Convergent evolution of modularity in metabolic networks through different community structures

PubMed Central

2012-01-01

Background It has been reported that the modularity of metabolic networks of bacteria is closely related to the variability of their living habitats. However, given the dependency of the modularity score on the community structure, it remains unknown whether organisms achieve certain modularity via similar or different community structures. Results In this work, we studied the relationship between similarities in modularity scores and similarities in community structures of the metabolic networks of 1021 species. Both similarities are then compared against the genetic distances. We revisited the association between modularity and variability of the microbial living environments and extended the analysis to other aspects of their life style such as temperature and oxygen requirements. We also tested both topological and biological intuition of the community structures identified and investigated the extent of their conservation with respect to the taxomony. Conclusions We find that similar modularities are realized by different community structures. We find that such convergent evolution of modularity is closely associated with the number of (distinct) enzymes in the organism’s metabolome, a consequence of different life styles of the species. We find that the order of modularity is the same as the order of the number of the enzymes under the classification based on the temperature preference but not on the oxygen requirement. Besides, inspection of modularity-based communities reveals that these communities are graph-theoretically meaningful yet not reflective of specific biological functions. From an evolutionary perspective, we find that the community structures are conserved only at the level of kingdoms. Our results call for more investigation into the interplay between evolution and modularity: how evolution shapes modularity, and how modularity affects evolution (mainly in terms of fitness and evolvability). Further, our results call for exploring new

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

PubMed Central

Triplet, Thomas; Shortridge, Matthew D.; Griep, Mark A.; Stark, Jaime L.; Powers, Robert; Revesz, Peter

2010-01-01

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks. Database URL: http://cse.unl.edu/∼profess/ PMID:20624718

Planetary Origin Evolution and Structure

NASA Technical Reports Server (NTRS)

Stevenson, David J.

2005-01-01

This wide-ranging grant supported theoretical modeling on many aspects of the formation, evolution and structure of planets and satellites. Many topics were studied during this grant period, including the evolution of icy bodies; the origin of magnetic fields in Ganymede; the thermal histories of terrestrial planets; the nature of flow inside giant planets (especially the coupling to the magnetic field) and the dynamics of silicate/iron mixing during giant impacts and terrestrial planet core formation. Many of these activities are ongoing and have not reached completion. This is the nature of this kind of research.

Understanding the evolution of Mammalian brain structures; the need for a (new) cerebrotype approach.

PubMed

Willemet, Romain

2012-05-18

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular ("mosaic evolution") to coordinated changes in brain structure size ("concerted evolution") or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a "taxon cerebrotype". In other taxa, no clear pattern is found, reflecting heterogeneity of the species' lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex "space" of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution.

Structural evolution of maize stalk/char particles during pyrolysis.

PubMed

Fu, Peng; Hu, Song; Sun, Lushi; Xiang, Jun; Yang, Tao; Zhang, Anchao; Zhang, Junying

2009-10-01

The structural evolution characteristics of maize stalk/char particles during pyrolysis were investigated. The char was prepared by pyrolyzing at temperatures ranging from 200 to 900 degrees C. Maize stalk and chars were characterized by thermogravimetric analysis, ultimate analysis (TGA), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), helium density measurement and N(2) adsorption/desorption method. The char yield decreased rapidly with increasing temperature until 400 degrees C. As temperature increased, the char became progressively more aromatic and carbonaceous. The hydroxyl, aliphatic C-H, carbonyl and olefinic C=C groups were lost at high temperatures. Below 500 degrees C, the removal of volatile matter made pore opening. High temperatures led to the occurrence of softening, melting, fusing and carbon structural ordering. The aromatization process started at approximately 350 degrees C and continued to higher temperatures. The shrinkage of carbon structure occurred above 500 degrees C, which was concurrent with the aromatization process.

The concurrent evolution of cooperation and the population structures that support it.

PubMed

Powers, Simon T; Penn, Alexandra S; Watson, Richard A

2011-06-01

The evolution of cooperation often depends upon population structure, yet nearly all models of cooperation implicitly assume that this structure remains static. This is a simplifying assumption, because most organisms possess genetic traits that affect their population structure to some degree. These traits, such as a group size preference, affect the relatedness of interacting individuals and hence the opportunity for kin or group selection. We argue that models that do not explicitly consider their evolution cannot provide a satisfactory account of the origin of cooperation, because they cannot explain how the prerequisite population structures arise. Here, we consider the concurrent evolution of genetic traits that affect population structure, with those that affect social behavior. We show that not only does population structure drive social evolution, as in previous models, but that the opportunity for cooperation can in turn drive the creation of population structures that support it. This occurs through the generation of linkage disequilibrium between socio-behavioral and population-structuring traits, such that direct kin selection on social behavior creates indirect selection pressure on population structure. We illustrate our argument with a model of the concurrent evolution of group size preference and social behavior. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Evolution of groundwater chemistry along fault structures in sandstone

NASA Astrophysics Data System (ADS)

Dausse, A.; Guiheneuf, N.; Pierce, A. A.; Cherry, J. A.; Parker, B. L.

2016-12-01

Fluid-rock interaction across geological structures plays a major role on evolution of groundwater chemistry and physical properties of reservoirs. In particular, groundwater chemistry evolve on different facies according to residence times which can be linked to hydraulic properties of the geological unit. In this study, we analyze groundwater samples collected at an 11 km² site located in southern California (USA) to evaluate the evolution of groundwater chemistry according to different geological structures. Major and minor elements were sampled at the same period of time from 40 wells located along the main structures in the northeast of the site, where major NE-SW trending faults and other oriented ESE-WNW are present in sandstone Chatsworth formation. By analyzing the spatial distribution of ions concentration at the site scale, several hydrochemical compartments (main- and sub-compartments) can be distinguished and are in agreement with structural and hydrological information. In particular, as previously observed from piezometric informations, the shear zone fault serves as a barrier for groundwater flow and separates the site on two mains compartments. In addition, the analysis along major faults oriented orthogonal to this shear zone (ESE-WNW) in the eastern part of the site, shows an increase in mineralization following the hydraulic gradient. This salinization has been confirmed by ionic ratio and Gibbs plots and is attributed to fluid-rock interaction processes. In particular, groundwater chemistry seems to evolve from bicarbonate to sodium facies. Moreover, the gradient of concentrations vary depending on fault locations and can be related to their hydraulic properties and hence to different characteristic times from point to point. To conclude, major faults across the site display different degrees of groundwater chemistry evolution, linked to their physical properties, which may in turn have a large impact on contaminant transport and attenuation.

Precambrian evolution of the Salalah Crystalline Basement from structural analysis and 40Ar/39Ar geochronology

NASA Astrophysics Data System (ADS)

Al-Doukhi, Hanadi Abulateef

The Salalah Crystalline Basement (SCB) is the largest Precambrian exposure in Oman located on the southern margin of the Arabian Plate at the Arabian Sea shore. This work used remote sensing, detailed structural analysis and the analysis of ten samples using 40Ar/39Ar age dating to establish the Precambrian evolution of the SCB by focusing on its central and southwestern parts. This work found that the SCB evolved through four deformational events that shaped its final architecture: (1) Folding and thrusting event that resulted in the emplacement of the Sadh complex atop the Juffa complex. This event resulted in the formation of possibly N-verging nappe structure; (2) Regional folding event around SE- and SW-plunging axes that deformed the regional fabric developed during the N-verging nappe structure and produced map-scale SE- and SW-plunging antiforms shaping the complexes into a semi-dome structure; (3) Strike-slip shearing event that produced a conjugate set of NE-trending sinistral and NW-trending dextral strike-slip shear zones; and (4) Localized SE-directed gravitational collapse manifested by top-to-the-southeast kinematic indicators. Deformation within the SCB might have ceased by 752.2+/-2.7 Ma as indicated by an age given by an undeformed granite. The thermochron of samples collected throughout the SCB complexes shows a single cooling event that occurred between about 800 and 760 Ma. This cooling event could be accomplished by crustal exhumation resulting in regional collapse following the prolonged period of the contractional deformation of the SCB. This makes the SCB a possible metamorphic core complex.

Matrix metalloproteinases: structures, evolution, and diversification.

PubMed

Massova, I; Kotra, L P; Fridman, R; Mobashery, S

1998-09-01

A comprehensive sequence alignment of 64 members of the family of matrix metalloproteinases (MMPs) for the entire sequences, and subsequently the catalytic and the hemopexin-like domains, have been performed. The 64 MMPs were selected from plants, invertebrates, and vertebrates. The analyses disclosed that as many as 23 distinct subfamilies of these proteins are known to exist. Information from the sequence alignments was correlated with structures, both crystallographic as well as computational, of the catalytic domains for the 23 representative members of the MMP family. A survey of the metal binding sites and two loops containing variable sequences of amino acids, which are important for substrate interactions, are discussed. The collective data support the proposal that the assembly of the domains into multidomain enzymes was likely to be an early evolutionary event. This was followed by diversification, perhaps in parallel among the MMPs, in a subsequent evolutionary time scale. Analysis indicates that a retrograde structure simplification may have accounted for the evolution of MMPs with simple domain constituents, such as matrilysin, from the larger and more elaborate enzymes.

Coda Wave Interferometry Method Applied in Structural Monitoring to Assess Damage Evolution in Masonry and Concrete Structures

NASA Astrophysics Data System (ADS)

Masera, D.; Bocca, P.; Grazzini, A.

2011-07-01

In this experimental program the main goal is to monitor the damage evolution in masonry and concrete structures by Acoustic Emission (AE) signal analysis applying a well-know seismic method. For this reason the concept of the coda wave interferometry is applied to AE signal recorded during the tests. Acoustic Emission (AE) are very effective non-destructive techniques applied to identify micro and macro-defects and their temporal evolution in several materials. This technique permits to estimate the velocity of ultrasound waves propagation and the amount of energy released during fracture propagation to obtain information on the criticality of the ongoing process. By means of AE monitoring, an experimental analysis on a set of reinforced masonry walls under variable amplitude loading and strengthening reinforced concrete (RC) beams under monotonic static load has been carried out. In the reinforced masonry wall, cyclic fatigue stress has been applied to accelerate the static creep and to forecast the corresponding creep behaviour of masonry under static long-time loading. During the tests, the evaluation of fracture growth is monitored by coda wave interferometry which represents a novel approach in structural monitoring based on AE relative change velocity of coda signal. In general, the sensitivity of coda waves has been used to estimate velocity changes in fault zones, in volcanoes, in a mining environment, and in ultrasound experiments. This method uses multiple scattered waves, which travelled through the material along numerous paths, to infer tiny temporal changes in the wave velocity. The applied method has the potential to be used as a "damage-gauge" for monitoring velocity changes as a sign of damage evolution into masonry and concrete structures.

Sunspot Umbra: Structure and Evolution

NASA Astrophysics Data System (ADS)

Vázquez, M.; Murdin, P.

2000-11-01

Sunspots show two main structures: a central dark region, the umbra, surrounded by a brighter and filamentary zone, the SUNSPOT PENUMBRA (see figure 1 in the article on SUNSPOT EVOLUTION). Sunspots without penumbra are usually called SUNSPOT PORES. Observed with low spatial resolution, the umbra appears homogeneous. However, even by the nineteenth century astronomers were able to detect fine deta...

Structure and evolution of plant centromeres.

PubMed

Nagaki, Kiyotaka; Walling, Jason; Hirsch, Cory; Jiang, Jiming; Murata, Minoru

2009-01-01

Investigations of centromeric DNA and proteins and centromere structures in plants have lagged behind those conducted with yeasts and animals; however, many attractive results have been obtained from plants during this decade. In particular, intensive investigations have been conducted in Arabidopsis and Gramineae species. We will review our understanding of centromeric components, centromere structures, and the evolution of these attributes of centromeres among plants using data mainly from Arabidopsis and Gramineae species.

Exaggeration and suppression of iridescence: the evolution of two-dimensional butterfly structural colours

PubMed Central

Wickham, Shelley; Large, Maryanne C.J; Poladian, Leon; Jermiin, Lars S

2005-01-01

Many butterfly species possess ‘structural’ colour, where colour is due to optical microstructures found in the wing scales. A number of such structures have been identified in butterfly scales, including three variations on a simple multi-layer structure. In this study, we optically characterize examples of all three types of multi-layer structure, as found in 10 species. The optical mechanism of the suppression and exaggeration of the angle-dependent optical properties (iridescence) of these structures is described. In addition, we consider the phylogeny of the butterflies, and are thus able to relate the optical properties of the structures to their evolutionary development. By applying two different types of analysis, the mechanism of adaptation is addressed. A simple parsimony analysis, in which all evolutionary changes are given an equal weighting, suggests convergent evolution of one structure. A Dollo parsimony analysis, in which the evolutionary ‘cost’ of losing a structure is less than that of gaining it, implies that ‘latent’ structures can be reused. PMID:16849221

Evol and ProDy for bridging protein sequence evolution and structural dynamics

PubMed Central

Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R.; Bahar, Ivet

2014-01-01

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. Availability and implementation: ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. Contact: bahar@pitt.edu PMID:24849577

Structure and evolution analysis of pollen receptor-like kinase in Zea mays and Arabidopsis thaliana.

PubMed

Wang, Dongxu; Wang, He; Irfan, Muhammad; Fan, Mingxia; Lin, Feng

2014-08-01

Receptor-like kinase (RLKs) is an important member in protein kinase family which is widely involved in plant growth, development and defense responses. It is significant to analyze the kinase structure and evolution of pollen RLKs in order to study their mechanisms. In our study, 64 and 73 putative pollen RLKs were chosen from maize and Arabidopsis. Phylogenetic analysis showed that the pollen RLKs were conservative and might had existed before divergence between monocot and dicot which were mainly concentrated in RLCK-VII and LRR-III two subfamilies. Chromosomal localization and gene duplication analysis showed the expansion of pollen RLKs were mainly caused by segmental duplication. By calculating Ka/Ks value of extracellular domain, intracellular domain and kinase domain in pollen RLKs, we found that the pollen RLKs duplicated genes had mainly experienced the purifying selection, while maize might have experienced weaker purifying selection. Meanwhile, extracellular domain might have experienced stronger diversifying selection than intracellular domain in both species. Estimation of duplication time showed that the duplication events of Arabidopsis have occurred approximately between 18 and 69 million years ago, compared to 0.67-170 million years ago of maize. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining protein sequence, structure, and dynamics: A novel approach for functional evolution analysis of PAS domain superfamily.

PubMed

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

PAS domains are widespread in archaea, bacteria, and eukaryota, and play important roles in various functions. In this study, we aim to explore functional evolutionary relationship among proteins in the PAS domain superfamily in view of the sequence-structure-dynamics-function relationship. We collected protein sequences and crystal structure data from RCSB Protein Data Bank of the PAS domain superfamily belonging to three biological functions (nucleotide binding, photoreceptor activity, and transferase activity). Protein sequences were aligned and then used to select sequence-conserved residues and build phylogenetic tree. Three-dimensional structure alignment was also applied to obtain structure-conserved residues. The protein dynamics were analyzed using elastic network model (ENM) and validated by molecular dynamics (MD) simulation. The result showed that the proteins with same function could be grouped by sequence similarity, and proteins in different functional groups displayed statistically significant difference in their vibrational patterns. Interestingly, in all three functional groups, conserved amino acid residues identified by sequence and structure conservation analysis generally have a lower fluctuation than other residues. In addition, the fluctuation of conserved residues in each biological function group was strongly correlated with the corresponding biological function. This research suggested a direct connection in which the protein sequences were related to various functions through structural dynamics. This is a new attempt to delineate functional evolution of proteins using the integrated information of sequence, structure, and dynamics. © 2017 The Protein Society.

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

NASA Astrophysics Data System (ADS)

Kalligeris, Nikos; Lynett, Patrick

2017-11-01

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

Understanding the Evolution of Mammalian Brain Structures; the Need for a (New) Cerebrotype Approach

PubMed Central

Willemet, Romain

2012-01-01

The mammalian brain varies in size by a factor of 100,000 and is composed of anatomically and functionally distinct structures. Theoretically, the manner in which brain composition can evolve is limited, ranging from highly modular (“mosaic evolution”) to coordinated changes in brain structure size (“concerted evolution”) or anything between these two extremes. There is a debate about the relative importance of these distinct evolutionary trends. It is shown here that the presence of taxa-specific allometric relationships between brain structures makes a taxa-specific approach obligatory. In some taxa, the evolution of the size of brain structures follows a unique, coordinated pattern, which, in addition to other characteristics at different anatomical levels, defines what has been called here a “taxon cerebrotype”. In other taxa, no clear pattern is found, reflecting heterogeneity of the species’ lifestyles. These results suggest that the evolution of brain size and composition depends on the complex interplay between selection pressures and constraints that have changed constantly during mammalian evolution. Therefore the variability in brain composition between species should not be considered as deviations from the normal, concerted mammalian trend, but in taxa and species-specific versions of the mammalian brain. Because it forms homogenous groups of species within this complex “space” of constraints and selection pressures, the cerebrotype approach developed here could constitute an adequate level of analysis for evo-devo studies, and by extension, for a wide range of disciplines related to brain evolution. PMID:24962772

Lithosphere structure and subsidence evolution of the conjugate S-African and Argentine margins

NASA Astrophysics Data System (ADS)

Dressel, Ingo; Scheck-Wenderoth, Magdalena; Cacace, Mauro; Götze, Hans-Jürgen; Franke, Dieter

2016-04-01

The bathymetric evolution of the South Atlantic passive continental margins is a matter of debate. Though it is commonly accepted that passive margins experience thermal subsidence as a result of lithospheric cooling as well as load induced subsidence in response to sediment deposition it is disputed if the South Atlantic passive margins were affected by additional processes affecting the subsidence history after continental breakup. We present a subsidence analysis along the SW African margin and offshore Argentina and restore paleobathymetries to assess the subsidence evolution of the margin. These results are discussed with respect to mechanisms behind margin evolution. Therefore, we use available information about the lithosphere-scale present-day structural configuration of these margins as a starting point for the subsidence analysis. A multi 1D backward modelling method is applied to separate individual subsidence components such as the thermal- as well as the load induced subsidence and to restore paleobathymetries for the conjugate margins. The comparison of the restored paleobathymetries shows that the conjugate margins evolve differently: Continuous subsidence is obtained offshore Argentina whereas the subsidence history of the SW African margin is interrupted by phases of uplift. This differing results for both margins correlate also with different structural configurations of the subcrustal mantle. In the light of these results we discuss possible implications for uplift mechanisms.

Application of integrated fluid-thermal-structural analysis methods

NASA Technical Reports Server (NTRS)

Wieting, Allan R.; Dechaumphai, Pramote; Bey, Kim S.; Thornton, Earl A.; Morgan, Ken

1988-01-01

Hypersonic vehicles operate in a hostile aerothermal environment which has a significant impact on their aerothermostructural performance. Significant coupling occurs between the aerodynamic flow field, structural heat transfer, and structural response creating a multidisciplinary interaction. Interfacing state-of-the-art disciplinary analysis methods is not efficient, hence interdisciplinary analysis methods integrated into a single aerothermostructural analyzer are needed. The NASA Langley Research Center is developing such methods in an analyzer called LIFTS (Langley Integrated Fluid-Thermal-Structural) analyzer. The evolution and status of LIFTS is reviewed and illustrated through applications.

Study of grain structure evolution during annealing of a twin-roll-cast Mg alloy

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

Tripathi, A.; Department of Metallurgical Engineering and Materials Science, IIT Bombay; Department of Materials Engineering, Monash University

2016-04-15

The evolution of microstructure under static annealing was studied for mid-thickness section of a twin-roll-cast (TRC) magnesium alloy. Annealing was performed at 300 °C and 500 °C for different times. Microstructural evolution was quantitatively analyzed, from optical micrographs, using grain path envelope analysis. Additional information from electron backscatter diffraction (EBSD) was used for addressing the possible mechanism(s). It was found that the TRC structure had a bimodal grain size, which was preserved even after annealing at 300 °C. However, the annealing at 500 °C led to a unimodal grain size. This difference in the grain size distribution created a contrastingmore » behavior in the normalized standard deviations. This was primarily attributed to a competition between recovery and recrystallization, and their respective dominance at 300° and 500 °C. A deformation induced recrystallization recovery (DIRR) model was proposed. The proposed model could successfully address the experimental microstructural evolution. - Highlights: • Annealing of twin roll cast (TRC) magnesium alloy was done at temperatures of 300 °C and 500 °C. • TRC had bimodal structure. Bimodality preserved for annealing at 300 °C. Annealing at 500 °C led to unimodal structure. • Grain evolution was described based on the competition between recovery and recrystallization. • Deformation induced recrystallization recovery (DIRR) mechanistic model was developed.« less

Molecular evolution and diversification of snake toxin genes, revealed by analysis of intron sequences.

PubMed

Fujimi, T J; Nakajyo, T; Nishimura, E; Ogura, E; Tsuchiya, T; Tamiya, T

2003-08-14

The genes encoding erabutoxin (short chain neurotoxin) isoforms (Ea, Eb, and Ec), LsIII (long chain neurotoxin) and a novel long chain neurotoxin pseudogene were cloned from a Laticauda semifasciata genomic library. Short and long chain neurotoxin genes were also cloned from the genome of Laticauda laticaudata, a closely related species of L. semifasciata, by PCR. A putative matrix attached region (MAR) sequence was found in the intron I of the LsIII gene. Comparative analysis of 11 structurally relevant snake toxin genes (three-finger-structure toxins) revealed the molecular evolution of these toxins. Three-finger-structure toxin genes diverged from a common ancestor through two types of evolutionary pathways (long and short types), early in the course of evolution. At a later stage of evolution in each gene, the accumulation of mutations in the exons, especially exon II, by accelerated evolution may have caused the increased diversification in their functions. It was also revealed that the putative MAR sequence found in the LsIII gene was integrated into the gene after the species-level divergence.

Modeling the mesozoic-cenozoic structural evolution of east texas

USGS Publications Warehouse

Pearson, Ofori N.; Rowan, Elisabeth L.; Miller, John J.

2012-01-01

The U.S. Geological Survey (USGS) recently assessed the undiscovered technically recoverable oil and gas resources within Jurassic and Cretaceous strata of the onshore coastal plain and State waters of the U.S. Gulf Coast. Regional 2D seismic lines for key parts of the Gulf Coast basin were interpreted in order to examine the evolution of structural traps and the burial history of petroleum source rocks. Interpretation and structural modeling of seismic lines from eastern Texas provide insights into the structural evolution of this part of the Gulf of Mexico basin. Since completing the assessment, the USGS has acquired additional regional seismic lines in east Texas; interpretation of these new lines, which extend from the Texas-Oklahoma state line to the Gulf Coast shoreline, show how some of the region's prominent structural elements (e.g., the Talco and Mount Enterprise fault zones, the East Texas salt basin, and the Houston diapir province) vary along strike. The interpretations also indicate that unexplored structures may lie beneath the current drilling floor. Structural restorations based upon interpretation of these lines illustrate the evolution of key structures and show the genetic relation between structural growth and movement of the Jurassic Louann Salt. 1D thermal models that integrate kinetics and burial histories were also created for the region's two primary petroleum source rocks, the Oxfordian Smackover Formation and the Cenomanian-Turonian Eagle Ford Shale. Integrating results from the thermal models with the structural restorations provides insights into the distribution and timing of petroleum expulsion from the Smackover Formation and Eagle Ford Shale in eastern Texas.

Evol and ProDy for bridging protein sequence evolution and structural dynamics.

PubMed

Bakan, Ahmet; Dutta, Anindita; Mao, Wenzhi; Liu, Ying; Chennubhotla, Chakra; Lezon, Timothy R; Bahar, Ivet

2014-09-15

Correlations between sequence evolution and structural dynamics are of utmost importance in understanding the molecular mechanisms of function and their evolution. We have integrated Evol, a new package for fast and efficient comparative analysis of evolutionary patterns and conformational dynamics, into ProDy, a computational toolbox designed for inferring protein dynamics from experimental and theoretical data. Using information-theoretic approaches, Evol coanalyzes conservation and coevolution profiles extracted from multiple sequence alignments of protein families with their inferred dynamics. ProDy and Evol are open-source and freely available under MIT License from http://prody.csb.pitt.edu/. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Rapid Modeling and Analysis Tools: Evolution, Status, Needs and Directions

NASA Technical Reports Server (NTRS)

Knight, Norman F., Jr.; Stone, Thomas J.; Ransom, Jonathan B. (Technical Monitor)

2002-01-01

Advanced aerospace systems are becoming increasingly more complex, and customers are demanding lower cost, higher performance, and high reliability. Increased demands are placed on the design engineers to collaborate and integrate design needs and objectives early in the design process to minimize risks that may occur later in the design development stage. High performance systems require better understanding of system sensitivities much earlier in the design process to meet these goals. The knowledge, skills, intuition, and experience of an individual design engineer will need to be extended significantly for the next generation of aerospace system designs. Then a collaborative effort involving the designer, rapid and reliable analysis tools and virtual experts will result in advanced aerospace systems that are safe, reliable, and efficient. This paper discusses the evolution, status, needs and directions for rapid modeling and analysis tools for structural analysis. First, the evolution of computerized design and analysis tools is briefly described. Next, the status of representative design and analysis tools is described along with a brief statement on their functionality. Then technology advancements to achieve rapid modeling and analysis are identified. Finally, potential future directions including possible prototype configurations are proposed.

The European Spacelab structural design evolution

NASA Technical Reports Server (NTRS)

Thirkettle, A. J.

1982-01-01

Spacelab is a manned, reusable laboratory which is being developed for the European Space Agency (ESA). In its working mode it will fly in low earth orbit in the cargo bay of the Shuttle Transportation System (STS) Orbiter. A description is presented of the structural development of the various features of Spacelab. System requirements are considered along with structural requirements, quasi-static loads, acoustic loads, pressure loads, crash loads, ground loads, and the fatigue profile. Aspects of thermal environment generation are discussed, and questions regarding the design evolution of the pallet structure are examined. Details of pallet structure testing are reported, taking into account static strength tests, acoustic tests, the modal survey test, crash tests, and fatigue/fracture mechanics testing.

The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement

PubMed Central

Peng, Yanhui; Loparev, Vladimir; Batra, Dhwani; Bowden, Katherine E.; Burroughs, Mark; Cassiday, Pamela K.; Davis, Jamie K.; Johnson, Taccara; Juieng, Phalasy; Knipe, Kristen; Mathis, Marsenia H.; Pruitt, Andrea M.; Rowe, Lori; Sheth, Mili; Tondella, M. Lucia; Williams, Margaret M.

2017-01-01

ABSTRACT Despite high pertussis vaccine coverage, reported cases of whooping cough (pertussis) have increased over the last decade in the United States and other developed countries. Although Bordetella pertussis is well known for its limited gene sequence variation, recent advances in long-read sequencing technology have begun to reveal genomic structural heterogeneity among otherwise indistinguishable isolates, even within geographically or temporally defined epidemics. We have compared rearrangements among complete genome assemblies from 257 B. pertussis isolates to examine the potential evolution of the chromosomal structure in a pathogen with minimal gene nucleotide sequence diversity. Discrete changes in gene order were identified that differentiated genomes from vaccine reference strains and clinical isolates of various genotypes, frequently along phylogenetic boundaries defined by single nucleotide polymorphisms. The observed rearrangements were primarily large inversions centered on the replication origin or terminus and flanked by IS481, a mobile genetic element with >240 copies per genome and previously suspected to mediate rearrangements and deletions by homologous recombination. These data illustrate that structural genome evolution in B. pertussis is not limited to reduction but also includes rearrangement. Therefore, although genomes of clinical isolates are structurally diverse, specific changes in gene order are conserved, perhaps due to positive selection, providing novel information for investigating disease resurgence and molecular epidemiology. IMPORTANCE Whooping cough, primarily caused by Bordetella pertussis, has resurged in the United States even though the coverage with pertussis-containing vaccines remains high. The rise in reported cases has included increased disease rates among all vaccinated age groups, provoking questions about the pathogen's evolution. The chromosome of B. pertussis includes a large number of repetitive mobile

Monogamy, strongly bonded groups, and the evolution of human social structure.

PubMed

Chapais, Bernard

2013-01-01

Human social evolution has most often been treated in a piecemeal fashion, with studies focusing on the evolution of specific components of human society such as pair-bonding, cooperative hunting, male provisioning, grandmothering, cooperative breeding, food sharing, male competition, male violence, sexual coercion, territoriality, and between-group conflicts. Evolutionary models about any one of those components are usually concerned with two categories of questions, one relating to the origins of the component and the other to its impact on the evolution of human cognition and social life. Remarkably few studies have been concerned with the evolution of the entity that integrates all components, the human social system itself. That social system has as its core feature human social structure, which I define here as the common denominator of all human societies in terms of group composition, mating system, residence patterns, and kinship structures. The paucity of information on the evolution of human social structure poses substantial problems because that information is useful, if not essential, to assess both the origins and impact of any particular aspect of human society. Copyright © 2013 Wiley Periodicals, Inc.

Ultrasonic influence on evolution of disordered dislocation structures

NASA Astrophysics Data System (ADS)

Bachurin, D. V.; Murzaev, R. T.; Nazarov, A. A.

2017-12-01

Evolution of disordered dislocation structures under ultrasonic influence is studied in a model two-dimensional grain within the discrete-dislocation approach. Non-equilibrium grain boundary state is mimicked by a mesodefect located at the corners of the grain, stress field of which is described by that of a wedge junction disclination quadrupole. Significant rearrangement related to gliding of lattice dislocations towards the grain boundaries is found, which results in a noticeable reduction of internal stress fields and cancel of disclination quadrupole. The process of dislocation structure evolution passes through two stages: rapid and slow. The main dislocation rearrangement occurs during the first stage. Reduction of internal stress fields is associated with the number of dislocations entered into the grain boundaries. The change of misorientation angle due to lattice dislocations absorbed by the grain boundaries is evaluated. Amplitude of ultrasonic treatment significantly influences the relaxation of dislocation structure. Preliminary elastic relaxation of dislocation structure does not affect substantially the results of the following ultrasonic treatment. Substantial grain size dependence of relaxation of disordered dislocation systems is found. Simulation results are consistent with experimental data.

Myosin MyTH4-FERM structures highlight important principles of convergent evolution.

PubMed

Planelles-Herrero, Vicente José; Blanc, Florian; Sirigu, Serena; Sirkia, Helena; Clause, Jeffrey; Sourigues, Yannick; Johnsrud, Daniel O; Amigues, Beatrice; Cecchini, Marco; Gilbert, Susan P; Houdusse, Anne; Titus, Margaret A

2016-05-24

Myosins containing MyTH4-FERM (myosin tail homology 4-band 4.1, ezrin, radixin, moesin, or MF) domains in their tails are found in a wide range of phylogenetically divergent organisms, such as humans and the social amoeba Dictyostelium (Dd). Interestingly, evolutionarily distant MF myosins have similar roles in the extension of actin-filled membrane protrusions such as filopodia and bind to microtubules (MT), suggesting that the core functions of these MF myosins have been highly conserved over evolution. The structures of two DdMyo7 signature MF domains have been determined and comparison with mammalian MF structures reveals that characteristic features of MF domains are conserved. However, across millions of years of evolution conserved class-specific insertions are seen to alter the surfaces and the orientation of subdomains with respect to each other, likely resulting in new sites for binding partners. The MyTH4 domains of Myo10 and DdMyo7 bind to MT with micromolar affinity but, surprisingly, their MT binding sites are on opposite surfaces of the MyTH4 domain. The structural analysis in combination with comparison of diverse MF myosin sequences provides evidence that myosin tail domain features can be maintained without strict conservation of motifs. The results illustrate how tuning of existing features can give rise to new structures while preserving the general properties necessary for myosin tails. Thus, tinkering with the MF domain enables it to serve as a multifunctional platform for cooperative recruitment of various partners, allowing common properties such as autoinhibition of the motor and microtubule binding to arise through convergent evolution.

The Divided Bacterial Genome: Structure, Function, and Evolution.

PubMed

diCenzo, George C; Finan, Turlough M

2017-09-01

Approximately 10% of bacterial genomes are split between two or more large DNA fragments, a genome architecture referred to as a multipartite genome. This multipartite organization is found in many important organisms, including plant symbionts, such as the nitrogen-fixing rhizobia, and plant, animal, and human pathogens, including the genera Brucella , Vibrio , and Burkholderia . The availability of many complete bacterial genome sequences means that we can now examine on a broad scale the characteristics of the different types of DNA molecules in a genome. Recent work has begun to shed light on the unique properties of each class of replicon, the unique functional role of chromosomal and nonchromosomal DNA molecules, and how the exploitation of novel niches may have driven the evolution of the multipartite genome. The aims of this review are to (i) outline the literature regarding bacterial genomes that are divided into multiple fragments, (ii) provide a meta-analysis of completed bacterial genomes from 1,708 species as a way of reviewing the abundant information present in these genome sequences, and (iii) provide an encompassing model to explain the evolution and function of the multipartite genome structure. This review covers, among other topics, salient genome terminology; mechanisms of multipartite genome formation; the phylogenetic distribution of multipartite genomes; how each part of a genome differs with respect to genomic signatures, genetic variability, and gene functional annotation; how each DNA molecule may interact; as well as the costs and benefits of this genome structure. Copyright © 2017 American Society for Microbiology.

RNA structural constraints in the evolution of the influenza A virus genome NP segment

PubMed Central

Gultyaev, Alexander P; Tsyganov-Bodounov, Anton; Spronken, Monique IJ; van der Kooij, Sander; Fouchier, Ron AM; Olsthoorn, René CL

2014-01-01

Conserved RNA secondary structures were predicted in the nucleoprotein (NP) segment of the influenza A virus genome using comparative sequence and structure analysis. A number of structural elements exhibiting nucleotide covariations were identified over the whole segment length, including protein-coding regions. Calculations of mutual information values at the paired nucleotide positions demonstrate that these structures impose considerable constraints on the virus genome evolution. Functional importance of a pseudoknot structure, predicted in the NP packaging signal region, was confirmed by plaque assays of the mutant viruses with disrupted structure and those with restored folding using compensatory substitutions. Possible functions of the conserved RNA folding patterns in the influenza A virus genome are discussed. PMID:25180940

Monitoring Data-Structure Evolution in Distributed Message-Passing Programs

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; Beers, Andrew; Woodrow, Thomas S. (Technical Monitor)

1996-01-01

Monitoring the evolution of data structures in parallel and distributed programs, is critical for debugging its semantics and performance. However, the current state-of-art in tracking and presenting data-structure information on parallel and distributed environments is cumbersome and does not scale. In this paper we present a methodology that automatically tracks memory bindings (not the actual contents) of static and dynamic data-structures of message-passing C programs, using PVM. With the help of a number of examples we show that in addition to determining the impact of memory allocation overheads on program performance, graphical views can help in debugging the semantics of program execution. Scalable animations of virtual address bindings of source-level data-structures are used for debugging the semantics of parallel programs across all processors. In conjunction with light-weight core-files, this technique can be used to complement traditional debuggers on single processors. Detailed information (such as data-structure contents), on specific nodes, can be determined using traditional debuggers after the data structure evolution leading to the semantic error is observed graphically.

EVOLUTION OF FAST MAGNETOACOUSTIC PULSES IN RANDOMLY STRUCTURED CORONAL PLASMAS

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

Yuan, D.; Li, B.; Pascoe, D. J.

2015-02-01

We investigate the evolution of fast magnetoacoustic pulses in randomly structured plasmas, in the context of large-scale propagating waves in the solar atmosphere. We perform one-dimensional numerical simulations of fast wave pulses propagating perpendicular to a constant magnetic field in a low-β plasma with a random density profile across the field. Both linear and nonlinear regimes are considered. We study how the evolution of the pulse amplitude and width depends on their initial values and the parameters of the random structuring. Acting as a dispersive medium, a randomly structured plasma causes amplitude attenuation and width broadening of the fast wavemore » pulses. After the passage of the main pulse, secondary propagating and standing fast waves appear. Width evolution of both linear and nonlinear pulses can be well approximated by linear functions; however, narrow pulses may have zero or negative broadening. This arises because narrow pulses are prone to splitting, while broad pulses usually deviate less from their initial Gaussian shape and form ripple structures on top of the main pulse. Linear pulses decay at an almost constant rate, while nonlinear pulses decay exponentially. A pulse interacts most efficiently with a random medium with a correlation length of about half of the initial pulse width. This detailed model of fast wave pulses propagating in highly structured media substantiates the interpretation of EIT waves as fast magnetoacoustic waves. Evolution of a fast pulse provides us with a novel method to diagnose the sub-resolution filamentation of the solar atmosphere.« less

Object Recognition and Random Image Structure Evolution

ERIC Educational Resources Information Center

Sadr, Jvid; Sinha, Pawan

2004-01-01

We present a technique called Random Image Structure Evolution (RISE) for use in experimental investigations of high-level visual perception. Potential applications of RISE include the quantitative measurement of perceptual hysteresis and priming, the study of the neural substrates of object perception, and the assessment and detection of subtle…

Multi-Scale Modeling of Microstructural Evolution in Structural Metallic Systems

NASA Astrophysics Data System (ADS)

Zhao, Lei

Metallic alloys are a widely used class of structural materials, and the mechanical properties of these alloys are strongly dependent on the microstructure. Therefore, the scientific design of metallic materials with superior mechanical properties requires the understanding of the microstructural evolution. Computational models and simulations offer a number of advantages over experimental techniques in the prediction of microstructural evolution, because they can allow studies of microstructural evolution in situ, i.e., while the material is mechanically loaded (meso-scale simulations), and bring atomic-level insights into the microstructure (atomistic simulations). In this thesis, we applied a multi-scale modeling approach to study the microstructural evolution in several metallic systems, including polycrystalline materials and metallic glasses (MGs). Specifically, for polycrystalline materials, we developed a coupled finite element model that combines phase field method and crystal plasticity theory to study the plasticity effect on grain boundary (GB) migration. Our model is not only coupled strongly (i.e., we include plastic driving force on GB migration directly) and concurrently (i.e., coupled equations are solved simultaneously), but also it qualitatively captures such phenomena as the dislocation absorption by mobile GBs. The developed model provides a tool to study the microstructural evolution in plastically deformed metals and alloys. For MGs, we used molecular dynamics (MD) simulations to investigate the nucleation kinetics in the primary crystallization in Al-Sm system. We calculated the time-temperature-transformation curves for low Sm concentrations, from which the strong suppressing effect of Sm solute on Al nucleation and its influencing mechanism are revealed. Also, through the comparative analysis of both Al attachment and Al diffusion in MGs, it has been found that the nucleation kinetics is controlled by interfacial attachment of Al, and that

Multidimensional Simulations of Filament Channel Structure and Evolution

NASA Astrophysics Data System (ADS)

Karpen, J. T.

2007-10-01

Over the past decade, the NRL Solar Theory group has made steady progress toward formulating a comprehensive model of filament-channel structure and evolution, combining the results of our sheared 3D arcade model for the magnetic field with our thermal nonequilibrium model for the cool, dense material suspended in the corona. We have also discovered that, when a sheared arcade is embedded within the global dipolar field, the resulting stressed filament channel can erupt through the mechanism of magnetic breakout. Our progress has been largely enabled by the development and implementation of state-of-the-art 1D hydrodynamic and 3D magnetohydrodynamic (MHD) codes to simulate the field-aligned plasma thermodynamics and large-scale magnetic-field evolution, respectively. Significant questions remain, however, which could be answered with the advanced observations anticipated from Solar-B. In this review, we summarize what we have learned from our simulations about the magnetic and plasma structure, evolution, and eruption of filament channels, and suggest key observational objectives for Solar-B that will test our filament-channel and CME-initiation models and augment our understanding of the underlying physical processes.

Structuring evolution: biochemical networks and metabolic diversification in birds.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2016-08-25

Recurrence and predictability of evolution are thought to reflect the correspondence between genomic and phenotypic dimensions of organisms, and the connectivity in deterministic networks within these dimensions. Direct examination of the correspondence between opportunities for diversification imbedded in such networks and realized diversity is illuminating, but is empirically challenging because both the deterministic networks and phenotypic diversity are modified in the course of evolution. Here we overcome this problem by directly comparing the structure of a "global" carotenoid network - comprising of all known enzymatic reactions among naturally occurring carotenoids - with the patterns of evolutionary diversification in carotenoid-producing metabolic networks utilized by birds. We found that phenotypic diversification in carotenoid networks across 250 species was closely associated with enzymatic connectivity of the underlying biochemical network - compounds with greater connectivity occurred the most frequently across species and were the hotspots of metabolic pathway diversification. In contrast, we found no evidence for diversification along the metabolic pathways, corroborating findings that the utilization of the global carotenoid network was not strongly influenced by history in avian evolution. The finding that the diversification in species-specific carotenoid networks is qualitatively predictable from the connectivity of the underlying enzymatic network points to significant structural determinism in phenotypic evolution.

Understanding the Global Structure and Evolution of Coronal Mass Ejections in the Solar Wind

NASA Technical Reports Server (NTRS)

Riley, Pete

2004-01-01

This report summarizes the technical progress made during the first six months of the second year of the NASA Living with a Star program contract Understanding the global structure and evolution of coronal mass ejections in the solar wind, between NASA and Science Applications International Corporation, and covers the period November 18, 2003 - May 17,2004. Under this contract SAIC has conducted numerical and data analysis related to fundamental issues concerning the origin, intrinsic properties, global structure, and evolution of coronal mass ejections in the solar wind. During this working period we have focused on a quantitative assessment of 5 flux rope fitting techniques. In the following sections we summarize the main aspects of this work and our proposed investigation plan for the next reporting period. Thus far, our investigation has resulted in 6 refereed scientific publications and we have presented the results at a number of scientific meetings and workshops.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Structural evolution of tunneling oxide passivating contact upon thermal annealing.

PubMed

Choi, Sungjin; Min, Kwan Hong; Jeong, Myeong Sang; Lee, Jeong In; Kang, Min Gu; Song, Hee-Eun; Kang, Yoonmook; Lee, Hae-Seok; Kim, Donghwan; Kim, Ka-Hyun

2017-10-16

We report on the structural evolution of tunneling oxide passivating contact (TOPCon) for high efficient solar cells upon thermal annealing. The evolution of doped hydrogenated amorphous silicon (a-Si:H) into polycrystalline-silicon (poly-Si) by thermal annealing was accompanied with significant structural changes. Annealing at 600 °C for one minute introduced an increase in the implied open circuit voltage (V oc ) due to the hydrogen motion, but the implied V oc decreased again at 600 °C for five minutes. At annealing temperature above 800 °C, a-Si:H crystallized and formed poly-Si and thickness of tunneling oxide slightly decreased. The thickness of the interface tunneling oxide gradually decreased and the pinholes are formed through the tunneling oxide at a higher annealing temperature up to 1000 °C, which introduced the deteriorated carrier selectivity of the TOPCon structure. Our results indicate a correlation between the structural evolution of the TOPCon passivating contact and its passivation property at different stages of structural transition from the a-Si:H to the poly-Si as well as changes in the thickness profile of the tunneling oxide upon thermal annealing. Our result suggests that there is an optimum thickness of the tunneling oxide for passivating electron contact, in a range between 1.2 to 1.5 nm.

Structural Evolution of Q-Carbon and Nanodiamonds

NASA Astrophysics Data System (ADS)

Gupta, Siddharth; Bhaumik, Anagh; Sachan, Ritesh; Narayan, Jagdish

2018-04-01

This article provides insights pertaining to the first-order phase transformation involved in the growth of densely packed Q-carbon and nanodiamonds by nanosecond laser melting and quenching of diamond-like carbon (DLC) thin films. DLC films with different sp 3 content were melted rapidly in a controlled way in super-undercooled state and quenched, leading to formation of distinct nanostructures, i.e., nanodiamonds, Q-carbon, and Q-carbon nanocomposites. This analysis provides direct evidence of the dependence of the super-undercooling on the structural evolution of Q-carbon. Finite element heat flow calculations showed that the super-undercooling varies monotonically with the sp 3 content. The phenomenon of solid-liquid interfacial instability during directional solidification from the melt state is studied in detail. The resulting lateral segregation leads to formation of cellular filamentary Q-carbon nanostructures. The dependence of the cell size and wavelength at the onset of instability on the sp 3 content of DLC thin films was modeled based on perturbation theory.

Friction-induced nano-structural evolution of graphene as a lubrication additive

NASA Astrophysics Data System (ADS)

Zhao, Jun; Mao, Junyuan; Li, Yingru; He, Yongyong; Luo, Jianbin

2018-03-01

Graphene has attracted enormous attention in the field of lubrication based on its excellent physical and chemical properties. Although many studies have obtained thermally or chemically- exfoliated graphene and investigated their wide and important application, few studies have reported their physical nano-structural evolution under friction. In this study, we investigated the lubrication properties of graphene additives with different layer numbers and interlayer spacing by exfoliating. The additives with a higher degrees of exfoliation changed to ordering under friction, and had better lubrication properties, while that with a lower degrees exhibited obvious structural defects and high friction. Therefore, the original degrees of exfoliation plays a key role in the structural evolution of graphene and superior lubrication can be achieved through the physical nano-structure changing to ordering, even graphitization. Furthermore, the ordered tribofilm on the frictional interfaces was parallel to the sliding direction, meaning the highly exfoliated graphene indeed reaching slippage between its layers, which wasn't experimentally discovered in previous studies. This work provides a new understanding of the relationship between friction-induced nano-structural evolution and lubrication properties of graphene as a lubrication additive, and has great potential for the structural design of graphene as a lubrication additive.

Evolution of structure and reactivity in a series of iconic carbenes.

PubMed

Zhang, Min; Moss, Robert A; Thompson, Jack; Krogh-Jespersen, Karsten

2012-01-20

We present experimental activation parameters for the reactions of six carbenes (CCl(2), CClF, CF(2), ClCOMe, FCOMe, and (MeO)(2)C) with six alkenes (tetramethylethylene, cyclohexene, 1-hexene, methyl acrylate, acrylonitrile, and α-chloroacrylonitrile). Activation energies range from -1 kcal/mol for the addition of CCl(2) to tetramethylethylene to 11 kcal/mol for the addition of FCOMe to acrylonitrile. A generally satisfactory analysis of major trends in the evolution of carbenic structure and reactivity is afforded by qualitative applications of frontier molecular orbital theory, although the observed entropies of activation appear to fall in a counterintuitive pattern. An analysis of computed cyclopropanation transition state parameters reveals significant nucleophilic selectivity of (MeO)(2)C toward α-chloroacrylonitrile.

Evolution of specialization in resource utilization in structured metapopulations.

PubMed

Nurmi, Tuomas; Geritz, Stefan; Parvinen, Kalle; Gyllenberg, Mats

2008-07-01

We study the evolution of resource utilization in a structured discrete-time metapopulation model with an infinite number of patches, prone to local catastrophes. The consumer faces a trade-off in the abilities to consume two resources available in different amounts in each patch. We analyse how the evolution of specialization in the utilization of the resources is affected by different ecological factors: migration, local growth, local catastrophes, forms of the trade-off and distribution of the resources in the patches. Our modelling approach offers a natural way to include more than two patch types into the models. This has not been usually possible in the previous spatially heterogeneous models focusing on the evolution of specialization.

Joint evolution of specialization and dispersal in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2011-04-21

We study the joint evolution of dispersal and specialization concerning resource usage in a mechanistically underpinned structured discrete-time metapopulation model. We show that dispersal significantly affects the evolution of specialization and that specialization is a key factor that determines the possibility of evolutionary branching in dispersal propensity. Allowing both dispersal propensity and specialization to evolve as a consequence of natural selection is necessary in order to understand the evolutionary dynamics. The joint evolution of dispersal and specialization forms a natural evolutionary path leading to the coexistence of generalists and specialists. We show that in this process, the number of different patch types and the resource distribution are essential. Copyright © 2011 Elsevier Ltd. All rights reserved.

Evolution of the Mount Woods Inlier, northern Gawler Craton, Southern Australia: an integrated structural and aeromagnetic analysis

NASA Astrophysics Data System (ADS)

Betts, Peter G.; Valenta, Rick K.; Finlay, Jim

2003-05-01

Structural mapping integrated with interpretation and forward modelling of aeromagnetic data form complimentary and powerful tools for regional structural analysis because both techniques focus on architecture and overprinting relationships. This approach is used to constrain the geometry and evolution of the sparsely exposed Mount Woods Inlier in the northern Gawler Craton. The Mount Woods Inlier records a history of poly-phase deformation, high-temperature metamorphism, and syn- and post-orogenic magmatism between ca. 1736 and 1584 Ma. The earliest deformation involved isoclinal folding, and the development of bedding parallel and axial planar gneissic foliation (S 1). This was accompanied by high-temperature, upper amphibolite to granulite facies metamorphism at ca. 1736 Ma. During subsequent north-south shortening (D 2), open to isoclinal south-southeast-oriented F 2 folds developed as the Palaeoproterozoic successions of the inlier were thrust over the Archaean nuclei of the Gawler Craton. The syn-D 2 Engenina Adamellite was emplaced at ca. 1692 Ma. The post-D 2 history involved shear zone development and localised folding, exhumation of metamorphic rocks, and deposition of clastic sediments prior to the emplacement of the ca. 1584 Ma Granite Balta Suite. The Mount Woods Inlier is interpreted as the northern continuation of the Kimban Orogen.

Energy-driven surface evolution in beta-MnO2 structures

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

Yao, Wentao; Yuan, Yifei; Asayesh-Ardakani, Hasti

Exposed crystal facets directly affect the electrochemical/catalytic performance of MnO2 materials during their applications in supercapacitors, rechargeable batteries, and fuel cells. Currently, the facet-controlled synthesis of MnO2 is facing serious challenges due to the lack of an in-depth understanding of their surface evolution mechanisms. Here, combining aberration-corrected scanning transmission electron microscopy (STEM) and high-resolution TEM, we revealed a mutual energy-driven mechanism between beta-MnO2 nanowires and microstructures that dominated the evolution of the lateral facets in both structures. The evolution of the lateral surfaces followed the elimination of the {100} facets and increased the occupancy of {110} facets with the increasemore » in hydrothermal retention time. Both self-growth and oriented attachment along their {100} facets were observed as two different ways to reduce the surface energies of the beta-MnO2 structures. High-density screw dislocations with the 1/2 < 100 > Burgers vector were generated consequently. The observed surface evolution phenomenon offers guidance for the facet-controlled growth of beta-MnO2 materials with high performances for its application in metal-air batteries, fuel cells, supercapacitors, etc.« less

Recapitulating the Structural Evolution of Redox Regulation in Adenosine 5'-Phosphosulfate Kinase from Cyanobacteria to Plants.

PubMed

Herrmann, Jonathan; Nathin, David; Lee, Soon Goo; Sun, Tony; Jez, Joseph M

2015-10-09

In plants, adenosine 5'-phosphosulfate (APS) kinase (APSK) is required for reproductive viability and the production of 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a sulfur donor in specialized metabolism. Previous studies of the APSK from Arabidopsis thaliana (AtAPSK) identified a regulatory disulfide bond formed between the N-terminal domain (NTD) and a cysteine on the core scaffold. This thiol switch is unique to mosses, gymnosperms, and angiosperms. To understand the structural evolution of redox control of APSK, we investigated the redox-insensitive APSK from the cyanobacterium Synechocystis sp. PCC 6803 (SynAPSK). Crystallographic analysis of SynAPSK in complex with either APS and a non-hydrolyzable ATP analog or APS and sulfate revealed the overall structure of the enzyme, which lacks the NTD found in homologs from mosses and plants. A series of engineered SynAPSK variants reconstructed the structural evolution of the plant APSK. Biochemical analyses of SynAPSK, SynAPSK H23C mutant, SynAPSK fused to the AtAPSK NTD, and the fusion protein with the H23C mutation showed that the addition of the NTD and cysteines recapitulated thiol-based regulation. These results reveal the molecular basis for structural changes leading to the evolution of redox control of APSK in the green lineage from cyanobacteria to plants. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Structure and Evolution of the Foreign Exchange Networks

NASA Astrophysics Data System (ADS)

Kwapień, J.; Gworek, S.; Drożdż, S.

2009-01-01

We investigate topology and temporal evolution of the foreign currency exchange market viewed from a weighted network perspective. Based on exchange rates for a set of 46 currencies (including precious metals), we construct different representations of the FX network depending on a choice of the base currency. Our results show that the network structure is not stable in time, but there are main clusters of currencies, which persist for a long period of time despite the fact that their size and content are variable. We find a long-term trend in the network's evolution which affects the USD and EUR nodes. In all the network representations, the USD node gradually loses its centrality, while, on contrary, the EUR node has become slightly more central than it used to be in its early years. Despite this directional trend, the overall evolution of the network is noisy.

Molecular dynamics simulations of the structure evolutions of Cu-Zr metallic glasses under irradiation

NASA Astrophysics Data System (ADS)

Lang, Lin; Tian, Zean; Xiao, Shifang; Deng, Huiqiu; Ao, Bingyun; Chen, Piheng; Hu, Wangyu

2017-02-01

Molecular dynamics simulations have been performed to investigate the structural evolution of Cu64.5Zr35.5 metallic glasses under irradiation. The largest standard cluster analysis (LSCA) method was used to quantify the microstructure within the collision cascade regions. It is found that the majority of clusters within the collision cascade regions are full and defective icosahedrons. Not only the smaller structures (common neighbor subcluster) but also primary clusters greatly changed during the collision cascades; while most of these radiation damages self-recover quickly in the following quench states. These findings indicate the Cu-Zr metallic glasses have excellent irradiation-resistance properties.

Comparative empirical analysis of flow-weighted transit route networks in R-space and evolution modeling

NASA Astrophysics Data System (ADS)

Huang, Ailing; Zang, Guangzhi; He, Zhengbing; Guan, Wei

2017-05-01

Urban public transit system is a typical mixed complex network with dynamic flow, and its evolution should be a process coupling topological structure with flow dynamics, which has received little attention. This paper presents the R-space to make a comparative empirical analysis on Beijing’s flow-weighted transit route network (TRN) and we found that both the Beijing’s TRNs in the year of 2011 and 2015 exhibit the scale-free properties. As such, we propose an evolution model driven by flow to simulate the development of TRNs with consideration of the passengers’ dynamical behaviors triggered by topological change. The model simulates that the evolution of TRN is an iterative process. At each time step, a certain number of new routes are generated driven by travel demands, which leads to dynamical evolution of new routes’ flow and triggers perturbation in nearby routes that will further impact the next round of opening new routes. We present the theoretical analysis based on the mean-field theory, as well as the numerical simulation for this model. The results obtained agree well with our empirical analysis results, which indicate that our model can simulate the TRN evolution with scale-free properties for distributions of node’s strength and degree. The purpose of this paper is to illustrate the global evolutional mechanism of transit network that will be used to exploit planning and design strategies for real TRNs.

Social dilemmas in an online social network: The structure and evolution of cooperation

NASA Astrophysics Data System (ADS)

Fu, Feng; Chen, Xiaojie; Liu, Lianghuan; Wang, Long

2007-11-01

We investigate two paradigms for studying the evolution of cooperation—Prisoner's Dilemma and Snowdrift game in an online friendship network, obtained from a social networking site. By structural analysis, it is revealed that the empirical social network has small-world and scale-free properties. Besides, it exhibits assortative mixing pattern. Then, we study the evolutionary version of the two types of games on it. It is found that cooperation is substantially promoted with small values of game matrix parameters in both games. Whereas the competent cooperators induced by the underlying network of contacts will be dramatically inhibited with increasing values of the game parameters. Further, we explore the role of assortativity in evolution of cooperation by random edge rewiring. We find that increasing amount of assortativity will to a certain extent diminish the cooperation level. We also show that connected large hubs are capable of maintaining cooperation. The evolution of cooperation on empirical networks is influenced by various network effects in a combined manner, compared with that on model networks. Our results can help understand the cooperative behaviors in human groups and society.

A teaching module about stellar structure and evolution

NASA Astrophysics Data System (ADS)

Colantonio, Arturo; Galano, Silvia; Leccia, Silvio; Puddu, Emanuella; Testa, Italo

2017-01-01

In this paper, we present a teaching module about stellar structure, functioning and evolution. Drawing from literature in astronomy education, we designed the activities around three key ideas: spectral analysis, mechanical and thermal equilibrium, energy and nuclear reactions. The module is divided into four phases, in which the key ideas for describing stars' functioning and physical mechanisms are gradually introduced. The activities (20 hours) build on previously learned laws in mechanics, thermodynamics, and electromagnetism and help students combine them meaningfully in order to get a complete picture of processes that happens in stars. The module was piloted with two intact classes of secondary school students (N = 59 students, 17-18 years old), using a ten-question multiple-choice questionnaire as research instrument. Results support the effectiveness of the proposed activities. Implications for the teaching of advanced physics topics using stars as fruitful context are briefly discussed.

Exploring social structure effect on language evolution based on a computational model

NASA Astrophysics Data System (ADS)

Gong, Tao; Minett, James; Wang, William

2008-06-01

A compositionality-regularity coevolution model is adopted to explore the effect of social structure on language emergence and maintenance. Based on this model, we explore language evolution in three experiments, and discuss the role of a popular agent in language evolution, the relationship between mutual understanding and social hierarchy, and the effect of inter-community communications and that of simple linguistic features on convergence of communal languages in two communities. This work embodies several important interactions during social learning, and introduces a new approach that manipulates individuals' probabilities to participate in social interactions to study the effect of social structure. We hope it will stimulate further theoretical and empirical explorations on language evolution in a social environment.

Phylogenetic analysis of honey bee behavioral evolution.

PubMed

Raffiudin, Rika; Crozier, Ross H

2007-05-01

DNA sequences from three mitochondrial (rrnL, cox2, nad2) and one nuclear gene (itpr) from all 9 known honey bee species (Apis), a 10th possible species, Apis dorsata binghami, and three outgroup species (Bombus terrestris, Melipona bicolor and Trigona fimbriata) were used to infer Apis phylogenetic relationships using Bayesian analysis. The dwarf honey bees were confirmed as basal, and the giant and cavity-nesting species to be monophyletic. All nodes were strongly supported except that grouping Apis cerana with A. nigrocincta. Two thousand post-burnin trees from the phylogenetic analysis were used in a Bayesian comparative analysis to explore the evolution of dance type, nest structure, comb structure and dance sound within Apis. The ancestral honey bee species was inferred with high support to have nested in the open, and to have more likely than not had a silent vertical waggle dance and a single comb. The common ancestor of the giant and cavity-dwelling bees is strongly inferred to have had a buzzing vertical directional dance. All pairwise combinations of characters showed strong association, but the multiple comparisons problem reduces the ability to infer associations between states between characters. Nevertheless, a buzzing dance is significantly associated with cavity-nesting, several vertical combs, and dancing vertically, a horizontal dance is significantly associated with a nest with a single comb wrapped around the support, and open nesting with a single pendant comb and a silent waggle dance.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

PubMed

Furnham, Nicholas; Dawson, Natalie L; Rahman, Syed A; Thornton, Janet M; Orengo, Christine A

2016-01-29

Enzymes, as biological catalysts, form the basis of all forms of life. How these proteins have evolved their functions remains a fundamental question in biology. Over 100 years of detailed biochemistry studies, combined with the large volumes of sequence and protein structural data now available, means that we are able to perform large-scale analyses to address this question. Using a range of computational tools and resources, we have compiled information on all experimentally annotated changes in enzyme function within 379 structurally defined protein domain superfamilies, linking the changes observed in functions during evolution to changes in reaction chemistry. Many superfamilies show changes in function at some level, although one function often dominates one superfamily. We use quantitative measures of changes in reaction chemistry to reveal the various types of chemical changes occurring during evolution and to exemplify these by detailed examples. Additionally, we use structural information of the enzymes active site to examine how different superfamilies have changed their catalytic machinery during evolution. Some superfamilies have changed the reactions they perform without changing catalytic machinery. In others, large changes of enzyme function, in terms of both overall chemistry and substrate specificity, have been brought about by significant changes in catalytic machinery. Interestingly, in some superfamilies, relatives perform similar functions but with different catalytic machineries. This analysis highlights characteristics of functional evolution across a wide range of superfamilies, providing insights that will be useful in predicting the function of uncharacterised sequences and the design of new synthetic enzymes. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Structural Evolution of Sub-10 nm Octahedral Platinum$-$Nickel Bimetallic Nanocrystals

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

Chang, Qiaowan; Xu, Yuan; Duan, Zhiyuan

Octahedral Pt alloy nanocrystals (NCs) have shown excellent activities as electrocatalysts toward oxygen reduction reaction (ORR). As the activity and stability of NCs are highly dependent on their structure and the elemental distribution, it is of great importance to understand the formation mechanism of octahedral NCs and to rationally synthesize shape-controlled alloy catalysts with optimized ORR activity and stability. However, the factors controlling the structural and compositional evolution during the synthesis have not been well understood yet. Here in this paper, we systematically investigated the structure and composition evolution pathways of Pt–Ni octahedra synthesized with the assistance of W(CO) 6more » and revealed a unique core–shell structure consisting of a Pt core and a Pt–Ni alloy shell. Below 140 °C, sphere-like pure Pt NCs with the diameter of 3–4 nm first nucleated, followed by the isotropic growth of Pt–Ni alloy on the seeds at temperatures between 170 and 230 °C forming Pt@Pt–Ni core–shell octahedra with {111} facets. Owing to its unique structure, the Pt@Pt–Ni octahedra show an unparalleled stability during potential cycling, that is, no activity drop after 10 000 cycles between 0.6 and 1.0 V. This work proposes the Pt@Pt–Ni octahedra as a high profile electrocatalyst for ORR and reveals the structural and composition evolution pathways of Pt-based bimetallic NCs.« less

Structural Evolution of Sub-10 nm Octahedral Platinum$-$Nickel Bimetallic Nanocrystals

DOE PAGES

Chang, Qiaowan; Xu, Yuan; Duan, Zhiyuan; ...

2017-05-11

Octahedral Pt alloy nanocrystals (NCs) have shown excellent activities as electrocatalysts toward oxygen reduction reaction (ORR). As the activity and stability of NCs are highly dependent on their structure and the elemental distribution, it is of great importance to understand the formation mechanism of octahedral NCs and to rationally synthesize shape-controlled alloy catalysts with optimized ORR activity and stability. However, the factors controlling the structural and compositional evolution during the synthesis have not been well understood yet. Here in this paper, we systematically investigated the structure and composition evolution pathways of Pt–Ni octahedra synthesized with the assistance of W(CO) 6more » and revealed a unique core–shell structure consisting of a Pt core and a Pt–Ni alloy shell. Below 140 °C, sphere-like pure Pt NCs with the diameter of 3–4 nm first nucleated, followed by the isotropic growth of Pt–Ni alloy on the seeds at temperatures between 170 and 230 °C forming Pt@Pt–Ni core–shell octahedra with {111} facets. Owing to its unique structure, the Pt@Pt–Ni octahedra show an unparalleled stability during potential cycling, that is, no activity drop after 10 000 cycles between 0.6 and 1.0 V. This work proposes the Pt@Pt–Ni octahedra as a high profile electrocatalyst for ORR and reveals the structural and composition evolution pathways of Pt-based bimetallic NCs.« less

Evolutions of fluctuation modes and inner structures of global stock markets

NASA Astrophysics Data System (ADS)

Yan, Yan; Wang, Lei; Liu, Maoxin; Chen, Xiaosong

2016-09-01

The paper uses empirical data, including 42 globally main stock indices in the period 1996-2014, to systematically study the evolution of fluctuation modes and inner structures of global stock markets. The data are large in scale considering both time and space. A covariance matrix-based principle fluctuation mode analysis (PFMA) is used to explore the properties of the global stock markets. It has been ignored by previous studies that covariance matrix is more suitable than the correlation matrix to be the basis of PFMA. It is found that the principle fluctuation modes of global stock markets are in the same directions, and global stock markets are divided into three clusters, which are found to be closely related to the countries’ locations with exceptions of China, Russia and Czech Republic. A time-stable correlation network constructing method is proposed to solve the problem of high-level statistical uncertainty when the estimated periods are very short, and the complex dynamic network (CDN) is constructed to investigate the evolution of inner structures. The results show when the clusters emerge and how long the clusters exist. When the 2008 financial crisis broke out, the indices form one cluster. After these crises, only the European cluster still exists. These findings complement the previous studies, and can help investors and regulators to understand the global stock markets.

Transverse zones controlling the structural evolution of the Zipaquira Anticline (Eastern Cordillera, Colombia): Regional implications

NASA Astrophysics Data System (ADS)

García, Helbert; Jiménez, Giovanny

2016-08-01

We report paleomagnetic, magnetic fabric and structural results from 21 sites collected in Cretaceous marine mudstones and Paleogene continental sandstones from the limbs, hinge and transverse zones of the Zipaquira Anticline (ZA). The ZA is an asymmetrical fold with one limb completely overturned by processes like gravity and salt tectonics, and marked by several axis curvatures. The ZA is controlled by at least two (2) transverse zones known as the Neusa and Zipaquira Transverse Zones (NTZ and ZTZ, respectively). Magnetic mineralogy methods were applied at different sites and the main carriers of the magnetic properties are paramagnetic components with some sites being controlled by hematite and magnetite. Magnetic fabric analysis shows rigid-body rotation for the back-limb in the ZA, while the forelimb is subjected to internal deformation. Structural and paleomagnetic data shows the influence of the NTZ and ZTZ in the evolution of the different structures like the ZA and the Zipaquira, Carupa, Rio Guandoque, Las Margaritas and Neusa faults, controlling several factors as vergence, extension, fold axis curvature and stratigraphic detatchment. Clockwise rotations unraveled a block segmentation following a discontinuos model caused by transverse zones and one site reported a counter clockwise rotation associated with a left-lateral strike slip component for transverse faults (e.g. the Neusa Fault). We propose that diverse transverse zones have been active since Paleogene times, playing an important role in the tectonic evolution of the Cundinamarca sub-basin and controlling the structural evolution of folds and faults with block segmentation and rotations.

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation.

PubMed

Karasawa, N; Mitsutake, A; Takano, H

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n]polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μs molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Two-step relaxation mode analysis with multiple evolution times applied to all-atom molecular dynamics protein simulation

NASA Astrophysics Data System (ADS)

Karasawa, N.; Mitsutake, A.; Takano, H.

2017-12-01

Proteins implement their functionalities when folded into specific three-dimensional structures, and their functions are related to the protein structures and dynamics. Previously, we applied a relaxation mode analysis (RMA) method to protein systems; this method approximately estimates the slow relaxation modes and times via simulation and enables investigation of the dynamic properties underlying the protein structural fluctuations. Recently, two-step RMA with multiple evolution times has been proposed and applied to a slightly complex homopolymer system, i.e., a single [n ] polycatenane. This method can be applied to more complex heteropolymer systems, i.e., protein systems, to estimate the relaxation modes and times more accurately. In two-step RMA, we first perform RMA and obtain rough estimates of the relaxation modes and times. Then, we apply RMA with multiple evolution times to a small number of the slowest relaxation modes obtained in the previous calculation. Herein, we apply this method to the results of principal component analysis (PCA). First, PCA is applied to a 2-μ s molecular dynamics simulation of hen egg-white lysozyme in aqueous solution. Then, the two-step RMA method with multiple evolution times is applied to the obtained principal components. The slow relaxation modes and corresponding relaxation times for the principal components are much improved by the second RMA.

Evolution of human brain functions: the functional structure of human consciousness.

PubMed

Cloninger, C Robert

2009-11-01

The functional structure of self-aware consciousness in human beings is described based on the evolution of human brain functions. Prior work on heritable temperament and character traits is extended to account for the quantum-like and holographic properties (i.e. parts elicit wholes) of self-aware consciousness. Cladistic analysis is used to identify the succession of ancestors leading to human beings. The functional capacities that emerge along this lineage of ancestors are described. The ecological context in which each cladogenesis occurred is described to illustrate the shifting balance of evolution as a complex adaptive system. Comparative neuroanatomy is reviewed to identify the brain structures and networks that emerged coincident with the emergent brain functions. Individual differences in human temperament traits were well developed in the common ancestor shared by reptiles and humans. Neocortical development in mammals proceeded in five major transitions: from early reptiles to early mammals, early primates, simians, early Homo, and modern Homo sapiens. These transitions provide the foundation for human self-awareness related to sexuality, materiality, emotionality, intellectuality, and spirituality, respectively. The functional structure of human self-aware consciousness is concerned with the regulation of five planes of being: sexuality, materiality, emotionality, intellectuality, and spirituality. Each plane elaborates neocortical functions organized around one of the five special senses. The interactions among these five planes gives rise to a 5 x 5 matrix of subplanes, which are functions that coarsely describe the focus of neocortical regulation. Each of these 25 neocortical functions regulates each of five basic motives or drives that can be measured as temperaments or basic emotions related to fear, anger, disgust, surprise, and happiness/sadness. The resulting 5 x 5 x 5 matrix of human characteristics provides a general and testable model of the

Deformations and Structural Evolution of Mesozoic Complexes in Western Chukotka

NASA Astrophysics Data System (ADS)

Golionko, B. G.; Vatrushkina, E. V.; Verzhbitskii, V. E.; Sokolov, S. D.; Tuchkova, M. I.

2018-01-01

Detailed structural investigations have been carried out in the Pevek district to specify tectonic evolution of the Chukotka mesozoids. The earliest south-verging folds F1 formed in Triassic rocks at the first deformation stage DI. These structures are overlapped by the northern-verging folds F2 and overthrusts pertain to the second deformation stage DII. Folding structures F1 and F2 were deformed by shear folds F3, completing stage DII. The DI and DII structures are complicated by roughly NS-trending normal faults marking deformation stage DIII. It has been established that DI is related to the onset of opening of the Amerasian Basin in the Early Jurassic, or, alternatively, to the later accretion of the Kulpolnei ensimatic arc toward the Chukotka microcontinent. DII marks the collision of Siberia and the Chukotka microcontinent in the Late Neocomian. Normal faulting under the roughly E-W-trending extension during DIII is likely related to rift opening of the Podvodnikov and Makarov-Toll basins in the deep Amerasian Basin. Formation of the Okhotsk-Chukotka volcanoplutonic belt completed the structural evolution of the studied region.

The relativistic equations of stellar structure and evolution

NASA Technical Reports Server (NTRS)

Thorne, K. S.

1975-01-01

The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. A general relativistic version of the mixing-length formalism for convection is presented. It is argued that in work on spherical systems, general relativity theorists have identified the wrong quantity as total mass-energy inside radius r.

Rifting to India-Asia Reactivation: Multi-phase Structural Evolution of the Barmer Basin, Rajasthan, northwest India

NASA Astrophysics Data System (ADS)

Kelly, M. J.; Bladon, A.; Clarke, S.; Najman, Y.; Copley, A.; Kloppenburg, A.

2015-12-01

The Barmer Basin, situated within the West Indian Rift System, is an intra-cratonic rift basin produced during Gondwana break-up. Despite being a prominent oil and gas province, the structural evolution and context of the rift within northwest India remains poorly understood. Substantial subsurface datasets acquired during hydrocarbon exploration provide an unrivalled tool to investigate the tectonic evolution of the Barmer Basin rift and northwest India during India-Asia collision. Here we present a structural analysis using seismic datasets to investigate Barmer Basin evolution and place findings within the context of northwest India development. Present day rift structural architectures result from superposition of two non-coaxial extensional events; an early mid-Cretaceous rift-oblique event (NW-SE), followed by a main Paleocene rifting phase (NE-SW). Three phases of fault reactivation follow rifting: A transpressive, Late Paleocene inversion along localised E-W and NNE-SSW-trending faults; a widespread Late Paleocene-Early Eocene inversion and Late Miocene-Present Day transpressive strike-slip faulting along NW-SE-trending faults and isolated inversion structures. A major Late Eocene-Miocene unconformity in the basin is also identified, approximately coeval with those identified within the Himalayan foreland basin, suggesting a common cause related to India-Asia collision, and calling into question previous explanations that are not compatible with spatial extension of the unconformity beyond the foreland basin. Although, relatively poorly age constrained, extensional and compressional events within the Barmer Basin can be correlated with regional tectonic processes including the fragmentation of Gondwana, the rapid migration of the Greater Indian continent, to subsequent collision with Asia. New insights into the Barmer Basin development have important implications not only for ongoing hydrocarbon exploration but the temporal evolution of northwest India.

Data Management System (DMS) Evolution Analysis

NASA Technical Reports Server (NTRS)

Douglas, Katherine

1990-01-01

The all encompassing goal for the Data Management System (DMS) Evolution Analysis task is to develop an advocacy for ensuring that growth and technology insertion issues are properly and adequately addressed during DMS requirements specification, design, and development. The most efficient methods of addressing those issues are via planned and graceful evolution, technology transparency, and system growth margins. It is necessary that provisions, such as those previously mentioned, are made to accommodate advanced missions requirements (e.g., Human Space Exploration Programs) in addition to evolving Space Station Freedom operations and user requirements .

Comparable contributions of structural-functional constraints and expression level to the rate of protein sequence evolution

PubMed Central

Wolf, Maxim Y; Wolf, Yuri I; Koonin, Eugene V

2008-01-01

Background Proteins show a broad range of evolutionary rates. Understanding the factors that are responsible for the characteristic rate of evolution of a given protein arguably is one of the major goals of evolutionary biology. A long-standing general assumption used to be that the evolution rate is, primarily, determined by the specific functional constraints that affect the given protein. These constrains were traditionally thought to depend both on the specific features of the protein's structure and its biological role. The advent of systems biology brought about new types of data, such as expression level and protein-protein interactions, and unexpectedly, a variety of correlations between protein evolution rate and these variables have been observed. The strongest connections by far were repeatedly seen between protein sequence evolution rate and the expression level of the respective gene. It has been hypothesized that this link is due to the selection for the robustness of the protein structure to mistranslation-induced misfolding that is particularly important for highly expressed proteins and is the dominant determinant of the sequence evolution rate. Results This work is an attempt to assess the relative contributions of protein domain structure and function, on the one hand, and expression level on the other hand, to the rate of sequence evolution. To this end, we performed a genome-wide analysis of the effect of the fusion of a pair of domains in multidomain proteins on the difference in the domain-specific evolutionary rates. The mistranslation-induced misfolding hypothesis would predict that, within multidomain proteins, fused domains, on average, should evolve at substantially closer rates than the same domains in different proteins because, within a mutlidomain protein, all domains are translated at the same rate. We performed a comprehensive comparison of the evolutionary rates of mammalian and plant protein domains that are either joined in

Structural evolution across the insulator-metal transition in oxygen-deficient BaTiO 3-δ studied using neutron total scattering and Rietveld analysis

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

Jeong, I.-K.; Lee, Seunghun; Jeong, Se-Young

2011-08-29

Oxygen-deficient BaTiO 3-δ exhibits an insulator-metal transition with increasing δ. We performed neutron total scattering measurements to study structural evolution across an insulator-metal transition in BaTiO 3-δ. Despite its significant impact on resistivity, slight oxygen reduction (δ=0.09) caused only a small disturbance on the local doublet splitting of Ti-O bond. This finding implies that local polarization is well preserved under marginal electric conduction. In the highly oxygen-deficient metallic state (δ=0.25), however, doublet splitting of the Ti-O bond became smeared. The smearing of the local Ti-O doublet is complemented with long-range structural analysis and demonstrates that the metallic conduction in themore » highly oxygen-reduced BaTiO 3-δ is due to the appearance of nonferroelectric cubic lattice.« less

Structural Evolution of central part of the Tuzgolu (Salt Lake) Basin, Central Anatolia, Turkey

NASA Astrophysics Data System (ADS)

Ada, M.; Cemen, I.; Çaptuğ, A.; Demirci, M.; Engin, C.

2017-12-01

The Tuzgolu Basin in Central Anatolia, Turkey, covers low-relief areas located between the Pontide Mountains to the North and Tauride Mountains to the South. The basin started to form as a rift basin during the Late Maastrichtian. The main Tuzgolu-Aksaray fault zone on the eastern margin of the basin and the northwest trending Yeniceoba and Cihanbeyli fault zones on the western margin of the basin were probably developed during that time. The basin has also experienced westward extension in response to westward escape of the Anatolian plate since Late Miocene. Several geologic studies have been conducted in the Tuz Gölü (Salt Lake) Basin and surrounding areas to determine structural and tectono-stratigraphic development of the basin. However, there are still many questions regarding the structural evolution of the basin. The main purpose of this study is to investigate the structural evolution of the central Tuzgolu Basin based on the structural interpretation of available 2-D seismic reflection profiles, well log analysis and construction of structural cross sections. The cross-sections will be based on depth converted seismic lines to determine structural geometry of the faults and folds. A preliminary Petrel project has been prepared using available seismic profiles. Our preliminary structural interpretations suggest that a well-developed rollover anticline was developed with respect to the westward extension in Central Anatolia. The rollover anticline is faulted in its crest area by both down-to-the west and down-to-the east normal faults. The geometry of the main boundary fault at depth still remains in question. We anticipate that this question will be resolved based on depth converted structural cross-sections and their restoration.

Principal Component Analysis reveals correlation of cavities evolution and functional motions in proteins.

PubMed

Desdouits, Nathan; Nilges, Michael; Blondel, Arnaud

2015-02-01

Protein conformation has been recognized as the key feature determining biological function, as it determines the position of the essential groups specifically interacting with substrates. Hence, the shape of the cavities or grooves at the protein surface appears to drive those functions. However, only a few studies describe the geometrical evolution of protein cavities during molecular dynamics simulations (MD), usually with a crude representation. To unveil the dynamics of cavity geometry evolution, we developed an approach combining cavity detection and Principal Component Analysis (PCA). This approach was applied to four systems subjected to MD (lysozyme, sperm whale myoglobin, Dengue envelope protein and EF-CaM complex). PCA on cavities allows us to perform efficient analysis and classification of the geometry diversity explored by a cavity. Additionally, it reveals correlations between the evolutions of the cavities and structures, and can even suggest how to modify the protein conformation to induce a given cavity geometry. It also helps to perform fast and consensual clustering of conformations according to cavity geometry. Finally, using this approach, we show that both carbon monoxide (CO) location and transfer among the different xenon sites of myoglobin are correlated with few cavity evolution modes of high amplitude. This correlation illustrates the link between ligand diffusion and the dynamic network of internal cavities. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The evolution of void-filled cosmological structures

NASA Technical Reports Server (NTRS)

Regos, Eniko; Geller, Margaret J.

1991-01-01

1D, 2D, and 3D simulations are used here to investigate the salient features in the evolution of void-filled cosmological structures in universes with arbitrary values of Omega. It is found that the growth of a void as a function of time decreases significantly at the time corresponding to Omega = 0.5. In models constructed in 2D and 3D, suitable initial conditions lead to cellular structure with faceted voids similar to those observed in redshift surveys. Matter compressed to planes flows more rapidly toward condensations at the intersections than would be expected for spherical infall. The peculiar streaming velocities for void diameters of 5000 km/s should be observable. The simulations provide a more physical basis and dynamics for the bubbly and Voronois tesselation models used to derive statistical properties of cellular large-scale structure.

Quantitative Restoration of the Evolution of Mantle Structures Using Data Assimilation

NASA Astrophysics Data System (ADS)

Ismail-Zadeh, A.; Schubert, G.; Tsepelev, I.

2008-12-01

Rapid progress in imaging deep Earth structures and in studies of physical and chemical properties of mantle rocks facilitates research in assimilation of data related to mantle dynamics. We present a quantitative approach to assimilation of geophysical and geodetic data, which allows for incorporating observations and unknown initial conditions for mantle temperature and flow into a three-dimensional dynamic model in order to determine the initial conditions in the geological past. Once the conditions are determined the evolution of mantle structures can be restore backward in time. We apply data assimilation techniques to model the evolution of mantle plumes and lithospheric slabs. We show that the geometry of the mantle structures changes with time diminishing the degree of surface curvature of the structures, because the heat conduction smoothes the complex thermal surfaces of mantle bodies with time. Present seismic tomography images of mantle structures do not allow definition of the sharp shapes of these structures. Assimilation of mantle temperature and flow to the geological past instead provides a quantitative tool to restore thermal shapes of prominent structures in the past from their diffusive shapes at present.

Evolution in vitro: analysis of a lineage of ribozymes

NASA Technical Reports Server (NTRS)

Lehman, N.; Joyce, G. F.

1993-01-01

Background: Catalytic RNAs, or ribozymes, possessing both a genotype and a phenotype, are ideal molecules for evolution experiments in vitro. A large, heterogeneous pool of RNAs can be subjected to multiple rounds of selection, amplification and mutation, leading to the development of variants that have some desired phenotype. Such experiments allow the investigator to correlate specific genetic changes with quantifiable alterations of the catalytic properties of the RNA. In addition, patterns of evolutionary change can be discerned through a detailed examination of the genotypic composition of the evolving RNA population. Results: Beginning with a pool of 10(13) variants of the Tetrahymena ribozyme, we carried out in vitro evolution experiments that led to the generation of ribozymes with the ability to cleave an RNA substrate in the presence of Ca2+ ions, an activity that does not exist for the wild-type molecule. Over the course of 12 generations, a seven-error variant emerged that has substantial Ca(2+)-dependent RNA-cleavage activity. Advantageous mutations increased in frequency in the population according to three distinct dynamics--logarithmic, linear and transient. Through a comparative analysis of 31 individual variants, we infer how certain mutations influence the catalytic properties of the ribozyme. Conclusions: In vitro evolution experiments make it possible to elucidate important aspects of both evolutionary biology and structural biochemistry on a reasonable short time scale.

Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery

PubMed Central

2018-01-01

Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA). Here, small molecules from phenotypic screens with demonstrated antiparasitic activity are used in genome-based target discovery methods. In this Review, we discuss the newest, most promising druggable targets discovered or further validated by evolution-based methods, as well as some exceptions. PMID:29451780

Evolution and structure of Mercury's interior from MESSENGER observations

NASA Astrophysics Data System (ADS)

Tosi, Nicola

2015-04-01

During the past four years, the MESSENGER mission (MErcury Surface, Space Environment, GEochemistry and Ranging) has delivered a wealth of information that has been dramatically advancing the understanding of the geological, chemical, and physical state of Mercury. Taking into account the latest constraints on the interior structure, surface composition, volcanic and tectonic history, we employed numerical models to simulate the thermo-chemical evolution of the planet's interior [1]. Typical evolution scenarios that allow the observational constraints to be satisfied consist of an initial phase of mantle heating accompanied by planetary expansion and the production of a substantial amount of partial melt. The evolution subsequent to 2 Ga is characterised by secular cooling that proceeds approximately at a constant rate and implies that contraction should be still ongoing. Most of the models also predict mantle convection to cease after 3-4 Ga, indicating that Mercury may be no longer dynamically active. In addition, the topography, measured by laser altimetry and the gravity field, obtained from radio-tracking, represent fundamental observations that can be interpreted in terms of the chemical and mechanical structure of the interior. The observed geoid-to-topography ratios at intermediate wavelengths are well explained by the isostatic compensation of the topography associated with lateral variations of the crustal thickness, whose mean value can be estimated to be ~35 km, broadly confirming the predictions of the evolution simulations [2]. Finally, we will show that the degree-2 and 4 of the topography and geoid spectra can be explained in terms of the long-wavelength deformation of the lithosphere resulting from deep thermal anomalies caused by the large latitudinal and longitudinal variations in temperature experienced by Mercury's surface. [1] Tosi N., M. Grott, A.-C. Plesa and D. Breuer (2013). Thermo-chemical evolution of Mercury's interior. Journal of

Structure and evolution of fossil H II regions

NASA Technical Reports Server (NTRS)

Mccray, R.; Schwarz, J.

1971-01-01

The structure and evolution of a fossil H II region created by a burst of ionizing radiation from a supernova is considered. The cooling time scale for the shell is about 10 to the 6th power years. Superposition of million-year-old fossil H II regions may account for the temperature and ionization of the interstellar medium. Fossil H II regions are unstable to growth of thermal condensations. Highly ionized filamentary structures form and dissipate in about 10,000 years. Partially ionized clouds form and dissipate in about 10 to the 6th power years.

Improvisation in evolution of genes and genomes: whose structure is it anyway?

PubMed

Shakhnovich, Boris E; Shakhnovich, Eugene I

2008-06-01

Significant progress has been made in recent years in a variety of seemingly unrelated fields such as sequencing, protein structure prediction, and high-throughput transcriptomics and metabolomics. At the same time, new microscopic models have been developed that made it possible to analyze the evolution of genes and genomes from first principles. The results from these efforts enable, for the first time, a comprehensive insight into the evolution of complex systems and organisms on all scales--from sequences to organisms and populations. Every newly sequenced genome uncovers new genes, families, and folds. Where do these new genes come from? How do gene duplication and subsequent divergence of sequence and structure affect the fitness of the organism? What role does regulation play in the evolution of proteins and folds? Emerging synergism between data and modeling provides first robust answers to these questions.

Clostridium perfringens: insight into virulence evolution and population structure.

PubMed

Sawires, Youhanna S; Songer, J Glenn

2006-02-01

Clostridium perfringens is an important pathogen in veterinary and medical fields. Diseases caused by this organism are in many cases life threatening or fatal. At the same time, it is part of the ecological community of the intestinal tract of man and animals. Virulence in this species is not fully understood and it does seem that there is erratic distribution of the toxin/enzyme genes within C. perfringens population. We used the recently developed multiple-locus variable-number tandem repeat analysis (MLVA) scheme to investigate the evolution of virulence and population structure of this species. Analysis of the phylogenetic signal indicates that acquisition of the major toxin genes as well as other plasmid-borne toxin genes is a recent evolutionary event and their maintenance is essentially a function of the selective advantage they confer in certain niches under different conditions. In addition, it indicates the ability of virulent strains to cause disease in different host species. More interestingly, there is evidence that certain normal flora strains are virulent when they gain access to a different host species. Analysis of the population structure indicates that recombination events are the major tool that shapes the population and this panmixia is interrupted by frequent clonal expansion that mostly corresponds to disease processes. The signature of positive selection was detected in alpha toxin gene, suggesting the possibility of adaptive alleles on the other chromosomally encoded determinants. Finally, C. perfringens proved to have a dynamic population and availability of more genome sequences and use of comparative proteomics and animal modeling would provide more insight into the virulence of this organism.

[Analysis on property of meridian supramolecules by biological evolution path].

PubMed

Deng, Kaiwen; Tao, Yeqin; Tang, Wenhan; He, Fuyuan; Liu, Wenlong; Shi, Jilian; Yang, Yantao; Zhou, Yiqun; Chang, Xiaorong

2017-03-12

With human placed in the whole nature, by following the biologic evolution path, the property of channel structure for "imprinting template" in meridian and zang-fu was explored with supramolecular chemistry. In the history of biologic evolution, each molecule in "molecule society" gradually developed into various highly-ordered supramolecular bodies based on self-identification, self-assembly, self-organization, self-replicating of"imprinting template", and thereby the original biochemical system was established, and finally evolved into human. In the forming process of supramolecular bodies, the channel structure of"imprinting template" in guest supramolecular bodies would be kept by host supramolecular bodies, and communicate with the outside to exchange materials, energy, information, otherwise life phenomenon could not continue, for which it was the chemical nature of biolo-gical supramolecular bodies for body to develop meridian. Therefore, the human was a gigantic and complicated supramolecules body in biological nature, and possessed the supramolecules "imprinting template" at each stage of evolution, for which the meridians were formed. When meridians converged, acupoints appeared; when acupointsconverged, zang-fu appeared. With the promotion of the blood from heart, according to"imprinting template", the guest supramolecular bodies and host meridian produced qi -analysis, which was the qi -phenomenon of guest in meridian. It presented as zang-fu image of physiology and pathology as well as action regularities of medication and acupuncture tolerance, by which current various meridian viewpoints could be explained and propose the hypothesis of meridian supramolecular bodies. The meridian and its phenomenon was decide by its "imprinting template" of supramolecular bodies and self-reaction regularities, which abided through the living nature. This was the substance for meridian biology.

Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data

DOE PAGES

Murugesan, Sugeerth; Bouchard, Kristofer; Chang, Edward; ...

2016-10-02

Here, we present ECoG ClusterFlow, a novel interactive visual analysis tool for the exploration of high-resolution Electrocorticography (ECoG) data. Our system detects and visualizes dynamic high-level structures, such as communities, using the time-varying spatial connectivity network derived from the high-resolution ECoG data. ECoG ClusterFlow provides a multi-scale visualization of the spatio-temporal patterns underlying the time-varying communities using two views: 1) an overview summarizing the evolution of clusters over time and 2) a hierarchical glyph-based technique that uses data aggregation and small multiples techniques to visualize the propagation of clusters in their spatial domain. ECoG ClusterFlow makes it possible 1) tomore » compare the spatio-temporal evolution patterns across various time intervals, 2) to compare the temporal information at varying levels of granularity, and 3) to investigate the evolution of spatial patterns without occluding the spatial context information. Lastly, we present case studies done in collaboration with neuroscientists on our team for both simulated and real epileptic seizure data aimed at evaluating the effectiveness of our approach.« less

Maintenance of a Protein Structure in the Dynamic Evolution of TIMPs over 600 Million Years

PubMed Central

Nicosia, Aldo; Maggio, Teresa; Costa, Salvatore; Salamone, Monica; Tagliavia, Marcello; Mazzola, Salvatore; Gianguzza, Fabrizio; Cuttitta, Angela

2016-01-01

Deciphering the events leading to protein evolution represents a challenge, especially for protein families showing complex evolutionary history. Among them, TIMPs represent an ancient eukaryotic protein family widely distributed in the animal kingdom. They are known to control the turnover of the extracellular matrix and are considered to arise early during metazoan evolution, arguably tuning essential features of tissue and epithelial organization. To probe the structure and molecular evolution of TIMPs within metazoans, we report the mining and structural characterization of a large data set of TIMPs over approximately 600 Myr. The TIMPs repertoire was explored starting from the Cnidaria phylum, coeval with the origins of connective tissue, to great apes and humans. Despite dramatic sequence differences compared with highest metazoans, the ancestral proteins displayed the canonical TIMP fold. Only small structural changes, represented by an α-helix located in the N-domain, have occurred over the evolution. Both the occurrence of such secondary structure elements and the relative solvent accessibility of the corresponding residues in the three-dimensional structures raises the possibility that these sites represent unconserved element prone to accept variations. PMID:26957029

Evolution of bacterial life-history traits is sensitive to community structure.

PubMed

Ketola, Tarmo; Mikonranta, Lauri; Mappes, Johanna

2016-06-01

Very few studies have experimentally assessed the evolutionary effects of species interactions within the same trophic level. Here we show that when Serratia marcescens evolve in multispecies communities, their growth rate exceeds the growth rate of the bacteria that evolved alone, whereas the biomass yield gets lower. In addition to the community effects per se, we found that few species in the communities caused strong effects on S. marcescens evolution. The results indicate that evolutionary responses (of a focal species) are different in communities, compared to species evolving alone. Moreover, selection can lead to very different outcomes depending on the community structure. Such context dependencies cast doubt on our ability to predict the course of evolution in the wild, where species often inhabit very different kinds of communities. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Protein structure and evolution: are they constrained globally by a principle derived from information theory?

PubMed

Hatton, Leslie; Warr, Gregory

2015-01-01

That the physicochemical properties of amino acids constrain the structure, function and evolution of proteins is not in doubt. However, principles derived from information theory may also set bounds on the structure (and thus also the evolution) of proteins. Here we analyze the global properties of the full set of proteins in release 13-11 of the SwissProt database, showing by experimental test of predictions from information theory that their collective structure exhibits properties that are consistent with their being guided by a conservation principle. This principle (Conservation of Information) defines the global properties of systems composed of discrete components each of which is in turn assembled from discrete smaller pieces. In the system of proteins, each protein is a component, and each protein is assembled from amino acids. Central to this principle is the inter-relationship of the unique amino acid count and total length of a protein and its implications for both average protein length and occurrence of proteins with specific unique amino acid counts. The unique amino acid count is simply the number of distinct amino acids (including those that are post-translationally modified) that occur in a protein, and is independent of the number of times that the particular amino acid occurs in the sequence. Conservation of Information does not operate at the local level (it is independent of the physicochemical properties of the amino acids) where the influences of natural selection are manifest in the variety of protein structure and function that is well understood. Rather, this analysis implies that Conservation of Information would define the global bounds within which the whole system of proteins is constrained; thus it appears to be acting to constrain evolution at a level different from natural selection, a conclusion that appears counter-intuitive but is supported by the studies described herein.

Morphological bubble evolution induced by air diffusion on submerged hydrophobic structures

NASA Astrophysics Data System (ADS)

Lv, Pengyu; Xiang, Yaolei; Xue, Yahui; Lin, Hao; Duan, Huiling

2017-03-01

Bubbles trapped in the cavities always play important roles in the underwater applications of structured hydrophobic surfaces. Air exchange between bubbles and surrounding water has a significant influence on the morphological bubble evolution, which in turn frequently affects the functionalities of the surfaces, such as superhydrophobicity and drag reduction. In this paper, air diffusion induced bubble evolution on submerged hydrophobic micropores under reduced pressures is investigated experimentally and theoretically. The morphological behaviors of collective and single bubbles are observed using confocal microscopy. Four representative evolution phases of bubbles are captured in situ. After depressurization, bubbles will not only grow and coalesce but also shrink and split although the applied pressure remains negative. A diffusion-based model is used to analyze the evolution behavior and the results are consistent with the experimental data. A criterion for bubble growth and shrinkage is also derived along with a phase diagram, revealing that the competition of effective gas partial pressures across the two sides of the diffusion layer dominates the bubble evolution process. Strategies for controlling the bubble evolution behavior are also proposed based on the phase diagram. The current work provides a further understanding of the general behavior of bubble evolution induced by air diffusion and can be employed to better designs of functional microstructured hydrophobic surfaces.

Cultural Transmission and Evolution of Melodic Structures in Multi-generational Signaling Games.

PubMed

Lumaca, Massimo; Baggio, Giosuè

2017-01-01

It has been proposed that languages evolve by adapting to the perceptual and cognitive constraints of the human brain, developing, in the course of cultural transmission, structural regularities that maximize or optimize learnability and ease of processing. To what extent would perceptual and cognitive constraints similarly affect the evolution of musical systems? We conducted an experiment on the cultural evolution of artificial melodic systems, using multi-generational signaling games as a laboratory model of cultural transmission. Signaling systems, using five-tone sequences as signals, and basic and compound emotions as meanings, were transmitted from senders to receivers along diffusion chains in which the receiver in each game became the sender in the next game. During transmission, structural regularities accumulated in the signaling systems, following principles of proximity, symmetry, and good continuation. Although the compositionality of signaling systems did not increase significantly across generations, we did observe a significant increase in similarity among signals from the same set. We suggest that our experiment tapped into the cognitive and perceptual constraints operative in the cultural evolution of musical systems, which may differ from the mechanisms at play in language evolution and change.

Morphology evolution in strain-compensated multiple quantum well structures

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

Ledentsov, N. N., E-mail: nikolay.ledentsov@v-i-systems.com; Shchukin, V. A.; Rouvimov, S.

2014-01-20

Morphology evolution in (In,Ga)As-Ga(As,P) strain-compensated multilayer structures is studied. The effects of nanoscale interface corrugation and phase separation are evident after the third period of the multilayer structure and become more pronounced with each new stack until the sixth period. Then, the interface stabilizes pointing to the formation of strain-balanced equilibrium interface structure. The epitaxial structure remains defect-free up to the maximum number (twenty) of periods studied. In a structure with a high lattice mismatch between the neighboring layers, In{sub 0.40}Ga{sub 0.60}As/GaAs{sub 0.85}P{sub 0.15}, clusters of dislocations are revealed already in the third period. The observed phenomena are critical formore » proper engineering of optoelectronic devices.« less

3D WHOLE-PROMINENCE FINE STRUCTURE MODELING. II. PROMINENCE EVOLUTION

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

Gunár, Stanislav; Mackay, Duncan H.

2015-10-20

We use the new three-dimensional (3D) whole-prominence fine structure model to study the evolution of prominences and their fine structures in response to changes in the underlying photospheric magnetic flux distribution. The applied model combines a detailed 3D prominence magnetic field configuration with a realistic description of the prominence plasma distributed along multiple fine structures. In addition, we utilize an approximate Hα visualization technique to study the evolution of the visible cool prominence plasma both in emission (prominence) and absorption (filament). We show that the initial magnetic field configuration of the modeled prominence is significantly disturbed by the changing positionmore » of a single polarity of a magnetic bipole as the bipole is advected toward the main body of the filament. This leads to the creation of a barb, which becomes the dominant feature visible in the synthetic Hα images of both the prominence and filament views. The evolution of the bipole also creates conditions that lead to the disappearance and reappearance of large portions of the main body. We also show that an arch-like region containing a dark void (a bubble) can be naturally produced in the synthetic prominence Hα images. While not visible in terms of the magnetic field lines, it is due to a lack of Hα emission from low-pressure, low-density plasma located in shallow magnetic dips lying along the lines of sight intersecting the dark void. In addition, a quasi-vertical small-scale feature consisting of short and deep dips, piled one above the other, is produced.« less

Coronal Structures in Cool Stars: XMM-NEWTON Hybrid Stars and Coronal Evolution

NASA Technical Reports Server (NTRS)

Dupree, Andrea K.; Mushotzky, Richard (Technical Monitor)

2003-01-01

This program addresses the evolution of stellar coronas by comparing a solar-like corona in the supergiant Beta Dra (G2 Ib-IIa) to the corona in the allegedly more evolved state of a hybrid star, alpha TrA (K2 II-III). Because the hybrid star has a massive wind, it appears likely that the corona will be cooler and less dense as the magnetic loop structures are no longer closed. By analogy with solar coronal holes, when the topology of the magnetic field is configured with open magnetic structures, both the coronal temperature and density are lower than in atmospheres dominated by closed loops. The hybrid stars assume a pivotal role in the definition of coronal evolution, atmospheric heating processes and mechanisms to drive winds of cool stars. We are attempting to determine if this model of coronal evolution is correct by using XMM-NEWTON RGS spectra for the 2 targets we were allocated through the Guest Observer program.

Structure and evolution of N-domains in AAA metalloproteases.

PubMed

Scharfenberg, Franka; Serek-Heuberger, Justyna; Coles, Murray; Hartmann, Marcus D; Habeck, Michael; Martin, Jörg; Lupas, Andrei N; Alva, Vikram

2015-02-27

Metalloproteases of the AAA (ATPases associated with various cellular activities) family play a crucial role in protein quality control within the cytoplasmic membrane of bacteria and the inner membrane of eukaryotic organelles. These membrane-anchored hexameric enzymes are composed of an N-terminal domain with one or two transmembrane helices, a central AAA ATPase module, and a C-terminal Zn(2+)-dependent protease. While the latter two domains have been well studied, so far, little is known about the N-terminal regions. Here, in an extensive bioinformatic and structural analysis, we identified three major, non-homologous groups of N-domains in AAA metalloproteases. By far, the largest one is the FtsH-like group of bacteria and eukaryotic organelles. The other two groups are specific to Yme1: one found in plants, fungi, and basal metazoans and the other one found exclusively in animals. Using NMR and crystallography, we determined the subunit structure and hexameric assembly of Escherichia coli FtsH-N, exhibiting an unusual α+β fold, and the conserved part of fungal Yme1-N from Saccharomyces cerevisiae, revealing a tetratricopeptide repeat fold. Our bioinformatic analysis showed that, uniquely among these proteins, the N-domain of Yme1 from the cnidarian Hydra vulgaris contains both the tetratricopeptide repeat region seen in basal metazoans and a region of homology to the N-domains of animals. Thus, it is a modern-day representative of an intermediate in the evolution of animal Yme1 from basal eukaryotic precursors. Copyright © 2015. Published by Elsevier Ltd.

Time evolution of fine structures in the solar chromosphere.

NASA Astrophysics Data System (ADS)

Tsiropoula, G.; Alissandrakis, C. E.; Schmieder, B.

1994-10-01

We have studied the temporal evolution of two quiet chromospheric regions, one with a typical rosette and another with chains of mottles at the junction of three supergranules. The observations were obtained during 15 minutes with the Multichannel Subtractive Double Pass spectrograph (MSDP) operating in Hα at the Pic du Midi Observatory. We derived intensity maps and Doppler shift velocities at different wavelengths along the Hα profile over a two dimensional field of view. The observed contrast profiles were matched with theoretical contrast profiles using Beckers' cloud model for a more accurate determination of the line of sight velocity. A statistical analysis with cross correlation functions showed that the fine structures were stable in intensity over the observation period (15 min), but the line of sight velocity showed important changes within a few minutes. A detailed analysis of the velocities along the axes of dark mottles showed that the predominant pattern of bulk motion is that of downflow at their footpoints and alternating phases of upflow and downflow at their tops. This motion is consistent with Pikel'ner's model for spicules, which attributes this pattern to the reconnection of opposite magnetic filed lines. This picture is also consistent with the velocity reversals with time observed in spicules and may be associated to the systematic downflows observed in the transition region. Doppler shift velocities in dark mottles are too low compared to those derived with the cloud model; the latter are comparable to those reported for spicules, strengthening the view that these structures are identical.

Structure Evolution of BaTiO3 on Co Doping: X-ray diffraction and Raman study

NASA Astrophysics Data System (ADS)

Mansuri, Amantulla; Mishra, Ashutosh

2016-10-01

In the present study, we have synthesize polycrystalline samples of BaTi1-xCoxO3 (x = 0, 0.05 and 0.1) with standard solid state reaction technique. The obtained samples are characterized by X-ray diffraction (XRD) and Raman spectroscopy. The detail structural analysis has been performed by Rietveld refinement using Fullprof program. The structural analysis reveal the samples are chemical pure and crystallize in tetragonal phase with space group Pm3m. We observe an increase in lattice parameters which results due to substitution of Co2+ with large ionic radii (0.9) for smaller ionic radii (0.6) Ti4+. Moreover peak at 45.5° shift to 45° on Co doping, which is due to structure phase transition from tetragonal to cubic. Raman study infers that the intensity of characteristic peaks decreases and linewidth increases with Co doping. The bands linked with the tetragonal structure (307 cm1) decreased due to the tetragonal-towards-cubic phase transition with Co doping. Our structural study reveals the expansion of BTO unit cell and tetragonal-to-cubic phase transformation takes place, results from different characterization techniques are conclusive and show structural evolution with Co doping.

Magnetic resonance imaging and image analysis for assessment of HPMC matrix tablets structural evolution in USP Apparatus 4.

PubMed

Kulinowski, Piotr; Dorożyński, Przemysław; Młynarczyk, Anna; Węglarz, Władysław P

2011-05-01

The purpose of the study was to present a methodology for the processing of Magnetic Resonance Imaging (MRI) data for the quantification of the dosage form matrix evolution during drug dissolution. The results of the study were verified by comparison with other approaches presented in literature. A commercially available, HPMC-based quetiapine fumarate tablet was studied with a 4.7T MR system. Imaging was performed inside an MRI probe-head coupled with a flow-through cell for 12 h in circulating water. The images were segmented into three regions using threshold-based segmentation algorithms due to trimodal structure of the image intensity histograms. Temporal evolution of dry glassy, swollen glassy and gel regions was monitored. The characteristic features were observed: initial high expansion rate of the swollen glassy and gel layers due to initial water uptake, dry glassy core disappearance and maximum area of swollen glassy region at 4 h, and subsequent gel layer thickness increase at the expense of swollen glassy layer. The temporal evolution of an HPMC-based tablet by means of noninvasive MRI integrated with USP Apparatus 4 was found to be consistent with both the theoretical model based on polymer disentanglement concentration and experimental VIS/FTIR studies.

SINEs, evolution and genome structure in the opossum.

PubMed

Gu, Wanjun; Ray, David A; Walker, Jerilyn A; Barnes, Erin W; Gentles, Andrew J; Samollow, Paul B; Jurka, Jerzy; Batzer, Mark A; Pollock, David D

2007-07-01

Short INterspersed Elements (SINEs) are non-autonomous retrotransposons, usually between 100 and 500 base pairs (bp) in length, which are ubiquitous components of eukaryotic genomes. Their activity, distribution, and evolution can be highly informative on genomic structure and evolutionary processes. To determine recent activity, we amplified more than one hundred SINE1 loci in a panel of 43 M. domestica individuals derived from five diverse geographic locations. The SINE1 family has expanded recently enough that many loci were polymorphic, and the SINE1 insertion-based genetic distances among populations reflected geographic distance. Genome-wide comparisons of SINE1 densities and GC content revealed that high SINE1 density is associated with high GC content in a few long and many short spans. Young SINE1s, whether fixed or polymorphic, showed an unbiased GC content preference for insertion, indicating that the GC preference accumulates over long time periods, possibly in periodic bursts. SINE1 evolution is thus broadly similar to human Alu evolution, although it has an independent origin. High GC content adjacent to SINE1s is strongly correlated with bias towards higher AT to GC substitutions and lower GC to AT substitutions. This is consistent with biased gene conversion, and also indicates that like chickens, but unlike eutherian mammals, GC content heterogeneity (isochore structure) is reinforced by substitution processes in the M. domestica genome. Nevertheless, both high and low GC content regions are apparently headed towards lower GC content equilibria, possibly due to a relative shift to lower recombination rates in the recent Monodelphis ancestral lineage. Like eutherians, metatherian (marsupial) mammals have evolved high CpG substitution rates, but this is apparently a convergence in process rather than a shared ancestral state.

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing

PubMed Central

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-01-01

ABSTRACT Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure. PMID:28277933

Role and convergent evolution of competing RNA secondary structures in mutually exclusive splicing.

PubMed

Yue, Yuan; Hou, Shouqing; Wang, Xiu; Zhan, Leilei; Cao, Guozheng; Li, Guoli; Shi, Yang; Zhang, Peng; Hong, Weiling; Lin, Hao; Liu, Baoping; Shi, Feng; Yang, Yun; Jin, Yongfeng

2017-10-03

Exon or cassette duplication is an important means of expanding protein and functional diversity through mutually exclusive splicing. However, the mechanistic basis of this process in non-arthropod species remains poorly understood. Here, we demonstrate that MRP1 genes underwent tandem exon duplication in Nematoda, Platyhelminthes, Annelida, Mollusca, Arthropoda, Echinodermata, and early-diverging Chordata but not in late-diverging vertebrates. Interestingly, these events were of independent origin in different phyla, suggesting convergent evolution of alternative splicing. Furthermore, we showed that multiple sets of clade-conserved RNA pairings evolved to guide species-specific mutually exclusive splicing in Arthropoda. Importantly, we also identified a similar structural code in MRP exon clusters of the annelid, Capitella teleta, and chordate, Branchiostoma belcheri, suggesting an evolutionarily conserved competing pairing-guided mechanism in bilaterians. Taken together, these data reveal the molecular determinants and RNA pairing-guided evolution of species-specific mutually exclusive splicing spanning more than 600 million years of bilaterian evolution. These findings have a significant impact on our understanding of the evolution of and mechanism underpinning isoform diversity and complex gene structure.

Structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Kanzyuba, Vasily; Dong, Sining; Liu, Xinyu; Li, Xiang; Rouvimov, Sergei; Okuno, Hanako; Mariette, Henri; Zhang, Xueqiang; Ptasinska, Sylwia; Tracy, Brian D.; Smith, David J.; Dobrowolska, Margaret; Furdyna, Jacek K.

2017-02-01

We describe the structural evolution of dilute magnetic (Sn,Mn)Se films grown by molecular beam epitaxy on GaAs (111) substrates, as revealed by transmission electron microscopy, X-ray diffraction, and X-ray photoelectron spectroscopy. When the Mn concentration is increased, the lattice of the ternary (Sn,Mn)Se films evolves quasi-coherently from a SnSe2 two-dimensional (2D) crystal structure into a more complex quasi-2D lattice rearrangement, ultimately transforming into the magnetically concentrated antiferromagnetic MnSe 3D rock-salt structure as Mn approaches 50 at. % of this material. These structural transformations are expected to underlie the evolution of magnetic properties of this ternary system reported earlier in the literature.

The interface of protein structure, protein biophysics, and molecular evolution

PubMed Central

Liberles, David A; Teichmann, Sarah A; Bahar, Ivet; Bastolla, Ugo; Bloom, Jesse; Bornberg-Bauer, Erich; Colwell, Lucy J; de Koning, A P Jason; Dokholyan, Nikolay V; Echave, Julian; Elofsson, Arne; Gerloff, Dietlind L; Goldstein, Richard A; Grahnen, Johan A; Holder, Mark T; Lakner, Clemens; Lartillot, Nicholas; Lovell, Simon C; Naylor, Gavin; Perica, Tina; Pollock, David D; Pupko, Tal; Regan, Lynne; Roger, Andrew; Rubinstein, Nimrod; Shakhnovich, Eugene; Sjölander, Kimmen; Sunyaev, Shamil; Teufel, Ashley I; Thorne, Jeffrey L; Thornton, Joseph W; Weinreich, Daniel M; Whelan, Simon

2012-01-01

Abstract The interface of protein structural biology, protein biophysics, molecular evolution, and molecular population genetics forms the foundations for a mechanistic understanding of many aspects of protein biochemistry. Current efforts in interdisciplinary protein modeling are in their infancy and the state-of-the art of such models is described. Beyond the relationship between amino acid substitution and static protein structure, protein function, and corresponding organismal fitness, other considerations are also discussed. More complex mutational processes such as insertion and deletion and domain rearrangements and even circular permutations should be evaluated. The role of intrinsically disordered proteins is still controversial, but may be increasingly important to consider. Protein geometry and protein dynamics as a deviation from static considerations of protein structure are also important. Protein expression level is known to be a major determinant of evolutionary rate and several considerations including selection at the mRNA level and the role of interaction specificity are discussed. Lastly, the relationship between modeling and needed high-throughput experimental data as well as experimental examination of protein evolution using ancestral sequence resurrection and in vitro biochemistry are presented, towards an aim of ultimately generating better models for biological inference and prediction. PMID:22528593

PIECE 2.0: an update for the plant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparision and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron-exon organization and provides valuable insights into the evolution of gene structure in ...

Evolution Analysis of Simple Sequence Repeats in Plant Genome.

PubMed

Qin, Zhen; Wang, Yanping; Wang, Qingmei; Li, Aixian; Hou, Fuyun; Zhang, Liming

2015-01-01

Simple sequence repeats (SSRs) are widespread units on genome sequences, and play many important roles in plants. In order to reveal the evolution of plant genomes, we investigated the evolutionary regularities of SSRs during the evolution of plant species and the plant kingdom by analysis of twelve sequenced plant genome sequences. First, in the twelve studied plant genomes, the main SSRs were those which contain repeats of 1-3 nucleotides combination. Second, in mononucleotide SSRs, the A/T percentage gradually increased along with the evolution of plants (except for P. patens). With the increase of SSRs repeat number the percentage of A/T in C. reinhardtii had no significant change, while the percentage of A/T in terrestrial plants species gradually declined. Third, in dinucleotide SSRs, the percentage of AT/TA increased along with the evolution of plant kingdom and the repeat number increased in terrestrial plants species. This trend was more obvious in dicotyledon than monocotyledon. The percentage of CG/GC showed the opposite pattern to the AT/TA. Forth, in trinucleotide SSRs, the percentages of combinations including two or three A/T were in a rising trend along with the evolution of plant kingdom; meanwhile with the increase of SSRs repeat number in plants species, different species chose different combinations as dominant SSRs. SSRs in C. reinhardtii, P. patens, Z. mays and A. thaliana showed their specific patterns related to evolutionary position or specific changes of genome sequences. The results showed that, SSRs not only had the general pattern in the evolution of plant kingdom, but also were associated with the evolution of the specific genome sequence. The study of the evolutionary regularities of SSRs provided new insights for the analysis of the plant genome evolution.

Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...

Evolution of plant δ 1-pyrroline-5-carboxylate reductases from phylogenetic and structural perspectives

DOE PAGES

Forlani, Giuseppe; Makarova, Kira S.; Ruszkowski, Milosz; ...

2015-08-03

Proline plays a crucial role in cell growth and stress responses, and its accumulation is essential for the tolerance of adverse environmental conditions in plants. Two routes are used to biosynthesize proline in plants. The main route uses glutamate as a precursor, while in the other route proline is derived from ornithine. The terminal step of both pathways, the conversion of δ 1-pyrroline-5-carboxylate (P5C) to L-proline, is catalyzed by P5C reductase (P5CR) using NADH or NADPH as a cofactor. Since P5CRs are important housekeeping enzymes, they are conserved across all domains of life and appear to be relatively unaffected throughoutmore » evolution. However, global analysis of these enzymes unveiled significant functional diversity in the preference for cofactors (NADPH vs. NADH), variation in metal dependence and the differences in the oligomeric state. In our study we investigated evolutionary patterns through phylogenetic and structural analysis of P5CR representatives from all kingdoms of life, with emphasis on the plant species. We attempted to correlate local sequence/structure variation among the functionally and structurally characterized members of the family.« less

Structural Biology and Evolution of the TGF-β Family

PubMed Central

Hinck, Andrew P.; Mueller, Thomas D.; Springer, Timothy A.

2017-01-01

We review the evolution and structure of members of the transforming growth factor β (TGF-β) family, antagonistic or agonistic modulators, and receptors that regulate TGF-β signaling in extracellular environments. The growth factor (GF) domain common to all family members and many of their antagonists evolved from a common cystine knot growth factor (CKGF) domain. The CKGF superfamily comprises six distinct families in primitive metazoans, including the TGF-β and Dan families. Compared with Wnt/Frizzled and Notch/Delta families that also specify body axes, cell fate, tissues, and other families that contain CKGF domains that evolved in parallel, the TGF-β family was the most fruitful in evolution. Complexes between the prodomains and GFs of the TGF-β family suggest a new paradigm for regulating GF release by conversion from closed- to open-arm procomplex conformations. Ternary complexes of the final step in extracellular signaling show how TGF-β GF dimers bind type I and type II receptors on the cell surface, and enable understanding of much of the specificity and promiscuity in extracellular signaling. However, structures suggest that when GFs bind repulsive guidance molecule (RGM) family coreceptors, type I receptors do not bind until reaching an intracellular, membrane-enveloped compartment, blurring the line between extra- and intracellular signaling. Modulator protein structures show how structurally diverse antagonists including follistatins, noggin, and members of the chordin family bind GFs to regulate signaling; complexes with the Dan family remain elusive. Much work is needed to understand how these molecular components assemble to form signaling hubs in extracellular environments in vivo. PMID:27638177

Image Analysis Technique for Material Behavior Evaluation in Civil Structures

PubMed Central

Moretti, Michele; Rossi, Gianluca

2017-01-01

The article presents a hybrid monitoring technique for the measurement of the deformation field. The goal is to obtain information about crack propagation in existing structures, for the purpose of monitoring their state of health. The measurement technique is based on the capture and analysis of a digital image set. Special markers were used on the surface of the structures that can be removed without damaging existing structures as the historical masonry. The digital image analysis was done using software specifically designed in Matlab to follow the tracking of the markers and determine the evolution of the deformation state. The method can be used in any type of structure but is particularly suitable when it is necessary not to damage the surface of structures. A series of experiments carried out on masonry walls of the Oliverian Museum (Pesaro, Italy) and Palazzo Silvi (Perugia, Italy) have allowed the validation of the procedure elaborated by comparing the results with those derived from traditional measuring techniques. PMID:28773129

Image Analysis Technique for Material Behavior Evaluation in Civil Structures.

PubMed

Speranzini, Emanuela; Marsili, Roberto; Moretti, Michele; Rossi, Gianluca

2017-07-08

The article presents a hybrid monitoring technique for the measurement of the deformation field. The goal is to obtain information about crack propagation in existing structures, for the purpose of monitoring their state of health. The measurement technique is based on the capture and analysis of a digital image set. Special markers were used on the surface of the structures that can be removed without damaging existing structures as the historical masonry. The digital image analysis was done using software specifically designed in Matlab to follow the tracking of the markers and determine the evolution of the deformation state. The method can be used in any type of structure but is particularly suitable when it is necessary not to damage the surface of structures. A series of experiments carried out on masonry walls of the Oliverian Museum (Pesaro, Italy) and Palazzo Silvi (Perugia, Italy) have allowed the validation of the procedure elaborated by comparing the results with those derived from traditional measuring techniques.

The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

Leith, Alex P.; Ratan, Rabindra A.; Wohn, Donghee Yvette

2016-08-01

Given the diversity and complexity of education game mechanisms and topics, this article contributes to a theoretical understanding of how game mechanisms "map" to educational topics through inquiry-based learning. Namely, the article examines the presence of evolution through natural selection (ENS) in digital games. ENS is a fundamentally important and widely misunderstood theory. This analysis of ENS portrayal in digital games provides insight into the use of games in teaching ENS. Systematic database search results were coded for the three principles of ENS: phenotypic variation, differential fitness, and fitness heritability. Though thousands of games use the term evolution, few presented elements of evolution, and even fewer contained all principles of ENS. Games developed to specifically teach evolution were difficult to find through Web searches. These overall deficiencies in ENS games reflect the inherent incompatibility between game control elements and the automatic process of ENS.

Paleostress maps and structural evolution of the Pontides

NASA Astrophysics Data System (ADS)

Hippolyte, Jean-Claude; Espurt, Nicolas; Kaymakci, Nuretdin; Sangu, Ercan; Müller, Carla

2014-05-01

In the frame of DARIUS programme we worked from 2010 to 2012 in the central and eastern Pontides. We aimed at understanding the timing and the characteristics of the extensional and compressional episodes that occurred along the southern margin of the Black Sea (Pontides belt). We used stress inversion technique (Angelier's softwares) for analyzing fault kinematics and characterizing the successive tectonic episodes in terms of paleostresses. The age of the tectonic episodes was constrained by combining structural analysis with nannoplankton dating of the sedimentary units. 1) In the central Pontides, structural analysis shows that deposition of the Barremian-Albian terrigenous sediments of the "syn-rift" Çaglayan Group was controlled by large normal faults under an ESE-WNW extension probably related to the SE-directed opening of the western Black Sea Basin. In contrast, the Coniacian-Santonian and the Paleocene "post-rift" sequences were deposited under NE-SW extension probably related to the SW-directed opening of the eastern Black Sea Basin. At the beginning of Eocene the stress regime changed from extensional to compressional which resulted in the formation of syn-compressional basins. In order to illustrate the two-dimensional structural evolution of the central Pontides we built a NNE-trending 75 km long balanced and restored cross section between Boyabat and Sinop cities. The section is constrained by 183 sites of field data, 5 seismic lines and 8 wells. We model the Pontides as a bi-vergent structure resulting from the structural inversion of Cretaceous normal faults of the southern Black Sea margin. Apatite fission track data along this section suggest that inversion started in the earliest Eocene (~55 Ma). Eocene-Miocene shortening reached ~28 km. 2) In the eastern Pontides, an early Campanian to late Paleocene NW-SE extension was followed by three successive compressional events. A Paleocene to early Eocene NW-SE compression resulted in the formation of

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Astrophysics Data System (ADS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-03-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

Time-dependent evolution of cosmic-ray-modified shock structure: Transition to steady state

NASA Technical Reports Server (NTRS)

Donohue, D. J.; Zank, G. P.; Webb, G. M.

1994-01-01

Steady state solutions to the two-fluid equations of cosmic-ray-modified shock structure were investigated first by Drury and Volk (1981). Their analysis revealed, among other properties, that there exist regions of upstream parameter space where the equations possess three different downstream solutions for a given upstream state. In this paper we investigate whether or not all these solutions can occur as time-asymptotic states in a physically realistic evolution. To do this, we investigate the time-dependent evolution of the two-fluid cosmic-ray equations in going from a specified initial condition to a steady state. Our results indicate that the time-asymptotic solution is strictly single-valued, and it undergoes a transition from weakly to strongly cosmic-ray-modified at a critical value of the upstream cosmic ray energy density. The expansion of supernova remnant shocks is considered as an example, and it is shown that the strong to weak transition is in fact more likely. The third intermediate solution is shown to influence the time-dependent evolution of the shock, but it is not found to be a stable time-asymptotic state. Timescales for convergence to these states and their implications for the efficiency of shock acceleration are considered. We also investigate the effects of a recently introduced model for the injection of seed particles into the shock accelerated cosmic-ray population. The injection is found to result in a more strongly cosmic-ray-dominated shock, which supports our conclusion that for most classes of intermediate and strong cosmic-ray-modified shocks, the downstream cosmic-ray pressure component is at least as large as the thermal gas pressure, independent of the upstream state. As a result, cosmic rays almost always play a significant role in determining the shock structure and dissipation and they cannot be regarded as test particles.

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function

PubMed Central

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A.

2012-01-01

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that the functional evolution can be inferred from the changes in the protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced Cα representation of the protein structure while enzymatic function is described by Enzyme Commission (EC) numbers. Similarity of the binding pocket dynamics at each branch of the protein family’s phylogeny was analyzed in two ways: 1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and 2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the alpha-amylase, D-isomer specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal modes analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. PMID:22651983

A phylogenetic analysis of normal modes evolution in enzymes and its relationship to enzyme function.

PubMed

Lai, Jason; Jin, Jing; Kubelka, Jan; Liberles, David A

2012-09-21

Since the dynamic nature of protein structures is essential for enzymatic function, it is expected that functional evolution can be inferred from the changes in protein dynamics. However, dynamics can also diverge neutrally with sequence substitution between enzymes without changes of function. In this study, a phylogenetic approach is implemented to explore the relationship between enzyme dynamics and function through evolutionary history. Protein dynamics are described by normal mode analysis based on a simplified harmonic potential force field applied to the reduced C(α) representation of the protein structure while enzymatic function is described by Enzyme Commission numbers. Similarity of the binding pocket dynamics at each branch of the protein family's phylogeny was analyzed in two ways: (1) explicitly by quantifying the normal mode overlap calculated for the reconstructed ancestral proteins at each end and (2) implicitly using a diffusion model to obtain the reconstructed lineage-specific changes in the normal modes. Both explicit and implicit ancestral reconstruction identified generally faster rates of change in dynamics compared with the expected change from neutral evolution at the branches of potential functional divergences for the α-amylase, D-isomer-specific 2-hydroxyacid dehydrogenase, and copper-containing amine oxidase protein families. Normal mode analysis added additional information over just comparing the RMSD of static structures. However, the branch-specific changes were not statistically significant compared to background function-independent neutral rates of change of dynamic properties and blind application of the analysis would not enable prediction of changes in enzyme specificity. Copyright © 2012 Elsevier Ltd. All rights reserved.

Focused Evolution of HIV-1 Neutralizing Antibodies Revealed by Structures and Deep Sequencing

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

Wu, Xueling; Zhou, Tongqing; Zhu, Jiang

2013-03-04

Antibody VRC01 is a human immunoglobulin that neutralizes about 90% of HIV-1 isolates. To understand how such broadly neutralizing antibodies develop, we used x-ray crystallography and 454 pyrosequencing to characterize additional VRC01-like antibodies from HIV-1-infected individuals. Crystal structures revealed a convergent mode of binding for diverse antibodies to the same CD4-binding-site epitope. A functional genomics analysis of expressed heavy and light chains revealed common pathways of antibody-heavy chain maturation, confined to the IGHV1-2*02 lineage, involving dozens of somatic changes, and capable of pairing with different light chains. Broadly neutralizing HIV-1 immunity associated with VRC01-like antibodies thus involves the evolution ofmore » antibodies to a highly affinity-matured state required to recognize an invariant viral structure, with lineages defined from thousands of sequences providing a genetic roadmap of their development.« less

Atomic study of effects of crystal structure and temperature on structural evolution of Au nanowires under torsion

NASA Astrophysics Data System (ADS)

Wu, Cheng-Da; Tsai, Hsing-Wei

2018-06-01

The effect of temperature on the structural evolution of nanocrystalline (NC) and single-crystalline (SC) Au nanowires (NWs) under torsional deformation is studied using molecular dynamics simulations based on the many-body embedded-atom potential. The effect is investigated using common neighbor analysis and discussed in terms of shear strain distribution and atomic flow field. The simulation results show that deformation for NC NWs is mainly driven by the nucleation and propagation of dislocations and the gliding of grain boundaries (GBs) and that for SC NWs is mainly driven by dislocations and the formation of disordered structures. Dislocations for NC and SC NWs easily nucleate at GBs and free surfaces, respectively. For NC NWs, torsional buckling occurs easily at GBs with large gliding. SC NWs have a more uniform and larger elastic deformation under torsion compared to that for NC NWs due to the former's lack of grains. SC NWs have a long period of elastic deformation transforming into plastic deformation. Increasing temperature facilitates stress transmission throughout NWs.

Evolution of stochastic demography with life history tradeoffs in density-dependent age-structured populations.

PubMed

Lande, Russell; Engen, Steinar; Sæther, Bernt-Erik

2017-10-31

We analyze the stochastic demography and evolution of a density-dependent age- (or stage-) structured population in a fluctuating environment. A positive linear combination of age classes (e.g., weighted by body mass) is assumed to act as the single variable of population size, [Formula: see text], exerting density dependence on age-specific vital rates through an increasing function of population size. The environment fluctuates in a stationary distribution with no autocorrelation. We show by analysis and simulation of age structure, under assumptions often met by vertebrate populations, that the stochastic dynamics of population size can be accurately approximated by a univariate model governed by three key demographic parameters: the intrinsic rate of increase and carrying capacity in the average environment, [Formula: see text] and [Formula: see text], and the environmental variance in population growth rate, [Formula: see text] Allowing these parameters to be genetically variable and to evolve, but assuming that a fourth parameter, [Formula: see text], measuring the nonlinearity of density dependence, remains constant, the expected evolution maximizes [Formula: see text] This shows that the magnitude of environmental stochasticity governs the classical trade-off between selection for higher [Formula: see text] versus higher [Formula: see text] However, selection also acts to decrease [Formula: see text], so the simple life-history trade-off between [Formula: see text]- and [Formula: see text]-selection may be obscured by additional trade-offs between them and [Formula: see text] Under the classical logistic model of population growth with linear density dependence ([Formula: see text]), life-history evolution in a fluctuating environment tends to maximize the average population size. Published under the PNAS license.

Evolution of amino acid metabolism inferred through cladistic analysis.

PubMed

Cunchillos, Chomin; Lecointre, Guillaume

2003-11-28

Because free amino acids were most probably available in primitive abiotic environments, their metabolism is likely to have provided some of the very first metabolic pathways of life. What were the first enzymatic reactions to emerge? A cladistic analysis of metabolic pathways of the 16 aliphatic amino acids and 2 portions of the Krebs cycle was performed using four criteria of homology. The analysis is not based on sequence comparisons but, rather, on coding similarities in enzyme properties. The properties used are shared specific enzymatic activity, shared enzymatic function without substrate specificity, shared coenzymes, and shared functional family. The tree shows that the earliest pathways to emerge are not portions of the Krebs cycle but metabolisms of aspartate, asparagine, glutamate, and glutamine. The views of Horowitz (Horowitz, N. H. (1945) Proc. Natl. Acad. Sci. U. S. A. 31, 153-157) and Cordón (Cordón, F. (1990) Tratado Evolucionista de Biologia, Aguilar, Madrid, Spain), according to which the upstream reactions in the catabolic pathways and the downstream reactions in the anabolic pathways are the earliest in evolution, are globally corroborated; however, with some exceptions. These are due to later opportunistic connections of pathways (actually already suggested by these authors). Earliest enzymatic functions are mostly catabolic; they were deaminations, transaminations, and decarboxylations. From the consensus tree we extracted four time spans for amino acid metabolism development. For some amino acids catabolism and biosynthesis occurred at the same time (Asp, Glu, Lys, Leu, Ala, Val, Ile, Pro, Arg). For others ultimate reactions that use amino acids as a substrate or as a product are distinct in time, with catabolism preceding anabolism for Asn, Gln, and Cys and anabolism preceding catabolism for Ser, Met, and Thr. Cladistic analysis of the structure of biochemical pathways makes hypotheses in biochemical evolution explicit and parsimonious.

Structural evolution of nanoscale metallic glasses during high-pressure torsion: A molecular dynamics analysis

NASA Astrophysics Data System (ADS)

Feng, S. D.; Jiao, W.; Jing, Q.; Qi, L.; Pan, S. P.; Li, G.; Ma, M. Z.; Wang, W. H.; Liu, R. P.

2016-11-01

Structural evolution in nanoscale Cu50Zr50 metallic glasses during high-pressure torsion is investigated using molecular dynamics simulations. Results show that the strong cooperation of shear transformations can be realized by high-pressure torsion in nanoscale Cu50Zr50 metallic glasses at room temperature. It is further shown that high-pressure torsion could prompt atoms to possess lower five-fold symmetries and higher potential energies, making them more likely to participate in shear transformations. Meanwhile, a higher torsion period leads to a greater degree of forced cooperative flow. And the pronounced forced cooperative flow at room temperature under high-pressure torsion permits the study of the shear transformation, its activation and characteristics, and its relationship to the deformations behaviors. This research not only provides an important platform for probing the atomic-level understanding of the fundamental mechanisms of high-pressure torsion in metallic glasses, but also leads to higher stresses and homogeneous flow near lower temperatures which is impossible previously.

Evolution of the insulin molecule: insights into structure-activity and phylogenetic relationships.

PubMed

Conlon, J M

2001-07-01

The conformation of insulin in the crystalline state has been known for more than 30 years but there remains uncertainty regarding the biologically active conformation and the structural features that constitute the receptor-binding domain. The primary structure of insulin has been determined for at least 100 vertebrate species. In addition to the invariant cysteines, only ten amino acids (GlyA1, IleA2, ValA3, TyrA19, LeuB6, GlyB8, LeuB11, ValB12, GlyB23 and PheB24) have been fully conserved during vertebrate evolution. This observation supports the hypothesis derived from alanine-scanning mutagenesis studies that five of these invariant residues (IleA2, ValA3, TyrA19, GlyB23, and Phe24) interact directly with the receptor and five additional conserved residues (LeuB6, GlyB8, LeuB11, GluB13 and PheB25) are important in maintaining the receptor-binding conformation. With the exception of the hagfish, only conservative substitutions are found at B13 (Glu --> Asp) and B25(Phe --> Tyr). In contrast, amino acid residues that were also considered to be important in receptor binding based upon the crystal structure of insulin (GluA4, GlnA5, AsnA21, TyrB16, TyrB26) have been much less well conserved and are probably not components of the receptor-binding domain. The hypothesis that LeuA13 and LeuB17 form part of a second receptor-binding site in the insulin molecule finds some support in terms of their conservation during vertebrate evolution, although the site is probably absent in some hystricomorph insulins. In general, the amino acid sequences of insulins are not useful in cladistic analyses especially when evolutionary distant taxa are compared but, among related species in a particular order or family, the presence of unusual structural features in the insulin molecule may permit a meaningful phylogenetic inference. For example, analysis of insulin sequences supports monophyletic status for Dipnoi, Elasmobranchii, Holocephali and Petromyzontiformes.

Empirical analysis of RNA robustness and evolution using high-throughput sequencing of ribozyme reactions.

PubMed

Hayden, Eric J

2016-08-15

RNA molecules provide a realistic but tractable model of a genotype to phenotype relationship. This relationship has been extensively investigated computationally using secondary structure prediction algorithms. Enzymatic RNA molecules, or ribozymes, offer access to genotypic and phenotypic information in the laboratory. Advancements in high-throughput sequencing technologies have enabled the analysis of sequences in the lab that now rivals what can be accomplished computationally. This has motivated a resurgence of in vitro selection experiments and opened new doors for the analysis of the distribution of RNA functions in genotype space. A body of computational experiments has investigated the persistence of specific RNA structures despite changes in the primary sequence, and how this mutational robustness can promote adaptations. This article summarizes recent approaches that were designed to investigate the role of mutational robustness during the evolution of RNA molecules in the laboratory, and presents theoretical motivations, experimental methods and approaches to data analysis. Copyright © 2016 Elsevier Inc. All rights reserved.

Vector-Borne Pathogen and Host Evolution in a Structured Immuno-Epidemiological System.

PubMed

Gulbudak, Hayriye; Cannataro, Vincent L; Tuncer, Necibe; Martcheva, Maia

2017-02-01

Vector-borne disease transmission is a common dissemination mode used by many pathogens to spread in a host population. Similar to directly transmitted diseases, the within-host interaction of a vector-borne pathogen and a host's immune system influences the pathogen's transmission potential between hosts via vectors. Yet there are few theoretical studies on virulence-transmission trade-offs and evolution in vector-borne pathogen-host systems. Here, we consider an immuno-epidemiological model that links the within-host dynamics to between-host circulation of a vector-borne disease. On the immunological scale, the model mimics antibody-pathogen dynamics for arbovirus diseases, such as Rift Valley fever and West Nile virus. The within-host dynamics govern transmission and host mortality and recovery in an age-since-infection structured host-vector-borne pathogen epidemic model. By considering multiple pathogen strains and multiple competing host populations differing in their within-host replication rate and immune response parameters, respectively, we derive evolutionary optimization principles for both pathogen and host. Invasion analysis shows that the [Formula: see text] maximization principle holds for the vector-borne pathogen. For the host, we prove that evolution favors minimizing case fatality ratio (CFR). These results are utilized to compute host and pathogen evolutionary trajectories and to determine how model parameters affect evolution outcomes. We find that increasing the vector inoculum size increases the pathogen [Formula: see text], but can either increase or decrease the pathogen virulence (the host CFR), suggesting that vector inoculum size can contribute to virulence of vector-borne diseases in distinct ways.

Evolution and development of gas exchange structures in Mammalia: the placenta and the lung.

PubMed

Mess, Andrea M; Ferner, Kirsten J

2010-08-31

Appropriate oxygen supply is crucial for organisms. Here we examine the evolution of structures associated with the delivery of oxygen in the pre- and postnatal phases in mammals. There is an enormous structural and functional variability in the placenta that has facilitated the evolution of specialized reproductive strategies, such as precociality. In particular the cell layers separating fetal and maternal blood differ markedly: a non-invasive epitheliochorial placenta, which increases the diffusion distance, represents a derived state in ungulates. Rodents and their relatives have an invasive haemochorial placental type as optimum for the diffusion distance. In contrast, lung development is highly conserved and differences in the lungs of neonates can be explained by different developmental rates. Monotremes and marsupials have altricial stages with lungs at the early saccular phase, whereas newborn eutherians have lungs at the late saccular or alveolar phase. In conclusion, the evolution of exchange structures in the pre- and postnatal periods does not follow similar principles. Copyright (c) 2010 Elsevier B.V. All rights reserved.

Evolution of Protein Domain Repeats in Metazoa

PubMed Central

Schüler, Andreas; Bornberg-Bauer, Erich

2016-01-01

Repeats are ubiquitous elements of proteins and they play important roles for cellular function and during evolution. Repeats are, however, also notoriously difficult to capture computationally and large scale studies so far had difficulties in linking genetic causes, structural properties and evolutionary trajectories of protein repeats. Here we apply recently developed methods for repeat detection and analysis to a large dataset comprising over hundred metazoan genomes. We find that repeats in larger protein families experience generally very few insertions or deletions (indels) of repeat units but there is also a significant fraction of noteworthy volatile outliers with very high indel rates. Analysis of structural data indicates that repeats with an open structure and independently folding units are more volatile and more likely to be intrinsically disordered. Such disordered repeats are also significantly enriched in sites with a high functional potential such as linear motifs. Furthermore, the most volatile repeats have a high sequence similarity between their units. Since many volatile repeats also show signs of recombination, we conclude they are often shaped by concerted evolution. Intriguingly, many of these conserved yet volatile repeats are involved in host-pathogen interactions where they might foster fast but subtle adaptation in biological arms races. Key Words: protein evolution, domain rearrangements, protein repeats, concerted evolution. PMID:27671125

Models of protocellular structures, functions and evolution

NASA Technical Reports Server (NTRS)

Pohorille, Andrew; New, Michael H.; DeVincenzi, Donald L. (Technical Monitor)

2000-01-01

The central step in the origin of life was the emergence of organized structures from organic molecules available on the early earth. These predecessors to modern cells, called 'proto-cells,' were simple, membrane bounded structures able to maintain themselves, grow, divide, and evolve. Since there is no fossil record of these earliest of life forms, it is a scientific challenge to discover plausible mechanisms for how these entities formed and functioned. To meet this challenge, it is essential to create laboratory models of protocells that capture the main attributes associated with living systems, while remaining consistent with known, or inferred, protobiological conditions. This report provides an overview of a project which has focused on protocellular metabolism and the coupling of metabolism to energy transduction. We have assumed that the emergence of systems endowed with genomes and capable of Darwinian evolution was preceded by a pre-genomic phase, in which protocells functioned and evolved using mostly proteins, without self-replicating nucleic acids such as RNA.

Spatially structured superinfection and the evolution of disease virulence.

PubMed

Caraco, Thomas; Glavanakov, Stephan; Li, Shengua; Maniatty, William; Szymanski, Boleslaw K

2006-06-01

When pathogen strains differing in virulence compete for hosts, spatial structuring of disease transmission can govern both evolved levels of virulence and patterns in strain coexistence. We develop a spatially detailed model of superinfection, a form of contest competition between pathogen strains; the probability of superinfection depends explicitly on the difference in levels of virulence. We apply methods of adaptive dynamics to address the interplay of spatial dynamics and evolution. The mean-field approximation predicts evolution to criticality; any small increase in virulence capable of dynamical persistence is favored. Both pair approximation and simulation of the detailed model indicate that spatial structure constrains disease virulence. Increased spatial clustering reduces the maximal virulence capable of single-strain persistence and, more importantly, reduces the convergent-stable virulence level under strain competition. The spatially detailed model predicts that increasing the probability of superinfection, for given difference in virulence, increases the likelihood of between-strain coexistence. When strains differing in virulence can coexist ecologically, our results may suggest policies for managing diseases with localized transmission. Comparing equilibrium densities from the pair approximation, we find that introducing a more virulent strain into a host population infected by a less virulent strain can sometimes reduce total host mortality and increase global host density.

Evolution of an arsenal: structural and functional diversification of the venom system in the advanced snakes (Caenophidia).

PubMed

Fry, Bryan G; Scheib, Holger; van der Weerd, Louise; Young, Bruce; McNaughtan, Judith; Ramjan, S F Ryan; Vidal, Nicolas; Poelmann, Robert E; Norman, Janette A

2008-02-01

Venom is a key innovation underlying the evolution of advanced snakes (Caenophidia). Despite this, very little is known about venom system structural diversification, toxin recruitment event timings, or toxin molecular evolution. A multidisciplinary approach was used to examine the diversification of the venom system and associated toxins across the full range of the approximately 100 million-year-old advanced snake clade with a particular emphasis upon families that have not secondarily evolved a front-fanged venom system ( approximately 80% of the 2500 species). Analysis of cDNA libraries revealed complex venom transcriptomes containing multiple toxin types including three finger toxins, cobra venom factor, cysteine-rich secretory protein, hyaluronidase, kallikrein, kunitz, lectin, matrix metalloprotease, phospholipase A(2), snake venom metalloprotease/a disintegrin and metalloprotease, and waprin. High levels of sequence diversity were observed, including mutations in structural and functional residues, changes in cysteine spacing, and major deletions/truncations. Morphological analysis comprising gross dissection, histology, and magnetic resonance imaging also demonstrated extensive modification of the venom system architecture in non-front-fanged snakes in contrast to the conserved structure of the venom system within the independently evolved front-fanged elapid or viperid snakes. Further, a reduction in the size and complexity of the venom system was observed in species in which constriction has been secondarily evolved as the preferred method of prey capture or dietary preference has switched from live prey to eggs or to slugs/snails. Investigation of the timing of toxin recruitment events across the entire advanced snake radiation indicates that the evolution of advanced venom systems in three front-fanged lineages is associated with recruitment of new toxin types or explosive diversification of existing toxin types. These results support the role of venom

The evolution and population structure of Lactobacillus fermentum from different naturally fermented products as determined by multilocus sequence typing (MLST).

PubMed

Dan, Tong; Liu, Wenjun; Song, Yuqin; Xu, Haiyan; Menghe, Bilige; Zhang, Heping; Sun, Zhihong

2015-05-20

Lactobacillus fermentum is economically important in the production and preservation of fermented foods. A repeatable and discriminative typing method was devised to characterize L. fermentum at the molecular level. The multilocus sequence typing (MLST) scheme developed was based on analysis of the internal sequence of 11 housekeeping gene fragments (clpX, dnaA, dnaK, groEL, murC, murE, pepX, pyrG, recA, rpoB, and uvrC). MLST analysis of 203 isolates of L. fermentum from Mongolia and seven provinces/ autonomous regions in China identified 57 sequence types (ST), 27 of which were represented by only a single isolate, indicating high genetic diversity. Phylogenetic analyses based on the sequence of the 11 housekeeping gene fragments indicated that the L. fermentum isolates analyzed belonged to two major groups. A standardized index of association (I A (S)) indicated a weak clonal population structure in L. fermentum. Split decomposition analysis indicated that recombination played an important role in generating the genetic diversity observed in L. fermentum. The results from the minimum spanning tree strongly suggested that evolution of L. fermentum STs was not correlated with geography or food-type. The MLST scheme developed will be valuable for further studies on the evolution and population structure of L. fermentum isolates used in food products.

Forest structure analysis combining laser scanning with digital airborne photogrammetry

NASA Astrophysics Data System (ADS)

Lissak, Candide; Onda, Yuichi; Kato, Hiroaki

2017-04-01

The interest of Light Detection and Ranging (LiDAR) for vegetation structure analysis has been demonstrated in several research context. Indeed, airborne or ground Lidar surveys can provide detailed three-dimensional data of the forest structure from understorey forest to the canopy. To characterize at different timescale the vegetation components in dense cedar forests we can combine several sources point clouds from Lidar survey and photogrammetry data. For our study, Terrestrial Laser Scanning (TLS-Leica ScanStation C10 processed with Cyclone software) have been lead in three forest areas (≈ 200m2 each zone) mainly composed of japanese cedar (Japonica cryptomeria), in the region of Fukushima (Japan). The study areas are characterized by various vegetation densities. For the 3 areas, Terrestrial laser scanning has been performed from several location points and several heights. Various floors shootings (ground, 4m, 6m and 18m high) were able with the use of a several meters high tower implanted to study the canopy evolution following the Fukushima Daiishi nuclear power plant accident. The combination of all scanners provides a very dense 3D point cloud of ground and canopy structure (average 300 000 000 points). For the Tochigi forest area, a first test of a low-cost Unmanned Aerial Vehicle (UAV) photogrammetry has been lead and calibrated by ground GPS measurements to determine the coordinates of points. TLS combined to UAV photogrammetry make it possible to obtain information on vertical and horizontal structure of the Tochigi forest. This combination of technologies will allow the forest structure mapping, morphometry analysis and the assessment of biomass volume evolution from multi-temporal point clouds. In our research, we used a low-cost UAV 3 Advanced (200 m2 cover, 1300 pictures...). Data processing were performed using PotoScan Pro software to obtain a very dense point clouds to combine to TLS data set. This low-cost UAV photogrammetry data has been

Observed Evolution of the Upper-level Thermal Structure in Tropical Cyclones

NASA Astrophysics Data System (ADS)

Rivoire, L.; Birner, T.; Knaff, J. A.

2016-12-01

Tropical cyclones (TCs) are associated with tropopause-level cooling above the well-known tropospheric warm core. While the investigation of tropopause-level structures started as early as 1951, there is no clear consensus on the mechanisms involved. In addition, the large-scale average vertical and radial structure of the tropopause-level cooling is yet to be examined. Tropopause-level cooling destabilizes the upper atmosphere to convection, which potentially allows existing convection to reach higher altitudes. This is of particular importance during the early stages of tropical cyclogenesis. Other important characteristics of the tropopause-level cooling include its amplitude, its position relative to that of the warm core, its radial extent, and its evolution during the lifetime of TCs. These potentially influence TC structure, surface pressure gradients and maximum winds, intensity evolution, and outflow entropy. We use the 322 hurricane-strength TCs from the best-track archive in 2007-2014, along with high vertical resolution temperature measurements from the Constellation Observing System for Meteorology, Ionosphere, and Climate (COSMIC). These measurements are composited about the Lifetime Maximum Intensity (LMI) to examine the evolution of the fine-scale upper-level thermal structure inside TCs. We find that the tropopause-cooling has an amplitude similar to that of the warm core. Relative to the far-field structure (the area average between 1300-1500 km radii), tropopause-level cooling is found to occur several days before the warm core is established. Cold anomalies extend up to 1000 km away from the storm center, and may take part in a large-scale poleward transport of cold, dry air in the UTLS. Lastly, cold air masses move away from the storm center (and warm core) after LMI, and their remains lie around the 400-700 km radius -essentially inward of the radius of maximum tangential anticyclonic winds in the outflow layer. We discuss these results in the

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution

PubMed Central

Chursov, Andrey; Frishman, Dmitrij; Shneider, Alexander

2013-01-01

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the ‘long-term evolution experiment’. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation. Our principal finding is that purifying selection tends to eliminate those mutations in essential genes that lead to greater changes of MFE values and, therefore, may be more disruptive for the corresponding mRNA secondary structures. This effect implies that synonymous mutations disrupting mRNA secondary structures may directly affect the fitness of the organism. These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. PMID:23783573

A passive mutualistic interaction promotes the evolution of spatial structure within microbial populations.

PubMed

Marchal, Marie; Goldschmidt, Felix; Derksen-Müller, Selina N; Panke, Sven; Ackermann, Martin; Johnson, David R

2017-04-24

While mutualistic interactions between different genotypes are pervasive in nature, their evolutionary origin is not clear. The dilemma is that, for mutualistic interactions to emerge and persist, an investment into the partner genotype must pay off: individuals of a first genotype that invest resources to promote the growth of a second genotype must receive a benefit that is not equally accessible to individuals that do not invest. One way for exclusive benefits to emerge is through spatial structure (i.e., physical barriers to the movement of individuals and resources). Here we propose that organisms can evolve their own spatial structure based on physical attachment between individuals, and we hypothesize that attachment evolves when spatial proximity to members of another species is advantageous. We tested this hypothesis using experimental evolution with combinations of E. coli strains that depend on each other to grow. We found that attachment between cells repeatedly evolved within 8 weeks of evolution and observed that many different types of mutations potentially contributed to increased attachment. We postulate a general principle by which passive beneficial interactions between organisms select for attachment, and attachment then provides spatial structure that could be conducive for the evolution of active mutualistic interactions.

Dynamic analysis of evolutive conservative systems. Discussion of eigenmode crossings

NASA Technical Reports Server (NTRS)

Morand, H. J. P.

1984-01-01

After an analysis of the close connection between the symmetries of a dynamical system and the multiplicity of its vibrational natural frequencies, it is proved by variational arguments that for a system of invariable symmetry the eigenfrequencies associated with the eigenmodes of a given symmetry type do not cross, in general, during the evolution of this system. The theory is implemented by some numerical calculations applied to the analysis of the evolution of the axisymmetric hydroelastic modes of the Ariane launch vehicle during burning of the first stage.

Roles of NN-interaction components in shell-structure evolution

NASA Astrophysics Data System (ADS)

Umeya, Atsushi; Muto, Kazuo

2016-11-01

Since the importance of the monopole interaction was first emphasized in 1960s, roles of monopole strengths of two-body nucleon-nucleon interaction in shell structure have been discussed. Through the monopole strengths, we study the roles in shell-structure evolution, starting from explicit forms of the interaction. For the tensor component of the interaction, we show the derivation of the relation, (2j> + 1)Vjj> + (2j< + 1)Vjj< = 0, with a detailed manipulation. We show that one-body spin-orbit term appears in the multipole expansion of two-body spin-orbit interaction. Only the spin-orbit components can affect the spin-orbit energy splitting between spin-orbit partners, when the spin-orbit partner orbits are fully occupied.

Time evolution of coherent structures in networks of Hindmarch Rose neurons

NASA Astrophysics Data System (ADS)

Mainieri, M. S.; Erichsen, R.; Brunnet, L. G.

2005-08-01

In the regime of partial synchronization, networks of diffusively coupled Hindmarch-Rose neurons show coherent structures developing in a region of the phase space which is wider than in the correspondent single neuron. Such structures are kept, without important changes, during several bursting periods. In this work, we study the time evolution of these structures and their dynamical stability under damage. This system may model the behavior of ensembles of neurons coupled through a bidirectional gap junction or, in a broader sense, it could also account for the molecular cascades present in the formation of flash and short time memory.

A global analysis of adaptive evolution of operons in cyanobacteria.

PubMed

Memon, Danish; Singh, Abhay K; Pakrasi, Himadri B; Wangikar, Pramod P

2013-02-01

Operons are an important feature of prokaryotic genomes. Evolution of operons is hypothesized to be adaptive and has contributed significantly towards coordinated optimization of functions. Two conflicting theories, based on (i) in situ formation to achieve co-regulation and (ii) horizontal gene transfer of functionally linked gene clusters, are generally considered to explain why and how operons have evolved. Furthermore, effects of operon evolution on genomic traits such as intergenic spacing, operon size and co-regulation are relatively less explored. Based on the conservation level in a set of diverse prokaryotes, we categorize the operonic gene pair associations and in turn the operons as ancient and recently formed. This allowed us to perform a detailed analysis of operonic structure in cyanobacteria, a morphologically and physiologically diverse group of photoautotrophs. Clustering based on operon conservation showed significant similarity with the 16S rRNA-based phylogeny, which groups the cyanobacterial strains into three clades. Clade C, dominated by strains that are believed to have undergone genome reduction, shows a larger fraction of operonic genes that are tightly packed in larger sized operons. Ancient operons are in general larger, more tightly packed, better optimized for co-regulation and part of key cellular processes. A sub-clade within Clade B, which includes Synechocystis sp. PCC 6803, shows a reverse trend in intergenic spacing. Our results suggest that while in situ formation and vertical descent may be a dominant mechanism of operon evolution in cyanobacteria, optimization of intergenic spacing and co-regulation are part of an ongoing process in the life-cycle of operons.

Thermally Induced Structural Evolution and Performance of Mesoporous Block Copolymer-Directed Alumina Perovskite Solar Cells

PubMed Central

2015-01-01

Structure control in solution-processed hybrid perovskites is crucial to design and fabricate highly efficient solar cells. Here, we utilize in situ grazing incidence wide-angle X-ray scattering and scanning electron microscopy to investigate the structural evolution and film morphologies of methylammonium lead tri-iodide/chloride (CH3NH3PbI3–xClx) in mesoporous block copolymer derived alumina superstructures during thermal annealing. We show the CH3NH3PbI3–xClx material evolution to be characterized by three distinct structures: a crystalline precursor structure not described previously, a 3D perovskite structure, and a mixture of compounds resulting from degradation. Finally, we demonstrate how understanding the processing parameters provides the foundation needed for optimal perovskite film morphology and coverage, leading to enhanced block copolymer-directed perovskite solar cell performance. PMID:24684494

The Mass, Color, and Structural Evolution of Today’s Massive Galaxies Since z ˜ 5

NASA Astrophysics Data System (ADS)

Hill, Allison R.; Muzzin, Adam; Franx, Marijn; Clauwens, Bart; Schreiber, Corentin; Marchesini, Danilo; Stefanon, Mauro; Labbe, Ivo; Brammer, Gabriel; Caputi, Karina; Fynbo, Johan; Milvang-Jensen, Bo; Skelton, Rosalind E.; van Dokkum, Pieter; Whitaker, Katherine E.

2017-03-01

In this paper, we use stacking analysis to trace the mass growth, color evolution, and structural evolution of present-day massive galaxies ({log}({M}* /{M}⊙ )=11.5) out to z = 5. We utilize the exceptional depth and area of the latest UltraVISTA data release, combined with the depth and unparalleled seeing of CANDELS to gather a large, mass-selected sample of galaxies in the NIR (rest-frame optical to UV). Progenitors of present-day massive galaxies are identified via an evolving cumulative number density selection, which accounts for the effects of merging to correct for the systematic biases introduced using a fixed cumulative number density selection, and find progenitors grow in stellar mass by ≈ 1.5 {dex} since z = 5. Using stacking, we analyze the structural parameters of the progenitors and find that most of the stellar mass content in the central regions was in place by z˜ 2, and while galaxies continue to assemble mass at all radii, the outskirts experience the largest fractional increase in stellar mass. However, we find evidence of significant stellar mass build-up at r< 3 {kpc} beyond z> 4 probing an era of significant mass assembly in the interiors of present-day massive galaxies. We also compare mass assembly from progenitors in this study to the EAGLE simulation and find qualitatively similar assembly with z at r< 3 {kpc}. We identify z˜ 1.5 as a distinct epoch in the evolution of massive galaxies where progenitors transitioned from growing in mass and size primarily through in situ star formation in disks to a period of efficient growth in r e consistent with the minor merger scenario.

GALACTIC CHEMICAL EVOLUTION: THE IMPACT OF THE {sup 13}C-POCKET STRUCTURE ON THE s -PROCESS DISTRIBUTION

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

Bisterzo, S.; Travaglio, C.; Wiescher, M.

2017-01-20

The solar s -process abundances have been analyzed in the framework of a Galactic Chemical Evolution (GCE) model. The aim of this work is to implement the study by Bisterzo et al., who investigated the effect of one of the major uncertainties of asymptotic giant branch (AGB) yields, the internal structure of the {sup 13}C pocket. We present GCE predictions of s -process elements computed with additional tests in the light of suggestions provided in recent publications. The analysis is extended to different metallicities, by comparing GCE results and updated spectroscopic observations of unevolved field stars. We verify that themore » GCE predictions obtained with different tests may represent, on average, the evolution of selected neutron-capture elements in the Galaxy. The impact of an additional weak s -process contribution from fast-rotating massive stars is also explored.« less

Damage evolution analysis of coal samples under cyclic loading based on single-link cluster method

NASA Astrophysics Data System (ADS)

Zhang, Zhibo; Wang, Enyuan; Li, Nan; Li, Xuelong; Wang, Xiaoran; Li, Zhonghui

2018-05-01

In this paper, the acoustic emission (AE) response of coal samples under cyclic loading is measured. The results show that there is good positive relation between AE parameters and stress. The AE signal of coal samples under cyclic loading exhibits an obvious Kaiser Effect. The single-link cluster (SLC) method is applied to analyze the spatial evolution characteristics of AE events and the damage evolution process of coal samples. It is found that a subset scale of the SLC structure becomes smaller and smaller when the number of cyclic loading increases, and there is a negative linear relationship between the subset scale and the degree of damage. The spatial correlation length ξ of an SLC structure is calculated. The results show that ξ fluctuates around a certain value from the second cyclic loading process to the fifth cyclic loading process, but spatial correlation length ξ clearly increases in the sixth loading process. Based on the criterion of microcrack density, the coal sample failure process is the transformation from small-scale damage to large-scale damage, which is the reason for changes in the spatial correlation length. Through a systematic analysis, the SLC method is an effective method to research the damage evolution process of coal samples under cyclic loading, and will provide important reference values for studying coal bursts.

NASA Structure and Evolution of the Universe Theme: Science Overview

NASA Technical Reports Server (NTRS)

White, Nicholas E.; Margon, Bruce

2001-01-01

The NASA Office of Space Science Structure and Evolution of the Universe (SEU) theme covers a wide variety of scientific investigations, from the nearest bodies to the farthest observable distances just after the time of the Big Bang. SEU supports experiments that sense radiation of all wavelengths, together with particle and gravitational wave detection. Recently completed road mapping and strategic planning exercises have identified a number of near- and medium-term space initiatives for the 2003-2023 time frame. Each of these experiments pushes the state of the art technically, but will return incredible new insights on the formation and evolution of the universe, as well as probe fundamental laws of physics in regimes never before tested. The scientific goals and technological highlights of each mission are described.

Influence of Game Evolution and the Phase of Competition on Temporal Game Structure in High-Level Table Tennis Tournaments.

PubMed

Leite, Jorge Vieira de Mello; Barbieri, Fabio Augusto; Miyagi, Willian; Malta, Elvis de Souza; Zagatto, Alessandro Moura

2017-01-01

The aims of this study were: a) to investigate the game temporal structure in high-level table tennis competitions; b) to verify the influence of game evolution in international competitions from 2009 to 2012 (World Table Tennis Championships and the Olympic Games) on game temporal structure; c) to compare game temporal structure according to the phase of competition. Comparisons between the three international tournaments demonstrated that rally duration decreased significantly (p < 0.05) during the analyzed period (2009-2012), while the rest time increased (p < 0.05) from 2009 to 2011, but decreased (p < 0.05) from 2011 to 2012. In the competition phase analysis, it was found that rally duration decreased (p < 0.05) in the quarterfinals in relation to the semifinals and finals, while the rest time increased (p < 0.05) from the quarterfinals to semifinals and finals. Based on our findings and previous literature, we concluded that the performance level, game evolution and the competition phase influenced the game temporal structure of table tennis, considering longer rest periods adopted by elite athletes in relation to non-elite athletes, the reduction in rally duration and an increase in rest time over the 2009-2012 period and through the competition phases (quarterfinals to finals).

Comparative Structural Models of Similarities and Differences between "Vehicle" and "Target" in Order to Teach Darwinian "Evolution"

ERIC Educational Resources Information Center

Marcelos, Maria Fatima; Nagem, Ronaldo L.

2010-01-01

Our objective is to contribute to the teaching of Classical Darwinian "Evolution" by means of a study of analogies and metaphors. Throughout the history of knowledge about "Evolution" and in Science teaching, tree structures have been used an analogs to refer to "Evolution," such as by Darwin in the "Tree of Life" passage contained in "On The…

Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea).

PubMed

Gao, Feng; Song, Weibo; Katz, Laura A

2014-08-01

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family-a protein kinase domain containing protein (PKc)-from two C. uncinata strains. Analysis of the PKc sequences reveals that (1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and (2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Valence-band electronic structure evolution of graphene oxide upon thermal annealing for optoelectronics

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

Yamaguchi, Hisato; Ogawa, Shuichi; Watanabe, Daiki

We report valence band electronic structure evolution of graphene oxide (GO) upon its thermal reduction. Degree of oxygen functionalization was controlled by annealing temperatures, and an electronic structure evolution was monitored using real-time ultraviolet photoelectron spectroscopy. We observed a drastic increase in density of states around the Fermi level upon thermal annealing at ~600 °C. The result indicates that while there is an apparent band gap for GO prior to a thermal reduction, the gap closes after an annealing around that temperature. This trend of band gap closure was correlated with electrical, chemical, and structural properties to determine a setmore » of GO material properties that is optimal for optoelectronics. The results revealed that annealing at a temperature of ~500 °C leads to the desired properties, demonstrated by a uniform and an order of magnitude enhanced photocurrent map of an individual GO sheet compared to as-synthesized counterpart.« less

Valence-band electronic structure evolution of graphene oxide upon thermal annealing for optoelectronics

DOE PAGES

Yamaguchi, Hisato; Ogawa, Shuichi; Watanabe, Daiki; ...

2016-09-01

We report valence band electronic structure evolution of graphene oxide (GO) upon its thermal reduction. Degree of oxygen functionalization was controlled by annealing temperatures, and an electronic structure evolution was monitored using real-time ultraviolet photoelectron spectroscopy. We observed a drastic increase in density of states around the Fermi level upon thermal annealing at ~600 °C. The result indicates that while there is an apparent band gap for GO prior to a thermal reduction, the gap closes after an annealing around that temperature. This trend of band gap closure was correlated with electrical, chemical, and structural properties to determine a setmore » of GO material properties that is optimal for optoelectronics. The results revealed that annealing at a temperature of ~500 °C leads to the desired properties, demonstrated by a uniform and an order of magnitude enhanced photocurrent map of an individual GO sheet compared to as-synthesized counterpart.« less

Pollen sensitivity to ultraviolet-B (UV-B) suggests floral structure evolution in alpine plants.

PubMed

Zhang, Chan; Yang, Yong-Ping; Duan, Yuan-Wen

2014-03-31

Various biotic and abiotic factors are known to exert selection pressures on floral traits, but the influence of ultraviolet-B (UV-B) light on the evolution of flower structure remains relatively unexplored. We have examined the effectiveness of flower structure in blocking radiation and the effects of UV-B on pollen viability in 42 species of alpine plants in the Hengduan Mountains, China. Floral forms were categorized as either protecting or exposing pollen grains to UV-B. The floral materials of plants with exposed and protected pollen grains were able to block UV-B at similar levels. Exposure to UV-B radiation in vitro resulted in a significantly greater loss of viability in pollen from plant species with protective floral structures. The pronounced sensitivity of protected pollen to UV-B radiation was associated with the type of flower structure. These findings demonstrate that UV-B plays an important role in the evolution of protective floral forms in alpine plants.

Morphological diversity and evolution of egg and clutch structure in amphibians

USGS Publications Warehouse

Altig, Ronald; McDiarmid, Roy W.

2007-01-01

The first part of this synthesis summarizes the morphology of the jelly layers surrounding an amphibian ovum. We propose a standard terminology and discuss the evolution of jelly layers. The second part reviews the morphological diversity and arrangement of deposited eggs?the ovipositional mode; we recognize 5 morphological classes including 14 modes. We discuss some of the oviductal, ovipositional, and postovipositional events that contribute to these morphologies. We have incorporated data from taxa from throughout the world but recognize that other types will be discovered that may modify understanding of these modes. Finally, we discuss the evolutionary context of the diversity of clutch structure and present a first estimate of its evolution.

Temperature evolution of the structural properties of monodomain ferroelectric thin film

NASA Astrophysics Data System (ADS)

Janolin, Pierre-Eymeric; Le Marrec, Françoise; Chevreul, Jacques; Dkhil, Brahim

2007-05-01

The structural evolution of epitaxial monodomain (only 180° domains) ferroelectric PbTiO3 thin film has been investigated, using high-resolution, temperature-dependent, x-ray diffraction. The full set of lattice parameters was obtained from room temperature up to 850K. It allowed the calculation of the different strains stored in the film at room temperature, underlying the difference between the mechanical strain and the misfit strain. The evolution of the misfit strain as a function of temperature was also calculated and was found to be consistent with the theoretical temperature-misfit strain phase diagram. These data strongly suggest that the film remains ferroelectric and tetragonal up to 940K.

Atmospheric chemical and thermal structure evolution after one Titanian year

NASA Astrophysics Data System (ADS)

Coustenis, A.; Bampasidis, G.; Vinatier, S.; Achterberg, R.; Lavvas, P.; Nixon, C.; Jennings, D.; Teanby, N.; Flasar, F. M.; Carlson, R.; Orton, G.; Romani, P.; Guandique, E. A.

2012-09-01

We analyze Cassini Composite Infrared Spectrometer (CIRS) data taken during the numerous Titan flybys from 2004-2010 and compare them to the 1980 Voyager 1 flyby values inferred from the re-analysis of the Infrared Radiometer Spectrometer (IRIS) spectra. Seven years after Cassini's Saturn orbit insertion, we look at the evolution of the chemical composition by combining these recordings and the intervening ground- and space- based observations, we have in hand almost a complete picture of the stratospheric evolution within a Titan year. The fulfillment of one Titanian year of observations provides us for the first time with the opportunity to evaluate the relative role of different physical processes in the long-term evolution of this complex environment. By comparing V1 (1980), ISO (1997) and Cassini (2010) we find that a reversal of composition near the equator from autumnal equinox to vernal equinox (1996 min -2009 max, half a year), as well as some differences in polar enhancement at the same era as Voyager.

Non-Dissipative Structural Evolutions in Granular Materials

NASA Astrophysics Data System (ADS)

Pouragha, Mehdi; Wan, Richard

2017-06-01

The structure of the contact network in granular assemblies can evolve due to either dissipative mechanisms such as sliding at contact points, or non-dissipative mechanisms through the phenomenon of contact gain and loss. Being associated with negligible deformations, non-dissipative mechanisms is actually active even in the small strain range of 10-3, especially in the case of densely packed assemblies. Hence, from a constitutive modelling point of view, it is crucial to be able to estimate such non-dissipative evolutions since both elastic and plastic properties of granular assemblies highly depend on contact network characteristics. The current study proposes an analytical scheme that allows us to estimate the non-dissipative contact gain/loss regime in terms of directional changes in the average contact force. The probability distribution of contact forces is used to compute the number of lost contact for each direction. Similarly, the number of newly formed contacts is estimated by considering the probability distribution of the gap between neighbouring particles. Based on the directional contact gain/loss computed, the changes in coordination number and fabric anisotropy can be found which, together with statistical treatments of Love-Weber stress expression, form a complete system of equations describing the evolution of other controlling microvariables. Finally, the results of the calculations have been compared with DEM simulations which verify the accuracy of the proposed scheme.

Evolution and dynamics of shear-layer structures in near-wall turbulence

NASA Technical Reports Server (NTRS)

Johansson, Arne V.; Alfredsson, P. H.; Kim, John

1991-01-01

Near-wall flow structures in turbulent shear flows are analyzed, with particular emphasis on the study of their space-time evolution and connection to turbulence production. The results are obtained from investigation of a database generated from direct numerical simulation of turbulent channel flow at a Reynolds number of 180 based on half-channel width and friction velocity. New light is shed on problems associated with conditional sampling techniques, together with methods to improve these techniques, for use both in physical and numerical experiments. The results clearly indicate that earlier conceptual models of the processes associated with near-wall turbulence production, based on flow visualization and probe measurements need to be modified. For instance, the development of asymmetry in the spanwise direction seems to be an important element in the evolution of near-wall structures in general, and for shear layers in particular. The inhibition of spanwise motion of the near-wall streaky pattern may be the primary reason for the ability of small longitudinal riblets to reduce turbulent skin friction below the value for a flat surface.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

PubMed Central

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-01-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions. PMID:26355955

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co(2+) Solution: Interactional Performance and Mechanism.

PubMed

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-10

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co(2+) solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co(2+) reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the "structural influence" crucial for the full and dynamical understanding of nZVI reactions.

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+ Solution: Interactional Performance and Mechanism

NASA Astrophysics Data System (ADS)

Zhang, Yalei; Chen, Wen; Dai, Chaomeng; Zhou, Chuanlong; Zhou, Xuefei

2015-09-01

The structures of nanoscale zero-valent iron (nZVI) particles evolving during reactions, and the reactions are influenced by the evolved structures. To understand the removal process in detail, it is important to investigate the relationships between the reactions and structural evolution. Using high resolution-transmission electron microscopy (HR-TEM), typical evolved structures (sheet coprecipitation and cavity corrosion) of nZVI in anoxic Co2+ solutions were revealed. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the nZVI corrosion rate, were found to be the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results indicated that the formation and dissolution of sheet structure impacts on the ratio of Fe(0) on the nZVI surface and the surface Co2+ reduction. The cavity structure provides the possibility of Co migration from the surface to the bulk of nZVI, leading to continuous removal. Subacidity conditions could accelerate the evolution and improve the removal; the results of structurally controlled reactions further indicated that the removal was suspended by the sheet structure and enhanced by cavity structure. The results and discussion in this paper revealed the “structural influence” crucial for the full and dynamical understanding of nZVI reactions.

Stable Isotope Analysis of Precipitation Samples Obtained via Crowdsourcing Reveals the Spatiotemporal Evolution of Superstorm Sandy

PubMed Central

Good, Stephen P.; Mallia, Derek V.; Lin, John C.; Bowen, Gabriel J.

2014-01-01

Extra-tropical cyclones, such as 2012 Superstorm Sandy, pose a significant climatic threat to the northeastern United Sates, yet prediction of hydrologic and thermodynamic processes within such systems is complicated by their interaction with mid-latitude water patterns as they move poleward. Fortunately, the evolution of these systems is also recorded in the stable isotope ratios of storm-associated precipitation and water vapor, and isotopic analysis provides constraints on difficult-to-observe cyclone dynamics. During Superstorm Sandy, a unique crowdsourced approach enabled 685 precipitation samples to be obtained for oxygen and hydrogen isotopic analysis, constituting the largest isotopic sampling of a synoptic-scale system to date. Isotopically, these waters span an enormous range of values (21‰ for O, 160‰ for H) and exhibit strong spatiotemporal structure. Low isotope ratios occurred predominantly in the west and south quadrants of the storm, indicating robust isotopic distillation that tracked the intensity of the storm's warm core. Elevated values of deuterium-excess (25‰) were found primarily in the New England region after Sandy made landfall. Isotope mass balance calculations and Lagrangian back-trajectory analysis suggest that these samples reflect the moistening of dry continental air entrained from a mid-latitude trough. These results demonstrate the power of rapid-response isotope monitoring to elucidate the structure and dynamics of water cycling within synoptic-scale systems and improve our understanding of storm evolution, hydroclimatological impacts, and paleo-storm proxies. PMID:24618882

Asymmetric 3d Electronic Structure for Enhanced Oxygen Evolution Catalysis.

PubMed

Liu, Yang; Yin, Shibin; Shen, Pei Kang

2018-06-27

The oxygen evolution reaction (OER) is an essential process for renewable energy, and designing a bifunctional oxygen electrocatalyst with high catalytic performance plays a significant role. In this work, FeS, Ni 3 S 2 , Fe 5 Ni 4 S 8 , and N, O, S-doped meshy carbon base were successfully synthesized. The sample containing Fe 5 Ni 4 S 8 exhibited excellent OER performance. The density functional theory calculations indicate that the partial density of states for 3d electrons (3d-PDOS) of Fe and Ni atoms are changed from monometallic sulfide to bimetallic sulfide at the sulfur vacancy. The asymmetric 3d electronic structure optimizes the 3d-PDOS of Fe and Ni atoms, and leads to an enhanced OER activity. This work provides a new strategy to prepare a low-cost electrocatalyst for oxygen evolution with high-efficiency.

Evolution processes of the corrosion behavior and structural characteristics of plasma electrolytic oxidation coatings on AZ31 magnesium alloy

NASA Astrophysics Data System (ADS)

Chen, Dong; Wang, Ruiqiang; Huang, Zhiquan; Wu, Yekang; Zhang, Yi; Wu, Guorui; Li, Dalong; Guo, Changhong; Jiang, Guirong; Yu, Shengxue; Shen, Dejiu; Nash, Philip

2018-03-01

Evolution processes of the corrosion behavior and structural characteristics of the plasma electrolytic oxidation (PEO) coated AZ31 magnesium alloy were investigated by using scanning electron microscope (SEM) equipped with energy dispersive X-ray spectroscopy (EDS), X-ray diffraction (XRD), potentio-dynamic polarization curves and electrochemical impedance spectroscopy (EIS) measurements. Detached coating samples were fabricated by an electrochemical method and more details of the internal micro-structure of coatings were clearly observed on the fractured cross-section morphologies of the samples compared to general polished cross-section morphologies. Evolution mechanisms of the coating corrosion behavior in relation to the evolution of micro-structural characteristics were discussed in detail.

Evolution of community structure in the world trade web

NASA Astrophysics Data System (ADS)

Tzekina, I.; Danthi, K.; Rockmore, D. N.

2008-06-01

In this note we study the bilateral merchandise trade flows between 186 countries over the 1948 2005 period using data from the International Monetary Fund. We use the network visualization package Pajek to identify network structure and behavior across thresholds and over time. In particular, we focus on the evolution of trade “islands” in a world trade network in which countries are linked with directed edges weighted according to the fraction of total dollars sent from one country to another. We find mixed evidence for globalization.

Biophysical and structural considerations for protein sequence evolution

PubMed Central

2011-01-01

Background Protein sequence evolution is constrained by the biophysics of folding and function, causing interdependence between interacting sites in the sequence. However, current site-independent models of sequence evolutions do not take this into account. Recent attempts to integrate the influence of structure and biophysics into phylogenetic models via statistical/informational approaches have not resulted in expected improvements in model performance. This suggests that further innovations are needed for progress in this field. Results Here we develop a coarse-grained physics-based model of protein folding and binding function, and compare it to a popular informational model. We find that both models violate the assumption of the native sequence being close to a thermodynamic optimum, causing directional selection away from the native state. Sampling and simulation show that the physics-based model is more specific for fold-defining interactions that vary less among residue type. The informational model diffuses further in sequence space with fewer barriers and tends to provide less support for an invariant sites model, although amino acid substitutions are generally conservative. Both approaches produce sequences with natural features like dN/dS < 1 and gamma-distributed rates across sites. Conclusions Simple coarse-grained models of protein folding can describe some natural features of evolving proteins but are currently not accurate enough to use in evolutionary inference. This is partly due to improper packing of the hydrophobic core. We suggest possible improvements on the representation of structure, folding energy, and binding function, as regards both native and non-native conformations, and describe a large number of possible applications for such a model. PMID:22171550

Evolution of population structure in a highly social top predator, the killer whale.

PubMed

Hoelzel, A Rus; Hey, Jody; Dahlheim, Marilyn E; Nicholson, Colin; Burkanov, Vladimir; Black, Nancy

2007-06-01

Intraspecific resource partitioning and social affiliations both have the potential to structure populations, though it is rarely possible to directly assess the impact of these mechanisms on genetic diversity and population divergence. Here, we address this for killer whales (Orcinus orca), which specialize on prey species and hunting strategy and have long-term social affiliations involving both males and females. We used genetic markers to assess the structure and demographic history of regional populations and test the hypothesis that known foraging specializations and matrifocal sociality contributed significantly to the evolution of population structure. We find genetic structure in sympatry between populations of foraging specialists (ecotypes) and evidence for isolation by distance within an ecotype. Fitting of an isolation with migration model suggested ongoing, low-level migration between regional populations (within and between ecotypes) and small effective sizes for extant local populations. The founding of local populations by matrifocal social groups was indicated by the pattern of fixed mtDNA haplotypes in regional populations. Simulations indicate that this occurred within the last 20,000 years (after the last glacial maximum). Our data indicate a key role for social and foraging behavior in the evolution of genetic structure among conspecific populations of the killer whale.

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

PubMed

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

2016-06-01

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

The energy cycle and structural evolution of cyclones over southeastern South America in three case studies

NASA Astrophysics Data System (ADS)

Dias Pinto, JoãO. Rafael; Da Rocha, Rosmeri PorfíRio

2011-07-01

In this paper, the Lorenz energy cycle over a limited area was applied for three cyclones with different origins and evolutions, where each of them was formed in an important cyclogenetic region near southeastern South America. The synoptic conditions and energetics were analyzed during each system's life cycle and showed important relationships between their energy cycle and the evolution of their vertical structure. In the case of the weak baroclinic cyclone which formed on Brazil's south-southeastern coast, the analysis showed that it originated through a midlevel cutoff low with contribution from barotropic instability. Its evolution would indicate potential transition to a hybrid system if the convective activity were stronger. The system that occurred in the La Plata River mouth had features of an oceanic bomb-type cyclogenesis and showed an important contribution from the available potential energy generation term through the latent heat release by the convection. Meanwhile, the system of the southern Argentina coast presented a classical baroclinic development of extratropical cyclogenesis in the energy cycle, from the wave amplification up to the final occlusion of the associated frontal system. These analyses revealed that the development of some cyclones that occur in eastern South America can present different mechanisms that are not related to the classical extratropical cyclogenesis.

The importance of inherited structures in slope evolution: the Ridnaun Valley case, Italy

NASA Astrophysics Data System (ADS)

Zorzi, L.; Flaim, L.; Massironi, M.; Genevois, R.; Stead, D.

2013-12-01

The south facing slope of the Ridnaun Valley (South Tyrol, Italy) comprises the crystalline units belonging to the Austoalpine Nappe of the Alpine orogenic wedge and shows evidence of quaternary gravitational evolution which is highly dependent on the interaction between the slope trend and the brittle/ductile structural setting. The slope valley is incised within the paragneiss rocks of the Oetztal - Stubei Unit and the micaschists of the Schneeberg Unit. These two units are separated by a NNW gentle dipping tectonic contact, which obliquely intersects the E-W slope, and is characterized by multiple ultracataclasitic layers that follow the regional low angle north-dipping schistosity. Folds with sub-horizontal E-trending axes induce a change in the dip direction of the regional schistosity from N dipping (unfavorable to the slip) to SE dipping (favorable to the slip). NNE-SSW and N-S trending faults, having a mean thickness of incoherent fault breccias of 1 m, affect the entire slope. These along with the folds and the ultracataclastic layers, have significant influence on rock mass mechanical properties and on mechanisms and timing of the observed gravitational phenomena. Field work and ALS-HRDEM analysis has revealed different gravitational movements along the slope. A fully evolved gravitational collapse, having the features of a Rock Avalanche (RA), characterizes the central part covering an area of about 2.4 km2; whereas to the east and west of the RA, deep seated gravitational slope deformations (DSGSDs) still affect the slope. An ongoing gravitational deformation is apparent in the uphill sections of the slope, next to the crown area of the RA. PS and DS - SAR interferometry data (provided by the Geological Survey of the Autonomous Province of Bolzano, Italy), testify an ongoing movement on both the DSGSDs bordering the RA, highlighting a most unstable area at the western sector. The heterogeneous behavior of the slope is most likely controlled by the

The correlated evolution of three-dimensional reproductive structures between male and female damselflies.

PubMed

McPeek, Mark A; Shen, Li; Farid, Hany

2009-01-01

For many taxa, species are defined by the morphologies of reproductive structures. In many odonates, these structures are the cerci of males (used to hold females during mating) and the thoracic plates of females where the male cerci contact the females' bodies. A previous study showed that the shapes of cerci of Enallagma males (Zygoptera: Coenagrionidae) are best explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the entire phylogeny of the genus. In the present study, we examine the evolution of shape change in the corresponding female plates. We found that, like male cerci, the shapes of Enallagma female thoracic plates could best be explained by an evolutionary model of punctuated change at the time of speciation, with a homogeneous rate of change across the clade. Moreover, the evolutionary contrasts quantifying the rates of change in male cerci and female thoracic plates were positively related across the history of the clade, demonstrating that these male and female structures evolve in a correlated fashion. This pattern of evolution suggests that these structures are primary signals of species identity during mating.

Structural evolution of zirconium carbide under ion irradiation

NASA Astrophysics Data System (ADS)

Gosset, D.; Dollé, M.; Simeone, D.; Baldinozzi, G.; Thomé, L.

2008-02-01

Zirconium carbide is one of the candidate materials to be used for some fuel components of the high temperature nuclear reactors planned in the frame of the Gen-IV project. Few data exist regarding its behaviour under irradiation. We have irradiated ZrC samples at room temperature with slow heavy ions (4 MeV Au, fluence from 10 11 to 5 × 10 15 cm -2) in order to simulate neutron irradiations. Grazing incidence X-Ray diffraction (GIXRD) and transmission electron microscopy (TEM) analysis have been performed in order to study the microstructural evolution of the material versus ion fluence. A high sensitivity to oxidation is observed with the formation of zirconia precipitates during the ion irradiations. Three damage stages are observed. At low fluence (<10 12 cm -2), low modifications are observed. At intermediate fluence, high micro-strains appear together with small faulted dislocation loops. At the highest fluence (>10 14 cm -2), the micro-strains saturate and the loops coalesce to form a dense dislocation network. No other structural modification is observed. The material shows a moderate cell parameter increase, corresponding to a 0.6 vol.% swelling, which saturates around 10 14 ions/cm 2, i.e., a few Zr dpa. As a result, in spite of a strong covalent bonding component, ZrC seems to have a behaviour under irradiation close to cubic metals.

Structure and Evolution of the Central Appalachians from the Mantle to the Surface: Results from the MAGIC Project

NASA Astrophysics Data System (ADS)

Long, M. D.; Benoit, M. H.; Evans, R. L.; King, S. D.; Kirby, E.; Aragon, J. C.; Miller, S. R.; Liu, S.; Elsenbeck, J.

2017-12-01

stream profile analysis show particularly fast erosion rates just to the west of Harrisonburg. Integration of results from the MAGIC project is yielding new insight into the structure and evolution of the central Appalachians and into the processes associated with orogenesis, rifting, and post-rift evolution of the passive margin.

Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome.

PubMed

Sanseverino, Walter; Hénaff, Elizabeth; Vives, Cristina; Pinosio, Sara; Burgos-Paz, William; Morgante, Michele; Ramos-Onsins, Sebastián E; Garcia-Mas, Jordi; Casacuberta, Josep Maria

2015-10-01

The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). This is a strong limitation as structural variation (SV) and transposon insertion polymorphisms are frequent in plant species and have had an important mutational role in crop domestication and breeding. Here, we present the first comprehensive analysis of melon genetic diversity, which includes a detailed analysis of SNPs, SV, and transposon insertion polymorphisms. The variability found among seven melon varieties representing the species diversity and including wild accessions and highly breed lines, is relatively high due in part to the marked divergence of some lineages. The diversity is distributed nonuniformly across the genome, being lower at the extremes of the chromosomes and higher in the pericentromeric regions, which is compatible with the effect of purifying selection and recombination forces over functional regions. Additionally, this variability is greatly reduced among elite varieties, probably due to selection during breeding. We have found some chromosomal regions showing a high differentiation of the elite varieties versus the rest, which could be considered as strongly selected candidate regions. Our data also suggest that transposons and SV may be at the origin of an important fraction of the variability in melon, which highlights the importance of analyzing all types of genetic variability to understand crop genome evolution. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Methods for constraining fine structure constant evolution with OH microwave transitions.

PubMed

Darling, Jeremy

2003-07-04

We investigate the constraints that OH microwave transitions in megamasers and molecular absorbers at cosmological distances may place on the evolution of the fine structure constant alpha=e(2)/ variant Planck's over 2pi c. The centimeter OH transitions are a combination of hyperfine splitting and lambda doubling that can constrain the cosmic evolution of alpha from a single species, avoiding systematic errors in alpha measurements from multiple species which may have relative velocity offsets. The most promising method compares the 18 and 6 cm OH lines, includes a calibration of systematic errors, and offers multiple determinations of alpha in a single object. Comparisons of OH lines to the HI 21 cm line and CO rotational transitions also show promise.

Structural evolution of the J-fold; a multi-scalar approach to modeling kinematic fold evolution in the Cordilleran fold-thrust belt, southwestern Montana

NASA Astrophysics Data System (ADS)

Wallace, James W.

The Highway 2 structural complex (HW2SC) is part of the North American western Cordilleran fold-and-thrust belt that extends from northern Wyoming into northwestern Canada. More precisely, the HW2SC is located on the southeastern margin of the Helena salient in what is known as the southwest Montana transverse zone. Based on the location of the HW2SC it appears to have formed as footwall deformation associated with displacement along the southwestern Montana transverse zone. The most prominent structural feature in the HW2SC is the Late-Cretaceous "J-fold", a east-west trending, muliti-hinged, northeast plunging anticline with an associated northeast plunging syncline. The purpose of this study is to provide insight into whether the geometries of thrust-related folds correlate to particular mechanical responses taking place within the folded sedimentary sequences. This is accomplished by conducting a multifaceted examination of the J-fold using high-resolution terrestrial laser scanning combined with detailed field measurements of kinematic indicators, and petrographic analysis of microstructures in thin section. Based on the findings of this study four specific conclusions about the kinematic and mechanical evolution of the J-fold can be made: 1) the J-fold kinematically behaves as a fault-bend fold throughout its structural evolution; 2) the J-fold enjoyed two stages of fault-bend folding deformation that produced its present day geometry; 3) the J-fold has been tectonically thinned by >50% in the Permian Phosphoria and Jurassic Ellis-Rierdon formations located in the Overturned forelimb; and finally 4) the J-fold is mechanically accommodating the thinning in the Overturned forelimb by pressure solution and dissolution of chert grains in the Permian Phosphoria formation and by faulting and shearing in the Jurassic Ellis-Rierdon formation.

Evolution of the Chos Malal and Agrio fold and thrust belts, Andes of Neuquén: Insights from structural analysis and apatite fission track dating

NASA Astrophysics Data System (ADS)

Rojas Vera, E. A.; Mescua, J.; Folguera, A.; Becker, T. P.; Sagripanti, L.; Fennell, L.; Orts, D.; Ramos, V. A.

2015-12-01

The Chos Malal and Agrio fold and thrust belts are located in the western part of the Neuquén basin, an Andean retroarc basin of central-western Argentina. Both belts show evidence of tectonic inversion at the western part during Late Cretaceous times. The eastern part is dominated by late Miocene deformation which also partially reactivated the western structures. This work focuses on the study of the regional structure and the deformational event that shaped the relief of this part of the Andes. Based on new field work and structural data and previously published works a detailed map of the central part of the Neuquén basin is presented. Three regional structural cross sections were surveyed and balanced using the 2d Move™ software. In order to define a more accurate uplift history, new apatite fission track analyses were carried on selected structures. These data was used for new thermal history modeling of the inner part of the Agrio and Chos Malal fold and thrust belts. The results of the fission track analyses improve the knowledge of how these fold and thrust belts have grown trough time. Two main deformational events are defined in Late Cretaceous to Paleocene and Late Miocene times. Based on this regional structural analysis and the fission track data the precise location of the orogenic front for the Late Cretaceous-Paleocene times is reconstructed and it is proposed a structural evolution of this segment of the Andes. This new exhumation data show how the Late Cretaceous to Paleocene event was a continuous and uninterrupted deformational event.

Protein Flexibility Facilitates Quaternary Structure Assembly and Evolution

PubMed Central

Marsh, Joseph A.; Teichmann, Sarah A.

2014-01-01

The intrinsic flexibility of proteins allows them to undergo large conformational fluctuations in solution or upon interaction with other molecules. Proteins also commonly assemble into complexes with diverse quaternary structure arrangements. Here we investigate how the flexibility of individual protein chains influences the assembly and evolution of protein complexes. We find that flexibility appears to be particularly conducive to the formation of heterologous (i.e., asymmetric) intersubunit interfaces. This leads to a strong association between subunit flexibility and homomeric complexes with cyclic and asymmetric quaternary structure topologies. Similarly, we also observe that the more nonhomologous subunits that assemble together within a complex, the more flexible those subunits tend to be. Importantly, these findings suggest that subunit flexibility should be closely related to the evolutionary history of a complex. We confirm this by showing that evolutionarily more recent subunits are generally more flexible than evolutionarily older subunits. Finally, we investigate the very different explorations of quaternary structure space that have occurred in different evolutionary lineages. In particular, the increased flexibility of eukaryotic proteins appears to enable the assembly of heteromeric complexes with more unique components. PMID:24866000

Structural Evolution of Nanoscale Zero-Valent Iron (nZVI) in Anoxic Co2+Soultion : Interactional Performance and Mechanism

NASA Astrophysics Data System (ADS)

Dai, C.; Zhang, Y.

2015-12-01

The nanoscale particle and low oxidation reduction potential make nano zero-valent iron (nZVI) an efficient sorbent and reductant for treating many kinds of organic contaminants and heavy metals.The structures of nanoscale zero-valent iron (nZVI) particles are evolving in reactions, and the reactions are influenced by the evolved structures. In order to understand the detail removal process, it is important to investigate the interactions between reactions and structural evolution. In this work, reactions between nZVI and Co2+ at different initial concentrations in anoxic aqueous solutions (to eliminate the effects of O2) were tracked for 10 days using a variety of methods including inductively coupled plasma optical emission spectrometry (ICP-OES), high resolution-transmission electron microscopy (HR-TEM), energy dispersive spectrometer (EDS), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM). Continuous removal and reduction of Co2+ by nZVI caused by structural evolution were revealed in reaction processes. The system pH (pH measured in mixture), which controls the stability of coprecipitation and the corrosion rate of nZVI, was deemed as the determining factors of structural evolutions. X-ray photoelectron spectroscopy (XPS) results showed that the formation and dissolution of sheet structure impacts on the ratio of Fe (0) on nZVI's surface and the surface reduction of Co2+. The cavity structure provides the possibility of Co migrating from surface to inside of nZVI leading a continuous removal. A subacidity condition could accelerate the evolution to improve the removal of Co2+ and the results of structural controlled reactions further indicated that the removal was suspended by sheet structure and enhanced by cavity structure. The results in this study revealed "structural influence" for fully and dynamically understanding nZVI's reactions.

Structures and Evolutions of Explosive Cyclones over the Northwestern and Northeastern Pacific

NASA Astrophysics Data System (ADS)

Zhang, Shuqin; Fu, Gang

2018-06-01

In this study, the structures and evolutions of moderate (MO) explosive cyclones (ECs) over the Northwestern Pacific (NWP) and Northeastern Pacific (NEP) are investigated and compared using composite analysis with cyclone-relative coordinates. Final Operational Global Analysis data gathered during the cold seasons (October-April) of the 15 years from 2000 to 2015 are used. The results indicate that MO NWP ECs have strong baroclinicity and abundant latent heat release at low levels and strong upper-level forcing, which favors explosive cyclogenesis. The rapid development of MO NEP ECs results from their interaction with a northern cyclone and a large middle-level advection of cyclonic vorticity. The structural differences between MO NWP ECs and MO NEP ECs are significant. This results from their specific large-scale atmospheric and oceanic environments. MO NWP ECs usually develop rapidly in the east and southeast of the Japan Islands; the intrusion of cold dry air from the East Asian continent leads to strong baroclinicity, and the Kuroshio/Kuroshio Extension provides abundant latent heat release at low levels. The East Asian subtropical westerly jet stream supplies strong upper-level forcing. While MO NEP ECs mainly occur over the NEP, the low-level baroclinicity, upper-level jet stream, and warm ocean currents are relatively weaker. The merged cyclone associated with a strong middle-level trough transports large cyclonic vorticity to MO NEP ECs, which favors their rapid development.

Structural Evolutions of STOCK Markets Controlled by Generalized Entropy Principles of Complex Systems

NASA Astrophysics Data System (ADS)

Wang, Yi Jiao; Feng, Qing Yi; Chai, Li He

As one of the most important financial markets and one of the main parts of economic system, the stock market has become the research focus in economics. The stock market is a typical complex open system far from equilibrium. Many available models that make huge contribution to researches on market are strong in describing the market however, ignoring strong nonlinear interactions among active agents and weak in reveal underlying dynamic mechanisms of structural evolutions of market. From econophysical perspectives, this paper analyzes the complex interactions among agents and defines the generalized entropy in stock markets. Nonlinear evolutionary dynamic equation for the stock markets is then derived from Maximum Generalized Entropy Principle. Simulations are accordingly conducted for a typical case with the given data, by which the structural evolution of the stock market system is demonstrated. Some discussions and implications are finally provided.

Structure and Evolution of Mediterranean Forest Research: A Science Mapping Approach.

PubMed

Nardi, Pierfrancesco; Di Matteo, Giovanni; Palahi, Marc; Scarascia Mugnozza, Giuseppe

2016-01-01

This study aims at conducting the first science mapping analysis of the Mediterranean forest research in order to elucidate its research structure and evolution. We applied a science mapping approach based on co-term and citation analyses to a set of scientific publications retrieved from the Elsevier's Scopus database over the period 1980-2014. The Scopus search retrieved 2,698 research papers and reviews published by 159 peer-reviewed journals. The total number of publications was around 1% (N = 17) during the period 1980-1989 and they reached 3% (N = 69) in the time slice 1990-1994. Since 1995, the number of publications increased exponentially, thus reaching 55% (N = 1,476) during the period 2010-2014. Within the thirty-four years considered, the retrieved publications were published by 88 countries. Among them, Spain was the most productive country, publishing 44% (N = 1,178) of total publications followed by Italy (18%, N = 482) and France (12%, N = 336). These countries also host the ten most productive scientific institutions in terms of number of publications in Mediterranean forest subjects. Forest Ecology and Management and Annals of Forest Science were the most active journals in publishing research in Mediterranean forest. During the period 1980-1994, the research topics were poorly characterized, but they become better defined during the time slice 1995-1999. Since 2000s, the clusters become well defined by research topics. Current status of Mediterranean forest research (20092014) was represented by four clusters, in which different research topics such as biodiversity and conservation, land-use and degradation, climate change effects on ecophysiological responses and soil were identified. Basic research in Mediterranean forest ecosystems is mainly conducted by ecophysiological research. Applied research was mainly represented by land-use and degradation, biodiversity and conservation and fire research topics. The citation analyses revealed highly

Models of Protocellular Structure, Function and Evolution

NASA Technical Reports Server (NTRS)

New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.; DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

In the absence of any record of protocells, the most direct way to test our understanding, of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction.

Structural evolution of epitaxial SrCoO x films near topotactic phase transition

DOE PAGES

Jeen, Hyoung Jeen; Lee, Ho Nyung

2015-12-18

Control of oxygen stoichiometry in complex oxides via topotactic phase transition is an interesting avenue to not only modifying the physical properties, but utilizing in many energy technologies, such as energy storage and catalysts. However, detailed structural evolution in the close proximity of the topotactic phase transition in multivalent oxides has not been much studied. In this work, we used strontium cobaltites (SrCoO x) epitaxially grown by pulsed laser epitaxy (PLE) as a model system to study the oxidation-driven evolution of the structure, electronic, and magnetic properties. We grew coherently strained SrCoO 2.5thin films and performed post-annealing at various temperaturesmore » for topotactic conversion into the perovskite phase (SrCoO 3-δ). We clearly observed significant changes in electronic transport, magnetism, and microstructure near the critical temperature for the topotactic transformation from the brownmillerite to the perovskite phase. Furthermore, the overall crystallinity was well maintained without much structural degradation, indicating that topotactic phase control can be a useful tool to control the physical properties repeatedly via redox reactions.« less

Structural evolution of a granular medium during simultaneous penetration

NASA Astrophysics Data System (ADS)

González-Gutiérrez, Jorge; Carreón, Yojana J. P.; Moctezuma, R. E.

2018-01-01

Typically, fluidized beds are granular systems composed of solid particles through which a fluid flows. They are relevant to a wide variety of disciplines such as physics, chemistry, engineering, among others. Generally, the fluidized beds are characterized by different flow regimes such as particulate, bubbling, slugging, turbulent, fast fluidization, and pneumatic conveying. Here, we report the experimental study of the structural evolution of a granular system due to simultaneous penetration of intruders in the presence of an upward airflow. We found that the granular medium evolves from the static state to the turbulent regime showing the coexistence of three regions in different flow regimes. Interestingly, the cooperative dynamic of intruders correlate with the formation of such regions. As a non-invasive method, we use lacunarity and fractal dimension to quantitatively describe the patterns arising within the system during the different stages of the penetration process. Finally, we found that our results would allow us to relate the evolution of the visual patterns appearing in the process with different physical properties of the system.

A model for the evolution of the Earth's mantle structure since the Early Paleozoic

NASA Astrophysics Data System (ADS)

Zhang, Nan; Zhong, Shijie; Leng, Wei; Li, Zheng-Xiang

2010-06-01

Seismic tomography studies indicate that the Earth's mantle structure is characterized by African and Pacific seismically slow velocity anomalies (i.e., superplumes) and circum-Pacific seismically fast anomalies (i.e., a globally spherical harmonic degree 2 structure). However, the cause for and time evolution of the African and Pacific superplumes and the degree 2 mantle structure remain poorly understood with two competing proposals. First, the African and Pacific superplumes have remained largely unchanged for at least the last 300 Myr and possibly much longer. Second, the African superplume is formed sometime after the formation of Pangea (i.e., at 330 Ma) and the mantle in the African hemisphere is predominated by cold downwelling structures before and during the assembly of Pangea, while the Pacific superplume has been stable for the Pangea supercontinent cycle (i.e., globally a degree 1 structure before the Pangea formation). Here, we construct a proxy model of plate motions for the African hemisphere for the last 450 Myr since the Early Paleozoic using the paleogeographic reconstruction of continents constrained by paleomagnetic and geological observations. Coupled with assumed oceanic plate motions for the Pacific hemisphere, this proxy model for the plate motion history is used as time-dependent surface boundary condition in three-dimensional spherical models of thermochemical mantle convection to study the evolution of mantle structure, particularly the African mantle structure, since the Early Paleozoic. Our model calculations reproduce well the present-day mantle structure including the African and Pacific superplumes and generally support the second proposal with a dynamic cause for the superplume structure. Our results suggest that while the mantle in the African hemisphere before the assembly of Pangea is predominated by the cold downwelling structure resulting from plate convergence between Gondwana and Laurussia, it is unlikely that the bulk of

Analysis of the geological structure and tectonic evolution of Xingning-Jinghai sag in deep water area, northern South China Sea

NASA Astrophysics Data System (ADS)

Han, Xiaoying; Ren, Jianye; Lin, Zi; Yang, Linlong

2015-04-01

Recent years, oil and gas exploration of the Pearl River Mouth Basin in the northern margin of South China Sea continuously achieved historic breakthroughs. The Xingning-Jinghai sag, which is located in southeast of the Pearl River Mouth Basin, is a deep-water sag with a great exploration potential. Its tectonic evolution is extremely complex. It experienced Mesozoic subduction to Cenozoic intra-continental rifting background, and finally evolved into a deep-water sag of the northern continental margin of South China Sea. The geological characteristics and the tectonic evolution of Xingning-Jinghai sag was closely related to the process of formation and evolution of the passive continental margin of the northern South China Sea. It is confirmed by many geophysical data that compared with adjacent Chaoshan depression, the crustal thickness of Xingning-Jinghai sag was rapidly thinning, and it developed detachment faults with later magmatic intrusion. The development of detachment faults have dynamic significance for the spreading of the South China Sea. Based on the seismic geological interpretation of 2D seismic data in the study area, the characteristics of detachment fault and supra-detachment basin have been proposed in this study. The characteristics of the detachment fault are low angle and high ratio between heave and throw. The geometry of the detachment fault is a typical lisric shape, with the dip of fault decreasing generally from the seismic profile. The detachment basin where sediments are not deposited over a tilting hanging-wall block but onto a tectonically exhumed footwall which is different from the typical half graben basin. Seismic profiles indicate two different structural styles in the east and west part of Xingning-Jinghai sag. In the west of the sag, there developed two large detachment faults, which control their detachment basin systems and the typical H block, and the two detachment faults are dipping landward and seaward, respectively. In

EVOLUTION OF NEAR-SURFACE FLOWS INFERRED FROM HIGH-RESOLUTION RING-DIAGRAM ANALYSIS

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

Bogart, Richard S.; Baldner, Charles S.; Basu, Sarbani

2015-07-10

Ring-diagram analysis of acoustic waves observed at the photosphere can provide a relatively robust determination of the sub-surface flows at a particular time under a particular region. The depth of penetration of the waves is related to the size of the region, hence the depth extent of the measured flows is inversely proportional to the spatial resolution. Most ring-diagram analysis has focused on regions of extent ∼15° (180 Mm) or more in order to provide reasonable mode sets for inversions. Helioseismic and Magnetic Imager (HMI) data analysis also provides a set of ring fit parameters on a scale three timesmore » smaller. These provide flow estimates for the outer 1% (7 Mm) of the Sun only, with very limited depth resolution, but with spatial resolution adequate to map structures potentially associated with the belts and regions of magnetic activity. There are a number of systematic effects affecting the determination of flows from a local helioseismic analysis of regions over different parts of the observable disk, and not all of them are well understood. In this study we characterize those systematic effects with higher spatial resolution so that they may be accounted for more effectively in mapping the temporal and spatial evolution of the flows. Leaving open the question of the mean structure of the global meridional circulation and the differential rotation, we describe the near-surface flow anomalies in time and latitude corresponding to the torsional oscillation pattern in differential rotation and analogous patterns in the meridional cell structure as observed by the Solar Dynamics Observatory/HMI.« less

Fossil scales illuminate the early evolution of lepidopterans and structural colors

PubMed Central

Zhang, Qingqing; Starkey, Timothy A.; McNamara, Maria E.; Jarzembowski, Edmund A.; Kelly, Richard; Ren, Xiaoyin; Chen, Jun; Zhang, Haichun

2018-01-01

Lepidopteran scales exhibit remarkably complex ultrastructures, many of which produce structural colors that are the basis for diverse communication strategies. Little is known, however, about the early evolution of lepidopteran scales and their photonic structures. We report scale architectures from Jurassic Lepidoptera from the United Kingdom, Germany, Kazakhstan, and China and from Tarachoptera (a stem group of Amphiesmenoptera) from mid-Cretaceous Burmese amber. The Jurassic lepidopterans exhibit a type 1 bilayer scale vestiture: an upper layer of large fused cover scales and a lower layer of small fused ground scales. This scale arrangement, plus preserved herringbone ornamentation on the cover scale surface, is almost identical to those of some extant Micropterigidae. Critically, the fossil scale ultrastructures have periodicities measuring from 140 to 2000 nm and are therefore capable of scattering visible light, providing the earliest evidence of structural colors in the insect fossil record. Optical modeling confirms that diffraction-related scattering mechanisms dominate the photonic properties of the fossil cover scales, which would have displayed broadband metallic hues as in numerous extant Micropterigidae. The fossil tarachopteran scales exhibit a unique suite of characteristics, including small size, elongate-spatulate shape, ridged ornamentation, and irregular arrangement, providing novel insight into the early evolution of lepidopteran scales. Combined, our results provide the earliest evidence for structural coloration in fossil lepidopterans and support the hypothesis that fused wing scales and the type 1 bilayer covering are groundplan features of the group. Wing scales likely had deep origins in earlier amphiesmenopteran lineages before the appearance of the Lepidoptera. PMID:29651455

Fossil scales illuminate the early evolution of lepidopterans and structural colors.

PubMed

Zhang, Qingqing; Mey, Wolfram; Ansorge, Jörg; Starkey, Timothy A; McDonald, Luke T; McNamara, Maria E; Jarzembowski, Edmund A; Wichard, Wilfried; Kelly, Richard; Ren, Xiaoyin; Chen, Jun; Zhang, Haichun; Wang, Bo

2018-04-01

Lepidopteran scales exhibit remarkably complex ultrastructures, many of which produce structural colors that are the basis for diverse communication strategies. Little is known, however, about the early evolution of lepidopteran scales and their photonic structures. We report scale architectures from Jurassic Lepidoptera from the United Kingdom, Germany, Kazakhstan, and China and from Tarachoptera (a stem group of Amphiesmenoptera) from mid-Cretaceous Burmese amber. The Jurassic lepidopterans exhibit a type 1 bilayer scale vestiture: an upper layer of large fused cover scales and a lower layer of small fused ground scales. This scale arrangement, plus preserved herringbone ornamentation on the cover scale surface, is almost identical to those of some extant Micropterigidae. Critically, the fossil scale ultrastructures have periodicities measuring from 140 to 2000 nm and are therefore capable of scattering visible light, providing the earliest evidence of structural colors in the insect fossil record. Optical modeling confirms that diffraction-related scattering mechanisms dominate the photonic properties of the fossil cover scales, which would have displayed broadband metallic hues as in numerous extant Micropterigidae. The fossil tarachopteran scales exhibit a unique suite of characteristics, including small size, elongate-spatulate shape, ridged ornamentation, and irregular arrangement, providing novel insight into the early evolution of lepidopteran scales. Combined, our results provide the earliest evidence for structural coloration in fossil lepidopterans and support the hypothesis that fused wing scales and the type 1 bilayer covering are groundplan features of the group. Wing scales likely had deep origins in earlier amphiesmenopteran lineages before the appearance of the Lepidoptera.

Same Precursor, Two Different Products: Comparing the Structural Evolution of In–Ga–O “Gel-Derived” Powders and Solution-Cast Films Using Pair Distribution Function Analysis

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

Wood, Suzannah R.; Woods, Keenan N.; Plassmeyer, Paul N.

Amorphous metal oxides are central to a variety of technological applications. In particular, indium gallium oxide has garnered attention as a thin-film transistor channel layer material. In this work we examine the structural evolution of indium gallium oxide gel-derived powders and thin films using infrared vibrational spectroscopy, X-ray diffraction, and pair distribution function (PDF) analysis of X-ray total scattering from standard and normal incidence thin-film geometries (tfPDF). We find that the gel-derived powders and films from the same aqueous precursor evolve differently with temperature, forming mixtures of Ga-substituted In2O3 and In-substituted β-Ga2O3 with different degrees of substitution. X-ray total scatteringmore » and PDF analysis indicate that the majority phase for both the powders and films is an amorphous/nanocrystalline β-Ga2O3 phase, with a minor constituent of In2O3 with significantly larger coherence lengths. This amorphous β-Ga2O3 phase could not be identified using the conventional Bragg diffraction techniques traditionally used to study crystalline metal oxide thin films. The combination of Bragg diffraction and tfPDF provides a much more complete description of film composition and structure, which can be used to detail the effect of processing conditions and structure–property relationships. This study also demonstrates how structural features of amorphous materials, traditionally difficult to characterize by standard diffraction, can be elucidated using tfPDF.« less

Contamination of RR Lyrae stars from Binary Evolution Pulsators

NASA Astrophysics Data System (ADS)

Karczmarek, Paulina; Pietrzyński, Grzegorz; Belczyński, Krzysztof; Stępień, Kazimierz; Wiktorowicz, Grzegorz; Iłkiewicz, Krystian

2016-06-01

Binary Evolution Pulsator (BEP) is an extremely low-mass member of a binary system, which pulsates as a result of a former mass transfer to its companion. BEP mimics RR Lyrae-type pulsations but has different internal structure and evolution history. We present possible evolution channels to produce BEPs, and evaluate the contamination value, i.e. how many objects classified as RR Lyrae stars can be undetected BEPs. In this analysis we use population synthesis code StarTrack.

Analysis of very-high-resolution Galileo images of Europa: Implications for small-scale structure and surface evolution

NASA Astrophysics Data System (ADS)

Leonard, E. J.; Pappalardo, R. T.; Yin, A.; Prockter, L. M.; Patthoff, D. A.

2014-12-01

The Galileo Solid State Imager (SSI) recorded nine very high-resolution frames (8 at 12 m/pixel and 1 at 6 m/pixel) during the E12 flyby of Europa in Dec. 1997. To understand the implications for the small-scale structure and evolution of Europa, we mosaicked these frames (observations 12ESMOTTLE01 and 02, incidence ≈18°, emission ≈77°) into their regional context (part of observation 11ESREGMAP01, 220 m/pixel, incidence ≈74°, emission ≈23°), despite their very different viewing and lighting conditions. We created a map of geological units based on morphology, structure, and albedo along with stereoscopic images where the frames overlapped. The highly diverse units range from: high albedo sub-parallel ridge and grooved terrain; to variegated-albedo hummocky terrain; to low albedo and relatively smooth terrain. We classified and analyzed the diverse units solely based on the high-resolution image mosaic, prior to comparison to the context image, to obtain an in-depth look at possible surface evolution and underlying formational processes. We infer that some of these units represent different stages and forms of resurfacing, including cryovolcanic and tectonic resurfacing. However, significant morphological variation among units in the region indicates that there are different degrees of resurfacing at work. We have created candidate morphological sequences that provide insight into the conversion of ridged plains to chaotic terrain—generally, a process of subduing formerly sharp features through tectonic modification and/or cryovolcanism. When the map of the high-resolution area is compared to the regional context, features that appear to be one unit at regional resolution are comprised of several distinct units at high resolution, and features that appear to be smooth in the context image are found to show distinct textures. Moreover, in the context image, transitions from ridged units to disrupted units appear to be gradual; however the high

Binder-induced surface structure evolution effects on Li-ion battery performance

NASA Astrophysics Data System (ADS)

Rezvani, S. J.; Pasqualini, M.; Witkowska, A.; Gunnella, R.; Birrozzi, A.; Minicucci, M.; Rajantie, H.; Copley, M.; Nobili, F.; Di Cicco, A.

2018-03-01

A comparative investigation on binder induced chemical and morphological evolution of Li4Ti5O12 electrodes was performed via X-ray photoemission spectroscopy, scanning electron microscopy, and electrochemical measurements. Composite electrodes were obtained using three different binders (PAA, PVdF, and CMC) with 80:10:10 ratio of active material:carbon:binder. The electrochemical performances of the electrodes, were found to be intimately correlated with the evolution of the microstructure of the electrodes, probed by XPS and SEM analysis. Our analysis shows that the surface chemistry, thickness of the passivation layers and the morphology of the electrodes are strongly dependent on the type of binders that significantly influence the electrochemical properties of the electrodes. These results point to a key role played by binders in optimization of the battery performance and improve our understanding of the previously observed and unexplained electrochemical properties of these electrodes.

Multiphase Structural Evolution of a Continental Margin During Obduction Orogeny: Insights From the Jebel Akhdar Dome, Oman Mountains

NASA Astrophysics Data System (ADS)

Grobe, A.; Virgo, S.; von Hagke, C.; Urai, J. L.; Littke, R.

2018-03-01

The structural evolution of the carbonate platform in the footwall of the Semail ophiolite emplaced onto the passive continental margin of Arabia helps to better understand the early stages of obduction-related orogens. These early stages are rarely observable in other orogens as they are mostly overprinted by later mountain building phases. We present an extensive structural analysis of the Jebel Akhdar anticline, the largest tectonic window of the Oman Mountains, and integrate it on different scales. Outcrop observations can be linked to plate motion data, providing an absolute timeframe for structural generations consistent with radiometric dating of veins. Top-to-S overthrusting of the Semail ophiolite and Hawasina nappes onto the carbonate platform during high plate convergence rates between Arabia and Eurasia caused rapid burial and overpressure, generation and migration of hydrocarbons, and bedding-confined veins, but no major deformation in the carbonate platform. At reduced convergence rates, subsequent tectonic thinning of the ophiolite took place above a top-to-NNE, crustal-scale ductile shear zone, deforming existing veins and forming a cleavage in clay-rich layers in early Campanian times. Ongoing extension occurred along normal- to oblique-slip faults, forming horst-graben structures and a precursor of the Jebel Akhdar dome (Campanian to Maastrichtian). This was followed by NE-SW oriented ductile shortening and the formation of the Jebel Akhdar dome, deforming the earlier structures. Thereafter, exhumation was associated with low-angle normal faults on the northern flank of the anticline. We correlate the top-to-NNE crustal-scale shear zone with a similar structure in the Saih Hatat window to develop a unified model of the tectonic evolution of the Oman Mountains.

Thermodynamics, Kinetics and Structural Evolution of ε-LiVOPO 4 over Multiple Lithium Intercalation

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

Lin, Yuh-Chieh; Wen, Bohua; Wiaderek, Kamila M.

In this work, we demonstrate the stable cycling of more than one Li in solid-state-synthesized ε-LiVOPO4 over more than 20 cycles for the first time. Using a combination of density functional theory (DFT) calculations, X-ray pair distribution function (PDF) analysis and X-ray absorption near edge structure (XANES) measurements, we present a comprehensive analysis of the thermodynamics, kinetics, and structural evolution of ε-LixVOPO4 over the entire lithiation range. We identify two intermediate phases at x = 1.5 and 1.75 in the low-voltage regime using DFT calculations, and the computed and electrochemical voltage profiles are in excellent agreement. Operando PDF and EXAFSmore » techniques show a reversible hysteretic change in the short (<2 Å) V—O bond lengths coupled with an irreversible extension of the long V—O bond (>2.4 Å) during low-voltage cycling. Hydrogen intercalation from electrolyte decomposition is a possible explanation for the ~2.4 Å V—O bond and its irreversible extension. Finally, we show that ε-LixVOPO4 is likely a pseudo-1D ionic diffuser with low electronic conductivity using DFT calculations, which suggests that nanosizing and carbon coating is necessary to achieve good electrochemical performance in this material.« less

Studying the Thermal and Structural Evolution of Planetary Bodies

NASA Astrophysics Data System (ADS)

Karimi, Mohammadali

The focus of this research is to study the thermal and structural evolution of three planetary bodies, Mars, Venus and the asteroid Vesta. The almost uniform spatial distribution of craters on the surfaces of planets makes them excellent candidates to examine the evolution of planets as a whole. By modeling the viscoelastic deformation of craters at the surface and subsurface with the Finite Element Method (FEM), this study investigated the role of lower crustal flow in crater relaxation, and since lower crustal flow is sensitive to the thermal state, it serves as a probe into the thermal evolution of planets. The thermal history of Mars was explored by modeling the evolution of large craters and Quasi-Circular Depressions (QCDs) in the Southern Highlands and Northern Lowlands, respectively. Because of the spatial distribution of craters, this study yielded a thermal map for Mars that is more complete and less biased regionally relative to other studies. The results revealed a higher background heat flux for the Northern Lowlands relative to the Southern Highlands during the most ancient Noachian epoch, which suggests a thermal fingerprint to whatever process that formed the hemispherical crustal dichotomy, the oldest and most prominent geomorphic feature on Mars. Next, the largest crater on the surface of Venus, Mead, also appears to have undergone significant lower crustal flow. Modeling the viscoelastic deformation of Mead puts constraints on the thermal state of our sister planet in the vicinity of the basin. The background heat flux of Venus estimated here is higher than globally average values predicted by previous thermal models. Moreover, this study showed that Venus's crust and mantle seem to be dry relative to those of the Earth. Last, modeling the evolution of two large craters in the south polar region of Vesta (Rheasilvia and Veneneia) showed that the shallow topography and large central peak of these craters are likely the products of a planetary

Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria).

PubMed

Olsson, Sanna; Kaasalainen, Ulla; Rikkinen, Jouko

2012-02-01

In this study we reconstruct the structural evolution of the hyper-variable P6b region of the group I trnLeu intron in a monophyletic group of lichen-symbiotic Nostoc strains and establish it as a useful marker in the phylogenetic analysis of these organisms. The studied cyanobacteria occur as photosynthetic and/or nitrogen-fixing symbionts in lichen species of the diverse Nephroma guild. Phylogenetic analyses and secondary structure reconstructions are used to improve the understanding of the replication mechanisms in the P6b stem-loop and to explain the observed distribution patterns of indels. The variants of the P6b region in the Nostoc clade studied consist of different combinations of five sequence modules. The distribution of indels together with the ancestral character reconstruction performed enables the interpretation of the evolution of each sequence module. Our results indicate that the indel events are usually associated with single nucleotide changes in the P6b region and have occurred several times independently. In spite of their homoplasy, they provide phylogenetic information for closely related taxa. Thus we recognize that features of the P6b region can be used as molecular markers for species identification and phylogenetic studies involving symbiotic Nostoc cyanobacteria.

Evolution of the pore structure during the early stages of the alkali-activation reaction: An in situ small-angle neutron scattering investigation

DOE PAGES

White, Claire E.; Olds, Daniel P.; Hartl, Monika; ...

2017-02-01

The long-term durability of cement-based materials is influenced by the pore structure and associated permeability at the sub-micrometre length scale. With the emergence of new types of sustainable cements in recent decades, there is a pressing need to be able to predict the durability of these new materials, and therefore nondestructive experimental techniques capable of characterizing the evolution of the pore structure are increasingly crucial for investigating cement durability. Here, small-angle neutron scattering is used to analyze the evolution of the pore structure in alkali-activated materials over the initial 24 h of reaction in order to assess the characteristic poremore » sizes that emerge during these short time scales. By using a unified fitting approach for data modeling, information on the pore size and surface roughness is obtained for a variety of precursor chemistries and morphologies (metakaolin- and slag-based pastes). Furthermore, the impact of activator chemistry is elucidatedviathe analysis of pastes synthesized using hydroxide- and silicate-based activators. It is found that the main aspect influencing the size of pores that are accessible using small-angle neutron scattering analysis (approximately 10–500 Å in diameter) is the availability of free silica in the activating solution, which leads to a more refined pore structure with smaller average pore size. Furthermore, as the reaction progresses the gel pores visible using this scattering technique are seen to increase in size.« less

Structural evolution of the methane cation in subfemtosecond photodynamics

NASA Astrophysics Data System (ADS)

Mondal, T.; Varandas, A. J. C.

2015-07-01

An ab initio quantum dynamics study has been performed to explore the structural rearrangement of ground state CH 4+ in subfemtosecond resolved photodynamics. The method utilizes time-dependent wave-packet propagation on the X ˜ 2 T 2 electronic manifold of the title cation in full dimensionality, including nonadiabatic coupling of the three electronic sheets. Good agreement is obtained with recent experiments [Baker et al., Science 312, 424 (2006)] which use high-order harmonic generation to probe the attosecond proton dynamics. The novel results provide direct theoretical support of the observations while unravelling the underlying details. With the geometrical changes obtained by calculating the expectation values of the nuclear coordinates as a function of time, the structural evolution is predicted to begin through activation of the totally symmetric a1 and doubly degenerate e modes. While the former retains the original Td symmetry of the cation, the Jahn-Teller active e mode conducts it to a D2d structure. At ˜1.85 fs, the intermediate D2d structure is further predicted to rearrange to local C2v minimum geometry via Jahn-Teller active bending vibrations of t2 symmetry.

Evolution of the structure and the phase composition of a bainitic structural steel during plastic deformation

NASA Astrophysics Data System (ADS)

Nikitina, E. N.; Glezer, A. M.; Ivanov, Yu. F.; Aksenova, K. V.; Gromov, V. E.; Kazimirov, S. A.

2017-10-01

The evolution of the phase composition and the imperfect substructure of the 30Kh2N2MFA bainitic structural steel subjected to compressive deformation by 36% is quantitatively analyzed. It is shown that deformation is accompanied by an increase in the scalar dislocation density, a decrease in the longitudinal fragment sizes, an increase in the number of stress concentrators, the dissolution of cementite particles, and the transformation of retained austenite.

An Analysis on a Negotiation Model Based on Multiagent Systems with Symbiotic Learning and Evolution

NASA Astrophysics Data System (ADS)

Hossain, Md. Tofazzal

This study explores an evolutionary analysis on a negotiation model based on Masbiole (Multiagent Systems with Symbiotic Learning and Evolution) which has been proposed as a new methodology of Multiagent Systems (MAS) based on symbiosis in the ecosystem. In Masbiole, agents evolve in consideration of not only their own benefits and losses, but also the benefits and losses of opponent agents. To aid effective application of Masbiole, we develop a competitive negotiation model where rigorous and advanced intelligent decision-making mechanisms are required for agents to achieve solutions. A Negotiation Protocol is devised aiming at developing a set of rules for agents' behavior during evolution. Simulations use a newly developed evolutionary computing technique, called Genetic Network Programming (GNP) which has the directed graph-type gene structure that can develop and design the required intelligent mechanisms for agents. In a typical scenario, competitive negotiation solutions are reached by concessions that are usually predetermined in the conventional MAS. In this model, however, not only concession is determined automatically by symbiotic evolution (making the system intelligent, automated, and efficient) but the solution also achieves Pareto optimal automatically.

Detection of structural damage in multiwire cables by monitoring the entropy evolution of wavelet coefficients

NASA Astrophysics Data System (ADS)

Ibáñez, Flor; Baltazar, Arturo; Mijarez, Rito; Aranda, Jorge

2015-03-01

Multiwire cables are widely used in important civil structures. Since they are exposed to several dynamic and static loads, their structural health can be compromised. The cables can also be submitted to mechanical contact, tension and energy propagation in addition to changes in size and material within their wires. Due to the critical role played by multiwire cables, it is necessary to develop a non-destructive health monitoring method to maintain their structure and proper performance. Ultrasonic inspection using guided waves is a promising non-destructive damage monitoring technique for rods, single wires and multiwire cables. The propagated guided waves are composed by an infinite number of vibrational modes making their analysis difficult. In this work, an entropy-based method to identify small changes in non-stationary signals is proposed. A system to capture and post-process acoustic signals is implemented. The Discrete Wavelet Transform (DWT) is computed in order to obtain the reconstructed wavelet coefficients of the signals and to analyze the energy at different scales. The feasibility of using the concept of entropy evolution of non-stationary signals to detect damage in multiwire cables is evaluated. The results show that there is a high correlation between the entropy value and damage level of the cable. The proposed method has low sensitivity to noise and reduces the computational complexity found in a typical time-frequency analysis.

Structural Measures to Track the Evolution of SNOMED CT Hierarchies

PubMed Central

Wei, Duo; Gu, Huanying (Helen); Perl, Yehoshua; Halper, Michael; Ochs, Christopher; Elhanan, Gai; Chen, Yan

2015-01-01

The Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) is an extensive reference terminology with an attendant amount of complexity. It has been updated continuously and revisions have been released semi-annually to meet users’ needs and to reflect the results of quality assurance (QA) activities. Two measures based on structural features are proposed to track the effects of both natural terminology growth and QA activities based on aspects of the complexity of SNOMED CT. These two measures, called the structural density measure and accumulated structural measure, are derived based on two abstraction networks, the area taxonomy and the partial-area taxonomy. The measures derive from attribute relationship distributions and various concept groupings that are associated with the abstraction networks. They are used to track the trends in the complexity of structures as SNOMED CT changes over time. The measures were calculated for consecutive releases of five SNOMED CT hierarchies, including the Specimen hierarchy. The structural density measure shows that natural growth tends to move a hierarchy’s structure toward a more complex state, whereas the accumulated structural measure shows that QA processes tend to move a hierarchy’s structure toward a less complex state. It is also observed that both the structural density and accumulated structural measures are useful tools to track the evolution of an entire SNOMED CT hierarchy and reveal internal concept migration within it. PMID:26260003

Invasion fitness for gene-culture co-evolution in family-structured populations and an application to cumulative culture under vertical transmission.

PubMed

Mullon, Charles; Lehmann, Laurent

2017-08-01

Human evolution depends on the co-evolution between genetically determined behaviors and socially transmitted information. Although vertical transmission of cultural information from parent to offspring is common in hominins, its effects on cumulative cultural evolution are not fully understood. Here, we investigate gene-culture co-evolution in a family-structured population by studying the invasion fitness of a mutant allele that influences a deterministic level of cultural information (e.g., amount of knowledge or skill) to which diploid carriers of the mutant are exposed in subsequent generations. We show that the selection gradient on such a mutant, and the concomitant level of cultural information it generates, can be evaluated analytically under the assumption that the cultural dynamic has a single attractor point, thereby making gene-culture co-evolution in family-structured populations with multigenerational effects mathematically tractable. We apply our result to study how genetically determined phenotypes of individual and social learning co-evolve with the level of adaptive information they generate under vertical transmission. We find that vertical transmission increases adaptive information due to kin selection effects, but when information is transmitted as efficiently between family members as between unrelated individuals, this increase is moderate in diploids. By contrast, we show that the way resource allocation into learning trades off with allocation into reproduction (the "learning-reproduction trade-off") significantly influences levels of adaptive information. We also show that vertical transmission prevents evolutionary branching and may therefore play a qualitative role in gene-culture co-evolutionary dynamics. More generally, our analysis of selection suggests that vertical transmission can significantly increase levels of adaptive information under the biologically plausible condition that information transmission between relatives is

The evolution of antibiotic resistance in a structured host population.

PubMed

Blanquart, François; Lehtinen, Sonja; Lipsitch, Marc; Fraser, Christophe

2018-06-01

The evolution of antibiotic resistance in opportunistic pathogens such as Streptococcus pneumoniae , Escherichia coli or Staphylococcus aureus is a major public health problem, as infection with resistant strains leads to prolonged hospital stay and increased risk of death. Here, we develop a new model of the evolution of antibiotic resistance in a commensal bacterial population adapting to a heterogeneous host population composed of untreated and treated hosts, and structured in different host classes with different antibiotic use. Examples of host classes include age groups and geographic locations. Explicitly modelling the antibiotic treatment reveals that the emergence of a resistant strain is favoured by more frequent but shorter antibiotic courses, and by higher transmission rates. In addition, in a structured host population, localized transmission in host classes promotes both local adaptation of the bacterial population and the global maintenance of coexistence between sensitive and resistant strains. When transmission rates are heterogeneous across host classes, resistant strains evolve more readily in core groups of transmission. These findings have implications for the better management of antibiotic resistance: reducing the rate at which individuals receive antibiotics is more effective to reduce resistance than reducing the duration of treatment. Reducing the rate of treatment in a targeted class of the host population allows greater reduction in resistance, but determining which class to target is difficult in practice. © 2018 The Authors.

Technology for Space Station Evolution. Volume 5: Structures and Materials/Thermal Control System

NASA Technical Reports Server (NTRS)

1990-01-01

NASA's Office of Aeronautics and Space Technology (OAST) conducted a workshop on technology for space station evolution on 16-19 Jan. 1990. The purpose of this workshop was to collect and clarify Space Station Freedom technology requirements for evolution and to describe technologies that can potentially fill those requirements. These proceedings are organized into an Executive Summary and Overview and five volumes containing the Technology Discipline Presentations. Volume 5 consists of the technology discipline sections for Structures/Materials and the Thermal Control System. For each technology discipline, there is a level 3 subsystem description, along with papers.

The role of unsteady buoyancy flux on transient eruption plume velocity structure and evolution

NASA Astrophysics Data System (ADS)

Chojnicki, K. N.; Clarke, A. B.; Phillips, J. C.

2010-12-01

Volcanic vent exit velocities, eruption column velocity profiles, and atmospheric entrainment are important parameters that control the evolution of explosive volcanic eruption plumes. New data sets tracking short-term variability in such parameters are becoming more abundant in volcanology and are being used to indirectly estimate eruption source conditions such vent flux, material properties of the plume, and source mechanisms. However, inadequate theory describing the relationships between time-varying source fluxes and evolution of unsteady turbulent flows such as eruption plumes, limits the interpretation potential of these data sets. In particular, the relative roles of gas-thrust and buoyancy in volcanic explosions is known to generate distinct differences in the ascent dynamics. Here we investigate the role of initial buoyancy in unsteady, short-duration eruption dynamics through scaled laboratory experiments and provide an empirical description of the relationship between unsteady source flux and plume evolution. The experiments involved source fluids of various densities (960-1000 kg/m3) injected, with a range of initial momentum and buoyancy, into a tank of fresh water through a range of vent diameters (3-15 mm). A scaled analysis was used to determine the fundamental parameters governing the evolution of the laboratory plumes as a function of unsteady source conditions. The subsequent model can be applied to predict flow front propagation speeds, and maximum flow height and width of transient volcanic eruption plumes which can not be adequately described by existing steady approximations. In addition, the model describes the relative roles of momentum or gas-thrust and buoyancy in plume motion which is suspected to be a key parameter in quantitatively defining explosive eruption style. The velocity structure of the resulting flows was measured using the Particle Image Velocimetry (PIV) technique in which velocity vector fields were generated from

Functional evolution and structural conservation in chimeric cytochromes p450: calibrating a structure-guided approach.

PubMed

Otey, Christopher R; Silberg, Jonathan J; Voigt, Christopher A; Endelman, Jeffrey B; Bandara, Geethani; Arnold, Frances H

2004-03-01

Recombination generates chimeric proteins whose ability to fold depends on minimizing structural perturbations that result when portions of the sequence are inherited from different parents. These chimeric sequences can display functional properties characteristic of the parents or acquire entirely new functions. Seventeen chimeras were generated from two CYP102 members of the functionally diverse cytochrome p450 family. Chimeras predicted to have limited structural disruption, as defined by the SCHEMA algorithm, displayed CO binding spectra characteristic of folded p450s. Even this small population exhibited significant functional diversity: chimeras displayed altered substrate specificities, a wide range in thermostabilities, up to a 40-fold increase in peroxidase activity, and ability to hydroxylate a substrate toward which neither parent heme domain shows detectable activity. These results suggest that SCHEMA-guided recombination can be used to generate diverse p450s for exploring function evolution within the p450 structural framework.

Pressure-Induced Structural Evolution and Band Gap Shifts of Organometal Halide Perovskite-Based Methylammonium Lead Chloride.

PubMed

Wang, Lingrui; Wang, Kai; Xiao, Guanjun; Zeng, Qiaoshi; Zou, Bo

2016-12-15

Organometal halide perovskites are promising materials for optoelectronic devices. Further development of these devices requires a deep understanding of their fundamental structure-property relationships. The effect of pressure on the structural evolution and band gap shifts of methylammonium lead chloride (MAPbCl 3 ) was investigated systematically. Synchrotron X-ray diffraction and Raman experiments provided structural information on the shrinkage, tilting distortion, and amorphization of the primitive cubic unit cell. In situ high pressure optical absorption and photoluminescence spectra manifested that the band gap of MAPbCl 3 could be fine-tuned to the ultraviolet region by pressure. The optical changes are correlated with pressure-induced structural evolution of MAPbCl 3 , as evidenced by band gap shifts. Comparisons between Pb-hybrid perovskites and inorganic octahedra provided insights on the effects of halogens on pressure-induced transition sequences of these compounds. Our results improve the understanding of the structural and optical properties of organometal halide perovskites.

Microrheology: Structural evolution under static and dynamic conditions by simultaneous analysis of confocal microscopy and diffusing wave spectroscopy

NASA Astrophysics Data System (ADS)

Nicolas, Yves; Paques, Marcel; Knaebel, Alexandra; Steyer, Alain; Munch, Jean-Pierre; Blijdenstein, Theo B. J.; van Aken, George A.

2003-08-01

An oscillatory shear configuration was developed to improve understanding of structural evolution during deformation. It combines an inverted confocal scanning laser microscope (CSLM) and a special sample holder that can apply to the sample specific deformation: oscillatory shear or steady strain. In this configuration, a zero-velocity plane is created in the sample by moving two plates in opposite directions, thereby providing stable observation conditions of the structural behavior under deformation. The configuration also includes diffusion wave spectroscopy (DWS) to monitor the network properties via particle mobility under static and dynamic conditions. CSLM and DWS can be performed simultaneously and three-dimensional images can be obtained under static conditions. This configuration is mainly used to study mechanistic phenomena like particle interaction, aggregation, gelation and network disintegration, interactions at interfaces under static and dynamic conditions in semisolid food materials (desserts, dressings, sauces, dairy products) and in nonfood materials (mineral emulsions, etc.). Preliminary data obtained with this new oscillatory shear configuration are described that demonstrate their capabilities and the potential contribution to other areas of application also.

Chloroplast evolution, structure and functions

PubMed Central

Jensen, Poul Erik

2014-01-01

In this review, we consider a selection of recent advances in chloroplast biology. These include new findings concerning chloroplast evolution, such as the identification of Chlamydiae as a third partner in primary endosymbiosis, a second instance of primary endosymbiosis represented by the chromatophores found in amoebae of the genus Paulinella, and a new explanation for the longevity of captured chloroplasts (kleptoplasts) in sacoglossan sea slugs. The controversy surrounding the three-dimensional structure of grana, its recent resolution by tomographic analyses, and the role of the CURVATURE THYLAKOID1 (CURT1) proteins in supporting grana formation are also discussed. We also present an updated inventory of photosynthetic proteins and the factors involved in the assembly of thylakoid multiprotein complexes, and evaluate findings that reveal that cyclic electron flow involves NADPH dehydrogenase (NDH)- and PGRL1/PGR5-dependent pathways, both of which receive electrons from ferredoxin. Other topics covered in this review include new protein components of nucleoids, an updated inventory of the chloroplast proteome, new enzymes in chlorophyll biosynthesis and new candidate messengers in retrograde signaling. Finally, we discuss the first successful synthetic biology approaches that resulted in chloroplasts in which electrons from the photosynthetic light reactions are fed to enzymes derived from secondary metabolism. PMID:24991417

Structural evolution of fluorinated graphene upon molten-alkali treatment probed by X-ray absorption near-edge structure spectroscopy

NASA Astrophysics Data System (ADS)

Liang, Xianqing; Pan, Deyou; Lao, Ming; Liang, Shuiying; Huang, Dan; Zhou, Wenzheng; Guo, Jin

2017-05-01

The structural evolution of fluorinated graphene (FG) nanosheets upon molten-alkali treatment has been systematically investigated utilizing X-ray absorption near-edge structure (XANES) spectroscopy. It is found that the hydroxyl groups can progressively displace fluorine atoms to form covalent bonds to the graphene sheets under designed molten-alkali condition. The XANES spectra also reveal the formation of epoxide groups through intramolecular dehydration of neighbouring hydroxyl groups after substitution reaction. At high alkali-FG weight ratio, the restoration of the π-conjugated structure in graphene sheets can be observed due to the gradual decomposition of epoxide groups. Our experimental results indicate that the surface chemistry and electronic structure of hydroxyl-functionalized FG (HFG) can be readily tuned by varying the ratio of reactants.

Scale covariant gravitation. V - Kinetic theory. VI - Stellar structure and evolution

NASA Technical Reports Server (NTRS)

Hsieh, S.-H.; Canuto, V. M.

1981-01-01

A scale covariant kinetic theory for particles and photons is developed. The mathematical framework of the theory is given by the tangent bundle of a Weyl manifold. The Liouville equation is derived, and solutions to corresponding equilibrium distributions are presented and shown to yield thermodynamic results identical to the ones obtained previously. The scale covariant theory is then used to derive results of interest to stellar structure and evolution. A radiative transfer equation is derived that can be used to study stellar evolution with a variable gravitational constant. In addition, it is shown that the sun's absolute luminosity scales as L approximately equal to GM/kappa, where kappa is the stellar opacity. Finally, a formula is derived for the age of globular clusters as a function of the gravitational constant using a previously derived expression for the absolute luminosity.

A spatial analysis of hierarchical waste transport structures under growing demand.

PubMed

Tanguy, Audrey; Glaus, Mathias; Laforest, Valérie; Villot, Jonathan; Hausler, Robert

2016-10-01

The design of waste management systems rarely accounts for the spatio-temporal evolution of the demand. However, recent studies suggest that this evolution affects the planning of waste management activities like the choice and location of treatment facilities. As a result, the transport structure could also be affected by these changes. The objective of this paper is to study the influence of the spatio-temporal evolution of the demand on the strategic planning of a waste transport structure. More particularly this study aims at evaluating the effect of varying spatial parameters on the economic performance of hierarchical structures (with one transfer station). To this end, three consecutive generations of three different spatial distributions were tested for hierarchical and non-hierarchical transport structures based on costs minimization. Results showed that a hierarchical structure is economically viable for large and clustered spatial distributions. The distance parameter was decisive but the loading ratio of trucks and the formation of clusters of sources also impacted the attractiveness of the transfer station. Thus the territories' morphology should influence strategies as regards to the installation of transfer stations. The use of spatial-explicit tools such as the transport model presented in this work that take into account the territory's evolution are needed to help waste managers in the strategic planning of waste transport structures. © The Author(s) 2016.

Inclusive fitness analysis of cumulative cultural evolution in an island-structured population.

PubMed

Ohtsuki, Hisashi; Wakano, Joe Yuichiro; Kobayashi, Yutaka

2017-06-01

The success of humans on the globe is largely supported by our cultural excellence. Our culture is cumulative, meaning that it is improved from generation to generation. Previous works have revealed that two modes of learning, individual learning and social learning, play pivotal roles in the accumulation of culture. However, under the trade-off between learning and reproduction, one's investment into learning is easily exploited by those who copy the knowledge of skillful individuals and selfishly invest more efforts in reproduction. It has been shown that in order to prevent such a breakdown, the rate of vertical transmission (i.e. transmission from parents to their offspring) of culture must be unrealistically close to one. Here we investigate what if the population is spatially structured. In particular, we hypothesize that spatial structure should favor highly cumulative culture through endogenously arising high kinship. We employ Wright's island model and assume that cultural transmission occurs within a local island. Our inclusive fitness analysis reveals combined effects of direct fitness of the actor, indirect fitness through relatives in the current generation, and indirect fitness through relatives in future generations. The magnitude of those indirect benefits is measured by intergenerational coefficients of genetic relatedness. Our result suggests that the introduction of spatial structure raises the stationary level of culture in the population, but that the extent of its improvement compared with a well-mixed population is marginal unless spatial localization is extreme. Overall, our model implies that we need an alternative mechanism to explain highly cumulative culture of modern humans. Copyright © 2017 Elsevier Inc. All rights reserved.

Experimental evolution in biofilm populations

PubMed Central

Steenackers, Hans P.; Parijs, Ilse; Foster, Kevin R.; Vanderleyden, Jozef

2016-01-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. PMID:26895713

Experimental evolution in biofilm populations.

PubMed

Steenackers, Hans P; Parijs, Ilse; Dubey, Akanksha; Foster, Kevin R; Vanderleyden, Jozef

2016-05-01

Biofilms are a major form of microbial life in which cells form dense surface associated communities that can persist for many generations. The long-life of biofilm communities means that they can be strongly shaped by evolutionary processes. Here, we review the experimental study of evolution in biofilm communities. We first provide an overview of the different experimental models used to study biofilm evolution and their associated advantages and disadvantages. We then illustrate the vast amount of diversification observed during biofilm evolution, and we discuss (i) potential ecological and evolutionary processes behind the observed diversification, (ii) recent insights into the genetics of adaptive diversification, (iii) the striking degree of parallelism between evolution experiments and real-life biofilms and (iv) potential consequences of diversification. In the second part, we discuss the insights provided by evolution experiments in how biofilm growth and structure can promote cooperative phenotypes. Overall, our analysis points to an important role of biofilm diversification and cooperation in bacterial survival and productivity. Deeper understanding of both processes is of key importance to design improved antimicrobial strategies and diagnostic techniques. © FEMS 2016.

Structural evolution under uniaxial drawing of Poly(D, L-lactide) Films

NASA Astrophysics Data System (ADS)

Stoclet, Grégory; Lefebvre, Jean-Marc; Seguela, Roland

2009-03-01

Aliphatic polyesters are an important class of biodegradable polymers. They have drawn particular attention in the last few years as food packaging materials because they can be derived from renewable resources. Among this family, polylactide (PLA) is considered as one of the most promising ``green'' polymer for use as a substitute to petroleum-based polymers. In the present work, we investigate the mechanical behaviour of amorphous poly(D, L-lactide) films in relation to the structural evolution upon stretching at various draw temperatures (Td) above the glass transition temperature. Examination of the drawing behaviour shows that PLA initially behaves like a rubbery material until a true strain of the order of 1. Strain hardening occurs beyond this strain level, up to film fracture. Such strain hardening is generally ascribed to a strain induced crystallization phenomenon. In the present case, it is clearly more pronounced for Td = 90 C than for Td = 70 C. The corresponding structural evolutions are investigated by means of WAXS. The diffraction patterns reveal the marked influence of draw temperature. Indeed for Td = 70 C a mesophase is induced whereas strain-induced crystallisation takes place at Td = 90 C. Further work is in progress, in order to elucidate mesophase development and mechanical response.

Origin and evolution of the deep thermochemical structure beneath Eurasia.

PubMed

Flament, N; Williams, S; Müller, R D; Gurnis, M; Bower, D J

2017-01-18

A unique structure in the Earth's lowermost mantle, the Perm Anomaly, was recently identified beneath Eurasia. It seismologically resembles the large low-shear velocity provinces (LLSVPs) under Africa and the Pacific, but is much smaller. This challenges the current understanding of the evolution of the plate-mantle system in which plumes rise from the edges of the two LLSVPs, spatially fixed in time. New models of mantle flow over the last 230 million years reproduce the present-day structure of the lower mantle, and show a Perm-like anomaly. The anomaly formed in isolation within a closed subduction network ∼22,000 km in circumference prior to 150 million years ago before migrating ∼1,500 km westward at an average rate of 1 cm year -1 , indicating a greater mobility of deep mantle structures than previously recognized. We hypothesize that the mobile Perm Anomaly could be linked to the Emeishan volcanics, in contrast to the previously proposed Siberian Traps.

Intermediate states and structure evolution in the free-falling process of the dislocation in graphene

NASA Astrophysics Data System (ADS)

Wang, Shaofeng; Yao, Yin; Bai, Jianhui; Wang, Rui

2017-04-01

This paper investigated the intermediate states and the structure evolution of the dislocation in graphene when it falls freely from the saddle point of the energy landscape. The O-type dislocation, an unstable equilibrium structure located at the saddle point, is obtained from the lattice theory of the dislocation structure and improved by the ab initio calculation to take the buckling into account. Intermediate states along the kinetics path in the falling process are obtained from the ab initio simulation. Once the dislocation falls from the saddle point to the energy valley, this O-type dislocation transforms into the stable structure that is referred to as the B-type dislocation, and in the meantime, it moves a distance that equals half a Burgers vector. The structure evolution and the energy variation in the free-falling process are revealed explicitly. It is observed that rather than smooth change, a platform manifests itself in the energy curve. The unusual behaviour in the energy curve is mainly originated from symmetry breaking and bond formation in the dislocation core. The results can provide deep insight in the mechanism of the brittle feature of covalent materials.

The structure and evolution of coronal holes

NASA Technical Reports Server (NTRS)

Timothy, A. F.; Krieger, A. S.; Vaiana, G. S.

1975-01-01

Soft X-ray observations of coronal holes are analyzed to determine the structure, temporal evolution, and rotational properties of those features as well as possible mechanisms which may account for their almost rigid rotational characteristics. It is shown that coronal holes are open features with a divergent magnetic-field configuration resulting from a particular large-scale magnetic-field topology. They are apparently formed when the successive emergence and dispersion of active-region fields produce a swath of unipolar field founded by fields of opposite polarity, and they die when large-scale field patterns emerge which significantly distort the original field configuration. Two types of holes are described (compact and elongated), and three possible rotation mechanisms are considered: a rigidly rotating subphotospheric phenomenon, a linking of high and low latitudes by closed field lines, and an interaction between moving coronal material and open field lines.

A highly-active and stable hydrogen evolution catalyst based on pyrite-structured cobalt phosphosulfide

DOE PAGES

Liu, Wen; Hu, Enyuan; Jiang, Hong; ...

2016-02-19

Rational design and controlled synthesis of hybrid structures comprising multiple components with distinctive functionalities are an intriguing and challenging approach to materials development for important energy applications like electrocatalytic hydrogen production, where there is a great need for cost effective, active and durable catalyst materials to replace the precious platinum. Here we report a structure design and sequential synthesis of a highly active and stable hydrogen evolution electrocatalyst material based on pyrite-structured cobalt phosphosulfide nanoparticles grown on carbon nanotubes. The three synthetic steps in turn render electrical conductivity, catalytic activity and stability to the material. The hybrid material exhibits superiormore » activity for hydrogen evolution, achieving current densities of 10 mA cm –2 and 100 mA cm –2 at overpotentials of 48 mV and 109 mV, respectively. Lastly, phosphorus substitution is crucial for the chemical stability and catalytic durability of the material, the molecular origins of which are uncovered by X-ray absorption spectroscopy and computational simulation.« less

Discovering structure and evolution within the coronae of Seyfert galaxies

NASA Astrophysics Data System (ADS)

Wilkins, Daniel; Gallo, Luigi C.; Silva, Catia; Costantini, Elisa

2017-08-01

Detailed analysis of the reflection and reverberation of X-rays from the innermost regions of AGN accretion discs reveals the structure and processes that produce the intense continuum emission and the extreme variability we see, right down to the innermost stable orbit and event horizon of the black hole. Observations of Seyfert galaxies spanning more than a decade have enabled measurement of the geometry of the corona and how it evolves, leading to orders of magnitude in variability. They reveal processes the corona undergoes during transient events, notably the collimation and ejection of the corona during X-ray flares, reminiscent of the aborted launching of a jet.Recent reverberation studies, of the Seyfert galaxy I Zwicky 1 with XMM-Newton, are revealing structures within the corona for the very first time. A persistent collimated core is discovered, akin to the base of a jet embedded in the innermost regions alongside an extended corona related to the accretion disc. The detection of the flare in the X-ray emission enables the evolution of both the collimated and extended portions of the corona to be tracked. The flare is seen originating as an increase in activity above the accretion disc before propagating inwards, energising the collimated core at a later time, leading to a second sharp increase in the X-ray luminosity.This gives us important constraints on the processes by which energy is liberated from black hole accretion flows, how they are governed over time and how jets are launched, giving us the deepest insight to date of how these extreme objects are powered.

Long-term phenotypic evolution of bacteria.

PubMed

Plata, Germán; Henry, Christopher S; Vitkup, Dennis

2015-01-15

For many decades comparative analyses of protein sequences and structures have been used to investigate fundamental principles of molecular evolution. In contrast, relatively little is known about the long-term evolution of species' phenotypic and genetic properties. This represents an important gap in our understanding of evolution, as exactly these proprieties play key roles in natural selection and adaptation to diverse environments. Here we perform a comparative analysis of bacterial growth and gene deletion phenotypes using hundreds of genome-scale metabolic models. Overall, bacterial phenotypic evolution can be described by a two-stage process with a rapid initial phenotypic diversification followed by a slow long-term exponential divergence. The observed average divergence trend, with approximately similar fractions of phenotypic properties changing per unit time, continues for billions of years. We experimentally confirm the predicted divergence trend using the phenotypic profiles of 40 diverse bacterial species across more than 60 growth conditions. Our analysis suggests that, at long evolutionary distances, gene essentiality is significantly more conserved than the ability to utilize different nutrients, while synthetic lethality is significantly less conserved. We also find that although a rapid phenotypic evolution is sometimes observed within the same species, a transition from high to low phenotypic similarity occurs primarily at the genus level.

Using Time Evolution of the Bunch Structure to Extract the Muon Momentum Distribution in the Fermilab Muon g-2 Experiment

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

Wu, W.; Quinn, B.; Crnkovic, J. D.

Beam dynamics plays an important role in achieving the unprecedented precision on measurement of the muon anomalous magnetic moment in the Fermilab Muon g-2 Experiment. It needs to find the muon momentum distribution in the storage ring in order to evaluate the electric field correction to muon anomalous precession frequency. We will show how to use time evolution of the beam bunch structure to extract the muon momentum distribution by applying a fast rotation analysis on the decay electron signals.

Multilocus genetics to reconstruct aeromonad evolution

PubMed Central

2012-01-01

Background Aeromonas spp. are versatile bacteria that exhibit a wide variety of lifestyles. In an attempt to improve the understanding of human aeromonosis, we investigated whether clinical isolates displayed specific characteristics in terms of genetic diversity, population structure and mode of evolution among Aeromonas spp. A collection of 195 Aeromonas isolates from human, animal and environmental sources was therefore genotyped using multilocus sequence analysis (MLSA) based on the dnaK, gltA, gyrB, radA, rpoB, tsf and zipA genes. Results The MLSA showed a high level of genetic diversity among the population, and multilocus-based phylogenetic analysis (MLPA) revealed 3 major clades: the A. veronii, A. hydrophila and A. caviae clades, among the eleven clades detected. Lower genetic diversity was observed within the A. caviae clade as well as among clinical isolates compared to environmental isolates. Clonal complexes, each of which included a limited number of strains, mainly corresponded to host-associated subsclusters of strains, i.e., a fish-associated subset within A. salmonicida and 11 human-associated subsets, 9 of which included only disease-associated strains. The population structure was shown to be clonal, with modes of evolution that involved mutations in general and recombination events locally. Recombination was detected in 5 genes in the MLSA scheme and concerned approximately 50% of the STs. Therefore, these recombination events could explain the observed phylogenetic incongruities and low robustness. However, the MLPA globally confirmed the current systematics of the genus Aeromonas. Conclusions Evolution in the genus Aeromonas has resulted in exceptionally high genetic diversity. Emerging from this diversity, subsets of strains appeared to be host adapted and/or “disease specialized” while the A. caviae clade displayed an atypical tempo of evolution among aeromonads. Considering that A. salmonicida has been described as a genetically

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in Al-Zr-Y alloy

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

Gao, Haiyan, E-mail: gaohaiyan@sjtu.edu.cn

Structural and compositional evolution of Al{sub 3}(Zr,Y) precipitates in aged Al-Zr-Y alloy was investigated through atom probe tomography (APT) and transmission electron microscope (TEM) analysis and first principles calculations. The results show that short-bar-shaped D0{sub 19}-Al{sub 3}Y with some Zr atoms dissolved in precipitated at the very beginning of decomposition and worked as heterogeneous nuclei for L1{sub 2}-Al{sub 3}Zr with spherical morphology after being aged at 400 °C for 2 h. Quasi-static coarsening happened as the aging treatment lasted from 2 h to 200 h. However, distribution of Zr and Y atoms in Al{sub 3}(Zr,Y) is nearly uniform and Al{submore » 3}(Zr,Y) do not have the typical “Al{sub 3}RE core-Al{sub 3}Zr shell” structure which observed in other RE containing Al-Zr-RE alloys with L1{sub 2}-Al{sub 3}RE as nuclei. First principles calculations revealed that binding energy between Y and Zr is strong during the growth of Al{sub 3}(Zr,Y), which led to the co-precipitation of Y and Zr atoms and attribute to the evolution of Al{sub 3}(Zr,Y). - Highlights: •Al{sub 3}Y precipitated firstly and then became nuclei for Al{sub 3}Zr during aging of Al-Zr-Y. •Al{sub 3}(Zr,Y) precipitates do not have the typical “Al{sub 3}Y core-Al{sub 3}Zr shell” structure. •Strong binding between Y and Zr led to the co-precipitation of Y and Zr atoms.« less

The evolution of plant secretory structures and emergence of terpenoid chemical diversity.

PubMed

Lange, Bernd Markus

2015-01-01

Secretory structures in terrestrial plants appear to have first emerged as intracellular oil bodies in liverworts. In vascular plants, internal secretory structures, such as resin ducts and laticifers, are usually found in conjunction with vascular bundles, whereas subepidermal secretory cavities and epidermal glandular trichomes generally have more complex tissue distribution patterns. The primary function of plant secretory structures is related to defense responses, both constitutive and induced, against herbivores and pathogens. The ability to sequester secondary (or specialized) metabolites and defense proteins in secretory structures was a critical adaptation that shaped plant-herbivore and plant-pathogen interactions. Although this review places particular emphasis on describing the evolution of pathways leading to terpenoids, it also assesses the emergence of other metabolite classes to outline the metabolic capabilities of different plant lineages.

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

PubMed Central

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-01-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth

NASA Astrophysics Data System (ADS)

Foley, Joseph; Hill, Shannon E.; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-01

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

Structural fingerprints and their evolution during oligomeric vs. oligomer-free amyloid fibril growth.

PubMed

Foley, Joseph; Hill, Shannon E; Miti, Tatiana; Mulaj, Mentor; Ciesla, Marissa; Robeel, Rhonda; Persichilli, Christopher; Raynes, Rachel; Westerheide, Sandy; Muschol, Martin

2013-09-28

Deposits of fibrils formed by disease-specific proteins are the molecular hallmark of such diverse human disorders as Alzheimer's disease, type II diabetes, or rheumatoid arthritis. Amyloid fibril formation by structurally and functionally unrelated proteins exhibits many generic characteristics, most prominently the cross β-sheet structure of their mature fibrils. At the same time, amyloid formation tends to proceed along one of two separate assembly pathways yielding either stiff monomeric filaments or globular oligomers and curvilinear protofibrils. Given the focus on oligomers as major toxic species, the very existence of an oligomer-free assembly pathway is significant. Little is known, though, about the structure of the various intermediates emerging along different pathways and whether the pathways converge towards a common or distinct fibril structures. Using infrared spectroscopy we probed the structural evolution of intermediates and late-stage fibrils formed during in vitro lysozyme amyloid assembly along an oligomeric and oligomer-free pathway. Infrared spectroscopy confirmed that both pathways produced amyloid-specific β-sheet peaks, but at pathway-specific wavenumbers. We further found that the amyloid-specific dye thioflavin T responded to all intermediates along either pathway. The relative amplitudes of thioflavin T fluorescence responses displayed pathway-specific differences and could be utilized for monitoring the structural evolution of intermediates. Pathway-specific structural features obtained from infrared spectroscopy and Thioflavin T responses were identical for fibrils grown at highly acidic or at physiological pH values and showed no discernible effects of protein hydrolysis. Our results suggest that late-stage fibrils formed along either pathway are amyloidogenic in nature, but have distinguishable structural fingerprints. These pathway-specific fingerprints emerge during the earliest aggregation events and persist throughout the

Evolution of the cosmic web

NASA Astrophysics Data System (ADS)

Cautun, Marius; van de Weygaert, Rien; Jones, Bernard J. T.; Frenk, Carlos S.

2014-07-01

The cosmic web is the largest scale manifestation of the anisotropic gravitational collapse of matter. It represents the transitional stage between linear and non-linear structures and contains easily accessible information about the early phases of structure formation processes. Here we investigate the characteristics and the time evolution of morphological components. Our analysis involves the application of the NEXUS Multiscale Morphology Filter technique, predominantly its NEXUS+ version, to high resolution and large volume cosmological simulations. We quantify the cosmic web components in terms of their mass and volume content, their density distribution and halo populations. We employ new analysis techniques to determine the spatial extent of filaments and sheets, like their total length and local width. This analysis identifies clusters and filaments as the most prominent components of the web. In contrast, while voids and sheets take most of the volume, they correspond to underdense environments and are devoid of group-sized and more massive haloes. At early times the cosmos is dominated by tenuous filaments and sheets, which, during subsequent evolution, merge together, such that the present-day web is dominated by fewer, but much more massive, structures. The analysis of the mass transport between environments clearly shows how matter flows from voids into walls, and then via filaments into cluster regions, which form the nodes of the cosmic web. We also study the properties of individual filamentary branches, to find long, almost straight, filaments extending to distances larger than 100 h-1 Mpc. These constitute the bridges between massive clusters, which seem to form along approximatively straight lines.

Genome structure drives patterns of gene family evolution in ciliates, a case study using Chilodonella uncinata (Protista, Ciliophora, Phyllopharyngea)

PubMed Central

Gao, Feng; Song, Weibo; Katz, Laura A.

2014-01-01

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that: 1) alternative processing is extensive among gene families; and 2) such gene families are likely to be C. uncinata-specific. We characterized additional macronuclear and micronuclear copies of one candidate alternatively processed gene family -- a protein kinase domain containing protein (PKc) -- from two C. uncinata strains. Analysis of the PKc sequences reveals: 1) multiple PKc gene family members in the macronucleus share some identical regions flanked by divergent regions; and 2) the shared identical regions are processed from a single micronuclear chromosome. We discuss analogous processes in lineages across the eukaryotic tree of life to provide further insights on the impact of genome structure on gene family evolution in eukaryotes. PMID:24749903

The relativistic equations of stellar structure and evolution. Stars with degenerate neutron cores. 1: Structure of equilibrium models

NASA Technical Reports Server (NTRS)

Thorne, K. S.; Zytkow, A. N.

1976-01-01

The general relativistic equations of stellar structure and evolution are reformulated in a notation which makes easy contact with Newtonian theory. Also, a general relativistic version of the mixing-length formalism for convection is presented. Finally, it is argued that in previous work on spherical systems general relativity theorists have identified the wrong quantity as "total mass-energy inside radius r."

Intra-individual variation and evolution of modular structure in Draba plants.

PubMed

Grigorieva, Olga V; Cherdantsev, Vladimir G

2014-09-01

We studied the evolution of quantitative traits related to shoot system architecture in a large genus Draba (Brassicaceae) making emphasis on the dynamics of relationship between individual and intra-individual variation. The results suggest that selection leading to origin of different life forms arises mainly from a necessity of moderation of the non-adaptive contest between the egoistic plant modules, taking care of self-reproduction of their own. We separated two evolutionary trends, one leading to the formation of short-lived monocarpic, and the other to long-lived polycarpic forms from the short-lived polycarpic plants. The first trend concerns with transformation of the innovation shoots into the axillary inflorescences by shortening of their vegetative developmental phase, while the second one - with individuation of the plant modules owing to acquisition of the capacity of rooting and separating from the mother plant. In both trends, the turning points of the evolution are those of originating of the negative for individual plants interactions between the plant modules being indirect non-adaptive consequences of the previous adaptive evolution and initiating selection for rebuilding of the plant modular structure. The difference between selection operating on intra-individual and individual variations is that, in the first case, combining of the characters of different individuals is infeasible. This leaves no choice for the evolution but to change the developmental mechanisms. In the case considered in this work, this is a change in shoot architecture using the material afforded by the natural variability of developmental pathways of the plant modules. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

ProteomeVis: a web app for exploration of protein properties from structure to sequence evolution across organisms' proteomes.

PubMed

Razban, Rostam M; Gilson, Amy I; Durfee, Niamh; Strobelt, Hendrik; Dinkla, Kasper; Choi, Jeong-Mo; Pfister, Hanspeter; Shakhnovich, Eugene I

2018-05-08

Protein evolution spans time scales and its effects span the length of an organism. A web app named ProteomeVis is developed to provide a comprehensive view of protein evolution in the S. cerevisiae and E. coli proteomes. ProteomeVis interactively creates protein chain graphs, where edges between nodes represent structure and sequence similarities within user-defined ranges, to study the long time scale effects of protein structure evolution. The short time scale effects of protein sequence evolution are studied by sequence evolutionary rate (ER) correlation analyses with protein properties that span from the molecular to the organismal level. We demonstrate the utility and versatility of ProteomeVis by investigating the distribution of edges per node in organismal protein chain universe graphs (oPCUGs) and putative ER determinants. S. cerevisiae and E. coli oPCUGs are scale-free with scaling constants of 1.79 and 1.56, respectively. Both scaling constants can be explained by a previously reported theoretical model describing protein structure evolution (Dokholyan et al., 2002). Protein abundance most strongly correlates with ER among properties in ProteomeVis, with Spearman correlations of -0.49 (p-value<10-10) and -0.46 (p-value<10-10) for S. cerevisiae and E. coli, respectively. This result is consistent with previous reports that found protein expression to be the most important ER determinant (Zhang and Yang, 2015). ProteomeVis is freely accessible at http://proteomevis.chem.harvard.edu. Supplementary data are available at Bioinformatics. shakhnovich@chemistry.harvard.edu.

Extortion provides alternative routes to the evolution of cooperation in structured populations

NASA Astrophysics Data System (ADS)

Xu, Xiongrui; Rong, Zhihai; Wu, Zhi-Xi; Zhou, Tao; Tse, Chi Kong

2017-05-01

In this paper, we study the evolution of cooperation in structured populations (individuals are located on either a regular lattice or a scale-free network) in the context of repeated games by involving three types of strategies, namely, unconditional cooperation, unconditional defection, and extortion. The strategy updating of the players is ruled by the replicator-like dynamics. We find that extortion strategies can act as catalysts to promote the emergence of cooperation in structured populations via different mechanisms. Specifically, on regular lattice, extortioners behave as both a shield, which can enwrap cooperators inside and keep them away from defectors, and a spear, which can defeat those surrounding defectors with the help of the neighboring cooperators. Particularly, the enhancement of cooperation displays a resonance-like behavior, suggesting the existence of optimal extortion strength mostly favoring the evolution of cooperation, which is in good agreement with the predictions from the generalized mean-field approximation theory. On scale-free network, the hubs, who are likely occupied by extortioners or defectors at the very beginning, are then prone to be conquered by cooperators on small-degree nodes as time elapses, thus establishing a bottom-up mechanism for the emergence and maintenance of cooperation.

Evolution of Venomous Cartilaginous and Ray-Finned Fishes.

PubMed

Smith, W Leo; Stern, Jennifer H; Girard, Matthew G; Davis, Matthew P

2016-11-01

Venom and its associated delivery systems have evolved in numerous animal groups ranging from jellyfishes to spiders, lizards, shrews, and the male platypus. Building off new data and previously published anatomical and molecular studies, we explore the evolution of and variation within venomous fishes. We show the results of the first multi-locus, ordinal-level phylogenetic analysis of cartilaginous (Chondrichthyes) and ray-finned (Actinopterygii) fishes that hypothesizes 18 independent evolutions of this specialization. Ancestral-states reconstruction indicates that among the 2386-2962 extant venomous fishes, envenomed structures have evolved four times in cartilaginous fishes, once in eels (Anguilliformes), once in catfishes (Siluriformes), and 12 times in spiny-rayed fishes (Acanthomorpha). From our anatomical studies and phylogenetic reconstruction, we show that dorsal spines are the most common envenomed structures (∼95% of venomous fish species and 15 independent evolutions). In addition to envenomed spines, fishes have also evolved venomous fangs (2% of venomous fish species, two independent evolutions), cleithral spines (2% of venomous fish species, one independent evolution), and opercular or subopercular spines (1% of venomous fish species, three independent evolutions). © The Author 2016. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

The structural and electrical evolution of graphene by oxygen plasma-induced disorder.

PubMed

Kim, Dong Chul; Jeon, Dae-Young; Chung, Hyun-Jong; Woo, YunSung; Shin, Jai Kwang; Seo, Sunae

2009-09-16

Evolution of a single graphene layer with disorder generated by remote oxygen plasma irradiation is investigated using atomic force microscopy, Raman spectroscopy and electrical measurement. Gradual changes of surface morphology from planar graphene to isolated granular structure associated with a decrease of transconductance are accounted for by two-dimensional percolative conduction by disorder and the oxygen plasma-induced doping effect. The corresponding evolution of Raman spectra of graphene shows several peculiarities such as a sudden appearance of a saturated D peak followed by a linear decrease in its intensity, a relatively inert characteristic of a D' peak and a monotonic increase of a G peak position as the exposure time to oxygen plasma increases. These are discussed in terms of a disorder-induced change of Raman spectra in the graphite system.

In situ visualization of domain structure evolution during field cooling in 0.67PMN-0.33PT single crystal

NASA Astrophysics Data System (ADS)

Ushakov, A. D.; Esin, A. A.; Chezganov, D. S.; Turygin, A. P.; Akhmatkhanov, A. R.; Hu, Q.; Sun, L.; Wei, X.; Shur, V. Ya

2017-10-01

The evolution of the domain structure during in-field cooling was in situ studied in [001]-cut single crystals of relaxor ferroelectric (1-x)Pb(Mg1/3Nb2/3)O3-xPbTiO3 (PMN-PT) with x = 0.33 with maximum of dielectric permittivity at 150°C. The main stages of domain evolution have been separated. The visualization of the static as-grown and polarized domain structures with high spatial resolution by piezoresponse force microscopy and scanning electron microscopy allowed measuring the characteristic features of maze and needle-like domain structures.

Neoproterozoic Evolution and Najd‒Related Transpressive Shear Deformations Along Nugrus Shear Zone, South Eastern Desert, Egypt (Implications from Field‒Structural Data and AMS‒Technique)

NASA Astrophysics Data System (ADS)

Hagag, W.; Moustafa, R.; Hamimi, Z.

2018-01-01

The tectonometamorphic evolution of Nugrus Shear Zone (NSZ) in the south Eastern Desert of Egypt was reevaluated through an integrated study including field-structural work and magnetofabric analysis using Anisotropy of Magnetic Susceptibility (AMS) technique, complemented by detailed microstructural investigation. Several lines of evidence indicate that the Neoproterozoic juvenile crust within this high strain zone suffered an impressive tectonic event of left-lateral transpressional regime, transposed the majority of the earlier formed structures into a NNW to NW-directed wrench corridor depicts the northwestern extension of the Najd Shear System (NSS) along the Eastern Desert of Egypt. The core of the southern Hafafit dome underwent a high metamorphic event ( M 1) developed during the end of the main collisional orogeny in the Arabian-Nubian Shield (ANS). The subsequent M 2 metamorphic event was retrogressive and depicts the tectonic evolution and exhumation of the Nugrus-Hafafit area including the Hafafit gneissic domes, during the origination of the left-lateral transpressive wrench corridor of the NSS. The early tectonic fabric within the NSZ and associated highly deformed rocks was successfully detected by the integration of AMS-technique and microstructural observations. Such fabric grain was checked through a field-structural work. The outcomes of the present contribution advocate a complex tectonic evolution with successive and overlapped deformation events for the NSZ.

Structural evolution and electronic properties of n-type doped hydrogenated amorphous silicon thin films

NASA Astrophysics Data System (ADS)

He, Jian; Li, Wei; Xu, Rui; Qi, Kang-Cheng; Jiang, Ya-Dong

2011-12-01

The relationship between structure and electronic properties of n-type doped hydrogenated amorphous silicon (a-Si:H) thin films was investigated. Samples with different features were prepared by plasma enhanced chemical vapor deposition (PECVD) at various substrate temperatures. Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy were used to evaluate the structural evolution, meanwhile, electronic-spin resonance (ESR) and optical measurement were applied to explore the electronic properties of P-doped a-Si:H thin films. Results reveal that the changes in materials structure affect directly the electronic properties and the doping efficiency of dopant.

Evolution of complex dynamics

NASA Astrophysics Data System (ADS)

Wilds, Roy; Kauffman, Stuart A.; Glass, Leon

2008-09-01

We study the evolution of complex dynamics in a model of a genetic regulatory network. The fitness is associated with the topological entropy in a class of piecewise linear equations, and the mutations are associated with changes in the logical structure of the network. We compare hill climbing evolution, in which only mutations that increase the fitness are allowed, with neutral evolution, in which mutations that leave the fitness unchanged are allowed. The simple structure of the fitness landscape enables us to estimate analytically the rates of hill climbing and neutral evolution. In this model, allowing neutral mutations accelerates the rate of evolutionary advancement for low mutation frequencies. These results are applicable to evolution in natural and technological systems.

Evolution of the IBDM Structural Latch Development into a Generic Simplified Design

NASA Technical Reports Server (NTRS)

DeVriendt, K.; Dittmer, H.; Vrancken, D.; Urmston, P.; Gracia, O.

2010-01-01

This paper presents the evolution in the development of the structural latch for the International Berthing Docking Mechanism (IBDM, see Figure 1). It reports on the lessons learned since completion of the test program on the engineering development unit of the first generation latching system in 2007. The initial latch design has been through a second generation concept in 2008, and now evolved into a third generation of this mechanism. Functional and structural testing on the latest latch hardware has recently been completed with good results. The IBDM latching system will provide the structural connection between two mated space vehicles after berthing or docking. The mechanism guarantees that the interface seals become compressed to form a leak-tight pressure system that creates a passageway for the astronauts.

Structural evolution of nrDNA ITS in Pinaceae and its phylogenetic implications.

PubMed

Kan, Xian-Zhao; Wang, Shan-Shan; Ding, Xin; Wang, Xiao-Quan

2007-08-01

Nuclear ribosomal DNA (nrDNA) has been considered as an important tool for inferring phylogenetic relationships at many taxonomic levels. In comparison with its fast concerted evolution in angiosperms, nrDNA is symbolized by slow concerted evolution and substantial ITS region length variation in gymnosperms, particularly in Pinaceae. Here we studied structure characteristics, including subrepeat composition, size, GC content and secondary structure, of nrDNA ITS regions of all Pinaceae genera. The results showed that the ITS regions of all taxa studied contained subrepeat units, ranging from 2 to 9 in number, and these units could be divided into two types, longer subrepeat (LSR) without the motif (5'-GGCCACCCTAGTC) and shorter subrepeat (SSR) with the motif. Phylogenetic analyses indicate that the homology of some SSRs still can be recognized, providing important informations for the evolutionary history of nrDNA ITS and phylogeny of Pinaceae. In particular, the adjacent tandem SSRs are not more closely related to one another than they are to remote SSRs in some genera, which may imply that multiple structure variations such as recombination have occurred in the ITS1 region of these groups. This study also found that GC content in the ITS1 region is relevant to its sequence length and subrepeat number, and could provide some phylogenetic information, especially supporting the close relationships among Picea, Pinus, and Cathaya. Moreover, several characteristics of the secondary structure of Pinaceae ITS1 were found as follows: (1) the structure is dominated by several extended hairpins; (2) the configuration complexity is positively correlated with subrepeat number; (3) paired subrepeats often partially overlap at the conserved motif (5'-GGCCACCCTAGTC), and form a long stem, while other subrepeats fold onto itself, leaving part of the conserved motif exposed in hairpin loops.

The proteome: structure, function and evolution

PubMed Central

Fleming, Keiran; Kelley, Lawrence A; Islam, Suhail A; MacCallum, Robert M; Muller, Arne; Pazos, Florencio; Sternberg, Michael J.E

2006-01-01

This paper reports two studies to model the inter-relationships between protein sequence, structure and function. First, an automated pipeline to provide a structural annotation of proteomes in the major genomes is described. The results are stored in a database at Imperial College, London (3D-GENOMICS) that can be accessed at www.sbg.bio.ic.ac.uk. Analysis of the assignments to structural superfamilies provides evolutionary insights. 3D-GENOMICS is being integrated with related proteome annotation data at University College London and the European Bioinformatics Institute in a project known as e-protein (http://www.e-protein.org/). The second topic is motivated by the developments in structural genomics projects in which the structure of a protein is determined prior to knowledge of its function. We have developed a new approach PHUNCTIONER that uses the gene ontology (GO) classification to supervise the extraction of the sequence signal responsible for protein function from a structure-based sequence alignment. Using GO we can obtain profiles for a range of specificities described in the ontology. In the region of low sequence similarity (around 15%), our method is more accurate than assignment from the closest structural homologue. The method is also able to identify the specific residues associated with the function of the protein family. PMID:16524832

Triassic structural and stratigraphic evolution of the Central German North Sea sector

NASA Astrophysics Data System (ADS)

Wolf, Marco; Jähne-Klingberg, Fabian

2017-04-01

The subsurface of the Central German North Sea sector is characterized by a complex sequence of tectonic events that span from the Permo-Carboniferous initiation of the Southern Permian Basin to the present day. The Triassic period is one of the most prominent stratigraphic intervals in this area due to alternating phases of relatively tectonic quiescence and intense tectonic activity with the development of grabens, salt-tectonics movements, various regional and local erosional events and strong local and regional changes in subsidence over time. The heterogeneous geological history led to complex structural and lithological patterns. The presented results are part of a comprehensive investigation of the Central German North Sea sector. It was carried out within the scope of the project TUNB (www.bgr.bund.de). The main goal was to enhance the understanding of the Triassic geological development in the area of interest due to detailed seismic interpretation of several hundred 2D seismic lines and as well 3D seismic data sets. A seismostratigraphic concept was used to interpret most formations of the Triassic resulting in a detailed subdivision of the Triassic unit. Depth and thickness maps for every stratigraphic unit and geological cross sections provided new insights regarding an overall basin evolution as well as the timing and mechanisms of rifting and salt-tectonics. New results concerning the evolution of the Keuper in the German North Sea and especially the Triassic evolution of the Horn Graben, as one of the major Triassic rift-structures in the North Sea, will be highlighted. We will show aspects of strong tectonic subsidence in the Horn Graben in the Lower Triassic. In parts of the study area, halotectonic movements started in the Upper Triassic, earlier than previously proposed. Besides mapping of regional seismic reflectors, distinct sedimentary features like fluvial channel systems of the Stuttgart formation (Middle Keuper) or subrosion-like structures

Analyzing the Scientific Evolution of Social Work Using Science Mapping

ERIC Educational Resources Information Center

Martínez, Ma Angeles; Cobo, Manuel Jesús; Herrera, Manuel; Herrera-Viedma, Enrique

2015-01-01

Objectives: This article reports the first science mapping analysis of the social work field, which shows its conceptual structure and scientific evolution. Methods: Science Mapping Analysis Software Tool, a bibliometric science mapping tool based on co-word analysis and h-index, is applied using a sample of 18,794 research articles published from…

Structural controls on Eocene to Pliocene tectonic and metallogenic evolution of the southernmost Lesser Caucasus, Armenia: paleostress field reconstruction and fault-slip analysis

NASA Astrophysics Data System (ADS)

Hovakimyan, Samvel; Moritz, Robert; Tayan, Rodrik

2017-04-01

The Cenozoic evolution of the central segment of the Tethyan belt is dominated by oblique convergence and final collision of Gondwana-derived terranes and the Arabian plate with Eurasia, which created a favorable setting for the formation of the highly mineralized Meghri-Ordubad pluton in the southernmost Lesser Caucasus. Regional strike-slip faults played an important role in the control of the porphyry Cu-Mo and epithermal systems hosted by the Meghri-Ordubad pluton. In this contribution we discuss the paleostress and the kinematic environment of the major strike-slip and oblique-slip ore-controlling faults throughout the Eocene subduction to Mio-Pliocene post-collisional tectonic evolution of the Meghri-Ordubad pluton based on detailed structural field mapping of the ore districts, stereonet compilation of ore-bearing fractures and vein orientations in the major porphyry and epithermal deposits, and the paleostress reconstructions. Paleostress reconstructions indicate that during the Eocene and Early Oligocene, the main paleostress axe orientations reveal a dominant NE-SW-oriented compression, which is compatible with the subduction geometry of the Neotethys along Eurasia. This tectonic setting was favorable for dextral displacements along the two major, regional NNW-oriented Khustup-Giratakh and Salvard-Ordubad strike-slip faults. This resulted in the formation of a NS-oriented transrotational basin, known as the Central magma and ore- controlling zone (Tayan, 1998). It caused a horizontal clockwise rotation of blocks. The EW-oriented faults separating the blocks formed as en-échelon antithetic faults (Voghji, Meghrasar, Bughakyar and Meghriget-Cav faults). The Central zone consists of a network of EW-oriented sinistral and NS-oriented subparallel strike-slip faults (Tashtun, Spetry, Tey, Meghriget and Terterasar faults). They are active since the Eocene and were reactivated during the entire tectonic evolution of the pluton, but with different behaviors

Evolution of Integrated Causal Structures in Animats Exposed to Environments of Increasing Complexity

PubMed Central

Albantakis, Larissa; Hintze, Arend; Koch, Christof; Adami, Christoph; Tononi, Giulio

2014-01-01

Natural selection favors the evolution of brains that can capture fitness-relevant features of the environment's causal structure. We investigated the evolution of small, adaptive logic-gate networks (“animats”) in task environments where falling blocks of different sizes have to be caught or avoided in a ‘Tetris-like’ game. Solving these tasks requires the integration of sensor inputs and memory. Evolved networks were evaluated using measures of information integration, including the number of evolved concepts and the total amount of integrated conceptual information. The results show that, over the course of the animats' adaptation, i) the number of concepts grows; ii) integrated conceptual information increases; iii) this increase depends on the complexity of the environment, especially on the requirement for sequential memory. These results suggest that the need to capture the causal structure of a rich environment, given limited sensors and internal mechanisms, is an important driving force for organisms to develop highly integrated networks (“brains”) with many concepts, leading to an increase in their internal complexity. PMID:25521484

Structure-property evolution during polymer crystallization

NASA Astrophysics Data System (ADS)

Arora, Deepak

The main theme of this research is to understand the structure-property evolution during crystallization of a semicrystalline thermoplastic polymer. A combination of techniques including rheology, small angle light scattering, differential scanning calorimetry and optical microscopy are applied to follow the mechanical and optical properties along with crystallinity and the morphology. Isothermal crystallization experiments on isotactic poly-1-butene at early stages of spherulite growth provide quantitative information about nucleation density, volume fraction of spherulites and their crystallinity, and the mechanism of connecting into a sample spanning structure. Optical microscopy near the fluid-to-solid transition suggests that the transition, as determined by time-resolved mechanical spectroscopy, is not caused by packing/jamming of spherulites but by the formation of a percolating network structure. The effect of strain, Weissenberg number (We ) and specific mechanical work (w) on rate of crystallization (nucleation followed by growth) and on growth of anisotropy was studied for shear-induced crystallization of isotactic poly-1-butene. The samples were sheared for a finite strain at the beginning of the experiment and then crystallized without further flow (Janeschitz-Kriegl protocol). Strain requirements to attain steady state/leveling off of the rate of crystallization were found to be much larger than the strain needed to achieve steady state of flow. The large strain and We>1 criteria were also observed for morphological transition from spherulitic growth to oriented growth. An apparatus for small angle light scattering (SALS) and light transmission measurements under shear was built and tested at the University of Massachusetts Amherst. As a new development, the polarization direction can be rotated by a liquid crystal polarization rotator (LCPR) with a short response time of 20 ms. The experiments were controlled and analyzed with a LabVIEW(TM) based

Strategy evolution driven by switching probabilities in structured multi-agent systems

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Chen, Zengqiang; Li, Zhiqi

2017-10-01

Evolutionary mechanism driving the commonly seen cooperation among unrelated individuals is puzzling. Related models for evolutionary games on graphs traditionally assume that players imitate their successful neighbours with higher benefits. Notably, an implicit assumption here is that players are always able to acquire the required pay-off information. To relax this restrictive assumption, a contact-based model has been proposed, where switching probabilities between strategies drive the strategy evolution. However, the explicit and quantified relation between a player's switching probability for her strategies and the number of her neighbours remains unknown. This is especially a key point in heterogeneously structured system, where players may differ in the numbers of their neighbours. Focusing on this, here we present an augmented model by introducing an attenuation coefficient and evaluate its influence on the evolution dynamics. Results show that the individual influence on others is negatively correlated with the contact numbers specified by the network topologies. Results further provide the conditions under which the coexisting strategies can be calculated analytically.

Directed evolution approach to a structural genomics project: Rv2002 from Mycobacterium tuberculosis.

PubMed

Yang, Jin Kuk; Park, Min S; Waldo, Geoffrey S; Suh, Se Won

2003-01-21

One of the serious bottlenecks in structural genomics projects is overexpression of the target proteins in soluble form. We have applied the directed evolution technique and prepared soluble mutants of the Mycobacterium tuberculosis Rv2002 gene product, the wild type of which had been expressed as inclusion bodies in Escherichia coli. A triple mutant I6TV47MT69K (Rv2002-M3) was chosen for structural and functional characterizations. Enzymatic assays indicate that the Rv2002-M3 protein has a high catalytic activity as a NADH-dependent 3alpha, 20beta-hydroxysteroid dehydrogenase. We have determined the crystal structures of a binary complex with NAD(+) and a ternary complex with androsterone and NADH. The structure reveals that Asp-38 determines the cofactor specificity. The catalytic site includes the triad Ser-140Tyr-153Lys-157. Additionally, it has an unusual feature, Glu-142. Enzymatic assays of the E142A mutant of Rv2002-M3 indicate that Glu-142 reverses the effect of Lys-157 in influencing the pKa of Tyr-153. This study suggests that the Rv2002 gene product is a unique member of the SDR family and is likely to be involved in steroid metabolism in M. tuberculosis. Our work demonstrates the power of the directed evolution technique as a general way of overcoming the difficulties in overexpressing the target proteins in soluble form.

Structure and evolution of the large scale solar and heliospheric magnetic fields. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Hoeksema, J. T.

1984-01-01

Structure and evolution of large scale photospheric and coronal magnetic fields in the interval 1976-1983 were studied using observations from the Stanford Solar Observatory and a potential field model. The solar wind in the heliosphere is organized into large regions in which the magnetic field has a componenet either toward or away from the sun. The model predicts the location of the current sheet separating these regions. Near solar minimum, in 1976, the current sheet lay within a few degrees of the solar equator having two extensions north and south of the equator. Soon after minimum the latitudinal extent began to increase. The sheet reached to at least 50 deg from 1978 through 1983. The complex structure near maximum occasionally included multiple current sheets. Large scale structures persist for up to two years during the entire interval. To minimize errors in determining the structure of the heliospheric field particular attention was paid to decreasing the distorting effects of rapid field evolution, finding the optimum source surface radius, determining the correction to the sun's polar field, and handling missing data. The predicted structure agrees with direct interplanetary field measurements taken near the ecliptic and with coronameter and interplanetary scintillation measurements which infer the three dimensional interplanetary magnetic structure. During most of the solar cycle the heliospheric field cannot be adequately described as a dipole.

[Petrological Analysis of Astrophysical Dust Analog Evolution

NASA Technical Reports Server (NTRS)

Rietmeijer, Frans J. M.

1997-01-01

This project "Petrological analysis of astrophysical dust analog evolution" was initiated to try to understand the vapor phase condensation, and the nature of the reaction products, in circumstellar environments, such as the solar nebula 4,500 Myrs ago, and in the interstellar medium. Telescope-based infrared [IR] spectroscopy offers a broad-scale inventory of the various types of dust in these environments but no details on small-scale variations in terms of chemistry and morphology and petrological phase relationships. Vapor phase condensation in these environments is almost certainly a non-equilibrium process. The main challenge to this research was to document the nature of this process that, based on astrophysical observations, seems to yield compositionally consistent materials. This observation may suggest a predictable character during non-equilibrium condensation. These astrophysical environments include two chemically distinct, that is, oxygen-rich and carbon-rich environments. The former is characterized by silicates the latter by carbon-bearing solids. According to cosmological models of stellar evolution circumstellar dust accreted into protoplanets wherein thermal and/or aqueous processes will alter the dust under initially, non-equilibrium conditions.

Compact structure and proteins of pasta retard in vitro digestive evolution of branched starch molecular structure.

PubMed

Zou, Wei; Sissons, Mike; Warren, Frederick J; Gidley, Michael J; Gilbert, Robert G

2016-11-05

The roles that the compact structure and proteins in pasta play in retarding evolution of starch molecular structure during in vitro digestion are explored, using four types of cooked samples: whole pasta, pasta powder, semolina (with proteins) and extracted starch without proteins. These were subjected to in vitro digestion with porcine α-amylase, collecting samples at different times and characterizing the weight distribution of branched starch molecules using size-exclusion chromatography. Measurement of α-amylase activity showed that a protein (or proteins) from semolina or pasta powder interacted with α-amylase, causing reduced enzymatic activity and retarding digestion of branched starch molecules with hydrodynamic radius (Rh)<100nm; this protein(s) was susceptible to proteolysis. Thus the compact structure of pasta protects the starch and proteins in the interior of the whole pasta, reducing the enzymatic degradation of starch molecules, especially for molecules with Rh>100nm. Copyright © 2016 Elsevier Ltd. All rights reserved.

The Sucrose Synthase Gene Family in Chinese Pear (Pyrus bretschneideri Rehd.): Structure, Expression, and Evolution.

PubMed

Abdullah, Muhammad; Cao, Yungpeng; Cheng, Xi; Meng, Dandan; Chen, Yu; Shakoor, Awais; Gao, Junshan; Cai, Yongping

2018-05-11

Sucrose synthase (SS) is a key enzyme involved in sucrose metabolism that is critical in plant growth and development, and particularly quality of the fruit. Sucrose synthase gene families have been identified and characterized in plants various plants such as tobacco, grape, rice, and Arabidopsis . However, there is still lack of detailed information about sucrose synthase gene in pear. In the present study, we performed a systematic analysis of the pear ( Pyrus bretschneideri Rehd.) genome and reported 30 sucrose synthase genes. Subsequently, gene structure, phylogenetic relationship, chromosomal localization, gene duplications, promoter regions, collinearity, RNA-Seq data and qRT-PCR were conducted on these sucrose synthase genes. The transcript analysis revealed that 10 PbSSs genes (30%) were especially expressed in pear fruit development. Additionally, qRT-PCR analysis verified the RNA-seq data and shown that PbSS30 , PbSS24 , and PbSS15 have a potential role in the pear fruit development stages. This study provides important insights into the evolution of sucrose synthase gene family in pear and will provide assistance for further investigation of sucrose synthase genes functions in the process of fruit development, fruit quality and resistance to environmental stresses.

Seafloor Structural Geomorphic Evolution in Response to Seamount Subduction, Poverty Bay Indentation, New Zealand

NASA Astrophysics Data System (ADS)

Bodger, K. L.; Pettinga, J. R.; Barnes, P. M.

2006-12-01

More than 4000 km2 of high quality bathymetric and backscatter imaging of the Poverty Bay Indentation across the northern part of the Hikurangi subduction zone provide new insights into the relationship between seafloor morphology and active structures. The swath bathymetry extends from the edge of the continental shelf to the abyssal plain, at depths of between 100 to 3500 metres. The origin of the slope re-entrant is inferred to be related to multiple seamount impacts, and these collisions have initiated numerous large-scale gravitational collapse structures, multiple debris flow and avalanche deposits, which range in down-slope length from a few hundred metres to more than 40 km. The Poverty Bay Indentation has been simultaneously eroded by canyon systems that exhibit many of the features of incised river systems onshore. The swath images are complemented by the availability of excellent high-quality processed multi-channel seismic reflection data, single channel high-resolution 3.5 kHz seismic reflection data, as well as a limited number of core samples. Seismic reflection profiles and seafloor morphology are used to provide three morpho-structural sections. The comparison of these sections highlights the different effects of seamount subduction on the evolution of the margin and the re-entrant. The northern two sections are located to the north side of the re-entrant and reveal the role of seamount impact on the interrelationship between the structural evolution with respect to seafloor morphology. Here the development of an over-steepened margin with fault reactivation, inversion and over- printing leads to very complex structural styles of deformation and geometry in both seismic reflection profiles and seafloor morphology. There is evidence of an older, inactive thrust front buried beneath the upper and mid- slope basins. Beneath the mid-slope a subducted seamount is revealed by the presence of relief on the subduction interface and associated structural

Dynamic New World: Refining Our View of Protein Structure, Function and Evolution

PubMed Central

Mannige, Ranjan V.

2014-01-01

Proteins are crucial to the functioning of all lifeforms. Traditional understanding posits that a single protein occupies a single structure (“fold”), which performs a single function. This view is radically challenged with the recognition that high structural dynamism—the capacity to be extra “floppy”—is more prevalent in functional proteins than previously assumed. As reviewed here, this dynamic take on proteins affects our understanding of protein “structure”, function, and evolution, and even gives us a glimpse into protein origination. Specifically, this review will discuss historical developments concerning protein structure, and important new relationships between dynamism and aspects of protein sequence, structure, binding modes, binding promiscuity, evolvability, and origination. Along the way, suggestions will be provided for how key parts of textbook definitions—that so far have excluded membership to intrinsically disordered proteins (IDPs)—could be modified to accommodate our more dynamic understanding of proteins. PMID:28250374

Recent advances on the understanding of structural and composition evolution of LMR cathodes for Li-ion batteries

DOE PAGES

Yan, Pengfei; Zheng, Jianming; Xiao, Jie; ...

2015-06-08

Lithium-rich, magnesium-rich (LMR) cathode materials have been regarded as one of the very promising cathodes for Li-ion battery applications. However, their practical application is still limited by several challenges, especially by their limited electrochemical stability rate capability. In this work, we present recent progresses on the understanding of the structural and composition evolution of LMR cathode materials with emphasis being placed on the correlation between structural/chemical evolution and electrochemical properties. In particular, using Li [Li 0.2Ni 0.2Mn 0.6O 2 as a typical example, we clearly illustrate the structural characteristics of the pristine materials and their dependence on the materials processingmore » history, cycling induced structural degradation/chemical partition and their correlation with degradation of electrochemical performance. The fundamental understanding obtained in this work may also guide the design and preparation of new cathode materials based on ternary system of transitional metal oxide.« less

Structural evolution of trimesic acid (TMA)/Zn2 + ion network on Au(111) to final structure of (10√3 × 10√3)

NASA Astrophysics Data System (ADS)

Kim, Jandee; Lee, Jaesung; Rhee, Choong Kyun

2016-02-01

Presented is a scanning tunneling microscopy (STM) study of structural evolution of TMA/Zn2 + ion network on Au(111) to the final structure of (10√3 × 10√3) during solution phase post-modification of pristine trimesic acid (TMA) network of a (5√3 × 5√3) structure with Zn2 + ions. Coordination of Zn2 + ions into adsorbed TMA molecules transforms crown-like TMA hexamers in pristine TMA network to chevron pairs in TMA/Zn2 + ion network. Two ordered transient structures of TMA/Zn2 + ion network were observed. One is a (5√7 × 5√7) structure consisting of Zn2 + ion-containing chevron pairs and Zn2 + ion-free TMA dimers. The other is a (5√39 × 5√21) structure made of chevron pairs and chevron-pair-missing sites. An STM image showing domains of different stages of crystallization of chevron pairs demonstrates that the TMA/Zn2 + network before reaching to the final one is quite dynamic. The observed structural evolution of the TMA/Zn2 + ion network is discussed in terms of modification of configurations of adsorbed TMA as accommodating Zn2 + ions and re-ordering of Zn2 + ion-containing chevron pairs.

A multi-populations multi-strategies differential evolution algorithm for structural optimization of metal nanoclusters

NASA Astrophysics Data System (ADS)

Fan, Tian-E.; Shao, Gui-Fang; Ji, Qing-Shuang; Zheng, Ji-Wen; Liu, Tun-dong; Wen, Yu-Hua

2016-11-01

Theoretically, the determination of the structure of a cluster is to search the global minimum on its potential energy surface. The global minimization problem is often nondeterministic-polynomial-time (NP) hard and the number of local minima grows exponentially with the cluster size. In this article, a multi-populations multi-strategies differential evolution algorithm has been proposed to search the globally stable structure of Fe and Cr nanoclusters. The algorithm combines a multi-populations differential evolution with an elite pool scheme to keep the diversity of the solutions and avoid prematurely trapping into local optima. Moreover, multi-strategies such as growing method in initialization and three differential strategies in mutation are introduced to improve the convergence speed and lower the computational cost. The accuracy and effectiveness of our algorithm have been verified by comparing the results of Fe clusters with Cambridge Cluster Database. Meanwhile, the performance of our algorithm has been analyzed by comparing the convergence rate and energy evaluations with the classical DE algorithm. The multi-populations, multi-strategies mutation and growing method in initialization in our algorithm have been considered respectively. Furthermore, the structural growth pattern of Cr clusters has been predicted by this algorithm. The results show that the lowest-energy structure of Cr clusters contains many icosahedra, and the number of the icosahedral rings rises with increasing size.

Coherent Structures and Evolution of Vorticity in Short-Crested Breaking Surface Waves

NASA Astrophysics Data System (ADS)

Kirby, James; Derakhti, Morteza

2017-11-01

We employ a multi-phase LES/VOF code to study turbulence and coherent structures generated during breaking of short-crested surface water waves. We examine the evolution of coherent vortex structures evolving at the scale of the width of the breaking event, and their long-time interaction with smaller vortex loops formed by the local instability of the breaking crest. Long-time results are often characterized by the detachment of the larger scale vortex loop from the surface and formation of a closed vortex ring. The evolution of circulation for the vortical flow field is examined. The initial concentration of forcing close to the free surface leads to spatial distributions of both span-wise and vertical vorticity distributions which are concentrated close to the surface. This result, which persists into shallow water, is at odds with the basic simplicity of the Peregrine mechanism, suggesting that even shallow flows such as the surf zone should be regarded as being forced (in dissipative situations) by a wave-induced surface stress rather than a uniform-over-depth body force. The localized forcing leads to the development of a complex pattern of stream-wise vorticity, comparable in strength to the vertical and span-wise components, and also persist into shallow water. NSF OCE-1435147.

Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B 12

DOE PAGES

Miller, Nicholas A.; Deb, Aniruddha; Alonso-Mori, Roberto; ...

2017-01-30

Ultrafast, polarization-selective time-resolved X-ray absorption near-edge structure (XANES) was used to characterize the photochemistry of vitamin B 12, cyanocobalamin (CNCbl), in solution. Cobalamins are important biological cofactors involved in methyl transfer, radical rearrangement, and light-activated gene regulation, while also holding promise as light-activated agents for spatiotemporal controlled delivery of therapeutics. We introduce polarized femtosecond XANES, combined with UV–visible spectroscopy, to reveal sequential structural evolution of CNCbl in the excited electronic state. Femtosecond polarized XANES provides the crucial structural dynamics link between computed potential energy surfaces and optical transient absorption spectroscopy. Polarization selectivity can be used to uniquely identify electronic contributionsmore » and structural changes, even in isotropic samples when well-defined electronic transitions are excited. Our XANES measurements reveal that the structural changes upon photoexcitation occur mainly in the axial direction, where elongation of the axial Co–CN bond and Co–N Im bond on a 110 fs time scale is followed by corrin ring relaxation on a 260 fs time scale. In conclusion, these observations expose features of the potential energy surfaces controlling cobalamin reactivity and deactivation.« less

Polarized XANES Monitors Femtosecond Structural Evolution of Photoexcited Vitamin B 12

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

Miller, Nicholas A.; Deb, Aniruddha; Alonso-Mori, Roberto

Ultrafast, polarization-selective time-resolved X-ray absorption near-edge structure (XANES) was used to characterize the photochemistry of vitamin B 12, cyanocobalamin (CNCbl), in solution. Cobalamins are important biological cofactors involved in methyl transfer, radical rearrangement, and light-activated gene regulation, while also holding promise as light-activated agents for spatiotemporal controlled delivery of therapeutics. We introduce polarized femtosecond XANES, combined with UV–visible spectroscopy, to reveal sequential structural evolution of CNCbl in the excited electronic state. Femtosecond polarized XANES provides the crucial structural dynamics link between computed potential energy surfaces and optical transient absorption spectroscopy. Polarization selectivity can be used to uniquely identify electronic contributionsmore » and structural changes, even in isotropic samples when well-defined electronic transitions are excited. Our XANES measurements reveal that the structural changes upon photoexcitation occur mainly in the axial direction, where elongation of the axial Co–CN bond and Co–N Im bond on a 110 fs time scale is followed by corrin ring relaxation on a 260 fs time scale. In conclusion, these observations expose features of the potential energy surfaces controlling cobalamin reactivity and deactivation.« less

Local Structure Evolution and Modes of Charge Storage in Secondary Li–FeS 2 Cells

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

Butala, Megan M.; Mayo, Martin; Doan-Nguyen, Vicky V. T.

2017-03-27

In the pursuit of high-capacity electrochemical energy storage, a promising domain of research involves conversion reaction schemes, wherein electrode materials are fully transformed during charge and discharge. There are, however, numerous difficulties in realizing theoretical capacity and high rate capability in many conversion schemes. Here we employ operando studies to understand the conversion material FeS2, focusing on the local structure evolution of this relatively reversible material. X-ray absorption spectroscopy, pair distribution function analysis, and first-principles calculations of intermediate structures shed light on the mechanism of charge storage in the Li-FeS2 system, with some general principles emerging for charge storage inmore » chalcogenide materials. Focusing on second and later charge/discharge cycles, we find small, disordered domains that locally resemble Fe and Li2S at the end of the first discharge. Upon charge, this is converted to a Li-Fe-S composition whose local structure reveals tetrahedrally coordinated Fe. With continued charge, this ternary composition displays insertion extraction behavior at higher potentials and lower Li content. The finding of hybrid modes of charge storage, rather than simple conversion, points to the important role of intermediates that appear to store charge by mechanisms that more closely resemble intercalation.« less

Multidimensional Solitons in Complex Media with Variable Dispersion: Structure and Evolution

DTIC Science & Technology

2003-07-20

the results of numerical experiments on Kadomtsev - Petviashvili (KP) equation study of structure and evolution of the nonlinear waves Sx described by...the KP equation with 13 = 3 (t,r) are con- at + auaxu + 03’u =K fAjudx, (1) sidered distracting from a concrete type of media. The -o• numerical...0i)(cot 0- mIM). It is well known that cluding the solutions of the mixed "soliton - non-soliton" the ID solutions of the KdV equation with 3 = const

Probabilistic structural analysis methods of hot engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Hopkins, D. A.

1989-01-01

Development of probabilistic structural analysis methods for hot engine structures at Lewis Research Center is presented. Three elements of the research program are: (1) composite load spectra methodology; (2) probabilistic structural analysis methodology; and (3) probabilistic structural analysis application. Recent progress includes: (1) quantification of the effects of uncertainties for several variables on high pressure fuel turbopump (HPFT) turbine blade temperature, pressure, and torque of the space shuttle main engine (SSME); (2) the evaluation of the cumulative distribution function for various structural response variables based on assumed uncertainties in primitive structural variables; and (3) evaluation of the failure probability. Collectively, the results demonstrate that the structural durability of hot engine structural components can be effectively evaluated in a formal probabilistic/reliability framework.

Electric field driven evolution of topological domain structure in hexagonal manganites

NASA Astrophysics Data System (ADS)

Yang, K. L.; Zhang, Y.; Zheng, S. H.; Lin, L.; Yan, Z. B.; Liu, J.-M.; Cheong, S.-W.

2017-10-01

Controlling and manipulating the topological state represents an important topic in condensed matters for both fundamental researches and applications. In this work, we focus on the evolution of a real-space topological domain structure in hexagonal manganites driven by electric field, using the analytical and numerical calculations based on the Ginzburg-Landau theory. It is revealed that the electric field drives a transition of the topological domain structure from the type-I pattern to the type-II one. In particular, it is identified that a high electric field can enforce the two antiphase-plus-ferroelectric (AP +FE ) domain walls with Δ Φ =π /3 to approach each other and to merge into one domain wall with Δ Φ = 2 π /3 eventually if the electric field is sufficiently high, where Δ Φ is the difference in the trimerization phase between two neighboring domains. Our simulations also reveal that the vortex cores of the topological structure can be disabled at a sufficiently high critical electric field by suppressing the structural trimerization therein, beyond which the vortex core region is replaced by a single ferroelectric domain without structural trimerization (Q = 0 ). Our results provide a stimulating reference for understanding the manipulation of real-space topological domain structure in hexagonal manganites.

Integrated analysis of engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.

1981-01-01

The need for light, durable, fuel efficient, cost effective aircraft requires the development of engine structures which are flexible, made from advaced materials (including composites), resist higher temperatures, maintain tighter clearances and have lower maintenance costs. The formal quantification of any or several of these requires integrated computer programs (multilevel and/or interdisciplinary analysis programs interconnected) for engine structural analysis/design. Several integrated analysis computer prorams are under development at Lewis Reseach Center. These programs include: (1) COBSTRAN-Composite Blade Structural Analysis, (2) CODSTRAN-Composite Durability Structural Analysis, (3) CISTRAN-Composite Impact Structural Analysis, (4) STAEBL-StruTailoring of Engine Blades, and (5) ESMOSS-Engine Structures Modeling Software System. Three other related programs, developed under Lewis sponsorship, are described.

Nonlinear Structural Analysis

NASA Technical Reports Server (NTRS)

1984-01-01

Nonlinear structural analysis techniques for engine structures and components are addressed. The finite element method and boundary element method are discussed in terms of stress and structural analyses of shells, plates, and laminates.

Turbulent Compressible Convection with Rotation. Part 1; Flow Structure and Evolution

NASA Technical Reports Server (NTRS)

Brummell, Nicholas H.; Hurlburt, Neal E.; Toomre, Juri

1996-01-01

The effects of Coriolis forces on compressible convection are studied using three-dimensional numerical simulations carried out within a local modified f-plane model. The physics is simplified by considering a perfect gas occupying a rectilinear domain placed tangentially to a rotating sphere at various latitudes, through which a destabilizing heat flux is driven. The resulting convection is considered for a range of Rayleigh, Taylor, and Prandtl (and thus Rossby) numbers, evaluating conditions where the influence of rotation is both weak and strong. Given the computational demands of these high-resolution simulations, the parameter space is explored sparsely to ascertain the differences between laminar and turbulent rotating convection. The first paper in this series examines the effects of rotation on the flow structure within the convection, its evolution, and some consequences for mixing. Subsequent papers consider the large-scale mean shear flows that are generated by the convection, and the effects of rotation on the convective energetics and transport properties. It is found here that the structure of rotating turbulent convection is similar to earlier nonrotating studies, with a laminar, cellular surface network disguising a fully turbulent interior punctuated by vertically coherent structures. However, the temporal signature of the surface flows is modified by inertial motions to yield new cellular evolution patterns and an overall increase in the mobility of the network. The turbulent convection contains vortex tubes of many scales, including large-scale coherent structures spanning the full vertical extent of the domain involving multiple density scale heights. Remarkably, such structures align with the rotation vector via the influence of Coriolis forces on turbulent motions, in contrast with the zonal tilting of streamlines found in laminar flows. Such novel turbulent mechanisms alter the correlations which drive mean shearing flows and affect the

Equatorial Density Irregularity Structures at Intermediate Scales and Their Temporal Evolution

NASA Technical Reports Server (NTRS)

Kil, Hyosub; Heelis, R. A.

1998-01-01

We examine high resolution measurements of ion density in the equatorial ionosphere from the AE-E satellite during the years 1977-1981. Structure over spatial scales from 18 km to 200 m is characterized by the spectrum of irregularities at larger and smaller scales and at altitudes above 350 km and below 300 km. In the low-altitude region, only small amplitude large-scale (lambda greater than 5 km) density modulations are often observed, and thus the power spectrum of these density structures exhibits a steep spectral slope at kilometer scales. In the high-altitude region, sinusoidal density fluctuations, characterized by enhanced power near 1-km scale, are frequently observed during 2000-0200 LT. However, such fluctuations are confined to regions at the edges of larger bubble structures where the average background density is high. Small amplitude irregularity structures, observed at early local time hours, grow rapidly to high-intensity structures in about 90 min. Fully developed structures, which are observed at late local time hours, decay very slowly producing only-small differences in spectral characteristics even 4 hours later. The local time evolution of irregularity structure is investigated by using average statistics for low-(1% less than sigma less than 5%) and high-intensity (sigma greater than 10%) structures. At lower altitudes, little chance in the spectral slope is seen as a function of local time, while at higher attitudes the growth and maintenance of structures near 1 km scales dramatically affects the spectral slope.

Coordination polymer structure and revisited hydrogen evolution catalytic mechanism for amorphous molybdenum sulfide

PubMed Central

Tran, Phong D.; Tran, Thu V.; Orio, Maylis; Torelli, Stephane; Truong, Quang Duc; Nayuki, Keiichiro; Sasaki, Yoshikazu; Chiam, Sing Yang; Yi, Ren; Honma, Itaru; Barber, James; Artero, Vincent

2017-01-01

Molybdenum sulfides are very attractive noble-metal free electrocatalysts for the hydrogen evolution reaction (HER) from water. Atomic structure and identity of the catalytically active sites have been well established for crystalline molybdenum disulfide (c-MoS2) but not for amorphous molybdenum sulfide (a-MoSx) which displays significantly higher HER activity compared to its crystalline counterpart. Here we show that HER–active a-MoSx, prepared either as nanoparticles or as films, is a molecular–based coordination polymer consisting of discrete [Mo3S13]2– building blocks. Of the three terminal disulfide (S22–) ligands within these clusters, two are shared to form the polymer chain. The third one remains free and generates molybdenum hydride moieties as the active site under H2 evolution conditions. Such a molecular structure therefore provides a basis for revisiting the mechanism of a-MoSx catalytic activity, as well as explaining some of its special properties such as reductive activation and corrosion. Our findings open up new avenues for the rational optimisation of this HER electrocatalyst as an alternative to platinum. PMID:26974410

The role of disc self-gravity in circumbinary planet systems - I. Disc structure and evolution

NASA Astrophysics Data System (ADS)

Mutter, Matthew M.; Pierens, Arnaud; Nelson, Richard P.

2017-03-01

We present the results of two-dimensional hydrodynamic simulations of self-gravitating circumbinary discs around binaries whose parameters match those of the circumbinary planet-hosting systems Kepler-16, Kepler-34 and Kepler-35. Previous work has shown that non-self-gravitating discs in these systems form an eccentric precessing inner cavity due to tidal truncation by the binary, and planets which form at large radii migrate until stalling at this cavity. Whilst this scenario appears to provide a natural explanation for the observed orbital locations of the circumbinary planets, previous simulations have failed to match the observed planet orbital parameters. The aim of this work is to examine the role of self-gravity in modifying circumbinary disc structure as a function of disc mass, prior to considering the evolution of embedded circumbinary planets. In agreement with previous work, we find that for disc masses between one and five times the minimum mass solar nebula (MMSN), disc self-gravity affects modest changes in the structure and evolution of circumbinary discs. Increasing the disc mass to 10 or 20 MMSN leads to two dramatic changes in disc structure. First, the scale of the inner cavity shrinks substantially, bringing its outer edge closer to the binary. Secondly, in addition to the eccentric inner cavity, additional precessing eccentric ring-like features develop in the outer regions of the discs. If planet formation starts early in the disc lifetime, these changes will have a significant impact on the formation and evolution of planets and precursor material.

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa

PubMed Central

2015-01-01

Background Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. Results One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. Conclusions These results characterize the features of the coding exon-intron structure that affect the

Computer analysis of protein functional sites projection on exon structure of genes in Metazoa.

PubMed

Medvedeva, Irina V; Demenkov, Pavel S; Ivanisenko, Vladimir A

2015-01-01

Study of the relationship between the structural and functional organization of proteins and their coding genes is necessary for an understanding of the evolution of molecular systems and can provide new knowledge for many applications for designing proteins with improved medical and biological properties. It is well known that the functional properties of proteins are determined by their functional sites. Functional sites are usually represented by a small number of amino acid residues that are distantly located from each other in the amino acid sequence. They are highly conserved within their functional group and vary significantly in structure between such groups. According to this facts analysis of the general properties of the structural organization of the functional sites at the protein level and, at the level of exon-intron structure of the coding gene is still an actual problem. One approach to this analysis is the projection of amino acid residue positions of the functional sites along with the exon boundaries to the gene structure. In this paper, we examined the discontinuity of the functional sites in the exon-intron structure of genes and the distribution of lengths and phases of the functional site encoding exons in vertebrate genes. We have shown that the DNA fragments coding the functional sites were in the same exons, or in close exons. The observed tendency to cluster the exons that code functional sites which could be considered as the unit of protein evolution. We studied the characteristics of the structure of the exon boundaries that code, and do not code, functional sites in 11 Metazoa species. This is accompanied by a reduced frequency of intercodon gaps (phase 0) in exons encoding the amino acid residue functional site, which may be evidence of the existence of evolutionary limitations to the exon shuffling. These results characterize the features of the coding exon-intron structure that affect the functionality of the encoded protein and

From mantle peridotites to hybrid troctolites: Textural, structural and geochemical evolution during multi-stage melt-rock interaction history

NASA Astrophysics Data System (ADS)

Basch, V.; Rampone, E.; Crispini, L.; Ferrando, C.; Ildefonse, B.; Godard, M.

2017-12-01

Recent studies investigate the replacive formation of hybrid troctolites from mantle peridotites after multiple stages of melt-rock reactions. However, none of these studies are conducted in a field-controlled geological setting displaying the clear evolution from peridotite to dunite to troctolite. We investigated the Mt.Maggiore and Erro Tobbio ophiolitic peridotites. They both preserve structural and chemical records of two distinct melt-rock interaction stages, from a reactive melt percolation at spinel facies to plagioclase-bearing melt impregnation at shallower lithospheric depths. We performed EBSD and in situ geochemical analyses to document the textural, structural and geochemical variations of the olivine matrix during melt-rock interactions and the associated evolution from peridotite to dunite to troctolite. The olivine-saturated reactive melt percolation leads to the dissolution of mantle pyroxenes in peridotite, and to the formation of replacive dunite. At shallower level, melt impregnation leads to the crystallization of plagioclase in the dunite, and to the formation of hybrid troctolite. The latter is characterized by textural, structural and geochemical features acquired during dunitization and impregnation processes. We documented a textural evolution of the olivine matrix (decrease in grain area, tortuosity and aspect ratio) during impregnation, with a progressive corrosion of mantle olivines by a reactive melt. As a result, olivine in the hybrid troctolites occurs both as coarse deformed relicts and disrupted undeformed grains. During melt-rock interactions, the variation in olivine Crystallographic Preferred Orientation is related to the local melt/rock ratio involved in the percolation process. At high melt/rock ratio, a change from axial-[100] to axial-[010] is observed, with the disaggregation of the solid matrix. REE-enriched compositions are observed in olivine of dunites and troctolites. A geochemical modeling of melt-rock interactions

Oxygen vacancy induced structural evolution of SrFeO3 -x epitaxial thin film from brownmillerite to perovskite

NASA Astrophysics Data System (ADS)

Roh, Seulki; Lee, Seokbae; Lee, Myounghoon; Seo, Yu-Seong; Khare, Amit; Yoo, Taesup; Woo, Sungmin; Choi, Woo Seok; Hwang, Jungseek; Glamazda, A.; Choi, K.-Y.

2018-02-01

We investigated SrFeO3 -x thin films on a SrTiO3 (001) substrate prepared via pulsed laser epitaxy using an optical spectroscopy technique. The oxygen vacancy level (x ) was controlled by post-annealing processes at different oxygen partial pressures. We achieved a brownmillerite (BM) structure at x =0.5 and observed the evolution of the crystal structure from BM into perovskite (PV) as the oxygen concentration increased. We observed the evolution of infrared-active phonons with respect to the oxygen concentration, which was closely related to the structural evolution observed via x-ray diffraction. We identified the phonons using the shell-model calculation. Furthermore, we studied temperature-dependent behaviors of the phonon modes of three representative samples: PV and two BMs (BMoop and BMip) with different orientations of the oxygen vacancy channel. In the BMoop sample, we observed a phonon mode, which exhibited an unusual redshift with decreasing temperature; this behavior may have been due to the apical oxygen instability in the FeO6 octahedron. Our results provide important information regarding the ionic conduction mechanism in SrFeO3 -x material systems.

Directed evolution of the periodic table: probing the electronic structure of late actinides.

PubMed

Marsh, M L; Albrecht-Schmitt, T E

2017-07-25

Recent investigations of the coordination chemistry and physical properties of berkelium (Z = 97) and californium (Z = 98) have revealed fundamental differences between post-curium elements and lighter members of the actinide series. This review highlights these developments and chronicles key findings and concepts from the last half-century that have helped usher in a new understanding of the evolution of electronic structure in the periodic table.

Evolutions of lamellar structure during melting and solidification of Fe9577 nanoparticle from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Wu, Yongquan; Shen, Tong; Lu, Xionggang

2013-03-01

A structural evolution during solidification and melting processes of nanoparticle Fe9577 was investigated from MD simulations. A perfect lamellar structure, consisting alternately of fcc and hcp layers, was obtained from solidification process. A structural heredity of early embryo is proposed to explain the structural preference of solidification. Defects were found inside the solid core and play the same role as surface premelting on melting. hcp was found more stable than fcc in high temperature. The difference between melting and solidification points can be deduced coming fully from the overcoming of thermodynamic energy barrier, instead of kinetic delay of structural relaxation.

Tailoring characteristic thermal stability of Ni-Au binary nanocrystals via structure and composition engineering: theoretical insights into structural evolution and atomic inter-diffusion

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

Li, Bangquan; Wang, Hailong; Xing, Guozhong

We report on the structural evolution and atomic inter-diffusion characteristics of the bimetallic Ni-Au nanocrystals (NCs) by molecular dynamics simulations studies. Our results reveal that the thermal stability dynamics of Ni-Au NCs strongly depends on the atomic configurations. By engineering the structural construction with Ni:Au = 1:1 atomic composition, compared with core-shell Au@Ni and alloy NCs, the melting point of core-shell Ni@Au NCs is significantly enhanced up to 1215 K. Unexpectedly, with atomic ratio of Au:Ni= 1:9, the melting process initiates from the atoms in the shell of Ni@Au and alloy NCs, while starts from the core of Au@Ni NCs.more » The corresponding features and evolution process of structural motifs, mixing and segregation are illustrated via a series of dynamic simulations videos. Moreover, our results revealed that the face centered cubic phase Au{sub 0.75}Ni{sub 0.25} favorably stabilizes in NCs form but does not exist in the bulk counterpart, which elucidates the anomalies of previously reported experimental results on such bimetallic NCs.« less

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat1[W][OA

PubMed Central

Akhunov, Eduard D.; Sehgal, Sunish; Liang, Hanquan; Wang, Shichen; Akhunova, Alina R.; Kaur, Gaganpreet; Li, Wanlong; Forrest, Kerrie L.; See, Deven; Šimková, Hana; Ma, Yaqin; Hayden, Matthew J.; Luo, Mingcheng; Faris, Justin D.; Doležel, Jaroslav; Gill, Bikram S.

2013-01-01

Cycles of whole-genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied by comparing the patterns of gene structure changes, alternative splicing (AS), and codon substitution rates among wheat and model grass genomes. In orthologous gene sets, significantly more acquired and lost exonic sequences were detected in wheat than in model grasses. In wheat, 35% of these gene structure rearrangements resulted in frame-shift mutations and premature termination codons. An increased codon mutation rate in the wheat lineage compared with Brachypodium distachyon was found for 17% of orthologs. The discovery of premature termination codons in 38% of expressed genes was consistent with ongoing pseudogenization of the wheat genome. The rates of AS within the individual wheat subgenomes (21%–25%) were similar to diploid plants. However, we uncovered a high level of AS pattern divergence between the duplicated homeologous copies of genes. Our results are consistent with the accelerated accumulation of AS isoforms, nonsynonymous mutations, and gene structure rearrangements in the wheat lineage, likely due to genetic redundancy created by WGDs. Whereas these processes mostly contribute to the degeneration of a duplicated genome and its diploidization, they have the potential to facilitate the origin of new functional variations, which, upon selection in the evolutionary lineage, may play an important role in the origin of novel traits. PMID:23124323

A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation.

PubMed

Ross, Caitlin; Rychtář, Jan; Rueppell, Olav

2015-03-21

Social organization correlates with longevity across animal taxa. This correlation has been explained by selection for longevity by social evolution. The reverse causality is also conceivable but has not been sufficiently considered. We constructed a simple, spatially structured population model of asexually reproducing individuals to study the effect of temporal life history structuring on the evolution of cooperation. Individuals employed fixed strategies of cooperation or defection towards all neighbours in a basic Prisoner's Dilemma paradigm. Individuals aged and transitioned through different life history stages asynchronously without migration. An individual's death triggered a reproductive event by one immediate neighbour. The specific neighbour was chosen probabilistically according to the cumulative payoff from all local interactions. Varying the duration of pre-reproductive, reproductive, and post-reproductive life history stages, long-term simulations allowed a systematic evaluation of the influence of the duration of these specific life history stages. Our results revealed complex interactions among the effects of the three basic life history stages and the benefit to defect. Overall, a long post-reproductive stage promoted the evolution of cooperation, while a prolonged pre-reproductive stage has a negative effect. In general, the total length of life also increased the probability of the evolution of cooperation. Thus, our specific model suggests that the timing of life history transitions and total duration of life history stages may affect the evolution of cooperative behaviour. We conclude that the causation of the empirically observed association of life expectancy and sociality may be more complex than previously realized. Copyright © 2015 Elsevier Ltd. All rights reserved.

A structured population model suggests that long life and post-reproductive lifespan promote the evolution of cooperation

PubMed Central

Ross, Caitlin; Rychtář, Jan; Rueppell, Olav

2015-01-01

Social organization correlates with longevity across animal taxa. This correlation has been explained by selection for longevity by social evolution. The reverse causality is also conceivable but has not been sufficiently considered. We constructed a simple, spatially structured population model of asexually reproducing individuals to study the effect of temporal life history structuring on the evolution of cooperation. Individuals employed fixed strategies of cooperation or defection towards all neighbours in a basic Prisoner’s Dilemma paradigm. Individuals aged and transitioned through different life history stages asynchronously without migration. An individual’s death triggered a reproductive event by one immediate neighbour. The specific neighbour was chosen probabilistically according to the cumulative payoff from all local interactions. Varying the duration of pre-reproductive, reproductive, and post-reproductive life history stages, long-term simulations allowed a systematic evaluation of the influence of the duration of these specific life history stages. Our results revealed complex interactions among the effects of the three basic life history stages and the benefit to defect. Overall, a long post-reproductive stage promoted the evolution of cooperation, while a prolonged pre-reproductive stage has a negative effect. In general, the total length of life also increased the probability of the evolution of cooperation. Thus, our specific model suggests that the timing of life history transitions and total duration of life history stages may affect the evolution of cooperative behaviour. We conclude that the causation of the empirically observed association of life expectancy and sociality may be more complex than previously realized. PMID:25637763

Historical contingency and its biophysical basis in glucocorticoid receptor evolution.

PubMed

Harms, Michael J; Thornton, Joseph W

2014-08-14

Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative 'might-have-been' trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements--they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures--thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.

Oh sister, where art thou? Spatial population structure and the evolution of an altruistic defence trait.

PubMed

Pamminger, T; Foitzik, S; Metzler, D; Pennings, P S

2014-11-01

The evolution of parasite virulence and host defences is affected by population structure. This effect has been confirmed in studies focusing on large spatial scales, whereas the importance of local structure is not well understood. Slavemaking ants are social parasites that exploit workers of another species to rear their offspring. Enslaved workers of the host species Temnothorax longispinosus have been found to exhibit an effective post-enslavement defence behaviour: enslaved workers were observed killing a large proportion of the parasites' offspring. As enslaved workers do not reproduce, they gain no direct fitness benefit from this 'rebellion' behaviour. However, there may be an indirect benefit: neighbouring host nests that are related to 'rebel' nests can benefit from a reduced raiding pressure, as a result of the reduction in parasite nest size due to the enslaved workers' killing behaviour. We use a simple mathematical model to examine whether the small-scale population structure of the host species could explain the evolution of this potentially altruistic defence trait against slavemaking ants. We find that this is the case if enslaved host workers are related to nearby host nests. In a population genetic study, we confirm that enslaved workers are, indeed, more closely related to host nests within the raiding range of their resident slavemaker nest, than to host nests outside the raiding range. This small-scale population structure seems to be a result of polydomy (e.g. the occupation of several nests in close proximity by a single colony) and could have enabled the evolution of 'rebellion' by kin selection. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

The fine-scale genetic structure and evolution of the Japanese population.

PubMed

Takeuchi, Fumihiko; Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua; Teo, Yik-Ying; Kato, Norihiro

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups-Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.

The fine-scale genetic structure and evolution of the Japanese population

PubMed Central

Katsuya, Tomohiro; Kimura, Ryosuke; Nabika, Toru; Isomura, Minoru; Ohkubo, Takayoshi; Tabara, Yasuharu; Yamamoto, Ken; Yokota, Mitsuhiro; Liu, Xuanyao; Saw, Woei-Yuh; Mamatyusupu, Dolikun; Yang, Wenjun; Xu, Shuhua

2017-01-01

The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics. PMID:29091727

Both Epistasis and Diversifying Selection Drive the Structural Evolution of the Ebola Virus Glycoprotein Mucin-Like Domain.

PubMed

Ibeh, Neke; Nshogozabahizi, Jean Claude; Aris-Brosou, Stéphane

2016-06-01

Throughout the last 3 decades, Ebola virus (EBOV) outbreaks have been confined to isolated areas within Central Africa; however, the 2014 variant reached unprecedented transmission and mortality rates. While the outbreak was still under way, it was reported that the variant leading up to this outbreak evolved faster than previous EBOV variants, but evidence for diversifying selection was undetermined. Here, we test this selection hypothesis and show that while previous EBOV outbreaks were preceded by bursts of diversification, evidence for site-specific diversifying selection during the emergence of the 2014 EBOV clade is weak. However, we show strong evidence supporting an interplay between selection and correlated evolution (epistasis), particularly in the mucin-like domain (MLD) of the EBOV glycoprotein. By reconstructing ancestral structures of the MLD, we further propose a structural mechanism explaining how the substitutions that accumulated between 1918 and 1969 distorted the MLD, while more recent epistatic substitutions restored part of the structure, with the most recent substitution being adaptive. We suggest that it is this complex interplay between weak selection, epistasis, and structural constraints that has shaped the evolution of the 2014 EBOV variant. The role that selection plays in the emergence of viral epidemics remains debated, particularly in the context of the 2014 EBOV outbreak. Most critically, should such evidence exist, it is generally unclear how this relates to function and increased virulence. Here, we show that the viral lineage leading up to the 2014 outbreak underwent a complex interplay between selection and correlated evolution (epistasis) in a protein region that is critical for immune evasion. We then reconstructed the three-dimensional structure of this domain and showed that the initial mutations in this lineage deformed the structure, while subsequent mutations restored part of the structure. Along this mutational path, the

Structural power and the evolution of collective fairness in social networks.

PubMed

Santos, Fernando P; Pacheco, Jorge M; Paiva, Ana; Santos, Francisco C

2017-01-01

From work contracts and group buying platforms to political coalitions and international climate and economical summits, often individuals assemble in groups that must collectively reach decisions that may favor each part unequally. Here we quantify to which extent our network ties promote the evolution of collective fairness in group interactions, modeled by means of Multiplayer Ultimatum Games (MUG). We show that a single topological feature of social networks-which we call structural power-has a profound impact on the tendency of individuals to take decisions that favor each part equally. Increased fair outcomes are attained whenever structural power is high, such that the networks that tie individuals allow them to meet the same partners in different groups, thus providing the opportunity to strongly influence each other. On the other hand, the absence of such close peer-influence relationships dismisses any positive effect created by the network. Interestingly, we show that increasing the structural power of a network leads to the appearance of well-defined modules-as found in human social networks that often exhibit community structure-providing an interaction environment that maximizes collective fairness.

Enhanced dewaterability of sludge during anaerobic digestion with thermal hydrolysis pretreatment: New insights through structure evolution.

PubMed

Zhang, Jingsi; Li, Ning; Dai, Xiaohu; Tao, Wenquan; Jenkinson, Ian R; Li, Zhuo

2017-12-19

Comprehensive insights into the sludge digestate dewaterability were gained through porous network structure of sludge. We measured the evolution of digestate dewaterability, represented by the solid content of centrifugally dewatered cake, in high-solids sequencing batch digesters with and without thermal hydrolysis pretreatment (THP). The results show that the dewaterability of the sludge after digestion was improved by 3.5% (±0.5%) for unpretreated sludge and 5.1% (±0.4%) for thermally hydrolyzed sludge. Compared to the unpretreated sludge digestate, thermal hydrolysis pretreatment eventually resulted in an improvement of dewaterability by 4.6% (±0.5%). Smaller particle size and larger surface area of sludge were induced by thermal hydrolysis and anaerobic digestion treatments. The structure strength and compactness of sludge, represented by elastic modulus and fractal dimension respectively, decreased with increase of digestion time. The porous network structure was broken up by thermal hydrolysis pretreatment and was further weakened during anaerobic digestion, which correspondingly improved the dewaterability of digestates. The logarithm of elastic modulus increased linearly with fractal dimension regardless of the pretreatment. Both fractal dimension and elastic modulus showed linear relationship with dewaterability. The rheological characterization combined with the analysis of fractal dimension of sewage sludge porous network structure was found applicable in quantitative evaluation of sludge dewaterability, which depended positively on both thermal hydrolysis and anaerobic digestion. Copyright © 2017 Elsevier Ltd. All rights reserved.

An 1-2-1 Cyclic Model for the Evolution of Mantle Structure

NASA Astrophysics Data System (ADS)

Zhong, S.; Zhang, N.

2006-12-01

The present-day Earth`s mantle is predominated by long-wavelength structures including circum-Pacific subducted slabs and Africa and Pacific super-plumes. These long-wavelength structures are largely controlled by the history of plate tectonic motion. Although it dictates the evolution of mantle structure, global plate tectonic history prior to 120 Ma is poorly constrained except for continental motions that can be reliably traced back to >1 Ga. An important observation of continental motions in the last 1 Ga is the two episodes of formation and breakup of super-continents Pangea and Rodinia. We formulated 3D global models of mantle convection with temperature- and depth-dependent viscosity to study the formation of mantle structure. We found that for the upper mantle with 30 times smaller viscosity than the lower mantle, in the absence of continents, mantle convection is characterized by a hemispherically asymmetric structure in which one hemisphere is largely upwellings, while the other hemisphere contains downwellings (i.e., degree-1 convection). This is the first study in which degree-1 mantle convection is observed in mobile-lid/plate-tectonic convection regime at high Rayleigh number. This result suggests that degree-1 convection is a dynamically preferred state for the Earth`s mantle. We suggest that the evolution of mantle structure is controlled by a cyclic process of formation and breakdown of degree-1 convection modulated strongly by continents. The formation and breakup of supercontinents are surface manifestation of this cyclic process. During the degree-1 convection state, the upwellings in one hemisphere push all continents into the other hemisphere with the downwellings to form a supercontinent. The non-subducting nature of continents dictates that subduction in the downwelling hemisphere occurs along the edge of the supercontinent upon its formation. The insulating effect of a supercontinent and return flow from the circum-supercontinent subduction

A mathematical model of the structure and evolution of small-scale discrete auroral arcs

NASA Technical Reports Server (NTRS)

Seyler, Charles E.

1990-01-01

A three-dimensional fluid model for the structure and evolution of small-scale discrete auroral arcs originating from Alfven waves is developed and used to study the nonlinear macroscopic plasma dynamics of these auroral arcs. The results of simulations show that stationary auroral arcs can be unstable to a collisionless tearing mode which may be responsible for the observed transverse structuring in the form of folds and curls. At late times, the plasma becomes turbulent having transverse electric field power spectra that tend toward a universal k exp -5/3 spectral form.

Characterizing the propagation evolution of wave patterns and vortex structures in astigmatic transformations of Hermite-Gaussian beams

NASA Astrophysics Data System (ADS)

Chen, Y. F.; Chang, C. C.; Lee, C. Y.; Tung, J. C.; Liang, H. C.; Huang, K. F.

2018-01-01

Theoretical wave functions are analytically derived to characterize the propagation evolution of the Hermite-Gaussian (HG) beams transformed by a single-lens astigmatic mode converter with arbitrary angle. The derived wave functions are related to the combination of the rotation transform and the antisymmetric fractional Fourier transform. The derived formula is systematically validated by using an off-axis diode-pumped solid-state laser to generate various high-order HG beams for mode conversions. In addition to validation, the creation and evolution of vortex structures in the transformed HG beams are numerically manifested. The present theoretical analyses can be used not only to characterize the evolution of the transformed beams but to design the optical vortex beams with various forms.

Evolution of the ATLAS PanDA Production and Distributed Analysis System

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

Maeno, T.; De, K.; Wenaus, T.

2012-12-13

Evolution of the ATLAS PanDA Production and Distributed Analysis System T Maeno1,5, K De2, T Wenaus1, P Nilsson2, R Walker3, A Stradling2, V Fine1, M Potekhin1, S Panitkin1 and G Compostella4 Published under licence by IOP Publishing Ltd Journal of Physics: Conference Series, Volume 396, Part 3 Article PDF References Citations Metrics 101 Total downloads Cited by 8 articles Turn on MathJax Share this article Article information Abstract The PanDA (Production and Distributed Analysis) system has been developed to meet ATLAS production and analysis requirements for a data-driven workload management system capable of operating at LHC data processing scale. PanDAmore » has performed well with high reliability and robustness during the two years of LHC data-taking, while being actively evolved to meet the rapidly changing requirements for analysis use cases. We will present an overview of system evolution including automatic rebrokerage and reattempt for analysis jobs, adaptation for the CernVM File System, support for the multi-cloud model through which Tier-2 sites act as members of multiple clouds, pledged resource management and preferential brokerage, and monitoring improvements. We will also describe results from the analysis of two years of PanDA usage statistics, current issues, and plans for the future.« less

BOOK REVIEW: Structures in the Universe by Exact Methods: Formation, Evolutions, Interactions (Cambridge Monographs on Mathematical Physics) Structures in the Universe by Exact Methods: Formation, Evolutions, Interactions (Cambridge Monographs on Mathematical Physics)

NASA Astrophysics Data System (ADS)

Coley, Alan

2010-05-01

Szekeres model) is studied regarding structure formation. I thought that the authors describe the advantages and drawbacks of the idealized exact solutions used in the physical modelling in a reasonable manner (although more concise conclusions might have been useful). The authors also address the formation of a galaxy with a central black hole, the formation and evolution of rich galactic clusters and voids and other structures, and the effects of radiation in the models. The most interesting application is presented in chapter 5; namely, the effects of inhomogeneities on observations such as the luminosity distance relation and the explanation of the observed dimming of distant SN Ia (which is usually interpreted within the standard FLRW model in terms of the existence of dark energy). The main conclusion of this work is that data can be reproduced within the LT model (via inhomogeneities in general relativity, but without introducing dark energy). In particular, a number of exact LT solutions were surveyed, and a full discussion of various models in the literature (and a critique of the various assumptions) is presented. In the next chapter the possible resolution of the horizon problem without inflation, in terms of shell crossing in a LT model, is discussed. This is perhaps the most controversial chapter of the book. In the final chapter 7, the influence of inhomogeneous structures in the path of a light ray (for both center and off-center observers in a special Szekeres Swiss cheese model) on the observed temperature distribution of the CMB is discussed. This is a very important topic, but only a heuristic and qualitative study is presented here; more work on the multipole moments of higher order would be necessary for a more comprehensive analysis.

Evolution of basin and range structure in the Ruby Mountains and vicinity, Nevada

NASA Technical Reports Server (NTRS)

Blackwell, D. D.; Reese, N. M.; Kelley, S. A.

1985-01-01

Results from various age dating techniques, seismic reflection profiling hydrocarbon maturation studies, and structural analysis were used to evaluate the Cenozoic deformation in the Ruby Mountains and adjoining ranges (pinyon Range and Cortez Range) in Elko and Eureka Counties, Nevada. Age dating techniques used include potassium-argon ages of biotites from granites published by Kistler et al. (1981) and fission track ages from apatite and zircon. Fission track ages from apatite reflect a closing temperature of 100 plus or minus 20 deg C. Zircon fission track ages reflect a closing temperature of 175 plus or minus 25 deg C and potassium-argon ages from brotite reflect a closing temperature of 250 plus or minus 30 deg C. Thus these results allow a reasonably precise tracking of the evolution of the ranges during the Cenozoic. Seismic reflection data are available from Huntington Valley. Access to seismic reflection data directly to the west of the Harrison Pass Pluton in the central Ruby Mountains was obtained. In addition results are available from several deep exploration holes in Huntington Valley.

Structural Evolution of Reversible Mg Insertion into a Bilayer Structure of V 2 O 5 · n H 2 O Xerogel Material

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

Sa, Niya; Kinnibrugh, Tiffany L.; Wang, Hao

Functional multivalent intercalation cathodes represent one of the largest hurdles in the development of Mg batteries. While there are many reports of Mg cathodes, many times the evidence of intercalation chemistry is only circumstantial. In this work, direct evidence of Mg intercalation into a bilayer structure of V2O5·nH2O xerogel is confirmed, and the nature of the Mg intercalated species is reported. The interlayer spacing of V2O5·nH2O contracts upon Mg intercalation and expands for Mg deintercalation due to the strong electrostatic interaction between the divalent cation and the cathode. A combination of NMR, pair distribution function (PDF) analysis, and X-ray absorptionmore » near edge spectroscopy (XANES) confirmed reversible Mg insertion into the V2O5·nH2O material, and structural evolution of Mg intercalation leads to the formation of multiple new phases. Structures of V2O5·nH2O with Mg intercalation were further supported by the first principle simulations. A solvent cointercalated Mg in V2O5·nH2O is observed for the first time, and the 25Mg magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy was used to elucidate the structure obtained upon electrochemical cycling. Specifically, existence of a well-defined Mg–O environment is revealed for the Mg intercalated structures. Information reported here reveals the fundamental Mg ion intercalation mechanism in a bilayer structure of V2O5·nH2O material and provides insightful design metrics for future Mg cathodes.« less

The triple helix of collagens - an ancient protein structure that enabled animal multicellularity and tissue evolution.

PubMed

Fidler, Aaron L; Boudko, Sergei P; Rokas, Antonis; Hudson, Billy G

2018-04-09

The cellular microenvironment, characterized by an extracellular matrix (ECM), played an essential role in the transition from unicellularity to multicellularity in animals (metazoans), and in the subsequent evolution of diverse animal tissues and organs. A major ECM component are members of the collagen superfamily -comprising 28 types in vertebrates - that exist in diverse supramolecular assemblies ranging from networks to fibrils. Each assembly is characterized by a hallmark feature, a protein structure called a triple helix. A current gap in knowledge is understanding the mechanisms of how the triple helix encodes and utilizes information in building scaffolds on the outside of cells. Type IV collagen, recently revealed as the evolutionarily most ancient member of the collagen superfamily, serves as an archetype for a fresh view of fundamental structural features of a triple helix that underlie the diversity of biological activities of collagens. In this Opinion, we argue that the triple helix is a protein structure of fundamental importance in building the extracellular matrix, which enabled animal multicellularity and tissue evolution. © 2018. Published by The Company of Biologists Ltd.

Untangling the origin of viruses and their impact on cellular evolution.

PubMed

Nasir, Arshan; Sun, Feng-Jie; Kim, Kyung Mo; Caetano-Anollés, Gustavo

2015-04-01

The origin and evolution of viruses remain mysterious. Here, we focus on the distribution of viral replicons in host organisms, their morphological features, and the evolution of highly conserved protein and nucleic acid structures. The apparent inability of RNA viral replicons to infect contemporary akaryotic species suggests an early origin of RNA viruses and their subsequent loss in akaryotes. A census of virion morphotypes reveals that advanced forms were unique to viruses infecting a specific supergroup, while simpler forms were observed in viruses infecting organisms in all forms of cellular life. Results hint toward an ancient origin of viruses from an ancestral virus harboring either filamentous or spherical virions. Finally, phylogenetic trees built from protein domain and tRNA structures in thousands of genomes suggest that viruses evolved via reductive evolution from ancient cells. The analysis presents a complete account of the evolutionary history of cells and viruses and identifies viruses as crucial agents influencing cellular evolution. © 2015 New York Academy of Sciences.

Imprints of the large-scale structure on AGN formation and evolution

NASA Astrophysics Data System (ADS)

Porqueres, Natàlia; Jasche, Jens; Enßlin, Torsten A.; Lavaux, Guilhem

2018-04-01

Black hole masses are found to correlate with several global properties of their host galaxies, suggesting that black holes and galaxies have an intertwined evolution and that active galactic nuclei (AGN) have a significant impact on galaxy evolution. Since the large-scale environment can also affect AGN, this work studies how their formation and properties depend on the environment. We have used a reconstructed three-dimensional high-resolution density field obtained from a Bayesian large-scale structure reconstruction method applied to the 2M++ galaxy sample. A web-type classification relying on the shear tensor is used to identify different structures on the cosmic web, defining voids, sheets, filaments, and clusters. We confirm that the environmental density affects the AGN formation and their properties. We found that the AGN abundance is equivalent to the galaxy abundance, indicating that active and inactive galaxies reside in similar dark matter halos. However, occurrence rates are different for each spectral type and accretion rate. These differences are consistent with the AGN evolutionary sequence suggested by previous authors, Seyferts and Transition objects transforming into low-ionization nuclear emission line regions (LINERs), the weaker counterpart of Seyferts. We conclude that AGN properties depend on the environmental density more than on the web-type. More powerful starbursts and younger stellar populations are found in high densities, where interactions and mergers are more likely. AGN hosts show smaller masses in clusters for Seyferts and Transition objects, which might be due to gas stripping. In voids, the AGN population is dominated by the most massive galaxy hosts.

Using asteroseismology to probe the structure and evolution of the Galaxy

NASA Astrophysics Data System (ADS)

Stello, Dennis

2015-08-01

Recent space missions have transformed our ability to use asteroseismology on vast numbers of stars. This advance has opened up for exploration of the structure and evolution of the Galaxy using oscillating red giant stars as distant tracers of stellar populations including the halo, the bulge and the thin and thick disks. Asteroseismology provides a powerful way to obtain precise estimates of stellar bulk properties such as radius, mass, and age. The radius, and hence distance, places a star accurately in the Galaxy, the mass reveals the mass function and, in combination with composition, provide ages for red giants. Initial results from the CoRoT and Kepler missions have demonstrated the enormous potential there is in the marriage between asteroseismology and contemporary Galactic Archaeology based on single-epoch spectroscopy, photometry, and parallax measurements. The scope for this research received a significant boost last year on several fronts. The re-purposed Kepler telescope, K2, started observing tens of thousands of red giants along the ecliptic covering all main constituents of the Galaxy, and in a few years time NASA's TESS mission will stars observing up to 1 mio red giants full sky. Finally, ESA's decision to fund PLATO guaranties that high quality seismic measurements will continue to flow beyond the nextdecade. In this talk I will give an overview of how seismology can aid the study of the structure and evolution of the Galaxy. I will include the most recent results that we have obtained with our K2 Galactic Archaeology Program.

Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

NASA Technical Reports Server (NTRS)

Mcknight, R. L.; Huang, H.; Hartle, M.

1992-01-01

Accomplishments are described for the third years effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures. These accomplishments include: (1) structural analysis capability specialized for graded composite structures including large deformation and deformation position eigenanalysis technologies; (2) a thermal analyzer specialized for graded composite structures; (3) absorption of electromagnetic waves by graded composite structures; and (4) coupled structural thermal/electromagnetic analysis of graded composite structures.

On the temporal evolution of long-wavelength mantle structure of the Earth since the early Paleozoic

NASA Astrophysics Data System (ADS)

Zhong, Shijie; Rudolph, Maxwell L.

2015-05-01

The seismic structure of the Earth's lower mantle is characterized by a dominantly degree-2 pattern with the African and Pacific large low shear velocity provinces (i.e., LLSVP) that are separated by circum-Pacific seismically fast anomalies. It is important to understand the origin of such a degree-2 mantle structure and its temporal evolution. In this study, we investigated the effects of plate motion history and mantle viscosity on the temporal evolution of the lower mantle structure since the early Paleozoic by formulating 3-D spherical shell models of thermochemical convection. For convection models with realistic mantle viscosity and no initial structure, it takes about ˜50 Myr to develop dominantly degree-2 lower mantle structure using the published plate motion models for the last either 120 Ma or 250 Ma. However, it takes longer time to develop the mantle structure for more viscous mantle. While the circum-Pangea subduction in plate motion history models promotes the formation of degree-2 mantle structure, the published pre-Pangea plate motions before 330 Ma produce relatively cold lower mantle in the African hemisphere and significant degree-1 structure in the early Pangea (˜300 Ma) or later times, even if the lower mantle has an initially degree-2 structure and a viscosity as high as 1023 Pas. This suggests that the African LLSVP may not be stationary since the early Paleozoic. With the published plate motion models and lower mantle viscosity of 1022 Pas, our mantle convection models suggest that the present-day degree-2 mantle structure may have largely been formed by ˜200 Ma.

Decoupling of the Leading Order DGLAP Evolution Equation with Spin Dependent Structure Functions

NASA Astrophysics Data System (ADS)

Azadbakht, F. Teimoury; Boroun, G. R.

2018-02-01

We propose an analytical solution for DGLAP evolution equations with polarized splitting functions at the Leading Order (LO) approximation based on the Laplace transform method. It is shown that the DGLAP evolution equations can be decoupled completely into two second order differential equations which then are solved analytically by using the initial conditions δ FS(x,Q2)=F[partial δ FS0(x), δ FS0(x)] and {δ G}(x,Q2)=G[partial δ G0(x), δ G0(x)]. We used this method to obtain the polarized structure function of the proton as well as the polarized gluon distribution function inside the proton and compared the numerical results with experimental data of COMPASS, HERMES, and AAC'08 Collaborations. It was found that there is a good agreement between our predictions and the experiments.

Galaxy evolution in the densest environments: HST imaging

NASA Astrophysics Data System (ADS)

Jorgensen, Inger

2013-10-01

We propose to process in a consistent fashion all available HST/ACS and WFC3 imaging of seven rich clusters of galaxies at z=1.2-1.6. The clusters are part of our larger project aimed at constraining models for galaxy evolution in dense environments from observations of stellar populations in rich z=1.2-2 galaxy clusters. The main objective is to establish the star formation {SF} history and structural evolution over this epoch during which large changes in SF rates and galaxy structure are expected to take place in cluster galaxies.The observational data required to meet our main objective are deep HST imaging and high S/N spectroscopy of individual cluster members. The HST imaging already exists for the seven rich clusters at z=1.2-1.6 included in this archive proposal. However, the data have not been consistently processed to derive colors, magnitudes, sizes and morphological parameters for all potential cluster members bright enough to be suitable for spectroscopic observations with 8-m class telescopes. We propose to carry out this processing and make all derived parameters publicly available. We will use the parameters derived from the HST imaging to {1} study the structural evolution of the galaxies, {2} select clusters and galaxies for spectroscopic observations, and {3} use the photometry and spectroscopy together for a unified analysis aimed at the SF history and structural changes. The analysis will also utilize data from the Gemini/HST Cluster Galaxy Project, which covers rich clusters at z=0.2-1.0 and for which we have similar HST imaging and high S/N spectroscopy available.

An in situ USAXS-SAXS-WAXS study of precipitate size distribution evolution in a model Ni-based alloy.

PubMed

Andrews, Ross N; Serio, Joseph; Muralidharan, Govindarajan; Ilavsky, Jan

2017-06-01

Intermetallic γ' precipitates typically strengthen nickel-based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their temporal evolution characteristics determine the high-temperature alloy stability. Combined ultra-small-, small- and wide-angle X-ray scattering (USAXS-SAXS-WAXS) analysis can be used to evaluate the temporal evolution of an alloy's precipitate size distribution (PSD) and phase structure during in situ heat treatment. Analysis of PSDs from USAXS-SAXS data employs either least-squares fitting of a preordained PSD model or a maximum entropy (MaxEnt) approach, the latter avoiding a priori definition of a functional form of the PSD. However, strong low- q scattering from grain boundaries and/or structure factor effects inhibit MaxEnt analysis of typical alloys. This work describes the extension of Bayesian-MaxEnt analysis methods to data exhibiting structure factor effects and low- q power law slopes and demonstrates their use in an in situ study of precipitate size evolution during heat treatment of a model Ni-Al-Si alloy.

Observations of the structure and evolution of solar flares with a soft X-ray telescope

NASA Technical Reports Server (NTRS)

Vorpahl, J. A.; Gibson, E. G.; Landecker, P. B.; Mckenzie, D. L.; Underwood, J. M.

1975-01-01

Soft X ray flare events were observed with the S-056 X-ray telescope that was part of the ATM complement of instruments aboard SKYLAB. Analyses of these data are reported. The observations are summarized and a detailed discussion of the X-ray flare structures is presented. The data indicated that soft X-ray emitted by a flare come primarily from an intense well-defined core surrounded by a region of fainter, more diffuse emission. An analysis of flare evolution indicates evidence for preliminary heating and energy release prior to the main phase of the flare. Core features are found to be remarkably stable and retain their shape throughout a flare. Most changes in the overall configuration seem to be result of the appearance, disappearance or change in brightness of individual features, rather than the restructuring or reorientation of these features. Brief comparisons with several theories are presented.

Understanding the process of social network evolution: Online-offline integrated analysis of social tie formation

PubMed Central

Kwak, Doyeon

2017-01-01

It is important to consider the interweaving nature of online and offline social networks when we examine social network evolution. However, it is difficult to find any research that examines the process of social tie formation from an integrated perspective. In our study, we quantitatively measure offline interactions and examine the corresponding evolution of online social network in order to understand the significance of interrelationship between online and offline social factors in generating social ties. We analyze the radio signal strength indicator sensor data from a series of social events to understand offline interactions among the participants and measure the structural attributes of their existing online Facebook social networks. By monitoring the changes in their online social networks before and after offline interactions in a series of social events, we verify that the ability to develop an offline interaction into an online friendship is tied to the number of social connections that participants previously had, while the presence of shared mutual friends between a pair of participants disrupts potential new connections within the pre-designed offline social events. Thus, while our integrative approach enables us to confirm the theory of preferential attachment in the process of network formation, the common neighbor theory is not supported. Our dual-dimensional network analysis allows us to observe the actual process of social network evolution rather than to make predictions based on the assumption of self-organizing networks. PMID:28542367

Understanding the process of social network evolution: Online-offline integrated analysis of social tie formation.

PubMed

Kwak, Doyeon; Kim, Wonjoon

2017-01-01

It is important to consider the interweaving nature of online and offline social networks when we examine social network evolution. However, it is difficult to find any research that examines the process of social tie formation from an integrated perspective. In our study, we quantitatively measure offline interactions and examine the corresponding evolution of online social network in order to understand the significance of interrelationship between online and offline social factors in generating social ties. We analyze the radio signal strength indicator sensor data from a series of social events to understand offline interactions among the participants and measure the structural attributes of their existing online Facebook social networks. By monitoring the changes in their online social networks before and after offline interactions in a series of social events, we verify that the ability to develop an offline interaction into an online friendship is tied to the number of social connections that participants previously had, while the presence of shared mutual friends between a pair of participants disrupts potential new connections within the pre-designed offline social events. Thus, while our integrative approach enables us to confirm the theory of preferential attachment in the process of network formation, the common neighbor theory is not supported. Our dual-dimensional network analysis allows us to observe the actual process of social network evolution rather than to make predictions based on the assumption of self-organizing networks.

Evolution of the Busbar Structure in Large-Scale Aluminum Reduction Cells

NASA Astrophysics Data System (ADS)

Zhang, Hongliang; Liang, Jinding; Li, Jie; Sun, Kena; Xiao, Jin

2017-02-01

Studies of magnetic field and magneto-hydro-dynamics are regarded as the foundation for the development of large-scale aluminum reduction cells, while due to the direct relationship between the busbar configuration and magnetic compensation, the actual key content is the configuration of the busbar. As the line current has been increased from 160 kA to 600 kA, the configuration of the busbar was becoming more complex. To summarize and explore the evolution of busbar configuration in aluminum reduction cells, this paper has reviewed various representative large-scale pre-baked aluminum reduction cell busbar structures, such as end-to-end potlines, side-by-side potlines and external compensation current. The advantages and disadvantages in the magnetic distribution or technical specifications have also been introduced separately, especially for the configurations of the mainstream 400-kA potlines. In the end, the development trends of the bus structure configuration were prospected, based on the recent successful applications of super-scale cell busbar structures in China (500-600 kA).

A practical approach to calculate the time evolutions of magnetic field effects on photochemical reactions in nano-structured materials.

PubMed

Yago, Tomoaki; Wakasa, Masanobu

2015-04-21

A practical method to calculate time evolutions of magnetic field effects (MFEs) on photochemical reactions involving radical pairs is developed on the basis of the theory of the chemically induced dynamic spin polarization proposed by Pedersen and Freed. In theory, the stochastic Liouville equation (SLE), including the spin Hamiltonian, diffusion motions of the radical pair, chemical reactions, and spin relaxations, is solved by using the Laplace and the inverse Laplace transformation technique. In our practical approach, time evolutions of the MFEs are successfully calculated by applying the Miller-Guy method instead of the final value theorem to the inverse Laplace transformation process. Especially, the SLE calculations are completed in a short time when the radical pair dynamics can be described by the chemical kinetics consisting of diffusions, reactions and spin relaxations. The SLE analysis with a short calculation time enables one to examine the various parameter sets for fitting the experimental date. Our study demonstrates that simultaneous fitting of the time evolution of the MFE and of the magnetic field dependence of the MFE provides valuable information on the diffusion motions of the radical pairs in nano-structured materials such as micelles where the lifetimes of radical pairs are longer than hundreds of nano-seconds and the magnetic field dependence of the spin relaxations play a major role for the generation of the MFE.

Neuroanatomy of the killer whale (Orcinus orca): a magnetic resonance imaging investigation of structure with insights on function and evolution.

PubMed

Wright, Alexandra; Scadeng, Miriam; Stec, Dominik; Dubowitz, Rebecca; Ridgway, Sam; Leger, Judy St

2017-01-01

The evolutionary process of adaptation to an obligatory aquatic existence dramatically modified cetacean brain structure and function. The brain of the killer whale (Orcinus orca) may be the largest of all taxa supporting a panoply of cognitive, sensory, and sensorimotor abilities. Despite this, examination of the O. orca brain has been limited in scope resulting in significant deficits in knowledge concerning its structure and function. The present study aims to describe the neural organization and potential function of the O. orca brain while linking these traits to potential evolutionary drivers. Magnetic resonance imaging was used for volumetric analysis and three-dimensional reconstruction of an in situ postmortem O. orca brain. Measurements were determined for cortical gray and cerebral white matter, subcortical nuclei, cerebellar gray and white matter, corpus callosum, hippocampi, superior and inferior colliculi, and neuroendocrine structures. With cerebral volume comprising 81.51 % of the total brain volume, this O. orca brain is one of the most corticalized mammalian brains studied to date. O. orca and other delphinoid cetaceans exhibit isometric scaling of cerebral white matter with increasing brain size, a trait that violates an otherwise evolutionarily conserved cerebral scaling law. Using comparative neurobiology, it is argued that the divergent cerebral morphology of delphinoid cetaceans compared to other mammalian taxa may have evolved in response to the sensorimotor demands of the aquatic environment. Furthermore, selective pressures associated with the evolution of echolocation and unihemispheric sleep are implicated in substructure morphology and function. This neuroanatomical dataset, heretofore absent from the literature, provides important quantitative data to test hypotheses regarding brain structure, function, and evolution within Cetacea and across Mammalia.

Microstructural properties and evolution of nanoclusters in liquid Si during a rapid cooling process

NASA Astrophysics Data System (ADS)

Gao, T.; Hu, X.; Li, Y.; Tian, Z.; Xie, Q.; Chen, Q.; Liang, Y.; Luo, X.; Ren, L.; Luo, J.

2017-11-01

The formation of amorphous structures in Si during the rapid quenching process was studied based on molecular dynamics simulation by using the Stillinger-Weber potential. The evolution characteristics of nanoclusters during the solidification were analyzed by several structural analysis methods. The amorphous Si has been formed with many tetrahedral clusters and few nanoclusters. During the solidification, tetrahedral polyhedrons affect the local structures by their different positions and connection modes. The main kinds of polyhedrons randomly linked with one another to form an amorphous network structures in the system. The structural evolution of crystal nanocluster demonstrates that the nanocluster has difficulty to growth because of the high cooling rate of 1012 K/s.

Evolution of Structure and Composition in Saturn's Rings Due to Ballistic Transport of Micrometeoroid Impact Ejecta

NASA Astrophysics Data System (ADS)

Estrada, P. R.; Durisen, R. H.; Cuzzi, J. N.

2014-04-01

We introduce improved numerical techniques for simulating the structural and compositional evolution of planetary rings due to micrometeoroid bombardment and subsequent ballistic transport of impact ejecta. Our current, robust code, which is based on the original structural code of [1] and on the pollution transport code of [3], is capable of modeling structural changes and pollution transport simultaneously over long times on both local and global scales. We provide demonstrative simulations to compare with, and extend upon previous work, as well as examples of how ballistic transport can maintain the observed structure in Saturn's rings using available Cassini occultation optical depth data.

A Complex Network Analysis of Granular Fabric Evolution in Three-Dimensions

DTIC Science & Technology

2011-01-01

organized pattern formation (e.g., strain localization), and co-evolution of emergent in- ternal structures (e.g., force cycles and force chains) [15...these networks, particularly recurring patterns or motifs, and understanding how these co-evolve are crucial to the robust characterization and...the lead up to and during failure. Since failure patterns and boundaries of flow in three-dimensional specimens can be quite complicated and difficult

Influence of pre-existing basement faults on the structural evolution of the Zagros Simply Folded belt: 3D numerical modelling

NASA Astrophysics Data System (ADS)

Ruh, Jonas B.; Gerya, Taras

2015-04-01

The Simply Folded Belt of the Zagros orogen is characterized by elongated fold trains symptomatically defining the geomorphology along this mountain range. The Zagros orogen results from the collision of the Arabian and the Eurasian plates. The Simply Folded Belt is located southwest of the Zagros suture zone. An up to 2 km thick salt horizon below the sedimentary sequence enables mechanical and structural detachment from the underlying Arabian basement. Nevertheless, deformation within the basement influences the structural evolution of the Simply Folded Belt. It has been shown that thrusts in form of reactivated normal faults can trigger out-of-sequence deformation within the sedimentary stratigraphy. Furthermore, deeply rooted strike-slip faults, such as the Kazerun faults between the Fars zone in the southeast and the Dezful embayment and the Izeh zone, are largely dispersing into the overlying stratigraphy, strongly influencing the tectonic evolution and mechanical behaviour. The aim of this study is to reveal the influence of basement thrusts and strike-slip faults on the structural evolution of the Simply Folded Belt depending on the occurrence of intercrustal weak horizons (Hormuz salt) and the rheology and thermal structure of the basement. Therefore, we present high-resolution 3D thermo-mechnical models with pre-existing, inversively reactivated normal faults or strike-slip faults within the basement. Numerical models are based on finite difference, marker-in-cell technique with (power-law) visco-plastic rheology accounting for brittle deformation. Preliminary results show that deep tectonic structures present in the basement may have crucial effects on the morphology and evolution of a fold-and-thrust belt above a major detachment horizon.

Probabilistic structural analysis methods of hot engine structures

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Hopkins, D. A.

1989-01-01

Development of probabilistic structural analysis methods for hot engine structures is a major activity at Lewis Research Center. Recent activities have focused on extending the methods to include the combined uncertainties in several factors on structural response. This paper briefly describes recent progress on composite load spectra models, probabilistic finite element structural analysis, and probabilistic strength degradation modeling. Progress is described in terms of fundamental concepts, computer code development, and representative numerical results.

Design Strategy of Multi-electron Transfer Catalysts Based on a Bioinformatic Analysis of Oxygen Evolution and Reduction Enzymes.

PubMed

Ooka, Hideshi; Hashimoto, Kazuhito; Nakamura, Ryuhei

2018-05-14

Understanding the design strategy of photosynthetic and respiratory enzymes is important to develop efficient artificial catalysts for oxygen evolution and reduction reactions. Here, based on a bioinformatic analysis of cyanobacterial oxygen evolution and reduction enzymes (photosystem II: PS II and cytochrome c oxidase: COX, respectively), the gene encoding the catalytic D1 subunit of PS II was found to be expressed individually across 38 phylogenetically diverse strains, which is in contrast to the operon structure of the genes encoding major COX subunits. Selective synthesis of the D1 subunit minimizes the repair cost of PS II, which allows compensation for its instability by lowering the turnover number required to generate a net positive energy yield. The different bioenergetics observed between PS II and COX suggest that in addition to the catalytic activity rationalized by the Sabatier principle, stability factors have also provided a major influence on the design strategy of biological multi-electron transfer enzymes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transition Characteristic Analysis of Traffic Evolution Process for Urban Traffic Network

PubMed Central

Chen, Hong; Li, Yang

2014-01-01

The characterization of the dynamics of traffic states remains fundamental to seeking for the solutions of diverse traffic problems. To gain more insights into traffic dynamics in the temporal domain, this paper explored temporal characteristics and distinct regularity in the traffic evolution process of urban traffic network. We defined traffic state pattern through clustering multidimensional traffic time series using self-organizing maps and construct a pattern transition network model that is appropriate for representing and analyzing the evolution progress. The methodology is illustrated by an application to data flow rate of multiple road sections from Network of Shenzhen's Nanshan District, China. Analysis and numerical results demonstrated that the methodology permits extracting many useful traffic transition characteristics including stability, preference, activity, and attractiveness. In addition, more information about the relationships between these characteristics was extracted, which should be helpful in understanding the complex behavior of the temporal evolution features of traffic patterns. PMID:24982969

Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications

PubMed Central

Mail, M.; Neinhuis, C.

2016-01-01

A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing. This article is part of the themed issue ‘Bioinspired hierarchically structured surfaces for green science’. PMID:27354736

Superhydrophobic hierarchically structured surfaces in biology: evolution, structural principles and biomimetic applications.

PubMed

Barthlott, W; Mail, M; Neinhuis, C

2016-08-06

A comprehensive survey of the construction principles and occurrences of superhydrophobic surfaces in plants, animals and other organisms is provided and is based on our own scanning electron microscopic examinations of almost 20 000 different species and the existing literature. Properties such as self-cleaning (lotus effect), fluid drag reduction (Salvinia effect) and the introduction of new functions (air layers as sensory systems) are described and biomimetic applications are discussed: self-cleaning is established, drag reduction becomes increasingly important, and novel air-retaining grid technology is introduced. Surprisingly, no evidence for lasting superhydrophobicity in non-biological surfaces exists (except technical materials). Phylogenetic trees indicate that superhydrophobicity evolved as a consequence of the conquest of land about 450 million years ago and may be a key innovation in the evolution of terrestrial life. The approximate 10 million extant species exhibit a stunning diversity of materials and structures, many of which are formed by self-assembly, and are solely based on a limited number of molecules. A short historical survey shows that bionics (today often called biomimetics) dates back more than 100 years. Statistical data illustrate that the interest in biomimetic surfaces is much younger still. Superhydrophobicity caught the attention of scientists only after the extreme superhydrophobicity of lotus leaves was published in 1997. Regrettably, parabionic products play an increasing role in marketing.This article is part of the themed issue 'Bioinspired hierarchically structured surfaces for green science'. © 2016 The Author(s).

Evolution of the Structure of Cu-1% Sn Bronze under High Pressure Torsion and Subsequent Annealing

NASA Astrophysics Data System (ADS)

Popov, V. V.; Popova, E. N.; Stolbovsky, A. V.; Falahutdinov, R. M.

2018-04-01

The evolution of the structure of tin bronze under the room-temperature high-pressure torsion with different degrees of deformation and the subsequent annealing has been investigated. The thermal stability of the structure formed, namely, its behavior upon annealing in the temperature range of 150-400°C has been studied. The possibility of alloying copper with tin has been analyzed with the purpose of obtaining a thermally stable nanostructure with high strength characteristics.

Evolution of crystal structure during the initial stages of ZnO atomic layer deposition

DOE PAGES

Boichot, R.; Tian, L.; Richard, M. -I.; ...

2016-01-05

In this study, a complementary suite of in situ synchrotron X-ray techniques is used to investigate both structural and chemical evolution during ZnO growth by atomic layer deposition. Focusing on the first 10 cycles of growth, we observe that the structure formed during the coalescence stage largely determines the overall microstructure of the film. Furthermore, by comparing ZnO growth on silicon with a native oxide with that on Al 2O 3(001), we find that even with lattice-mismatched substrates and low deposition temperatures, the crystalline texture of the films depend strongly on the nature of the interfacial bonds.

Structural evolution of fault zones in sandstone by multiple deformation mechanisms: Moab fault, southeast Utah

USGS Publications Warehouse

Davatzes, N.C.; Eichhubl, P.; Aydin, A.

2005-01-01

Faults in sandstone are frequently composed of two classes of structures: (1) deformation bands and (2) joints and sheared joints. Whereas the former structures are associated with cataclastic deformation, the latter ones represent brittle fracturing, fragmentation, and brecciation. We investigated the distribution of these structures, their formation, and the underlying mechanical controls for their occurrence along the Moab normal fault in southeastern Utah through the use of structural mapping and numerical elastic boundary element modeling. We found that deformation bands occur everywhere along the fault, but with increased density in contractional relays. Joints and sheared joints only occur at intersections and extensional relays. In all locations , joints consistently overprint deformation bands. Localization of joints and sheared joints in extensional relays suggests that their distribution is controlled by local variations in stress state that are due to mechanical interaction between the fault segments. This interpretation is consistent with elastic boundary element models that predict a local reduction in mean stress and least compressive principal stress at intersections and extensional relays. The transition from deformation band to joint formation along these sections of the fault system likely resulted from the combined effects of changes in remote tectonic loading, burial depth, fluid pressure, and rock properties. In the case of the Moab fault, we conclude that the structural heterogeneity in the fault zone is systematically related to the geometric evolution of the fault, the local state of stress associated with fault slip , and the remote loading history. Because the type and distribution of structures affect fault permeability and strength, our results predict systematic variations in these parameters with fault evolution. ?? 2004 Geological Society of America.

An in situ USAXS–SAXS–WAXS study of precipitate size distribution evolution in a model Ni-based alloy1

PubMed Central

Andrews, Ross N.; Serio, Joseph; Muralidharan, Govindarajan; Ilavsky, Jan

2017-01-01

Intermetallic γ′ precipitates typically strengthen nickel-based superalloys. The shape, size and spatial distribution of strengthening precipitates critically influence alloy strength, while their temporal evolution characteristics determine the high-temperature alloy stability. Combined ultra-small-, small- and wide-angle X-ray scattering (USAXS–SAXS–WAXS) analysis can be used to evaluate the temporal evolution of an alloy’s precipitate size distribution (PSD) and phase structure during in situ heat treatment. Analysis of PSDs from USAXS–SAXS data employs either least-squares fitting of a preordained PSD model or a maximum entropy (MaxEnt) approach, the latter avoiding a priori definition of a functional form of the PSD. However, strong low-q scattering from grain boundaries and/or structure factor effects inhibit MaxEnt analysis of typical alloys. This work describes the extension of Bayesian–MaxEnt analysis methods to data exhibiting structure factor effects and low-q power law slopes and demonstrates their use in an in situ study of precipitate size evolution during heat treatment of a model Ni–Al–Si alloy. PMID:28656039

Detection of early landscape evolution through controlled experimentation, data analysis, and numerical modeling at the Landscape Evolution Observatory

NASA Astrophysics Data System (ADS)

Troch, Peter A.; Pangle, Luke; Niu, Guo-Yue; Dontsova, Katerina; Barron-Gafford, Greg; van Haren, Joost; Pavao-Zuckerman, Mitch

2014-05-01

The Landscape Evolution Observatory (LEO) at Biosphere 2-The University of Arizona consists of three identical, sloping, 333 m2 convergent landscapes inside a 5,000 m2 environmentally controlled facility. These engineered landscapes contain 1-meter depth of basaltic tephra, ground to homogenous loamy sand that will undergo physical, chemical, and mineralogical changes over many years. Each landscape contains a spatially dense sensor and sampler network capable of resolving meter-scale lateral heterogeneity and sub-meter scale vertical heterogeneity in moisture, energy and carbon states and fluxes. The density of sensors and frequency at which they can be polled allows for data collection at spatial and temporal scales that are impossible in natural field settings. Embedded solution and gas samplers allow for quantification of biogeochemical processes, and facilitate the use of chemical tracers to study water movement at very high spatial resolutions. Each ~600 metric ton landscape has load cells embedded into the structure to measure changes in total system mass with 0.05% full-scale repeatability (equivalent to less than 1 cm of precipitation). This facilitates the real time accounting of hydrological partitioning at the hillslope scale. Each hillslope is equipped with an engineered rain system capable of raining at rates between 3 and 45 mm/hr in a range of spatial patterns. The rain systems are capable of creating long-term steady state conditions or running complex simulations. The precipitation water supply storage system is flexibly designed to facilitate addition of tracers at constant or time-varying rates for any of the three hillslopes. This presentation will discuss detection of early landscape evolution in terms of hydrological, geochemical and microbial processes through controlled experimentation, data analysis, and numerical modeling during the commissioning phase of the first hillslope at LEO.

If the cap fits, wear it: an overview of telomeric structures over evolution.

PubMed

Fulcher, Nick; Derboven, Elisa; Valuchova, Sona; Riha, Karel

2014-03-01

Genome organization into linear chromosomes likely represents an important evolutionary innovation that has permitted the development of the sexual life cycle; this process has consequently advanced nuclear expansion and increased complexity of eukaryotic genomes. Chromosome linearity, however, poses a major challenge to the internal cellular machinery. The need to efficiently recognize and repair DNA double-strand breaks that occur as a consequence of DNA damage presents a constant threat to native chromosome ends known as telomeres. In this review, we present a comparative survey of various solutions to the end protection problem, maintaining an emphasis on DNA structure. This begins with telomeric structures derived from a subset of prokaryotes, mitochondria, and viruses, and will progress into the typical telomere structure exhibited by higher organisms containing TTAGG-like tandem sequences. We next examine non-canonical telomeres from Drosophila melanogaster, which comprise arrays of retrotransposons. Finally, we discuss telomeric structures in evolution and possible switches between canonical and non-canonical solutions to chromosome end protection.

Clouds on Neptune: Motions, Evolution, and Structure

NASA Technical Reports Server (NTRS)

Sromovsky, Larry A.; Morgan, Thomas (Technical Monitor)

2001-01-01

The aims of our original proposal were these: (1) improving measurements of Neptune's circulation, (2) understanding the spatial distribution of cloud features, (3) discovery of new cloud features and understanding their evolutionary process, (4) understanding the vertical structure of zonal cloud patterns, (5) defining the structure of discrete cloud features, and (6) defining the near IR albedo and light curve of Triton. Towards these aims we proposed analysis of existing 1996 groundbased NSFCAM/IRTF observations and nearly simultaneous WFPC2 observations from the Hubble Space Telescope. We also proposed to acquire new observations from both HST and the IRTF.

Adaptive potential of genomic structural variation in human and mammalian evolution.

PubMed

Radke, David W; Lee, Charles

2015-09-01

Because phenotypic innovations must be genetically heritable for biological evolution to proceed, it is natural to consider new mutation events as well as standing genetic variation as sources for their birth. Previous research has identified a number of single-nucleotide polymorphisms that underlie a subset of adaptive traits in organisms. However, another well-known class of variation, genomic structural variation, could have even greater potential to produce adaptive phenotypes, due to the variety of possible types of alterations (deletions, insertions, duplications, among others) at different genomic positions and with variable lengths. It is from these dramatic genomic alterations, and selection on their phenotypic consequences, that adaptations leading to biological diversification could be derived. In this review, using studies in humans and other mammals, we highlight examples of how phenotypic variation from structural variants might become adaptive in populations and potentially enable biological diversification. Phenotypic change arising from structural variants will be described according to their immediate effect on organismal metabolic processes, immunological response and physical features. Study of population dynamics of segregating structural variation can therefore provide a window into understanding current and historical biological diversification. © The Author 2015. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Structure and Evolution of Insect Sperm: New Interpretations in the Age of Phylogenomics.

PubMed

Dallai, Romano; Gottardo, Marco; Beutel, Rolf Georg

2016-01-01

This comprehensive review of the structure of sperm in all orders of insects evaluates phylogenetic implications, with the background of a phylogeny based on transcriptomes. Sperm characters strongly support several major branches of the phylogeny of insects-for instance, Cercophora, Dicondylia, and Psocodea-and also different infraordinal groups. Some closely related taxa, such as Trichoptera and Lepidoptera (Amphiesmenoptera), differ greatly in sperm structure. Sperm characters are very conservative in some groups (Heteroptera, Odonata) but highly variable in others, including Zoraptera, a small and morphologically uniform group with a tremendously accelerated rate of sperm evolution. Unusual patterns such as sperm dimorphism, the formation of bundles, or aflagellate and immotile sperm have evolved independently in several groups.

Accelerated probabilistic inference of RNA structure evolution

PubMed Central

Holmes, Ian

2005-01-01

Background Pairwise stochastic context-free grammars (Pair SCFGs) are powerful tools for evolutionary analysis of RNA, including simultaneous RNA sequence alignment and secondary structure prediction, but the associated algorithms are intensive in both CPU and memory usage. The same problem is faced by other RNA alignment-and-folding algorithms based on Sankoff's 1985 algorithm. It is therefore desirable to constrain such algorithms, by pre-processing the sequences and using this first pass to limit the range of structures and/or alignments that can be considered. Results We demonstrate how flexible classes of constraint can be imposed, greatly reducing the computational costs while maintaining a high quality of structural homology prediction. Any score-attributed context-free grammar (e.g. energy-based scoring schemes, or conditionally normalized Pair SCFGs) is amenable to this treatment. It is now possible to combine independent structural and alignment constraints of unprecedented general flexibility in Pair SCFG alignment algorithms. We outline several applications to the bioinformatics of RNA sequence and structure, including Waterman-Eggert N-best alignments and progressive multiple alignment. We evaluate the performance of the algorithm on test examples from the RFAM database. Conclusion A program, Stemloc, that implements these algorithms for efficient RNA sequence alignment and structure prediction is available under the GNU General Public License. PMID:15790387

Structure-activity correlations in a nickel-borate oxygen evolution catalyst.

PubMed

Bediako, D Kwabena; Lassalle-Kaiser, Benedikt; Surendranath, Yogesh; Yano, Junko; Yachandra, Vittal K; Nocera, Daniel G

2012-04-18

An oxygen evolution catalyst that forms as a thin film from Ni(aq)(2+) solutions containing borate electrolyte (Ni-B(i)) has been studied by in situ X-ray absorption spectroscopy. A dramatic increase in catalytic rate, induced by anodic activation of the electrodeposited films, is accompanied by structure and oxidation state changes. Coulometric measurements correlated with X-ray absorption near-edge structure spectra of the active catalyst show that the nickel centers in activated films possess an average oxidation state of +3.6, indicating that a substantial proportion of nickel centers exist in a formal oxidation state of Ni(IV). In contrast, nickel centers in nonactivated films exist predominantly as Ni(III). Extended X-ray absorption fine structure reveals that activated catalyst films comprise bis-oxo/hydroxo-bridged nickel centers organized into sheets of edge-sharing NiO(6) octahedra. Diminished long-range ordering in catalyst films is due to their ostensibly amorphous nature. Nonactivated films display a similar oxidic nature but exhibit a distortion in the local coordination geometry about nickel centers, characteristic of Jahn-Teller distorted Ni(III) centers. Our findings indicate that the increase in catalytic activity of films is accompanied by changes in oxidation state and structure that are reminiscent of those observed for conversion of β-NiOOH to γ-NiOOH and consequently challenge the long-held notion that the β-NiOOH phase is a more efficient oxygen-evolving catalyst. © 2012 American Chemical Society

Evolution of the three-dimensional collagen structure in vascular walls during deformation: an in situ mechanical testing under multiphoton microscopy observation.

PubMed

Nierenberger, Mathieu; Fargier, Guillaume; Ahzi, Saïd; Rémond, Yves

2015-08-01

The collagen fibers' three-dimensional architecture has a strong influence on the mechanical behavior of biological tissues. To accurately model this behavior, it is necessary to get some knowledge about the structure of the collagen network. In the present paper, we focus on the in situ characterization of the collagenous structure, which is present in porcine jugular vein walls. An observation of the vessel wall is first proposed in an unloaded configuration. The vein is then put into a mechanical tensile testing device. As the vein is stretched, three-dimensional images of its collagenous structure are acquired using multiphoton microscopy. Orientation analyses are provided for the multiple images recorded during the mechanical test. From these analyses, the reorientation of the two families of collagen fibers existing in the vein wall is quantified. We noticed that the reorientation of the fibers stops as the tissue stiffness starts decreasing, corresponding to the onset of damage. Besides, no relevant evolutions of the out of plane collagen orientations were observed. Due to the applied loading, our analysis also allowed for linking the stress relaxation within the tissue to its internal collagenous structure. Finally, this analysis constitutes the first mechanical test performed under a multiphoton microscope with a continuous three-dimensional observation of the tissue structure all along the test. It allows for a quantitative evaluation of microstructural parameters combined with a measure of the global mechanical behavior. Such data are useful for the development of structural mechanical models for living tissues.

Sequence analysis of serum albumins reveals the molecular evolution of ligand recognition properties.

PubMed

Fanali, Gabriella; Ascenzi, Paolo; Bernardi, Giorgio; Fasano, Mauro

2012-01-01

Serum albumin (SA) is a circulating protein providing a depot and carrier for many endogenous and exogenous compounds. At least seven major binding sites have been identified by structural and functional investigations mainly in human SA. SA is conserved in vertebrates, with at least 49 entries in protein sequence databases. The multiple sequence analysis of this set of entries leads to the definition of a cladistic tree for the molecular evolution of SA orthologs in vertebrates, thus showing the clustering of the considered species, with lamprey SAs (Lethenteron japonicum and Petromyzon marinus) in a separate outgroup. Sequence analysis aimed at searching conserved domains revealed that most SA sequences are made up by three repeated domains (about 600 residues), as extensively characterized for human SA. On the contrary, lamprey SAs are giant proteins (about 1400 residues) comprising seven repeated domains. The phylogenetic analysis of the SA family reveals a stringent correlation with the taxonomic classification of the species available in sequence databases. A focused inspection of the sequences of ligand binding sites in SA revealed that in all sites most residues involved in ligand binding are conserved, although the versatility towards different ligands could be peculiar of higher organisms. Moreover, the analysis of molecular links between the different sites suggests that allosteric modulation mechanisms could be restricted to higher vertebrates.

Comparative genomics and evolution of eukaryotic phospholipidbiosynthesis

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

Lykidis, Athanasios

2006-12-01

Phospholipid biosynthetic enzymes produce diverse molecular structures and are often present in multiple forms encoded by different genes. This work utilizes comparative genomics and phylogenetics for exploring the distribution, structure and evolution of phospholipid biosynthetic genes and pathways in 26 eukaryotic genomes. Although the basic structure of the pathways was formed early in eukaryotic evolution, the emerging picture indicates that individual enzyme families followed unique evolutionary courses. For example, choline and ethanolamine kinases and cytidylyltransferases emerged in ancestral eukaryotes, whereas, multiple forms of the corresponding phosphatidyltransferases evolved mainly in a lineage specific manner. Furthermore, several unicellular eukaryotes maintain bacterial-type enzymesmore » and reactions for the synthesis of phosphatidylglycerol and cardiolipin. Also, base-exchange phosphatidylserine synthases are widespread and ancestral enzymes. The multiplicity of phospholipid biosynthetic enzymes has been largely generated by gene expansion in a lineage specific manner. Thus, these observations suggest that phospholipid biosynthesis has been an actively evolving system. Finally, comparative genomic analysis indicates the existence of novel phosphatidyltransferases and provides a candidate for the uncharacterized eukaryotic phosphatidylglycerol phosphate phosphatase.« less

Evolution and Advances in Satellite Analysis of Volcanoes

NASA Astrophysics Data System (ADS)

Dean, K. G.; Dehn, J.; Webley, P.; Bailey, J.

2008-12-01

Over the past 20 years satellite data used for monitoring and analysis of volcanic eruptions has evolved in terms of timeliness, access, distribution, resolution and understanding of volcanic processes. Initially satellite data was used for retrospective analysis but has evolved to proactive monitoring systems. Timely acquisition of data and the capability to distribute large data files paralleled advances in computer technology and was a critical component for near real-time monitoring. The sharing of these data and resulting discussions has improved our understanding of eruption processes and, even more importantly, their impact on society. To illustrate this evolution, critical scientific discoveries will be highlighted, including detection of airborne ash and sulfur dioxide, cloud-height estimates, prediction of ash cloud movement, and detection of thermal anomalies as precursor-signals to eruptions. AVO has been a leader in implementing many of these advances into an operational setting such as, automated eruption detection, database analysis systems, and remotely accessible web-based analysis systems. Finally, limitations resulting from trade-offs between resolution and how they impact some weakness in detection techniques and hazard assessments will be presented.

Comparative Bioinformatic Analysis of Active Site Structures in Evolutionarily Remote Homologues of α,β-Hydrolase Superfamily Enzymes.

PubMed

Suplatov, D A; Arzhanik, V K; Svedas, V K

2011-01-01

Comparative bioinformatic analysis is the cornerstone of the study of enzymes' structure-function relationship. However, numerous enzymes that derive from a common ancestor and have undergone substantial functional alterations during natural selection appear not to have a sequence similarity acceptable for a statistically reliable comparative analysis. At the same time, their active site structures, in general, can be conserved, while other parts may largely differ. Therefore, it sounds both plausible and appealing to implement a comparative analysis of the most functionally important structural elements - the active site structures; that is, the amino acid residues involved in substrate binding and the catalytic mechanism. A computer algorithm has been developed to create a library of enzyme active site structures based on the use of the PDB database, together with programs of structural analysis and identification of functionally important amino acid residues and cavities in the enzyme structure. The proposed methodology has been used to compare some α,β-hydrolase superfamily enzymes. The insight has revealed a high structural similarity of catalytic site areas, including the conservative organization of a catalytic triad and oxyanion hole residues, despite the wide functional diversity among the remote homologues compared. The methodology can be used to compare the structural organization of the catalytic and substrate binding sites of various classes of enzymes, as well as study enzymes' evolution and to create of a databank of enzyme active site structures.

The Structure and Evolution of Self-Gravitating Molecular Clouds

NASA Astrophysics Data System (ADS)

Holliman, John Herbert, II

1995-01-01

We present a theoretical formalism to evaluate the structure of molecular clouds and to determine precollapse conditions in star-forming regions. Models consist of pressure-bounded, self-gravitating spheres of a single -fluid ideal gas. We treat the case without rotation. The analysis is generalized to consider states in hydrostatic equilibrium maintained by multiple pressure components. Individual pressures vary with density as P_i(r) ~ rho^{gamma {rm p},i}(r), where gamma_{rm p},i is the polytropic index. Evolution depends additionally on whether conduction occurs on a dynamical time scale and on the adiabatic index gammai of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. Special attention is given to properly representing the major contributors to dynamical support in molecular clouds: the pressures due to static magnetic fields, Alfven waves, and thermal motions. Straightforward adjustments to the model allow us to treat the intrinsically anisotropic support provided by the static fields. We derive structure equations, as well as perturbation equations for performing a linear stability analysis. The analysis provides insight on the nature of dynamical motions due to collapse from an equilibrium state and estimates the mass of condensed objects that form in such a process. After presenting a set of general results, we describe models of star-forming regions that include the major pressure components. We parameterize the extent of ambipolar diffusion. The analysis contributes to the physical understanding of several key results from observations of these regions. Commonly observed quantities are explicitly cross-referenced with model results. We theoretically determine density and linewidth profiles on scales ranging from that of molecular cloud cores to that of giant molecular clouds (GMCs). The model offers an explanation of the mean pressures in GMCs, which are observed to be high relative

Structure and functions of water-membrane interfaces and their role in proto-biological evolution

NASA Technical Reports Server (NTRS)

Pohorille, A.; Wilson, M.; Macelroy, R. D.

1991-01-01

Among the most important developments in proto-biological evolution was the emergence of membrane-like structures. These are formed by spontaneous association of relatively simple amphiphilic molecules that would have been readily available in the primordial environment. The resulting interfacial regions between water and nonpolar interior of the membrane have several properties which made them uniquely suitable for promoting subsequent evolution. They can (1) selectively attract organic material and mediate its transport, (2) serve as simple catalysts for chemical reactions, and (3) promote the formation of trans-membrane electrical and chemical gradients which could provide energy sources for proto-cells. Understanding the structure of interfaces, their interactions with organic molecules and molecular mechanisms of their functions is an essential step to understanding proto-biological evolution. In our computer simulation studies, we showed that the structure of water at interfaces with nonpolar media is significantly different from that in the bulk. In particular, the average surface dipole density points from the vapor to the liquid. As a result, negative ions can approach the interface more easily than positive ions. Amphiphilic molecules composed of hydrocarbon conjugated rings and polar substituents (e.g., phenol) assume at the interface rigid orientations in which polar groups are buried in water while hydrocarbon parts are located in the nonpolar environment. These orientational differences are of special interest in connection with the ability of some of these molecules to efficiently absorb photons. Flexible molecules with polar substituents often adopt at interfaces conformations different from those in the bulk aquaeous solution and in the gas phase. As a result, in many instances both specificity and kinetics of chemical reactions in which these molecules can participate is modified by the presence of surfaces. Of special interest is the mechanism by

Allopolyploidization and evolution of species with reduced floral structures in Lepidium L. (Brassicaceae)

PubMed Central

Lee, Ji-Young; Mummenhoff, Klaus; Bowman, John L.

2002-01-01

Understanding the pattern of speciation in a group of plants is critical for understanding its morphological evolution. Lepidium is the genus with the largest variation in floral structure in Brassicaceae, a family in which the floral ground plan is remarkably stable. However, flowers in more than half of Lepidium species have reduced stamen numbers, and most of these also have reduced petals. The species with reduced flowers are geographically biased, distributed mostly in the Americas and Australia/ New Zealand. Previous phylogenetic studies using noncoding regions of chloroplast DNA and rDNA internal transcribed spacer were incongruent in most New World species relationships. These data, combined with the presence of many polyploid Lepidium species, implied a reticulate history of the genus but did not provide enough information to infer the evolutionary pattern of flower structures. To address this question more thoroughly, sequences of the first intron of a single copy nuclear gene, PISTILLATA, were determined from 43 species. Phylogenetic analysis of the PI intron suggests that many species in the New World have originated from allopolyploidization, and that this is correlated with floral reduction. Interspecific hybrids were generated to understand why allopolyploidization is associated with reduced flowers. The phenotypes of F1 flowers indicate allelic dominance of the absence of lateral stamens, suggesting that propagation of dominant alleles through interspecific hybridization could account for the abundance of the allopolyploid species without lateral stamens. PMID:12481035

Effect of small perturbations on the evolution of polycrystalline structure during plastic deformation

NASA Astrophysics Data System (ADS)

Korznikova, E. A.; Baimova, Yu. A.; Kistanov, A. A.; Dmitriev, S. V.; Korznikov, A. V.

2014-09-01

The method of molecular dynamics has been used to study the influence of initial perturbations on the evolution of grain boundaries during the shear plastic deformation of a two-dimensional polycrystalline material with nanoscale grains. It has been shown that short-term thermalization-induced small perturbations result in noticeable differences in grain boundaries configurations at the deformation of 0.05 and the polycrystal completely loses its initial grain boundary structure at the deformation of 0.4.

Evolution of Linux operating system network

NASA Astrophysics Data System (ADS)

Xiao, Guanping; Zheng, Zheng; Wang, Haoqin

2017-01-01

Linux operating system (LOS) is a sophisticated man-made system and one of the most ubiquitous operating systems. However, there is little research on the structure and functionality evolution of LOS from the prospective of networks. In this paper, we investigate the evolution of the LOS network. 62 major releases of LOS ranging from versions 1.0 to 4.1 are modeled as directed networks in which functions are denoted by nodes and function calls are denoted by edges. It is found that the size of the LOS network grows almost linearly, while clustering coefficient monotonically decays. The degree distributions are almost the same: the out-degree follows an exponential distribution while both in-degree and undirected degree follow power-law distributions. We further explore the functionality evolution of the LOS network. It is observed that the evolution of functional modules is shown as a sequence of seven events (changes) succeeding each other, including continuing, growth, contraction, birth, splitting, death and merging events. By means of a statistical analysis of these events in the top 4 largest components (i.e., arch, drivers, fs and net), it is shown that continuing, growth and contraction events occupy more than 95% events. Our work exemplifies a better understanding and describing of the dynamics of LOS evolution.

Self-assembly of core-shell structure PtO2@Pt nanodots and their formation evolution

NASA Astrophysics Data System (ADS)

Yang, Weijia; Liu, Junjie; Liu, Mingquan; Zhao, Zhicheng; Song, Yapeng; Tang, Xiufeng; Luo, Jianyi; Zeng, Qingguang; He, Xin

2018-05-01

Core-shell structure PtO2@Pt nanodots have been self-assembly by vacuum sputtering and high temperature annealing. First, Pt thin films with a small amount of PtO2 are grown on the sapphire substrates by vacuum sputtering. And then high temperature annealing on the thin films is carried out at 800 °C for 2 min to form Pt nanodots. During the cooling process, the atmosphere is deployed to supplant the nitrogen. Finally, even distributed core-shell structure PtO2@Pt nanodots with a diameter from 100 to 300 nm are achieved. Furthermore, the formation evolution of core-shell structure PtO2@Pt nanodots is also proposed. This work open up a new approach for fabricating core-shell structure nanodots.

Chemical structure influence on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux

NASA Astrophysics Data System (ADS)

Padgett, Mark C.; Tick, Geoffrey R.; Carroll, Kenneth C.; Burke, William R.

2017-03-01

The influence of chemical structure on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux was examined. The variability of measured and UNIFAC modeled NAPL activity coefficients as a function of mole fraction was compared for two NAPL mixtures containing structurally-different contaminants of concern including toluene (TOL) or trichloroethene (TCE) within a hexadecane (HEXDEC) matrix. The results showed that dissolution from the NAPL mixtures transitioned from ideality for mole fractions > 0.05 to nonideality as mole fractions decreased. In particular, the TCE generally exhibited more ideal dissolution behavior except at lower mole fractions, and may indicate greater structural/polarity similarity between the two compounds. Raoult's Law and UNIFAC generally under-predicted the batch experiment results for TOL:HEXDEC mixtures especially for mole fractions ≤ 0.05. The dissolution rate coefficients were similar for both TOL and TCE over all mole fractions tested. Mass flux reduction (MFR) analysis showed that more efficient removal behavior occurred for TOL and TCE with larger mole fractions compared to the lower initial mole fraction mixtures (i.e. < 0.2). However, compared to TOL, TCE generally exhibited more efficient removal behavior over all mole fractions tested and may have been the result of structural and molecular property differences between the compounds. Activity coefficient variability as a function of mole fraction was quantified through regression analysis and incorporated into dissolution modeling analyses for the dynamic flushing experiments. TOL elution concentrations were modeled (predicted) reasonable well using ideal and equilibrium assumptions, but the TCE elution concentrations could not be predicted using the ideal model. Rather, the dissolution modeling demonstrated that TCE elution was better described by the nonideal model whereby NAPL-phase activity coefficient varied as a function of COC mole

Evolution of the Structural-Phase State of a Ti-Al- V-Mo Alloy During Severe Plastic Deformation and SubSequent Annealing

NASA Astrophysics Data System (ADS)

Grabovetskaya, G. P.; Ratochka, I. V.; Mishin, I. P.; Zabudchenko, O. V.; Lykova, O. N.

2016-05-01

The effect of the initial phase composition of a Ti-Al-V-Mo alloy (VT16 according to Russian classification) on the evolution of its structural-phase state during the formation of ultrafine-grained structure and subsequent annealing is investigated by methods of optical and transmission electron microscopy and x-ray diffraction analysis. The structure is produced by cyclic pressing with a change of the deformation axis in each cycle combined with a gradual decrease of the pressing temperature from 1073 to 723 K. As this takes place, α″ → α + β and β → α phase transitions are found to develop in the test alloy. The phase state of the ultrafinegrained material thus produced depends for the most part on its elemental composition and severe plastic deformation regime. Annealing below the recrystallization temperature is shown to give rise to a β→α phase transition and alloying element redistribution. The foregoing processes allow for retaining a high level of the strength properties of the alloy.

An Integrated Geophysical and Tectonic Study of the Structure and Evolution of the Crust in the Snake River Plain Region, Pacific Northwest

NASA Astrophysics Data System (ADS)

Keller, G. R.; Khatiwada, M.

2016-12-01

The Snake River Plain region in the Pacific Northwest of North America has been the target of a number of recent studies that have revealed further complexities in its structure and tectonic evolution. Based on surface morphology and Late Cenozoic volcanic activity, the Snake River Plain consists of an eastern and western arm (ESRP and WSRP) that are similar in many respects but also quite different in other respects. Thus, its origin, evolution, structural complexities, the role of extension and magmatism in its formation, and the tectonic drivers are still subjects of debate. Numerous seismic studies have specifically focused on the structure of the ESRP and Yellowstone area. However, crustal-scale studies of the WSRP are limited. We added new gravity data to the existing coverage in the WSRP region and undertook a regional, integrated analysis approach that included magnetic, seismic reflection and refraction profiling, receiver function results, geological and geospatial data, and interpreted well logs. Our integrated geophysical modeling focused on the structure of the WSRP. We generated two crustal models across it at locations where the most existing geophysical and geological constraints were available. We observed both differences and similarities in the structure of the WSRP and ESRP. Although, the shallow crustal structures are different, a mid-crustal mafic intrusion is a major source of the high gravity anomaly values. Within the context of recent studies in the surrounding region, the intersection of the two arms of the Snake River Plain emerges as a major element of a complex tectonic intersection that includes the High Lava Plains of eastern Oregon, the Northern Nevada Rift, a southwestern extension of the ESRP into northern Nevada, as well as, faulting and volcanism extending northwestward to connect with the Columbia River Basalts region.

Structure and Evolution of Kuiper Belt Objects and Dwarf Planets

NASA Astrophysics Data System (ADS)

McKinnon, W. B.; Prialnik, D.; Stern, S. A.; Coradini, A.

Kuiper belt objects (KBOs) accreted from a mélange of volatile ices, carbonaceous matter, and rock of mixed interstellar and solar nebular provenance. The transneptunian region, where this accretion took place, was likely more radially compact than today. This and the influence of gas drag during the solar nebula epoch argue for more rapid KBO accretion than usually considered. Early evolution of KBOs was largely the result of heating due to radioactive decay, the most important potential source being 26Al, whereas long-term evolution of large bodies is controlled by the decay of U, Th, and 40K. Several studies are reviewed dealing with the evolution of KBO models, calculated by means of one-dimensional numerical codes that solve the heat and mass balance equations. It is shown that, depending on parameters (principally rock content and porous conductivity), KBO interiors may have reached relatively high temperatures. The models suggest that KBOs likely lost ices of very volatile species during early evolution, whereas ices of less-volatile species should be retained in cold, less-altered subsurface layers. Initially amorphous ice may have crystallized in KBO interiors, releasing volatiles trapped in the amorphous ice, and some objects may have lost part of these volatiles as well. Generally, the outer layers are far less affected by internal evolution than the inner part, which in the absence of other effects (such as collisions) predicts a stratified composition and altered porosity distribution. Kuiper belt objects are thus unlikely to be "the most pristine objects in the solar system," but they do contain key information as to how the early solar system accreted and dynamically evolved. For large (dwarf planet) KBOs, long-term radiogenic heating alone may lead to differentiated structures -- rock cores, ice mantles, volatile-ice-rich "crusts," and even oceans. Persistence of oceans and (potential) volcanism to the present day depends strongly on body size and

Evolution and structure of sustainability science.

PubMed

Bettencourt, Luís M A; Kaur, Jasleen

2011-12-06

The concepts of sustainable development have experienced extraordinary success since their advent in the 1980s. They are now an integral part of the agenda of governments and corporations, and their goals have become central to the mission of research laboratories and universities worldwide. However, it remains unclear how far the field has progressed as a scientific discipline, especially given its ambitious agenda of integrating theory, applied science, and policy, making it relevant for development globally and generating a new interdisciplinary synthesis across fields. To address these questions, we assembled a corpus of scholarly publications in the field and analyzed its temporal evolution, geographic distribution, disciplinary composition, and collaboration structure. We show that sustainability science has been growing explosively since the late 1980s when foundational publications in the field increased its pull on new authors and intensified their interactions. The field has an unusual geographic footprint combining contributions and connecting through collaboration cities and nations at very different levels of development. Its decomposition into traditional disciplines reveals its emphasis on the management of human, social, and ecological systems seen primarily from an engineering and policy perspective. Finally, we show that the integration of these perspectives has created a new field only in recent years as judged by the emergence of a giant component of scientific collaboration. These developments demonstrate the existence of a growing scientific field of sustainability science as an unusual, inclusive and ubiquitous scientific practice and bode well for its continued impact and longevity.

The supramolecular structure of bone: X-ray scattering analysis and lateral structure modeling

PubMed Central

Zhou, Hong-Wen; Burger, Christian; Wang, Hao; Hsiao, Benjamin S.; Chu, Benjamin; Graham, Lila

2016-01-01

The evolution of vertebrates required a key development in supramolecular evolution: internally mineralized collagen fibrils. In bone, collagen molecules and mineral crystals form a nanocomposite material comparable to cast iron in tensile strength, but several times lighter and more flexible. Current understanding of the internal nanoscale structure of collagen fibrils, derived from studies of rat tail tendon (RTT), does not explain how nucleation and growth of mineral crystals can occur inside a collagen fibril. Experimental obstacles encountered in studying bone have prevented a solution to this problem for several decades. This report presents a lateral packing model for collagen molecules in bone fibrils, based on the unprecedented observation of multiple resolved equatorial reflections for bone tissue using synchrotron small-angle X-ray scattering (SAXS; ∼1 nm resolution). The deduced structure for pre-mineralized bone fibrils includes features that are not present in RTT: spatially discrete microfibrils. The data are consistent with bone microfibrils similar to pentagonal Smith microfibrils, but are not consistent with the (nondiscrete) quasi-hexagonal microfibrils reported for RTT. These results indicate that collagen fibrils in bone and tendon differ in their internal structure in a manner that allows bone fibrils, but not tendon fibrils, to internally mineralize. In addition, the unique pattern of collagen cross-link types and quantities in mineralized tissues can be can be accounted for, in structural/functional terms, based on a discrete microfibril model. PMID:27599731

Differential evolution-simulated annealing for multiple sequence alignment

NASA Astrophysics Data System (ADS)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

Making Plants Break a Sweat: the Structure, Function, and Evolution of Plant Salt Glands

PubMed Central

Dassanayake, Maheshi; Larkin, John C.

2017-01-01

Salt stress is a complex trait that poses a grand challenge in developing new crops better adapted to saline environments. Some plants, called recretohalophytes, that have naturally evolved to secrete excess salts through salt glands, offer an underexplored genetic resource for examining how plant development, anatomy, and physiology integrate to prevent excess salt from building up to toxic levels in plant tissue. In this review we examine the structure and evolution of salt glands, salt gland-specific gene expression, and the possibility that all salt glands have originated via evolutionary modifications of trichomes. Salt secretion via salt glands is found in more than 50 species in 14 angiosperm families distributed in caryophyllales, asterids, rosids, and grasses. The salt glands of these distantly related clades can be grouped into four structural classes. Although salt glands appear to have originated independently at least 12 times, they share convergently evolved features that facilitate salt compartmentalization and excretion. We review the structural diversity and evolution of salt glands, major transporters and proteins associated with salt transport and secretion in halophytes, salt gland relevant gene expression regulation, and the prospect for using new genomic and transcriptomic tools in combination with information from model organisms to better understand how salt glands contribute to salt tolerance. Finally, we consider the prospects for using this knowledge to engineer salt glands to increase salt tolerance in model species, and ultimately in crops. PMID:28400779

Mathematical methods to analysis of topology, functional variability and evolution of metabolic systems based on different decomposition concepts.

PubMed

Mrabet, Yassine; Semmar, Nabil

2010-05-01

Complexity of metabolic systems can be undertaken at different scales (metabolites, metabolic pathways, metabolic network map, biological population) and under different aspects (structural, functional, evolutive). To analyse such a complexity, metabolic systems need to be decomposed into different components according to different concepts. Four concepts are presented here consisting in considering metabolic systems as sets of metabolites, chemical reactions, metabolic pathways or successive processes. From a metabolomic dataset, such decompositions are performed using different mathematical methods including correlation, stiochiometric, ordination, classification, combinatorial and kinetic analyses. Correlation analysis detects and quantifies affinities/oppositions between metabolites. Stoichiometric analysis aims to identify the organisation of a metabolic network into different metabolic pathways on the hand, and to quantify/optimize the metabolic flux distribution through the different chemical reactions of the system. Ordination and classification analyses help to identify different metabolic trends and their associated metabolites in order to highlight chemical polymorphism representing different variability poles of the metabolic system. Then, metabolic processes/correlations responsible for such a polymorphism can be extracted in silico by combining metabolic profiles representative of different metabolic trends according to a weighting bootstrap approach. Finally evolution of metabolic processes in time can be analysed by different kinetic/dynamic modelling approaches.

Evolution of surface structure in laser-preheated, perturbed materials

DOE PAGES

Di Stefano, Carlos; Merritt, Elizabeth Catherine; Doss, Forrest William; ...

2017-02-03

Here, we report an experimental and computational study investigating the effects of laser preheat on the hydrodynamic behavior of a material layer. In particular, we find that perturbation of the surface of the layer results in a complex interaction, in which the bulk of the layer develops density, pressure, and temperature structure and in which the surface experiences instability-like behavior, including mode coupling. A uniform one-temperature preheat model is used to reproduce the experimentally observed behavior, and we find that this model can be used to capture the evolution of the layer, while also providing evidence of complexities in themore » preheat behavior. Lastly, this result has important consequences for inertially confined fusion plasmas, which can be difficult to diagnose in detail, as well as for laser hydrodynamics experiments, which generally depend on assumptions about initial conditions in order to interpret their results.« less

Constraints on Composition, Structure and Evolution of the Lithosphere

NASA Astrophysics Data System (ADS)

Bianchini, Gianluca; Bonadiman, Costanza; Aulbach, Sonja; Schutt, Derek

2015-05-01

The idea for this special issue was triggered at the Goldschmidt Conference held in Florence (August 25-30, 2013), where we convened a session titled "Integrated Geophysical-Geochemical Constraints on Composition and Structure of the Lithosphere". The invitation to contribute was extended not only to the session participants but also to a wider spectrum of colleagues working on related topics. Consequently, a diverse group of Earth scientists encompassing geophysicists, geodynamicists, geochemists and petrologists contributed to this Volume, providing a comprehensive overview on the nature and evolution of lithospheric mantle by combining studies that exploit different types of data and interpretative approaches. The integration of geochemical and geodynamic datasets and their interpretation represents the state of the art in our knowledge of the lithosphere and beyond, and could serve as a blueprint for future strategies in concept and methodology to advance our knowledge of this and other terrestrial reservoirs.

Insights into the Ecology and Evolution of Polyploid Plants through Network Analysis.

PubMed

Gallagher, Joseph P; Grover, Corrinne E; Hu, Guanjing; Wendel, Jonathan F

2016-06-01

Polyploidy is a widespread phenomenon throughout eukaryotes, with important ecological and evolutionary consequences. Although genes operate as components of complex pathways and networks, polyploid changes in genes and gene expression have typically been evaluated as either individual genes or as a part of broad-scale analyses. Network analysis has been fruitful in associating genomic and other 'omic'-based changes with phenotype for many systems. In polyploid species, network analysis has the potential not only to facilitate a better understanding of the complex 'omic' underpinnings of phenotypic and ecological traits common to polyploidy, but also to provide novel insight into the interaction among duplicated genes and genomes. This adds perspective to the global patterns of expression (and other 'omic') change that accompany polyploidy and to the patterns of recruitment and/or loss of genes following polyploidization. While network analysis in polyploid species faces challenges common to other analyses of duplicated genomes, present technologies combined with thoughtful experimental design provide a powerful system to explore polyploid evolution. Here, we demonstrate the utility and potential of network analysis to questions pertaining to polyploidy with an example involving evolution of the transgressively superior cotton fibres found in polyploid Gossypium hirsutum. By combining network analysis with prior knowledge, we provide further insights into the role of profilins in fibre domestication and exemplify the potential for network analysis in polyploid species. © 2016 John Wiley & Sons Ltd.

Coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures

NASA Technical Reports Server (NTRS)

Mcknight, R. L.; Chen, P. C.; Dame, L. T.; Huang, H.

1992-01-01

Accomplishments are described for the first year effort of a 5-year program to develop a methodology for coupled structural/thermal/electromagnetic analysis/tailoring of graded composite structures. These accomplishments include: (1) the results of the selective literature survey; (2) 8-, 16-, and 20-noded isoparametric plate and shell elements; (3) large deformation structural analysis; (4) eigenanalysis; (5) anisotropic heat transfer analysis; and (6) anisotropic electromagnetic analysis.

Analysis of the Science and Technology Preservice Teachers' Opinions on Teaching Evolution and Theory of Evolution

ERIC Educational Resources Information Center

Töman, Ufuk; Karatas, Faik Özgür; Çimer, Sabiha Odabasi

2014-01-01

In this study, we investigate of science and technology teachers' opinions about the theory of evolution and the evolution teaching. The aim of this study, we investigate of science and technology teachers' opinions about the theory of evolution and the evolution teaching. This study is a descriptive study. Open-ended questions were used to…

Context-aided analysis of community evolution in networks

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

Pallotta, Giuliana; Konjevod, Goran; Cadena, Jose

Here, we are interested in detecting and analyzing global changes in dynamic networks (networks that evolve with time). More precisely, we consider changes in the activity distribution within the network, in terms of density (ie, edge existence) and intensity (ie, edge weight). Detecting change in local properties, as well as individual measurements or metrics, has been well studied and often reduces to traditional statistical process control. In contrast, detecting change in larger scale structure of the network is more challenging and not as well understood. We address this problem by proposing a framework for detecting change in network structure basedmore » on separate pieces: a probabilistic model for partitioning nodes by their behavior, a label-unswitching heuristic, and an approach to change detection for sequences of complex objects. We examine the performance of one instantiation of such a framework using mostly previously available pieces. The dataset we use for these investigations is the publicly available New York City Taxi and Limousine Commission dataset covering all taxi trips in New York City since 2009. Using it, we investigate the evolution of an ensemble of networks under different spatiotemporal resolutions. We identify the community structure by fitting a weighted stochastic block model. In conclusion, we offer insights on different node ranking and clustering methods, their ability to capture the rhythm of life in the Big Apple, and their potential usefulness in highlighting changes in the underlying network structure.« less

Context-aided analysis of community evolution in networks

DOE PAGES

Pallotta, Giuliana; Konjevod, Goran; Cadena, Jose; ...

2017-09-15

Here, we are interested in detecting and analyzing global changes in dynamic networks (networks that evolve with time). More precisely, we consider changes in the activity distribution within the network, in terms of density (ie, edge existence) and intensity (ie, edge weight). Detecting change in local properties, as well as individual measurements or metrics, has been well studied and often reduces to traditional statistical process control. In contrast, detecting change in larger scale structure of the network is more challenging and not as well understood. We address this problem by proposing a framework for detecting change in network structure basedmore » on separate pieces: a probabilistic model for partitioning nodes by their behavior, a label-unswitching heuristic, and an approach to change detection for sequences of complex objects. We examine the performance of one instantiation of such a framework using mostly previously available pieces. The dataset we use for these investigations is the publicly available New York City Taxi and Limousine Commission dataset covering all taxi trips in New York City since 2009. Using it, we investigate the evolution of an ensemble of networks under different spatiotemporal resolutions. We identify the community structure by fitting a weighted stochastic block model. In conclusion, we offer insights on different node ranking and clustering methods, their ability to capture the rhythm of life in the Big Apple, and their potential usefulness in highlighting changes in the underlying network structure.« less

Corrosion detection and evolution monitoring in reinforced concrete structures by the use of fiber Bragg grating sensor

NASA Astrophysics Data System (ADS)

Ali-Alvarez, S.; Ferdinand, P.; Magne, S.; Nogueira, R. P.

2013-04-01

Corrosion of reinforced bar (rebar) in concrete structures represents a major issue in civil engineering works, being its detection and evolution a challenge for the applied research. In this work, we present a new methodology to corrosion detection in reinforced concrete structures, by combining Fiber Bragg Grating (FBG) sensors with the electrochemical and physical properties of rebar in a simplified assembly. Tests in electrolytic solutions and concrete were performed for pitting and general corrosion. The proposed Structural Health Monitoring (SHM) methodology constitutes a direct corrosion measurement potentially useful to implement or improve Condition-Based Maintenance (CBM) program for civil engineering concrete structures.

Helicity evolution at small-x

DOE PAGES

Kovchegov, Yuri V.; Pitonyak, Daniel; Sievert, Matthew D.

2016-01-13

We construct small-x evolution equations which can be used to calculate quark and anti-quark helicity TMDs and PDFs, along with the g1 structure function. These evolution equations resum powers of α s ln 2(1/x) in the polarization-dependent evolution along with the powers of α s ln(1/x) in the unpolarized evolution which includes saturation efects. The equations are written in an operator form in terms of polarization-dependent Wilson line-like operators. While the equations do not close in general, they become closed and self-contained systems of non-linear equations in the large-N c and large-N c & N f limits. As a cross-check,more » in the ladder approximation, our equations map onto the same ladder limit of the infrared evolution equations for g 1 structure function derived previously by Bartels, Ermolaev and Ryskin.« less

The diverse crustal structure and magmatic evolution of the Manihiki Plateau, central Pacific

NASA Astrophysics Data System (ADS)

Hochmuth, K.; Gohl, K.; Uenzelmann-Neben, G.; Werner, R.

2014-07-01

The Manihiki Plateau is a Large Igneous Province (LIP) in the central Pacific. It was emplaced as part of the "Super-LIP" Ontong Java Nui and experienced fragmentation into three sub-plateaus, possibly during the break-up of Ontong Java Nui. The Manihiki Plateau is presumably the centerpiece of this "Super-LIP" and its investigation can therefore decipher the break-up mechanisms as well as the evolution of the plateau after its initial emplacement. By analyzing two seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the High Plateau and the Western Plateaus, we give new insights into their crustal structure and magmatic evolution. The High Plateau shows a crustal structure of 20 km thickness and a seismic P wave velocity distribution, which is comparable to other LIPs. The High Plateau experienced a strong secondary volcanism, which can be seen in relicts of seamount chain volcanism. The Western Plateaus on the other hand show no extensive secondary volcanism and are mainly structured by fault systems and sedimentary basins. A constant decrease in Moho depth (9-17 km) is a further indicator of crustal stretching on the Western Plateaus. Those findings lead to the conclusion, that the two sub-plateaus of the Manihiki Plateau experienced a different magmatic and tectonic history. Whereas the High Plateau experienced a secondary volcanism, the Western Plateaus underwent crustal stretching during and after the break-up of Ontong Java Nui. This indicates, that the sub-plateaus of the Manihiki Plateau play an individual part in the break-up history of Ontong Java Nui.

The structural evolution of magnesium acetate complex in aerosols by FTIR-ATR spectra

NASA Astrophysics Data System (ADS)

Pang, Shu-Feng; Wu, Chang-Qin; Zhang, Qing-Nuan; Zhang, Yun-Hong

2015-05-01

The structural evolution of magnesium acetate complex in aerosols with the relative humidity (RH) has been studied by ATR-FTIR technique. When the RH is higher than 66%, the ν4 band lies at 929 cm-1 meaning the free CH3COO- ions in Mg(CH3COO)2 droplets. At the 66% RH, ν4 band positioned at 939 cm-1, accompanying the ν8 band shift to 1554 cm-1, which indicats that the free CH3COO- ions are bounded to Mg2+ ions to form [Mg(H2O)5(CH3COO)]+ species. At the 57.7% RH, the ν8-COO band shifts to 1556 cm-1 accompanying the ν3 band at 1421 cm-1 and the appearance of shoulder at 1452 cm-1, which suggests the formation of chain-structure connected by the bridging bidentate of Mg2(CH3COO)4(H2O)2. In the region of 57.7-18.7% RH, the shoulder at 1452 cm-1 increases with the decrease in RH, showing the increase of Mg2(CH3COO)4(H2O)2. From the water-content, the water-transfer from and to the surface of the aerosols became limited, showing the aerosols enter the gel state. Below 18.7%RH, water-loss becomes rapid and the ν8 band performs blue-shift. At 3.8%RH, the ν8 band positioned at 1581 cm-1, showing the anhydrous Mg(CH3COO)2 solid, which can be reflected by the ν4 band at 947 cm-1. During the humidification process, the reverse structural evolution can be found.

Temporal evolution of ion spectral structures during a geomagnetic storm: Observations and modeling

NASA Astrophysics Data System (ADS)

Ferradas, C.; Zhang, J.; Spence, H. E.; Kistler, L. M.; Larsen, B.; Reeves, G. D.; Skoug, R. M.; Funsten, H. O.

2016-12-01

During the last decades several missions have recorded the presence of dynamic spectral features of energetic ions in the inner magnetosphere. We present a case study of the temporal evolution of H+, He+, and O+ spectral structures throughout the geomagnetic storm of 2 October 2013. We use data from the Helium, Oxygen, Proton, and Electron (HOPE) mass spectrometer onboard Van Allen Probe A to analyze the spectral structures in the energy range of 1- 50 keV. We find that the characteristics of the ion structures follow a cyclic pattern, the observed features changing dramatically as the storm starts and then returning to its initial pre-storm state. Quiet, pre-storm times are characterized by multiple and often complex flux structures at narrow energy bands. During the storm main phase, the observed features become simple, with no nose structures or only one nose structure present in the energy-time spectrograms. As the inner magnetosphere recovers from the storm, more complex structures appear once again. Additionally, the heavy ion spectral features are generally more complex than the H+ features, with multiple noses being observed more often in the heavy ion spectra. We use a model of ion drift and losses due to charge exchange to understand the formation of the spectral features and their species dependence.

Evolvability of flower geometry: Convergence in pollinator-driven morphological evolution of flowers.

PubMed

Woźniak, Natalia Joanna; Sicard, Adrien

2018-07-01

Flowers represent a key innovation during plant evolution. Driven by reproductive optimization, evolution of flower morphology has been central in boosting species diversification. In most cases, this has happened through specialized interactions with animal pollinators and subsequent reduction of gene flow between specialized morphs. While radiation has led to an enormous variability in flower forms and sizes, recurrent evolutionary patterns can be observed. Here, we discuss the targets of selection involved in major trends of pollinator-driven flower evolution. We review recent findings on their adaptive values, developmental grounds and genetic bases, in an attempt to better understand the repeated nature of pollinator-driven flower evolution. This analysis highlights how structural innovation can provide flexibility in phenotypic evolution, adaptation and speciation. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Taxonomy of Blue Amorphous Galaxies. II. Structure and Evolution

NASA Astrophysics Data System (ADS)

Marlowe, Amanda T.; Meurer, Gerhardt R.; Heckman, Timothy M.

1999-09-01

Dwarf galaxies play an important role in our understanding of galaxy formation and evolution, and starbursts are believed to affect the structure and evolution of dwarf galaxies strongly. We have therefore embarked on a systematic study of 12 of the nearest dwarf galaxies thought to be undergoing bursts of star formation. These were selected primarily by their morphological type (blue ``amorphous'' galaxies). We show that these blue amorphous galaxies are not physically distinguishable from dwarfs selected as starbursting by other methods, such as blue compact dwarfs (BCDs) and H II galaxies. All these classes exhibit surface brightness profiles that are exponential in the outer regions (r>~1.5re) but often have a predominantly central blue excess, suggesting a young burst in an older, redder galaxy. Typically, the starbursting ``cores'' are young (~107-108 yr) events compared to the older (~109-1010 yr) underlying galaxy (the ``envelope''). The ratio of the core to envelope in blue light ranges from essentially zero to about 2. These starbursts are therefore modest events involving only a few percent of the stellar mass. The envelopes have surface brightnesses that are much higher than typical dwarf irregular (dI) galaxies, so it is unlikely that there is a straightforward evolutionary relation between typical dIs and dwarf starburst galaxies. Instead we suggest that amorphous galaxies may repeatedly cycle through starburst and quiescent phases, corresponding to the galaxies with strong and weak/absent cores, respectively. Once amorphous galaxies use up the available gas (either through star formation or galactic winds) so that star formation is shut off, the faded remnants would strongly resemble dwarf elliptical galaxies. However, in the current cosmological epoch, this is evidently a slow process that is the aftermath of a series of many weak, recurring bursts. Present-day dE's must have experienced more rapid and intense evolution than this in the distant past.

The Molecular Clock of Neutral Evolution Can Be Accelerated or Slowed by Asymmetric Spatial Structure

PubMed Central

Allen, Benjamin; Sample, Christine; Dementieva, Yulia; Medeiros, Ruben C.; Paoletti, Christopher; Nowak, Martin A.

2015-01-01

Over time, a population acquires neutral genetic substitutions as a consequence of random drift. A famous result in population genetics asserts that the rate, K, at which these substitutions accumulate in the population coincides with the mutation rate, u, at which they arise in individuals: K = u. This identity enables genetic sequence data to be used as a “molecular clock” to estimate the timing of evolutionary events. While the molecular clock is known to be perturbed by selection, it is thought that K = u holds very generally for neutral evolution. Here we show that asymmetric spatial population structure can alter the molecular clock rate for neutral mutations, leading to either Ku. Our results apply to a general class of haploid, asexually reproducing, spatially structured populations. Deviations from K = u occur because mutations arise unequally at different sites and have different probabilities of fixation depending on where they arise. If birth rates are uniform across sites, then K ≤ u. In general, K can take any value between 0 and Nu. Our model can be applied to a variety of population structures. In one example, we investigate the accumulation of genetic mutations in the small intestine. In another application, we analyze over 900 Twitter networks to study the effect of network topology on the fixation of neutral innovations in social evolution. PMID:25719560