized sites for active ion transport, although other factors may be involved. PMID:1254642

The Effects of Non-Redox Active Metal Ions on the Activation of Dioxygen: Isolation and Characterization of a Heterobimetallic Complex Containing a MnIII–(μ-OH)–CaII core

PubMed Central

Park, Young Jun; Ziller, Joseph W.; Borovik, A. S.

2011-01-01

Rate enhancements for the reduction of dioxygen by a MnII complex were observed in the presence of redox inactive Group 2 metal ions. The rate changes correlated with an increase in the Lewis acidity of the Group 2 metal ions. These studies led to the isolation of heterobimetallic complexes that contain MnIII-(μ-OH)-MII cores (MII = CaII, BaII), in which the hydroxo oxygen atom is derived from O2. This type of core structure has relevance to the oxygen evolving complexes within photosystem II. PMID:21595481

Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures.

PubMed

Krystek, S; Stouch, T; Novotny, J

1993-12-05

An empirical function was used to calculate free energy change (delta G) of complex formation between the following inhibitors and enzymes: Kunitz inhibitor (BPTI) with trypsin, trypsinogen and kallikrein; turkey ovomucoid 3rd domain (OMTKY3) with alpha-chymotrypsin and the Streptomyces griseus protease B; the potato chymotrypsin inhibitor with the protease B; and the barely chymotrypsin inhibitor and eglin-c with subtilisin and thermitase. Using X-ray coordinates of the nine complexes, we estimated the contributions that hydrophobic effect, electrostatic interactions and side-chain conformational entropy make towards the stability of the complexes. The calculated delta G values showed good agreement with the experimentally measured ones, the only exception being the kallikrein/BPTI complex whose X-ray structure was solved at an exceptionally low pH. In complexes with different enzymes, the same inhibitor residues contributed identically towards complex formation (delta G(residue) Spearman rank correlation coefficient 0.7 to 1.0). The most productive enzyme-contacting residues in OMTKY3, eglin-c, and the chymotrypsin inhibitors were found in analogous positions on their respective binding loops; thus, our calculations identified a functional (energetic) motif that parallels the well-known structural similarity of the binding loops. The delta G values calculated for BPTI complexed with trypsin (-21.7 kcal) and trypsinogen (-23.4 kcal) were similar and close to the experimental delta G value of the trypsin/BPTI complex (-18.1 kcal), lending support to the suggestion that the 10(7) difference in the observed stabilities (KA) of these two complexes reflects the energetic cost of conformational changes induced in trypsinogen during the pre-equilibrium stages of complex formation. In almost all of the complexes studied, the stabilization free energy contributed by the inhibitors was larger than that donated by the enzymes. In the trypsin-BPTI complex, the calculated delta G contribution of the amino group from the BPTI residue Lys15 (9.7 kcal) was somewhat higher than that arrived at in experiments with semisynthetic inhibitor analogs (7.5 kcal). In OMTKY3, different binding loop residues are known to affect differently the binding (delta delta G) to alpha-chymotrypsin and protease B; a good qualitative agreement was found between the calculated delta G(residue) estimates and the experimental delta delta G data (correlation coefficient 0.7). Large variations were observed in local surface complementarity and related interfacial volume in the two OMTKY3 complexes (by 20 to 60% for some side-chains).(ABSTRACT TRUNCATED AT 400 WORDS)

Unravelling the spin-state of solvated [Fe(bpp)2]2+ spin-crossover complexes: structure-function relationship.

PubMed

Giménez-López, Maria Del Carmen; Clemente-León, Miguel; Giménez-Saiz, Carlos

2018-05-23

This paper reports firstly the syntheses, crystal structures, and thermal and magnetic properties of spin crossover salts of formulae [Fe(bpp)2]3[Cr(CN)6]2·13H2O (1) and [Fe(bpp)2][N(CN)2]2·H2O (2) (bpp = 2,6-bis(pyrazol-3-yl)pyridine) exhibiting hydrogen-bonded networks of low-spin [Fe(bpp)2]2+ complexes and [Cr(CN)6]3- or [N(CN)2]- anions, with solvent molecules located in the voids. Desolvation of 1 is accompanied by a complete low-spin (LS) to a high-spin (HS) transformation that becomes reversible after rehydration by exposing the sample to the humidity of air. The influence of the lattice water on the magnetic properties of spin-crossover [Fe(bpp)2]X2 complex salts has been documented. In most cases, it stabilises the LS state over the HS one. In other cases, it is rather the contrary. The second part of this paper is devoted to unravelling the reasons why the lattice solvent stabilises one form over the other through magneto-structural correlations of [Fe(bpp)2]2+ salts bearing anions with different charge/size ratios (Xn-). The [Fe(bpp)2]2+ stacking explaining these two different behaviours is correlated here with the composition of the second coordination sphere of the Fe centers and the ability of these anions to form hydrogen bonds and/or π-π stacking interactions between them or the bpp ligand.

Spatial organization and correlation properties quantify structural changes on mesoscale of parenchymatous plant tissue

NASA Astrophysics Data System (ADS)

Valous, N. A.; Delgado, A.; Drakakis, K.; Sun, D.-W.

2014-02-01

The study of plant tissue parenchyma's intercellular air spaces contributes to the understanding of anatomy and physiology. This is challenging due to difficulty in making direct measurements of the pore space and the complex mosaic of parenchymatous tissue. The architectural complexity of pore space has shown that single geometrical measurements are not sufficient for characterization. The inhomogeneity of distribution depends not only on the percentage content of phase, but also on how the phase fills the space. The lacunarity morphometric, as multiscale measure, provides information about the distribution of gaps that correspond to degree of spatial organization in parenchyma. Additionally, modern theories have suggested strategies, where the focus has shifted from the study of averages and histograms to the study of patterns in data fluctuations. Detrended fluctuation analysis provides information on the correlation properties of the parenchyma at different spatial scales. The aim is to quantify (with the aid of the aforementioned metrics), the mesostructural changes—that occur from one cycle of freezing and thawing—in the void phase of pome fruit parenchymatous tissue, acquired with X-ray microcomputed tomography. Complex systems methods provide numerical indices and detailed insights regarding the freezing-induced modifications upon the arrangement of cells and voids. These structural changes have the potential to lead to physiological disorders. The work can further stimulate interest for the analysis of internal plant tissue structures coupled with other physico-chemical processes or phenomena.

Relating geomorphic change and grazing to avian communities in riparian forests

USGS Publications Warehouse

Scott, M.L.; Skagen, S.K.; Merligliano, M.F.

2003-01-01

Avian conservation in riparian or bottomland forests requires an understanding of the physical and biotic factors that sustain the structural complexity of riparian vegetation. Riparian forests of western North America are dependent upon flow-related geomorphic processes necessary for establishment of new cottonwood and willow patches. In June 1995, we examined how fluvial geomorphic processes and long-term grazing influence the structural complexity of riparian vegetation and the abundance and diversity of breeding birds along the upper Missouri River in central Montana, a large, flow-regulated, and geomorphically constrained reach. Use by breeding birds was linked to fluvial geomorphic processes that influence the structure of these patches. Species richness and bird diversity increased with increasing structural complexity of vegetation (F1,32 = 75.49, p < 0.0001; F1,32 = 79.76, p < 0.0001, respectively). Bird species composition was significantly correlated with vegetation strata diversity (rs,33 = 0.98, p < 0.0001). Bird abundance in canopy and tall-shrub foraging guilds increased significantly with increasing tree cover and tall-shrub cover (F1,22 = 34.68, p < 0.0001; F1,20 = 22.22, p < 0.0001, respectively). Seventeen bird species, including five species of concern (e.g., Red-eyed Vireo [Vireo olivaceus]), were significantly associated (p < 0.10) with structurally complex forest patches, whereas only six bird species were significantly associated with structurally simple forest patches. We related the structural complexity of 34 riparian vegetation patches to geomorphic change, woody vegetation establishment, and grazing history over a 35-year post-dam period (1953–1988). The structural complexity of habitat patches was positively related to recent sediment accretion (t33 = 3.31, p = 0.002) and vegetation establishment (t20.7 = −3.63, p = 0.002) and negatively related to grazing activity (t19.6 = 3.75, p = 0.001). Avian conservation along rivers like the upper Missouri requires maintenance of the geomorphic processes responsible for tree establishment and management of land-use activities in riparian forests.

Modulation of in vivo distribution through chelator: Synthesis and evaluation of a 2-nitroimidazole-dipicolylamine-(99m)Tc(CO)3 complex for detecting tumor hypoxia.

PubMed

Mallia, Madhava B; Mittal, Sweety; Sarma, Haladhar D; Banerjee, Sharmila

2016-01-01

Previous studies have clearly demonstrated strong correlation between in vivo distribution and blood clearance of radiopharmaceuticals for the detection of hypoxia. Present study describes an attempt to improve the in vivo distribution of a previously reported 2-nitroimidazole-(99m)Tc(CO)3 complex by tuning its blood clearance pattern through structural modification of the ligand. Herein, a 2-nitroimidazole-dipicolylamine ligand (2-nitroimidazole-DPA) was synthesized in a two-step procedure and radiolabeled with (99m)Tc(CO)3 core. Subsequently, the complex was evaluated in Swiss mice bearing fibrosarcoma tumor. As intended by its design, 2-nitroimidazole-DPA-(99m)Tc(CO)3 complex was more lipophilic than previously reported 2-nitroimidazole-DETA-(99m)Tc(CO)3 complex (DETA-diethylenetriamine) and showed slower blood clearance. Consequently it showed higher tumor uptake than 2-nitroimidazole-DETA-(99m)Tc(CO)3 complex. Significantly, despite structural modifications, other parameters such as the tumor to blood ratio and tumor to muscle ratio of the 2-nitroimidazole-DPA-(99m)Tc(CO)3 complex remained comparable to that of 2-nitroimidazole-DETA-(99m)Tc(CO)3 complex. Present study demonstrates the feasibility of structural modifications for improving in vivo tumor uptake of hypoxia detecting radiopharmaceuticals. This might encourage researchers to improve suboptimal properties of a potential radiopharmaceuticals rather than ignoring it altogether. Copyright © 2015 Elsevier Ltd. All rights reserved.

Long-range correlation and market segmentation in bond market

NASA Astrophysics Data System (ADS)

Wang, Zhongxing; Yan, Yan; Chen, Xiaosong

2017-09-01

This paper investigates the long-range auto-correlations and cross-correlations in bond market. Based on Detrended Moving Average (DMA) method, empirical results present a clear evidence of long-range persistence that exists in one year scale. The degree of long-range correlation related to maturities has an upward tendency with a peak in short term. These findings confirm the expectations of fractal market hypothesis (FMH). Furthermore, we have developed a method based on a complex network to study the long-range cross-correlation structure and applied it to our data, and found a clear pattern of market segmentation in the long run. We also detected the nature of long-range correlation in the sub-period 2007-2012 and 2011-2016. The result from our research shows that long-range auto-correlations are decreasing in the recent years while long-range cross-correlations are strengthening.

Asymmetric correlation matrices: an analysis of financial data

NASA Astrophysics Data System (ADS)

Livan, G.; Rebecchi, L.

2012-06-01

We analyse the spectral properties of correlation matrices between distinct statistical systems. Such matrices are intrinsically non-symmetric, and lend themselves to extend the spectral analyses usually performed on standard Pearson correlation matrices to the realm of complex eigenvalues. We employ some recent random matrix theory results on the average eigenvalue density of this type of matrix to distinguish between noise and non-trivial correlation structures, and we focus on financial data as a case study. Namely, we employ daily prices of stocks belonging to the American and British stock exchanges, and look for the emergence of correlations between two such markets in the eigenvalue spectrum of their non-symmetric correlation matrix. We find several non trivial results when considering time-lagged correlations over short lags, and we corroborate our findings by additionally studying the asymmetric correlation matrix of the principal components of our datasets.

Palladium complexes with simple iminopyridines as catalysts for polyketone synthesis.

PubMed

Rosar, V; Dedeic, D; Nobile, T; Fini, F; Balducci, G; Alessio, E; Carfagna, C; Milani, B

2016-10-07

Four iminopyridines (N-N') differing in the nature of the substituents on the iminic carbon and on the ortho positions of the aryl ring (H or CH3) on the iminic nitrogen were used for the synthesis of neutral and monocationic palladium(ii) complexes of general formulae [Pd(CH3)Cl(N-N')] and [Pd(CH3)(NCCH3)(N-N')][PF6]. The detailed NMR characterization in solution highlighted that: (i) for both series of complexes, the Pd-CH3 signal is progressively shifted to a lower frequency on increasing the number of methyl groups on the ligand skeleton; (ii) for the neutral derivatives, the chemical shift of the (15)N NMR signals, determined through {(1)H,(15)N}-HMBC spectra, is significantly affected by the coordination to palladium; (iii) the coordination induced shift (CIS) of the nitrogen atom trans to the CH3 ligand is smaller than the other. The structure in the solid state for the neutral derivatives with all the four ligands was solved, pointing out that: (iv) the Pd-C bond distance increases with the basicity of the nitrogen-donor ligand; (v) the Pd-N bond distance correlates well with the CIS value. The combining of the solution and solid state structural features allows stating that: (vi) the Pd-CH3 singlet is a good probe for the electron donor capability of the ligand; (vii) the CIS value might be used as a probe for the strength of the Pd-N bond. All monocationic complexes generated active catalysts for the CO/vinyl arene copolymerization, leading to prevailingly syndiotactic polyketones. The catalyst performances, both in terms of catalyst productivity and polymer molecular weight, correlate well with the precatalyst structural features.

Structural basis of Arp2/3 complex inhibition by GMF, Coronin, and Arpin

PubMed Central

Sokolova, Olga S.; Chemeris, Angelina; Guo, Siyang; Alioto, Salvatore L.; Gandhi, Meghal; Padrick, Shae; Pechnikova, Evgeniya; David, Violaine; Gautreau, Alexis; Goode, Bruce L.

2017-01-01

The evolutionarily conserved Arp2/3 complex plays a central role in nucleating the branched actin filament arrays that drive cell migration, endocytosis, and other processes. To better understand Arp2/3 complex regulation, we used single particle electron microscopy to compare the structures of Arp2/3 complex bound to three different inhibitory ligands: GMF, Coronin, and Arpin. Although the three inhibitors have distinct binding sites on Arp2/3 complex, they each induced an ‘open’ nucleation-inactive conformation. Coronin promoted a standard (previously described) open conformation of Arp2/3 complex, with the N-terminal β-propeller domain of Coronin positioned near the p35/ARPC2 subunit of Arp2/3 complex. GMF induced two distinct open conformations of Arp2/3 complex, which correlated with two suggested binding sites for GMF. Further, GMF synergized with Coronin in inhibiting actin nucleation by Arp2/3 complex. Arpin, which uses VCA-related acidic (A) motifs to interact with the Arp2/3 complex, induced the standard open conformation, and two new masses appeared at positions near Arp2 and Arp3. Further, Arpin showed additive inhibitory effects on Arp2/3 complex with Coronin and GMF. Together, these data suggest that Arp2/3 complex conformation is highly polymorphic and that its activities can be controlled combinatorially by different inhibitory ligands. PMID:27939292

High refuge availability on coral reefs increases the vulnerability of reef-associated predators to overexploitation.

PubMed

Rogers, Alice; Blanchard, Julia L; Newman, Steven P; Dryden, Charlie S; Mumby, Peter J

2018-02-01

Refuge availability and fishing alter predator-prey interactions on coral reefs, but our understanding of how they interact to drive food web dynamics, community structure and vulnerability of different trophic groups is unclear. Here, we apply a size-based ecosystem model of coral reefs, parameterized with empirical measures of structural complexity, to predict fish biomass, productivity and community structure in reef ecosystems under a broad range of refuge availability and fishing regimes. In unfished ecosystems, the expected positive correlation between reef structural complexity and biomass emerges, but a non-linear effect of predation refuges is observed for the productivity of predatory fish. Reefs with intermediate complexity have the highest predator productivity, but when refuge availability is high and prey are less available, predator growth rates decrease, with significant implications for fisheries. Specifically, as fishing intensity increases, predators in habitats with high refuge availability exhibit vulnerability to over-exploitation, resulting in communities dominated by herbivores. Our study reveals mechanisms for threshold dynamics in predators living in complex habitats and elucidates how predators can be food-limited when most of their prey are able to hide. We also highlight the importance of nutrient recycling via the detrital pathway, to support high predator biomasses on coral reefs. © 2018 by the Ecological Society of America.

Correlational structure of ‘frontal’ tests and intelligence tests indicates two components with asymmetrical neurostructural correlates in old age

PubMed Central

Cox, Simon R.; MacPherson, Sarah E.; Ferguson, Karen J.; Nissan, Jack; Royle, Natalie A.; MacLullich, Alasdair M.J.; Wardlaw, Joanna M.; Deary, Ian J.

2014-01-01

Both general fluid intelligence (gf) and performance on some ‘frontal tests’ of cognition decline with age. Both types of ability are at least partially dependent on the integrity of the frontal lobes, which also deteriorate with age. Overlap between these two methods of assessing complex cognition in older age remains unclear. Such overlap could be investigated using inter-test correlations alone, as in previous studies, but this would be enhanced by ascertaining whether frontal test performance and gf share neurobiological variance. To this end, we examined relationships between gf and 6 frontal tests (Tower, Self-Ordered Pointing, Simon, Moral Dilemmas, Reversal Learning and Faux Pas tests) in 90 healthy males, aged ~ 73 years. We interpreted their correlational structure using principal component analysis, and in relation to MRI-derived regional frontal lobe volumes (relative to maximal healthy brain size). gf correlated significantly and positively (.24 ≤ r ≤ .53) with the majority of frontal test scores. Some frontal test scores also exhibited shared variance after controlling for gf. Principal component analysis of test scores identified units of gf-common and gf-independent variance. The former was associated with variance in the left dorsolateral (DL) and anterior cingulate (AC) regions, and the latter with variance in the right DL and AC regions. Thus, we identify two biologically-meaningful components of variance in complex cognitive performance in older age and suggest that age-related changes to DL and AC have the greatest cognitive impact. PMID:25278641

Correlational structure of 'frontal' tests and intelligence tests indicates two components with asymmetrical neurostructural correlates in old age.

PubMed

Cox, Simon R; MacPherson, Sarah E; Ferguson, Karen J; Nissan, Jack; Royle, Natalie A; MacLullich, Alasdair M J; Wardlaw, Joanna M; Deary, Ian J

2014-09-01

Both general fluid intelligence ( g f ) and performance on some 'frontal tests' of cognition decline with age. Both types of ability are at least partially dependent on the integrity of the frontal lobes, which also deteriorate with age. Overlap between these two methods of assessing complex cognition in older age remains unclear. Such overlap could be investigated using inter-test correlations alone, as in previous studies, but this would be enhanced by ascertaining whether frontal test performance and g f share neurobiological variance. To this end, we examined relationships between g f and 6 frontal tests (Tower, Self-Ordered Pointing, Simon, Moral Dilemmas, Reversal Learning and Faux Pas tests) in 90 healthy males, aged ~ 73 years. We interpreted their correlational structure using principal component analysis, and in relation to MRI-derived regional frontal lobe volumes (relative to maximal healthy brain size). g f correlated significantly and positively (.24 ≤  r  ≤ .53) with the majority of frontal test scores. Some frontal test scores also exhibited shared variance after controlling for g f . Principal component analysis of test scores identified units of g f -common and g f -independent variance. The former was associated with variance in the left dorsolateral (DL) and anterior cingulate (AC) regions, and the latter with variance in the right DL and AC regions. Thus, we identify two biologically-meaningful components of variance in complex cognitive performance in older age and suggest that age-related changes to DL and AC have the greatest cognitive impact.

A general and fast scoring function for protein-ligand interactions: a simplified potential approach.

PubMed

Muegge, I; Martin, Y C

1999-03-11

A fast, simplified potential-based approach is presented that estimates the protein-ligand binding affinity based on the given 3D structure of a protein-ligand complex. This general, knowledge-based approach exploits structural information of known protein-ligand complexes extracted from the Brookhaven Protein Data Bank and converts it into distance-dependent Helmholtz free interaction energies of protein-ligand atom pairs (potentials of mean force, PMF). The definition of an appropriate reference state and the introduction of a correction term accounting for the volume taken by the ligand were found to be crucial for deriving the relevant interaction potentials that treat solvation and entropic contributions implicitly. A significant correlation between experimental binding affinities and computed score was found for sets of diverse protein-ligand complexes and for sets of different ligands bound to the same target. For 77 protein-ligand complexes taken from the Brookhaven Protein Data Bank, the calculated score showed a standard deviation from observed binding affinities of 1.8 log Ki units and an R2 value of 0.61. The best results were obtained for the subset of 16 serine protease complexes with a standard deviation of 1.0 log Ki unit and an R2 value of 0.86. A set of 33 inhibitors modeled into a crystal structure of HIV-1 protease yielded a standard deviation of 0.8 log Ki units from measured inhibition constants and an R2 value of 0.74. In contrast to empirical scoring functions that show similar or sometimes better correlation with observed binding affinities, our method does not involve deriving specific parameters that fit the observed binding affinities of protein-ligand complexes of a given training set. We compared the performance of the PMF score, Böhm's score (LUDI), and the SMOG score for eight different test sets of protein-ligand complexes. It was found that for the majority of test sets the PMF score performs best. The strength of the new approach presented here lies in its generality as no knowledge about measured binding affinities is needed to derive atomic interaction potentials. The use of the new scoring function in docking studies is outlined.

Small-Molecule Effectors of Hepatitis B Virus Capsid Assembly Give Insight into Virus Life Cycle▿

PubMed Central

Bourne, Christina; Lee, Sejin; Venkataiah, Bollu; Lee, Angela; Korba, Brent; Finn, M. G.; Zlotnick, Adam

2008-01-01

The relationship between the physical chemistry and biology of self-assembly is poorly understood, but it will be critical to quantitatively understand infection and for the design of antivirals that target virus genesis. Here we take advantage of heteroaryldihydropyrimidines (HAPs), which affect hepatitis B virus (HBV) assembly, to gain insight and correlate in vitro assembly with HBV replication in culture. Based on a low-resolution crystal structure of a capsid-HAP complex, a closely related series of HAPs were designed and synthesized. These differentially strengthen the association between neighboring capsid proteins, alter the kinetics of assembly, and give rise to aberrant structures incompatible with a functional capsid. The chemical nature of the HAP variants correlated well with the structure of the HAP binding pocket. The thermodynamics and kinetics of in vitro assembly had strong and predictable effects on product morphology. However, only the kinetics of in vitro assembly had a strong correlation with inhibition of HBV replication in HepG2.2.15 cells; there was at best a weak correlation between assembly thermodynamics and replication. The correlation between assembly kinetics and virus suppression implies a competition between successful assembly and misassembly, small molecule induced or otherwise. This is a predictive and testable model for the mechanism of action of assembly effectors. PMID:18684823

Hierarchical Coarse-Graining Via a Generalized Yvon-Born Green Framework: Many-Body Correlations, Mappings, and Structural Accuracy

NASA Astrophysics Data System (ADS)

Rudzinski, Joseph F.

Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of "hierarchical" approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this "consistency" between the models is to parameterize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distributions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic constructs to directly relate the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correlation functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing models for systems with complex intramolecular structure. Overall, our results demonstrate the power of the g-YBG framework for developing accurate CG models and for investigating the driving forces of equilibrium structures for complex condensed-phase systems. This work also explicitly motivates future development of bottom-up CG methods and highlights some outstanding problems in the field. iii.

The structure and resilience of financial market networks

NASA Astrophysics Data System (ADS)

Kauê Dal'Maso Peron, Thomas; da Fontoura Costa, Luciano; Rodrigues, Francisco A.

2012-03-01

Financial markets can be viewed as a highly complex evolving system that is very sensitive to economic instabilities. The complex organization of the market can be represented in a suitable fashion in terms of complex networks, which can be constructed from stock prices such that each pair of stocks is connected by a weighted edge that encodes the distance between them. In this work, we propose an approach to analyze the topological and dynamic evolution of financial networks based on the stock correlation matrices. An entropy-related measurement is adopted to quantify the robustness of the evolving financial market organization. It is verified that the network topological organization suffers strong variation during financial instabilities and the networks in such periods become less robust. A statistical robust regression model is proposed to quantity the relationship between the network structure and resilience. The obtained coefficients of such model indicate that the average shortest path length is the measurement most related to network resilience coefficient. This result indicates that a collective behavior is observed between stocks during financial crisis. More specifically, stocks tend to synchronize their price evolution, leading to a high correlation between pair of stock prices, which contributes to the increase in distance between them and, consequently, decrease the network resilience.

Backbone dynamics in an intramolecular prolylpeptide-SH3 complex from the diphtheria toxin repressor, DtxR

PubMed Central

Bhattacharya, Nilakshee; Yi, Myunggi; Zhou, Huan-Xiang; Logan, Timothy M.

2008-01-01

Summary The diphtheria toxin repressor contains an SH3-like domain that forms an intramolecular complex with a proline-rich (Pr) peptide segment and stabilizes the inactive state of the repressor. Upon activation of DtxR by transition metals, this intramolecular complex must dissociate as the SH3 domain and Pr segment form different interactions in the active repressor. In this study we investigate the dynamics of this intramolecular complex using backbone amide nuclear spin relaxation rates determined using NMR spectroscopy and molecular dynamics trajectories. The SH3 domain in the unbound and bound states showed typical dynamics in that the secondary structures were fairly ordered with high generalized order parameters and low effective correlation times while residues in the loops connecting β-strands exhibited reduced generalized order parameters and required additional motional terms to adequately model the relaxation rates. Residues forming the Pr segment exhibited low order parameters with internal rotational correlation times on the order of 0.6 – 1 ns. Further analysis showed that the SH3 domain was rich in millisecond timescale motions while the Pr segment was rich in motions on the 100s μs timescale. Molecular dynamics simultations indicated structural rearrangements that may contribute to the observed relaxation rates and, together with the observed relaxation rate data, suggested that the Pr segment exhibits a binding ↔ unbinding equilibrium. The results of this study provide new insights into the nature of the intramolecular complex and provide a better understanding of the biological role of the SH3 domain in regulating DtxR activity. PMID:17976643

Unusual Complex Formation and Chemical Reaction of Haloacetate Anion on the Exterior Surface of Cucurbit[6]uril in the Gas Phase

NASA Astrophysics Data System (ADS)

Choi, Tae Su; Ko, Jae Yoon; Heo, Sung Woo; Ko, Young Ho; Kim, Kimoon; Kim, Hugh I.

2012-10-01

Noncovalent interactions of cucurbit[6]uril (CB[6]) with haloacetate and halide anions are investigated in the gas phase using electrospray ionization ion mobility mass spectrometry. Strong noncovalent interactions of monoiodoacetate, monobromoacetate, monochloroacetate, dichloroacetate, and trichloroacetate on the exterior surface of CB[6] are observed in the negative mode electrospray ionization mass spectra. The strong binding energy of the complex allows intramolecular SN2 reaction of haloacetate, which yields externally bound CB[6]-halide complex, by collisional activation. Utilizing ion mobility technique, structures of exteriorly bound CB[6] complexes of haloacetate and halide anions are confirmed. Theoretically determined low energy structures using density functional theory (DFT) further support results from ion mobility studies. The DFT calculation reveals that the binding energy and conformation of haloacetate on the CB[6] surface affect the efficiency of the intramolecular SN2 reaction of haloacetate, which correlate well with the experimental observation.

The Structure of Lombricine Kinase: Implications for Phosphagen Conformational Changes

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

Bush, D. Jeffrey; Kirillova, Olga; Clark, Shawn A.

2012-05-29

Lombricine kinase is a member of the phosphagen kinase family and a homolog of creatine and arginine kinases, enzymes responsible for buffering cellular ATP levels. Structures of lombricine kinase from the marine worm Urechis caupo were determined by x-ray crystallography. One form was crystallized as a nucleotide complex, and the other was substrate-free. The two structures are similar to each other and more similar to the substrate-free forms of homologs than to the substrate-bound forms of the other phosphagen kinases. Active site specificity loop 309-317, which is disordered in substrate-free structures of homologs and is known from the NMR ofmore » arginine kinase to be inherently dynamic, is resolved in both lombricine kinase structures, providing an improved basis for understanding the loop dynamics. Phosphagen kinases undergo a segmented closing on substrate binding, but the lombricine kinase ADP complex is in the open form more typical of substrate-free homologs. Through a comparison with prior complexes of intermediate structure, a correlation was revealed between the overall enzyme conformation and the substrate interactions of His{sup 178}. Comparative modeling provides a rationale for the more relaxed specificity of these kinases, of which the natural substrates are among the largest of the phosphagen substrates.« less

Structure-wise discrimination of adenine and guanine by proteins on the basis of their nonbonded interactions.

PubMed

Usha, S; Selvaraj, S

2015-01-01

We have analyzed the nonbonded interactions of the structurally similar moieties, adenine and guanine forming complexes with proteins. The results comprise (a) the amino acid-ligand atom preferences, (b) solvent accessibility of ligand atoms before and after complex formation with proteins, and (c) preferred amino acid residue atoms involved in the interactions. We have observed that the amino acid preferences involved in the hydrogen bonding interactions vary for adenine and guanine. The structural variation between the purine atoms is clearly reflected by their burial tendency in the solvent environment. Correlation of the mean amino acid preference values show the variation that exists between adenine and guanine preferences of all the amino acid residues. All our observations provide evidence for the discriminating nature of the proteins in recognizing adenine and guanine.

Vibronic Boson Sampling: Generalized Gaussian Boson Sampling for Molecular Vibronic Spectra at Finite Temperature.

PubMed

Huh, Joonsuk; Yung, Man-Hong

2017-08-07

Molecular vibroic spectroscopy, where the transitions involve non-trivial Bosonic correlation due to the Duschinsky Rotation, is strongly believed to be in a similar complexity class as Boson Sampling. At finite temperature, the problem is represented as a Boson Sampling experiment with correlated Gaussian input states. This molecular problem with temperature effect is intimately related to the various versions of Boson Sampling sharing the similar computational complexity. Here we provide a full description to this relation in the context of Gaussian Boson Sampling. We find a hierarchical structure, which illustrates the relationship among various Boson Sampling schemes. Specifically, we show that every instance of Gaussian Boson Sampling with an initial correlation can be simulated by an instance of Gaussian Boson Sampling without initial correlation, with only a polynomial overhead. Since every Gaussian state is associated with a thermal state, our result implies that every sampling problem in molecular vibronic transitions, at any temperature, can be simulated by Gaussian Boson Sampling associated with a product of vacuum modes. We refer such a generalized Gaussian Boson Sampling motivated by the molecular sampling problem as Vibronic Boson Sampling.

Correlation Analysis of Reactivity in the Photo- and Electro-Reduction of Cobalt(III) Complexes in Binary Organic Solvent/Water Mixtures

NASA Astrophysics Data System (ADS)

Sivaraj, Kumarasamy; Elango, Kuppanagounder P.

2008-08-01

The photo- and electro-reduction of a series of cobalt(III) complexes of the type cis-β - [Co(trien)(RC6H4NH2)Cl]Cl2 with R = H, p-OMe, p-OEt, p-Me, p-Et, p-F, and m-Me has been studied in binary propan-2-ol/water mixtures. The redox potential (E1/2) and photo-reduction quantum yield (ΦCo(II)) data were correlated with solvent and structural parameters with the aim to shed some light on the mechanism of these reactions. The correlation of E1/2 and ΦCo(II) with macroscopic solvent parameters, viz. relative permittivity, indicated that the reactivity is influenced by both specific and non-specific solute-solvent interactions. The Kamlet-Taft solvatochromic comparison method was used to separate and quantify these effects: An increase in the percentage of organic cosolvent in the medium enhances both reduction processes, and there exists a good linear correlation between E1/2 and ΦCo(II), suggesting a similar solvation of the participants in these redox processes.

Upper crustal structures beneath Yogyakarta imaged by ambient seismic noise tomography

NASA Astrophysics Data System (ADS)

Zulfakriza, Saygin, E.; Cummins, P.; Widiyantoro, S.; Nugraha, Andri Dian

2013-09-01

Delineating the upper crustal structures beneath Yogyakarta is necessary for understanding its tectonic setting. The presence of Mt. Merapi, fault line and the alluvial deposits contributes to the complex geology of Yogyakarta. Recently, ambient seismic noise tomography can be used to image the subsurface structure. The cross correlations of ambient seismic noise of pair stations were applied to extract the Green's function. The total of 27 stations from 134 seismic stations available in MERapi Amphibious EXperiment (MERAMEX) covering Yogyakarta region were selected to conduct cross correlation. More than 500 Rayleigh waves of Green's functions could be extracted by cross-correlating available the station pairs of short-period and broad-band seismometers. The group velocities were obtained by filtering the extracted Green's function between 0.5 and 20 s. 2-D inversion was applied to the retrieved travel times. Features in the derived tomographic images correlate with the surface geology of Yogyakarta. The Merapi active volcanoes and alluvial deposit in Yogyakarta are clearly described by lower group velocities. The high velocity anomaly contrasts which are visible in the images obtained from the period range between 1 and 5 s, correspond to subsurface imprints of fault that could be the Opak Fault.

Canopy structural complexity as a continental predictor of primary production: Using NEON to transform understanding of forest structure-function

NASA Astrophysics Data System (ADS)

Atkins, J. W.; Fahey, R. T.; Gough, C. M.; Hardiman, B. S.

2016-12-01

Ecosystem structure-function relationships represent a long-standing research area for ecosystem science. Relationships between canopy structural complexity (CSC) and net primary productivity (NPP), have been characterized for a limited number of sites, yet whether these relationships are conserved across eco-climatic boundaries remains unknown. We hypothesize an underlying mechanistic basis for global NPP-CSC linkages to include improved resource-use efficiency as CSC increases, examined here by correlating CSC with measures of light-use efficiency and nitrogen-use efficiency. Here we present a broad, continental scale analysis of CSC-NPP linkages. We are using multiple NEON sites coupled with other sites across a diverse array of temperate forest types spanning six eco-climatic domains of the continental United States to examine CSC-NPP relationships. Portable canopy LiDAR (PCL) data were used to calculate a suite of CSC metrics at the plot-level within each site. Ongoing work compares CSC to co-located measurements of wood net primary production estimated from the incremental change in woody biomass calculated using tree allometries. Results to date show CSC is highly variable across forest sites and may provide additional explanatory power for predicting NPP that is independent of other commonly used forest structural attributes such as leaf area index. CSC metrics such as rugosity vary widely across sites—ranging from high values (30 - 35) in complex canopies such as the Great Smoky Mountains to low values in open, savanna systems like North-Central Florida (< 0.5 - 2). NPP, and light- and nitrogen-use calculations are underway and will be paired with site-level CSC, with the expectation that CSC, resource-use efficiency, and NPP are positively correlated. Advancing understanding of how and why CSC affects forest NPP across a broad spatial dimension could transform mechanistic understanding of ecosystem structure-carbon cycling relationships, and greatly improve carbon cycling models and remote sensing applications, while providing a crucial linkage between the two.

X-ray diffraction, inelastic neutron scattering (INS) and infrared (IR) studies on 2:1 hexamethylbenzene (HMB) tetracyanoethylene (TCNE) complex

NASA Astrophysics Data System (ADS)

Pawlukojć, A.; Sawka-Dobrowolska, W.; Bator, G.; Sobczyk, L.; Grech, E.; Nowicka-Scheibe, J.

2006-09-01

The structure of the 2:1 hexamethylbenzene (HMB)-tetracyanoethylene (TCNE) complex was determined at 100 K. In the crystalline lattice the molecules of HMB (D) and TCNE (A) are arranged in DDADDADD stacks along the b-axis. Based on the red shift of the ν(C tbnd N) IR frequencies the charge transfer (CT) degree ( Z) was estimated to be equal to 0.14. It is markedly higher than that for the complex of HMB with tetracyanoquinodimethane (TCNQ) for which Z = 0.06. The analysis of vibrational modes connected with torsional motion in the low frequency region was performed based on the inelastic neutron scattering (INS) experiments and DFT theoretical calculations. The correlation between νexp/ νcalc and νcalc shows a deviation of experimental values from calculated ones. It is the higher the lower is the frequency of the analysed mode. The comparison of correlations for neat HMB and its complexes with TCNQ and TCNE suggests that some role in decreasing the barrier to rotation can be played by the charge transfer between D and A molecules.

Complex-Morphology Metal-Based Nanostructures: Fabrication, Characterization, and Applications

PubMed Central

Gentile, Antonella; Ruffino, Francesco; Grimaldi, Maria Grazia

2016-01-01

Due to their peculiar qualities, metal-based nanostructures have been extensively used in applications such as catalysis, electronics, photography, and information storage, among others. New applications for metals in areas such as photonics, sensing, imaging, and medicine are also being developed. Significantly, most of these applications require the use of metals in the form of nanostructures with specific controlled properties. The properties of nanoscale metals are determined by a set of physical parameters that include size, shape, composition, and structure. In recent years, many research fields have focused on the synthesis of nanoscale-sized metallic materials with complex shape and composition in order to optimize the optical and electrical response of devices containing metallic nanostructures. The present paper aims to overview the most recent results—in terms of fabrication methodologies, characterization of the physico-chemical properties and applications—of complex-morphology metal-based nanostructures. The paper strongly focuses on the correlation between the complex morphology and the structures’ properties, showing how the morphological complexity (and its nanoscale control) can often give access to a wide range of innovative properties exploitable for innovative functional device production. We begin with an overview of the basic concepts on the correlation between structural and optical parameters of nanoscale metallic materials with complex shape and composition, and the possible solutions offered by nanotechnology in a large range of applications (catalysis, electronics, photonics, sensing). The aim is to assess the state of the art, and then show the innovative contributions that can be proposed in this research field. We subsequently report on innovative, versatile and low-cost synthesis techniques, suitable for providing a good control on the size, surface density, composition and geometry of the metallic nanostructures. The main purpose of this study is the fabrication of functional nanoscale-sized materials, whose properties can be tailored (in a wide range) simply by controlling the structural characteristics. The modulation of the structural parameters is required to tune the plasmonic properties of the nanostructures for applications such as biosensors, opto-electronic or photovoltaic devices and surface-enhanced Raman scattering (SERS) substrates. The structural characterization of the obtained nanoscale materials is employed in order to define how the synthesis parameters affect the structural characteristics of the resulting metallic nanostructures. Then, macroscopic measurements are used to probe their electrical and optical properties. Phenomenological growth models are drafted to explain the processes involved in the growth and evolution of such composite systems. After the synthesis and characterization of the metallic nanostructures, we study the effects of the incorporation of the complex morphologies on the optical and electrical responses of each specific device. PMID:28335236

Entropy, complexity, and Markov diagrams for random walk cancer models.

PubMed

Newton, Paul K; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

2014-12-19

The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.

Entropy, complexity, and Markov diagrams for random walk cancer models

NASA Astrophysics Data System (ADS)

Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

2014-12-01

The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential.

X-ray scattering measurements of strong ion-ion correlations in shock-compressed aluminum.

PubMed

Ma, T; Döppner, T; Falcone, R W; Fletcher, L; Fortmann, C; Gericke, D O; Landen, O L; Lee, H J; Pak, A; Vorberger, J; Wünsch, K; Glenzer, S H

2013-02-08

The strong ion-ion correlation peak characteristic of warm dense matter (WDM) is observed for the first time using simultaneous angularly, temporally, and spectrally resolved x-ray scattering measurements in laser-driven shock-compressed aluminum. Laser-produced molybdenum x-ray line emission at an energy of 17.9 keV is employed to probe aluminum compressed to a density of ρ>8 g/cm(3). We observe a well pronounced peak in the static structure factor at a wave number of k=4.0 Å(-1). The measurements of the magnitude and position of this correlation peak are precise enough to test different theoretical models for the ion structure and show that only models taking the complex interaction in WDM into account agree with the data. This also demonstrates a new highly accurate diagnostic to directly measure the state of compression of warm dense matter.

Formation of orbital-selective electron states in LaTiO3/SrTiO3 superlattices

NASA Astrophysics Data System (ADS)

Lechermann, Frank; Boehnke, Lewin; Grieger, Daniel

2013-06-01

The interface electronic structure of correlated LaTiO3/SrTiO3 superlattices is investigated by means of the charge self-consistent combination of the local density approximation (LDA) to density functional theory with dynamical mean-field theory. Utilizing a pseudopotential technique together with a continuous-time quantum Monte Carlo approach, the resulting complex multiorbital electronic states are addressed in a coherent fashion beyond static mean field. General structural relaxations are taken into account on the LDA level and cooperate with the driving forces from strong electronic correlations. This alliance leads to a Ti(3dxy) dominated low-energy quasiparticle peak and a lower Hubbard band in line with photoemission studies. Furthermore correlation effects close to the band-insulating bulk SrTiO3 limit as well as the Mott-insulating bulk LaTiO3 limit are studied via realistic single-layer embeddings.

Self-amplified photo-induced gap quenching in a correlated electron material

PubMed Central

Mathias, S.; Eich, S.; Urbancic, J.; Michael, S.; Carr, A. V.; Emmerich, S.; Stange, A.; Popmintchev, T.; Rohwer, T.; Wiesenmayer, M.; Ruffing, A.; Jakobs, S.; Hellmann, S.; Matyba, P.; Chen, C.; Kipp, L.; Bauer, M.; Kapteyn, H. C.; Schneider, H. C.; Rossnagel, K.; Murnane, M. M.; Aeschlimann, M.

2016-01-01

Capturing the dynamic electronic band structure of a correlated material presents a powerful capability for uncovering the complex couplings between the electronic and structural degrees of freedom. When combined with ultrafast laser excitation, new phases of matter can result, since far-from-equilibrium excited states are instantaneously populated. Here, we elucidate a general relation between ultrafast non-equilibrium electron dynamics and the size of the characteristic energy gap in a correlated electron material. We show that carrier multiplication via impact ionization can be one of the most important processes in a gapped material, and that the speed of carrier multiplication critically depends on the size of the energy gap. In the case of the charge-density wave material 1T-TiSe2, our data indicate that carrier multiplication and gap dynamics mutually amplify each other, which explains—on a microscopic level—the extremely fast response of this material to ultrafast optical excitation. PMID:27698341

Differential Effects of the Factor Structure of the Wechsler Memory Scale-Revised on the Cortical Thickness and Complexity of Patients Aged Over 75 Years in a Memory Clinic Setting.

PubMed

Kinno, Ryuta; Shiromaru, Azusa; Mori, Yukiko; Futamura, Akinori; Kuroda, Takeshi; Yano, Satoshi; Murakami, Hidetomo; Ono, Kenjiro

2017-01-01

The Wechsler Memory Scale-Revised (WMS-R) is one of the internationally well-known batteries for memory assessment in a general memory clinic setting. Several factor structures of the WMS-R for patients aged under 74 have been proposed. However, little is known about the factor structure of the WMS-R for patients aged over 75 years and its neurological significance. Thus, we conducted exploratory factor analysis to determine the factor structure of the WMS-R for patients aged over 75 years in a memory clinic setting. Regional cerebral blood flow (rCBF) was calculated from single-photon emission computed tomography data. Cortical thickness and cortical fractal dimension, as the marker of cortical complexity, were calculated from high resolution magnetic resonance imaging data. We found that the four factors appeared to be the most appropriate solution to the model, including recognition memory, paired associate memory, visual-and-working memory, and attention as factors. Patients with mild cognitive impairments showed significantly higher factor scores for paired associate memory, visual-and-working memory, and attention than patients with Alzheimer's disease. Regarding the neuroimaging data, the factor scores for paired associate memory positively correlated with rCBF in the left pericallosal and hippocampal regions. Moreover, the factor score for paired associate memory showed most robust correlations with the cortical thickness in the limbic system, whereas the factor score for attention correlated with the cortical thickness in the bilateral precuneus. Furthermore, each factor score correlated with the cortical fractal dimension in the bilateral frontotemporal regions. Interestingly, the factor scores for the visual-and-working memory and attention selectively correlated with the cortical fractal dimension in the right posterior cingulate cortex and right precuneus cortex, respectively. These findings demonstrate that recognition memory, paired associate memory, visual-and-working memory, and attention can be crucial factors for interpreting the WMS-R results of elderly patients aged over 75 years in a memory clinic setting. Considering these findings, the results of WMS-R in elderly patients aged over 75 years in a memory clinic setting should be cautiously interpreted.

Correlations Between Clinical Judgement and Learning Style Preferences of Nursing Students in the Simulation Room.

PubMed

Hallin, Karin; Haggstrom, Marie; Backstrom, Britt; Kristiansen, Lisbeth Porskrog

2015-09-28

Health care educators account for variables affecting patient safety and are responsible for developing the highly complex process of education planning. Clinical judgement is a multidimensional process, which may be affected by learning styles. The aim was to explore three specific hypotheses to test correlations between nursing students' team achievements in clinical judgement and emotional, sociological and physiological learning style preferences. A descriptive cross-sectional study was conducted with Swedish university nursing students in 2012-2013. Convenience sampling was used with 60 teams with 173 nursing students in the final semester of a three-year Bachelor of Science in nursing programme. Data collection included questionnaires of personal characteristics, learning style preferences, determined by the Dunn and Dunn Productivity Environmental Preference Survey, and videotaped complex nursing simulation scenarios. Comparison with Lasater Clinical Judgement Rubric and Non-parametric analyses were performed. Three significant correlations were found between the team achievements and the students' learning style preferences: significant negative correlation with 'Structure' and 'Kinesthetic' at the individual level, and positive correlation with the 'Tactile' variable. No significant correlations with students' 'Motivation', 'Persistence', 'Wish to learn alone' and 'Wish for an authoritative person present' were seen. There were multiple complex interactions between the tested learning style preferences and the team achievements of clinical judgement in the simulation room, which provides important information for the becoming nurses. Several factors may have influenced the results that should be acknowledged when designing further research. We suggest conducting mixed methods to determine further relationships between team achievements, learning style preferences, cognitive learning outcomes and group processes.

Correlations Between Micromagnetic, Microstructural and Microchemical Properties in Ultrathin Epitaxial Magnetic Structures

DTIC Science & Technology

1993-12-31

substrates. 2-17,19- 24-17-34 These films possess corn- temperature. It is the complexity of both the structural and plec two-dimensional magnetic...free energy differences, diffusion lengths,were taken to ensure that these measurements represent su~ rt tepraue and deposition rates. At room tern...Arnion, G. Jennings, and Rt F. Willis, Surface taneous multilayered growth made due to the lack of Science 192, LS43 (1987). breaks in the normalized MWV

Sequence-dependent DNA flexibility mediates DNase I cleavage.

PubMed

Heddi, Brahim; Abi-Ghanem, Josephine; Lavigne, Marc; Hartmann, Brigitte

2010-01-08

Understanding the preference of nonspecific proteins for certain DNA structural features requires an accurate description of the properties of free DNA, especially regarding their possible predisposition to adopt a conformation that favors the formation of a complex. Exploiting previous exhaustive NMR studies performed on free DNA oligomers, we investigated the molecular basis of DNase I sensitivity under conditions where DNase I binding limits the probability of cleavage. We showed that cleavage intensity was correlated with adjacent 3' phosphate linkage flexibility, monitored by (31)P chemical shifts. Examining NMR-refined DNA structures highlighted that sequence-dependent flexible phosphates were associated with large minor groove variations that may promote the affinity of DNase I, according to relevant DNA-protein complexes. In sum, this work demonstrates that specificity in DNA-DNase I interaction is mediated by DNA flexibility, which influences the induced-fit transitions required to form productive complexes.

GRAIL gravity observations of the transition from complex crater to peak-ring basin on the Moon: Implications for crustal structure and impact basin formation

NASA Astrophysics Data System (ADS)

Baker, David M. H.; Head, James W.; Phillips, Roger J.; Neumann, Gregory A.; Bierson, Carver J.; Smith, David E.; Zuber, Maria T.

2017-08-01

High-resolution gravity data from the Gravity Recovery and Interior Laboratory (GRAIL) mission provide the opportunity to analyze the detailed gravity and crustal structure of impact features in the morphological transition from complex craters to peak-ring basins on the Moon. We calculate average radial profiles of free-air anomalies and Bouguer anomalies for peak-ring basins, protobasins, and the largest complex craters. Complex craters and protobasins have free-air anomalies that are positively correlated with surface topography, unlike the prominent lunar mascons (positive free-air anomalies in areas of low elevation) associated with large basins. The Bouguer gravity anomaly profiles of complex craters are highly irregular, with central positive anomalies that are generally absent or not clearly tied to interior morphology. In contrast, gravity profiles for peak-ring basins (∼200 km to 580 km) are much more regular and are highly correlated with surface morphology. A central positive Bouguer anomaly is confined within the peak ring and a negative Bouguer anomaly annulus extends from the edge of the positive anomaly outward to about the rim crest. A number of degraded basins lacking interior peak rings have diameters and gravity patterns similar to those of well-preserved peak-ring basins. If these structures represent degraded peak-ring basins, the number of peak-ring basins on the Moon would increase by more than a factor of two to 34. The gravity anomalies within basins are interpreted to be due to uplift of the mantle confined within the peak ring and an annulus of thickened crust between the peak ring and rim crest. We hypothesize that mantle uplift is influenced by interaction between the transient cavity and the mantle. Further, mascon formation is generally disconnected from the number of basin rings formed and occurs over a wide range of basin sizes. These observations have important implications for models of basin and mascon formation on the Moon and other planetary bodies.

Causal effect of disconnection lesions on interhemispheric functional connectivity in rhesus monkeys

PubMed Central

O’Reilly, Jill X.; Croxson, Paula L.; Jbabdi, Saad; Sallet, Jerome; Noonan, MaryAnn P.; Mars, Rogier B.; Browning, Philip G.F.; Wilson, Charles R. E.; Mitchell, Anna S.; Miller, Karla L.; Rushworth, Matthew F. S.; Baxter, Mark G.

2013-01-01

In the absence of external stimuli or task demands, correlations in spontaneous brain activity (functional connectivity) reflect patterns of anatomical connectivity. Hence, resting-state functional connectivity has been used as a proxy measure for structural connectivity and as a biomarker for brain changes in disease. To relate changes in functional connectivity to physiological changes in the brain, it is important to understand how correlations in functional connectivity depend on the physical integrity of brain tissue. The causal nature of this relationship has been called into question by patient data suggesting that decreased structural connectivity does not necessarily lead to decreased functional connectivity. Here we provide evidence for a causal but complex relationship between structural connectivity and functional connectivity: we tested interhemispheric functional connectivity before and after corpus callosum section in rhesus monkeys. We found that forebrain commissurotomy severely reduced interhemispheric functional connectivity, but surprisingly, this effect was greatly mitigated if the anterior commissure was left intact. Furthermore, intact structural connections increased their functional connectivity in line with the hypothesis that the inputs to each node are normalized. We conclude that functional connectivity is likely driven by corticocortical white matter connections but with complex network interactions such that a near-normal pattern of functional connectivity can be maintained by just a few indirect structural connections. These surprising results highlight the importance of network-level interactions in functional connectivity and may cast light on various paradoxical findings concerning changes in functional connectivity in disease states. PMID:23924609

Statistical analysis of EGFR structures' performance in virtual screening

NASA Astrophysics Data System (ADS)

Li, Yan; Li, Xiang; Dong, Zigang

2015-11-01

In this work the ability of EGFR structures to distinguish true inhibitors from decoys in docking and MM-PBSA is assessed by statistical procedures. The docking performance depends critically on the receptor conformation and bound state. The enrichment of known inhibitors is well correlated with the difference between EGFR structures rather than the bound-ligand property. The optimal structures for virtual screening can be selected based purely on the complex information. And the mixed combination of distinct EGFR conformations is recommended for ensemble docking. In MM-PBSA, a variety of EGFR structures have identically good performance in the scoring and ranking of known inhibitors, indicating that the choice of the receptor structure has little effect on the screening.

How Can Music Influence the Autonomic Nervous System Response in Patients with Severe Disorder of Consciousness?

PubMed

Riganello, Francesco; Cortese, Maria D; Arcuri, Francesco; Quintieri, Maria; Dolce, Giuliano

2015-01-01

Activations to pleasant and unpleasant musical stimuli were observed within an extensive neuronal network and different brain structures, as well as in the processing of the syntactic and semantic aspects of the music. Previous studies evidenced a correlation between autonomic activity and emotion evoked by music listening in patients with Disorders of Consciousness (DoC). In this study, we analyzed retrospectively the autonomic response to musical stimuli by mean of normalized units of Low Frequency (nuLF) and Sample Entropy (SampEn) of Heart Rate Variability (HRV) parameters, and their possible correlation to the different complexity of four musical samples (i.e., Mussorgsky, Tchaikovsky, Grieg, and Boccherini) in Healthy subjects and Vegetative State/Unresponsive Wakefulness Syndrome (VS/UWS) patients. The complexity of musical sample was based on Formal Complexity and General Dynamics parameters defined by Imberty's semiology studies. The results showed a significant difference between the two groups for SampEn during the listening of Mussorgsky's music and for nuLF during the listening of Boccherini and Mussorgsky's music. Moreover, the VS/UWS group showed a reduction of nuLF as well as SampEn comparing music of increasing Formal Complexity and General Dynamics. These results put in evidence how the internal structure of the music can change the autonomic response in patients with DoC. Further investigations are required to better comprehend how musical stimulation can modify the autonomic response in DoC patients, in order to administer the stimuli in a more effective way.

Neural Correlates of Dutch Verb Second in Speech Production

ERIC Educational Resources Information Center

den Ouden, Dirk-Bart; Hoogduin, Hans; Stowe, Laurie A.; Bastiaanse, Roelien

2008-01-01

Dutch speakers with agrammatic Broca's aphasia are known to have problems with the production of finite verbs in main clauses. This performance pattern has been accounted for in terms of the specific syntactic complexity of the Dutch main clause structure, which requires an extra syntactic operation (Verb Second), relative to the basic…

The Complexities of Teaching Prime Decomposition and Multiplicative Structure with Tools to Preservice Elementary Teachers

ERIC Educational Resources Information Center

Kurz, Terri L.; Garcia, Jorge

2012-01-01

Preservice elementary teachers often struggle with prime decomposition and other mathematical topics that correlate with number theory. This paper provides a framework for integrating prime factor tiles into their curriculum with a particular emphasis on prime decomposition. Using this framework, preservice teachers explored and evaluated numbers…

Psychofamilial Correlates of School Disorders.

ERIC Educational Resources Information Center

Ehrlich, Marc I.

A child's school disorder can, and most often does, exist within the complexity of the family's transactional patterns and must be dealt with in this context. To do so, a conceptual model of family dynamics is needed. Minuchin (1979) offers a theoretical framework to help structure such a model. He and his colleagues identified five common…

Extent of resection in temporal lobectomy for epilepsy. I. Interobserver analysis and correlation with seizure outcome.

PubMed

Awad, I A; Katz, A; Hahn, J F; Kong, A K; Ahl, J; Lüders, H

1989-01-01

The extent of resection was assessed in 45 temporal lobectomies for medically intractable epilepsy with mapped temporal lobe foci. Postoperative magnetic resonance imaging (MRI) in the coronal plane was used to quantify the extent of resection of superior lateral, inferior lateral, basal, and medial structures, including the amygdalohippocampal complex. A new 20-compartment model of the temporal lobe was used for this assessment. Blinded interobserver variability was minimal. Intraoperative measurements and maps routinely overestimated the actual extent of resection, especially of medial structures. One year after surgery, 70% of patients remained seizure-free (except for auras). Seizure-free outcome was accomplished despite varying degrees of resection, but was more likely achieved with more extensive resections in all compartments. Among patients with mesiobasal foci, seizure-free outcome correlated significantly with extent of resection of amygdalohippocampal complex. We conclude that assessment of extent of resection by postoperative MRI provides an objective basis of evaluating outcome after temporal lobectomy. It allows a rational approach to understanding of operative failures and is potentially useful in comparing efficacy of various surgical approaches.

Investigation of a protein complex network

NASA Astrophysics Data System (ADS)

Mashaghi, A. R.; Ramezanpour, A.; Karimipour, V.

2004-09-01

The budding yeast Saccharomyces cerevisiae is the first eukaryote whose genome has been completely sequenced. It is also the first eukaryotic cell whose proteome (the set of all proteins) and interactome (the network of all mutual interactions between proteins) has been analyzed. In this paper we study the structure of the yeast protein complex network in which weighted edges between complexes represent the number of shared proteins. It is found that the network of protein complexes is a small world network with scale free behavior for many of its distributions. However we find that there are no strong correlations between the weights and degrees of neighboring complexes. To reveal non-random features of the network we also compare it with a null model in which the complexes randomly select their proteins. Finally we propose a simple evolutionary model based on duplication and divergence of proteins.

Redox potential tuning by redox-inactive cations in nature's water oxidizing catalyst and synthetic analogues.

PubMed

Krewald, Vera; Neese, Frank; Pantazis, Dimitrios A

2016-04-28

The redox potential of synthetic oligonuclear transition metal complexes has been shown to correlate with the Lewis acidity of a redox-inactive cation connected to the redox-active transition metals of the cluster via oxo or hydroxo bridges. Such heterometallic clusters are important cofactors in many metalloenzymes, where it is speculated that the redox-inactive constituent ion of the cluster serves to optimize its redox potential for electron transfer or catalysis. A principal example is the oxygen-evolving complex in photosystem II of natural photosynthesis, a Mn4CaO5 cofactor that oxidizes water into dioxygen, protons and electrons. Calcium is critical for catalytic function, but its precise role is not yet established. In analogy to synthetic complexes it has been suggested that Ca(2+) fine-tunes the redox potential of the manganese cluster. Here we evaluate this hypothesis by computing the relative redox potentials of substituted derivatives of the oxygen-evolving complex with the cations Sr(2+), Gd(3+), Cd(2+), Zn(2+), Mg(2+), Sc(3+), Na(+) and Y(3+) for two sequential transitions of its catalytic cycle. The theoretical approach is validated with a series of experimentally well-characterized Mn3AO4 cubane complexes that are structural mimics of the enzymatic cluster. Our results reproduce perfectly the experimentally observed correlation between the redox potential and the Lewis acidities of redox-inactive cations for the synthetic complexes. However, it is conclusively demonstrated that this correlation does not hold for the oxygen evolving complex. In the enzyme the redox potential of the cluster only responds to the charge of the redox-inactive cations and remains otherwise insensitive to their precise identity, precluding redox-tuning of the metal cluster as a primary role for Ca(2+) in biological water oxidation.

Determination of binding constants of cyclodextrin inclusion complexes with amino acids and dipeptides by potentiometric titration.

PubMed

Kahle, Claudia; Holzgrabe, Ulrike

2004-10-01

Cyclodextrins are well known for their ability to separate enantiomers of drugs, natural products, and other chiral substances using HPLC, GC, or CE. The resolution of the enantiomers is due to the formation of diastereomeric complexes between the cyclodextrin and the pairs of enantiomers. The aim of this study was to determine the binding constants of the complexes between alpha- and beta-cyclodextrin and the enantiomers of a series of aliphatic and aromatic amino acids, and dipeptides, using a potentiometric titration method. The results of this method are compared to other methods, and correlated to findings in cyclodextrin-modified capillary electrophoresis and possible complex structures. Potentiometric titration was found to be an appropriate tool to determine the binding constants of cyclodextrin inclusion complexes.

The staff of the department of diagnostic imaging: radical changes and training.

PubMed

Marano, P; Pastore, G; Vecchioli Scaldazza, A

1998-01-01

When a complex reality as the Department of Diagnostic Imaging and its staff is aimed at the provision of a service, it may be extremely difficult to identify all present correlations and in turn, correlate them with the final goal. The relationship between human and technical resources, between organization and environment are of the utmost importance in planning the structure design. It should be kept in mind that "the person" is the pivot of any innovation for change. Participation by all members, a more flexible, structure, is required. In education and teaching, the global network we are heading for, could become the determining factor in a continuing training process and multispecialized research, facilitating the circulation of information in an interactive, formative dialogue.

Performance of Ultra Wideband On-Body Communication Based on Statistical Channel Model

NASA Astrophysics Data System (ADS)

Wang, Qiong; Wang, Jianqing

Ultra wideband (UWB) on-body communication is attracting much attention in biomedical applications. In this paper, the performance of UWB on-body communication is investigated based on a statistically extracted on-body channel model, which provides detailed characteristics of the multi-path-affected channel with an emphasis on various body postures or body movement. The possible data rate, the possible communication distance, as well as the bit error rate (BER) performance are clarified via computer simulation. It is found that the conventional correlation receiver is incompetent in the multi-path-affected on-body channel, while the RAKE receiver outperforms the conventional correlation receiver at a cost of structure complexity. Different RAKE receiver structures are compared to show the improvement of the BER performance.

Differential Dynamic Engagement within 24 SH3 Domain: Peptide Complexes Revealed by Co-Linear Chemical Shift Perturbation Analysis

PubMed Central

Stollar, Elliott J.; Lin, Hong; Davidson, Alan R.; Forman-Kay, Julie D.

2012-01-01

There is increasing evidence for the functional importance of multiple dynamically populated states within single proteins. However, peptide binding by protein-protein interaction domains, such as the SH3 domain, has generally been considered to involve the full engagement of peptide to the binding surface with minimal dynamics and simple methods to determine dynamics at the binding surface for multiple related complexes have not been described. We have used NMR spectroscopy combined with isothermal titration calorimetry to comprehensively examine the extent of engagement to the yeast Abp1p SH3 domain for 24 different peptides. Over one quarter of the domain residues display co-linear chemical shift perturbation (CCSP) behavior, in which the position of a given chemical shift in a complex is co-linear with the same chemical shift in the other complexes, providing evidence that each complex exists as a unique dynamic rapidly inter-converting ensemble. The extent the specificity determining sub-surface of AbpSH3 is engaged as judged by CCSP analysis correlates with structural and thermodynamic measurements as well as with functional data, revealing the basis for significant structural and functional diversity amongst the related complexes. Thus, CCSP analysis can distinguish peptide complexes that may appear identical in terms of general structure and percent peptide occupancy but have significant local binding differences across the interface, affecting their ability to transmit conformational change across the domain and resulting in functional differences. PMID:23251481

Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes [Structural Relaxation and Dynamics of Ionic-Neutral Block Copolymer Surfactant Complexes

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

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Dynamics of Charged Species in Ionic-Neutral Block Copolymer and Surfactant Complexes [Structural Relaxation and Dynamics of Ionic-Neutral Block Copolymer Surfactant Complexes

DOE PAGES

Borreguero, Jose M.; Pincus, Philip A.; Sumpter, Bobby G.; ...

2017-06-21

Structure–property relationships of ionic block copolymer (BCP) surfactant complexes are critical toward the progress of favorable engineering design of efficient charge-transport materials. In this paper, molecular dynamics simulations are used to understand the dynamics of charged-neutral BCP and surfactant complexes. The dynamics are examined for two different systems: charged-neutral double-hydrophilic and hydrophobic–hydrophilic block copolymers with oppositely charged surfactant moieties. The dynamics of the surfactant head, tails, and charges are studied for five different BCP volume fractions. We observe that the dynamics of the different species solely depend on the balance between electrostatic and entropic interactions between the charged species andmore » the neutral monomers. The favorable hydrophobic–hydrophobic interactions and the unfavorable hydrophobic–hydrophilic interactions determine the mobilities of the monomers. The dynamical properties of the charge species influence complex formation. Structural relaxations exhibit length-scale dependent behavior, with slower relaxation at the radius of gyration length-scale and faster relaxation at the segmental length-scale, consistent with previous results. The dynamical analysis correlates ion-exchange kinetics to the self-assembly behavior of the complexes.« less

Universal Spatial Correlation Functions for Describing and Reconstructing Soil Microstructure

PubMed Central

Skvortsova, Elena B.; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity. PMID:26010779

Universal spatial correlation functions for describing and reconstructing soil microstructure.

PubMed

Karsanina, Marina V; Gerke, Kirill M; Skvortsova, Elena B; Mallants, Dirk

2015-01-01

Structural features of porous materials such as soil define the majority of its physical properties, including water infiltration and redistribution, multi-phase flow (e.g. simultaneous water/air flow, or gas exchange between biologically active soil root zone and atmosphere) and solute transport. To characterize soil microstructure, conventional soil science uses such metrics as pore size and pore-size distributions and thin section-derived morphological indicators. However, these descriptors provide only limited amount of information about the complex arrangement of soil structure and have limited capability to reconstruct structural features or predict physical properties. We introduce three different spatial correlation functions as a comprehensive tool to characterize soil microstructure: 1) two-point probability functions, 2) linear functions, and 3) two-point cluster functions. This novel approach was tested on thin-sections (2.21×2.21 cm2) representing eight soils with different pore space configurations. The two-point probability and linear correlation functions were subsequently used as a part of simulated annealing optimization procedures to reconstruct soil structure. Comparison of original and reconstructed images was based on morphological characteristics, cluster correlation functions, total number of pores and pore-size distribution. Results showed excellent agreement for soils with isolated pores, but relatively poor correspondence for soils exhibiting dual-porosity features (i.e. superposition of pores and micro-cracks). Insufficient information content in the correlation function sets used for reconstruction may have contributed to the observed discrepancies. Improved reconstructions may be obtained by adding cluster and other correlation functions into reconstruction sets. Correlation functions and the associated stochastic reconstruction algorithms introduced here are universally applicable in soil science, such as for soil classification, pore-scale modelling of soil properties, soil degradation monitoring, and description of spatial dynamics of soil microbial activity.

Structural insights into the catalytic mechanism of a family 18 exo-chitinase

PubMed Central

van Aalten, D. M. F.; Komander, D.; Synstad, B.; Gåseidnes, S.; Peter, M. G.; Eijsink, V. G. H.

2001-01-01

Chitinase B (ChiB) from Serratia marcescens is a family 18 exo-chitinase whose catalytic domain has a TIM-barrel fold with a tunnel-shaped active site. We have solved structures of three ChiB complexes that reveal details of substrate binding, substrate-assisted catalysis, and product displacement. The structure of an inactive ChiB mutant (E144Q) complexed with a pentameric substrate (binding in subsites −2 to +3) shows closure of the “roof” of the active site tunnel. It also shows that the sugar in the −1 position is distorted to a boat conformation, thus providing structural evidence in support of a previously proposed catalytic mechanism. The structures of the active enzyme complexed to allosamidin (an analogue of a proposed reaction intermediate) and of the active enzyme soaked with pentameric substrate show events after cleavage of the glycosidic bond. The latter structure shows reopening of the roof of the active site tunnel and enzyme-assisted product displacement in the +1 and +2 sites, allowing a water molecule to approach the reaction center. Catalysis is accompanied by correlated structural changes in the core of the TIM barrel that involve conserved polar residues whose functions were hitherto unknown. These changes simultaneously contribute to stabilization of the reaction intermediate and alternation of the pKa of the catalytic acid during the catalytic cycle. PMID:11481469

Visualization of HIV T Cell Virological Synapses and Virus-Containing Compartments by Three-Dimensional Correlative Light and Electron Microscopy

PubMed Central

Wang, Lili; Eng, Edward T.; Law, Kenneth; Gordon, Ronald E.; Rice, William J.

2016-01-01

ABSTRACT Virological synapses (VS) are adhesive structures that form between infected and uninfected cells to enhance the spread of HIV-1. During T cell VS formation, viral proteins are actively recruited to the site of cell-cell contact where the viral material is efficiently translocated to target cells into heterogeneous, protease-resistant, antibody-inaccessible compartments. Using correlative light and electron microscopy (CLEM), we define the membrane topography of the virus-containing compartments (VCC) where HIV is found following VS-mediated transfer. Focused ion beam scanning electron microscopy (FIB-SEM) and serial sectioning transmission electron microscopy (SS-TEM) were used to better resolve the fluorescent Gag-containing structures within the VCC. We found that small punctate fluorescent signals correlated with single viral particles in enclosed vesicular compartments or surface-localized virus particles and that large fluorescent signals correlated with membranous Gag-containing structures with unknown pathological function. CLEM imaging revealed distinct pools of newly deposited viral proteins within endocytic and nonendocytic compartments in VS target T cells. IMPORTANCE This study directly correlates individual virus-associated objects observed in light microscopy with ultrastructural features seen by electron microscopy in the HIV-1 virological synapse. This approach elucidates which infection-associated ultrastructural features represent bona fide HIV protein complexes. We define the morphology of some HIV cell-to-cell transfer intermediates as true endocytic compartments and resolve unique synapse-associated viral structures created by transfer across virological synapses. PMID:27847357

Gray matter correlates of creative potential: A latent variable voxel-based morphometry study

PubMed Central

Jauk, Emanuel; Neubauer, Aljoscha C.; Dunst, Beate; Fink, Andreas; Benedek, Mathias

2015-01-01

There is increasing research interest in the structural and functional brain correlates underlying creative potential. Recent investigations found that interindividual differences in creative potential relate to volumetric differences in brain regions belonging to the default mode network, such as the precuneus. Yet, the complex interplay between creative potential, intelligence, and personality traits and their respective neural bases is still under debate. We investigated regional gray matter volume (rGMV) differences that can be associated with creative potential in a heterogeneous sample of N = 135 individuals using voxel-based morphometry (VBM). By means of latent variable modeling and consideration of recent psychometric advancements in creativity research, we sought to disentangle the effects of ideational originality and fluency as two independent indicators of creative potential. Intelligence and openness to experience were considered as common covariates of creative potential. The results confirmed and extended previous research: rGMV in the precuneus was associated with ideational originality, but not with ideational fluency. In addition, we found ideational originality to be correlated with rGMV in the caudate nucleus. The results indicate that the ability to produce original ideas is tied to default-mode as well as dopaminergic structures. These structural brain correlates of ideational originality were apparent throughout the whole range of intellectual ability and thus not moderated by intelligence. In contrast, structural correlates of ideational fluency, a quantitative marker of creative potential, were observed only in lower intelligent individuals in the cuneus/lingual gyrus. PMID:25676914

Intrinsic Multi-Scale Dynamic Behaviors of Complex Financial Systems.

PubMed

Ouyang, Fang-Yan; Zheng, Bo; Jiang, Xiong-Fei

2015-01-01

The empirical mode decomposition is applied to analyze the intrinsic multi-scale dynamic behaviors of complex financial systems. In this approach, the time series of the price returns of each stock is decomposed into a small number of intrinsic mode functions, which represent the price motion from high frequency to low frequency. These intrinsic mode functions are then grouped into three modes, i.e., the fast mode, medium mode and slow mode. The probability distribution of returns and auto-correlation of volatilities for the fast and medium modes exhibit similar behaviors as those of the full time series, i.e., these characteristics are rather robust in multi time scale. However, the cross-correlation between individual stocks and the return-volatility correlation are time scale dependent. The structure of business sectors is mainly governed by the fast mode when returns are sampled at a couple of days, while by the medium mode when returns are sampled at dozens of days. More importantly, the leverage and anti-leverage effects are dominated by the medium mode.

A tool for filtering information in complex systems

PubMed Central

Tumminello, M.; Aste, T.; Di Matteo, T.; Mantegna, R. N.

2005-01-01

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties. PMID:16027373

A tool for filtering information in complex systems.

PubMed

Tumminello, M; Aste, T; Di Matteo, T; Mantegna, R N

2005-07-26

We introduce a technique to filter out complex data sets by extracting a subgraph of representative links. Such a filtering can be tuned up to any desired level by controlling the genus of the resulting graph. We show that this technique is especially suitable for correlation-based graphs, giving filtered graphs that preserve the hierarchical organization of the minimum spanning tree but containing a larger amount of information in their internal structure. In particular in the case of planar filtered graphs (genus equal to 0), triangular loops and four-element cliques are formed. The application of this filtering procedure to 100 stocks in the U.S. equity markets shows that such loops and cliques have important and significant relationships with the market structure and properties.

Complex oxides: Intricate disorder

DOE PAGES

Uberuaga, Blas Pedro

2016-02-29

In this study, complex oxides such as pyrochlores have a myriad of potential technological applications, including as fast ion conductors and radiation-tolerant nuclear waste forms. They are also of interest for their catalytic and spin ice properties. Many of these functional properties are enabled by the atomic structure of the cation sublattices. Pyrochlores (A2B2O7) contain two different cations (A and B), typically a 3+ rare earth and a 4+ transition metal such as Hf, Zr, or Ti. The large variety of chemistries that can form pyrochlores leads to a rich space in which to search for exotic new materials. Furthermore,more » how cations order or disorder on their respective sublattices for a given chemical composition influences the functional properties of the oxide. For example, oxygen ionic conductivity is directly correlated with the level of cation disorder — the swapping of A and B cations 1. Further, the resistance of these materials against amorphization has also been connected with the ability of the cations to disorder 2, 3. These correlations between cation structure and functionality have spurred great interest in the structure of the cation sublattice under irradiation, with significant focus on the disordering mechanisms and disordered structure. Previous studies have found that, upon irradiation, pyrochlores often undergo an order-to-disorder transformation, in which the resulting structure is, from a diffraction point of view, indistinguishable from fluorite (AO2) (ref. 3). Shamblin et al. now reveal that the structure of disordered pyrochlore is more complicated than previously thought 4.« less

PLASS: Protein-ligand affinity statistical score a knowledge-based force-field model of interaction derived from the PDB

NASA Astrophysics Data System (ADS)

Ozrin, V. D.; Subbotin, M. V.; Nikitin, S. M.

2004-04-01

We have developed PLASS (Protein-Ligand Affinity Statistical Score), a pair-wise potential of mean-force for rapid estimation of the binding affinity of a ligand molecule to a protein active site. This scoring function is derived from the frequency of occurrence of atom-type pairs in crystallographic complexes taken from the Protein Data Bank (PDB). Statistical distributions are converted into distance-dependent contributions to the Gibbs free interaction energy for 10 atomic types using the Boltzmann hypothesis, with only one adjustable parameter. For a representative set of 72 protein-ligand structures, PLASS scores correlate well with the experimentally measured dissociation constants: a correlation coefficient R of 0.82 and RMS error of 2.0 kcal/mol. Such high accuracy results from our novel treatment of the volume correction term, which takes into account the inhomogeneous properties of the protein-ligand complexes. PLASS is able to rank reliably the affinity of complexes which have as much diversity as in the PDB.

The scope and control of attention as separate aspects of working memory.

PubMed

Shipstead, Zach; Redick, Thomas S; Hicks, Kenny L; Engle, Randall W

2012-01-01

The present study examines two varieties of working memory (WM) capacity task: visual arrays (i.e., a measure of the amount of information that can be maintained in working memory) and complex span (i.e., a task that taps WM-related attentional control). Using previously collected data sets we employ confirmatory factor analysis to demonstrate that visual arrays and complex span tasks load on separate, but correlated, factors. A subsequent series of structural equation models and regression analyses demonstrate that these factors contribute both common and unique variance to the prediction of general fluid intelligence (Gf). However, while visual arrays does contribute uniquely to higher cognition, its overall correlation to Gf is largely mediated by variance associated with the complex span factor. Thus we argue that visual arrays performance is not strictly driven by a limited-capacity storage system (e.g., the focus of attention; Cowan, 2001), but may also rely on control processes such as selective attention and controlled memory search.

Characterizing air quality data from complex network perspective.

PubMed

Fan, Xinghua; Wang, Li; Xu, Huihui; Li, Shasha; Tian, Lixin

2016-02-01

Air quality depends mainly on changes in emission of pollutants and their precursors. Understanding its characteristics is the key to predicting and controlling air quality. In this study, complex networks were built to analyze topological characteristics of air quality data by correlation coefficient method. Firstly, PM2.5 (particulate matter with aerodynamic diameter less than 2.5 μm) indexes of eight monitoring sites in Beijing were selected as samples from January 2013 to December 2014. Secondly, the C-C method was applied to determine the structure of phase space. Points in the reconstructed phase space were considered to be nodes of the network mapped. Then, edges were determined by nodes having the correlation greater than a critical threshold. Three properties of the constructed networks, degree distribution, clustering coefficient, and modularity, were used to determine the optimal value of the critical threshold. Finally, by analyzing and comparing topological properties, we pointed out that similarities and difference in the constructed complex networks revealed influence factors and their different roles on real air quality system.

Composition and structure of whey protein/gum arabic coacervates.

PubMed

Weinbreck, F; Tromp, R H; de Kruif, C G

2004-01-01

Complex coacervation in whey protein/gum arabic (WP/GA) mixtures was studied as a function of three main key parameters: pH, initial protein to polysaccharide mixing ratio (Pr:Ps)(ini), and ionic strength. Previous studies had already revealed under which conditions a coacervate phase was obtained. This study is aimed at understanding how these parameters influence the phase separation kinetics, the coacervate composition, and the internal coacervate structure. At a defined (Pr:Ps)(ini), an optimum pH of complex coacervation was found (pH(opt)), at which the strength of electrostatic interaction was maximum. For (Pr:Ps)(ini) = 2:1, the phase separation occurred the fastest and the final coacervate volume was the largest at pH(opt) = 4.0. The composition of the coacervate phase was determined after 48 h of phase separation and revealed that, at pH(opt), the coacervate phase was the most concentrated. Varying the (Pr:Ps)(ini) shifted the pH(opt) to higher values when (Pr:Ps)(ini) was increased and to lower values when (Pr:Ps)(ini) was decreased. This phenomenon was due to the level of charge compensation of the WP/GA complexes. Finally, the structure of the coacervate phase was studied with small-angle X-ray scattering (SAXS). SAXS data confirmed that at pH(opt) the coacervate phase was dense and structured. Model calculations revealed that the structure factor of WP induced a peak at Q = 0.7 nm(-1), illustrating that the coacervate phase was more structured, inducing the stronger correlation length of WP molecules. When the pH was changed to more acidic values, the correlation peak faded away, due to a more open structure of the coacervate. A shoulder in the scattering pattern of the coacervates was visible at small Q. This peak was attributed to the presence of residual charges on the GA. The peak intensity was reduced when the strength of interaction was increased, highlighting a greater charge compensation of the polyelectrolyte. Finally, increasing the ionic strength led to a less concentrated, a more heterogeneous, and a less structured coacervate phase, induced by the screening of the electrostatic interactions.

Mesoscopic Community Structure of Financial Markets Revealed by Price and Sign Fluctuations

PubMed Central

Almog, Assaf; Besamusca, Ferry; MacMahon, Mel; Garlaschelli, Diego

2015-01-01

The mesoscopic organization of complex systems, from financial markets to the brain, is an intermediate between the microscopic dynamics of individual units (stocks or neurons, in the mentioned cases), and the macroscopic dynamics of the system as a whole. The organization is determined by “communities” of units whose dynamics, represented by time series of activity, is more strongly correlated internally than with the rest of the system. Recent studies have shown that the binary projections of various financial and neural time series exhibit nontrivial dynamical features that resemble those of the original data. This implies that a significant piece of information is encoded into the binary projection (i.e. the sign) of such increments. Here, we explore whether the binary signatures of multiple time series can replicate the same complex community organization of the financial market, as the original weighted time series. We adopt a method that has been specifically designed to detect communities from cross-correlation matrices of time series data. Our analysis shows that the simpler binary representation leads to a community structure that is almost identical with that obtained using the full weighted representation. These results confirm that binary projections of financial time series contain significant structural information. PMID:26226226

Detection of structurally similar adulterants in botanical dietary supplements by thin-layer chromatography and surface enhanced Raman spectroscopy combined with two-dimensional correlation spectroscopy.

PubMed

Li, Hao; Zhu, Qing xia; Chwee, Tsz sian; Wu, Lin; Chai, Yi feng; Lu, Feng; Yuan, Yong fang

2015-07-09

Thin-layer chromatography (TLC) coupled with surface enhanced Raman spectroscopy (SERS) has been widely used for the study of various complex systems, especially for the detection of adulterants in botanical dietary supplements (BDS). However, this method is not sufficient to distinguish structurally similar adulterants in BDS since the analogs have highly similar chromatographic and/or spectroscopic behaviors. Taking into account the fact that higher cost and more time will be required for comprehensive chromatographic separation, more efforts with respect to spectroscopy are now focused on analyzing the overlapped SERS peaks. In this paper, the combination of a TLC-SERS method with two-dimensional correlation spectroscopy (2DCOS), with duration of exposure to laser as the perturbation, is applied to solve this problem. Besides the usual advantages of the TLC-SERS method, such as its simplicity, rapidness, and sensitivity, more advantages are presented here, such as enhanced selectivity and good reproducibility, which are obtained by 2DCOS. Two chemicals with similar structures are successfully differentiated from the complex BDS matrices. The study provides a more accurate qualitative screening method for detection of BDS with adulterants, and offers a new universal approach for the analysis of highly overlapped SERS peaks. Copyright © 2015 Elsevier B.V. All rights reserved.

The 3D Structure of the Binding Pocket of the Human Oxytocin Receptor for Benzoxazine Antagonists, Determined by Molecular Docking, Scoring Functions and 3D-QSAR Methods

NASA Astrophysics Data System (ADS)

Jójárt, Balázs; Martinek, Tamás A.; Márki, Árpád

2005-05-01

Molecular docking and 3D-QSAR studies were performed to determine the binding mode for a series of benzoxazine oxytocin antagonists taken from the literature. Structural hypotheses were generated by docking the most active molecule to the rigid receptor by means of AutoDock 3.05. The cluster analysis yielded seven possible binding conformations. These structures were refined by using constrained simulated annealing, and the further ligands were aligned in the refined receptor by molecular docking. A good correlation was found between the estimated Δ G bind and the p K i values for complex F. The Connolly-surface analysis, CoMFA and CoMSIA models q CoMFA 2 = 0.653, q CoMSA 2 = 0.630 and r pred,CoMFA 2 = 0.852 , r pred,CoMSIA 2 = 0.815) confirmed the scoring function results. The structural features of the receptor-ligand complex and the CoMFA and CoMSIA fields are in closely connected. These results suggest that receptor-ligand complex F is the most likely binding hypothesis for the studied benzoxazine analogs.

Sulfonamido tripods: tuning redox potentials via ligand modifications

PubMed Central

Lau, Nathanael; Ziller, Joseph W.

2014-01-01

A series of FeII–OH2 complexes were synthesized with ligands based on the tetradentate sulfonamido tripod N,N',N"-[2,2',2"-nitrilotris(ethane-2,1-diyl)]-tris-({R-Ph}-sulfonamido). These complexes differ by the substituent on the aryl rings and were fully characterized, including their molecular structures via X-ray diffraction methods. All the complexes were five-coordinate with trigonal bipyramidal geometry. A linear correlation was observed between the electronic effects of each ligand, given by the Hammett constants of the para-substituents, and the potential of the FeII/FeIII redox couple, which were determined using cyclic voltammetry. It was found that the range of redox potentials for the complexes spanned approximately 160 mV. PMID:25419035

Sulfonamido tripods: tuning redox potentials via ligand modifications.

PubMed

Lau, Nathanael; Ziller, Joseph W; Borovik, A S

2015-01-08

A series of Fe II -OH 2 complexes were synthesized with ligands based on the tetradentate sulfonamido tripod N , N ', N "-[2,2',2"-nitrilotris(ethane-2,1-diyl)]-tris-({R-Ph}-sulfonamido). These complexes differ by the substituent on the aryl rings and were fully characterized, including their molecular structures via X-ray diffraction methods. All the complexes were five-coordinate with trigonal bipyramidal geometry. A linear correlation was observed between the electronic effects of each ligand, given by the Hammett constants of the para -substituents, and the potential of the Fe II /Fe III redox couple, which were determined using cyclic voltammetry. It was found that the range of redox potentials for the complexes spanned approximately 160 mV.

Analysis of the interface variability in NMR structure ensembles of protein-protein complexes.

PubMed

Calvanese, Luisa; D'Auria, Gabriella; Vangone, Anna; Falcigno, Lucia; Oliva, Romina

2016-06-01

NMR structures consist in ensembles of conformers, all satisfying the experimental restraints, which exhibit a certain degree of structural variability. We analyzed here the interface in NMR ensembles of protein-protein heterodimeric complexes and found it to span a wide range of different conservations. The different exhibited conservations do not simply correlate with the size of the systems/interfaces, and are most probably the result of an interplay between different factors, including the quality of experimental data and the intrinsic complex flexibility. In any case, this information is not to be missed when NMR structures of protein-protein complexes are analyzed; especially considering that, as we also show here, the first NMR conformer is usually not the one which best reflects the overall interface. To quantify the interface conservation and to analyze it, we used an approach originally conceived for the analysis and ranking of ensembles of docking models, which has now been extended to directly deal with NMR ensembles. We propose this approach, based on the conservation of the inter-residue contacts at the interface, both for the analysis of the interface in whole ensembles of NMR complexes and for the possible selection of a single conformer as the best representative of the overall interface. In order to make the analyses automatic and fast, we made the protocol available as a web tool at: https://www.molnac.unisa.it/BioTools/consrank/consrank-nmr.html. Copyright © 2016 Elsevier Inc. All rights reserved.

Microstructural Quantification, Property Prediction, and Stochastic Reconstruction of Heterogeneous Materials Using Limited X-Ray Tomography Data

NASA Astrophysics Data System (ADS)

Li, Hechao

An accurate knowledge of the complex microstructure of a heterogeneous material is crucial for quantitative structure-property relations establishment and its performance prediction and optimization. X-ray tomography has provided a non-destructive means for microstructure characterization in both 3D and 4D (i.e., structural evolution over time). Traditional reconstruction algorithms like filtered-back-projection (FBP) method or algebraic reconstruction techniques (ART) require huge number of tomographic projections and segmentation process before conducting microstructural quantification. This can be quite time consuming and computationally intensive. In this thesis, a novel procedure is first presented that allows one to directly extract key structural information in forms of spatial correlation functions from limited x-ray tomography data. The key component of the procedure is the computation of a "probability map", which provides the probability of an arbitrary point in the material system belonging to specific phase. The correlation functions of interest are then readily computed from the probability map. Using effective medium theory, accurate predictions of physical properties (e.g., elastic moduli) can be obtained. Secondly, a stochastic optimization procedure that enables one to accurately reconstruct material microstructure from a small number of x-ray tomographic projections (e.g., 20 - 40) is presented. Moreover, a stochastic procedure for multi-modal data fusion is proposed, where both X-ray projections and correlation functions computed from limited 2D optical images are fused to accurately reconstruct complex heterogeneous materials in 3D. This multi-modal reconstruction algorithm is proved to be able to integrate the complementary data to perform an excellent optimization procedure, which indicates its high efficiency in using limited structural information. Finally, the accuracy of the stochastic reconstruction procedure using limited X-ray projection data is ascertained by analyzing the microstructural degeneracy and the roughness of energy landscape associated with different number of projections. Ground-state degeneracy of a microstructure is found to decrease with increasing number of projections, which indicates a higher probability that the reconstructed configurations match the actual microstructure. The roughness of energy landscape can also provide information about the complexity and convergence behavior of the reconstruction for given microstructures and projection number.

Association of Structural Global Brain Network Properties with Intelligence in Normal Aging

PubMed Central

Fischer, Florian U.; Wolf, Dominik; Scheurich, Armin; Fellgiebel, Andreas

2014-01-01

Higher general intelligence attenuates age-associated cognitive decline and the risk of dementia. Thus, intelligence has been associated with cognitive reserve or resilience in normal aging. Neurophysiologically, intelligence is considered as a complex capacity that is dependent on a global cognitive network rather than isolated brain areas. An association of structural as well as functional brain network characteristics with intelligence has already been reported in young adults. We investigated the relationship between global structural brain network properties, general intelligence and age in a group of 43 cognitively healthy elderly, age 60–85 years. Individuals were assessed cross-sectionally using Wechsler Adult Intelligence Scale-Revised (WAIS-R) and diffusion-tensor imaging. Structural brain networks were reconstructed individually using deterministic tractography, global network properties (global efficiency, mean shortest path length, and clustering coefficient) were determined by graph theory and correlated to intelligence scores within both age groups. Network properties were significantly correlated to age, whereas no significant correlation to WAIS-R was observed. However, in a subgroup of 15 individuals aged 75 and above, the network properties were significantly correlated to WAIS-R. Our findings suggest that general intelligence and global properties of structural brain networks may not be generally associated in cognitively healthy elderly. However, we provide first evidence of an association between global structural brain network properties and general intelligence in advanced elderly. Intelligence might be affected by age-associated network deterioration only if a certain threshold of structural degeneration is exceeded. Thus, age-associated brain structural changes seem to be partially compensated by the network and the range of this compensation might be a surrogate of cognitive reserve or brain resilience. PMID:24465994

Ortho-para interconversion in cation-water complexes: The case of V + (H 2 O) and Nb + (H 2 O) clusters

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

Ward, T. B.; Miliordos, E.; Carnegie, P. D.

Vanadium and niobium cation-water complexes, V+(H2O) and Nb+(H2O), are produced by laser vaporization in a pulsed supersonic expansion, mass selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy using rare gas atom (Ar, Ne) complex predissociation. The vibrational bands measured in the O–H stretching region contain K-type rotational sub-band structure, which provides insight into the structures of these complexes. However, rotational sub-bands do not exhibit the simple patterns seen previously for other metal ion-water complexes. The A rotational constants are smaller than expected and the normal 1:3 intensity ratios for K = even:odd levels for independent ortho:para nuclearmore » spin states are missing for some complexes. We relied on highly correlated internally contracted Multi-Reference Configuration Interaction (icMRCI) and Coupled Cluster [CCSD(T)] electronic structure calculations of those complexes with and without the rare gas atoms to investigate these anomalies. Rare gas atoms were found to bind via asymmetric motifs to the hydrated complexes undergoing large amplitude motions that vibrationally average to quasi-C2v symmetry with significant probability off the C2 axis, thus explaining the reduced A values. Both vanadium and iobium cations exhibit unusually strong nuclear spin coupling to the hydrogen atoms of water, the values of which vary with their electronic state. This catalyzes ortho-para interconversion in some complexes and explains the rotational patterns. The rate of ortho-para relaxation in the equilibrated complexes must therefore be greater than the collisional cooling rate in the supersonic expansion (about 106 sec-1).« less

Ortho-para interconversion in cation-water complexes: The case of V+(H2O) and Nb+(H2O) clusters.

PubMed

Ward, T B; Miliordos, E; Carnegie, P D; Xantheas, S S; Duncan, M A

2017-06-14

Vanadium and niobium cation-water complexes, V + (H 2 O) and Nb + (H 2 O), are produced by laser vaporization in a pulsed supersonic expansion, mass selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy using rare gas atom (Ar, Ne) complex predissociation. The vibrational bands measured in the O-H stretching region contain K-type rotational sub-band structure, which provides insight into the structures of these complexes. However, rotational sub-bands do not exhibit the simple patterns seen previously for other metal ion-water complexes. The A rotational constants are smaller than expected and the normal 3:1 intensity ratios for K = odd:even levels for independent ortho:para nuclear spin states are missing for some complexes. We relied on highly correlated internally contracted multi-reference configuration interaction and Coupled Cluster [CCSD(T)] electronic structure calculations of those complexes with and without the rare gas atoms to investigate these anomalies. Rare gas atoms were found to bind via asymmetric motifs to the hydrated complexes undergoing large amplitude motions that vibrationally average to the quasi-C 2v symmetry with a significant probability off the C 2 axis, thus explaining the reduced A values. Both vanadium and niobium cations exhibit unusually strong nuclear spin coupling to the hydrogen atoms of water, the values of which vary with their electronic state. This catalyzes ortho-para interconversion in some complexes and explains the rotational patterns. The rate of ortho-para relaxation in the equilibrated complexes must therefore be greater than the collisional cooling rate in the supersonic expansion (about 10 6 s -1 ).

Ortho-para interconversion in cation-water complexes: The case of V+(H2O) and Nb+(H2O) clusters

NASA Astrophysics Data System (ADS)

Ward, T. B.; Miliordos, E.; Carnegie, P. D.; Xantheas, S. S.; Duncan, M. A.

2017-06-01

Vanadium and niobium cation-water complexes, V+(H2O) and Nb+(H2O), are produced by laser vaporization in a pulsed supersonic expansion, mass selected in a time-of-flight spectrometer, and studied with infrared photodissociation spectroscopy using rare gas atom (Ar, Ne) complex predissociation. The vibrational bands measured in the O-H stretching region contain K-type rotational sub-band structure, which provides insight into the structures of these complexes. However, rotational sub-bands do not exhibit the simple patterns seen previously for other metal ion-water complexes. The A rotational constants are smaller than expected and the normal 3:1 intensity ratios for K = odd:even levels for independent ortho:para nuclear spin states are missing for some complexes. We relied on highly correlated internally contracted multi-reference configuration interaction and Coupled Cluster [CCSD(T)] electronic structure calculations of those complexes with and without the rare gas atoms to investigate these anomalies. Rare gas atoms were found to bind via asymmetric motifs to the hydrated complexes undergoing large amplitude motions that vibrationally average to the quasi-C2v symmetry with a significant probability off the C2 axis, thus explaining the reduced A values. Both vanadium and niobium cations exhibit unusually strong nuclear spin coupling to the hydrogen atoms of water, the values of which vary with their electronic state. This catalyzes ortho-para interconversion in some complexes and explains the rotational patterns. The rate of ortho-para relaxation in the equilibrated complexes must therefore be greater than the collisional cooling rate in the supersonic expansion (about 106 s-1).

Temporal evolution of the spatial covariability of rainfall in South America

NASA Astrophysics Data System (ADS)

Ciemer, Catrin; Boers, Niklas; Barbosa, Henrique M. J.; Kurths, Jürgen; Rammig, Anja

2017-10-01

The climate of South America exhibits pronounced differences between rainy and dry seasons, associated with specific synoptic features such as the establishment of the South Atlantic convergence zone. Here, we analyze the spatiotemporal correlation structure and in particular teleconnections of daily rainfall associated with these features by means of evolving complex networks. A modification of Pearson's correlation coefficient is introduced to handle the intricate statistical properties of daily rainfall. On this basis, spatial correlation networks are constructed, and new appropriate network measures are introduced in order to analyze the temporal evolution of the networks' characteristics. We particularly focus on the identification of coherent areas of similar rainfall patterns and previously unknown teleconnection structures between remote areas. We show that the monsoon onset is characterized by an abrupt transition from erratic to organized regional connectivity that prevails during the monsoon season, while only the onset times themselves exhibit anomalous large-scale organization of teleconnections. Furthermore, we reveal that the two mega-droughts in the Amazon basin were already announced in the previous year by an anomalous behavior of the connectivity structure.

Structure and evolution of a European Parliament via a network and correlation analysis

NASA Astrophysics Data System (ADS)

Puccio, Elena; Pajala, Antti; Piilo, Jyrki; Tumminello, Michele

2016-11-01

We present a study of the network of relationships among elected members of the Finnish parliament, based on a quantitative analysis of initiative co-signatures, and its evolution over 16 years. To understand the structure of the parliament, we constructed a statistically validated network of members, based on the similarity between the patterns of initiatives they signed. We looked for communities within the network and characterized them in terms of members' attributes, such as electoral district and party. To gain insight on the nested structure of communities, we constructed a hierarchical tree of members from the correlation matrix. Afterwards, we studied parliament dynamics yearly, with a focus on correlations within and between parties, by also distinguishing between government and opposition. Finally, we investigated the role played by specific individuals, at a local level. In particular, whether they act as proponents who gather consensus, or as signers. Our results provide a quantitative background to current theories in political science. From a methodological point of view, our network approach has proven able to highlight both local and global features of a complex social system.

Newer mixed ligand Schiff base complexes from aquo-N-(2‧-hydroxy acetophenone) glycinatocopper(II) as synthon: DFT, antimicrobial activity and molecular docking study

NASA Astrophysics Data System (ADS)

Pramanik, Harun A. R.; Das, Dharitri; Paul, Pradip C.; Mondal, Paritosh; Bhattacharjee, Chira R.

2014-02-01

Synthesis of a series of newer mixed ligand copper(II) complexes of aminoacid Schiff base of the type [CuL(X)] (L = N-(2‧-hydroxy acetophenone) glycinate, X = imidazole (im) 2, benzimidazole (benz) 3, pyridine (py) 4, hydrazine (hz) 5,8-hydroxyquinoline (8-hq) 6, pyrrolidine (pyrr) 7, piperidine (pip) 8, and nicotinamide (nic) 9) have been accomplished from the interaction of an aquated Schiff base complex, [CuL(H2O)]·H2O, 1 with some selected neutral nitrogen-donor ligands. The copper(II) Schiff base complex, [CuL(H2O)]·H2O, L = N-(2‧-hydroxy acetophenone) glycinate was synthesized from the reaction of glycine and 2‧ hydroxy acetophenone and copper(II) acetate. The compounds were characterised by elemental analysis, spectral, magnetic and thermal studies. The density functional theory calculations were performed using LANL2DZ and 6-311 G(d, p) basis sets with B3LYP correlation functional to ascertain the stable electronic structure, HOMO-LUMO energy gap, chemical hardness and dipole moment of the mixed ligand complexes. A distorted square planar geometry has been conjectured for the complexes. Antibacterial activities of the ligand and its metal complexes have been tested against selected gram-positive and gram-negative strains and correlated with computational docking scores.

Foundational Principles for Large-Scale Inference: Illustrations Through Correlation Mining

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

Hero, Alfred O.; Rajaratnam, Bala

When can reliable inference be drawn in the ‘‘Big Data’’ context? This article presents a framework for answering this fundamental question in the context of correlation mining, with implications for general large-scale inference. In large-scale data applications like genomics, connectomics, and eco-informatics, the data set is often variable rich but sample starved: a regime where the number n of acquired samples (statistical replicates) is far fewer than the number p of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for ‘‘Big Data.’’ Sample complexity, however, hasmore » received relatively less attention, especially in the setting when the sample size n is fixed, and the dimension p grows without bound. To address this gap, we develop a unified statistical framework that explicitly quantifies the sample complexity of various inferential tasks. Sampling regimes can be divided into several categories: 1) the classical asymptotic regime where the variable dimension is fixed and the sample size goes to infinity; 2) the mixed asymptotic regime where both variable dimension and sample size go to infinity at comparable rates; and 3) the purely high-dimensional asymptotic regime where the variable dimension goes to infinity and the sample size is fixed. Each regime has its niche but only the latter regime applies to exa-scale data dimension. We illustrate this high-dimensional framework for the problem of correlation mining, where it is the matrix of pairwise and partial correlations among the variables that are of interest. Correlation mining arises in numerous applications and subsumes the regression context as a special case. We demonstrate various regimes of correlation mining based on the unifying perspective of high-dimensional learning rates and sample complexity for different structured covariance models and different inference tasks.« less

Foundational Principles for Large-Scale Inference: Illustrations Through Correlation Mining

PubMed Central

Hero, Alfred O.; Rajaratnam, Bala

2015-01-01

When can reliable inference be drawn in fue “Big Data” context? This paper presents a framework for answering this fundamental question in the context of correlation mining, wifu implications for general large scale inference. In large scale data applications like genomics, connectomics, and eco-informatics fue dataset is often variable-rich but sample-starved: a regime where the number n of acquired samples (statistical replicates) is far fewer than fue number p of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for “Big Data”. Sample complexity however has received relatively less attention, especially in the setting when the sample size n is fixed, and the dimension p grows without bound. To address fuis gap, we develop a unified statistical framework that explicitly quantifies the sample complexity of various inferential tasks. Sampling regimes can be divided into several categories: 1) the classical asymptotic regime where fue variable dimension is fixed and fue sample size goes to infinity; 2) the mixed asymptotic regime where both variable dimension and sample size go to infinity at comparable rates; 3) the purely high dimensional asymptotic regime where the variable dimension goes to infinity and the sample size is fixed. Each regime has its niche but only the latter regime applies to exa cale data dimension. We illustrate this high dimensional framework for the problem of correlation mining, where it is the matrix of pairwise and partial correlations among the variables fua t are of interest. Correlation mining arises in numerous applications and subsumes the regression context as a special case. we demonstrate various regimes of correlation mining based on the unifying perspective of high dimensional learning rates and sample complexity for different structured covariance models and different inference tasks. PMID:27087700

Foundational Principles for Large-Scale Inference: Illustrations Through Correlation Mining

DOE PAGES

Hero, Alfred O.; Rajaratnam, Bala

2015-12-09

When can reliable inference be drawn in the ‘‘Big Data’’ context? This article presents a framework for answering this fundamental question in the context of correlation mining, with implications for general large-scale inference. In large-scale data applications like genomics, connectomics, and eco-informatics, the data set is often variable rich but sample starved: a regime where the number n of acquired samples (statistical replicates) is far fewer than the number p of observed variables (genes, neurons, voxels, or chemical constituents). Much of recent work has focused on understanding the computational complexity of proposed methods for ‘‘Big Data.’’ Sample complexity, however, hasmore » received relatively less attention, especially in the setting when the sample size n is fixed, and the dimension p grows without bound. To address this gap, we develop a unified statistical framework that explicitly quantifies the sample complexity of various inferential tasks. Sampling regimes can be divided into several categories: 1) the classical asymptotic regime where the variable dimension is fixed and the sample size goes to infinity; 2) the mixed asymptotic regime where both variable dimension and sample size go to infinity at comparable rates; and 3) the purely high-dimensional asymptotic regime where the variable dimension goes to infinity and the sample size is fixed. Each regime has its niche but only the latter regime applies to exa-scale data dimension. We illustrate this high-dimensional framework for the problem of correlation mining, where it is the matrix of pairwise and partial correlations among the variables that are of interest. Correlation mining arises in numerous applications and subsumes the regression context as a special case. We demonstrate various regimes of correlation mining based on the unifying perspective of high-dimensional learning rates and sample complexity for different structured covariance models and different inference tasks.« less

Mind Operational Semantics and Brain Operational Architectonics: A Putative Correspondence

PubMed Central

Benedetti, Giulio; Marchetti, Giorgio; Fingelkurts, Alexander A; Fingelkurts, Andrew A

2010-01-01

Despite allowing for the unprecedented visualization of brain functional activity, modern neurobiological techniques have not yet been able to provide satisfactory answers to important questions about the relationship between brain and mind. The aim of this paper is to show how two different but complementary approaches, Mind Operational Semantics (OS) and Brain Operational Architectonics (OA), can help bridge the gap between a specific kind of mental activity—the higher-order reflective thought or linguistic thought—and brain. The fundamental notion that allows the two different approaches to be jointly used under a common framework is that of operation. According to OS, which is based on introspection and linguistic data, the meanings of words can be analyzed in terms of elemental mental operations (EOMC), amongst which those of attention play a key role. Linguistic thought is made possible by special kinds of elements, which OS calls “correlators”, which have the function of tying together the other elements of thought, which OS calls “correlata” (a "correlational network” that is, a sentence, is so formed). Therefore, OS conceives of linguistic thought as a hierarchy of operations of increasing complexity. Likewise, according to OA, which is based on the joint analysis of cognitive and electromagnetic data (EEG and MEG), every conscious phenomenon is brought to existence by the joint operations of many functional and transient neuronal assemblies in the brain. According to OA, the functioning of the brain is always operational (made up of operations), and its structure is characterized by a hierarchy of operations of increasing complexity: single neurons, single assemblies of neurons, synchronized neuronal assemblies or Operational Modules (OM), integrated or complex OMs. The authors put forward the hypothesis that the whole level of OS’s description (EOMC, correlators, and correlational networks) corresponds to the level of OMs (or set of them) of different complexity within OA’s theory: EOMC could correspond to simple OMs, correlators to complex OMs and the correlational network to a set of simple and complex OMs. Finally, a set of experiments is proposed to verify the putative correspondence between OS and OA and prove the existence of an integrated continuum between brain and mind. PMID:21113277

In situ Investigation of Magnetism in Metastable Phases of Levitated Fe83 B17 During Solidification

NASA Astrophysics Data System (ADS)

Quirinale, D. G.; Messina, D.; Rustan, G. E.; Kreyssig, A.; Prozorov, R.; Goldman, A. I.

2017-11-01

In situ measurements of structure, density, and magnetization on samples of Fe83 B17 using an electrostatic levitation furnace allow us to identify and correlate the magnetic and structural transitions in this system during its complex solidification process. In particular, we identify magnetic ordering in the metastable Fe23 B6 /fcc Fe coherently grown structures and primitive tetragonal Fe3 B metastable phase in addition to characterizing the equilibrium Fe2 B phase. Our measurements demonstrate that the incorporation of a tunnel-diode oscillator circuit within an electrostatic levitation furnace enables investigations of the physical properties of high-temperature metastable structures.

Photosensitization of Intact Heart Mitochondria by the Phthalocyanine Pc 4: Correlation of Structural and Functional Deficits with Cytochrome c Release

PubMed Central

Kim, Junhwan; Fujioka, Hisashi; Oleinick, Nancy L.; Anderson, Vernon E.

2010-01-01

Singlet oxygen is produced by absorption of red light by the phthalocyanine dye, Pc 4, followed by energy transfer to dissolved triplet oxygen. Mitochondria pre-incubated with Pc 4 were illuminated by red light and the damage to mitochondrial structure and function by the generated singlet oxygen was studied. At early illumination times (3–5 min. of red light exposure), state 3 respiration was inhibited (50%) while state 4 activity increased, resulting in effectively complete uncoupling. Individual complex activities were measured and only complex IV activity was significantly reduced and exhibited a dose response while the activities of electron transport complexes I, II and III were not significantly affected. Cyt c release was an increasing function of irradiation time with 30% being released following 5 min. of illumination. Mitochondrial expansion along with changes in the structure of the cristae were observed by transmission electron microscopy following 5 min. of irradiation with an increase of large vacuoles and membrane rupture occurring following more extensive exposures. PMID:20510354

Visualizing ligand molecules in twilight electron density

PubMed Central

Weichenberger, Christian X.; Pozharski, Edwin; Rupp, Bernhard

2013-01-01

Three-dimensional models of protein structures determined by X-ray crystallo­graphy are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein–ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein–ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein–ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/. PMID:23385767

Visualizing ligand molecules in Twilight electron density.

PubMed

Weichenberger, Christian X; Pozharski, Edwin; Rupp, Bernhard

2013-02-01

Three-dimensional models of protein structures determined by X-ray crystallography are based on the interpretation of experimentally derived electron-density maps. The real-space correlation coefficient (RSCC) provides an easily comprehensible, objective measure of the residue-based fit of atom coordinates to electron density. Among protein structure models, protein-ligand complexes are of special interest, given their contribution to understanding the molecular underpinnings of biological activity and to drug design. For consumers of such models, it is not trivial to determine the degree to which ligand-structure modelling is biased by subjective electron-density interpretation. A standalone script, Twilight, is presented for the analysis, visualization and annotation of a pre-filtered set of 2815 protein-ligand complexes deposited with the PDB as of 15 January 2012 with ligand RSCC values that are below a threshold of 0.6. It also provides simplified access to the visualization of any protein-ligand complex available from the PDB and annotated by the Uppsala Electron Density Server. The script runs on various platforms and is available for download at http://www.ruppweb.org/twilight/.

The crystallography of correlated disorder.

PubMed

Keen, David A; Goodwin, Andrew L

2015-05-21

Classical crystallography can determine structures as complicated as multi-component ribosomal assemblies with atomic resolution, but is inadequate for disordered systems--even those as simple as water ice--that occupy the complex middle ground between liquid-like randomness and crystalline periodic order. Correlated disorder nevertheless has clear crystallographic signatures that map to the type of disorder, irrespective of the underlying physical or chemical interactions and material involved. This mapping hints at a common language for disordered states that will help us to understand, control and exploit the disorder responsible for many interesting physical properties.

Automatic Information Processing and High Performance Skills: Individual Differences and Mechanisms of Performance Improvement in Search-Detection and Complex Task

DTIC Science & Technology

1992-09-01

abilities is fit along with the autoregressive process. Initially, the influences on search performance of within-group age and sex were included as control...Results: PerformanceLAbility Structure Measurement Model: Ability Structure The correlations between all the ability measures, age, and sex are...subsequent analyses for young adults. Age and sex were included as control variables. There was an age range of 15 years; this range is sufficiently large that

The role of complex emotions in inconsistent diagnoses of schizophrenia.

PubMed

Gara, Michael A; Vega, William A; Lesser, Ira; Escamilla, Michael; Lawson, William B; Wilson, Daniel R; Fleck, David E; Strakowski, Stephen M

2010-09-01

In the case of large-scale epidemiological studies, there is evidence of substantial disagreement when lay diagnoses of schizophrenia based on structured interviews are compared with expert diagnoses of the same patients. Reasons for this level of disagreement are investigated in the current study, which made use of advances in text-mining techniques and associated structural representations of language expressions. Specifically, the current study examined whether content analyses of transcribed diagnostic interviews obtained from 150 persons with serious psychiatric disorders yielded any discernable patterns that correlated with diagnostic inconsistencies of schizophrenia. In summary, it was found that the patterning or structure of spontaneous self-reports of emotion states in the diagnostic interview was associated with diagnostic inconsistencies of schizophrenia, irrespective of confounders; i.e., age of patient, gender, or ethnicity. In particular, complex emotion patterns were associated with greater disagreement between experts and trained lay interviewers than were simpler patterns.

Estimation of Dynamic Systems for Gene Regulatory Networks from Dependent Time-Course Data.

PubMed

Kim, Yoonji; Kim, Jaejik

2018-06-15

Dynamic system consisting of ordinary differential equations (ODEs) is a well-known tool for describing dynamic nature of gene regulatory networks (GRNs), and the dynamic features of GRNs are usually captured through time-course gene expression data. Owing to high-throughput technologies, time-course gene expression data have complex structures such as heteroscedasticity, correlations between genes, and time dependence. Since gene experiments typically yield highly noisy data with small sample size, for a more accurate prediction of the dynamics, the complex structures should be taken into account in ODE models. Hence, this study proposes an ODE model considering such data structures and a fast and stable estimation method for the ODE parameters based on the generalized profiling approach with data smoothing techniques. The proposed method also provides statistical inference for the ODE estimator and it is applied to a zebrafish retina cell network.

Interaction Analysis of FABP4 Inhibitors by X-ray Crystallography and Fragment Molecular Orbital Analysis.

PubMed

Tagami, Uno; Takahashi, Kazutoshi; Igarashi, Shunsuke; Ejima, Chieko; Yoshida, Tomomi; Takeshita, Sen; Miyanaga, Wataru; Sugiki, Masayuki; Tokumasu, Munetaka; Hatanaka, Toshihiro; Kashiwagi, Tatsuki; Ishikawa, Kohki; Miyano, Hiroshi; Mizukoshi, Toshimi

2016-04-14

X-ray crystal structural determination of FABP4 in complex with four inhibitors revealed the complex binding modes, and the resulting observations led to improvement of the inhibitory potency of FABP4 inhibitors. However, the detailed structure-activity relationship (SAR) could not be explained from these structural observations. For a more detailed understanding of the interactions between FABP4 and inhibitors, fragment molecular orbital analyses were performed. These analyses revealed that the total interfragment interaction energies of FABP4 and each inhibitor correlated with the ranking of the K i value for the four inhibitors. Furthermore, interactions between each inhibitor and amino acid residues in FABP4 were identified. The oxygen atom of Lys58 in FABP4 was found to be very important for strong interactions with FABP4. These results might provide useful information for the development of novel potent FABP4 inhibitors.

Extended x-ray absorption fine structure spectroscopy and x-ray absorption near edge spectroscopy study of aliovalent doped ceria to correlate local structural changes with oxygen vacancies clustering

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

Shirbhate, S. C.; Acharya, S. A., E-mail: saha275@yahoo.com; Yadav, A. K.

2016-04-04

This study provides atomic scale insight to understand the role of aliovalent dopants on oxygen vacancies clustering and dissociation mechanism in ceria system in order to enhance the performance of oxy-ion conductor. Dopants induced microscale changes in ceria are probed by extended X-ray absorption fine structure spectroscopy, X-ray absorption near edge spectra, and Raman spectroscopy. The results are explored to establish a correlation between atomic level structural changes (coordination number, interatomic spacing) → formation of dimer and trimer type cation-oxygen vacancies defect complex (intrinsic and extrinsic) → dissociation of oxygen vacancies from defect cluster → ionic conductivity temperature. It ismore » a strategic approach to understand key physics of ionic conductivity mechanism in order to reduce operating temperature of electrolytes for intermediate temperature (300–450 °C) electrochemical devices for the first time.« less

On the genre-fication of music: a percolation approach

NASA Astrophysics Data System (ADS)

Lambiotte, R.; Ausloos, M.

2006-03-01

We analyze web-downloaded data on people sharing their music library. By attributing to each music group usual music genres (Rock, Pop ...), and analysing correlations between music groups of different genres with percolation-idea based methods, we probe the reality of these subdivisions and construct a music genre cartography, with a tree representation. We also discuss an alternative objective way to classify music, that is based on the complex structure of the groups audience. Finally, a link is drawn with the theory of hidden variables in complex networks.

Dissortativity and duplications in oral cancer

NASA Astrophysics Data System (ADS)

Shinde, Pramod; Yadav, Alok; Rai, Aparna; Jalan, Sarika

2015-08-01

More than 300 000 new cases worldwide are being diagnosed with oral cancer annually. Complexity of oral cancer renders designing drug targets very difficult. We analyse protein-protein interaction network for the normal and oral cancer tissue and detect crucial changes in the structural properties of the networks in terms of the interactions of the hub proteins and the degree-degree correlations. Further analysis of the spectra of both the networks, while exhibiting universal statistical behaviour, manifest distinction in terms of the zero degeneracy, providing insight to the complexity of the underlying system.

Neural Correlates of Emotional Personality: A Structural and Functional Magnetic Resonance Imaging Study

PubMed Central

Koelsch, Stefan; Skouras, Stavros; Jentschke, Sebastian

2013-01-01

Studies addressing brain correlates of emotional personality have remained sparse, despite the involvement of emotional personality in health and well-being. This study investigates structural and functional brain correlates of psychological and physiological measures related to emotional personality. Psychological measures included neuroticism, extraversion, and agreeableness scores, as assessed using a standard personality questionnaire. As a physiological measure we used a cardiac amplitude signature, the so-called E κ value (computed from the electrocardiogram) which has previously been related to tender emotionality. Questionnaire scores and E κ values were related to both functional (eigenvector centrality mapping, ECM) and structural (voxel-based morphometry, VBM) neuroimaging data. Functional magnetic resonance imaging (fMRI) data were obtained from 22 individuals (12 females) while listening to music (joy, fear, or neutral music). ECM results showed that agreeableness scores correlated with centrality values in the dorsolateral prefrontal cortex, the anterior cingulate cortex, and the ventral striatum (nucleus accumbens). Individuals with higher E κ values (indexing higher tender emotionality) showed higher centrality values in the subiculum of the right hippocampal formation. Structural MRI data from an independent sample of 59 individuals (34 females) showed that neuroticism scores correlated with volume of the left amygdaloid complex. In addition, individuals with higher E κ showed larger gray matter volume in the same portion of the subiculum in which individuals with higher E κ showed higher centrality values. Our results highlight a role of the amygdala in neuroticism. Moreover, they indicate that a cardiac signature related to emotionality (E κ) correlates with both function (increased network centrality) and structure (grey matter volume) of the subiculum of the hippocampal formation, suggesting a role of the hippocampal formation for emotional personality. Results are the first to show personality-related differences using eigenvector centrality mapping, and the first to show structural brain differences for a physiological measure associated with personality. PMID:24312166

Does hemipelvis structure and position influence acetabulum orientation?

PubMed

Musielak, Bartosz; Jóźwiak, Marek; Rychlik, Michał; Chen, Brian Po-Jung; Idzior, Maciej; Grzegorzewski, Andrzej

2016-03-16

Although acetabulum orientation is well established anatomically and radiographically, its relation to the innominate bone has rarely been addressed. If explored, it could open the discussion on patomechanisms of such complex disorders as femoroacetabular impingement (FAI). We therefore evaluated the influence of pelvic bone position and structure on acetabular spatial orientation. We describe this relation and its clinical implications. This retrospective study was based on computed tomography scanning of three-dimensional models of 31 consecutive male pelvises (62 acetabulums). All measurements were based on CT spatial reconstruction with the use of highly specialized software (Rhinoceros). Relations between acetabular orientation (inclination, tilt, anteversion angles) and pelvic structure were evaluated. The following parameters were evaluated to assess the pelvic structure: iliac opening angle, iliac tilt angle, interspinous distance (ISD), intertuberous distance (ITD), height of the pelvis (HP), and the ISD/ITD/HP ratio. The linear and nonlinear dependence of the acetabular angles and hemipelvic measurements were examined with Pearson's product - moment correlation and Spearman's rank correlation coefficient. Correlations different from 0 with p < 0.05 were considered statistically significant. Comparison of the axis position with pelvis structure with orientation in the horizontal plane revealed a significant positive correlation between the acetabular anteversion angle and the iliac opening angle (p = 0.041 and 0.008, respectively). In the frontal plane, there was a positive correlation between the acetabular inclination angle and the iliac tilt angle (p = 0.025 and 0.014, respectively) and the acetabular inclination angle and the ISD/ITD/HP ratio (both p = 0.048). There is a significant correlation of the hemipelvic structure and acetabular orientation under anatomic conditions, especially in the frontal and horizontal planes. In the anteroposterior view, the more tilted-down innominate bone causes a more caudally oriented acetabulum axis, whereas in the horizontal view this relation is reversed. This study may serve as a basis for the discussion on the role of the pelvis in common disorders of the hip.

Digital Speckle Photography of Subpixel Displacements of Speckle Structures Based on Analysis of Their Spatial Spectra

NASA Astrophysics Data System (ADS)

Maksimova, L. A.; Ryabukho, P. V.; Mysina, N. Yu.; Lyakin, D. V.; Ryabukho, V. P.

2018-04-01

We have investigated the capabilities of the method of digital speckle interferometry for determining subpixel displacements of a speckle structure formed by a displaceable or deformable object with a scattering surface. An analysis of spatial spectra of speckle structures makes it possible to perform measurements with a subpixel accuracy and to extend the lower boundary of the range of measurements of displacements of speckle structures to the range of subpixel values. The method is realized on the basis of digital recording of the images of undisplaced and displaced speckle structures, their spatial frequency analysis using numerically specified constant phase shifts, and correlation analysis of spatial spectra of speckle structures. Transformation into the frequency range makes it possible to obtain quantities to be measured with a subpixel accuracy from the shift of the interference-pattern minimum in the diffraction halo by introducing an additional phase shift into the complex spatial spectrum of the speckle structure or from the slope of the linear plot of the function of accumulated phase difference in the field of the complex spatial spectrum of the displaced speckle structure. The capabilities of the method have been investigated in natural experiment.

Structural and electrical properties of In-implanted Ge

DOE PAGES

Feng, R.; Kremer, F.; Sprouster, D. J.; ...

2015-10-22

Here, we report on the effects of dopant concentration on the structural and electrical properties of In-implanted Ge. For In concentrations of ≤ 0.2 at. %, extended x-ray absorption fine structure and x-ray absorption near-edge structure measurements demonstrate that all In atoms occupy a substitutional lattice site while metallic In precipitates are apparent in transmission electron micrographs for In concentrations ≥0.6 at. %. Evidence of the formation of In-vacancy complexes deduced from extended x-ray absorption fine structure measurements is complimented by density functional theory simulations. Hall effect measurements of the conductivity, carrier density, and carrier mobility are then correlated withmore » the substitutional In fraction.« less

Network diffusion accurately models the relationship between structural and functional brain connectivity networks

PubMed Central

Abdelnour, Farras; Voss, Henning U.; Raj, Ashish

2014-01-01

The relationship between anatomic connectivity of large-scale brain networks and their functional connectivity is of immense importance and an area of active research. Previous attempts have required complex simulations which model the dynamics of each cortical region, and explore the coupling between regions as derived by anatomic connections. While much insight is gained from these non-linear simulations, they can be computationally taxing tools for predicting functional from anatomic connectivities. Little attention has been paid to linear models. Here we show that a properly designed linear model appears to be superior to previous non-linear approaches in capturing the brain’s long-range second order correlation structure that governs the relationship between anatomic and functional connectivities. We derive a linear network of brain dynamics based on graph diffusion, whereby the diffusing quantity undergoes a random walk on a graph. We test our model using subjects who underwent diffusion MRI and resting state fMRI. The network diffusion model applied to the structural networks largely predicts the correlation structures derived from their fMRI data, to a greater extent than other approaches. The utility of the proposed approach is that it can routinely be used to infer functional correlation from anatomic connectivity. And since it is linear, anatomic connectivity can also be inferred from functional data. The success of our model confirms the linearity of ensemble average signals in the brain, and implies that their long-range correlation structure may percolate within the brain via purely mechanistic processes enacted on its structural connectivity pathways. PMID:24384152

Temporal and spatial correlation patterns of air pollutants in Chinese cities

PubMed Central

Dai, Yue-Hua

2017-01-01

As a huge threat to the public health, China’s air pollution has attracted extensive attention and continues to grow in tandem with the economy. Although the real-time air quality report can be utilized to update our knowledge on air quality, questions about how pollutants evolve across time and how pollutants are spatially correlated still remain a puzzle. In view of this point, we adopt the PMFG network method to analyze the six pollutants’ hourly data in 350 Chinese cities in an attempt to find out how these pollutants are correlated temporally and spatially. In terms of time dimension, the results indicate that, except for O3, the pollutants have a common feature of the strong intraday patterns of which the daily variations are composed of two contraction periods and two expansion periods. Besides, all the time series of the six pollutants possess strong long-term correlations, and this temporal memory effect helps to explain why smoggy days are always followed by one after another. In terms of space dimension, the correlation structure shows that O3 is characterized by the highest spatial connections. The PMFGs reveal the relationship between this spatial correlation and provincial administrative divisions by filtering the hierarchical structure in the correlation matrix and refining the cliques as the tinny spatial clusters. Finally, we check the stability of the correlation structure and conclude that, except for PM10 and O3, the other pollutants have an overall stable correlation, and all pollutants have a slight trend to become more divergent in space. These results not only enhance our understanding of the air pollutants’ evolutionary process, but also shed lights on the application of complex network methods into geographic issues. PMID:28832599

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

Hypergraph topological quantities for tagged social networks.

PubMed

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Hypergraph topological quantities for tagged social networks

NASA Astrophysics Data System (ADS)

Zlatić, Vinko; Ghoshal, Gourab; Caldarelli, Guido

2009-09-01

Recent years have witnessed the emergence of a new class of social networks, which require us to move beyond previously employed representations of complex graph structures. A notable example is that of the folksonomy, an online process where users collaboratively employ tags to resources to impart structure to an otherwise undifferentiated database. In a recent paper, we proposed a mathematical model that represents these structures as tripartite hypergraphs and defined basic topological quantities of interest. In this paper, we extend our model by defining additional quantities such as edge distributions, vertex similarity and correlations as well as clustering. We then empirically measure these quantities on two real life folksonomies, the popular online photo sharing site Flickr and the bookmarking site CiteULike. We find that these systems share similar qualitative features with the majority of complex networks that have been previously studied. We propose that the quantities and methodology described here can be used as a standard tool in measuring the structure of tagged networks.

Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

PubMed

Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

2017-01-01

The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

Complex basis functions for molecular resonances: Methodology and applications

NASA Astrophysics Data System (ADS)

White, Alec; McCurdy, C. William; Head-Gordon, Martin

The computation of positions and widths of metastable electronic states is a challenge for molecular electronic structure theory because, in addition to the difficulty of the many-body problem, such states obey scattering boundary conditions. These resonances cannot be addressed with naïve application of traditional bound state electronic structure theory. Non-Hermitian electronic structure methods employing complex basis functions is one way that we may rigorously treat resonances within the framework of traditional electronic structure theory. In this talk, I will discuss our recent work in this area including the methodological extension from single determinant SCF-based approaches to highly correlated levels of wavefunction-based theory such as equation of motion coupled cluster and many-body perturbation theory. These approaches provide a hierarchy of theoretical methods for the computation of positions and widths of molecular resonances. Within this framework, we may also examine properties of resonances including the dependence of these parameters on molecular geometry. Some applications of these methods to temporary anions and dianions will also be discussed.

Structure-based multiscale approach for identification of interaction partners of PDZ domains.

PubMed

Tiwari, Garima; Mohanty, Debasisa

2014-04-28

PDZ domains are peptide recognition modules which mediate specific protein-protein interactions and are known to have a complex specificity landscape. We have developed a novel structure-based multiscale approach which identifies crucial specificity determining residues (SDRs) of PDZ domains from explicit solvent molecular dynamics (MD) simulations on PDZ-peptide complexes and uses these SDRs in combination with knowledge-based scoring functions for proteomewide identification of their interaction partners. Multiple explicit solvent simulations ranging from 5 to 50 ns duration have been carried out on 28 PDZ-peptide complexes with known binding affinities. MM/PBSA binding energy values calculated from these simulations show a correlation coefficient of 0.755 with the experimental binding affinities. On the basis of the SDRs of PDZ domains identified by MD simulations, we have developed a simple scoring scheme for evaluating binding energies for PDZ-peptide complexes using residue based statistical pair potentials. This multiscale approach has been benchmarked on a mouse PDZ proteome array data set by calculating the binding energies for 217 different substrate peptides in binding pockets of 64 different mouse PDZ domains. Receiver operating characteristic (ROC) curve analysis indicates that, the area under curve (AUC) values for binder vs nonbinder classification by our structure based method is 0.780. Our structure based method does not require experimental PDZ-peptide binding data for training.

On the origin of long-range correlations in texts.

PubMed

Altmann, Eduardo G; Cristadoro, Giampaolo; Esposti, Mirko Degli

2012-07-17

The complexity of human interactions with social and natural phenomena is mirrored in the way we describe our experiences through natural language. In order to retain and convey such a high dimensional information, the statistical properties of our linguistic output has to be highly correlated in time. An example are the robust observations, still largely not understood, of correlations on arbitrary long scales in literary texts. In this paper we explain how long-range correlations flow from highly structured linguistic levels down to the building blocks of a text (words, letters, etc..). By combining calculations and data analysis we show that correlations take form of a bursty sequence of events once we approach the semantically relevant topics of the text. The mechanisms we identify are fairly general and can be equally applied to other hierarchical settings.

Seismotectonic zoning of Azerbaijan territory

NASA Astrophysics Data System (ADS)

Kangarli, Talat; Aliyev, Ali; Aliyev, Fuad; Rahimov, Fuad

2017-04-01

Studying of the space-time correlation and consequences effect between tectonic events and other geological processes that have created modern earth structure still remains as one of the most important problems in geology. This problem is especially important for the East Caucasus-South Caspian geodynamic zone. Being situated at the eastern part of the Caucasian strait, this zone refers to a center of Alpine-Himalayan active folded belt, and is known as a complex tectonic unit with jointing heterogeneous structural-substantial complexes arising from different branches of the belt (Doburja-Caucasus-Kopetdag from the north and Pyrenean-Alborz from the south with Kura and South Caspian zone). According to GPS and precise leveling data, activity of regional geodynamic processes shows intensive horizontal and vertical movements of the Earth's crust as conditioned by collision of the Arabian and Eurasian continental plates continuing since the end of Miocene. So far studies related to the regional of geology-geophysical data, periodically used for the geological and tectonic modeling of the environment mainly based on the fixing ideology. There still remains a number of uncertainties in solution of issues related to regional geology, tectonics and magmatism, structure and interrelation of different structural zones, space-time interrelations between onshore and offshore complexes, etc. At the same time large dataset produced by surface geological surveys, deep geological mapping of on- and offshore areas with the use of seismic and electrical reconnaissance and geophysical field zoning methods, deep well drilling and remote sensing activities. Conducted new studies produced results including differentiation of formerly unknown nappe complexes of the different ages and scales within the structure of mountain-fold zones, identification of new zones containing ophiolites in their section, outlining of currently active faulting areas, geophysical interpretation of the deep structure of Greater and Lesser Caucasus, detailed description of the deep structure of Caspian zone, Kur and Caspian megadepressions, identification of nappe-folded structure of the Absheron Peninsula and the Absheron threshold at the border of Middle and South Caspian, justification of the possible hydrocarbon concentration at the tectonically stratified substantial complexes of mountain and foothill areas, etc. Based on the outcomes of implemented researches, some general conclusions and schemes were drawn for some parts of the project region within the plate tectonics conceptual frameworks, to include the territories of Lesser Caucasus and South Caspian. Analysis and comparison of these data with macroseismic and instrumental data allowed us to conduct seismotectonic studies in a region and develop a new scheme of seismotectonic map with outlined recent and forecasted seismic activity. There also correlated foci zones of earthquakes with subhorizontal and subvertical borders in earth crust, which shows their structure-dynamic relationship. In the one hand, the earthquake foci zones belong to the faults of the basement which extend to sedimentary cover and their intersection knots. On the other hand, there appearing inner-block seismogenic levels, namely, in seismic generation acts all the earth crust: tectonic stress results on movements along fault zones, as well as lateral displacements along non-stable contacts of the structure-substance complexes of different competency.

The Shock and Vibration Bulletin. Part 1. Summaries of Presented Papers

DTIC Science & Technology

1974-10-01

15 S. Smith, R. C. Stroud, G. A. Hamma, W. L. Hallaver, R. C. Yee MODALAB-A NEW SYSTEM FOR STRUCTURAL DYNAMIC TESTING, II, ANALYSIS ...PV -A ........................................................... 33 A. Burkhard and R. Scott ANALYSIS AND FLIGHT TEST CORRELATION OF VIBROACOUSTIC...METHODS FOR THE ANALYSIS OF ELASTICALLY SUPPORTED ISOLATION SYSTEMS ............................................. 41 G. L. Fox IMPACT ON COMPLEX

Similar Neural Correlates for Language and Sequential Learning: Evidence from Event-Related Brain Potentials

ERIC Educational Resources Information Center

Christiansen, Morten H.; Conway, Christopher M.; Onnis, Luca

2012-01-01

We used event-related potentials (ERPs) to investigate the time course and distribution of brain activity while adults performed (1) a sequential learning task involving complex structured sequences and (2) a language processing task. The same positive ERP deflection, the P600 effect, typically linked to difficult or ungrammatical syntactic…

[Dichlorido (2-(2-(1H-benzo[d]thiazol-2-yl)hydrazono)propan-1-ol) Cu(II)]: Crystal structure, Hirshfeld surface analysis and correlation of its ESI-MS behavior with [Dichlorido 3-(hydroxyimino)-2-butanone-2-(1H-benzo[d]thiazol-2-yl)hydrazone Cu(II)

NASA Astrophysics Data System (ADS)

Kamat, Vinayak; Kumara, Karthik; Naik, Krishna; Kotian, Avinash; Netalkar, Priya; Shivalingegowda, Naveen; Neratur, Krishnappagowda Lokanath; Revankar, Vidyanand

2017-12-01

In the present work, Cu(II) complexes of 2-(2-benzo[d]thiazol-2-yl)hydrazono)propan-1-ol (L1) and 3-(hydroxyimino)-2-butanone-2-(1H-benzo[d]thiazol-2-yl)hydrazone (L2) are synthesized and characterized by various spectro-analytical techniques. The structure of Cu(II) complex of L1 i.e., [CuL1Cl2], is unambiguously determined by single crystal X-ray diffraction method. While similar efforts were unsuccessful in the case of Cu(II) complex of L2 i.e., [CuL2Cl2]. Hence, to avail the structural facts, various cationic/anionic fragments or adducts formed during positive/negative mode electrospray ionization (ESI) of CuL1Cl2 and CuL2Cl2 have been identified with the help of their charge, monoisotopic masses and isotopic distributions. The similarity in the ESI behavior of two complexes has inferred their structural resemblance, which is further supported by DFT optimized structures, EPR spectral studies and analytical measurements. The EPR spectral behavior (g|| > g⊥ > 2.02) of the complexes are attributed to an axial symmetry with the dx2-y2 ground state having square pyramidal Cu(II) ion. CuL1Cl2 has crystallized in monoclinic crystal system in P21/c space group. The molecular complex has ring-metal (Cg-Me) interactions of the type Cg···>Cu, which contributes to the crystal packing. The Cl⋯H (30.6%) interactions have the major contribution among all intermolecular contacts and have played a vital role in the stabilization of the molecular structure, which is extended to 3D network through Csbnd H···Cg and Cg-Cg interactions.

Dorso-medial and ventro-lateral functional specialization of the human retrosplenial complex in spatial updating and orienting.

PubMed

Burles, Ford; Slone, Edward; Iaria, Giuseppe

2017-04-01

The retrosplenial complex is a region within the posterior cingulate cortex implicated in spatial navigation. Here, we investigated the functional specialization of this large and anatomically heterogeneous region using fMRI and resting-state functional connectivity combined with a spatial task with distinct phases of spatial 'updating' (i.e., integrating and maintaining object locations in memory during spatial displacement) and 'orienting' (i.e., recalling unseen locations from current position in space). Both spatial 'updating' and 'orienting' produced bilateral activity in the retrosplenial complex, among other areas. However, spatial 'updating' produced slightly greater activity in ventro-lateral portions, of the retrosplenial complex, whereas spatial 'orienting' produced greater activity in a more dorsal and medial portion of it (both regions localized along the parieto-occipital fissure). At rest, both ventro-lateral and dorso-medial subregions of the retrosplenial complex were functionally connected to the hippocampus and parahippocampus, regions both involved in spatial orientation and navigation. However, the ventro-lateral subregion of the retrosplenial complex displayed more positive functional connectivity with ventral occipital and temporal object recognition regions, whereas the dorso-medial subregion activity was more correlated to dorsal activity and frontal activity, as well as negatively correlated with more ventral parietal structures. These findings provide evidence for a dorso-medial to ventro-lateral functional specialization within the human retrosplenial complex that may shed more light on the complex neural mechanisms underlying spatial orientation and navigation in humans.

Complex Networks Dynamics Based on Events-Phase Synchronization and Intensity Correlation Applied to The Anomaly Patterns and Extremes in The Tropical African Climate System

NASA Astrophysics Data System (ADS)

Oluoch, K.; Marwan, N.; Trauth, M.; Loew, A.; Kurths, J.

2012-04-01

The African continent lie almost entirely within the tropics and as such its (tropical) climate systems are predominantly governed by the heterogeneous, spatial and temporal variability of the Hadley and Walker circulations. The variabilities in these meridional and zonal circulations lead to intensification or suppression of the intensities, durations and frequencies of the Inter-tropical Convergence Zone (ICTZ) migration, trade winds and subtropical high-pressure regions and the continental monsoons. The above features play a central role in determining the African rainfall spatial and temporal variability patterns. The current understanding of these climate features and their influence on the rainfall patterns is not sufficiently understood. Like many real-world systems, atmospheric-oceanic processes exhibit non-linear properties that can be better explored using non-linear (NL) methods of time-series analysis. Over the recent years, the complex network approach has evolved as a powerful new player in understanding spatio-temporal dynamics and evolution of complex systems. Together with NL techniques, it is continuing to find new applications in many areas of science and technology including climate research. We would like to use these two powerful methods to understand the spatial structure and dynamics of African rainfall anomaly patterns and extremes. The method of event synchronization (ES) developed by Quiroga et al., 2002 and first applied to climate networks by Malik et al., 2011 looks at correlations with a dynamic time lag and as such, it is a more intuitive way to correlate a complex and heterogeneous system like climate networks than a fixed time delay most commonly used. On the other hand, the short comings of ES is its lack of vigorous test statistics for the significance level of the correlations, and the fact that only the events' time indices are synchronized while all information about how the relative intensities propagate within network framework is lost. The new method we present is motivated by the ES and borrows ideas from signal processing where a signal is represented by its intensity and frequency. Even though the anomaly signals are not periodic, the idea of phase synchronization is not far fetched. It brings into one umbrella, the traditionally known linear Intensity correlation methods like Pearson correlation, spear-man's rank or non-linear ones like mutual information with the ES for non-linear temporal synchronization. The intensity correlation is only performed where there is a temporal synchronization. The former just measures how constant the intensity differences are. In other words, how monotonic are the two functions. The overall measure of correlation and synchronization is the product of the two coefficients. Complex networks constructed by this technique has all the advantages inherent in each of the techniques it borrows. But, it is more superior and able to uncover many known and unknown dynamical features in rainfall field or any variable of interest. The main aim of this work is to develop a method that can identify the footprints of coherent or incoherent structures within the ICTZ, the African and the Indian monsoons and the ENSO signal on the tropical African continent and their temporal evolution.

Long-range dipolar order and dispersion forces in polar liquids

NASA Astrophysics Data System (ADS)

Besford, Quinn Alexander; Christofferson, Andrew Joseph; Liu, Maoyuan; Yarovsky, Irene

2017-11-01

Complex solvation phenomena, such as specific ion effects, occur in polar liquids. Interpretation of these effects in terms of structure and dispersion forces will lead to a greater understanding of solvation. Herein, using molecular dynamics, we probe the structure of polar liquids through specific dipolar pair correlation functions that contribute to the potential of mean force that is "felt" between thermally rotating dipole moments. It is shown that unique dipolar order exists at separations at least up to 20 Å for all liquids studied. When the structural order is compared with a dipolar dispersion force that arises from local co-operative enhancement of dipole moments, a strong agreement is found. Lifshitz theory of dispersion forces was compared with the structural order, where the theory is validated for all liquids that do not have significant local dipole correlations. For liquids that do have significant local dipole correlations, specifically liquid water, Lifshitz theory underestimates the dispersion force by a factor of 5-10, demonstrating that the force that leads to the increased structure in liquid water is missed by Lifshitz theory of van der Waals forces. We apply similar correlation functions to an ionic aqueous system, where long-range order between water's dipole moment and a single chloride ion is found to exist at 20 Å of separation, revealing a long-range perturbation of water's structure by an ion. Furthermore, we found that waters within the 1st, 2nd, and 3rd solvation shells of a chloride ion exhibit significantly enhanced dipolar interactions, particularly with waters at larger distances of separation. Our results provide a link between structures, dispersion forces, and specific ion effects, which may lead to a more robust understanding of solvation.

Correlating Intravital Multi-Photon Microscopy to 3D Electron Microscopy of Invading Tumor Cells Using Anatomical Reference Points

PubMed Central

Karreman, Matthia A.; Mercier, Luc; Schieber, Nicole L.; Shibue, Tsukasa; Schwab, Yannick; Goetz, Jacky G.

2014-01-01

Correlative microscopy combines the advantages of both light and electron microscopy to enable imaging of rare and transient events at high resolution. Performing correlative microscopy in complex and bulky samples such as an entire living organism is a time-consuming and error-prone task. Here, we investigate correlative methods that rely on the use of artificial and endogenous structural features of the sample as reference points for correlating intravital fluorescence microscopy and electron microscopy. To investigate tumor cell behavior in vivo with ultrastructural accuracy, a reliable approach is needed to retrieve single tumor cells imaged deep within the tissue. For this purpose, fluorescently labeled tumor cells were subcutaneously injected into a mouse ear and imaged using two-photon-excitation microscopy. Using near-infrared branding, the position of the imaged area within the sample was labeled at the skin level, allowing for its precise recollection. Following sample preparation for electron microscopy, concerted usage of the artificial branding and anatomical landmarks enables targeting and approaching the cells of interest while serial sectioning through the specimen. We describe here three procedures showing how three-dimensional (3D) mapping of structural features in the tissue can be exploited to accurately correlate between the two imaging modalities, without having to rely on the use of artificially introduced markers of the region of interest. The methods employed here facilitate the link between intravital and nanoscale imaging of invasive tumor cells, enabling correlating function to structure in the study of tumor invasion and metastasis. PMID:25479106

Structural changes in the minimal spanning tree and the hierarchical network in the Korean stock market around the global financial crisis

NASA Astrophysics Data System (ADS)

Nobi, Ashadun; Maeng, Seong Eun; Ha, Gyeong Gyun; Lee, Jae Woo

2015-04-01

This paper considers stock prices in the Korean stock market during the 2008 global financial crisis by focusing on three time periods: before, during, and after the crisis. Complex networks are extracted from cross-correlation coefficients between the normalized logarithmic return of the stock price time series of firms. The minimal spanning trees (MSTs) and the hierarchical network (HN) are generated from cross-correlation coefficients. Before and after the crisis, securities firms are located at the center of the MST. During the crisis, however, the center of the MST changes to a firm in heavy industry and construction. During the crisis, the MST shrinks in comparison to that before and that after the crisis. This topological change in the MST during the crisis reflects a distinct effect of the global financial crisis. The cophenetic correlation coefficient increases during the crisis, indicating an increase in the hierarchical structure during in this period. When crisis hits the market, firms behave synchronously, and their correlations are higher than those during a normal period.

[The correlations of somatic, dermatoglyphic and psychological characteristics in the structure of general human constitution from the standpoint of systemic approach].

PubMed

Negasheva, M A

2008-01-01

669 young men and women aged 16-23 years were examined using a program including the measurements of 40 body, head and face parameters, fingerprinting and determination of personal psychological characteristics. On the basis of the study of the correlations between the different groups of characteristics, the evidence was obtained that supports the concept of a relative autonomy of the morpho-functional systems as an essential condition for the integrity of the organism as a whole. The coefficients of canonical correlation were calculated between the somatic and dermatoglyphic features (R=0.3), somatic sizes and psychological personality characteristics (R=0.4), psychological characteristics and the dermatoglyphic indices (R=0.4). An original model is suggested that describes the correlations of somatic, dermatoglyphic and psychological features in the structure of general human constitution on the basis of statistically significant canonical correlations (revealed by the author) and that takes in consideration the degree of the influence of genetic and social-economic complex of factors (on the basis of the literature data) on the development and formation of the investigated systems of characteristics.

Full waveform inversion using envelope-based global correlation norm

NASA Astrophysics Data System (ADS)

Oh, Ju-Won; Alkhalifah, Tariq

2018-05-01

To increase the feasibility of full waveform inversion on real data, we suggest a new objective function, which is defined as the global correlation of the envelopes of modelled and observed data. The envelope-based global correlation norm has the advantage of the envelope inversion that generates artificial low-frequency information, which provides the possibility to recover long-wavelength structure in an early stage. In addition, the envelope-based global correlation norm maintains the advantage of the global correlation norm, which reduces the sensitivity of the misfit to amplitude errors so that the performance of inversion on real data can be enhanced when the exact source wavelet is not available and more complex physics are ignored. Through the synthetic example for 2-D SEG/EAGE overthrust model with inaccurate source wavelet, we compare the performance of four different approaches, which are the least-squares waveform inversion, least-squares envelope inversion, global correlation norm and envelope-based global correlation norm. Finally, we apply the envelope-based global correlation norm on the 3-D Ocean Bottom Cable (OBC) data from the North Sea. The envelope-based global correlation norm captures the strong reflections from the high-velocity caprock and generates artificial low-frequency reflection energy that helps us recover long-wavelength structure of the model domain in the early stages. From this long-wavelength model, the conventional global correlation norm is sequentially applied to invert for higher-resolution features of the model.

Quantifying networks complexity from information geometry viewpoint

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

Felice, Domenico, E-mail: domenico.felice@unicam.it; Mancini, Stefano; INFN-Sezione di Perugia, Via A. Pascoli, I-06123 Perugia

We consider a Gaussian statistical model whose parameter space is given by the variances of random variables. Underlying this model we identify networks by interpreting random variables as sitting on vertices and their correlations as weighted edges among vertices. We then associate to the parameter space a statistical manifold endowed with a Riemannian metric structure (that of Fisher-Rao). Going on, in analogy with the microcanonical definition of entropy in Statistical Mechanics, we introduce an entropic measure of networks complexity. We prove that it is invariant under networks isomorphism. Above all, considering networks as simplicial complexes, we evaluate this entropy onmore » simplexes and find that it monotonically increases with their dimension.« less

Entropy, complexity, and Markov diagrams for random walk cancer models

PubMed Central

Newton, Paul K.; Mason, Jeremy; Hurt, Brian; Bethel, Kelly; Bazhenova, Lyudmila; Nieva, Jorge; Kuhn, Peter

2014-01-01

The notion of entropy is used to compare the complexity associated with 12 common cancers based on metastatic tumor distribution autopsy data. We characterize power-law distributions, entropy, and Kullback-Liebler divergence associated with each primary cancer as compared with data for all cancer types aggregated. We then correlate entropy values with other measures of complexity associated with Markov chain dynamical systems models of progression. The Markov transition matrix associated with each cancer is associated with a directed graph model where nodes are anatomical locations where a metastatic tumor could develop, and edge weightings are transition probabilities of progression from site to site. The steady-state distribution corresponds to the autopsy data distribution. Entropy correlates well with the overall complexity of the reduced directed graph structure for each cancer and with a measure of systemic interconnectedness of the graph, called graph conductance. The models suggest that grouping cancers according to their entropy values, with skin, breast, kidney, and lung cancers being prototypical high entropy cancers, stomach, uterine, pancreatic and ovarian being mid-level entropy cancers, and colorectal, cervical, bladder, and prostate cancers being prototypical low entropy cancers, provides a potentially useful framework for viewing metastatic cancer in terms of predictability, complexity, and metastatic potential. PMID:25523357

Quantum correlation properties in Matrix Product States of finite-number spin rings

NASA Astrophysics Data System (ADS)

Zhu, Jing-Min; He, Qi-Kai

2018-02-01

The organization and structure of quantum correlation (QC) of quantum spin-chains are very rich and complex. Hence the depiction and measures about the QC of finite-number spin rings deserved to be investigated intensively by using Matrix Product States(MPSs) in addition to the case with infinite-number. Here the dependencies of the geometric quantum discord(GQD) of two spin blocks on the total spin number, the spacing spin number and the environment parameter are presented in detail. We also compare the GQD with the total correlation(TC) and the classical correlation(CC) and illustrate its characteristics. Predictably, our findings may provide the potential of designing the optimal QC experimental detection proposals and pave the way for the designation of optimal quantum information processing schemes.

Colloidal Aggregate Structure under Shear by USANS

NASA Astrophysics Data System (ADS)

Chatterjee, Tirtha; van Dyk, Antony K.; Ginzburg, Valeriy V.; Nakatani, Alan I.

2015-03-01

Paints are complex formulations of polymeric binders, inorganic pigments, dispersants, surfactants, colorants, rheology modifiers, and other additives. A commercially successful paint exhibits a desired viscosity profile over a wide shear rate range from 10-5 s-1 for settling to >104 s-1 for rolling, and spray applications. Understanding paint formulation structure is critical as it governs the paint viscosity profile. However, probing paint formulation structure under shear is a challenging task due to the formulation complexity containing structures with different hierarchical length scales and their alterations under the influence of an external flow field. In this work mesoscale structures of paint formulations under shear are investigated using Ultra Small-Angle Neutron Scattering (rheo-USANS). Contrast match conditions were utilized to independently probe the structure of latex binder particle aggregates and the TiO2 pigment particle aggregates. Rheo-USANS data revealed that the aggregates are fractal in nature and their self-similarity dimensions and correlations lengths depend on the chemistry of the binder particles, the type of rheology modifier present and the shear stress imposed upon the formulation. These results can be explained in the framework of diffusion and reaction limited transient aggregates structure evolution under simple shear.

Nephrin phosphorylation regulates podocyte adhesion through the PINCH-1-ILK-α-parvin complex

PubMed Central

Zha, Dongqing; Chen, Cheng; Liang, Wei; Chen, Xinghua; Ma, Tean; Yang, Hongxia; van Goor, Harry; Ding, Guohua

2013-01-01

Nephrin, a structural molecule, is also a signaling molecule after phosphorylation. Inhibition of nephrin phosphorylation is correlated with podocyte injury. The PINCH-1-ILK-α-parvin (PIP) complex plays a crucial role in cell adhesion and cytoskeleton formation. We hypothesized that nephrin phosphorylation influenced cytoskeleton and cell adhesion in podocytes by regulating the PIP complex. The nephrin phosphorylation, PIP complex formation, and F-actin in Wistar rats intraperitoneally injected with puromycin aminonucleoside were gradually decreased but increased with time, coinciding with the recovery from glomerular/podocyte injury and proteinuria. In cultured podocytes, PIP complex knockdown resulted in cytoskeleton reorganization and decreased cell adhesion and spreading. Nephrin and its phosphorylation were unaffected after PIP complex knockdown. Furthermore, inhibition of nephrin phosphorylation suppressed PIP complex expression, disorganized podocyte cytoskeleton, and decreased cell adhesion and spreading. These findings indicate that alterations in nephrin phosphorylation disorganize podocyte cytoskeleton and decrease cell adhesion through a PIP complex-dependent mechanism. [BMB Reports 2013; 46(4): 230-235] PMID:23615266

On the multi-reference nature of plutonium oxides: PuO22+, PuO2, PuO3 and PuO2(OH)2.

PubMed

Boguslawski, Katharina; Réal, Florent; Tecmer, Paweł; Duperrouzel, Corinne; Gomes, André Severo Pereira; Legeza, Örs; Ayers, Paul W; Vallet, Valérie

2017-02-08

Actinide-containing complexes present formidable challenges for electronic structure methods due to the large number of degenerate or quasi-degenerate electronic states arising from partially occupied 5f and 6d shells. Conventional multi-reference methods can treat active spaces that are often at the upper limit of what is required for a proper treatment of species with complex electronic structures, leaving no room for verifying their suitability. In this work we address the issue of properly defining the active spaces in such calculations, and introduce a protocol to determine optimal active spaces based on the use of the Density Matrix Renormalization Group algorithm and concepts of quantum information theory. We apply the protocol to elucidate the electronic structure and bonding mechanism of volatile plutonium oxides (PuO 3 and PuO 2 (OH) 2 ), species associated with nuclear safety issues for which little is known about the electronic structure and energetics. We show how, within a scalar relativistic framework, orbital-pair correlations can be used to guide the definition of optimal active spaces which provide an accurate description of static/non-dynamic electron correlation, as well as to analyse the chemical bonding beyond a simple orbital model. From this bonding analysis we are able to show that the addition of oxo- or hydroxo-groups to the plutonium dioxide species considerably changes the π-bonding mechanism with respect to the bare triatomics, resulting in bent structures with a considerable multi-reference character.

Decreased centrality of cortical volume covariance networks in autism spectrum disorders.

PubMed

Balardin, Joana Bisol; Comfort, William Edgar; Daly, Eileen; Murphy, Clodagh; Andrews, Derek; Murphy, Declan G M; Ecker, Christine; Sato, João Ricardo

2015-10-01

Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions characterized by atypical structural and functional brain connectivity. Complex network analysis has been mainly used to describe altered network-level organization for functional systems and white matter tracts in ASD. However, atypical functional and structural connectivity are likely to be also linked to abnormal development of the correlated structure of cortical gray matter. Such covariations of gray matter are particularly well suited to the investigation of the complex cortical pathology of ASD, which is not confined to isolated brain regions but instead acts at the systems level. In this study, we examined network centrality properties of gray matter networks in adults with ASD (n = 84) and neurotypical controls (n = 84) using graph theoretical analysis. We derived a structural covariance network for each group using interregional correlation matrices of cortical volumes extracted from a surface-based parcellation scheme containing 68 cortical regions. Differences between groups in closeness network centrality measures were evaluated using permutation testing. We identified several brain regions in the medial frontal, parietal and temporo-occipital cortices with reductions in closeness centrality in ASD compared to controls. We also found an association between an increased number of autistic traits and reduced centrality of visual nodes in neurotypicals. Our study shows that ASD are accompanied by atypical organization of structural covariance networks by means of a decreased centrality of regions relevant for social and sensorimotor processing. These findings provide further evidence for the altered network-level connectivity model of ASD. Copyright © 2015 Elsevier Ltd. All rights reserved.

Chemical properties and biotoxicity of several chromium picolinate derivatives.

PubMed

Liu, Bin; Liu, Yanfei; Chai, Jie; Hu, Xiangquan; Wu, Duoming; Yang, Binsheng

2016-11-01

As a man-made additive, chromium picolinate Cr(pic) 3 has become a popular dietary supplement worldwide. In this paper Cr(pic) 3 and its new derivatives Cr(6-CH 3 -pic) 3 (1), [Cr(6-NH 2 -pic) 2 (H 2 O) 2 ]NO 3 (2) and Cr(3-NH 2 -pic) 3 (3) were synthesized, and complexes 1 and 2 were characterized by X-ray crystal structure (where pic=2-carboxypyridine). The relationship between the chemical properties and biotoxicity of these complexes was fully discussed: (1) The dynamics stability of chromium picolinate complexes mainly depends on the CrN bonds length. (2) There is a positive correlation between the dynamics stability, electrochemical potentials and generation of reactive oxygen species through Fenton-like reaction. (3) However, no biological toxicity was observed through MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) and sub-chronic oral toxicity study for these chromium picolinate compounds. Together, our findings establish a framework for understanding the structure-property-toxicity relationships of the chromium picolinate complexes. Copyright © 2016 Elsevier Inc. All rights reserved.

A wavelet analysis for the X-ray absorption spectra of molecules

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

Penfold, T. J.; Ecole polytechnique Federale de Lausanne, Laboratoire de chimie et biochimie computationnelles, ISIC, FSB-BCH, CH-1015 Lausanne; SwissFEL, Paul Scherrer Inst, CH-5232 Villigen

2013-01-07

We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rheniummore » diimine complex, [ReX(CO){sub 3}(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.« less

Computational structure analysis of biomacromolecule complexes by interface geometry.

PubMed

Mahdavi, Sedigheh; Salehzadeh-Yazdi, Ali; Mohades, Ali; Masoudi-Nejad, Ali

2013-12-01

The ability to analyze and compare protein-nucleic acid and protein-protein interaction interface has critical importance in understanding the biological function and essential processes occurring in the cells. Since high-resolution three-dimensional (3D) structures of biomacromolecule complexes are available, computational characterizing of the interface geometry become an important research topic in the field of molecular biology. In this study, the interfaces of a set of 180 protein-nucleic acid and protein-protein complexes are computed to understand the principles of their interactions. The weighted Voronoi diagram of the atoms and the Alpha complex has provided an accurate description of the interface atoms. Our method is implemented in the presence and absence of water molecules. A comparison among the three types of interaction interfaces show that RNA-protein complexes have the largest size of an interface. The results show a high correlation coefficient between our method and the PISA server in the presence and absence of water molecules in the Voronoi model and the traditional model based on solvent accessibility and the high validation parameters in comparison to the classical model. Copyright © 2013 Elsevier Ltd. All rights reserved.

Complex network view of evolving manifolds

NASA Astrophysics Data System (ADS)

da Silva, Diamantino C.; Bianconi, Ginestra; da Costa, Rui A.; Dorogovtsev, Sergey N.; Mendes, José F. F.

2018-03-01

We study complex networks formed by triangulations and higher-dimensional simplicial complexes representing closed evolving manifolds. In particular, for triangulations, the set of possible transformations of these networks is restricted by the condition that at each step, all the faces must be triangles. Stochastic application of these operations leads to random networks with different architectures. We perform extensive numerical simulations and explore the geometries of growing and equilibrium complex networks generated by these transformations and their local structural properties. This characterization includes the Hausdorff and spectral dimensions of the resulting networks, their degree distributions, and various structural correlations. Our results reveal a rich zoo of architectures and geometries of these networks, some of which appear to be small worlds while others are finite dimensional with Hausdorff dimension equal or higher than the original dimensionality of their simplices. The range of spectral dimensions of the evolving triangulations turns out to be from about 1.4 to infinity. Our models include simplicial complexes representing manifolds with evolving topologies, for example, an h -holed torus with a progressively growing number of holes. This evolving graph demonstrates features of a small-world network and has a particularly heavy-tailed degree distribution.

Complex Patterns of Local Adaptation in Teosinte

PubMed Central

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

2013-01-01

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

Analysis of the electrolyte convection inside the concentration boundary layer during structured electrodeposition of copper in high magnetic gradient fields.

PubMed

König, Jörg; Tschulik, Kristina; Büttner, Lars; Uhlemann, Margitta; Czarske, Jürgen

2013-03-19

To experimentally reveal the correlation between electrodeposited structure and electrolyte convection induced inside the concentration boundary layer, a highly inhomogeneous magnetic field, generated by a magnetized Fe-wire, has been applied to an electrochemical system. The influence of Lorentz and magnetic field gradient force to the local transport phenomena of copper ions has been studied using a novel two-component laser Doppler velocity profile sensor. With this sensor, the electrolyte convection within 500 μm of a horizontally aligned cathode is presented. The electrode-normal two-component velocity profiles below the electrodeposited structure show that electrolyte convection is induced and directed toward the rim of the Fe-wire. The measured deposited structure directly correlates to the observed boundary layer flow. As the local concentration of Cu(2+) ions is enhanced due to the induced convection, maximum deposit thicknesses can be found at the rim of the Fe-wire. Furthermore, a complex boundary layer flow structure was determined, indicating that electrolyte convection of second order is induced. Moreover, the Lorentz force-driven convection rapidly vanishes, while the electrolyte convection induced by the magnetic field gradient force is preserved much longer. The progress for research is the first direct experimental proof of the electrolyte convection inside the concentration boundary layer that correlates to the deposited structure and reveals that the magnetic field gradient force is responsible for the observed structuring effect.

Structural and tectonic setting of the Charleston, South Carolina, region: Evidence from the Tertiary stratigraphic record

USGS Publications Warehouse

Weems, R.E.; Lewis, W.C.

2002-01-01

Eleven upper Eocene through Pliocene stratigraphic units occur in the subsurface of the region surrounding Charleston, South Carolina. These units contain a wealth of information concerning the long-term tectonic and structural setting of that area. These stratigraphic units have a mosaic pattern of distribution, rather than a simple layered pattern, because deposition, erosion, and tectonic warping have interacted in a complex manner through time. By generating separate structure-contour maps for the base of each stratigraphic unit, an estimate of the original basal surface of each unit can be reconstructed over wide areas. Changes in sea level over geologic time generate patterns of deposition and erosion that are geographically unique for the time of each transgression. Such patterns fail to persist when compared sequentially over time. In some areas, however, there has been persistent, repetitive net downward of upward movement over the past 34 m.y. These repetitive patterns of persistent motion are most readily attributable to tectonism. The spatial pattern of these high and low areas is complex, but it appears to correlate well with known tectonic features of the region. This correlation suggests that the tectonic setting of the Charleston region is controlled by scissors-like compression on a crustal block located between the north-trending Adams Run fault and the northwest-trending Charleston fault. Tectonism is localized in the Charleston region because it lies within a discrete hinge zone that accommodates structural movement between the Cape Fear arch and the Southeast Georgia embayment.

Two-Step Adsorption of PtCl 6 2– Complexes at a Charged Langmuir Monolayer: Role of Hydration and Ion Correlations

DOE PAGES

Uysal, Ahmet; Rock, William; Qiao, Baofu; ...

2017-11-03

Anion exchange at positively charged interfaces plays an important role in a variety of physical and chemical processes. However, the molecular-scale details of these processes, especially with heavy and large anionic complexes, are not well-understood. Here, we studied the adsorption of PtCl 6 2– anionic complexes to floating DPTAP monolayers in the presence of excess Cl– as a function of the bulk chlorometalate concentration. This system aims to simulate the industrial conditions for heavy metal separations with solvent extraction. In situ X-ray scattering and fluorescence measurements, which are element and depth sensitive, show that the chlorometalate ions only adsorb inmore » the diffuse layer at lower concentrations, while they adsorb predominantly in the Stern layer at higher concentrations. The response of DPTAP molecules to the adsorbed ions is determined independently by grazing incidence X-ray diffraction and supports this picture. Molecular dynamics simulations further elucidate the nanoscale structure of the interfacial complexes. The results suggest that ion hydration and ion–ion correlations play a key role in the competitive adsorption process.« less

Spectrally formulated user-defined element in conventional finite element environment for wave motion analysis in 2-D composite structures

NASA Astrophysics Data System (ADS)

Khalili, Ashkan; Jha, Ratneshwar; Samaratunga, Dulip

2016-11-01

Wave propagation analysis in 2-D composite structures is performed efficiently and accurately through the formulation of a User-Defined Element (UEL) based on the wavelet spectral finite element (WSFE) method. The WSFE method is based on the first-order shear deformation theory which yields accurate results for wave motion at high frequencies. The 2-D WSFE model is highly efficient computationally and provides a direct relationship between system input and output in the frequency domain. The UEL is formulated and implemented in Abaqus (commercial finite element software) for wave propagation analysis in 2-D composite structures with complexities. Frequency domain formulation of WSFE leads to complex valued parameters, which are decoupled into real and imaginary parts and presented to Abaqus as real values. The final solution is obtained by forming a complex value using the real number solutions given by Abaqus. Five numerical examples are presented in this article, namely undamaged plate, impacted plate, plate with ply drop, folded plate and plate with stiffener. Wave motions predicted by the developed UEL correlate very well with Abaqus simulations. The results also show that the UEL largely retains computational efficiency of the WSFE method and extends its ability to model complex features.

Currency co-movement and network correlation structure of foreign exchange market

NASA Astrophysics Data System (ADS)

Mai, Yong; Chen, Huan; Zou, Jun-Zhong; Li, Sai-Ping

2018-02-01

We study the correlations of exchange rate volatility in the global foreign exchange(FX) market based on complex network graphs. Correlation matrices (CM) and the theoretical information flow method (Infomap) are employed to analyze the modular structure of the global foreign exchange network. The analysis demonstrates that there exist currency modules in the network, which is consistent with the geographical nature of currencies. The European and the East Asian currency modules in the FX network are most significant. We introduce a measure of the impact of individual currency based on its partial correlations with other currencies. We further incorporate an impact elimination method to filter out the impact of core nodes and construct subnetworks after the removal of these core nodes. The result reveals that (i) the US Dollar has prominent global influence on the FX market while the Euro has great impact on European currencies; (ii) the East Asian currency module is more strongly correlated than the European currency module. The strong correlation is a result of the strong co-movement of currencies in the region. The co-movement of currencies is further used to study the formation of international monetary bloc and the result is in good agreement with the consideration based on international trade.

The right inhibition? Callosal correlates of hand performance in healthy children and adolescents callosal correlates of hand performance.

PubMed

Kurth, Florian; Mayer, Emeran A; Toga, Arthur W; Thompson, Paul M; Luders, Eileen

2013-09-01

Numerous studies suggest that interhemispheric inhibition-relayed via the corpus callosum-plays an important role in unilateral hand motions. Interestingly, transcallosal inhibition appears to be indicative of a strong laterality effect, where generally the dominant hemisphere exerts inhibition on the nondominant one. These effects have been largely identified through functional studies in adult populations, but links between motor performance and callosal structure (especially during sensitive periods of neurodevelopment) remain largely unknown. We therefore investigated correlations between Purdue Pegboard performance (a test of motor function) and local callosal thickness in 170 right-handed children and adolescents (mean age: 11.5 ± 3.4 years; range, 6-17 years). Better task performance with the right (dominant) hand was associated with greater callosal thickness in isthmus and posterior midbody. Task performance using both hands yielded smaller and less significant correlations in the same regions, while task performance using the left (nondominant) hand showed no significant correlations with callosal thickness. There were no significant interactions with age and sex. These links between motor performance and callosal structure may constitute the neural correlate of interhemispheric inhibition, which is thought to be necessary for fast and complex unilateral motions and to be biased towards the dominant hand. Copyright © 2012 Wiley Periodicals, Inc., a Wiley company.

Update of the ATTRACT force field for the prediction of protein-protein binding affinity.

PubMed

Chéron, Jean-Baptiste; Zacharias, Martin; Antonczak, Serge; Fiorucci, Sébastien

2017-06-05

Determining the protein-protein interactions is still a major challenge for molecular biology. Docking protocols has come of age in predicting the structure of macromolecular complexes. However, they still lack accuracy to estimate the binding affinities, the thermodynamic quantity that drives the formation of a complex. Here, an updated version of the protein-protein ATTRACT force field aiming at predicting experimental binding affinities is reported. It has been designed on a dataset of 218 protein-protein complexes. The correlation between the experimental and predicted affinities reaches 0.6, outperforming most of the available protocols. Focusing on a subset of rigid and flexible complexes, the performance raises to 0.76 and 0.69, respectively. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Square-antiprismatic eight-coordinate complexes of divalent first-row transition metal cations: a density functional theory exploration of the electronic-structural landscape.

PubMed

Conradie, Jeanet; Patra, Ashis K; Harrop, Todd C; Ghosh, Abhik

2015-02-16

Density functional theory (in the form of the PW91, BP86, OLYP, and B3LYP exchange-correlation functionals) has been used to map out the low-energy states of a series of eight-coordinate square-antiprismatic (D2d) first-row transition metal complexes, involving Mn(II), Fe(II), Co(II), Ni(II), and Cu(II), along with a pair of tetradentate N4 ligands. Of the five complexes, the Mn(II) and Fe(II) complexes have been synthesized and characterized structurally and spectroscopically, whereas the other three are as yet unknown. Each N4 ligand consists of a pair of terminal imidazole units linked by an o-phenylenediimine unit. The imidazole units are the strongest ligands in these complexes and dictate the spatial disposition of the metal three-dimensional orbitals. Thus, the dx(2)-y(2) orbital, whose lobes point directly at the coordinating imidazole nitrogens, has the highest orbital energy among the five d orbitals, whereas the dxy orbital has the lowest orbital energy. In general, the following orbital ordering (in order of increasing orbital energy) was found to be operative: dxy < dxz = dyz ≤ dz(2) < dx(2)-y(2). The square-antiprism geometry does not lead to large energy gaps between the d orbitals, which leads to an S = 2 ground state for the Fe(II) complex. Nevertheless, the dxy orbital has significantly lower energy relative to that of the dxz and dyz orbitals. Accordingly, the ground state of the Fe(II) complex corresponds unambiguously to a dxy(2)dxz(1)dyz(1)dz(2)(1)dx(2)-y(2)(1) electronic configuration. Unsurprisingly, the Mn(II) complex has an S = 5/2 ground state and no low-energy d-d excited states within 1.0 eV of the ground state. The Co(II) complex, on the other hand, has both a low-lying S = 1/2 state and multiple low-energy S = 3/2 states. Very long metal-nitrogen bonds are predicted for the Ni(II) and Cu(II) complexes; these bonds may be too fragile to survive in solution or in the solid state, and the complexes may therefore not be isolable. Overall, the different exchange-correlation functionals provided a qualitatively consistent and plausible picture of the low-energy d-d excited states of the complexes.

Brain-behaviour relationships in people at high genetic risk of schizophrenia.

PubMed

Lymer, G Katherine S; Job, Dominic E; William, T; Moorhead, J; McIntosh, Andrew M; Owens, David G C; Johnstone, Eve C; Lawrie, Stephen M

2006-10-15

The brain is known to be structurally abnormal in schizophrenia, with replicated findings between anatomical deficits and some dysfunctions. These structure-function associations have, however, only very rarely been studied in relatives at risk of schizophrenia. We studied the relationships between structure and schizotypal features (assessed using RISC and SIS) and verbal learning and memory (measured using RAVLT) in relatives at high risk of developing schizophrenia and normal controls. Since these behavioural test scores are strong predictors of schizophrenia in the Edinburgh High Risk Study, we hypothesised that these relationships would differ between those high-risk subjects who will develop schizophrenia from those who will not. We performed multiple regressions of the grey matter segments of the subjects and controls, produced using grey matter optimised, voxel-based morphometry, with their RAVLT, SIS and RISC scores in SPM. Where significant relationships were found, we used SPSS to test for subject group by behavioural score interactions. In those high-risk subjects who became ill, grey matter density (GMD) was significantly correlated with RISC in the left superior temporal gyrus. In subjects who remained well, SIS was significantly correlated with GMD in the right pulvinar. Across the whole HR group, GMD in the right medial dorsal thalamic nucleus was significantly correlated with RAVLT. In those subjects who developed symptoms, RAVLT significantly correlated with GMD in right parahippocampal gyrus whereas in those who became ill, significant correlations existed bilaterally in the pulvinar. These results suggest complex and changing patterns of structural-functional relationships in those subjects at high-risk of schizophrenia.

NMR spectroscopy of the ligand binding core of ionotropic glutamate receptor 2 bound to 5-substituted willardiine partial agonists

PubMed Central

Fenwick, Michael K.; Oswald, Robert E.

2008-01-01

Glutamate receptors mediate neuronal intercommunication in the central nervous system by coupling extracellular neurotransmitter-receptor interactions to ion channel conductivity. To gain insight into structural and dynamical factors that underlie this coupling, solution NMR experiments were performed on the bi-lobed ligand-binding core of glutamate receptor 2 in complexes with a set of willardiine partial agonists. These agonists are valuable for studying structure-function relationships because their 5-position substituent size is correlated with ligand efficacy and extent of receptor desensitization whereas the substituent electronegativity is correlated with ligand potency. NMR results show that the protein backbone amide chemical shift deviations correlate mainly with efficacy and extent of desensitization. Pronounced deviations occur at specific residues in the ligand-binding site and in the two helical segments that join the lobes by a disulfide bond. Experiments detecting conformational exchange show that micro- to millisecond timescale motions also occur near the disulfide bond and vary largely with efficacy and extent of desensitization. These results thus identify regions displaying structural and dynamical dissimilarity arising from differences in ligand-protein interactions and lobe closure which may play a critical role in receptor response. Furthermore, measures of line broadening and conformational exchange for a portion of the ligand-binding site correlate with ligand EC50 data. These results do not have any correlate in the currently available crystal structures and thus provide a novel view of ligand-binding events that may be associated with agonist potency differences. PMID:18387631

Study of a binary interpenetrated polymeric complex by correlation of rheological parameters with zeta potential and conductivity.

PubMed

Nita, Loredana Elena; Chiriac, Aurica P; Neamtu, Iordana; Bercea, Maria

2010-03-01

The interpenetrated macromolecular chains complexation between poly(aspartic acid) and poly(vinyl alcohol) in aqueous solution it was investigated. The interpolymer complexation process was evaluated through dynamic rheology. The aspects concerning the stability of the tested homopolymers and the prepared interpolymeric complex there were achieved from the evaluation of the aqueous solutions'zeta potential and also by determining the pH influence upon the zeta potential and the conductivity. The data obtained through the rheological dynamic measurements were correlated with the composition of the polymeric mixture, the dependence of zeta potential and conductivity. The study reveals the conditions for the formation of interpenetrated polymeric complex as being a ratio of 70wt.% PAS to 30wt.% PVA at 22 degrees C and 50/50 PAS/PVA ratio at 37 degrees C temperature. From the pH influence upon the zeta potential values it was evidenced the PAS aqueous solution does not reach the isoelectric point. At the same time, PVA solution and the complex PAS/PVA reaches the isoelectric point at strongly acid pH. The better stability of PAS, PVA and their mixture in solution is recorded in the alkaline domain (7.5or=12). The conductivity increases with the rising of the PAS content, pH and temperature. Other characteristics of the prepared interpenetrated polymeric structure, as for example thermal stability, there are also presented.

Interaction of a common painkiller piroxicam and copper-piroxicam with chromatin causes structural alterations accompanied by modulation at the epigenomic/genomic level.

PubMed

Goswami, Sathi; Sanyal, Sulagna; Chakraborty, Payal; Das, Chandrima; Sarkar, Munna

2017-08-01

NSAIDs are the most common class of painkillers and anti-inflammatory agents. They also show other functions like chemoprevention and chemosuppression for which they act at the protein but not at the genome level since they are mostly anions at physiological pH, which prohibit their approach to the poly-anionic DNA. Complexing the drugs with bioactive metal obliterate their negative charge and allow them to bind to the DNA, thereby, opening the possibility of genome level interaction. To test this hypothesis, we present the interaction of a traditional NSAID, Piroxicam and its copper complex with core histone and chromatin. Spectroscopy, DLS, and SEM studies were applied to see the effect of the interaction on the structure of histone/chromatin. This was coupled with MTT assay, immunoblot analysis, confocal microscopy, micro array analysis and qRT-PCR. The interaction of Piroxicam and its copper complex with histone/chromatin results in structural alterations. Such structural alterations can have different biological manifestations, but to test our hypothesis, we have focused only on the accompanied modulations at the epigenomic/genomic level. The complex, showed alteration of key epigenetic signatures implicated in transcription in the global context, although Piroxicam caused no significant changes. We have correlated such alterations caused by the complex with the changes in global gene expression and validated the candidate gene expression alterations. Our results provide the proof of concept that DNA binding ability of the copper complexes of a traditional NSAID, opens up the possibility of modulations at the epigenomic/genomic level. Copyright © 2017 Elsevier B.V. All rights reserved.

Crystal Structures of Covalent Complexes of [beta]-Lactam Antibiotics with Escherichia coli Penicillin-Binding Protein 5: Toward an Understanding of Antibiotic Specificity

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

Nicola, George; Tomberg, Joshua; Pratt, R.F.

Penicillin-binding proteins (PBPs) are the molecular targets for the widely used {beta}-lactam class of antibiotics, but how these compounds act at the molecular level is not fully understood. We have determined crystal structures of Escherichia coli PBP 5 as covalent complexes with imipenem, cloxacillin, and cefoxitin. These antibiotics exhibit very different second-order rates of acylation for the enzyme. In all three structures, there is excellent electron density for the central portion of the {beta}-lactam, but weak or absent density for the R1 or R2 side chains. Areas of contact between the antibiotics and PBP 5 do not correlate with themore » rates of acylation. The same is true for conformational changes, because although a shift of a loop leading to an electrostatic interaction between Arg248 and the {beta}-lactam carboxylate, which occurs completely with cefoxitin and partially with imipenem and is absent with cloxacillin, is consistent with the different rates of acylation, mutagenesis of Arg248 decreased the level of cefoxitin acylation only 2-fold. Together, these data suggest that structures of postcovalent complexes of PBP 5 are unlikely to be useful vehicles for the design of new covalent inhibitors of PBPs. Finally, superimposition of the imipenem-acylated complex with PBP 5 in complex with a boronic acid peptidomimetic shows that the position corresponding to the hydrolytic water molecule is occluded by the ring nitrogen of the {beta}-lactam. Because the ring nitrogen occupies a similar position in all three complexes, this supports the hypothesis that deacylation is blocked by the continued presence of the leaving group after opening of the {beta}-lactam ring.« less

A Cryo-Electron Microscopy Study Identifies the Complete H16.V5 Epitope and Reveals Global Conformational Changes Initiated by Binding of the Neutralizing Antibody Fragment

PubMed Central

Lee, Hyunwook; Brendle, Sarah A.; Bywaters, Stephanie M.; Guan, Jian; Ashley, Robert E.; Yoder, Joshua D.; Makhov, Alexander M.; Conway, James F.; Christensen, Neil D.

2014-01-01

ABSTRACT Human papillomavirus 16 (HPV16) is a worldwide health threat and an etiologic agent of cervical cancer. To understand the antigenic properties of HPV16, we pursued a structural study to elucidate HPV capsids and antibody interactions. The cryo-electron microscopy (cryo-EM) structures of a mature HPV16 particle and an altered capsid particle were solved individually and as complexes with fragment of antibody (Fab) from the neutralizing antibody H16.V5. Fitted crystal structures provided a pseudoatomic model of the virus-Fab complex, which identified a precise footprint of H16.V5, including previously unrecognized residues. The altered-capsid–Fab complex map showed that binding of the Fab induced significant conformational changes that were not seen in the altered-capsid structure alone. These changes included more ordered surface loops, consolidated so-called “invading-arm” structures, and tighter intercapsomeric connections at the capsid floor. The H16.V5 Fab preferentially bound hexavalent capsomers likely with a stabilizing effect that directly correlated with the number of bound Fabs. Additional cryo-EM reconstructions of the virus-Fab complex for different incubation times and structural analysis provide a model for a hyperstabilization of the capsomer by H16.V5 Fab and showed that the Fab distinguishes subtle differences between antigenic sites. IMPORTANCE Our analysis of the cryo-EM reconstructions of the HPV16 capsids and virus-Fab complexes has identified the entire HPV.V5 conformational epitope and demonstrated a detailed neutralization mechanism of this clinically important monoclonal antibody against HPV16. The Fab bound and ordered the apical loops of HPV16. This conformational change was transmitted to the lower region of the capsomer, resulting in enhanced intercapsomeric interactions evidenced by the more ordered capsid floor and “invading-arm” structures. This study advances the understanding of the neutralization mechanism used by H16.V5. PMID:25392224

Inversion of 2-D DC resistivity data using rapid optimization and minimal complexity neural network

NASA Astrophysics Data System (ADS)

Singh, U. K.; Tiwari, R. K.; Singh, S. B.

2010-02-01

The backpropagation (BP) artificial neural network (ANN) technique of optimization based on steepest descent algorithm is known to be inept for its poor performance and does not ensure global convergence. Nonlinear and complex DC resistivity data require efficient ANN model and more intensive optimization procedures for better results and interpretations. Improvements in the computational ANN modeling process are described with the goals of enhancing the optimization process and reducing ANN model complexity. Well-established optimization methods, such as Radial basis algorithm (RBA) and Levenberg-Marquardt algorithms (LMA) have frequently been used to deal with complexity and nonlinearity in such complex geophysical records. We examined here the efficiency of trained LMA and RB networks by using 2-D synthetic resistivity data and then finally applied to the actual field vertical electrical resistivity sounding (VES) data collected from the Puga Valley, Jammu and Kashmir, India. The resulting ANN reconstruction resistivity results are compared with the result of existing inversion approaches, which are in good agreement. The depths and resistivity structures obtained by the ANN methods also correlate well with the known drilling results and geologic boundaries. The application of the above ANN algorithms proves to be robust and could be used for fast estimation of resistive structures for other complex earth model also.

Synthesis of Pyridine– and Pyrazine–BF 3 Complexes and Their Characterization in Solution and Solid State

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

Chénard, Etienne; Sutrisno, Andre; Zhu, Lingyang

2016-03-31

Following the discovery of the redox-active 1,4- bis-BF 3-quinoxaline complex, we undertook a structure- activity study with the objective to understand the active nature of the quinoxaline complex. Through systematic synthesis and characterization, we have compared complexes prepared from pyridine and pyrazine derivatives, as heterocyclic core analogues. This paper reports the structural requirements that give rise to the electrochemical features of the 1,4-bis-BF 3-quinoxaline adduct. Using solution and solidstate NMR spectroscopy, the role of aromatic ring fusion and nitrogen incorporation in bonding and electronics was elucidated. We establish the boron atom location and its interaction with its environment from 1Dmore » and 2D solution NMR, X-ray diffraction analysis, and 11B solid-state NMR experiments. Crystallographic analysis of single crystals helped to correlate the boron geometry with 11B quadrupolar coupling constant (CQ) and asymmetry parameter (ηQ), extracted from 11B solid-state NMR spectra. Additionally, computations based on density functional theory were performed to predict electrochemical behavior of the BF 3-heteroaromatic complexes. We then experimentally measured electrochemical potential using cyclic voltammetry and found that the redox potentials and CQ values are similarly affected by electronic changes in the complexes.« less

Synthesis, characterization and DFT studies of two new silver(I) complexes with 3,4-lutidine

NASA Astrophysics Data System (ADS)

Soliman, Saied M.; Assem, Rania; Abu-Youssef, Morsy A. M.; Kassem, Taher S.

2015-04-01

The synthesis, characterization and molecular structure of two new Ag(I) complexes with 3,4-lutidine (34lut) have been reported. The [Ag(34lut)3(OAC)]; 1 and [Ag(34lut)2(TFA)]; 2 complexes, where OAC and TFA are acetate and trifluoroacetate respectively, have been characterized using elemental analysis, FTIR, NMR and mass spectra. Their molecular structures were calculated using DFT quantum chemical calculations. Both 1 and 2 were found to have distorted tetrahedral geometry around the Ag(I). The spectroscopic properties of the studied complexes have been calculated using the same level of theory. The Infrared vibrational frequencies of the COO stretches confirmed that the OAC is monodentate in 1 while the TFA is bidentate in 2. The calculated polarizability (α0) and HOMO-LUMO energy gap (ΔE) values indicated that 1 has higher NLO activity than 2. The electronic spectra of these complexes are calculated using the TD-DFT calculations. The calculated 1H NMR chemical shift values using GIAO approach showed good correlations with the experimental data. The interaction energies using the second order perturbation theory have been used to study the different intramolecular charge transfer interactions in the studied complexes. The NBO calculations indicated that both the Agsbnd O bonds are almost identical in 2 but not in 1.

Self-amplified photo-induced gap quenching in a correlated electron material

DOE PAGES

Mathias, S.; Eich, S.; Urbancic, J.; ...

2016-10-04

Capturing the dynamic electronic band structure of a correlated material presents a powerful capability for uncovering the complex couplings between the electronic and structural degrees of freedom. When combined with ultrafast laser excitation, new phases of matter can result, since far-from-equilibrium excited states are instantaneously populated. Here, we elucidate a general relation between ultrafast non-equilibrium electron dynamics and the size of the characteristic energy gap in a correlated electron material. Here, we show that carrier multiplication via impact ionization can be one of the most important processes in a gapped material, and that the speed of carrier multiplication critically dependsmore » on the size of the energy gap. In the case of the charge-density wave material 1T-TiSe 2, our data indicate that carrier multiplication and gap dynamics mutually amplify each other, which explains—on a microscopic level—the extremely fast response of this material to ultrafast optical excitation.« less

[Meaning in life and mental health: personal meaning systems of psychotherapists and psychotherapy patients].

PubMed

Löffler, Sabine; Knappe, Rainer; Joraschky, Peter; Pöhlmann, Karin

2010-01-01

This study investigated differences in the personal meaning systems of psychotherapists and psychotherapy patients as well as correlations between meaning in life and mental health. We qualitatively assessed the content and structure of the personal meaning systems of 41 psychotherapists and 77 psychotherapy patients. In addition, the participants completed questionnaires measuring meaning in life (LRI-r-d), sense of coherence (SOC-9L), self-esteem (RSES), satisfaction with life (SWLS), self-efficacy (SWK), and depression (BDI). The personal meaning systems of psychotherapists were more complex and coherent compared to psychotherapy patients. In the group of psychotherapy patients, a more elaborate structure of the personal meaning system correlated with the subjective sense of meaning. We were able to confirm correlations between meaning in life and mental health for most of the instances. Psychotherapists had more elaborate and coherent meaning systems than psychotherapy patients. Especially for psychotherapy patients elaborate and coherent meaning systems turned out to be important for mental health.

Fluoroquinolone-Gyrase-DNA Complexes

PubMed Central

Mustaev, Arkady; Malik, Muhammad; Zhao, Xilin; Kurepina, Natalia; Luan, Gan; Oppegard, Lisa M.; Hiasa, Hiroshi; Marks, Kevin R.; Kerns, Robert J.; Berger, James M.; Drlica, Karl

2014-01-01

DNA gyrase and topoisomerase IV control bacterial DNA topology by breaking DNA, passing duplex DNA through the break, and then resealing the break. This process is subject to reversible corruption by fluoroquinolones, antibacterials that form drug-enzyme-DNA complexes in which the DNA is broken. The complexes, called cleaved complexes because of the presence of DNA breaks, have been crystallized and found to have the fluoroquinolone C-7 ring system facing the GyrB/ParE subunits. As expected from x-ray crystallography, a thiol-reactive, C-7-modified chloroacetyl derivative of ciprofloxacin (Cip-AcCl) formed cross-linked cleaved complexes with mutant GyrB-Cys466 gyrase as evidenced by resistance to reversal by both EDTA and thermal treatments. Surprisingly, cross-linking was also readily seen with complexes formed by mutant GyrA-G81C gyrase, thereby revealing a novel drug-gyrase interaction not observed in crystal structures. The cross-link between fluoroquinolone and GyrA-G81C gyrase correlated with exceptional bacteriostatic activity for Cip-AcCl with a quinolone-resistant GyrA-G81C variant of Escherichia coli and its Mycobacterium smegmatis equivalent (GyrA-G89C). Cip-AcCl-mediated, irreversible inhibition of DNA replication provided further evidence for a GyrA-drug cross-link. Collectively these data establish the existence of interactions between the fluoroquinolone C-7 ring and both GyrA and GyrB. Because the GyrA-Gly81 and GyrB-Glu466 residues are far apart (17 Å) in the crystal structure of cleaved complexes, two modes of quinolone binding must exist. The presence of two binding modes raises the possibility that multiple quinolone-enzyme-DNA complexes can form, a discovery that opens new avenues for exploring and exploiting relationships between drug structure and activity with type II DNA topoisomerases. PMID:24497635

Structural investigation of oxovanadium(IV) Schiff base complexes: X-ray crystallography, electrochemistry and kinetic of thermal decomposition.

PubMed

Asadi, Mozaffar; Asadi, Zahra; Savaripoor, Nooshin; Dusek, Michal; Eigner, Vaclav; Shorkaei, Mohammad Ranjkesh; Sedaghat, Moslem

2015-02-05

A series of new VO(IV) complexes of tetradentate N2O2 Schiff base ligands (L(1)-L(4)), were synthesized and characterized by FT-IR, UV-vis and elemental analysis. The structure of the complex VOL(1)⋅DMF was also investigated by X-ray crystallography which revealed a vanadyl center with distorted octahedral coordination where the 2-aza and 2-oxo coordinating sites of the ligand were perpendicular to the "-yl" oxygen. The electrochemical properties of the vanadyl complexes were investigated by cyclic voltammetry. A good correlation was observed between the oxidation potentials and the electron withdrawing character of the substituents on the Schiff base ligands, showing the following trend: MeO5-H>5-Br>5-Cl. Furthermore, the kinetic parameters of thermal decomposition were calculated by using the Coats-Redfern equation. According to the Coats-Redfern plots the kinetics of thermal decomposition of studied complexes is of the first-order in all stages, the free energy of activation for each following stage is larger than the previous one and the complexes have good thermal stability. The preparation of VOL(1)⋅DMF yielded also another compound, one kind of vanadium oxide [VO]X, with different habitus of crystals, (platelet instead of prisma) and without L(1) ligand, consisting of a V10O28 cage, diaminium moiety and dimethylamonium as a counter ions. Because its crystal structure was also new, we reported it along with the targeted complex. Copyright © 2014 Elsevier B.V. All rights reserved.

Sensitivity analysis of a sound absorption model with correlated inputs

NASA Astrophysics Data System (ADS)

Chai, W.; Christen, J.-L.; Zine, A.-M.; Ichchou, M.

2017-04-01

Sound absorption in porous media is a complex phenomenon, which is usually addressed with homogenized models, depending on macroscopic parameters. Since these parameters emerge from the structure at microscopic scale, they may be correlated. This paper deals with sensitivity analysis methods of a sound absorption model with correlated inputs. Specifically, the Johnson-Champoux-Allard model (JCA) is chosen as the objective model with correlation effects generated by a secondary micro-macro semi-empirical model. To deal with this case, a relatively new sensitivity analysis method Fourier Amplitude Sensitivity Test with Correlation design (FASTC), based on Iman's transform, is taken into application. This method requires a priori information such as variables' marginal distribution functions and their correlation matrix. The results are compared to the Correlation Ratio Method (CRM) for reference and validation. The distribution of the macroscopic variables arising from the microstructure, as well as their correlation matrix are studied. Finally the results of tests shows that the correlation has a very important impact on the results of sensitivity analysis. Assessment of correlation strength among input variables on the sensitivity analysis is also achieved.

Exciton transport in the PE545 complex: insight from atomistic QM/MM-based quantum master equations and elastic network models

NASA Astrophysics Data System (ADS)

Pouyandeh, Sima; Iubini, Stefano; Jurinovich, Sandro; Omar, Yasser; Mennucci, Benedetta; Piazza, Francesco

2017-12-01

In this paper, we work out a parameterization of environmental noise within the Haken-Strobl-Reinenker (HSR) model for the PE545 light-harvesting complex, based on atomic-level quantum mechanics/molecular mechanics (QM/MM) simulations. We use this approach to investigate the role of various auto- and cross-correlations in the HSR noise tensor, confirming that site-energy autocorrelations (pure dephasing) terms dominate the noise-induced exciton mobility enhancement, followed by site energy-coupling cross-correlations for specific triplets of pigments. Interestingly, several cross-correlations of the latter kind, together with coupling-coupling cross-correlations, display clear low-frequency signatures in their spectral densities in the 30-70 cm-1 region. These slow components lie at the limits of validity of the HSR approach, which requires that environmental fluctuations be faster than typical exciton transfer time scales. We show that a simple coarse-grained elastic-network-model (ENM) analysis of the PE545 protein naturally spotlights collective normal modes in this frequency range that represent specific concerted motions of the subnetwork of cysteines covalenty linked to the pigments. This analysis strongly suggests that protein scaffolds in light-harvesting complexes are able to express specific collective, low-frequency normal modes providing a fold-rooted blueprint of exciton transport pathways. We speculate that ENM-based mixed quantum classical methods, such as Ehrenfest dynamics, might be promising tools to disentangle the fundamental designing principles of these dynamical processes in natural and artificial light-harvesting structures.

Phenetic Comparison of Prokaryotic Genomes Using k-mers

PubMed Central

Déraspe, Maxime; Raymond, Frédéric; Boisvert, Sébastien; Culley, Alexander; Roy, Paul H.; Laviolette, François; Corbeil, Jacques

2017-01-01

Abstract Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets. PMID:28957508

Damage detection of structures with detrended fluctuation and detrended cross-correlation analyses

NASA Astrophysics Data System (ADS)

Lin, Tzu-Kang; Fajri, Haikal

2017-03-01

Recently, fractal analysis has shown its potential for damage detection and assessment in fields such as biomedical and mechanical engineering. For its practicability in interpreting irregular, complex, and disordered phenomena, a structural health monitoring (SHM) system based on detrended fluctuation analysis (DFA) and detrended cross-correlation analysis (DCCA) is proposed. First, damage conditions can be swiftly detected by evaluating ambient vibration signals measured from a structure through DFA. Damage locations can then be determined by analyzing the cross correlation of signals of different floors by applying DCCA. A damage index is also proposed based on multi-scale DCCA curves to improve the damage location accuracy. To verify the performance of the proposed SHM system, a four-story numerical model was used to simulate various damage conditions with different noise levels. Furthermore, an experimental verification was conducted on a seven-story benchmark structure to assess the potential damage. The results revealed that the DFA method could detect the damage conditions satisfactorily, and damage locations can be identified through the DCCA method with an accuracy of 75%. Moreover, damage locations can be correctly assessed by the damage index method with an improved accuracy of 87.5%. The proposed SHM system has promising application in practical implementations.

In situ Investigation of Magnetism in Metastable Phases of Levitated Fe 83 B 17 During Solidification

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

Quirinale, D. G.; Messina, D.; Rustan, G. E.

In situ measurements of structure, density, and magnetization on samples of Fe 83 B 17 using an electrostatic levitation furnace allow us to identify and correlate the magnetic and structural transitions in this system during its complex solidification process. In particular, we identify magnetic ordering in the metastable Fe 23 B 6 / fcc Fe coherently grown structures and primitive tetragonal Fe 3 B metastable phase in addition to characterizing the equilibrium Fe 2 B phase. Our measurements demonstrate that the incorporation of a tunnel-diode oscillator circuit within an electrostatic levitation furnace enables investigations of the physical properties of high-temperaturemore » metastable structures.« less

Structure of turbulent non-premixed flames modeled with two-step chemistry

NASA Technical Reports Server (NTRS)

Chen, J. H.; Mahalingam, S.; Puri, I. K.; Vervisch, L.

1992-01-01

Direct numerical simulations of turbulent diffusion flames modeled with finite-rate, two-step chemistry, A + B yields I, A + I yields P, were carried out. A detailed analysis of the turbulent flame structure reveals the complex nature of the penetration of various reactive species across two reaction zones in mixture fraction space. Due to this two zone structure, these flames were found to be robust, resisting extinction over the parameter ranges investigated. As in single-step computations, mixture fraction dissipation rate and the mixture fraction were found to be statistically correlated. Simulations involving unequal molecular diffusivities suggest that the small scale mixing process and, hence, the turbulent flame structure is sensitive to the Schmidt number.

Illustrating Catalysis with Interlocking Building Blocks: Correlation between Structure of a Metallocene Catalyst and the Stereoregularity of Polypropylene

ERIC Educational Resources Information Center

Horikoshi, Ryo; Kobayashi, Yoji; Kageyama, Hiroshi

2013-01-01

Catalysis with transition-metal complexes is a part of the inorganic chemistry curriculum and a challenging topic for upper-level undergraduate and graduate students. A hands-on teaching aid has been developed for use during conventional lectures to help students understand these catalytic reactions. A unique method of illustrating the…

Evolution of opto-electronic properties during film formation of complex semiconductors

NASA Astrophysics Data System (ADS)

Heinemann, M. D.; Mainz, R.; Österle, F.; Rodriguez-Alvarez, H.; Greiner, D.; Kaufmann, C. A.; Unold, T.

2017-04-01

Optical and electrical properties of complex semiconducting alloys like Cu(In,Ga)Se2 (CIGS) are strongly influenced by the reaction pathways occurring during their deposition process. This makes it desirable to observe and control these properties in real-time during the deposition. Here we show for the first time the evolution of the band gap and the sub-band-gap defect absorption of CIGS thin film as well as surface roughness during a three-stage co-evaporation process by means of an optical analysis technique, based on white light reflectometry (WLR). By simultaneously recording structural information with in-situ energy dispersive X-ray diffraction and X-ray fluorescence we can directly correlate the evolution of opto-electronic material parameters with the structural properties of the film during growth. We find that the surface roughness and the sub-gap light absorption can be correlated with the phase evolution during the transformation from (In,Ga)2Se3 to Cu(In,Ga)Se2 by the incorporation of Cu into the film. Sub-bandgap light absorption is found to be influenced by the Cu-saturated growth phase and is lowered close to the points of stoichiometry, allowing for an advanced process design.

Perspective: Two-dimensional resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Molesky, Brian P.; Guo, Zhenkun; Cheshire, Thomas P.; Moran, Andrew M.

2016-11-01

Two-dimensional resonance Raman (2DRR) spectroscopy has been developed for studies of photochemical reaction mechanisms and structural heterogeneity in complex systems. The 2DRR method can leverage electronic resonance enhancement to selectively probe chromophores embedded in complex environments (e.g., a cofactor in a protein). In addition, correlations between the two dimensions of the 2DRR spectrum reveal information that is not available in traditional Raman techniques. For example, distributions of reactant and product geometries can be correlated in systems that undergo chemical reactions on the femtosecond time scale. Structural heterogeneity in an ensemble may also be reflected in the 2D spectroscopic line shapes of both reactive and non-reactive systems. In this perspective article, these capabilities of 2DRR spectroscopy are discussed in the context of recent applications to the photodissociation reactions of triiodide and myoglobin. We also address key differences between the signal generation mechanisms for 2DRR and off-resonant 2D Raman spectroscopies. Most notably, it has been shown that these two techniques are subject to a tradeoff between sensitivity to anharmonicity and susceptibility to artifacts. Overall, recent experimental developments and applications of the 2DRR method suggest great potential for the future of the technique.

Chromatin ionic atmosphere analyzed by a mesoscale electrostatic approach.

PubMed

Gan, Hin Hark; Schlick, Tamar

2010-10-20

Characterizing the ionic distribution around chromatin is important for understanding the electrostatic forces governing chromatin structure and function. Here we develop an electrostatic model to handle multivalent ions and compute the ionic distribution around a mesoscale chromatin model as a function of conformation, number of nucleosome cores, and ionic strength and species using Poisson-Boltzmann theory. This approach enables us to visualize and measure the complex patterns of counterion condensation around chromatin by examining ionic densities, free energies, shielding charges, and correlations of shielding charges around the nucleosome core and various oligonucleosome conformations. We show that: counterions, especially divalent cations, predominantly condense around the nucleosomal and linker DNA, unburied regions of histone tails, and exposed chromatin surfaces; ionic screening is sensitively influenced by local and global conformations, with a wide ranging net nucleosome core screening charge (56-100e); and screening charge correlations reveal conformational flexibility and interactions among chromatin subunits, especially between the histone tails and parental nucleosome cores. These results provide complementary and detailed views of ionic effects on chromatin structure for modest computational resources. The electrostatic model developed here is applicable to other coarse-grained macromolecular complexes. Copyright © 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Molecular dynamics simulation of trp-repressor/operator complex: analysis of hydrogen bond patterns of protein DNA interaction

NASA Astrophysics Data System (ADS)

Suenaga, A.; Yatsu, C.; Komeiji, Y.; Uebayasi, M.; Meguro, T.; Yamato, I.

2000-08-01

Molecular dynamics simulation of Escherichia colitrp-repressor/operator complex was performed to elucidate protein-DNA interactions in solution for 800 ps on special-purpose computer MD-GRAPE. The Ewald summation method was employed to treat the electrostatic interaction without cutoff. DNA kept stable conformation in comparison with the result of the conventional cutoff method. Thus, the trajectories obtained were used to analyze the protein-DNA interaction and to understand the role of dynamics of water molecules forming sequence specific recognition interface. The dynamical cross-correlation map showed a significant positive correlation between the helix-turn-helix DNA-binding motifs and the major grooves of operator DNA. The extensive contact surface was stable during the simulation. Most of the contacts consisted of direct interactions between phosphates of DNA and the protein, but several water-mediated polar contacts were also observed. These water-mediated interactions, which were also seen in the crystal structure (Z. Otwinowski, et al., Nature, 335 (1998) 321) emerged spontaneously from the randomized initial configuration of the solvent. This result suggests the importance of the water-mediated interaction in specific recognition of DNA by the trp-repressor, consistent with X-ray structural information.

Peptide-dependent Conformational Fluctuation Determines the Stability of the Human Leukocyte Antigen Class I Complex*

PubMed Central

Yanaka, Saeko; Ueno, Takamasa; Shi, Yi; Qi, Jianxun; Gao, George F.; Tsumoto, Kouhei; Sugase, Kenji

2014-01-01

In immune-mediated control of pathogens, human leukocyte antigen (HLA) class I presents various antigenic peptides to CD8+ T-cells. Long-lived peptide presentation is important for efficient antigen-specific T-cell activation. Presentation time depends on the peptide sequence and the stability of the peptide-HLA complex (pHLA). However, the determinant of peptide-dependent pHLA stability remains elusive. Here, to reveal the pHLA stabilization mechanism, we examined the crystal structures of an HLA class I allomorph in complex with HIV-derived peptides and evaluated site-specific conformational fluctuations using NMR. Although the crystal structures of various pHLAs were almost identical independent of the peptides, fluctuation analyses identified a peptide-dependent minor state that would be more tightly packed toward the peptide. The minor population correlated well with the thermostability and cell surface presentation of pHLA, indicating that this newly identified minor state is important for stabilizing the pHLA and facilitating T-cell recognition. PMID:25028510

Flies and humans share a motion estimation strategy that exploits natural scene statistics

PubMed Central

Clark, Damon A.; Fitzgerald, James E.; Ales, Justin M.; Gohl, Daryl M.; Silies, Marion A.; Norcia, Anthony M.; Clandinin, Thomas R.

2014-01-01

Sighted animals extract motion information from visual scenes by processing spatiotemporal patterns of light falling on the retina. The dominant models for motion estimation exploit intensity correlations only between pairs of points in space and time. Moving natural scenes, however, contain more complex correlations. Here we show that fly and human visual systems encode the combined direction and contrast polarity of moving edges using triple correlations that enhance motion estimation in natural environments. Both species extract triple correlations with neural substrates tuned for light or dark edges, and sensitivity to specific triple correlations is retained even as light and dark edge motion signals are combined. Thus, both species separately process light and dark image contrasts to capture motion signatures that can improve estimation accuracy. This striking convergence argues that statistical structures in natural scenes have profoundly affected visual processing, driving a common computational strategy over 500 million years of evolution. PMID:24390225

Learning Bayesian Networks from Correlated Data

NASA Astrophysics Data System (ADS)

Bae, Harold; Monti, Stefano; Montano, Monty; Steinberg, Martin H.; Perls, Thomas T.; Sebastiani, Paola

2016-05-01

Bayesian networks are probabilistic models that represent complex distributions in a modular way and have become very popular in many fields. There are many methods to build Bayesian networks from a random sample of independent and identically distributed observations. However, many observational studies are designed using some form of clustered sampling that introduces correlations between observations within the same cluster and ignoring this correlation typically inflates the rate of false positive associations. We describe a novel parameterization of Bayesian networks that uses random effects to model the correlation within sample units and can be used for structure and parameter learning from correlated data without inflating the Type I error rate. We compare different learning metrics using simulations and illustrate the method in two real examples: an analysis of genetic and non-genetic factors associated with human longevity from a family-based study, and an example of risk factors for complications of sickle cell anemia from a longitudinal study with repeated measures.

Complex polarization-phase and spatial-frequency selections of laser images of blood-plasma films in diagnostics of changes in their polycrystalline structure

NASA Astrophysics Data System (ADS)

Ushenko, Yu. A.; Angelskii, P. O.; Dubolazov, A. V.; Karachevtsev, A. O.; Sidor, M. I.; Mintser, O. P.; Oleinichenko, B. P.; Bizer, L. I.

2013-10-01

We present a theoretical formalism of correlation phase analysis of laser images of human blood plasma with spatial-frequency selection of manifestations of mechanisms of linear and circular birefringence of albumin and globulin polycrystalline networks. Comparative results of the measurement of coordinate distributions of the correlation parameter—the modulus of the degree of local correlation of amplitudes—of laser images of blood plasma taken from patients of three groups—healthy patients (donors), rheumatoid-arthritis patients, and breast-cancer patients—are presented. We investigate values and ranges of change of statistical (the first to fourth statistical moments), correlation (excess of autocorrelation functions), and fractal (slopes of approximating curves and dispersion of extrema of logarithmic dependences of power spectra) parameters of coordinate distributions of the degree of local correlation of amplitudes. Objective criteria for diagnostics of occurrence and differentiation of inflammatory and oncological states are determined.

Structural studies of FIV and HIV-1 proteases complexed with an efficient inhibitor of FIV protease.

PubMed

Li, M; Morris, G M; Lee, T; Laco, G S; Wong, C H; Olson, A J; Elder, J H; Wlodawer, A; Gustchina, A

2000-01-01

Three forms of feline immunodeficiency virus protease (FIV PR), the wild type (wt) and two single point mutants, V59I and Q99V, as well as human immunodeficiency virus type 1 protease (HIV-1 PR), were cocrystallized with the C2-symmetric inhibitor, TL-3. The mutants of FIV PR were designed to replace residues involved in enzyme-ligand interactions by the corresponding HIV-1 PR residues at the structurally equivalent position. TL-3 shows decreased (improved) inhibition constants with these FIV PR mutants relative to wt FIV PR. Despite similar modes of binding of the inhibitor to all PRs (from P3 to P3'), small differences are evident in the conformation of the Phe side chains of TL-3 at the P1 and P1' positions in the complexes with the mutated FIV PRs. The differences mimick the observed binding of TL-3 in HIV-1 PR and correlate with a significant improvement in the inhibition constants of TL-3 with the two mutant FIV PRs. Large differences between the HIV-1 and FIV PR complexes are evident in the binding modes of the carboxybenzyl groups of TL-3 at P4 and P4'. In HIV-1 PR:TL-3, these groups bind over the flap region, whereas in the FIV PR complexes, the rings are located along the major axis of the active site. A significant difference in the location of the flaps in this region of the HIV-1 and FIV PRs correlates with the observed conformational changes in the binding mode of the peptidomimetic inhibitor at the P4 and P4' positions. These findings provide a structural explanation of the observed Ki values for TL-3 with the different PRs and will further assist in the development of improved inhibitors.

Distance descending ordering method: An O(n) algorithm for inverting the mass matrix in simulation of macromolecules with long branches

NASA Astrophysics Data System (ADS)

Xu, Xiankun; Li, Peiwen

2017-11-01

Fixman's work in 1974 and the follow-up studies have developed a method that can factorize the inverse of mass matrix into an arithmetic combination of three sparse matrices-one of them is positive definite and needs to be further factorized by using the Cholesky decomposition or similar methods. When the molecule subjected to study is of serial chain structure, this method can achieve O (n) time complexity. However, for molecules with long branches, Cholesky decomposition about the corresponding positive definite matrix will introduce massive fill-in due to its nonzero structure. Although there are several methods can be used to reduce the number of fill-in, none of them could strictly guarantee for zero fill-in for all molecules according to our test, and thus cannot obtain O (n) time complexity by using these traditional methods. In this paper we present a new method that can guarantee for no fill-in in doing the Cholesky decomposition, which was developed based on the correlations between the mass matrix and the geometrical structure of molecules. As a result, the inverting of mass matrix will remain the O (n) time complexity, no matter the molecule structure has long branches or not.

Hydration of nucleic acid fragments: comparison of theory and experiment for high-resolution crystal structures of RNA, DNA, and DNA-drug complexes.

PubMed Central

Hummer, G; García, A E; Soumpasis, D M

1995-01-01

A computationally efficient method to describe the organization of water around solvated biomolecules is presented. It is based on a statistical mechanical expression for the water-density distribution in terms of particle correlation functions. The method is applied to analyze the hydration of small nucleic acid molecules in the crystal environment, for which high-resolution x-ray crystal structures have been reported. Results for RNA [r(ApU).r(ApU)] and DNA [d(CpG).d(CpG) in Z form and with parallel strand orientation] and for DNA-drug complexes [d(CpG).d(CpG) with the drug proflavine intercalated] are described. A detailed comparison of theoretical and experimental data shows positional agreement for the experimentally observed water sites. The presented method can be used for refinement of the water structure in x-ray crystallography, hydration analysis of nuclear magnetic resonance structures, and theoretical modeling of biological macromolecules such as molecular docking studies. The speed of the computations allows hydration analyses of molecules of almost arbitrary size (tRNA, protein-nucleic acid complexes, etc.) in the crystal environment and in aqueous solution. Images FIGURE 1 FIGURE 2 FIGURE 5 FIGURE 6 FIGURE 9 FIGURE 12 FIGURE 13 PMID:7542034

Gray matter volume of the anterior insular cortex and social networking.

PubMed

Spagna, Alfredo; Dufford, Alexander J; Wu, Qiong; Wu, Tingting; Zheng, Weihao; Coons, Edgar E; Hof, Patrick R; Hu, Bin; Wu, Yanhong; Fan, Jin

2018-05-01

In human life, social context requires the engagement in complex interactions among individuals as the dynamics of social networks. The evolution of the brain as the neurological basis of the mind must be crucial in supporting social networking. Although the relationship between social networking and the amygdala, a small but core region for emotion processing, has been reported, other structures supporting sophisticated social interactions must be involved and need to be identified. In this study, we examined the relationship between morphology of the anterior insular cortex (AIC), a structure involved in basic and high-level cognition, and social networking. Two independent cohorts of individuals (New York group n = 50, Beijing group n = 100) were recruited. Structural magnetic resonance images were acquired and the social network index (SNI), a composite measure summarizing an individual's network diversity, size, and complexity, was measured. The association between morphological features of the AIC, in addition to amygdala, and the SNI was examined. Positive correlations between the measures of the volume as well as sulcal depth of the AIC and the SNI were found in both groups, while a significant positive correlation between the volume of the amygdala and the SNI was only found in the New York group. The converging results from the two groups suggest that the AIC supports network-level social interactions. © 2018 Wiley Periodicals, Inc.

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

PubMed Central

Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

2016-01-01

Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

A new theoretical approach to analyze complex processes in cytoskeleton proteins.

PubMed

Li, Xin; Kolomeisky, Anatoly B

2014-03-20

Cytoskeleton proteins are filament structures that support a large number of important biological processes. These dynamic biopolymers exist in nonequilibrium conditions stimulated by hydrolysis chemical reactions in their monomers. Current theoretical methods provide a comprehensive picture of biochemical and biophysical processes in cytoskeleton proteins. However, the description is only qualitative under biologically relevant conditions because utilized theoretical mean-field models neglect correlations. We develop a new theoretical method to describe dynamic processes in cytoskeleton proteins that takes into account spatial correlations in the chemical composition of these biopolymers. Our approach is based on analysis of probabilities of different clusters of subunits. It allows us to obtain exact analytical expressions for a variety of dynamic properties of cytoskeleton filaments. By comparing theoretical predictions with Monte Carlo computer simulations, it is shown that our method provides a fully quantitative description of complex dynamic phenomena in cytoskeleton proteins under all conditions.

Fractal dimension analysis of complexity in Ligeti piano pieces

NASA Astrophysics Data System (ADS)

Bader, Rolf

2005-04-01

Fractal correlation dimensional analysis has been performed with whole solo piano pieces by Gyrgy Ligeti at every 50ms interval of the pieces. The resulting curves of development of complexity represented by the fractal dimension showed up a very reasonable correlation with the perceptional density of events during these pieces. The seventh piece of Ligeti's ``Musica ricercata'' was used as a test case. Here, each new part of the piece was followed by an increase of the fractal dimension because of the increase of information at the part changes. The second piece ``Galamb borong,'' number seven of the piano Etudes was used, because Ligeti wrote these Etudes after studying fractal geometry. Although the piece is not fractal in the strict mathematical sense, the overall structure of the psychoacoustic event-density as well as the detailed event development is represented by the fractal dimension plot.

Spatial-frequency Fourier polarimetry of the complex degree of mutual anisotropy of linear and circular birefringence in the diagnostics of oncological changes in morphological structure of biological tissues

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

Ushenko, Yu A; Gorskii, M P; Dubolazov, A V

2012-08-31

Theory of polarisation-correlation analysis of laser images of histological sections of biopsy material from cervix tissue based on spatial frequency selection of linear and circular birefringence mechanisms is formulated. Comparative results of measuring the coordinate distributions of the complex degree of mutual anisotropy (CDMA), produced by fibrillar networks formed by myosin and collagen fibres of cervix tissue in different pathological conditions, namely, pre-cancer (dysplasia) and cancer (adenocarcinoma), are presented. The values and variation ranges of statistical (moments of the first - fourth order), correlation (excess-autocorrelation functions), and fractal (slopes of approximating curves and dispersion of extrema of logarithmic dependences ofmore » power spectra) parameters of the CDMA coordinate distributions are studied. Objective criteria for pathology diagnostics and differentiation of its severity degree are determined. (image processing)« less

Spatial-frequency Fourier polarimetry of the complex degree of mutual anisotropy of linear and circular birefringence in the diagnostics of oncological changes in morphological structure of biological tissues

NASA Astrophysics Data System (ADS)

Ushenko, Yu A.; Gorskii, M. P.; Dubolazov, A. V.; Motrich, A. V.; Ushenko, V. A.; Sidor, M. I.

2012-08-01

Theory of polarisation-correlation analysis of laser images of histological sections of biopsy material from cervix tissue based on spatial frequency selection of linear and circular birefringence mechanisms is formulated. Comparative results of measuring the coordinate distributions of the complex degree of mutual anisotropy (CDMA), produced by fibrillar networks formed by myosin and collagen fibres of cervix tissue in different pathological conditions, namely, pre-cancer (dysplasia) and cancer (adenocarcinoma), are presented. The values and variation ranges of statistical (moments of the first — fourth order), correlation (excess-autocorrelation functions), and fractal (slopes of approximating curves and dispersion of extrema of logarithmic dependences of power spectra) parameters of the CDMA coordinate distributions are studied. Objective criteria for pathology diagnostics and differentiation of its severity degree are determined.

Ion specific correlations in bulk and at biointerfaces.

PubMed

Kalcher, I; Horinek, D; Netz, R R; Dzubiella, J

2009-10-21

Ion specific effects are ubiquitous in any complex colloidal or biological fluid in bulk or at interfaces. The molecular origins of these 'Hofmeister effects' are not well understood and their theoretical description poses a formidable challenge to the modeling and simulation community. On the basis of the combination of atomistically resolved molecular dynamics (MD) computer simulations and statistical mechanics approaches, we present a few selected examples of specific electrolyte effects in bulk, at simple neutral and charged interfaces, and on a short α-helical peptide. The structural complexity in these strongly Coulomb-correlated systems is highlighted and analyzed in the light of available experimental data. While in general the comparison of MD simulations to experiments often lacks quantitative agreement, mostly because molecular force fields and coarse-graining procedures remain to be optimized, the consensus as regards trends provides important insights into microscopic hydration and binding mechanisms.

Spectrally formulated user-defined element in Abaqus for wave motion analysis and health monitoring of composite structures

NASA Astrophysics Data System (ADS)

Khalili, Ashkan

Wave propagation analysis in 1-D and 2-D composite structures is performed efficiently and accurately through the formulation of a User-Defined Element (UEL) based on the wavelet spectral finite element (WSFE) method. The WSFE method is based on the first order shear deformation theory which yields accurate results for wave motion at high frequencies. The wave equations are reduced to ordinary differential equations using Daubechies compactly supported, orthonormal, wavelet scaling functions for approximations in time and one spatial dimension. The 1-D and 2-D WSFE models are highly efficient computationally and provide a direct relationship between system input and output in the frequency domain. The UEL is formulated and implemented in Abaqus for wave propagation analysis in composite structures with complexities. Frequency domain formulation of WSFE leads to complex valued parameters, which are decoupled into real and imaginary parts and presented to Abaqus as real values. The final solution is obtained by forming a complex value using the real number solutions given by Abaqus. Several numerical examples are presented here for 1-D and 2-D composite waveguides. Wave motions predicted by the developed UEL correlate very well with Abaqus simulations using shear flexible elements. The results also show that the UEL largely retains computational efficiency of the WSFE method and extends its ability to model complex features. An enhanced cross-correlation method (ECCM) is developed in order to accurately predict damage location in plates. Three major modifications are proposed to the widely used cross-correlation method (CCM) to improve damage localization capabilities, namely actuator-sensor configuration, signal pre-processing method, and signal post-processing method. The ECCM is investigated numerically (FEM simulation) and experimentally. Experimental investigations for damage detection employ a PZT transducer as actuator and laser Doppler vibrometer as sensor. Both numerical and experimental results show that the developed method is capable of damage localization with high precision. Further, ECCM is used to detect and localize debonding in a composite material skin-stiffener joint. The UEL is used to represent the healthy case whereas the damaged case is simulated using Abaqus. It is shown that the ECCM successfully detects the location of the debond in the skin-stiffener joint.

Correlation effect and magnetic moments in Cr2Te3

NASA Astrophysics Data System (ADS)

Youn, S. J.; Kwon, S. K.; Min, B. I.

2007-05-01

The electronic and magnetic structures of Cr2Te3 have been studied theoretically using the linearized muffin-tin orbitals band method. Experimental photoemission spectra and magnetic moments can be described better when the on-site Coulomb correlation U of Cr 3d electrons is considered using the local spin-density approximation+U method. The proper size of U is found to be U ˜1.7eV. The complex magnetic behaviors of Cr2Te3 come from the degeneracy of parallel and antiparallel alignments of CrI spin to CrII and CrIII spins.

Transport Properties of Complex Oxides: New Ideas and Insights from Theory and Simulation

NASA Astrophysics Data System (ADS)

Benedek, Nicole

Complex oxides are one of the largest and most technologically important materials families. The ABO3 perovskite oxides in particular display an unparalleled variety of physical properties. The microscopic origin of these properties (how they arise from the structure of the material) is often complicated, but in many systems previous research has identified simple guidelines or `rules of thumb' that link structure and chemistry to the physics of interest. For example, the tolerance factor is a simple empirical measure that relates the composition of a perovskite to its tendency to adopt a distorted structure. First-principles calculations have shown that the tendency towards ferroelectricity increases systematically as the tolerance factor of the perovskite decreases. Can we uncover a similar set of simple guidelines to yield new insights into the ionic and thermal transport properties of perovskites? I will discuss recent research from my group on the link between crystal structure and chemistry, soft phonons and ionic transport in a family of layered perovskite oxides, the Ln2NiO4+δ Ruddlesden-Popper phases. In particular, we show how the lattice dynamical properties of these materials (their tendency to undergo certain structural distortions) can be correlated with oxide ion transport properties. Ultimately, we seek new ways to understand the microscopic origins of complex transport processes and to develop first-principles-based design rules for new materials based on our understanding.

Global industrial impact coefficient based on random walk process and inter-country input-output table

NASA Astrophysics Data System (ADS)

Xing, Lizhi; Dong, Xianlei; Guan, Jun

2017-04-01

Input-output table is very comprehensive and detailed in describing the national economic system with lots of economic relationships, which contains supply and demand information among industrial sectors. The complex network, a theory and method for measuring the structure of complex system, can describe the structural characteristics of the internal structure of the research object by measuring the structural indicators of the social and economic system, revealing the complex relationship between the inner hierarchy and the external economic function. This paper builds up GIVCN-WIOT models based on World Input-Output Database in order to depict the topological structure of Global Value Chain (GVC), and assumes the competitive advantage of nations is equal to the overall performance of its domestic sectors' impact on the GVC. Under the perspective of econophysics, Global Industrial Impact Coefficient (GIIC) is proposed to measure the national competitiveness in gaining information superiority and intermediate interests. Analysis of GIVCN-WIOT models yields several insights including the following: (1) sectors with higher Random Walk Centrality contribute more to transmitting value streams within the global economic system; (2) Half-Value Ratio can be used to measure robustness of open-economy macroeconomics in the process of globalization; (3) the positive correlation between GIIC and GDP indicates that one country's global industrial impact could reveal its international competitive advantage.

Intrinsic Multi-Scale Dynamic Behaviors of Complex Financial Systems

PubMed Central

Ouyang, Fang-Yan; Zheng, Bo; Jiang, Xiong-Fei

2015-01-01

The empirical mode decomposition is applied to analyze the intrinsic multi-scale dynamic behaviors of complex financial systems. In this approach, the time series of the price returns of each stock is decomposed into a small number of intrinsic mode functions, which represent the price motion from high frequency to low frequency. These intrinsic mode functions are then grouped into three modes, i.e., the fast mode, medium mode and slow mode. The probability distribution of returns and auto-correlation of volatilities for the fast and medium modes exhibit similar behaviors as those of the full time series, i.e., these characteristics are rather robust in multi time scale. However, the cross-correlation between individual stocks and the return-volatility correlation are time scale dependent. The structure of business sectors is mainly governed by the fast mode when returns are sampled at a couple of days, while by the medium mode when returns are sampled at dozens of days. More importantly, the leverage and anti-leverage effects are dominated by the medium mode. PMID:26427063

Wind-sea surface temperature-sea ice relationship in the Chukchi-Beaufort Seas during autumn

NASA Astrophysics Data System (ADS)

Zhang, Jing; Stegall, Steve T.; Zhang, Xiangdong

2018-03-01

Dramatic climate changes, especially the largest sea ice retreat during September and October, in the Chukchi-Beaufort Seas could be a consequence of, and further enhance, complex air-ice-sea interactions. To detect these interaction signals, statistical relationships between surface wind speed, sea surface temperature (SST), and sea ice concentration (SIC) were analyzed. The results show a negative correlation between wind speed and SIC. The relationships between wind speed and SST are complicated by the presence of sea ice, with a negative correlation over open water but a positive correlation in sea ice dominated areas. The examination of spatial structures indicates that wind speed tends to increase when approaching the ice edge from open water and the area fully covered by sea ice. The anomalous downward radiation and thermal advection, as well as their regional distribution, play important roles in shaping these relationships, though wind-driven sub-grid scale boundary layer processes may also have contributions. Considering the feedback loop involved in the wind-SST-SIC relationships, climate model experiments would be required to further untangle the underlying complex physical processes.

Correlation between ionic radii of metals and thermal decomposition of supramolecular structure of azodye complexes

NASA Astrophysics Data System (ADS)

El-Sonbati, A. Z.; Diab, M. A.; El-Bindary, A. A.; Eldesoky, A. M.; Morgan, Sh. M.

2015-01-01

An interesting azodye heterocyclic ligand of copper(II), cobalt(II), nickel(II) and uranyl(II) complexes have been synthesized by the reaction of metal salts with 5-(2,3-dimethyl-1-phenylpyrazol-5-one azo)-2-thioxo-4-thiazolidinone (HL) yields 1:1 and 1:2 (M:L) complexes depending on the reaction conditions. The elemental analysis, magnetic moments, spectral (UV-Vis, IR, 1H and 13C NMR and ESR) and thermal studies were used to characterize the isolated complexes. The molecular structures of the ligand tautomers are optimized theoretically and the quantum chemical parameters are calculated. The IR spectra showed that the ligand (HL) act as monobasic tridentate/neutral bidentate through the (sbnd Ndbnd N), enolic (Csbnd O)- and/or oxygen keto moiety groups forming a five/six-membered structures. According to intramolecular hydrogen bond leads to increasing of the complexes stability. The molar conductivities show that all the complexes are non-electrolytes. The ESR spectra indicate that the free electron is in dxy orbital. The calculated bonding parameter indicates that in-plane σ-bonding is more covalent than in-plane π-bonding. The coordination geometry is five/six-coordinated trigonal bipyramidal for complex (1) and octahedral for complexes (2-6). The value of covalency factor β12 and orbital reduction factor K accounts for the covalent nature of the complexes. The activation thermodynamic parameters are calculated using Coats-Redfern and Horowitz-Metzger methods. The synthesized ligand (HL) and its Cu(II) complexes (1, 2 and 4) are screened for their biological activity against bacterial and fungal species. The ligand (HL) showed antimicrobial activities against Escherichia coli. The ligand (HL) and its Cu(II) complexes (2 and 4) have very high antifungal activity against Penicillium italicum. The inhibitive action of ligand (HL), against the corrosion of C-steel in 2 M HCl solution has been investigated using potentiodynamic polarization and electrochemical impedance spectroscopy (EIS).

UHPC and NSFRC in Severe Environmental Conditions

NASA Astrophysics Data System (ADS)

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

2017-10-01

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

Positron annihilation spectroscopy: Applications to Si, ZnO, and multilayer semiconductor structures

NASA Astrophysics Data System (ADS)

Schaffer, J. P.; Rohatgi, A.; Dewald, A. B.; Frost, R. L.; Pang, S. K.

1989-11-01

The potential of positron annihilation spectroscopy (PAS) for defect characterization at the atomic scale in semiconductors is demonstrated for Si, ZnO, and multilayer structures, such as an AlGaAs/GaAs solar cell. The types of defects discussed include: i) vacancy complexes, oxygen impurities and dopants, ii) the influence of cooling rates on spatial non-uniformities in defects, and iii) characterization of buried interfaces. In sev-eral instances, the results of the PAS investigations are correlated with data from other established semiconductor characterization techniques.

The molecular shape and the field similarities as criteria to interpret SAR studies for fragment-based design of platinum(IV) anticancer agents. Correlation of physicochemical properties with cytotoxicity.

PubMed

Lorenzo, Julia; Montaña, Ángel M

2016-09-01

Molecular shape similarity and field similarity have been used to interpret, in a qualitative way, the structure-activity relationships in a selected series of platinum(IV) complexes with anticancer activity. MM and QM calculations have been used to estimate the electron density, electrostatic potential maps, partial charges, dipolar moments and other parameters to correlate the stereo-electronic properties with the differential biological activity of complexes. Extended Electron Distribution (XED) field similarity has been also evaluated for the free 1,4-diamino carrier ligands, in a fragment-based drug design approach, comparing Connolly solvent excluded surface, hydrophobicity field surface, Van der Waals field surface, nucleophilicity field surface, electrophilicity field surface and the extended electron-distribution maxima field points. A consistency has been found when comparing the stereo-electronic properties of the studied series of platinum(IV) complexes and/or the free ligands evaluated and their in vitro anticancer activity. Copyright © 2016 Elsevier Inc. All rights reserved.

Acoustic indices provide information on the status of coral reefs: an example from Moorea Island in the South Pacific

PubMed Central

Bertucci, Frédéric; Parmentier, Eric; Lecellier, Gaël; Hawkins, Anthony D.; Lecchini, David

2016-01-01

Different marine habitats are characterised by different soundscapes. How or which differences may be representative of the habitat characteristics and/or community structure remains however to be explored. A growing project in passive acoustics is to find a way to use soundscapes to have information on the habitat and on its changes. In this study we have successfully tested the potential of two acoustic indices, i.e. the average sound pressure level and the acoustic complexity index based on the frequency spectrum. Inside and outside marine protected areas of Moorea Island (French Polynesia), sound pressure level was positively correlated with the characteristics of the substratum and acoustic complexity was positively correlated with fish diversity. It clearly shows soundscape can be used to evaluate the acoustic features of marine protected areas, which presented a significantly higher ambient sound pressure level and were more acoustically complex than non-protected areas. This study further emphasizes the importance of acoustics as a tool in the monitoring of marine environments and in the elaboration and management of future conservation plans. PMID:27629650

Acoustic indices provide information on the status of coral reefs: an example from Moorea Island in the South Pacific.

PubMed

Bertucci, Frédéric; Parmentier, Eric; Lecellier, Gaël; Hawkins, Anthony D; Lecchini, David

2016-09-15

Different marine habitats are characterised by different soundscapes. How or which differences may be representative of the habitat characteristics and/or community structure remains however to be explored. A growing project in passive acoustics is to find a way to use soundscapes to have information on the habitat and on its changes. In this study we have successfully tested the potential of two acoustic indices, i.e. the average sound pressure level and the acoustic complexity index based on the frequency spectrum. Inside and outside marine protected areas of Moorea Island (French Polynesia), sound pressure level was positively correlated with the characteristics of the substratum and acoustic complexity was positively correlated with fish diversity. It clearly shows soundscape can be used to evaluate the acoustic features of marine protected areas, which presented a significantly higher ambient sound pressure level and were more acoustically complex than non-protected areas. This study further emphasizes the importance of acoustics as a tool in the monitoring of marine environments and in the elaboration and management of future conservation plans.

Correlating the magic numbers of inorganic nanomolecular assemblies with a {Pd84} molecular-ring Rosetta Stone

PubMed Central

Xu, Feng; Miras, Haralampos N.; Scullion, Rachel A.; Long, De-Liang; Thiel, Johannes; Cronin, Leroy

2012-01-01

Molecular self-assembly has often been suggested as the ultimate route for the bottom-up construction of building blocks atom-by-atom for functional nanotechnology, yet structural design or prediction of nanomolecular assemblies is still far from reach. Whereas nature uses complex machinery such as the ribosome, chemists use painstakingly engineered step-by-step approaches to build complex molecules but the size and complexity of such molecules, not to mention the accessible yields, can be limited. Herein we present the discovery of a palladium oxometalate {Pd84}-ring cluster 3.3 nm in diameter; [Pd84O42(OAc)28(PO4)42]70- ({Pd84} ≡ {Pd12}7) that is formed in water just by mixing two reagents at room temperature, giving crystals of the compound in just a few days. The structure of the {Pd84}-ring has sevenfold symmetry, comprises 196 building blocks, and we also show, using mass spectrometry, that a large library of other related nanostructures is present in solution. Finally, by analysis of the symmetry and the building block library that construct the {Pd84} we show that the correlation of the symmetry, subunit number, and overall cluster nuclearity can be used as a “Rosetta Stone” to rationalize the “magic numbers” defining a number of other systems. This is because the discovery of {Pd84} allows the relationship between seemingly unrelated families of molecular inorganic nanosystems to be decoded from the overall cluster magic-number nuclearity, to the symmetry and building blocks that define such structures allowing the prediction of other members of these nanocluster families. PMID:22753516

Fine structure of 25 extragalactic radio sources. [interferometric observations of quasars

NASA Technical Reports Server (NTRS)

Wittels, J. J.; Knight, C. A.; Shapiro, I. I.; Hinteregger, H. F.; Rogers, A. E. E.; Whitney, A. R.; Clark, T. A.; Hutton, L. K.; Marandino, G. E.; Niell, A. E.

1975-01-01

Interferometric observations taken at 7.8 GHz (gamma approximately = 3.8 cm) with five pairings of antennae of 25 extragalactic radio sources between April, 1972 and May, 1973 are reported. These sources exhibit a broad variety of fine structure from very simple to complex. The total flux and the correlated flux of some of the sources underwent large changes in a few weeks, while the structure and total power of others remained constant during the entire period of observation. Some aspects of the data processing and a discussion of errors are presented. Numerous figures are provided and explained. The individual radio sources are described in detail.

Relative Displacement Method for Track-Structure Interaction

PubMed Central

Ramos, Óscar Ramón; Pantaleón, Marcos J.

2014-01-01

The track-structure interaction effects are usually analysed with conventional FEM programs, where it is difficult to implement the complex track-structure connection behaviour, which is nonlinear, elastic-plastic and depends on the vertical load. The authors developed an alternative analysis method, which they call the relative displacement method. It is based on the calculation of deformation states in single DOF element models that satisfy the boundary conditions. For its solution, an iterative optimisation algorithm is used. This method can be implemented in any programming language or analysis software. A comparison with ABAQUS calculations shows a very good result correlation and compliance with the standard's specifications. PMID:24634610

GRAIL Gravity Observations of the Transition from Complex Crater to Peak-Ring Basin on the Moon: Implications for Crustal Structure and Impact Basin Formation

NASA Technical Reports Server (NTRS)

Baker, David M. H.; Head, James W.; Phillips, Roger J.; Neumann, Gregory A.; Bierson, Carver J.; Smith, David E.; Zuber, Maria T.

2017-01-01

High-resolution gravity data from the Gravity Recovery and Interior Laboratory (GRAIL) mission provide the opportunity to analyze the detailed gravity and crustal structure of impact features in the morphological transition from complex craters to peak-ring basins on the Moon. We calculate average radial profiles for free-air anomalies and Bouguer anomalies for peak-ring basins, proto-basins, and the largest complex craters. Complex craters and proto-basins have free-air anomalies that are positively correlated with surface topography, unlike the prominent lunar mascons (positive free-air anomalies in areas of low elevation) associated with large basins. The Bouguer gravity anomaly profiles of complex craters are highly irregular, with central positive anomalies that are generally absent or not clearly tied to interior morphology. In contrast, gravity profiles for peak-ring basins (approx. 200 km to 580 km) are much more regular and are highly correlated with surface morphology. A central positive Bouguer anomaly is confined within the peak ring and a negative Bouguer anomaly annulus extends from the edge of the positive anomaly outward to about the rim crest. A number of degraded basins lacking interior peak rings have diameters and gravity patterns similar to those of well-preserved peak-ring basins. If these structures represent degraded peak-ring basins, the number of peak-ring basins on the Moon would increase by more than a factor of two to 34. The gravity anomalies within basins are interpreted to be due to uplift of the mantle confined within the peak ring and an annulus of thickened crust between the peak ring and rim crest. We hypothesize that mantle uplift is influenced by interaction between the transient cavity and the mantle. Further, mascon formation is generally disconnected from the number of basin rings formed and occurs over a wide range of basin sizes. These observations have important implications for models of basin and mascon formation on the Moon and other planetary bodies.

Relative and combined effects of habitat and fishing on reef fish communities across a limited fishing gradient at Ningaloo.

PubMed

Wilson, Shaun K; Babcock, Russ C; Fisher, Rebecca; Holmes, Thomas H; Moore, James A Y; Thomson, Damian P

2012-10-01

Habitat degradation and fishing are major drivers of temporal and spatial changes in fish communities. The independent effects of these drivers are well documented, but the relative importance and interaction between fishing and habitat shifts is poorly understood, particularly in complex systems such as coral reefs. To assess the combined and relative effects of fishing and habitat we examined the composition of fish communities on patch reefs across a gradient of high to low structural complexity in fished and unfished areas of the Ningaloo Marine Park, Western Australia. Biomass and species richness of fish were positively correlated with structural complexity of reefs and negatively related to macroalgal cover. Total abundance of fish was also positively related to structural complexity, however this relationship was stronger on fished reefs than those where fishing is prohibited. The interaction between habitat condition and fishing pressure is primarily due to the high abundance of small bodied planktivorous fish on fished reefs. However, the influence of management zones on the abundance and biomass of predators and target species is small, implying spatial differences in fishing pressure are low and unlikely to be driving this interaction. Our results emphasise the importance of habitat in structuring reef fish communities on coral reefs especially when gradients in fishing pressure are low. The influence of fishing effort on this relationship may however become more important as fishing pressure increases. Copyright © 2012 Elsevier Ltd. All rights reserved.

Hybrid scatterometry measurement for BEOL process control

NASA Astrophysics Data System (ADS)

Timoney, Padraig; Vaid, Alok; Kang, Byeong Cheol; Liu, Haibo; Isbester, Paul; Cheng, Marjorie; Ng-Emans, Susan; Yellai, Naren; Sendelbach, Matt; Koret, Roy; Gedalia, Oram

2017-03-01

Scaling of interconnect design rules in advanced nodes has been accompanied by a reducing metrology budget for BEOL process control. Traditional inline optical metrology measurements of BEOL processes rely on 1-dimensional (1D) film pads to characterize film thickness. Such pads are designed on the assumption that solid copper blocks from previous metallization layers prevent any light from penetrating through the copper, thus simplifying the effective film stack for the 1D optical model. However, the reduction of the copper thickness in each metallization layer and CMP dishing effects within the pad, have introduced undesired noise in the measurement. To resolve this challenge and to measure structures that are more representative of product, scatterometry has been proposed as an alternative measurement. Scatterometry is a diffraction based optical measurement technique using Rigorous Coupled Wave Analysis (RCWA), where light diffracted from a periodic structure is used to characterize the profile. Scatterometry measurements on 3D structures have been shown to demonstrate strong correlation to electrical resistance parameters for BEOL Etch and CMP processes. However, there is significant modeling complexity in such 3D scatterometry models, in particlar due to complexity of front-end-of-line (FEOL) and middle-of-line (MOL) structures. The accompanying measurement noise associated with such structures can contribute significant measurement error. To address the measurement noise of the 3D structures and the impact of incoming process variation, a hybrid scatterometry technique is proposed that utilizes key information from the structure to significantly reduce the measurement uncertainty of the scatterometry measurement. Hybrid metrology combines measurements from two or more metrology techniques to enable or improve the measurement of a critical parameter. In this work, the hybrid scatterometry technique is evaluated for 7nm and 14nm node BEOL measurements of interlayer dielectric (ILD) thickness, hard mask thickness and dielectric trench etch in complex 3D structures. The data obtained from the hybrid scatterometry technique demonstrates stable measurement precision, improved within wafer and wafer to wafer range, robustness in cases where 3D scatterometry measurements incur undesired shifts in the measurements, accuracy as compared to TEM and correlation to process deposition time. Process capability indicator comparisons also demonstrate improvement as compared to conventional scatterometry measurements. The results validate the suitability of the method for monitoring of production BEOL processes.

A Biomimetic Structural Health Monitoring Approach Using Carbon Nanotubes

NASA Astrophysics Data System (ADS)

Liu, Yingtao; Rajadas, Abhishek; Chattopadhyay, Aditi

2012-07-01

A self-sensing nanocomposite material has been developed to track the presence of damage in complex composite structures. Multiwalled carbon nanotubes are integrated with polymer matrix to develop a novel bonding material with sensing capabilities. The changes of the piezoresistance in the presence of damage are used to monitor the condition of bonded joints, where the usual bonding material is replaced by the self-sensing nanocomposite. The feasibility of this concept is investigated through experiments conducted on single-lap joints subject to monotonic tensile loading conditions. The results show that the self-sensing nanocomposite is sensitive to crack propagation within the matrix material. An acoustic emission-based sensing technique has been used to validate these results and shows good correlation with damage growth. A digital image correlation system is used to measure the shear strain field in the joint area.

Complex path flows in geological media imaged by X-Ray computed tomography

NASA Astrophysics Data System (ADS)

Neuville, Amélie; Ebner, Marcus; Toussaint, Renaud; Renard, François; Koehn, Daniel; Flekkøy, Eirik; Cochard, Alain

2013-04-01

Stylolites as well as fractures are reported as major conduits in geological media (1, 2). The flow circulation has a strong influence on hydro-mecanico-chemical processes, in particular on crystallization and dissolution (3, 4). For instance hydrothermal ore deposits are frequently located in stylolites and fractures at depth. The fluid pressure also intervenes as a thermodynamic parameter in chemical reactions, and is in addition responsible for elastic deformations of the medium. Using tridimensional numerical simulations, we aim at better characterizing the flow circulation in complex structures, and at investigating on how the flow modifies the geological medium. First, X-Ray computed tomography scans of a complete stylolite structure (i.e. calcareous matrix, clay layering in the aperture, and the very thin aperture itself), and that of a fractured sandstone sample were performed. Then, image processing is required in order to extract the geometry of the porous medium of each sample. The geometries are actually more complicated than that of classical fractures, because of the existence of non connected -- or barely connected -- void spaces. We report on the influence of this image processing on the aperture geometry and on the computed permeability. This is addressed by first performing a numerical simulation of the tridimensional velocity field, using a coupled lattice Boltzmann method that solves the complete Navier-Stokes equation. After calculating the velocity field we then question the link between the geometry of complex stylolites and fractures, and the spatial auto-correlation of the velocity field. This correlation might indeed be important for dispersion processes. A first approach is to compute this correlation from the simulated velocity field. Another approach is to compute analytically the correlation function, from the knowledge of the aperture correlation. This is however developed in the perturbative limit of small aperture variations, that may not hold for the apertures found in stylolites. We then present the pressure field obtained within these complex structures, and give preliminary tracks on how variations of the pressure might be responsible for transformations of the medium, that affect its mechanical and transport properties. 1 A Neuville, R Toussaint, and J Schmittbuhl (2010) Hydro-thermal flows in a self-affine rough fracture. Physical Review E, 82, 036317 2 André G., C. Hibsch, S. Fourcade, M. Cathelineau and S. Buschaert (2010) Chronology of fracture sealing under a meteoric fluid environment: Microtectonic and isotopic evidence of major Cainozoic events in the eastern Paris Basin (France). Tectonophysics, 490, 214-228 3 Laronne Ben-Itzhak, L., E. Aharonov, R. Toussaint and A. Sagy (2012) Upper bound on stylolite roughness as indicator for the duration and amount of dissolution. Earth and Planetary Science Letters, 337-338, 186-196 4 Angheluta, L., J. Mathiesen, E. Aharonov (2012) Compaction of porous rock by dissolution on discrete stylolites: A one-dimensional model. Journal of Geophysical Research -- Solid Earth, 117, B08203

Signatures of correlated excitonic dynamics in two-dimensional spectroscopy of the Fenna-Matthew-Olson photosynthetic complex

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

Caram, Justin R.; Lewis, Nicholas H. C.; Fidler, Andrew F.

2012-03-14

Long-lived excitonic coherence in photosynthetic proteins has become an exciting area of research because it may provide design principles for enhancing the efficiency of energy transfer in a broad range of materials. In this publication, we provide new evidence that long-lived excitonic coherence in the Fenna-Mathew-Olson pigment-protein (FMO) complex is consistent with the assumption of cross correlation in the site basis, indicating that each site shares bath fluctuations. We analyze the structure and character of the beating crosspeak between the two lowest energy excitons in two-dimensional (2D) electronic spectra of the FMO Complex. To isolate this dynamic signature, we usemore » the two-dimensional linear prediction Z-transform as a platform for filtering coherent beating signatures within 2D spectra. By separating signals into components in frequency and decay rate representations, we are able to improve resolution and isolate specific coherences. This strategy permits analysis of the shape, position, character, and phase of these features. Simulations of the crosspeak between excitons 1 and 2 in FMO under different regimes of cross correlation verify that statistically independent site fluctuations do not account for the elongation and persistence of the dynamic crosspeak. To reproduce the experimental results, we invoke near complete correlation in the fluctuations experienced by the sites associated with excitons 1 and 2. This model contradicts ab initio quantum mechanic/molecular mechanics simulations that observe no correlation between the energies of individual sites. This contradiction suggests that a new physical model for long-lived coherence may be necessary. The data presented here details experimental results that must be reproduced for a physical model of quantum coherence in photosynthetic energy transfer.« less

[Beijing college students' self-consciousness: its level, structure and relationship with mental health].

PubMed

Fan, Zhiwei; He, Shuchang

2013-11-01

To investigate Beijing college students' self-consciousness and its relationship with mental health. Convenient samples of 928 college students from five universities in Beijing were inquired and assessed with the self-consciousness scale and the Kessler 10 psychological distress scale. Confirmatory factor analysis and structural equation modeling were used to analyze the data. College students' scores of self-consciousness did not differ in sex, age, grade and major type. 83.5% of the participants had relatively low scores (10-24) of psychological distress, but those of the students of liberal arts were higher (P < 0.05). The measurement data of self-consciousness supported Mittal and Balasubramanian' s five-factor structure. Self-reflectiveness was positively correlated with depression (P < 0.05). Internal state awareness was negatively associated with both anxiety and depression (P < 0.05). Style consciousness was positively correlated with both of them (P < 0.001). Beijing college students' self-consciousness is relatively high and has a relatively complex structure. While self-reflectiveness and style consciousness have negative effects, internal state awareness is good for mental health.

Implementation theory of distortion-invariant pattern recognition for optical and digital signal processing systems

NASA Astrophysics Data System (ADS)

Lhamon, Michael Earl

A pattern recognition system which uses complex correlation filter banks requires proportionally more computational effort than single-real valued filters. This introduces increased computation burden but also introduces a higher level of parallelism, that common computing platforms fail to identify. As a result, we consider algorithm mapping to both optical and digital processors. For digital implementation, we develop computationally efficient pattern recognition algorithms, referred to as, vector inner product operators that require less computational effort than traditional fast Fourier methods. These algorithms do not need correlation and they map readily onto parallel digital architectures, which imply new architectures for optical processors. These filters exploit circulant-symmetric matrix structures of the training set data representing a variety of distortions. By using the same mathematical basis as with the vector inner product operations, we are able to extend the capabilities of more traditional correlation filtering to what we refer to as "Super Images". These "Super Images" are used to morphologically transform a complicated input scene into a predetermined dot pattern. The orientation of the dot pattern is related to the rotational distortion of the object of interest. The optical implementation of "Super Images" yields feature reduction necessary for using other techniques, such as artificial neural networks. We propose a parallel digital signal processor architecture based on specific pattern recognition algorithms but general enough to be applicable to other similar problems. Such an architecture is classified as a data flow architecture. Instead of mapping an algorithm to an architecture, we propose mapping the DSP architecture to a class of pattern recognition algorithms. Today's optical processing systems have difficulties implementing full complex filter structures. Typically, optical systems (like the 4f correlators) are limited to phase-only implementation with lower detection performance than full complex electronic systems. Our study includes pseudo-random pixel encoding techniques for approximating full complex filtering. Optical filter bank implementation is possible and they have the advantage of time averaging the entire filter bank at real time rates. Time-averaged optical filtering is computational comparable to billions of digital operations-per-second. For this reason, we believe future trends in high speed pattern recognition will involve hybrid architectures of both optical and DSP elements.

Deformation in metallic glasses studied by synchrotron x-ray diffraction

DOE PAGES

Dmowski, Wojciech; Egami, Takeshi; Tong, Yang

2016-01-11

In this study, high mechanical strength is one of the superior properties of metallic glasses which render them promising as a structural material. However, understanding the process of mechanical deformation in strongly disordered matter, such as metallic glass, is exceedingly difficult because even an effort to describe the structure qualitatively is hampered by the absence of crystalline periodicity. In spite of such challenges, we demonstrate that high-energy synchrotron X-ray diffraction measurement under stress, using a two-dimensional detector coupled with the anisotropic pair-density function (PDF) analysis, has greatly facilitated the effort of unraveling complex atomic rearrangements involved in the elastic, anelastic,more » and plastic deformation of metallic glasses. Even though PDF only provides information on the correlation between two atoms and not on many-body correlations, which are often necessary in elucidating various properties, by using stress as means of exciting the system we can garner rich information on the nature of the atomic structure and local atomic rearrangements during deformation in glasses.« less

Design, Fabrication and Testing of a Crushable Energy Absorber for a Passive Earth Entry Vehicle

NASA Technical Reports Server (NTRS)

Kellas, Sotiris; Corliss, James M. (Technical Monitor)

2002-01-01

A conceptual study was performed to investigate the impact response of a crushable energy absorber for a passive Earth entry vehicle. The spherical energy-absorbing concept consisted of a foam-filled composite cellular structure capable of omni-directional impact-load attenuation as well as penetration resistance. Five composite cellular samples of hemispherical geometry were fabricated and tested dynamically with impact speeds varying from 30 to 42 meters per second. Theoretical crush load predictions were obtained with the aid of a generalized theory which accounts for the energy dissipated during the folding deformation of the cell-walls. Excellent correlation was obtained between theoretical predictions and experimental tests on characteristic cell-web intersections. Good correlation of theory with experiment was also found to exist for the more complex spherical cellular structures. All preliminary design requirements were met by the cellular structure concept, which exhibited a near-ideal sustained crush-load and approximately 90% crush stroke.

The nuclear contacts and short range correlations in nuclei

NASA Astrophysics Data System (ADS)

Weiss, R.; Cruz-Torres, R.; Barnea, N.; Piasetzky, E.; Hen, O.

2018-05-01

Atomic nuclei are complex strongly interacting systems and their exact theoretical description is a long-standing challenge. An approximate description of nuclei can be achieved by separating its short and long range structure. This separation of scales stands at the heart of the nuclear shell model and effective field theories that describe the long-range structure of the nucleus using a mean-field approximation. We present here an effective description of the complementary short-range structure using contact terms and stylized two-body asymptotic wave functions. The possibility to extract the nuclear contacts from experimental data is presented. Regions in the two-body momentum distribution dominated by high-momentum, close-proximity, nucleon pairs are identified and compared to experimental data. The amount of short-range correlated (SRC) nucleon pairs is determined and compared to measurements. Non-combinatorial isospin symmetry for SRC pairs is identified. The obtained one-body momentum distributions indicate dominance of SRC pairs above the nuclear Fermi-momentum.

A non-ideal MHD model for structure formation

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Sarma, Pankaj

2018-02-01

The evolutionary initiation dynamics of triggered planetary structure formation is indeed a complex process yet to be well understood. We herein develop a theoretical classical model to see the gravitational fragmentation kinetics of the viscoelastic non-ideal magneto-hydro-dynamic (MHD) fabric. The inhomogeneous planetary disk is primarily composed of heavier dust grains (strongly correlated) together with relatively lighter electrons, ions and neutrals (weakly correlated) in a mean-fluidic approximation. A normal harmonic mode analysis results in a quadratic dispersion relation of a unique shape. It is demonstrated that the growth rate of the MHD fluctuations (magnetosonic) contributing to the planet formation rate, apart from the wave vector and its projection orientation, has a pure explicit dependency on the viscoelastic parameters. The analysis specifically shows that the effective generalized viscosity (χ) , viscoelastic relaxation time (τm) , and K-orientation (θ) play as destabilizing agencies against the non-local gravitational disk collapse. The relevancy is briefly indicated in the real astronomical context of bounded planetary structure formation and evolution.

A simplified implementation of van der Waals density functionals for first-principles molecular dynamics applications

NASA Astrophysics Data System (ADS)

Wu, Jun; Gygi, François

2012-06-01

We present a simplified implementation of the non-local van der Waals correlation functional introduced by Dion et al. [Phys. Rev. Lett. 92, 246401 (2004)] and reformulated by Román-Pérez et al. [Phys. Rev. Lett. 103, 096102 (2009)]. The proposed numerical approach removes the logarithmic singularity of the kernel function. Complete expressions of the self-consistent correlation potential and of the stress tensor are given. Combined with various choices of exchange functionals, five versions of van der Waals density functionals are implemented. Applications to the computation of the interaction energy of the benzene-water complex and to the computation of the equilibrium cell parameters of the benzene crystal are presented. As an example of crystal structure calculation involving a mixture of hydrogen bonding and dispersion interactions, we compute the equilibrium structure of two polymorphs of aspirin (2-acetoxybenzoic acid, C9H8O4) in the P21/c monoclinic structure.

Structure-dependent metallokinetics of antidiabetic vanadyl-picolinate complexes in rats: studies on solution structure, insulinomimetic activity, and metallokinetics.

PubMed

Yasui, Hiroyuki; Tamura, Asuka; Takino, Toshikazu; Sakurai, Hiromu

2002-07-25

The insulinomimetic effect of vanadium is the most remarkable and important among its several biological actions. Vanadyl ion (+4 oxidation state of vanadium) and its complexes have been found to normalize the blood glucose levels of both type 1 and 2 diabetic animals. We have developed insulinomimetic vanadyl complexes having different coordination modes, emphasizing the possible usefulness of vanadyl-picolinate [VO(pa)(2)] and its related complexes with the VO(N(2)O(2)) coordination mode. In order to apply these complexes clinically in the future, the relationship between the chemical structure, insulinomimetic action, organ distribution of vanadium, and blood disposition of vanadyl species must be closely investigated. In the present investigation, we studied the blood disposition of the vanadyl-picolinate complexes in healthy rats, and tried to understand comprehensively the relationship between the structures, insulinomimetic activity, and metallokinetic parameters of the complexes, which had been recently prepared and specifically synthesized for the present study, by using an in vivo blood circulation monitoring -- electron spin resonance (BCM-ESR) method for analyzing ESR signals due to paramagnetic metal ions and complexes in the blood in real time. Metallokinetic parameters were estimated based on the blood clearance curves in terms of a two-compartment pharmacokinetic model, and vanadyl species were indicated to be distributed in peripheral tissues and gradually eliminated from the circulating blood, depending on their chemical structures. Vanadyl concentrations in the blood of rats given bis(5-iodopicolinato)oxovanadium(IV) [VO(5ipa)(2)] and bis(3-methylpicolinato)oxovanadium(IV) [VO(3mpa)(2)] with electron-withdrawing and donating groups, respectively, remained significantly higher and longer, due to their slower clearance rates from the blood, than in rats given other complexes, suggesting that the high exposure and long residence of vanadyl species bring about the high normoglyceric effect in diabetic animals. We then examined the relationship between insulinomimetic activity and metallokinetic parameters in the family of VO(pa)(2) for further development of insulinomimetic vanadyl complexes. IC(50), the 50% inhibitory concentration of the complexes on the free fatty acid release from isolated rat adipocytes treated with epinephrine, was found to be sufficiently correlated with metallokinetic parameters such as area under the concentration curve, mean residence time, total clearance, and distribution volume at steady-state. Furthermore, the in vivo antidiabetic activity of the complexes was enhanced with increasing exposure and residence of vanadyl species in the blood of animals. On the basis of these results, we concluded that in vitro insulinomimetic activity, metallokinetic character, and in vivo antidiabetic action of vanadyl-picolinate complexes are closely related to their chemical structures.