New sensitive micro-measurements of dynamic surface tension and diffusion coefficients: Validated and tested for the adsorption of 1-Octanol at a microscopic air-water interface and its dissolution into water.

PubMed

Kinoshita, Koji; Parra, Elisa; Needham, David

2017-02-15

Currently available dynamic surface tension (DST) measurement methods, such as Wilhelmy plate, droplet- or bubble-based methods, still have various experimental limitations such as the large size of the interface, convection in the solution, or a certain "dead time" at initial measurement. These limitations create inconsistencies for the kinetic analysis of surfactant adsorption/desorption, especially significant for ionic surfactants. Here, the "micropipette interfacial area-expansion method" was introduced and validated as a new DST measurement having a high enough sensitivity to detect diffusion controlled molecular adsorption at the air-water interfaces. To validate the new technique, the diffusion coefficient of 1-Octanol in water was investigated with existing models: the Ward Tordai model for the long time adsorption regime (1-100s), and the Langmuir and Frumkin adsorption isotherm models for surface excess concentration. We found that the measured diffusion coefficient of 1-Octanol, 7.2±0.8×10 -6 cm 2 /s, showed excellent agreement with the result from an alternative method, "single microdroplet catching method", to measure the diffusion coefficient from diffusion-controlled microdroplet dissolution, 7.3±0.1×10 -6 cm 2 /s. These new techniques for determining adsorption and diffusion coefficients can apply for a range of surface active molecules, especially the less-characterized ionic surfactants, and biological compounds such as lipids, peptides, and proteins. Copyright © 2016 Elsevier Inc. All rights reserved.

Applicability of contact angle techniques used in the analysis of contact lenses, part 1: comparative methodologies.

PubMed

Campbell, Darren; Carnell, Sarah Maria; Eden, Russell John

2013-05-01

Contact angle, as a representative measure of surface wettability, is often employed to interpret contact lens surface properties. The literature is often contradictory and can lead to confusion. This literature review is part of a series regarding the analysis of hydrogel contact lenses using contact angle techniques. Here we present an overview of contact angle terminology, methodology, and analysis. Having discussed this background material, subsequent parts of the series will discuss the analysis of contact lens contact angles and evaluate differences in published laboratory results. The concepts of contact angle, wettability and wetting are presented as an introduction. Contact angle hysteresis is outlined and highlights the advantages in using dynamic analytical techniques over static methods. The surface free energy of a material illustrates how contact angle analysis is capable of providing supplementary surface characterization. Although single values are able to distinguish individual material differences, surface free energy and dynamic methods provide an improved understanding of material behavior. The frequently used sessile drop, captive bubble, and Wilhelmy plate techniques are discussed. Their use as both dynamic and static methods, along with the advantages and disadvantages of each technique, is explained. No single contact angle technique fully characterizes the wettability of a material surface, and the application of complimenting methods allows increased characterization. At present, there is not an ISO standard method designed for soft materials. It is important that each contact angle technique has a standard protocol, as small protocol differences between laboratories often contribute to a variety of published data that are not easily comparable.

Developing a calibrated CONUS-wide watershed-scale simulation platform for quantifying the influence of different sources of uncertainty on streamflow forecast skill

NASA Astrophysics Data System (ADS)

Newman, A. J.; Sampson, K. M.; Wood, A. W.; Hopson, T. M.; Brekke, L. D.; Arnold, J.; Raff, D. A.; Clark, M. P.

2013-12-01

Skill in model-based hydrologic forecasting depends on the ability to estimate a watershed's initial moisture and energy conditions, to forecast future weather and climate inputs, and on the quality of the hydrologic model's representation of watershed processes. The impact of these factors on prediction skill varies regionally, seasonally, and by model. We are investigating these influences using a watershed simulation platform that spans the continental US (CONUS), encompassing a broad range of hydroclimatic variation, and that uses the current simulation models of National Weather Service streamflow forecasting operations. The first phase of this effort centered on the implementation and calibration of the SNOW-17 and Sacramento soil moisture accounting (SAC-SMA) based hydrologic modeling system for a range of watersheds. The base configuration includes 630 basins in the United States Geological Survey's Hydro-Climatic Data Network 2009 (HCDN-2009, Lins 2012) conterminous U.S. basin subset. Retrospective model forcings were derived from Daymet (http://daymet.ornl.gov/), and where available, a priori parameter estimates were based on or compared with the operational NWS model parameters. Model calibration was accomplished by several objective, automated strategies, including the shuffled complex evolution (SCE) optimization approach developed within the NWS in the early 1990s (Duan et al. 1993). This presentation describes outcomes from this effort, including insights about measuring simulation skill, and on relationships between simulation skill and model parameters, basin characteristics (climate, topography, vegetation, soils), and the quality of forcing inputs. References: %Z Thornton, P.; Thornton, M.; Mayer, B.; Wilhelmi, N.; Wei, Y.; Devarakonda, R; Cook, R. Daymet: Daily Surface Weather on a 1 km Grid for North America. 1980-2008; Oak Ridge National Laboratory Distributed Active Archive Center: Oak Ridge, TN, USA, 2012; Volume 10.

Synthesis of biocompatible hydrophobic silica-gelatin nano-hybrid by sol-gel process.

PubMed

Smitha, S; Shajesh, P; Mukundan, P; Nair, T D R; Warrier, K G K

2007-03-15

Silica-biopolymer hybrid has been synthesised using colloidal silica as the precursor for silica and gelatin as the biopolymer counterpart. The surface modification of the hybrid material has been done with methyltrimethoxysilane leading to the formation of biocompatible hydrophobic silica-gelatin hybrid. Here we are reporting hydrophobic silica-gelatin hybrid and coating precursor for the first time. The hybrid gel has been evaluated for chemical modification, thermal degradation, hydrophobicity, particle size, transparency under the UV-visible region and morphology. FTIR spectroscopy has been used to verify the presence of CH(3) groups which introduce hydrophobicity to the SiO2-MTMS-gelatin hybrids. The hydrophobic property has also been tailored by varying the concentration of methyltrimethoxysilane. Contact angle by Wilhelmy plate method of transparent hydrophobic silica-gelatin coatings has been found to be as high as approximately 95 degrees . Oxidation of the organic group which induces the hydrophobic character occurs at 530 degrees C which indicates that the surface hydrophobicity is retained up to that temperature. Optical transmittance of SiO2-MTMS-gelatin hybrid coatings on glass substrates has been found to be close to 100% which will enable the hybrid for possible optical applications and also for preparation of transparent biocompatible hydrophobic coatings on biological substrates such as leather.

Optoelectronic properties and interfacial durability of CNT and ITO on boro-silicate glass and PET substrates with nano- and heterostructural aspects

NASA Astrophysics Data System (ADS)

Park, Joung-Man; Wang, Zuo-Jia; Kwon, Dong-Jun; DeVries, Lawrence

2011-02-01

Nano- and hetero-structures of carbon nanotube (CNT) and indium tin oxide (ITO) can control significantly piezoelectric and optoelectronic properties in Microelectromechanical Systems (MEMS) as sensing and actuator under cyclic loading. Optimized preparing conditions were obtained for multi-functional purpose of the specimen by obtaining the best dispersion and turbidity in the solution. Optical transmittance and electrical properties were investigated for CNT and ITO dipping and spraying coating on boro-silicate glass and polyethylene terephthalate (PET) substrates by electrical resistance measurement under cyclic loading and wettability test. Uniform dip-coating was performed using Wilhelmy plate method due to its simple and convenience. Spraying coating was applied to the specimen additionally. The change in the electrical resistance and optical properties of coated layer were mainly dependent upon the number of dip-coating, the concentration of CNT and ITO solutions, and the surface treatment condition. Electric properties of coating layers were measured using four-point probe method, and surface resistance was calculated using a dual configuration method. Optical transmittance of CNT and ITO coated PET film was also evaluated using UV spectrum. Surface energy and their hydrophilic and hydrophobic properties of CNT and ITO coated substrates were investigated by wettability test via static and dynamic contact angle measurements. As the elapsing time of cyclic loading passed, the stability of surface resistance and thus comparative interfacial adhesion between coated layer and substrates was evaluated to compare the thermodynamic work of adhesion, Wa. As dip-coating number increased, surface resistance of coated CNT decreased, whereas the transmittance decreased step-by-step due to the thicker CNT and ITO networked layer. Nano- and heterostructural effects of CNT and ITO solution on the optical and electrical effects have been studied continuously.

Adsorption energies of poly(ethylene oxide)-based surfactants and nanoparticles on an air-water surface.

PubMed

Zell, Zachary A; Isa, Lucio; Ilg, Patrick; Leal, L Gary; Squires, Todd M

2014-01-14

The self-assembly of polymer-based surfactants and nanoparticles on fluid-fluid interfaces is central to many applications, including dispersion stabilization, creation of novel 2D materials, and surface patterning. Very often these processes involve compressing interfacial monolayers of particles or polymers to obtain a desired material microstructure. At high surface pressures, however, even highly interfacially active objects can desorb from the interface. Methods of directly measuring the energy which keeps the polymer or particles bound to the interface (adsorption/desorption energies) are therefore of high interest for these processes. Moreover, though a geometric description linking adsorption energy and wetting properties through the definition of a contact angle can be established for rigid nano- or microparticles, such a description breaks down for deformable or aggregating objects. Here, we demonstrate a technique to quantify desorption energies directly, by comparing surface pressure-density compression measurements using a Wilhelmy plate and a custom-microfabricated deflection tensiometer. We focus on poly(ethylene oxide)-based polymers and nanoparticles. For PEO-based homo- and copolymers, the adsorption energy of PEO chains scales linearly with molecular weight and can be tuned by changing the subphase composition. Moreover, the desorption surface pressure of PEO-stabilized nanoparticles corresponds to the saturation surface pressure for spontaneously adsorbed monolayers, yielding trapping energies of ∼10(3) k(B)T.

Dynamic surface tension measurement for the screening of biosurfactants produced by Lactobacillus plantarum subsp. plantarum PTCC 1896.

PubMed

Bakhshi, Nafiseh; Soleimanian-Zad, Sabihe; Sheikh-Zeinoddin, Mahmoud

2017-06-01

Currently, screening of microbial biosurfactants (BSs) is based on their equilibrium surface tension values obtained using static surface tension measurement. However, a good surfactant should not only have a low equilibrium surface tension, but its dynamic surface tension (DST) should also decrease rapidly with time. In this study, screening of BSs produced by Lactobacillus plantarum subsp. plantarum PTCC 1896 (probiotic) was performed based on their DST values measured by Wilhelmy plate tensiometry. The relationship between DST and structural and functional properties (anti-adhesive activity) of the BSs was investigated. The results showed that the changes in the yield, productivity and structure of the BSs were growth medium and incubation time dependent (p<0.05). Structurally different BSs produced exhibited identical equilibrium surface tension values. However, differences among the structure/yield of the BSs were observed through the measurement of their DST. The considerable dependence of DST on the concentration and composition of the BS proteins was observed (p<0.05). Moreover, the anti-adhesive activity of the BS was found to be positively correlated with its DST. The results suggest that the DST measurement could serve as an efficient method for the clever screening of BSs producer/production condition, and consequently, for the investigation of probiotic features of bacteria, since the anti-adhesive activity is an important criterion of probiotics. Copyright © 2017 Elsevier Inc. All rights reserved.

Greywater-induced soil hydrophobicity.

PubMed

Maimon, Adi; Gross, Amit; Arye, Gilboa

2017-10-01

Greywater (GW) reuse for irrigation is a common method of reducing domestic consumption of fresh water. Most of the scientific research and legislation efforts have focused on GW's health risks, while less attention has been given to its environmental outcomes. One of the environmental risks of GW irrigation is its possible effect on soil hydraulic properties. This research examined the ability of GW to induce soil hydrophobicity, as well as its degree and persistence. Fresh water (control) and three model GW solutions representing raw, treated and highly treated GW were used to wet fine-grained sand. Every treatment was subjected to five cycles of wetting, incubation (at 5 °C or 30 °C) and drying (60 °C). After each cycle, capillary rise was measured and the contact angle (CA) was calculated. Samples were also tested by the Wilhelmy plate method to retrieve advancing and receding CA and reservoir surface tension. Water repellence of the sand, as implied from the CA, increased with increasing GW concentration and was highest in the sand coated with the model raw GW and incubated at 5 °C. However, none of the treatments resulted in what is considered to be "water-repellent soil". Furthermore, when raw GW-coated sand was immersed in water, its surface tension was significantly reduced relative to the other treatments, implying a release of surface-active compounds from the sand into the water. It was postulated that untreated GW may induce sub-critical water repellence in sand. However, this effect is sensitive to biodegradation and washing processes and is therefore temporary. Copyright © 2017 Elsevier Ltd. All rights reserved.

MECHANICS OF THE LUNG IN THE 20TH CENTURY

PubMed Central

Mitzner, Wayne

2015-01-01

Major advances in respiratory mechanics occurred primarily in the latter half of the 20th century, and this is when much of our current understanding was secured. The earliest and ancient investigations involving respiratory physiology and mechanics were often done in conjunction with other scientific activities and often lacked the ability to make quantitative measurements. This situation changed rapidly in the 20th century, and this relatively recent history of lung mechanics has been greatly influenced by critical technological advances and applications, which have made quantitative experimental testing of ideas possible. From the spirometer of Hutchinson, to the pneumotachograph of Fleisch, to the measurement of esophageal pressure, to the use of the Wilhelmy balance by Clements, to the unassuming strain gauges for measuring pressure and rapid paper and electronic chart recorders, these enabling devices have generated numerous quantitative experimental studies with greatly increased physiologic understanding and validation of mechanistic theories of lung function in health and disease. PMID:23733695

San Isidoro Schools in Padul, Granada, Spain

NASA Astrophysics Data System (ADS)

Lafuente-Bolívar, Francisco Javier; Santiago Zaragoza, Juan Manuel; Fernández-Adarve, Gabriel; María Cruz-Valdivieso, Ana

2017-10-01

The small and unique building of “Las Escuelas de San Isidoro”, erected in Padul at the beginning of the 20th century, is a clear example of the new architectural type of the innovative educational model created in Granada by Father Manjón. That model supposed a radical change for the methods of the Spanish teaching and it was the origin of the current educational system. Andrés Manjón y Manjón (1846-1923), priest, jurist and pedagogue, broke with traditional pedagogy and revolutionized the old-fashion model of education that was in vogue until that moment and universalized and socialized education. That pioneer model promoted an education based on aptitudes and faculties, using games and practice, addressed to all ages and social classes, in conjunction with nature. Outdoor education should be used wherever possible. In a historical context of profound social changes, this typology was the answer to the new educational needs using a “spearing” architectural language based on a constructive system that was both efficient and economic: Spanish Regionalism. It was a new style from the first third of the 20th century that recreated historical forms. It was far from the breakthrough modern movement that, at that time, it took place in central Europe. However, the model of the Manjonian School runs away from historicist models and remains in the simplicity of brick-faced walls or brick-wrapping walls and masonry drawers, with no more decorative concession that window lintels, jambs and sill jut out. The façades highlight made with simple semicircular arches and some glazed ceramics. Wooden rounded slabs supported on walls and simple wooden cover structures. The steel was barely used in metal structural slabs and brick, and even less on the roof. Architects like Francisco Jiménez Arévalo, Juan Montserrat Pons or Fernando Wilhelmi Manzano will be the architects of this type of architecture that has as a mark of identity the massive use of brick in load walls; and as a way to show the facade creating a modest appearance image but of a certain nobility. Wilhelmi projected the Schools of Padul not belonging to the Manjonian type but following a similar way. Conclusion: The knowledge of this architectural typology is basic to protect these simple buildings for educational use, reinforcing the attachment and identity of the citizens of Padul. For them it symbolizes a time and its economic and social context. Through the dissemination in this municipality of the Endof- Grade Projects of the students of the School of Building of the University of Granada related to this building, the following objectives were achieved: revaluing, strengthening and fostering the sense of identity of a village towards one of its most peculiar buildings, The Schools where many of them began their education. Through its study, the process of preserving its values has begun, and with knowledge, are fully assumed contributing to the respect and conservation of this inherited heritage.

[Biophysical models in investigations of exogenous surfactant activities on the surface tension and their theurapeutic effectiveness].

PubMed

Todorov, R; Iordanova, A; Georgiev, G A; Petkova, Kh; Stoimenova, E; Georgieva, R; Khristova, E; Vasiliev, Kh; Lalchev, Z

2007-01-01

Surfactant therapy leads to significant clinical improvement in infants at risk for, or having, respiratory distress syndrome (RDS). The development of exogenous surfactant (ES) as a therapy for neonatal respiratory disorders was a significant advance in neonatal intensive care that has led to a decrease in neonatal mortality. Two broad categories of surfactants are available for exogenous therapy: surfactants derived from animal sources or 'natural' surfactants; and synthetic surfactants. The physical properties of natural and synthetic surfactants have been studied using techniques such as the Wilhelmy surface balance and the bilayer black film (BBF) method. Here we report some data from a comparative study of ES (Exosurf, Survanta, Curosurf and Alveofact) and clinical samples of tracheal aspirate (TA) of newborns with RDS treated with Curosurf. Measured interfacial physico-chemical parameters prove "better" properties in vitro of the surfactant proteins (SP-B and SP-C) containing preparations Curosurf and Alveofact. Their properties are similar, Alveofact showing a higher surface tension lowering capacity under dynamic conditions. A compendious comparison of results for dynamic surface properties of monolayers of TA from newborns treated with Curosurf with data for newborns treated with Exosurf is presented. Both ES yield the desired lowering of the surface tension during cyclic film compression, being larger after treatment with Curosurf. Observations concerning the properties of BFF of ES (dependence on surfactant concentration, adsorption time, film drainage time and BFF formation time) are also reported and discussed.

Hydrophobization potential of organic compounds deriving from olive oil production waste water

NASA Astrophysics Data System (ADS)

Egerer, Sina E.; Bandow, Nicole; Marschner, Bernd; Schaumann, Gabriele E.

2010-05-01

Olive oil production waste water (OPWW) is rich in dissolved organic carbon and nutrients (e.g. potassium). In order to use it as organic fertilizer, small-scale and family run olive oil production farms in Israel and Palestine often discharge it directly onto agricultural land without any previous treatment. One unwanted side effect that can be observed is the development of soil water repellency (SWR) which is probably induced by amphiphilic substances. Previous studies on the composition of OPWW have shown that it contains oil components such as phenols, fats and large-molecular organic compounds (e.g. Gonzalezvila et al., 1995), some of which have been reported to induce water repellency on soil mineral surfaces (e.g. Ma'shum et al., 1988; Leelamanie and Karube, 2007). For prioritization of compounds the individual hydrophobization potential of 16 common OPWW components was systematically evaluated using the sessile drop and the Wilhelmy plate method. Acid-washed sand was taken as model soil mineral material. In a batch experiment OPWW samples from Israel and Palestine were applied to sand and two different soils in order to investigate their hydrophobization potential under different temperature and humidity conditions. To facilitate the identification of the chemicals responsible for inducing SWR, a fractionation procedure was applied to fraction the OPWW samples using solvents of different polarity. The prioritized compounds were analyzed by GC-MS. First results of this identification will be presented as well.

Physical properties and application in the confined geometrical systems

NASA Astrophysics Data System (ADS)

Pak, Hunkyun

Surface viscoelasticity of a vitamin E modified polyethylene glycol (vitamin E-TPGS) monolayers at the air/water interface is deduced by the surface light scattering method and Wilhelmy plate method. It was found that the viscoelasticity of vitamin E-TPGS monolayer is similar to that of PEO monolayer at the surface pressure lower than the collapse pressure of the polyethylene oxide (PEO). However, at higher surface pressure than the collapse pressure of PEO, it deviates from the viscoelastic behavior of PEO. Lateral diffusion constants of a probe lipid (NBD-PC) in a binary monolayer of L-a-dilauroylphosphatidylcholine (DLPC) and poly-(di-isobutylene-alt-maleic acid) (PDIBMA) were determined by the fluorescence recovery after photobleaching (FRAP) method at the air/pH 7 buffer interface as a function of composition. The diffusion constant is found to retard down to less than one hundredth to that at pure DLPC monolayers as the mole fraction of PDIBMA increased. The free area model was used to interpret the probe diffusion retardation. Translational diffusion constants of a probe molecule, 4-octadecylamino-7-nitrobenzo-2-oxa-1,3-diazole (C18-NBD), in thin polyisoprene (PI) and polydimethyl siloxane (PDMS) films, spin coated on methylated and propylyaminated silicon wafers, are studied by the FRAP method as a function of film thickness. Reduction of the diffusion constant is observed as thickness of the films is decreased. Two empirical models, the two-layer model and the continuous layer model are proposed to account for the diffusion constant dependence on the film thickness vs. thickness. It was observed that the diffusion profiles in the films are dependet on the nature of the substrate surfaces. Self-assembled patterns of magnetic particles were made and fixed by applying magnetic field on the particles dispersed at the air/liquid interface, followed by gelling of the liquid subphase. With this method, the large patterns with controllable lattice constant can be made. The fixation of the subphase enhances the stability of the patterns. Further, three-dimensional self-assembled patterns can be made by this method when the fixation process is incorporated.

Precipitation thresholds for triggering floods in Corgo hydrographic basin (Northern Portugal)

NASA Astrophysics Data System (ADS)

Santos, Monica; Fragoso, Marcelo

2016-04-01

The precipitation is a major cause of natural hazards and is therefore related to the flood events (Borga et al., 2011; Gaál et al., 2014; Wilhelmi & Morss, 2013). The severity of a precipitation event and their potential damage is dependent on the total amount of rain but also on the intensity and duration event (Gaál et al., 2014). In this work, it was established thresholds based on critical combinations: amount / duration of flood events with daily rainfall data for Corgo hydrographic basin, in northern Portugal. In Corgo basin are recorded 31 floods events between 1865 and 2011 (Santos et al., 2015; Zêzere et al., 2014). We determined the minimum, maximum and pre-warning thresholds that define the boundaries so that an event may occur. Additionally, we applied these thresholds to different flood events occurred in the past in the study basin. The results show that the ratio between the flood events and precipitation events that occur above the minimum threshold has relatively low probability of a flood happen. These results may be related to the reduced number of floods events (only those that caused damage reported by the media and produced some type of damage). The maximum threshold is not useful for floods forecasting, since the majority of true positives are below this limit. The retrospective analysis of the thresholds defined suggests that the minimum and pre warning thresholds are well adjusted. The application of rainfall thresholds contribute to minimize possible situations of pre-crisis or immediate crisis, reducing the consequences and the resources involved in emergency response of flood events. References Borga, M., Anagnostou, E. N., Blöschl, G., & Creutin, J. D. (2011). Flash flood forecasting, warning and risk management: the HYDRATE project. Environmental Science & Policy, 14(7), 834-844. doi: 10.1016/j.envsci.2011.05.017 Gaál, L., Molnar, P., & Szolgay, J. (2014). Selection of intense rainfall events based on intensity thresholds and lightning data in Switzerland. Hydrol. Earth Syst. Sci., 18(5), 1561-1573. doi: 10.5194/hess-18-1561-2014 Santos, M., Santos, J. A., & Fragoso, M. (2015). Historical damaging flood records for 1871-2011 in Northern Portugal and underlying atmospheric forcings. Journal of Hydrology, 530, 591-603. doi: 10.1016/j.jhydrol.2015.10.011 Wilhelmi, O. V., & Morss, R. E. (2013). Integrated analysis of societal vulnerability in an extreme precipitation event: A Fort Collins case study. Environmental Science & Policy, 26, 49-62. doi: 10.1016/j.envsci.2012.07.005 Zêzere, J. L., Pereira, S., Tavares, A. O., Bateira, C., Trigo, R. M., Quaresma, I., Santos, P. P., Santos, M., & Verde, J. (2014). DISASTER: a GIS database on hydro-geomorphologic disasters in Portugal. Nat. Hazards, 1-30. doi: 10.1007/s11069-013-1018-y

Effect of temperature and concentration on the surface tension of chia seed mucilage

NASA Astrophysics Data System (ADS)

Fu, Yuting; Arye, Gilboa

2017-04-01

The production of mucilage by the seed coat during hydration is a common adaptation of many different plant species. The mucilage may play many ecological roles in adaptation and seed germination in diverse environments, especially in extreme desert conditions. The major compound of the seed mucilage is polysaccharides (e.g. pectins and hemicelluloses), which makes it highly hydrophilic. Consequently, it can hydrate quickly in the presence of water; forming a gel like coating surrounding the seed. However, the seed mucilage also reported to contain small amounts of protein and lipid which may exhibit surface activity at the water-air interface. As a result, decay in the surface tension of water can be occur and consequently a reduction in soil capillary pressure. This in turn may affect the water retention and transport during seed germination. The physical properties of the seeds mucilage have been studied mainly in conjunction with its rheological properties. To the best of our knowledge, its surface activity at the water-air interface has been reported mainly in the realms of food engineering, using a robust method of extraction. The main objective of this study was to quantify the effect of temperature and concentration on the surface tension of seed mucilage. The mucilage in this study was extracted from chia (Salvia hispanica L.) seeds, using distilled water (1:20 w/w) by shaking for 12 h at 4°C. The extracts were freeze dried after centrifuge (5000rpm for 20min). Fresh samples of different concentrations, ranging from 0.5 to 6 mg/ml, were prepared before each surface tension measurements. The equilibrium surface tension was measured by the Wilhelmy plate method using a tensiometer (DCAT 11, Data Physics) with temperature control unit. For a given mucilage concentration, surface tension measurements carried out at 5, 15, 25, 35, 45 °C. The quantitative and thermodynamic analysis of the results will be presented and discussed.

Human exposure to flash floods Relation between flood parameters and human vulnerability during a storm of September 2002 in Southern France

NASA Astrophysics Data System (ADS)

Ruin, Isabelle; Creutin, Jean-Dominique; Anquetin, Sandrine; Lutoff, Céline

2008-10-01

SummaryThe aim of this paper is to investigate the detailed hydrometeorological circumstances that lead to accidental casualties, and to better understand the prominent physical factors of risk. Based on an event that affected the Gard region (Southern France) in September 2002, it is a first attempt to combine analysis of the physical and human response to Mediterranean storms. After details concerning the methodology (for meteorological, hydrological and casualty analysis), the local context and the event, the authors examine two points: the dynamics of the event (flash-flood and riverine-flood response to the storm) together with human exposure on the one hand, and scale as a critical problem affecting flood risk on the other. This investigation stresses the specificity of small catchments, which are more dangerous both in hydrological and human terms. Moreover, this contribution linking social sciences and geophysics constitutes an important step in what [Morss, R.E., Wilhelmi, O.V., Downton, M.W., Gruntfest, E., 2005. Flood risk, uncertainty, and scientific information for decision making. Bull. Am. Meteor. Soc. 86 (11), 1593-1601] call the "End to end to end" process

Endoparasite fauna of five Gadiformes fish species from the coast of Chile: host ecology versus phylogeny.

PubMed

Chávez, R A; González, M T; Oliva, M E; Valdivia, I M

2012-03-01

The aims of the present study were to compare, using multivariate analyses, the degree of similarity of the endoparasite fauna of five fish species belonging to the order Gadiformes: Merluccius gayi, Merluccius australis, Macruronus magellanicus (Gadoidei) and Micromesistius australis and Nezumia pulchella (Macrouroidei), from the southern and central Chilean coast, and to evaluate whether the composition of the endoparasite fauna was determined by phylogenetic or ecological relationships. We employed our database of Merluccius australis, M. magellanicus and Micromesistius australis, which was complemented with published information for M. magellanicus, Merluccius australis, Micromesistius australis, M. gayi and N. pulchella. A higher number of endoparasite species was recorded for Merluccius australis, Micromesistius australis and M. magellanicus, namely Anisakis sp. and Hepatoxylon trichiuri, which is the most prevalent parasite among these hosts. Aporocotyle wilhelmi and Hysterothylacium sp. were detected only in M. gayi, whereas Lepidapedon sp. was found exclusively in N. pulchella. These results suggest that fish ecology rather than host phylogeny was the most important factor for the determination of similarity in parasite composition. This result could be explained by the similar trophic patterns of hosts and by the predominance of generalist larval species among these fish parasite communities.

The Accelerated Late Adsorption of Pulmonary Surfactant

PubMed Central

2011-01-01

Adsorption of pulmonary surfactant to an air−water interface lowers surface tension (γ) at rates that initially decrease progressively, but which then accelerate close to the equilibrium γ. The studies here tested a series of hypotheses concerning mechanisms that might cause the late accelerated drop in γ. Experiments used captive bubbles and a Wilhelmy plate to measure γ during adsorption of vesicles containing constituents from extracted calf surfactant. The faster fall in γ reflects faster adsorption rather than any feature of the equation of state that relates γ to surface concentration (Γ). Adsorption accelerates when γ reaches a critical value rather than after an interval required to reach that γ. The hydrophobic surfactant proteins (SPs) represent key constituents, both for reaching the γ at which the acceleration occurs and for producing the acceleration itself. The γ at which rates of adsorption increase, however, is unaffected by the Γ of protein in the films. In the absence of the proteins, a phosphatidylethanolamine, which, like the SPs, induces fusion of the vesicles with the interfacial film, also causes adsorption to accelerate. Our results suggest that the late acceleration is characteristic of adsorption by fusion of vesicles with the nascent film, which proceeds more favorably when the Γ of the lipids exceeds a critical value. PMID:21417351

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

Guttman, Shani; Sapir, Zvi; Ocko, Benjamin M.

Recent extensive studies reveal that surfactant-stabilized spherical alkane emulsion droplets spontaneously adopt polyhedral shapes upon cooling below a temperature T d while remaining liquid. Further cooling induces the growth of tails and spontaneous droplet splitting. Two mechanisms were offered to account for these intriguing effects. One assigns the effects to the formation of an intradroplet frame of tubules consisting of crystalline rotator phases with cylindrically curved lattice planes. The second assigns the sphere-to-polyhedron transition to the buckling of defects in a crystalline interfacial monolayer, known to form in these systems at some T s > T d. The buckling reducesmore » the extensional energy of the crystalline monolayer’s defects, unavoidably formed when wrapping a spherical droplet by a hexagonally packed interfacial monolayer. The tail growth, shape changes, and droplet splitting were assigned to the decrease and vanishing of surface tension, γ. Here we present temperature-dependent γ(T), optical microscopy measurements, and interfacial entropy determinations for several alkane/surfactant combinations. We demonstrate the advantages and accuracy of the in situ γ(T) measurements made simultaneously with the microscopy measurements on the same droplet. The in situ and coinciding ex situ Wilhelmy plate γ(T) measurements confirm the low interfacial tension, ≲0.1 mN/m, observed at T d. Here, our results provide strong quantitative support validating the crystalline monolayer buckling mechanism.« less

Methods and Systems for Measurement and Estimation of Normalized Contrast in Infrared Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M. (Inventor)

2017-01-01

Methods and systems for converting an image contrast evolution of an object to a temperature contrast evolution and vice versa are disclosed, including methods for assessing an emissivity of the object; calculating an afterglow heat flux evolution; calculating a measurement region of interest temperature change; calculating a reference region of interest temperature change; calculating a reflection temperature change; calculating the image contrast evolution or the temperature contrast evolution; and converting the image contrast evolution to the temperature contrast evolution or vice versa, respectively.

Methods and Systems for Measurement and Estimation of Normalized Contrast in Infrared Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M. (Inventor)

2015-01-01

Methods and systems for converting an image contrast evolution of an object to a temperature contrast evolution and vice versa are disclosed, including methods for assessing an emissivity of the object; calculating an afterglow heat flux evolution; calculating a measurement region of interest temperature change; calculating a reference region of interest temperature change; calculating a reflection temperature change; calculating the image contrast evolution or the temperature contrast evolution; and converting the image contrast evolution to the temperature contrast evolution or vice versa, respectively.

Complex Contact Angles Calculated from Capillary Rise Measurements on Rock Fracture Faces

NASA Astrophysics Data System (ADS)

Perfect, E.; Gates, C. H.; Brabazon, J. W.; Santodonato, L. J.; Dhiman, I.; Bilheux, H.; Bilheux, J. C.; Lokitz, B. S.

2017-12-01

Contact angles for fluids in unconventional reservoir rocks are needed for modeling hydraulic fracturing leakoff and subsequent oil and gas extraction. Contact angle measurements for wetting fluids on rocks are normally performed using polished flat surfaces. However, such prepared surfaces are not representative of natural rock fracture faces, which have been shown to be rough over multiple scales. We applied a variant of the Wilhelmy plate method for determining contact angle from the height of capillary rise on a vertical surface to the wetting of rock fracture faces by water in the presence of air. Cylindrical core samples (5.05 cm long x 2.54 cm diameter) of Mancos shale and 6 other rock types were investigated. Mode I fractures were created within the cores using the Brazilian method. Each fractured core was then separated into halves exposing the fracture faces. One fracture face from each rock type was oriented parallel to a collimated neutron beam in the CG-1D imaging instrument at ORNL's High Flux Isotope Reactor. Neutron radiography was performed using the multi-channel plate detector with a spatial resolution of 50 μm. Images were acquired every 60 s after a water reservoir contacted the base of the fracture face. The images were normalized to the initial dry condition so that the upward movement of water on the fracture face was clearly visible. The height of wetting at equilibrium was measured on the normalized images using ImageJ. Contact angles were also measured on polished flat surfaces using the conventional sessile drop method. Equilibrium capillary rise on the exposed fracture faces was up to 8.5 times greater than that predicted for polished flat surfaces from the sessile drop measurements. These results indicate that rock fracture faces are hyperhydrophilic (i.e., the height of capillary rise is greater than that predicted for a contact angle of zero degrees). The use of complex numbers permitted calculation of imaginary contact angles for such surfaces. This analysis yielded a continuum of contact angles (real above, and imaginary below, zero degrees) that can be used to investigate relationships with properties such surface roughness and porosity. It should be noted these are preliminary, unreplicated results and further research will be needed to verify them and refine the approach.

Novel Random Mutagenesis Method for Directed Evolution.

PubMed

Feng, Hong; Wang, Hai-Yan; Zhao, Hong-Yan

2017-01-01

Directed evolution is a powerful strategy for gene mutagenesis, and has been used for protein engineering both in scientific research and in the biotechnology industry. The routine method for directed evolution was developed by Stemmer in 1994 (Stemmer, Proc Natl Acad Sci USA 91, 10747-10751, 1994; Stemmer, Nature 370, 389-391, 1994). Since then, various methods have been introduced, each of which has advantages and limitations depending upon the targeted genes and procedure. In this chapter, a novel alternative directed evolution method which combines mutagenesis PCR with dITP and fragmentation by endonuclease V is described. The kanamycin resistance gene is used as a reporter gene to verify the novel method for directed evolution. This method for directed evolution has been demonstrated to be efficient, reproducible, and easy to manipulate in practice.

Temperature-Tuned Faceting and Shape Changes in Liquid Alkane Droplets

DOE PAGES

Guttman, Shani; Sapir, Zvi; Ocko, Benjamin M.; ...

2017-01-09

Recent extensive studies reveal that surfactant-stabilized spherical alkane emulsion droplets spontaneously adopt polyhedral shapes upon cooling below a temperature T d while remaining liquid. Further cooling induces the growth of tails and spontaneous droplet splitting. Two mechanisms were offered to account for these intriguing effects. One assigns the effects to the formation of an intradroplet frame of tubules consisting of crystalline rotator phases with cylindrically curved lattice planes. The second assigns the sphere-to-polyhedron transition to the buckling of defects in a crystalline interfacial monolayer, known to form in these systems at some T s > T d. The buckling reducesmore » the extensional energy of the crystalline monolayer’s defects, unavoidably formed when wrapping a spherical droplet by a hexagonally packed interfacial monolayer. The tail growth, shape changes, and droplet splitting were assigned to the decrease and vanishing of surface tension, γ. Here we present temperature-dependent γ(T), optical microscopy measurements, and interfacial entropy determinations for several alkane/surfactant combinations. We demonstrate the advantages and accuracy of the in situ γ(T) measurements made simultaneously with the microscopy measurements on the same droplet. The in situ and coinciding ex situ Wilhelmy plate γ(T) measurements confirm the low interfacial tension, ≲0.1 mN/m, observed at T d. Here, our results provide strong quantitative support validating the crystalline monolayer buckling mechanism.« less

Structural and shear characteristics of adsorbed sodium caseinate and monoglyceride mixed monolayers at the air-water interface.

PubMed

Rodríguez Patino, Juan M; Cejudo Fernández, Marta; Carrera Sánchez, Cecilio; Rodríguez Niño, Ma Rosario

2007-09-01

The structural and shear characteristics of mixed monolayers formed by an adsorbed Na-caseinate film and a spread monoglyceride (monopalmitin or monoolein) on the previously adsorbed protein film have been analyzed. Measurements of the surface pressure (pi)-area (A) isotherm and surface shear viscosity (eta(s)) were obtained at 20 degrees C and at pH 7 in a modified Wilhelmy-type film balance. The structural and shear characteristics of the mixed films depend on the surface pressure and on the composition of the mixed film. At surface pressures lower than the equilibrium surface pressure of Na-caseinate (at pipi(e)(CS) have important repercussions on the shear characteristics of the mixed films.

Impact of C-reactive protein (CRP) on surfactant function

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

Li, J.J.; Sanders, R.L.; McAdam, K.P.

1989-12-01

Plasma levels of the acute-phase reactant, C-reactive protein (CRP), increase up to one thousand-fold as a result of trauma or inflammation. CRP binds to phosphorylcholine (PC) in a calcium-ion dependent manner. The structural homology between PC and the major phospholipid component of surfactant, dipalmitoyl phosphatidylcholine (DPPC), led to the present study in which we examined if CRP levels might be increased in patients with adult respiratory distress syndrome (ARDS), and subsequently interfere with surfactant function. Our results showed that CRP levels in the bronchoalveolar fluid (BALF) was increased in patients with ARDS (97.8 +/- 84.2 micrograms/mg total protein vs. 4.04more » +/- 2.2 micrograms/mg total protein in normals). Our results show that CRP binds to liposomes containing DPPC and phosphatidylglycerol (PG). As a result of this interaction, CRP inhibits the surface activity of a PG-DPPC mixture when tested with a Wilhelmy surfactometer or with the Enhorning pulsating bubble apparatus. Furthermore, the surface activity of a clinically used surfactant replacement, Surfactant TA (2 mg/ml), was also severely impaired by CRP in a dose-dependent manner (doses used ranging from 24.5 to 1,175 micrograms/ml). In contrast, human serum albumin (HSA) at 500 and 900 micrograms/ml had no inhibitory effect on Surfactant TA surface activity. These results suggest that CRP, although not an initiating insult in ARDS, may contribute to the subsequent abnormalities of surfactant function and thus the pathogenesis of the pulmonary dysfunction seen in ARDS.« less

Effect of lipid/polysaccharide ratio on surface activity of model root mucilage in its solid and liquid states

NASA Astrophysics Data System (ADS)

Chen, Fengxian; Arye, Gilboa

2016-04-01

The rhizosphere can be defined as the volume of soil around living roots, which is influenced by root activity. The biological, chemical and physical conditions that prevail in the rhizosphere are significantly different from those of the bulk soil. Plant roots can release diverse organic materials in the rhizosphere which may have different effects on its bio-chemo-physical activity. Among these exudates is the root mucilage which can play a role on the maintenance of root-soil contact, lubrication of the root tip, protection of roots from desiccation and disease, stabilization of soil micro-aggregates and the selective absorption and storage of ions. The surface activity of the root mucilage at the liquid-air interface deduced from its surface tension depression relative to water, implying on its amphiphilic nature. Consequently as the rhizosphere dry out, hydrophobic functional groups may exhibit orientation at the solid-air interface and thus, the wettability of the rhizosphere may temporarily decrease. The major fraction of the root mucilage comprise of polysaccharides and to a much lesser extent, amino acids, organic acids, and phospholipids. The most frequent polysaccharide and phospholipids detected in root mucilage are polygalacturonic acid (PGA) and Phosphatidylcholine (PC), respectively. The latter, is thought to be main cause for the surface active nature of root mucilage. Nevertheless, the role and function of root mucilage in the rhizosphere is commonly studied based on model root mucilage that comprise of only one component, where the most frequent ones are PGA or PC (or lecithin). The main objective of this study was to quantify the effect of concentration and PGA/PC ratios on the wettability of a model rhizosphere soil and the surface tension of the model root mucilage at the liquid-air interface. The PGA/PC mixtures were measured for their equilibrium and dynamic surface tension using the Wilhelmy-Plate method. Quartz sand or glass slides were coated with PGA and/or PC using the above solutions and measured for their initial advancing contact angle and dynamic one, using the capillary rise and sessile drop methods, respectively. The results of this study will be presented and their implications for the wettability of the rhizosphere will be discussed.

The Effects of Predator Evolution and Genetic Variation on Predator-Prey Population-Level Dynamics.

PubMed

Cortez, Michael H; Patel, Swati

2017-07-01

This paper explores how predator evolution and the magnitude of predator genetic variation alter the population-level dynamics of predator-prey systems. We do this by analyzing a general eco-evolutionary predator-prey model using four methods: Method 1 identifies how eco-evolutionary feedbacks alter system stability in the fast and slow evolution limits; Method 2 identifies how the amount of standing predator genetic variation alters system stability; Method 3 identifies how the phase lags in predator-prey cycles depend on the amount of genetic variation; and Method 4 determines conditions for different cycle shapes in the fast and slow evolution limits using geometric singular perturbation theory. With these four methods, we identify the conditions under which predator evolution alters system stability and shapes of predator-prey cycles, and how those effect depend on the amount of genetic variation in the predator population. We discuss the advantages and disadvantages of each method and the relations between the four methods. This work shows how the four methods can be used in tandem to make general predictions about eco-evolutionary dynamics and feedbacks.

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

A key, yet often neglected, component of digital evolution and evolutionary models is the ‘selection method’ which assigns fitness (number of offspring) to individuals based on their performance scores (efficiency in performing tasks). Here, we study with formal analysis and numerical experiments the evolution of cooperation under the five most common selection methods (proportionate, rank, truncation-proportionate, truncation-uniform and tournament). We consider related individuals engaging in a Prisoner's Dilemma game where individuals can either cooperate or defect. A cooperator pays a cost, whereas its partner receives a benefit, which affect their performance scores. These performance scores are translated into fitness by one of the five selection methods. We show that cooperation is positively associated with the relatedness between individuals under all selection methods. By contrast, the change in the performance benefit of cooperation affects the populations’ average level of cooperation only under the proportionate methods. We also demonstrate that the truncation and tournament methods may introduce negative frequency-dependence and lead to the evolution of polymorphic populations. Using the example of the evolution of cooperation, we show that the choice of selection method, though it is often marginalized, can considerably affect the evolutionary dynamics. PMID:24152811

The orbital evolution of NEA 30825 1900 TG1

NASA Astrophysics Data System (ADS)

Timoshkova, E. I.

2008-02-01

The orbital evolution of the near-Earth asteroid (NEA) 30825 1990 TG1 has been studied by numerical integration of the equations of its motion over the 100 000-year time interval with allowance for perturbations from eight major planets and Pluto, and the variations in its osculating orbit over this time interval were determined. The numerical integrations were performed using two methods: the Bulirsch-Stoer method and the Everhart method. The comparative analysis of the two resulting orbital evolutions of motion is presented for the time interval examined. The evolution of the asteroid motion is qualitatively the same for both variants, but the rate of evolution of the orbital elements is different. Our research confirms the known fact that the application of different integrators to the study of the long-term evolution of the NEA orbit may lead to different evolution tracks.

A review: applications of the phase field method in predicting microstructure and property evolution of irradiated nuclear materials

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

Li, Yulan; Hu, Shenyang; Sun, Xin

Here, complex microstructure changes occur in nuclear fuel and structural materials due to the extreme environments of intense irradiation and high temperature. This paper evaluates the role of the phase field method in predicting the microstructure evolution of irradiated nuclear materials and the impact on their mechanical, thermal, and magnetic properties. The paper starts with an overview of the important physical mechanisms of defect evolution and the significant gaps in simulating microstructure evolution in irradiated nuclear materials. Then, the phase field method is introduced as a powerful and predictive tool and its applications to microstructure and property evolution in irradiatedmore » nuclear materials are reviewed. The review shows that (1) Phase field models can correctly describe important phenomena such as spatial-dependent generation, migration, and recombination of defects, radiation-induced dissolution, the Soret effect, strong interfacial energy anisotropy, and elastic interaction; (2) The phase field method can qualitatively and quantitatively simulate two-dimensional and three-dimensional microstructure evolution, including radiation-induced segregation, second phase nucleation, void migration, void and gas bubble superlattice formation, interstitial loop evolution, hydrate formation, and grain growth, and (3) The Phase field method correctly predicts the relationships between microstructures and properties. The final section is dedicated to a discussion of the strengths and limitations of the phase field method, as applied to irradiation effects in nuclear materials.« less

A review: applications of the phase field method in predicting microstructure and property evolution of irradiated nuclear materials

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

Li, Yulan; Hu, Shenyang; Sun, Xin

Complex microstructure changes occur in nuclear fuel and structural materials due to the extreme environments of intense irradiation and high temperature. This paper evaluates the role of the phase field (PF) method in predicting the microstructure evolution of irradiated nuclear materials and the impact on their mechanical, thermal, and magnetic properties. The paper starts with an overview of the important physical mechanisms of defect evolution and the significant gaps in simulating microstructure evolution in irradiated nuclear materials. Then, the PF method is introduced as a powerful and predictive tool and its applications to microstructure and property evolution in irradiated nuclearmore » materials are reviewed. The review shows that 1) FP models can correctly describe important phenomena such as spatial dependent generation, migration, and recombination of defects, radiation-induced dissolution, the Soret effect, strong interfacial energy anisotropy, and elastic interaction; 2) The PF method can qualitatively and quantitatively simulate 2-D and 3-D microstructure evolution, including radiation-induced segregation, second phase nucleation, void migration, void and gas bubble superlattice formation, interstitial loop evolution, hydrate formation, and grain growth, and 3) The FP method correctly predicts the relationships between microstructures and properties. The final section is dedicated to a discussion of the strengths and limitations of the PF method, as applied to irradiation effects in nuclear materials.« less

A review: applications of the phase field method in predicting microstructure and property evolution of irradiated nuclear materials

DOE PAGES

Li, Yulan; Hu, Shenyang; Sun, Xin; ...

2017-04-14

Here, complex microstructure changes occur in nuclear fuel and structural materials due to the extreme environments of intense irradiation and high temperature. This paper evaluates the role of the phase field method in predicting the microstructure evolution of irradiated nuclear materials and the impact on their mechanical, thermal, and magnetic properties. The paper starts with an overview of the important physical mechanisms of defect evolution and the significant gaps in simulating microstructure evolution in irradiated nuclear materials. Then, the phase field method is introduced as a powerful and predictive tool and its applications to microstructure and property evolution in irradiatedmore » nuclear materials are reviewed. The review shows that (1) Phase field models can correctly describe important phenomena such as spatial-dependent generation, migration, and recombination of defects, radiation-induced dissolution, the Soret effect, strong interfacial energy anisotropy, and elastic interaction; (2) The phase field method can qualitatively and quantitatively simulate two-dimensional and three-dimensional microstructure evolution, including radiation-induced segregation, second phase nucleation, void migration, void and gas bubble superlattice formation, interstitial loop evolution, hydrate formation, and grain growth, and (3) The Phase field method correctly predicts the relationships between microstructures and properties. The final section is dedicated to a discussion of the strengths and limitations of the phase field method, as applied to irradiation effects in nuclear materials.« less

High Oxygen Concentrations Adversely Affect the Performance of Pulmonary Surfactant.

PubMed

Smallwood, Craig D; Boloori-Zadeh, Parnian; Silva, Maricris R; Gouldstone, Andrew

2017-08-01

Although effective in the neonatal population, exogenous pulmonary surfactant has not demonstrated a benefit in pediatric and adult subjects with hypoxic lung injury despite a sound physiologic rationale. Importantly, neonatal surfactant replacement therapy is administered in conjunction with low fractional F IO 2 while pediatric/adult therapy is administered with high F IO 2 . We suspected a connection between F IO 2 and surfactant performance. Therefore, we sought to assess a possible mechanism by which the activity of pulmonary surfactant is adversely affected by direct oxygen exposure in in vitro experiments. The mechanical performance of pulmonary surfactant was evaluated using 2 methods. First, Langmuir-Wilhelmy balance was utilized to study the reduction in surface area (δA) of surfactant to achieve a low bound value of surface tension after repeated compression and expansion cycles. Second, dynamic light scattering was utilized to measure the size of pulmonary surfactant particles in aqueous suspension. For both experiments, comparisons were made between surfactant exposed to 21% and 100% oxygen. The δA of surfactant was 21.1 ± 2.0% and 35.8 ± 2.0% during exposure to 21% and 100% oxygen, respectively ( P = .02). Furthermore, dynamic light-scattering experiments revealed a micelle diameter of 336.0 ± 12.5 μm and 280.2 ± 11.0 μm in 21% and 100% oxygen, respectively ( P < .001), corresponding to a ∼16% decrease in micelle diameter following exposure to 100% oxygen. The characteristics of pulmonary surfactant were adversely affected by short-term exposure to oxygen. Specifically, surface tension studies revealed that short-term exposure of surfactant film to high concentrations of oxygen expedited the frangibility of pulmonary surfactant, as shown with the δA. This suggests that reductions in pulmonary compliance and associated adverse effects could begin to take effect in a very short period of time. If these findings can be demonstrated in vivo, a role for reduced F IO 2 during exogenous surfactant delivery may have a clinical benefit. Copyright © 2017 by Daedalus Enterprises.

Methods of geometrical integration in accelerator physics

NASA Astrophysics Data System (ADS)

Andrianov, S. N.

2016-12-01

In the paper we consider a method of geometric integration for a long evolution of the particle beam in cyclic accelerators, based on the matrix representation of the operator of particles evolution. This method allows us to calculate the corresponding beam evolution in terms of two-dimensional matrices including for nonlinear effects. The ideology of the geometric integration introduces in appropriate computational algorithms amendments which are necessary for preserving the qualitative properties of maps presented in the form of the truncated series generated by the operator of evolution. This formalism extends both on polarized and intense beams. Examples of practical applications are described.

Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data.

PubMed

Oakley, Todd H; Gu, Zhenglong; Abouheif, Ehab; Patel, Nipam H; Li, Wen-Hsiung

2005-01-01

Understanding the evolution of gene function is a primary challenge of modern evolutionary biology. Despite an expanding database from genomic and developmental studies, we are lacking quantitative methods for analyzing the evolution of some important measures of gene function, such as gene-expression patterns. Here, we introduce phylogenetic comparative methods to compare different models of gene-expression evolution in a maximum-likelihood framework. We find that expression of duplicated genes has evolved according to a nonphylogenetic model, where closely related genes are no more likely than more distantly related genes to share common expression patterns. These results are consistent with previous studies that found rapid evolution of gene expression during the history of yeast. The comparative methods presented here are general enough to test a wide range of evolutionary hypotheses using genomic-scale data from any organism.

Analytic Evolution of Singular Distribution Amplitudes in QCD

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

Tandogan Kunkel, Asli

2014-08-01

Distribution amplitudes (DAs) are the basic functions that contain information about the quark momentum. DAs are necessary to describe hard exclusive processes in quantum chromodynamics. We describe a method of analytic evolution of DAs that have singularities such as nonzero values at the end points of the support region, jumps at some points inside the support region and cusps. We illustrate the method by applying it to the evolution of a at (constant) DA, antisymmetric at DA, and then use the method for evolution of the two-photon generalized distribution amplitude. Our approach to DA evolution has advantages over the standardmore » method of expansion in Gegenbauer polynomials [1, 2] and over a straightforward iteration of an initial distribution with evolution kernel. Expansion in Gegenbauer polynomials requires an infinite number of terms in order to accurately reproduce functions in the vicinity of singular points. Straightforward iteration of an initial distribution produces logarithmically divergent terms at each iteration. In our method the logarithmic singularities are summed from the start, which immediately produces a continuous curve. Afterwards, in order to get precise results, only one or two iterations are needed.« less

High School Students' Perceptions of Evolution Instruction: Acceptance and Evolution Learning Experiences

ERIC Educational Resources Information Center

Donnelly, Lisa A.; Kazempour, Mahsa; Amirshokoohi, Aidin

2009-01-01

Evolution is an important and sometimes controversial component of high school biology. In this study, we used a mixed methods approach to explore students' evolution acceptance and views of evolution teaching and learning. Students explained their acceptance and rejection of evolution in terms of evidence and conflicts with religion and…

Echo movement and evolution from real-time processing.

NASA Technical Reports Server (NTRS)

Schaffner, M. R.

1972-01-01

Preliminary experimental data on the effectiveness of conventional radars in measuring the movement and evolution of meteorological echoes when the radar is connected to a programmable real-time processor are examined. In the processor programming is accomplished by conceiving abstract machines which constitute the actual programs used in the methods employed. An analysis of these methods, such as the center of gravity method, the contour-displacement method, the method of slope, the cross-section method, the contour crosscorrelation method, the method of echo evolution at each point, and three-dimensional measurements, shows that the motions deduced from them may differ notably (since each method determines different quantities) but the plurality of measurement may give additional information on the characteristics of the precipitation.

Effects of hydrophobic helix length and side chain chemistry on biomimicry in peptoid analogues of SP-C.

PubMed

Brown, Nathan J; Wu, Cindy W; Seurynck-Servoss, Shannon L; Barron, Annelise E

2008-02-12

The hydrophobic proteins of lung surfactant (LS), SP-B and SP-C, are critical constituents of an effective surfactant replacement therapy for the treatment of respiratory distress syndrome. Because of concerns and difficulties associated with animal-derived surfactants, recent investigations have focused on the creation of synthetic analogues of the LS proteins. However, creating an accurate mimic of SP-C that retains its biophysical surface activity is extraordinarily challenging given the lipopeptide's extreme hydrophobicity and propensity to misfold and aggregate. One successful approach that overcomes these difficulties is the use of poly-N-substituted glycines, or peptoids, to mimic SP-C. To develop a non-natural, bioactive mimic of SP-C and to investigate the effects of side chain chemistry and length of the helical hydrophobic region, we synthesized, purified, and performed in vitro testing of two classes of peptoid SP-C mimics: those having a rigid alpha-chiral aromatic helix and those having a biomimetic alpha-chiral aliphatic helix. The length of the two classes of mimics was also systematically altered. Circular dichroism spectroscopy gave evidence that all of the peptoid-based mimics studied here emulated SP-C's secondary structure, forming stable helical structures in solution. Langmuir-Wilhelmy surface balance, fluorescence microscopy, and pulsating bubble surfactometry experiments provide evidence that the aromatic-based SP-C peptoid mimics, in conjunction with a synthetic lipid mixture, have superior surface activity and biomimetic film morphology in comparison to the aliphatic-based mimics and that there is an increase in surface activity corresponding to increasing helical length.

Simulation of Heterogeneous Atom Probe Tip Shapes Evolution during Field Evaporation Using a Level Set Method and Different Evaporation Models

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

Xu, Zhijie; Li, Dongsheng; Xu, Wei

2015-04-01

In atom probe tomography (APT), accurate reconstruction of the spatial positions of field evaporated ions from measured detector patterns depends upon a correct understanding of the dynamic tip shape evolution and evaporation laws of component atoms. Artifacts in APT reconstructions of heterogeneous materials can be attributed to the assumption of homogeneous evaporation of all the elements in the material in addition to the assumption of a steady state hemispherical dynamic tip shape evolution. A level set method based specimen shape evolution model is developed in this study to simulate the evaporation of synthetic layered-structured APT tips. The simulation results ofmore » the shape evolution by the level set model qualitatively agree with the finite element method and the literature data using the finite difference method. The asymmetric evolving shape predicted by the level set model demonstrates the complex evaporation behavior of heterogeneous tip and the interface curvature can potentially lead to the artifacts in the APT reconstruction of such materials. Compared with other APT simulation methods, the new method provides smoother interface representation with the aid of the intrinsic sub-grid accuracy. Two evaporation models (linear and exponential evaporation laws) are implemented in the level set simulations and the effect of evaporation laws on the tip shape evolution is also presented.« less

Reply to Efford on ‘Integrating resource selection information with spatial capture-recapture’

USGS Publications Warehouse

Royle, Andy; Chandler, Richard; Sun, Catherine C.; Fuller, Angela K.

2014-01-01

3. A key point of Royle et al. (Methods in Ecology and Evolution, 2013, 4) was that active resource selection induces heterogeneity in encounter probability which, if unaccounted for, should bias estimates of population size or density. The models of Royle et al. (Methods in Ecology and Evolution, 2013, 4) and Efford (Methods in Ecology and Evolution, 2014, 000, 000) merely amount to alternative models of resource selection, and hence varying amounts of heterogeneity in encounter probability.

Exact traveling wave solutions for system of nonlinear evolution equations.

PubMed

Khan, Kamruzzaman; Akbar, M Ali; Arnous, Ahmed H

2016-01-01

In this work, recently deduced generalized Kudryashov method is applied to the variant Boussinesq equations, and the (2 + 1)-dimensional breaking soliton equations. As a result a range of qualitative explicit exact traveling wave solutions are deduced for these equations, which motivates us to develop, in the near future, a new approach to obtain unsteady solutions of autonomous nonlinear evolution equations those arise in mathematical physics and engineering fields. It is uncomplicated to extend this method to higher-order nonlinear evolution equations in mathematical physics. And it should be possible to apply the same method to nonlinear evolution equations having more general forms of nonlinearities by utilizing the traveling wave hypothesis.

Fitting models of continuous trait evolution to incompletely sampled comparative data using approximate Bayesian computation.

PubMed

Slater, Graham J; Harmon, Luke J; Wegmann, Daniel; Joyce, Paul; Revell, Liam J; Alfaro, Michael E

2012-03-01

In recent years, a suite of methods has been developed to fit multiple rate models to phylogenetic comparative data. However, most methods have limited utility at broad phylogenetic scales because they typically require complete sampling of both the tree and the associated phenotypic data. Here, we develop and implement a new, tree-based method called MECCA (Modeling Evolution of Continuous Characters using ABC) that uses a hybrid likelihood/approximate Bayesian computation (ABC)-Markov-Chain Monte Carlo approach to simultaneously infer rates of diversification and trait evolution from incompletely sampled phylogenies and trait data. We demonstrate via simulation that MECCA has considerable power to choose among single versus multiple evolutionary rate models, and thus can be used to test hypotheses about changes in the rate of trait evolution across an incomplete tree of life. We finally apply MECCA to an empirical example of body size evolution in carnivores, and show that there is no evidence for an elevated rate of body size evolution in the pinnipeds relative to terrestrial carnivores. ABC approaches can provide a useful alternative set of tools for future macroevolutionary studies where likelihood-dependent approaches are lacking. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Does probabilistic modelling of linkage disequilibrium evolution improve the accuracy of QTL location in animal pedigree?

PubMed

Cierco-Ayrolles, Christine; Dejean, Sébastien; Legarra, Andrés; Gilbert, Hélène; Druet, Tom; Ytournel, Florence; Estivals, Delphine; Oumouhou, Naïma; Mangin, Brigitte

2010-10-22

Since 2001, the use of more and more dense maps has made researchers aware that combining linkage and linkage disequilibrium enhances the feasibility of fine-mapping genes of interest. So, various method types have been derived to include concepts of population genetics in the analyses. One major drawback of many of these methods is their computational cost, which is very significant when many markers are considered. Recent advances in technology, such as SNP genotyping, have made it possible to deal with huge amount of data. Thus the challenge that remains is to find accurate and efficient methods that are not too time consuming. The study reported here specifically focuses on the half-sib family animal design. Our objective was to determine whether modelling of linkage disequilibrium evolution improved the mapping accuracy of a quantitative trait locus of agricultural interest in these populations. We compared two methods of fine-mapping. The first one was an association analysis. In this method, we did not model linkage disequilibrium evolution. Therefore, the modelling of the evolution of linkage disequilibrium was a deterministic process; it was complete at time 0 and remained complete during the following generations. In the second method, the modelling of the evolution of population allele frequencies was derived from a Wright-Fisher model. We simulated a wide range of scenarios adapted to animal populations and compared these two methods for each scenario. Our results indicated that the improvement produced by probabilistic modelling of linkage disequilibrium evolution was not significant. Both methods led to similar results concerning the location accuracy of quantitative trait loci which appeared to be mainly improved by using four flanking markers instead of two. Therefore, in animal half-sib designs, modelling linkage disequilibrium evolution using a Wright-Fisher model does not significantly improve the accuracy of the QTL location when compared to a simpler method assuming complete and constant linkage between the QTL and the marker alleles. Finally, given the high marker density available nowadays, the simpler method should be preferred as it gives accurate results in a reasonable computing time.

Evolution of solar magnetic fields - A new approach to MHD initial-boundary value problems by the method of nearcharacteristics

NASA Technical Reports Server (NTRS)

Nakagawa, Y.

1980-01-01

A method of analysis for the MHD initial-boundary problem is presented in which the model's formulation is based on the method of nearcharacteristics developed by Werner (1968) and modified by Shin and Kot (1978). With this method, the physical causality relationship can be traced from the perturbation to the response as in the method of characteristics, while achieving the advantage of a considerable reduction in mathematical procedures. The method offers the advantage of examining not only the evolution of nonforce free fields, but also the changes of physical conditions in the atmosphere accompanying the evolution of magnetic fields. The physical validity of the method is demonstrated with examples, and their significance in interpreting observations is discussed.

Black hole evolution by spectral methods

NASA Astrophysics Data System (ADS)

Kidder, Lawrence E.; Scheel, Mark A.; Teukolsky, Saul A.; Carlson, Eric D.; Cook, Gregory B.

2000-10-01

Current methods of evolving a spacetime containing one or more black holes are plagued by instabilities that prohibit long-term evolution. Some of these instabilities may be due to the numerical method used, traditionally finite differencing. In this paper, we explore the use of a pseudospectral collocation (PSC) method for the evolution of a spherically symmetric black hole spacetime in one dimension using a hyperbolic formulation of Einstein's equations. We demonstrate that our PSC method is able to evolve a spherically symmetric black hole spacetime forever without enforcing constraints, even if we add dynamics via a Klein-Gordon scalar field. We find that, in contrast with finite-differencing methods, black hole excision is a trivial operation using PSC applied to a hyperbolic formulation of Einstein's equations. We discuss the extension of this method to three spatial dimensions.

Research on social communication network evolution based on topology potential distribution

NASA Astrophysics Data System (ADS)

Zhao, Dongjie; Jiang, Jian; Li, Deyi; Zhang, Haisu; Chen, Guisheng

2011-12-01

Aiming at the problem of social communication network evolution, first, topology potential is introduced to measure the local influence among nodes in networks. Second, from the perspective of topology potential distribution the method of network evolution description based on topology potential distribution is presented, which takes the artificial intelligence with uncertainty as basic theory and local influence among nodes as essentiality. Then, a social communication network is constructed by enron email dataset, the method presented is used to analyze the characteristic of the social communication network evolution and some useful conclusions are got, implying that the method is effective, which shows that topology potential distribution can effectively describe the characteristic of sociology and detect the local changes in social communication network.

Comparative evolution of the inverse problems (Introduction to an interdisciplinary study of the inverse problems)

NASA Technical Reports Server (NTRS)

Sabatier, P. C.

1972-01-01

The progressive realization of the consequences of nonuniqueness imply an evolution of both the methods and the centers of interest in inverse problems. This evolution is schematically described together with the various mathematical methods used. A comparative description is given of inverse methods in scientific research, with examples taken from mathematics, quantum and classical physics, seismology, transport theory, radiative transfer, electromagnetic scattering, electrocardiology, etc. It is hoped that this paper will pave the way for an interdisciplinary study of inverse problems.

OncoNEM: inferring tumor evolution from single-cell sequencing data.

PubMed

Ross, Edith M; Markowetz, Florian

2016-04-15

Single-cell sequencing promises a high-resolution view of genetic heterogeneity and clonal evolution in cancer. However, methods to infer tumor evolution from single-cell sequencing data lag behind methods developed for bulk-sequencing data. Here, we present OncoNEM, a probabilistic method for inferring intra-tumor evolutionary lineage trees from somatic single nucleotide variants of single cells. OncoNEM identifies homogeneous cellular subpopulations and infers their genotypes as well as a tree describing their evolutionary relationships. In simulation studies, we assess OncoNEM's robustness and benchmark its performance against competing methods. Finally, we show its applicability in case studies of muscle-invasive bladder cancer and essential thrombocythemia.

Evolutionary Biology Digital Dissection Project: Web-Based Laboratory Learning Opportunities for Students

ERIC Educational Resources Information Center

Fabian, Carole Ann

2004-01-01

A university in Buffalo introduced its students to evolution by providing them with information on evidence of evolution, mechanisms for evolution, principles of genetics, selection, adaptation, evolution and sociobiology. This method of teaching with technology enabled students to improve and expand their learning opportunities.

Strain Characterization and Microstructure Evolution Under Deformation in 2060 Alloy

NASA Astrophysics Data System (ADS)

Jin, X.; Zhang, G. D.; Zhao, Y. F.; Xue, F.

2018-05-01

A new method of DIC combined with EBSD is developed for the characterization of strain and microstructure evolution during bending. The traditional microhardness point and DIC methods are used to study the microstructure evolution in 2060 alloy during bending; the interested area suffers under tensile stress, the microstructure evolution is collected by SEM, EBSD, digital image correlation (DIC) method during bending. The results shows that the DIC method can both realize the strain tensor characterization of the interested area, and can also express the local strain tensor in the micro-area even more. The degree of grain division in the process of deformation is related to the strain in this region; the grains have larger strain of small angle grain boundary (SLGBs), which results in a new micro-organizational structure. The misorientation is smaller with larger strain degree while the misorientation is larger with smaller strain.

From molecular engineering to process engineering: development of high-throughput screening methods in enzyme directed evolution.

PubMed

Ye, Lidan; Yang, Chengcheng; Yu, Hongwei

2018-01-01

With increasing concerns in sustainable development, biocatalysis has been recognized as a competitive alternative to traditional chemical routes in the past decades. As nature's biocatalysts, enzymes are able to catalyze a broad range of chemical transformations, not only with mild reaction conditions but also with high activity and selectivity. However, the insufficient activity or enantioselectivity of natural enzymes toward non-natural substrates limits their industrial application, while directed evolution provides a potent solution to this problem, thanks to its independence on detailed knowledge about the relationship between sequence, structure, and mechanism/function of the enzymes. A proper high-throughput screening (HTS) method is the key to successful and efficient directed evolution. In recent years, huge varieties of HTS methods have been developed for rapid evaluation of mutant libraries, ranging from in vitro screening to in vivo selection, from indicator addition to multi-enzyme system construction, and from plate screening to computation- or machine-assisted screening. Recently, there is a tendency to integrate directed evolution with metabolic engineering in biosynthesis, using metabolites as HTS indicators, which implies that directed evolution has transformed from molecular engineering to process engineering. This paper aims to provide an overview of HTS methods categorized based on the reaction principles or types by summarizing related studies published in recent years including the work from our group, to discuss assay design strategies and typical examples of HTS methods, and to share our understanding on HTS method development for directed evolution of enzymes involved in specific catalytic reactions or metabolic pathways.

Evolution of Advection Upstream Splitting Method Schemes

NASA Technical Reports Server (NTRS)

Liou, Meng-Sing

2010-01-01

This paper focuses on the evolution of advection upstream splitting method(AUSM) schemes. The main ingredients that have led to the development of modern computational fluid dynamics (CFD) methods have been reviewed, thus the ideas behind AUSM. First and foremost is the concept of upwinding. Second, the use of Riemann problem in constructing the numerical flux in the finite-volume setting. Third, the necessity of including all physical processes, as characterised by the linear (convection) and nonlinear (acoustic) fields. Fourth, the realisation of separating the flux into convection and pressure fluxes. The rest of this review briefly outlines the technical evolution of AUSM and more details can be found in the cited references. Keywords: Computational fluid dynamics methods, hyperbolic systems, advection upstream splitting method, conservation laws, upwinding, CFD

A Bivariate Chebyshev Spectral Collocation Quasilinearization Method for Nonlinear Evolution Parabolic Equations

PubMed Central

Motsa, S. S.; Magagula, V. M.; Sibanda, P.

2014-01-01

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature. PMID:25254252

A bivariate Chebyshev spectral collocation quasilinearization method for nonlinear evolution parabolic equations.

PubMed

Motsa, S S; Magagula, V M; Sibanda, P

2014-01-01

This paper presents a new method for solving higher order nonlinear evolution partial differential equations (NPDEs). The method combines quasilinearisation, the Chebyshev spectral collocation method, and bivariate Lagrange interpolation. In this paper, we use the method to solve several nonlinear evolution equations, such as the modified KdV-Burgers equation, highly nonlinear modified KdV equation, Fisher's equation, Burgers-Fisher equation, Burgers-Huxley equation, and the Fitzhugh-Nagumo equation. The results are compared with known exact analytical solutions from literature to confirm accuracy, convergence, and effectiveness of the method. There is congruence between the numerical results and the exact solutions to a high order of accuracy. Tables were generated to present the order of accuracy of the method; convergence graphs to verify convergence of the method and error graphs are presented to show the excellent agreement between the results from this study and the known results from literature.

Stress relaxation in quasi-two-dimensional self-assembled nanoparticle monolayers

NASA Astrophysics Data System (ADS)

Boucheron, Leandra S.; Stanley, Jacob T.; Dai, Yeling; You, Siheng Sean; Parzyck, Christopher T.; Narayanan, Suresh; Sandy, Alec R.; Jiang, Zhang; Meron, Mati; Lin, Binhua; Shpyrko, Oleg G.

2018-05-01

We experimentally probed the stress relaxation of a monolayer of iron oxide nanoparticles at the water-air interface. Upon drop-casting onto a water surface, the nanoparticles self-assembled into islands of two-dimensional hexagonally close packed crystalline domains surrounded by large voids. When compressed laterally, the voids gradually disappeared as the surface pressure increased. After the compression was stopped, the surface pressure (as measured by a Wilhelmy plate) evolved as a function of the film aging time with three distinct timescales. These aging dynamics were intrinsic to the stressed state built up during the non-equilibrium compression of the film. Utilizing x-ray photon correlation spectroscopy, we measured the characteristic relaxation time (τ ) of in-plane nanoparticle motion as a function of the aging time through both second-order and two-time autocorrelation analysis. Compressed and stretched exponential fitting of the intermediate scattering function yielded exponents (β ) indicating different relaxation mechanisms of the films under different compression stresses. For a monolayer compressed to a lower surface pressure (between 20 mN/m and 30 mN/m), the relaxation time (τ ) decreased continuously as a function of the aging time, as did the fitted exponent, which transitioned from being compressed (>1 ) to stretched (<1 ), indicating that the monolayer underwent a stress release through crystalline domain reorganization. However, for a monolayer compressed to a higher surface pressure (around 40 mN/m), the relaxation time increased continuously and the compressed exponent varied very little from a value of 1.6, suggesting that the system may have been highly stressed and jammed. Despite the interesting stress relaxation signatures seen in these samples, the structural ordering of the monolayer remained the same over the sample lifetime, as revealed by grazing incidence x-ray diffraction.

The surface activity of purified ocular mucin at the air-liquid interface and interactions with meibomian lipids.

PubMed

Millar, Thomas J; Tragoulias, Sophia T; Anderton, Philip J; Ball, Malcolm S; Miano, Fausto; Dennis, Gary R; Mudgil, Poonam

2006-01-01

Ocular mucins are thought to contribute to the stability of the tear film by reducing surface tension. The purpose of this study was to compare the effect of different mucins and hyaluronic acid (HA) alone and mixed with meibomian lipids on the surface pressure at an air-liquid interface. A Langmuir trough and Wilhelmy balance were used to measure and compare the surface activity of bovine submaxillary gland mucin (BSM), purified BSM, purified bovine ocular mucin and HA, and mixtures of these with meibomian lipids, phosphatidylcholine, and phosphatidylglycerol. Their appearance at the surface of an air-buffer interface was examined using epifluorescence microscopy. Purified ocular mucin had no surface activity even at concentrations that were 100 times more than normally occur in tears. By contrast, commercial BSM caused changes to surface pressure that were concentration dependent. The surface pressure-area profiles showed surface activity with maximum surface pressures of 12.3-22.5 mN/m depending on the concentration. Purified BSM showed no surface activity at low concentrations, whereas higher concentrations reached a maximum surface pressure of 25 mN/m. HA showed no surface activity, at low or high concentrations. Epifluorescence showed that the mucins were located at the air-buffer interface and changed the appearance of lipid films. Purified bovine ocular mucin and HA have no surface activity. However, despite having no surface activity in their own right, ocular mucins are likely to be present at the surface of the tear film, where they cause an increase in surface pressure by causing a compression of the lipids (a reorganization of the lipids) and alter the viscoelastic properties at the surface.

Predicting the evolution of complex networks via similarity dynamics

NASA Astrophysics Data System (ADS)

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

2017-01-01

Almost all real-world networks are subject to constant evolution, and plenty of them have been investigated empirically to uncover the underlying evolution mechanism. However, the evolution prediction of dynamic networks still remains a challenging problem. The crux of this matter is to estimate the future network links of dynamic networks. This paper studies the evolution prediction of dynamic networks with link prediction paradigm. To estimate the likelihood of the existence of links more accurate, an effective and robust similarity index is presented by exploiting network structure adaptively. Moreover, most of the existing link prediction methods do not make a clear distinction between future links and missing links. In order to predict the future links, the networks are regarded as dynamic systems in this paper, and a similarity updating method, spatial-temporal position drift model, is developed to simulate the evolutionary dynamics of node similarity. Then the updated similarities are used as input information for the future links' likelihood estimation. Extensive experiments on real-world networks suggest that the proposed similarity index performs better than baseline methods and the position drift model performs well for evolution prediction in real-world evolving networks.

Evolutionary decay and the prospects for long-term disease intervention using engineered insect vectors

PubMed Central

2015-01-01

After a long history of applying the sterile insect technique to suppress populations of disease vectors and agricultural pests, there is growing interest in using genetic engineering both to improve old methods and to enable new methods. The two goals of interventions are to suppress populations, possibly eradicating a species altogether, or to abolish the vector’s competence to transmit a parasite. New methods enabled by genetic engineering include the use of selfish genes toward either goal as well as a variety of killer-rescue systems that could be used for vector competence reduction. This article reviews old and new methods with an emphasis on the potential for evolution of resistance to these strategies. Established methods of population suppression did not obviously face a problem from resistance evolution, but newer technologies might. Resistance to these newer interventions will often be mechanism-specific, and while it is too early to know where resistance evolution will become a problem, it is at least possible to propose properties of interventions that will be more or less effective in blocking resistance evolution. PMID:26160736

Unifying time evolution and optimization with matrix product states

NASA Astrophysics Data System (ADS)

Haegeman, Jutho; Lubich, Christian; Oseledets, Ivan; Vandereycken, Bart; Verstraete, Frank

2016-10-01

We show that the time-dependent variational principle provides a unifying framework for time-evolution methods and optimization methods in the context of matrix product states. In particular, we introduce a new integration scheme for studying time evolution, which can cope with arbitrary Hamiltonians, including those with long-range interactions. Rather than a Suzuki-Trotter splitting of the Hamiltonian, which is the idea behind the adaptive time-dependent density matrix renormalization group method or time-evolving block decimation, our method is based on splitting the projector onto the matrix product state tangent space as it appears in the Dirac-Frenkel time-dependent variational principle. We discuss how the resulting algorithm resembles the density matrix renormalization group (DMRG) algorithm for finding ground states so closely that it can be implemented by changing just a few lines of code and it inherits the same stability and efficiency. In particular, our method is compatible with any Hamiltonian for which ground-state DMRG can be implemented efficiently. In fact, DMRG is obtained as a special case of our scheme for imaginary time evolution with infinite time step.

Adaptive Discontinuous Evolution Galerkin Method for Dry Atmospheric Flow

DTIC Science & Technology

2013-04-02

standard one-dimensional approximate Riemann solver used for the flux integration demonstrate better stability, accuracy as well as reliability of the...discontinuous evolution Galerkin method for dry atmospheric convection. Comparisons with the standard one-dimensional approximate Riemann solver used...instead of a standard one- dimensional approximate Riemann solver , the flux integration within the discontinuous Galerkin method is now realized by

Protein-protein interaction network-based detection of functionally similar proteins within species.

PubMed

Song, Baoxing; Wang, Fen; Guo, Yang; Sang, Qing; Liu, Min; Li, Dengyun; Fang, Wei; Zhang, Deli

2012-07-01

Although functionally similar proteins across species have been widely studied, functionally similar proteins within species showing low sequence similarity have not been examined in detail. Identification of these proteins is of significant importance for understanding biological functions, evolution of protein families, progression of co-evolution, and convergent evolution and others which cannot be obtained by detection of functionally similar proteins across species. Here, we explored a method of detecting functionally similar proteins within species based on graph theory. After denoting protein-protein interaction networks using graphs, we split the graphs into subgraphs using the 1-hop method. Proteins with functional similarities in a species were detected using a method of modified shortest path to compare these subgraphs and to find the eligible optimal results. Using seven protein-protein interaction networks and this method, some functionally similar proteins with low sequence similarity that cannot detected by sequence alignment were identified. By analyzing the results, we found that, sometimes, it is difficult to separate homologous from convergent evolution. Evaluation of the performance of our method by gene ontology term overlap showed that the precision of our method was excellent. Copyright © 2012 Wiley Periodicals, Inc.

Development of efficient time-evolution method based on three-term recurrence relation

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

Akama, Tomoko, E-mail: a.tomo---s-b-l-r@suou.waseda.jp; Kobayashi, Osamu; Nanbu, Shinkoh, E-mail: shinkoh.nanbu@sophia.ac.jp

The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function.more » Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.« less

Estimating selection through male fitness: three complementary methods illuminate the nature and causes of selection on flowering time

PubMed Central

Austen, Emily J.; Weis, Arthur E.

2016-01-01

Our understanding of selection through male fitness is limited by the resource demands and indirect nature of the best available genetic techniques. Applying complementary, independent approaches to this problem can help clarify evolution through male function. We applied three methods to estimate selection on flowering time through male fitness in experimental populations of the annual plant Brassica rapa: (i) an analysis of mating opportunity based on flower production schedules, (ii) genetic paternity analysis, and (iii) a novel approach based on principles of experimental evolution. Selection differentials estimated by the first method disagreed with those estimated by the other two, indicating that mating opportunity was not the principal driver of selection on flowering time. The genetic and experimental evolution methods exhibited striking agreement overall, but a slight discrepancy between the two suggested that negative environmental covariance between age at flowering and male fitness may have contributed to phenotypic selection. Together, the three methods enriched our understanding of selection on flowering time, from mating opportunity to phenotypic selection to evolutionary response. The novel experimental evolution method may provide a means of examining selection through male fitness when genetic paternity analysis is not possible. PMID:26911957

Time-dependent spectral renormalization method

NASA Astrophysics Data System (ADS)

Cole, Justin T.; Musslimani, Ziad H.

2017-11-01

The spectral renormalization method was introduced by Ablowitz and Musslimani (2005) as an effective way to numerically compute (time-independent) bound states for certain nonlinear boundary value problems. In this paper, we extend those ideas to the time domain and introduce a time-dependent spectral renormalization method as a numerical means to simulate linear and nonlinear evolution equations. The essence of the method is to convert the underlying evolution equation from its partial or ordinary differential form (using Duhamel's principle) into an integral equation. The solution sought is then viewed as a fixed point in both space and time. The resulting integral equation is then numerically solved using a simple renormalized fixed-point iteration method. Convergence is achieved by introducing a time-dependent renormalization factor which is numerically computed from the physical properties of the governing evolution equation. The proposed method has the ability to incorporate physics into the simulations in the form of conservation laws or dissipation rates. This novel scheme is implemented on benchmark evolution equations: the classical nonlinear Schrödinger (NLS), integrable PT symmetric nonlocal NLS and the viscous Burgers' equations, each of which being a prototypical example of a conservative and dissipative dynamical system. Numerical implementation and algorithm performance are also discussed.

A Hybrid Forward-Adjoint Data Assimilation Method for Reconstructing the Temporal Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Q.; Liu, L.

2017-12-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation method that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics to the best.

EFFECTS OF LASER RADIATION ON MATTER: Distribution function of microinclusions in polymethylmethacrylate and its evolution under the influence of a series of laser pulses

NASA Astrophysics Data System (ADS)

Glauberman, G. Ya; Savanin, S. Yu; Shkunov, V. V.; Shumov, D. E.

1990-08-01

A new method is proposed for the derivation of the distribution function of the experimentally determined breakdown thresholds of absorbing microinclusions in a transparent insulator. Expressions are obtained for describing the evolution of this function in the course of irradiation of the insulator with laser pulses of constant energy density. The method is applied to calculate the distribution function of microinclusions in polymethylmethacrylate and the evolution of this function.

A New Automated Design Method Based on Machine Learning for CMOS Analog Circuits

NASA Astrophysics Data System (ADS)

Moradi, Behzad; Mirzaei, Abdolreza

2016-11-01

A new simulation based automated CMOS analog circuit design method which applies a multi-objective non-Darwinian-type evolutionary algorithm based on Learnable Evolution Model (LEM) is proposed in this article. The multi-objective property of this automated design of CMOS analog circuits is governed by a modified Strength Pareto Evolutionary Algorithm (SPEA) incorporated in the LEM algorithm presented here. LEM includes a machine learning method such as the decision trees that makes a distinction between high- and low-fitness areas in the design space. The learning process can detect the right directions of the evolution and lead to high steps in the evolution of the individuals. The learning phase shortens the evolution process and makes remarkable reduction in the number of individual evaluations. The expert designer's knowledge on circuit is applied in the design process in order to reduce the design space as well as the design time. The circuit evaluation is made by HSPICE simulator. In order to improve the design accuracy, bsim3v3 CMOS transistor model is adopted in this proposed design method. This proposed design method is tested on three different operational amplifier circuits. The performance of this proposed design method is verified by comparing it with the evolutionary strategy algorithm and other similar methods.

Directed evolution: tailoring biocatalysts for industrial applications.

PubMed

Kumar, Ashwani; Singh, Suren

2013-12-01

Current challenges and promises of white biotechnology encourage protein engineers to use a directed evolution approach to generate novel and useful biocatalysts for various sets of applications. Different methods of enzyme engineering have been used in the past in an attempt to produce enzymes with improved functions and properties. Recent advancement in the field of random mutagenesis, screening, selection and computational design increased the versatility and the rapid development of enzymes under strong selection pressure with directed evolution experiments. Techniques of directed evolution improve enzymes fitness without understanding them in great detail and clearly demonstrate its future role in adapting enzymes for use in industry. Despite significant advances to date regarding biocatalyst improvement, there still remains a need to improve mutagenesis strategies and development of easy screening and selection tools without significant human intervention. This review covers fundamental and major development of directed evolution techniques, and highlights the advances in mutagenesis, screening and selection methods with examples of enzymes developed by using these approaches. Several commonly used methods for creating molecular diversity with their advantages and disadvantages including some recently used strategies are also discussed.

Experimental Investigation of Spectra of Dynamical Maps and their Relation to non-Markovianity

NASA Astrophysics Data System (ADS)

Yu, Shang; Wang, Yi-Tao; Ke, Zhi-Jin; Liu, Wei; Meng, Yu; Li, Zhi-Peng; Zhang, Wen-Hao; Chen, Geng; Tang, Jian-Shun; Li, Chuan-Feng; Guo, Guang-Can

2018-02-01

The spectral theorem of von Neumann has been widely applied in various areas, such as the characteristic spectral lines of atoms. It has been recently proposed that dynamical evolution also possesses spectral lines. As the most intrinsic property of evolution, the behavior of these spectra can, in principle, exhibit almost every feature of this evolution, among which the most attractive topic is non-Markovianity, i.e., the memory effects during evolution. Here, we develop a method to detect these spectra, and moreover, we experimentally examine the relation between the spectral behavior and non-Markovianity by engineering the environment to prepare dynamical maps with different non-Markovian properties and then detecting the dynamical behavior of the spectral values. These spectra will lead to a witness for essential non-Markovianity. We also experimentally verify another simplified witness method for essential non-Markovianity. Interestingly, in both cases, we observe the sudden transition from essential non-Markovianity to something else. Our work shows the role of the spectra of evolution in the studies of non-Makovianity and provides the alternative methods to characterize non-Markovian behavior.

Online evolution reconstruction from a single measurement record with random time intervals for quantum communication

NASA Astrophysics Data System (ADS)

Zhou, Hua; Su, Yang; Wang, Rong; Zhu, Yong; Shen, Huiping; Pu, Tao; Wu, Chuanxin; Zhao, Jiyong; Zhang, Baofu; Xu, Zhiyong

2017-10-01

Online reconstruction of a time-variant quantum state from the encoding/decoding results of quantum communication is addressed by developing a method of evolution reconstruction from a single measurement record with random time intervals. A time-variant two-dimensional state is reconstructed on the basis of recovering its expectation value functions of three nonorthogonal projectors from a random single measurement record, which is composed from the discarded qubits of the six-state protocol. The simulated results prove that our method is robust to typical metro quantum channels. Our work extends the Fourier-based method of evolution reconstruction from the version for a regular single measurement record with equal time intervals to a unified one, which can be applied to arbitrary single measurement records. The proposed protocol of evolution reconstruction runs concurrently with the one of quantum communication, which can facilitate the online quantum tomography.

Hydrogen evolution reaction catalyst

DOEpatents

Subbaraman, Ram; Stamenkovic, Vojislav; Markovic, Nenad; Tripkovic, Dusan

2016-02-09

Systems and methods for a hydrogen evolution reaction catalyst are provided. Electrode material includes a plurality of clusters. The electrode exhibits bifunctionality with respect to the hydrogen evolution reaction. The electrode with clusters exhibits improved performance with respect to the intrinsic material of the electrode absent the clusters.

Enzyme catalysis: Evolution made easy

NASA Astrophysics Data System (ADS)

Wee, Eugene J. H.; Trau, Matt

2014-09-01

Directed evolution is a powerful tool for the development of improved enzyme catalysts. Now, a method that enables an enzyme, its encoding DNA and a fluorescent reaction product to be encapsulated in a gel bead enables the application of directed evolution in an ultra-high-throughput format.

Cultural macroevolution matters

PubMed Central

Gray, Russell D.

2017-01-01

Evolutionary thinking can be applied to both cultural microevolution and macroevolution. However, much of the current literature focuses on cultural microevolution. In this article, we argue that the growing availability of large cross-cultural datasets facilitates the use of computational methods derived from evolutionary biology to answer broad-scale questions about the major transitions in human social organization. Biological methods can be extended to human cultural evolution. We illustrate this argument with examples drawn from our recent work on the roles of Big Gods and ritual human sacrifice in the evolution of large, stratified societies. These analyses show that, although the presence of Big Gods is correlated with the evolution of political complexity, in Austronesian cultures at least, they do not play a causal role in ratcheting up political complexity. In contrast, ritual human sacrifice does play a causal role in promoting and sustaining the evolution of stratified societies by maintaining and legitimizing the power of elites. We briefly discuss some common objections to the application of phylogenetic modeling to cultural evolution and argue that the use of these methods does not require a commitment to either gene-like cultural inheritance or to the view that cultures are like vertebrate species. We conclude that the careful application of these methods can substantially enhance the prospects of an evolutionary science of human history. PMID:28739960

Towards Complex Abiotic Systems for Chemical and Biological Sensing

DTIC Science & Technology

2009-11-01

such as phage display, cell surface display, and Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Other processes necessary to...Directed evolution by in vitro compartmentalization. Nat Methods 2006, 3, 561-570. l7Chelliserrykattil, J.; Ellington, A.D. Evolution of a T7 RNA

Quantifying selection and diversity in viruses by entropy methods, with application to the haemagglutinin of H3N2 influenza

PubMed Central

Pan, Keyao; Deem, Michael W.

2011-01-01

Many viruses evolve rapidly. For example, haemagglutinin (HA) of the H3N2 influenza A virus evolves to escape antibody binding. This evolution of the H3N2 virus means that people who have previously been exposed to an influenza strain may be infected by a newly emerged virus. In this paper, we use Shannon entropy and relative entropy to measure the diversity and selection pressure by an antibody in each amino acid site of H3 HA between the 1992–1993 season and the 2009–2010 season. Shannon entropy and relative entropy are two independent state variables that we use to characterize H3N2 evolution. The entropy method estimates future H3N2 evolution and migration using currently available H3 HA sequences. First, we show that the rate of evolution increases with the virus diversity in the current season. The Shannon entropy of the sequence in the current season predicts relative entropy between sequences in the current season and those in the next season. Second, a global migration pattern of H3N2 is assembled by comparing the relative entropy flows of sequences sampled in China, Japan, the USA and Europe. We verify this entropy method by describing two aspects of historical H3N2 evolution. First, we identify 54 amino acid sites in HA that have evolved in the past to evade the immune system. Second, the entropy method shows that epitopes A and B on the top of HA evolve most vigorously to escape antibody binding. Our work provides a novel entropy-based method to predict and quantify future H3N2 evolution and to describe the evolutionary history of H3N2. PMID:21543352

Numerical study of the vortex tube reconnection using vortex particle method on many graphics cards

NASA Astrophysics Data System (ADS)

Kudela, Henryk; Kosior, Andrzej

2014-08-01

Vortex Particle Methods are one of the most convenient ways of tracking the vorticity evolution. In the article we presented numerical recreation of the real life experiment concerning head-on collision of two vortex rings. In the experiment the evolution and reconnection of the vortex structures is tracked with passive markers (paint particles) which in viscous fluid does not follow the evolution of vorticity field. In numerical computations we showed the difference between vorticity evolution and movement of passive markers. The agreement with the experiment was very good. Due to problems with very long time of computations on a single processor the Vortex-in-Cell method was implemented on the multicore architecture of the graphics cards (GPUs). Vortex Particle Methods are very well suited for parallel computations. As there are myriads of particles in the flow and for each of them the same equations of motion have to be solved the SIMD architecture used in GPUs seems to be perfect. The main disadvantage in this case is the small amount of the RAM memory. To overcome this problem we created a multiGPU implementation of the VIC method. Some remarks on parallel computing are given in the article.

Deducing noninductive current profile from surface voltage evolution

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

Litwin, C.; Wukitch, S.; Hershkowitz, N.

Solving the resistive diffusion equation in the presence of a noninductive current source determines the time-evolution of the surface voltage. By inverting the problem the current drive profile can be determined from the surface voltage evolution. We show that under wide range of conditions the deduced profile is unique. If the conductivity profile is known, this method can be employed to infer the noninductive current profile, and, ipso facto, the profile of the total current. We discuss the application of this method to analyze the Alfven wave current drive experiments in Phaedrus-T.

MEvoLib v1.0: the first molecular evolution library for Python.

PubMed

Álvarez-Jarreta, Jorge; Ruiz-Pesini, Eduardo

2016-10-28

Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank's features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.

Concentration Places, Concentration Evolutions, and Online Information Retrieval Techniques for Calculating Them.

ERIC Educational Resources Information Center

Egghe, L.

1988-01-01

Presents a mathematical theory that can be used to define concentration places of objects within unordered classes. The application to research on the evolution of journals and subject areas is illustrated, and an online method of calculating concentration evolution is described. (1 references) (CLB)

Teaching Evolution: From SMART Objectives to Threshold Experience

ERIC Educational Resources Information Center

Wolf, Alexander; Akkaraju, Shylaja

2014-01-01

Despite the centrality of evolution to the study of biology, the pedagogical methods employed to teach the subject are often instructor-centered and rarely embedded in every topic throughout the curriculum. In addition, students' prior beliefs about evolution are often dismissed rather than incorporated into the classroom. In this article we…

Evolution dynamics modeling and simulation of logistics enterprise's core competence based on service innovation

NASA Astrophysics Data System (ADS)

Yang, Bo; Tong, Yuting

2017-04-01

With the rapid development of economy, the development of logistics enterprises in China is also facing a huge challenge, especially the logistics enterprises generally lack of core competitiveness, and service innovation awareness is not strong. Scholars in the process of studying the core competitiveness of logistics enterprises are mainly from the perspective of static stability, not from the perspective of dynamic evolution to explore. So the author analyzes the influencing factors and the evolution process of the core competence of logistics enterprises, using the method of system dynamics to study the cause and effect of the evolution of the core competence of logistics enterprises, construct a system dynamics model of evolution of core competence logistics enterprises, which can be simulated by vensim PLE. The analysis for the effectiveness and sensitivity of simulation model indicates the model can be used as the fitting of the evolution process of the core competence of logistics enterprises and reveal the process and mechanism of the evolution of the core competence of logistics enterprises, and provide management strategies for improving the core competence of logistics enterprises. The construction and operation of computer simulation model offers a kind of effective method for studying the evolution of logistics enterprise core competence.

Microstructural characterization and simulation of damage for geared sheet components

NASA Astrophysics Data System (ADS)

Gerstein, G.; Isik, K.; Gutknecht, F.; Sieczkarek, P.; Ewert, J.; Tekkaya, A. E.; Clausmeyer, T.; Nürnberger, F.

2017-09-01

The evolution of damage in geared components manufactured from steel sheets was investigated, to analyse the influence of damage caused by the sheet-bulk-metal forming. Due to the inhomogeneous and multi-axial deformation in the investigated parts, different aspects such as the location-dependent shape and size of voids are analysed by means of various microscopic methods. In particular, a method to characterize the state of damage evolution, i. e. void nucleation, growth and coalescence using scanning electron microscopy (SEM) is applied. The investigations reveal a strong dependence of the void area fraction, shape of voids and thus damage evolution on the loading mode. The microstructural analysis is complemented with FEM simulations using material models which consider the characteristics of the void evolution.

Arresting Evolution.

PubMed

Bull, James J; Barrick, Jeffrey E

2017-12-01

Evolution in the form of selective breeding has long been harnessed as a useful tool by humans. However, rapid evolution can also be a danger to our health and a stumbling block for biotechnology. Unwanted evolution can underlie the emergence of drug and pesticide resistance, cancer, and weeds. It makes live vaccines and engineered cells inherently unreliable and unpredictable, and therefore potentially unsafe. Yet, there are strategies that have been and can possibly be used to stop or slow many types of evolution. We review and classify existing population genetics-inspired methods for arresting evolution. Then, we discuss how genome editing techniques enable a radically new set of approaches to limit evolution. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Networks of lexical borrowing and lateral gene transfer in language and genome evolution

PubMed Central

List, Johann-Mattis; Nelson-Sathi, Shijulal; Geisler, Hans; Martin, William

2014-01-01

Like biological species, languages change over time. As noted by Darwin, there are many parallels between language evolution and biological evolution. Insights into these parallels have also undergone change in the past 150 years. Just like genes, words change over time, and language evolution can be likened to genome evolution accordingly, but what kind of evolution? There are fundamental differences between eukaryotic and prokaryotic evolution. In the former, natural variation entails the gradual accumulation of minor mutations in alleles. In the latter, lateral gene transfer is an integral mechanism of natural variation. The study of language evolution using biological methods has attracted much interest of late, most approaches focusing on language tree construction. These approaches may underestimate the important role that borrowing plays in language evolution. Network approaches that were originally designed to study lateral gene transfer may provide more realistic insights into the complexities of language evolution. PMID:24375688

Using hybridization networks to retrace the evolution of Indo-European languages.

PubMed

Willems, Matthieu; Lord, Etienne; Laforest, Louise; Labelle, Gilbert; Lapointe, François-Joseph; Di Sciullo, Anna Maria; Makarenkov, Vladimir

2016-09-06

Curious parallels between the processes of species and language evolution have been observed by many researchers. Retracing the evolution of Indo-European (IE) languages remains one of the most intriguing intellectual challenges in historical linguistics. Most of the IE language studies use the traditional phylogenetic tree model to represent the evolution of natural languages, thus not taking into account reticulate evolutionary events, such as language hybridization and word borrowing which can be associated with species hybridization and horizontal gene transfer, respectively. More recently, implicit evolutionary networks, such as split graphs and minimal lateral networks, have been used to account for reticulate evolution in linguistics. Striking parallels existing between the evolution of species and natural languages allowed us to apply three computational biology methods for reconstruction of phylogenetic networks to model the evolution of IE languages. We show how the transfer of methods between the two disciplines can be achieved, making necessary methodological adaptations. Considering basic vocabulary data from the well-known Dyen's lexical database, which contains word forms in 84 IE languages for the meanings of a 200-meaning Swadesh list, we adapt a recently developed computational biology algorithm for building explicit hybridization networks to study the evolution of IE languages and compare our findings to the results provided by the split graph and galled network methods. We conclude that explicit phylogenetic networks can be successfully used to identify donors and recipients of lexical material as well as the degree of influence of each donor language on the corresponding recipient languages. We show that our algorithm is well suited to detect reticulate relationships among languages, and present some historical and linguistic justification for the results obtained. Our findings could be further refined if relevant syntactic, phonological and morphological data could be analyzed along with the available lexical data.

Skulls and Human Evolution: The Use of Casts of Anthropoid Skulls in Teaching Concepts of Human Evolution.

ERIC Educational Resources Information Center

Gipps, John

1991-01-01

Proposes the use of a series of 11 casts of fossil skulls as a method of teaching about the theory of human evolution. Students explore the questions of which skulls are "human" and which came first in Homo Sapien development, large brain or upright stance. (MDH)

Teaching the Evolution of the Angiosperm Carpel.

ERIC Educational Resources Information Center

Laferriere, Joseph E.

1992-01-01

The carpel is a highly modified leaf enclosing the ovules. This article describes methods for teaching about the evolution of the carpel and the nature of carpel fusion. Presents an illustration of the evolution of the most common types of compound pistil arrangement from the ancestral single-carpel marginal type of placentation. (PR)

Non-linear hydrodynamical evolution of rotating relativistic stars: numerical methods and code tests

NASA Astrophysics Data System (ADS)

Font, José A.; Stergioulas, Nikolaos; Kokkotas, Kostas D.

2000-04-01

We present numerical hydrodynamical evolutions of rapidly rotating relativistic stars, using an axisymmetric, non-linear relativistic hydrodynamics code. We use four different high-resolution shock-capturing (HRSC) finite-difference schemes (based on approximate Riemann solvers) and compare their accuracy in preserving uniformly rotating stationary initial configurations in long-term evolutions. Among these four schemes, we find that the third-order piecewise parabolic method scheme is superior in maintaining the initial rotation law in long-term evolutions, especially near the surface of the star. It is further shown that HRSC schemes are suitable for the evolution of perturbed neutron stars and for the accurate identification (via Fourier transforms) of normal modes of oscillation. This is demonstrated for radial and quadrupolar pulsations in the non-rotating limit, where we find good agreement with frequencies obtained with a linear perturbation code. The code can be used for studying small-amplitude or non-linear pulsations of differentially rotating neutron stars, while our present results serve as testbed computations for three-dimensional general-relativistic evolution codes.

A Huygens immersed-finite-element particle-in-cell method for modeling plasma-surface interactions with moving interface

NASA Astrophysics Data System (ADS)

Cao, Huijun; Cao, Yong; Chu, Yuchuan; He, Xiaoming; Lin, Tao

2018-06-01

Surface evolution is an unavoidable issue in engineering plasma applications. In this article an iterative method for modeling plasma-surface interactions with moving interface is proposed and validated. In this method, the plasma dynamics is simulated by an immersed finite element particle-in-cell (IFE-PIC) method, and the surface evolution is modeled by the Huygens wavelet method which is coupled with the iteration of the IFE-PIC method. Numerical experiments, including prototypical engineering applications, such as the erosion of Hall thruster channel wall, are presented to demonstrate features of this Huygens IFE-PIC method for simulating the dynamic plasma-surface interactions.

Extant-only comparative methods fail to recover the disparity preserved in the bird fossil record.

PubMed

Mitchell, Jonathan S

2015-09-01

Most extant species are in clades with poor fossil records, and recent studies of comparative methods show they have low power to infer even highly simplified models of trait evolution without fossil data. Birds are a well-studied radiation, yet their early evolutionary patterns are still contentious. The fossil record suggests that birds underwent a rapid ecological radiation after the end-Cretaceous mass extinction, and several smaller, subsequent radiations. This hypothesized series of repeated radiations from fossil data is difficult to test using extant data alone. By uniting morphological and phylogenetic data on 604 extant genera of birds with morphological data on 58 species of extinct birds from 50 million years ago, the "halfway point" of avian evolution, I have been able to test how well extant-only methods predict the diversity of fossil forms. All extant-only methods underestimate the disparity, although the ratio of within- to between-clade disparity does suggest high early rates. The failure of standard models to predict high early disparity suggests that recent radiations are obscuring deep time patterns in the evolution of birds. Metrics from different models can be used in conjunction to provide more valuable insights than simply finding the model with the highest relative fit. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Biological intuition in alignment-free methods: response to Posada.

PubMed

Ragan, Mark A; Chan, Cheong Xin

2013-08-01

A recent editorial in Journal of Molecular Evolution highlights opportunities and challenges facing molecular evolution in the era of next-generation sequencing. Abundant sequence data should allow more-complex models to be fit at higher confidence, making phylogenetic inference more reliable and improving our understanding of evolution at the molecular level. However, concern that approaches based on multiple sequence alignment may be computationally infeasible for large datasets is driving the development of so-called alignment-free methods for sequence comparison and phylogenetic inference. The recent editorial characterized these approaches as model-free, not based on the concept of homology, and lacking in biological intuition. We argue here that alignment-free methods have not abandoned models or homology, and can be biologically intuitive.

Rotational stellar structures based on the Lagrangian variational principle

NASA Astrophysics Data System (ADS)

Yasutake, Nobutoshi; Fujisawa, Kotaro; Yamada, Shoichi

2017-06-01

A new method for multi-dimensional stellar structures is proposed in this study. As for stellar evolution calculations, the Heney method is the defacto standard now, but basically assumed to be spherical symmetric. It is one of the difficulties for deformed stellar-evolution calculations to trace the potentially complex movements of each fluid element. On the other hand, our new method is very suitable to follow such movements, since it is based on the Lagrange coordinate. This scheme is also based on the variational principle, which is adopted to the studies for the pasta structures inside of neutron stars. Our scheme could be a major break through for evolution calculations of any types of deformed stars: proto-planets, proto-stars, and proto-neutron stars, etc.

A single-shot spatial chirp method for measuring initial AC conductivity evolution of femtosecond laser pulse excited warm dense matter

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

Chen, Z.; Hering, P.; Brown, S. B.

To study the rapid evolution of AC conductivity from ultrafast laser excited warm dense matter (WDM), a spatial chirp single-shot method is developed utilizing a crossing angle pump-probe configuration. The pump beam is shaped individually in two spatial dimensions so that it can provide both sufficient laser intensity to excite the material to warm dense matter state and a uniform time window of up to 1 ps with sub-100 fs FWHM temporal resolution. Here, temporal evolution of AC conductivity in laser excited warm dense gold was also measured.

A single-shot spatial chirp method for measuring initial AC conductivity evolution of femtosecond laser pulse excited warm dense matter

DOE PAGES

Chen, Z.; Hering, P.; Brown, S. B.; ...

2016-09-19

To study the rapid evolution of AC conductivity from ultrafast laser excited warm dense matter (WDM), a spatial chirp single-shot method is developed utilizing a crossing angle pump-probe configuration. The pump beam is shaped individually in two spatial dimensions so that it can provide both sufficient laser intensity to excite the material to warm dense matter state and a uniform time window of up to 1 ps with sub-100 fs FWHM temporal resolution. Here, temporal evolution of AC conductivity in laser excited warm dense gold was also measured.

Averaging, passage through resonances, and capture into resonance in two-frequency systems

NASA Astrophysics Data System (ADS)

Neishtadt, A. I.

2014-10-01

Applying small perturbations to an integrable system leads to its slow evolution. For an approximate description of this evolution the classical averaging method prescribes averaging the rate of evolution over all the phases of the unperturbed motion. This simple recipe does not always produce correct results, because of resonances arising in the process of evolution. The phenomenon of capture into resonance consists in the system starting to evolve in such a way as to preserve the resonance property once it has arisen. This paper is concerned with application of the averaging method to a description of evolution in two-frequency systems. It is assumed that the trajectories of the averaged system intersect transversally the level surfaces of the frequency ratio and that certain other conditions of general position are satisfied. The rate of evolution is characterized by a small parameter \\varepsilon. The main content of the paper is a proof of the following result: outside a set of initial data with measure of order \\sqrt \\varepsilon the averaging method describes the evolution to within O(\\sqrt \\varepsilon \\vert\\ln\\varepsilon\\vert) for periods of time of order 1/\\varepsilon. This estimate is sharp. The exceptional set of measure \\sqrt \\varepsilon contains the initial data for phase points captured into resonance. A description of the motion of such phase points is given, along with a survey of related results on averaging. Examples of capture into resonance are presented for some problems in the dynamics of charged particles. Several open problems are stated. Bibliography: 65 titles.

A three-dimensional FEM-DEM technique for predicting the evolution of fracture in geomaterials and concrete

NASA Astrophysics Data System (ADS)

Zárate, Francisco; Cornejo, Alejandro; Oñate, Eugenio

2018-07-01

This paper extends to three dimensions (3D), the computational technique developed by the authors in 2D for predicting the onset and evolution of fracture in a finite element mesh in a simple manner based on combining the finite element method and the discrete element method (DEM) approach (Zárate and Oñate in Comput Part Mech 2(3):301-314, 2015). Once a crack is detected at an element edge, discrete elements are generated at the adjacent element vertexes and a simple DEM mechanism is considered in order to follow the evolution of the crack. The combination of the DEM with simple four-noded linear tetrahedron elements correctly captures the onset of fracture and its evolution, as shown in several 3D examples of application.

Incorporating information on predicted solvent accessibility to the co-evolution-based study of protein interactions.

PubMed

Ochoa, David; García-Gutiérrez, Ponciano; Juan, David; Valencia, Alfonso; Pazos, Florencio

2013-01-27

A widespread family of methods for studying and predicting protein interactions using sequence information is based on co-evolution, quantified as similarity of phylogenetic trees. Part of the co-evolution observed between interacting proteins could be due to co-adaptation caused by inter-protein contacts. In this case, the co-evolution is expected to be more evident when evaluated on the surface of the proteins or the internal layers close to it. In this work we study the effect of incorporating information on predicted solvent accessibility to three methods for predicting protein interactions based on similarity of phylogenetic trees. We evaluate the performance of these methods in predicting different types of protein associations when trees based on positions with different characteristics of predicted accessibility are used as input. We found that predicted accessibility improves the results of two recent versions of the mirrortree methodology in predicting direct binary physical interactions, while it neither improves these methods, nor the original mirrortree method, in predicting other types of interactions. That improvement comes at no cost in terms of applicability since accessibility can be predicted for any sequence. We also found that predictions of protein-protein interactions are improved when multiple sequence alignments with a richer representation of sequences (including paralogs) are incorporated in the accessibility prediction.

Symmetry reduction and exact solutions of two higher-dimensional nonlinear evolution equations.

PubMed

Gu, Yongyi; Qi, Jianming

2017-01-01

In this paper, symmetries and symmetry reduction of two higher-dimensional nonlinear evolution equations (NLEEs) are obtained by Lie group method. These NLEEs play an important role in nonlinear sciences. We derive exact solutions to these NLEEs via the [Formula: see text]-expansion method and complex method. Five types of explicit function solutions are constructed, which are rational, exponential, trigonometric, hyperbolic and elliptic function solutions of the variables in the considered equations.

REVIEWS OF TOPICAL PROBLEMS: Population synthesis in astrophysics

NASA Astrophysics Data System (ADS)

Popov, S. B.; Prokhorov, M. E.

2007-11-01

Population synthesis is a method for numerical simulation of the population of objects with a complex evolution. This method is widely used in astrophysics. We consider its main applications to studying astronomical objects. Examples of modeling evolution are given for populations of close binaries and isolated neutron stars. The application of the method to studying active galactic nuclei and the integral spectral characteristics of galaxies is briefly discussed. An extensive bibliography on all the topics covered is provided.

Unity and disunity in evolutionary sciences: process-based analogies open common research avenues for biology and linguistics.

PubMed

List, Johann-Mattis; Pathmanathan, Jananan Sylvestre; Lopez, Philippe; Bapteste, Eric

2016-08-20

For a long time biologists and linguists have been noticing surprising similarities between the evolution of life forms and languages. Most of the proposed analogies have been rejected. Some, however, have persisted, and some even turned out to be fruitful, inspiring the transfer of methods and models between biology and linguistics up to today. Most proposed analogies were based on a comparison of the research objects rather than the processes that shaped their evolution. Focusing on process-based analogies, however, has the advantage of minimizing the risk of overstating similarities, while at the same time reflecting the common strategy to use processes to explain the evolution of complexity in both fields. We compared important evolutionary processes in biology and linguistics and identified processes specific to only one of the two disciplines as well as processes which seem to be analogous, potentially reflecting core evolutionary processes. These new process-based analogies support novel methodological transfer, expanding the application range of biological methods to the field of historical linguistics. We illustrate this by showing (i) how methods dealing with incomplete lineage sorting offer an introgression-free framework to analyze highly mosaic word distributions across languages; (ii) how sequence similarity networks can be used to identify composite and borrowed words across different languages; (iii) how research on partial homology can inspire new methods and models in both fields; and (iv) how constructive neutral evolution provides an original framework for analyzing convergent evolution in languages resulting from common descent (Sapir's drift). Apart from new analogies between evolutionary processes, we also identified processes which are specific to either biology or linguistics. This shows that general evolution cannot be studied from within one discipline alone. In order to get a full picture of evolution, biologists and linguists need to complement their studies, trying to identify cross-disciplinary and discipline-specific evolutionary processes. The fact that we found many process-based analogies favoring transfer from biology to linguistics further shows that certain biological methods and models have a broader scope than previously recognized. This opens fruitful paths for collaboration between the two disciplines. This article was reviewed by W. Ford Doolittle and Eugene V. Koonin.

A simple and general method for solving detailed chemical evolution with delayed production of iron and other chemical elements

NASA Astrophysics Data System (ADS)

Vincenzo, F.; Matteucci, F.; Spitoni, E.

2017-04-01

We present a theoretical method for solving the chemical evolution of galaxies by assuming an instantaneous recycling approximation for chemical elements restored by massive stars and the delay time distribution formalism for delayed chemical enrichment by Type Ia Supernovae. The galaxy gas mass assembly history, together with the assumed stellar yields and initial mass function, represents the starting point of this method. We derive a simple and general equation, which closely relates the Laplace transforms of the galaxy gas accretion history and star formation history, which can be used to simplify the problem of retrieving these quantities in the galaxy evolution models assuming a linear Schmidt-Kennicutt law. We find that - once the galaxy star formation history has been reconstructed from our assumptions - the differential equation for the evolution of the chemical element X can be suitably solved with classical methods. We apply our model to reproduce the [O/Fe] and [Si/Fe] versus [Fe/H] chemical abundance patterns as observed at the solar neighbourhood by assuming a decaying exponential infall rate of gas and different delay time distributions for Type Ia Supernovae; we also explore the effect of assuming a non-linear Schmidt-Kennicutt law, with the index of the power law being k = 1.4. Although approximate, we conclude that our model with the single-degenerate scenario for Type Ia Supernovae provides the best agreement with the observed set of data. Our method can be used by other complementary galaxy stellar population synthesis models to predict also the chemical evolution of galaxies.

Perceptions of High School Biology Teachers in Christian Schools on Relationships between Religious Beliefs and Teaching Evolution

ERIC Educational Resources Information Center

Mangahas, Ana Marie E.

2017-01-01

This mixed method study explored Christian teachers' beliefs in religious schools on evolution, their attitudes toward evolution, and their perceptions on the effect of those beliefs on the teaching of evolutionary content. Teachers (N = 52) from Association for Christian Schools International (ACSI) accredited schools in California and Hawaii…

The orbital evolution of the asteroid 4179 Toutatis during 11,550 years

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Pushkaryov, A. N.

The orbital evolution of the asteroid 4179 Toutatis was followed by the Everhart method in the time interval 2250 AD to 9300 BC. The closest encounters with Earth are calculated in the evolution process. It is shown that this asteroid is not dangerous for Earth during the time interval 2250 AD to 9300 BC.

Methods for Prediction of High-Speed Reacting Flows in Aerospace Propulsion

NASA Technical Reports Server (NTRS)

Drummond, J. Philip

2014-01-01

Research to develop high-speed airbreathing aerospace propulsion systems was underway in the late 1950s. A major part of the effort involved the supersonic combustion ramjet, or scramjet, engine. Work had also begun to develop computational techniques for solving the equations governing the flow through a scramjet engine. However, scramjet technology and the computational methods to assist in its evolution would remain apart for another decade. The principal barrier was that the computational methods needed for engine evolution lacked the computer technology required for solving the discrete equations resulting from the numerical methods. Even today, computer resources remain a major pacing item in overcoming this barrier. Significant advances have been made over the past 35 years, however, in modeling the supersonic chemically reacting flow in a scramjet combustor. To see how scramjet development and the required computational tools finally merged, we briefly trace the evolution of the technology in both areas.

Exact stochastic unraveling of an optical coherence dynamics by cumulant expansion

NASA Astrophysics Data System (ADS)

Olšina, Jan; Kramer, Tobias; Kreisbeck, Christoph; Mančal, Tomáš

2014-10-01

A numerically exact Monte Carlo scheme for calculation of open quantum system dynamics is proposed and implemented. The method consists of a Monte Carlo summation of a perturbation expansion in terms of trajectories in Liouville phase-space with respect to the coupling between the excited states of the molecule. The trajectories are weighted by a complex decoherence factor based on the second-order cumulant expansion of the environmental evolution. The method can be used with an arbitrary environment characterized by a general correlation function and arbitrary coupling strength. It is formally exact for harmonic environments, and it can be used with arbitrary temperature. Time evolution of an optically excited Frenkel exciton dimer representing a molecular exciton interacting with a charge transfer state is calculated by the proposed method. We calculate the evolution of the optical coherence elements of the density matrix and linear absorption spectrum, and compare them with the predictions of standard simulation methods.

A Hybrid Approach to Data Assimilation for Reconstructing the Evolution of Mantle Dynamics

NASA Astrophysics Data System (ADS)

Zhou, Quan; Liu, Lijun

2017-11-01

Quantifying past mantle dynamic processes represents a major challenge in understanding the temporal evolution of the solid earth. Mantle convection modeling with data assimilation is one of the most powerful tools to investigate the dynamics of plate subduction and mantle convection. Although various data assimilation methods, both forward and inverse, have been created, these methods all have limitations in their capabilities to represent the real earth. Pure forward models tend to miss important mantle structures due to the incorrect initial condition and thus may lead to incorrect mantle evolution. In contrast, pure tomography-based models cannot effectively resolve the fine slab structure and would fail to predict important subduction-zone dynamic processes. Here we propose a hybrid data assimilation approach that combines the unique power of the sequential and adjoint algorithms, which can properly capture the detailed evolution of the downgoing slab and the tomographically constrained mantle structures, respectively. We apply this new method to reconstructing mantle dynamics below the western U.S. while considering large lateral viscosity variations. By comparing this result with those from several existing data assimilation methods, we demonstrate that the hybrid modeling approach recovers the realistic 4-D mantle dynamics the best.

Trends in the sand: Directional evolution in the shell shape of recessing scallops (Bivalvia: Pectinidae).

PubMed

Sherratt, Emma; Alejandrino, Alvin; Kraemer, Andrew C; Serb, Jeanne M; Adams, Dean C

2016-09-01

Directional evolution is one of the most compelling evolutionary patterns observed in macroevolution. Yet, despite its importance, detecting such trends in multivariate data remains a challenge. In this study, we evaluate multivariate evolution of shell shape in 93 bivalved scallop species, combining geometric morphometrics and phylogenetic comparative methods. Phylomorphospace visualization described the history of morphological diversification in the group; revealing that taxa with a recessing life habit were the most distinctive in shell shape, and appeared to display a directional trend. To evaluate this hypothesis empirically, we extended existing methods by characterizing the mean directional evolution in phylomorphospace for recessing scallops. We then compared this pattern to what was expected under several alternative evolutionary scenarios using phylogenetic simulations. The observed pattern did not fall within the distribution obtained under multivariate Brownian motion, enabling us to reject this evolutionary scenario. By contrast, the observed pattern was more similar to, and fell within, the distribution obtained from simulations using Brownian motion combined with a directional trend. Thus, the observed data are consistent with a pattern of directional evolution for this lineage of recessing scallops. We discuss this putative directional evolutionary trend in terms of its potential adaptive role in exploiting novel habitats. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Cascade Defect Evolution Processes: Comparison of Atomistic Methods

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

Xu, Haixuan; Stoller, Roger E; Osetskiy, Yury N

2013-11-01

Determining the defect evolution beyond the molecular dynamics (MD) time scale is critical in bridging the gap between atomistic simulations and experiments. The recently developed self-evolving atomistic kinetic Monte Carlo (SEAKMC) method provides new opportunities to simulate long-term defect evolution with MD-like fidelity. In this study, SEAKMC is applied to investigate the cascade defect evolution in bcc iron. First, the evolution of a vacancy rich region is simulated and compared with results obtained using autonomous basin climbing (ABC) +KMC and kinetic activation-relaxation technique (kART) simulations. Previously, it is found the results from kART are orders of magnitude faster than ABC+KMC.more » The results obtained from SEAKMC are similar to kART but the time predicted is about one order of magnitude faster than kART. The fidelity of SEAKMC is confirmed by statistically relevant MD simulations at multiple higher temperatures, which proves that the saddle point sampling is close to complete in SEAKMC. The second is the irradiation-induced formation of C15 Laves phase nano-size defect clusters. In contrast to previous studies, which claim the defects can grow by capturing self-interstitials, we found these highly stable clusters can transform to <111> glissile configuration on a much longer time scale. Finally, cascade-annealing simulations using SEAKMC is compared with traditional object KMC (OKMC) method. SEAKMC predicts substantially fewer surviving defects compared with OKMC. The possible origin of this difference is discussed and a possible way to improve the accuracy of OKMC based on SEAKMC results is outlined. These studies demonstrate the atomistic fidelity of SEAKMC in comparison with other on-the-fly KMC methods and provide new information on long-term defect evolution in iron.« less

Thermography detection on the fatigue damage

NASA Astrophysics Data System (ADS)

Yang, Bing

It has always been a great temptation in finding new methods to in-situ "watch" the material fatigue-damage processes so that in-time reparations will be possible, and failures or losses can be minimized to the maximum extent. Realizing that temperature patterns may serve as fingerprints for stress-strain behaviors of materials, a state-of-art infrared (IR) thermography camera has been used to "watch" the temperature evolutions of both crystalline and amorphous materials "cycle by cycle" during fatigue experiments in the current research. The two-dimensional (2D) thermography technique records the surface-temperature evolutions of materials. Since all plastic deformations are related to heat dissipations, thermography provides an innovative method to in-situ monitor the heat-evolution processes, including plastic-deformation, mechanical-damage, and phase-transformation characteristics. With the understanding of the temperature evolutions during fatigue, thermography could provide the direct information and evidence of the stress-strain distribution, crack initiation and propagation, shear-band growth, and plastic-zone evolution, which will open up wide applications in studying the structural integrity of engineering components in service. In the current research, theoretical models combining thermodynamics and heat-conduction theory have been developed. Key issues in fatigue, such as in-situ stress-strain states, cyclic softening and hardening observations, and fatigue-life predictions, have been resolved by simply monitoring the specimen-temperature variation during fatigue. Furthermore, in-situ visulizations as well as qualitative and quantitative analyses of fatigue-damage processes, such as Luders-band evolutions, crack propagation, plastic zones, and final fracture, have been performed by thermography. As a method requiring no special sample preparation or surface contact by sensors, thermography provides an innovative and convenient method to in-situ monitor and analyze the mechanical-damage processes of materials and components.

A novel method of multi-scale simulation of macro-scale deformation and microstructure evolution on metal forming

NASA Astrophysics Data System (ADS)

Huang, Shiquan; Yi, Youping; Li, Pengchuan

2011-05-01

In recent years, multi-scale simulation technique of metal forming is gaining significant attention for prediction of the whole deformation process and microstructure evolution of product. The advances of numerical simulation at macro-scale level on metal forming are remarkable and the commercial FEM software, such as Deform2D/3D, has found a wide application in the fields of metal forming. However, the simulation method of multi-scale has little application due to the non-linearity of microstructure evolution during forming and the difficulty of modeling at the micro-scale level. This work deals with the modeling of microstructure evolution and a new method of multi-scale simulation in forging process. The aviation material 7050 aluminum alloy has been used as example for modeling of microstructure evolution. The corresponding thermal simulated experiment has been performed on Gleeble 1500 machine. The tested specimens have been analyzed for modeling of dislocation density, nucleation and growth of recrystallization(DRX). The source program using cellular automaton (CA) method has been developed to simulate the grain nucleation and growth, in which the change of grain topology structure caused by the metal deformation was considered. The physical fields at macro-scale level such as temperature field, stress and strain fields, which can be obtained by commercial software Deform 3D, are coupled with the deformed storage energy at micro-scale level by dislocation model to realize the multi-scale simulation. This method was explained by forging process simulation of the aircraft wheel hub forging. Coupled the results of Deform 3D with CA results, the forging deformation progress and the microstructure evolution at any point of forging could be simulated. For verifying the efficiency of simulation, experiments of aircraft wheel hub forging have been done in the laboratory and the comparison of simulation and experiment result has been discussed in details.

Identifying heterogeneity in rates of morphological evolution: discrete character change in the evolution of lungfish (Sarcopterygii; Dipnoi).

PubMed

Lloyd, Graeme T; Wang, Steve C; Brusatte, Stephen L

2012-02-01

Quantifying rates of morphological evolution is important in many macroevolutionary studies, and critical when assessing possible adaptive radiations and episodes of punctuated equilibrium in the fossil record. However, studies of morphological rates of change have lagged behind those on taxonomic diversification, and most authors have focused on continuous characters and quantifying patterns of morphological rates over time. Here, we provide a phylogenetic approach, using discrete characters and three statistical tests to determine points on a cladogram (branches or entire clades) that are characterized by significantly high or low rates of change. These methods include a randomization approach that identifies branches with significantly high rates and likelihood ratio tests that pinpoint either branches or clades that have significantly higher or lower rates than the pooled rate of the remainder of the tree. As a test case for these methods, we analyze a discrete character dataset of lungfish, which have long been regarded as "living fossils" due to an apparent slowdown in rates since the Devonian. We find that morphological rates are highly heterogeneous across the phylogeny and recover a general pattern of decreasing rates along the phylogenetic backbone toward living taxa, from the Devonian until the present. Compared with previous work, we are able to report a more nuanced picture of lungfish evolution using these new methods. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Dynamic and quantitative method of analyzing service consistency evolution based on extended hierarchical finite state automata.

PubMed

Fan, Linjun; Tang, Jun; Ling, Yunxiang; Li, Benxian

2014-01-01

This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA). Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service's evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA) is constructed based on finite state automata (FSA), which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs) based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average) is the biggest influential factor, the noncomposition of atomic services (13.12%) is the second biggest one, and the service version's confusion (1.2%) is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA.

Dynamic and Quantitative Method of Analyzing Service Consistency Evolution Based on Extended Hierarchical Finite State Automata

PubMed Central

Fan, Linjun; Tang, Jun; Ling, Yunxiang; Li, Benxian

2014-01-01

This paper is concerned with the dynamic evolution analysis and quantitative measurement of primary factors that cause service inconsistency in service-oriented distributed simulation applications (SODSA). Traditional methods are mostly qualitative and empirical, and they do not consider the dynamic disturbances among factors in service's evolution behaviors such as producing, publishing, calling, and maintenance. Moreover, SODSA are rapidly evolving in terms of large-scale, reusable, compositional, pervasive, and flexible features, which presents difficulties in the usage of traditional analysis methods. To resolve these problems, a novel dynamic evolution model extended hierarchical service-finite state automata (EHS-FSA) is constructed based on finite state automata (FSA), which formally depict overall changing processes of service consistency states. And also the service consistency evolution algorithms (SCEAs) based on EHS-FSA are developed to quantitatively assess these impact factors. Experimental results show that the bad reusability (17.93% on average) is the biggest influential factor, the noncomposition of atomic services (13.12%) is the second biggest one, and the service version's confusion (1.2%) is the smallest one. Compared with previous qualitative analysis, SCEAs present good effectiveness and feasibility. This research can guide the engineers of service consistency technologies toward obtaining a higher level of consistency in SODSA. PMID:24772033

Surface phenomena and the evolution of radiating fluid spheres in general relativity

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

Herrera, L.; Jimenez, J.; Esculpi, M.

1989-10-01

A method used to study the evolution of radiating spheres (Herrera, Jimenez, and Ruggeri) is extended to the case in which surface phenomena are taken into account. The equations have been integrated numerically for a model derived from the Schwarzschild interior solution, bringing out the effects of surface tension on the evolution of the spheres. 17 refs.

Investigating Greek Biology Teachers' Attitudes towards Evolution Teaching with Respect to Their Pedagogical Content Knowledge: Suggestions for Their Professional Development

ERIC Educational Resources Information Center

Stasinakis, Panagiotis K.; Athanasiou, Kyriacos

2016-01-01

Evolution Teaching (ET) among in-service teachers in Greece was examined in an attempt to evaluate their Pedagogical Content Knowledge. Evolution teaching is a problematic issue. For this purpose, we constructed a questionnaire that was distributed to the target population and to which 181 teachers responded. We used quantitative method to…

Evolution of the orbit of asteroid 4179 Toutatis over 11,550 years.

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Pushkarev, A. N.

1994-05-01

The Everhart method is used to study evolution of the orbit of the asteroid 4179 Toutatis, a member of the Apollo group, over the time period 9300 B.C. to 2250 A.D. Minimum asteroid-Earth distances during the evolution process are calculated. It is shown that the asteroid presents no danger to the Earth over the interval studied.

Crustal Movement: A Major Force in Evolution. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Review of investigations performed in the USSR on close approaches of comets to Jupiter and the evolution of cometary orbits

NASA Technical Reports Server (NTRS)

Kazimirchak-Polonskaya, E. I.

1976-01-01

Methods are reviewed for calculating the evolution of cometary orbits with emphasis on the orbital changes that take place when comets pass within the spheres of action of giant planets. Topics discussed include: differences and difficulties in methods used for the calculation of large perturbations by Jupiter; the construction of numerical theories of motion covering the whole period of observations of each comet, allowing for planetary perturbations and the effects of nongravitational forces; and investigations of the evolution of cometary orbits over the 400 year interval 1660-2060. The classical theory of cometary capture is briefly discussed.

Evolution of statistical averages: An interdisciplinary proposal using the Chapman-Enskog method

NASA Astrophysics Data System (ADS)

Mariscal-Sanchez, A.; Sandoval-Villalbazo, A.

2017-08-01

This work examines the idea of applying the Chapman-Enskog (CE) method for approximating the solution of the Boltzmann equation beyond the realm of physics, using an information theory approach. Equations describing the evolution of averages and their fluctuations in a generalized phase space are established up to first-order in the Knudsen parameter which is defined as the ratio of the time between interactions (mean free time) and a characteristic macroscopic time. Although the general equations here obtained may be applied in a wide range of disciplines, in this paper, only a particular case related to the evolution of averages in speculative markets is examined.

Relatedness, conflict, and the evolution of eusociality.

PubMed

Liao, Xiaoyun; Rong, Stephen; Queller, David C

2015-03-01

The evolution of sterile worker castes in eusocial insects was a major problem in evolutionary theory until Hamilton developed a method called inclusive fitness. He used it to show that sterile castes could evolve via kin selection, in which a gene for altruistic sterility is favored when the altruism sufficiently benefits relatives carrying the gene. Inclusive fitness theory is well supported empirically and has been applied to many other areas, but a recent paper argued that the general method of inclusive fitness was wrong and advocated an alternative population genetic method. The claim of these authors was bolstered by a new model of the evolution of eusociality with novel conclusions that appeared to overturn some major results from inclusive fitness. Here we report an expanded examination of this kind of model for the evolution of eusociality and show that all three of its apparently novel conclusions are essentially false. Contrary to their claims, genetic relatedness is important and causal, workers are agents that can evolve to be in conflict with the queen, and eusociality is not so difficult to evolve. The misleading conclusions all resulted not from incorrect math but from overgeneralizing from narrow assumptions or parameter values. For example, all of their models implicitly assumed high relatedness, but modifying the model to allow lower relatedness shows that relatedness is essential and causal in the evolution of eusociality. Their modeling strategy, properly applied, actually confirms major insights of inclusive fitness studies of kin selection. This broad agreement of different models shows that social evolution theory, rather than being in turmoil, is supported by multiple theoretical approaches. It also suggests that extensive prior work using inclusive fitness, from microbial interactions to human evolution, should be considered robust unless shown otherwise.

F-Expansion Method and New Exact Solutions of the Schrödinger-KdV Equation

PubMed Central

Filiz, Ali; Ekici, Mehmet; Sonmezoglu, Abdullah

2014-01-01

F-expansion method is proposed to seek exact solutions of nonlinear evolution equations. With the aid of symbolic computation, we choose the Schrödinger-KdV equation with a source to illustrate the validity and advantages of the proposed method. A number of Jacobi-elliptic function solutions are obtained including the Weierstrass-elliptic function solutions. When the modulus m of Jacobi-elliptic function approaches to 1 and 0, soliton-like solutions and trigonometric-function solutions are also obtained, respectively. The proposed method is a straightforward, short, promising, and powerful method for the nonlinear evolution equations in mathematical physics. PMID:24672327

F-expansion method and new exact solutions of the Schrödinger-KdV equation.

PubMed

Filiz, Ali; Ekici, Mehmet; Sonmezoglu, Abdullah

2014-01-01

F-expansion method is proposed to seek exact solutions of nonlinear evolution equations. With the aid of symbolic computation, we choose the Schrödinger-KdV equation with a source to illustrate the validity and advantages of the proposed method. A number of Jacobi-elliptic function solutions are obtained including the Weierstrass-elliptic function solutions. When the modulus m of Jacobi-elliptic function approaches to 1 and 0, soliton-like solutions and trigonometric-function solutions are also obtained, respectively. The proposed method is a straightforward, short, promising, and powerful method for the nonlinear evolution equations in mathematical physics.

FFT-based computation of the bioheat transfer equation for the HCC ultrasound surgery therapy modeling.

PubMed

Dillenseger, Jean-Louis; Esneault, Simon; Garnier, Carole

2008-01-01

This paper describes a modeling method of the tissue temperature evolution over time in hyperthermia. More precisely, this approach is used to simulate the hepatocellular carcinoma curative treatment by a percutaneous high intensity ultrasound surgery. The tissue temperature evolution over time is classically described by Pennes' bioheat transfer equation which is generally solved by a finite difference method. In this paper we will present a method where the bioheat transfer equation can be algebraically solved after a Fourier transformation over the space coordinates. The implementation and boundary conditions of this method will be shown and compared with the finite difference method.

Bayesian nonparametric clustering in phylogenetics: modeling antigenic evolution in influenza.

PubMed

Cybis, Gabriela B; Sinsheimer, Janet S; Bedford, Trevor; Rambaut, Andrew; Lemey, Philippe; Suchard, Marc A

2018-01-30

Influenza is responsible for up to 500,000 deaths every year, and antigenic variability represents much of its epidemiological burden. To visualize antigenic differences across many viral strains, antigenic cartography methods use multidimensional scaling on binding assay data to map influenza antigenicity onto a low-dimensional space. Analysis of such assay data ideally leads to natural clustering of influenza strains of similar antigenicity that correlate with sequence evolution. To understand the dynamics of these antigenic groups, we present a framework that jointly models genetic and antigenic evolution by combining multidimensional scaling of binding assay data, Bayesian phylogenetic machinery and nonparametric clustering methods. We propose a phylogenetic Chinese restaurant process that extends the current process to incorporate the phylogenetic dependency structure between strains in the modeling of antigenic clusters. With this method, we are able to use the genetic information to better understand the evolution of antigenicity throughout epidemics, as shown in applications of this model to H1N1 influenza. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Evolution of self-reporting methods for identifying discrete emotions in science classrooms

NASA Astrophysics Data System (ADS)

Ritchie, Stephen M.; Hudson, Peter; Bellocchi, Alberto; Henderson, Senka; King, Donna; Tobin, Kenneth

2016-09-01

Emotion researchers have grappled with challenging methodological issues in capturing emotions of participants in naturalistic settings such as school or university classrooms. Self-reporting methods have been used frequently, yet these methods are inadequate when used alone. We argue that the self-reporting methods of emotion diaries and cogenerative dialogues can be helpful in identifying in-the-moment emotions when used in conjunction with the microanalysis of video recordings of classroom events. We trace the evolution of our use of innovative self-reporting methods through three cases from our research projects, and propose new directions for our ongoing development and application of these methods in both school and university classrooms.

Vorticity vector-potential method based on time-dependent curvilinear coordinates for two-dimensional rotating flows in closed configurations

NASA Astrophysics Data System (ADS)

Fu, Yuan; Zhang, Da-peng; Xie, Xi-lin

2018-04-01

In this study, a vorticity vector-potential method for two-dimensional viscous incompressible rotating driven flows is developed in the time-dependent curvilinear coordinates. The method is applicable in both inertial and non-inertial frames of reference with the advantage of a fixed and regular calculation domain. The numerical method is applied to triangle and curved triangle configurations in constant and varying rotational angular velocity cases respectively. The evolutions of flow field are studied. The geostrophic effect, unsteady effect and curvature effect on the evolutions are discussed.

Vorticity vector-potential method based on time-dependent curvilinear coordinates for two-dimensional rotating flows in closed configurations

NASA Astrophysics Data System (ADS)

Fu, Yuan; Zhang, Da-peng; Xie, Xi-lin

2018-03-01

In this study, a vorticity vector-potential method for two-dimensional viscous incompressible rotating driven flows is developed in the time-dependent curvilinear coordinates. The method is applicable in both inertial and non-inertial frames of reference with the advantage of a fixed and regular calculation domain. The numerical method is applied to triangle and curved triangle configurations in constant and varying rotational angular velocity cases respectively. The evolutions of flow field are studied. The geostrophic effect, unsteady effect and curvature effect on the evolutions are discussed.

Directed evolution: an approach to engineer enzymes.

PubMed

Kaur, Jasjeet; Sharma, Rohit

2006-01-01

Directed evolution is being used increasingly in industrial and academic laboratories to modify and improve commercially important enzymes. Laboratory evolution is thought to make its biggest contribution in explorations of non-natural functions, by allowing us to distinguish the properties nurtured by evolution. In this review we report the significant advances achieved with respect to the methods of biocatalyst improvement and some critical properties and applications of the modified enzymes. The application of directed evolution has been elaborately demonstrated for protein solubility, stability and catalytic efficiency. Modification of certain enzymes for their application in enantioselective catalysis has also been elucidated. By providing a simple and reliable route to enzyme improvement, directed evolution has emerged as a key technology for enzyme engineering and biocatalysis.

Simulation of Corrosion Process for Structure with the Cellular Automata Method

NASA Astrophysics Data System (ADS)

Chen, M. C.; Wen, Q. Q.

2017-06-01

In this paper, from the mesoscopic point of view, under the assumption of metal corrosion damage evolution being a diffusive process, the cellular automata (CA) method was proposed to simulate numerically the uniform corrosion damage evolution of outer steel tube of concrete filled steel tubular columns subjected to corrosive environment, and the effects of corrosive agent concentration, dissolution probability and elapsed etching time on the corrosion damage evolution were also investigated. It was shown that corrosion damage increases nonlinearly with increasing elapsed etching time, and the longer the etching time, the more serious the corrosion damage; different concentration of corrosive agents had different impacts on the corrosion damage degree of the outer steel tube, but the difference between the impacts was very small; the heavier the concentration, the more serious the influence. The greater the dissolution probability, the more serious the corrosion damage of the outer steel tube, but with the increase of dissolution probability, the difference between its impacts on the corrosion damage became smaller and smaller. To validate present method, corrosion damage measurements for concrete filled square steel tubular columns (CFSSTCs) sealed at both their ends and immersed fully in a simulating acid rain solution were conducted, and Faraday’s law was used to predict their theoretical values. Meanwhile, the proposed CA mode was applied for the simulation of corrosion damage evolution of the CFSSTCs. It was shown by the comparisons of results from the three methods aforementioned that they were in good agreement, implying that the proposed method used for the simulation of corrosion damage evolution of concrete filled steel tubular columns is feasible and effective. It will open a new approach to study and evaluate further the corrosion damage, loading capacity and lifetime prediction of concrete filled steel tubular structures.

An adaptively refined phase-space element method for cosmological simulations and collisionless dynamics

NASA Astrophysics Data System (ADS)

Hahn, Oliver; Angulo, Raul E.

2016-01-01

N-body simulations are essential for understanding the formation and evolution of structure in the Universe. However, the discrete nature of these simulations affects their accuracy when modelling collisionless systems. We introduce a new approach to simulate the gravitational evolution of cold collisionless fluids by solving the Vlasov-Poisson equations in terms of adaptively refineable `Lagrangian phase-space elements'. These geometrical elements are piecewise smooth maps between Lagrangian space and Eulerian phase-space and approximate the continuum structure of the distribution function. They allow for dynamical adaptive splitting to accurately follow the evolution even in regions of very strong mixing. We discuss in detail various one-, two- and three-dimensional test problems to demonstrate the performance of our method. Its advantages compared to N-body algorithms are: (I) explicit tracking of the fine-grained distribution function, (II) natural representation of caustics, (III) intrinsically smooth gravitational potential fields, thus (IV) eliminating the need for any type of ad hoc force softening. We show the potential of our method by simulating structure formation in a warm dark matter scenario. We discuss how spurious collisionality and large-scale discreteness noise of N-body methods are both strongly suppressed, which eliminates the artificial fragmentation of filaments. Therefore, we argue that our new approach improves on the N-body method when simulating self-gravitating cold and collisionless fluids, and is the first method that allows us to explicitly follow the fine-grained evolution in six-dimensional phase-space.

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.

Study of travelling wave solutions for some special-type nonlinear evolution equations

NASA Astrophysics Data System (ADS)

Song, Junquan; Hu, Lan; Shen, Shoufeng; Ma, Wen-Xiu

2018-07-01

The tanh-function expansion method has been improved and used to construct travelling wave solutions of the form U={\\sum }j=0n{a}j{\\tanh }jξ for some special-type nonlinear evolution equations, which have a variety of physical applications. The positive integer n can be determined by balancing the highest order linear term with the nonlinear term in the evolution equations. We improve the tanh-function expansion method with n = 0 by introducing a new transform U=-W\\prime (ξ )/{W}2. A nonlinear wave equation with source terms, and mKdV-type equations, are considered in order to show the effectiveness of the improved scheme. We also propose the tanh-function expansion method of implicit function form, and apply it to a Harry Dym-type equation as an example.

The orbital evolution of the Aten asteroids over 11,550 years (9300 BC to 2250 AD)

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Pushkarev, A. N.

1991-04-01

The orbital evolution of five Aten asteroids was monitored by the Everhart method in the time interval from 9300 BC to 2250 AD. The closest encounters with large planets in the evolution process are calculated. Four out of five asteroids exhibit stable resonances with earth and Venus over the period from 9300 BC to 2250 AD.

Pulse retrieval algorithm for interferometric frequency-resolved optical gating based on differential evolution.

PubMed

Hyyti, Janne; Escoto, Esmerando; Steinmeyer, Günter

2017-10-01

A novel algorithm for the ultrashort laser pulse characterization method of interferometric frequency-resolved optical gating (iFROG) is presented. Based on a genetic method, namely, differential evolution, the algorithm can exploit all available information of an iFROG measurement to retrieve the complex electric field of a pulse. The retrieval is subjected to a series of numerical tests to prove the robustness of the algorithm against experimental artifacts and noise. These tests show that the integrated error-correction mechanisms of the iFROG method can be successfully used to remove the effect from timing errors and spectrally varying efficiency in the detection. Moreover, the accuracy and noise resilience of the new algorithm are shown to outperform retrieval based on the generalized projections algorithm, which is widely used as the standard method in FROG retrieval. The differential evolution algorithm is further validated with experimental data, measured with unamplified three-cycle pulses from a mode-locked Ti:sapphire laser. Additionally introducing group delay dispersion in the beam path, the retrieval results show excellent agreement with independent measurements with a commercial pulse measurement device based on spectral phase interferometry for direct electric-field retrieval. Further experimental tests with strongly attenuated pulses indicate resilience of differential-evolution-based retrieval against massive measurement noise.

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

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

Nakamachi, Eiji; Yoshida, Takashi; Yamaguchi, Toshihiko

2014-10-06

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture andmore » hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.« less

Process metallurgy simulation for metal drawing process optimization by using two-scale finite element method

NASA Astrophysics Data System (ADS)

Nakamachi, Eiji; Yoshida, Takashi; Kuramae, Hiroyuki; Morimoto, Hideo; Yamaguchi, Toshihiko; Morita, Yusuke

2014-10-01

We developed two-scale FE analysis procedure based on the crystallographic homogenization method by considering the hierarchical structure of poly-crystal aluminium alloy metal. It can be characterized as the combination of two-scale structure, such as the microscopic polycrystal structure and the macroscopic elastic plastic continuum. Micro polycrystal structure can be modeled as a three dimensional representative volume element (RVE). RVE is featured as by 3×3×3 eight-nodes solid finite elements, which has 216 crystal orientations. This FE analysis code can predict the deformation, strain and stress evolutions in the wire drawing processes in the macro- scales, and further the crystal texture and hardening evolutions in the micro-scale. In this study, we analyzed the texture evolution in the wire drawing processes by our two-scale FE analysis code under conditions of various drawing angles of dice. We evaluates the texture evolution in the surface and center regions of the wire cross section, and to clarify the effects of processing conditions on the texture evolution.

Subsonic aircraft: Evolution and the matching of size to performance

NASA Technical Reports Server (NTRS)

Loftin, L. K., Jr.

1980-01-01

Methods for estimating the approximate size, weight, and power of aircraft intended to meet specified performance requirements are presented for both jet-powered and propeller-driven aircraft. The methods are simple and require only the use of a pocket computer for rapid application to specific sizing problems. Application of the methods is illustrated by means of sizing studies of a series of jet-powered and propeller-driven aircraft with varying design constraints. Some aspects of the technical evolution of the airplane from 1918 to the present are also briefly discussed.

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

PubMed Central

Cruz-Aceves, I.; Avina-Cervantes, J. G.; Lopez-Hernandez, J. M.; Rostro-Gonzalez, H.; Garcia-Capulin, C. H.; Torres-Cisneros, M.; Guzman-Cabrera, R.

2013-01-01

This paper presents a new image segmentation method based on multiple active contours guided by differential evolution, called MACDE. The segmentation method uses differential evolution over a polar coordinate system to increase the exploration and exploitation capabilities regarding the classical active contour model. To evaluate the performance of the proposed method, a set of synthetic images with complex objects, Gaussian noise, and deep concavities is introduced. Subsequently, MACDE is applied on datasets of sequential computed tomography and magnetic resonance images which contain the human heart and the human left ventricle, respectively. Finally, to obtain a quantitative and qualitative evaluation of the medical image segmentations compared to regions outlined by experts, a set of distance and similarity metrics has been adopted. According to the experimental results, MACDE outperforms the classical active contour model and the interactive Tseng method in terms of efficiency and robustness for obtaining the optimal control points and attains a high accuracy segmentation. PMID:23983809

Advantages of formulating an evolution equation directly for elastic distortional deformation in finite deformation plasticity

NASA Astrophysics Data System (ADS)

Rubin, M. B.; Cardiff, P.

2017-11-01

Simo (Comput Methods Appl Mech Eng 66:199-219, 1988) proposed an evolution equation for elastic deformation together with a constitutive equation for inelastic deformation rate in plasticity. The numerical algorithm (Simo in Comput Methods Appl Mech Eng 68:1-31, 1988) for determining elastic distortional deformation was simple. However, the proposed inelastic deformation rate caused plastic compaction. The corrected formulation (Simo in Comput Methods Appl Mech Eng 99:61-112, 1992) preserves isochoric plasticity but the numerical integration algorithm is complicated and needs special methods for calculation of the exponential map of a tensor. Alternatively, an evolution equation for elastic distortional deformation can be proposed directly with a simplified constitutive equation for inelastic distortional deformation rate. This has the advantage that the physics of inelastic distortional deformation is separated from that of dilatation. The example of finite deformation J2 plasticity with linear isotropic hardening is used to demonstrate the simplicity of the numerical algorithm.

SU-E-T-644: Evaluation of Angular Dependence Correction for 2D Array Detector Using for Quality Assurance of Volumetric Modulated Arc Therapy

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

Karthikeyan, N; Ganesh, K M; Vikraman, S

2014-06-15

Purpose: To evaluate the angular dependence correction for Matrix Evolution 2D array detector in quality assurance of volumetric modulated arc therapy(VMAT). Methods: Total ten patients comprising of different sites were planned for VMAT and taken for the study. Each plan was exposed on Matrix Evolution 2D array detector with Omnipro IMRT software based on the following three different methods using 6MV photon beams from Elekta Synergy linear accelerator. First method, VMAT plan was delivered on Matrix Evolution detector as it gantry mounted with dedicated holder with build-up of 2.3cm. Second, the VMAT plan was delivered with the static gantry anglemore » on to the table mounted setup. Third, the VMAT plan was delivered with actual gantry angle on Matrix Evolution detector fixed in Multicube phantom with gantry angle sensor and angular dependence correction were applied to quantify the plan quality. For all these methods, the corresponding QA plans were generated in TPS and the dose verification was done for both point and 2D fluence analysis with pass criteria of 3% dose difference and 3mm distance to agreement. Results: The measured point dose variation for the first method was observed as 1.58±0.6% of mean and SD with TPS calculated. For second and third method, the mean and standard deviation(SD) was observed as 1.67±0.7% and 1.85±0.8% respectively. The 2D fluence analysis of measured and TPS calculated has the mean and SD of 97.9±1.1%, 97.88±1.2% and 97.55±1.3% for first, second and third methods respectively. The calculated two-tailed Pvalue for point dose and 2D fluence analysis shows the insignificance with values of 0.9316 and 0.9015 respectively, among the different methods of QA. Conclusion: The qualitative evaluation of angular dependence correction for Matrix Evolution 2D array detector shows its competency in accuracy of quality assurance measurement of composite dose distribution of volumetric modulated arc therapy.« less

Towards investigation of evolution of dynamical systems with independence of time accuracy: more classes of systems

NASA Astrophysics Data System (ADS)

Gurzadyan, V. G.; Kocharyan, A. A.

2015-07-01

The recently developed method (Paper 1) enabling one to investigate the evolution of dynamical systems with an accuracy not dependent on time is developed further. The classes of dynamical systems which can be studied by that method are much extended, now including systems that are: (1) non-Hamiltonian, conservative; (2) Hamiltonian with time-dependent perturbation; (3) non-conservative (with dissipation). These systems cover various types of N-body gravitating systems of astrophysical and cosmological interest, such as the orbital evolution of planets, minor planets, artificial satellites due to tidal, non-tidal perturbations and thermal thrust, evolving close binary stellar systems, and the dynamics of accretion disks.

The Independent Evolution Method Is Not a Viable Phylogenetic Comparative Method

PubMed Central

2015-01-01

Phylogenetic comparative methods (PCMs) use data on species traits and phylogenetic relationships to shed light on evolutionary questions. Recently, Smaers and Vinicius suggested a new PCM, Independent Evolution (IE), which purportedly employs a novel model of evolution based on Felsenstein’s Adaptive Peak Model. The authors found that IE improves upon previous PCMs by producing more accurate estimates of ancestral states, as well as separate estimates of evolutionary rates for each branch of a phylogenetic tree. Here, we document substantial theoretical and computational issues with IE. When data are simulated under a simple Brownian motion model of evolution, IE produces severely biased estimates of ancestral states and changes along individual branches. We show that these branch-specific changes are essentially ancestor-descendant or “directional” contrasts, and draw parallels between IE and previous PCMs such as “minimum evolution”. Additionally, while comparisons of branch-specific changes between variables have been interpreted as reflecting the relative strength of selection on those traits, we demonstrate through simulations that regressing IE estimated branch-specific changes against one another gives a biased estimate of the scaling relationship between these variables, and provides no advantages or insights beyond established PCMs such as phylogenetically independent contrasts. In light of our findings, we discuss the results of previous papers that employed IE. We conclude that Independent Evolution is not a viable PCM, and should not be used in comparative analyses. PMID:26683838

A note on improved F-expansion method combined with Riccati equation applied to nonlinear evolution equations.

PubMed

Islam, Md Shafiqul; Khan, Kamruzzaman; Akbar, M Ali; Mastroberardino, Antonio

2014-10-01

The purpose of this article is to present an analytical method, namely the improved F-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin-Bona-Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering.

A note on improved F-expansion method combined with Riccati equation applied to nonlinear evolution equations

PubMed Central

Islam, Md. Shafiqul; Khan, Kamruzzaman; Akbar, M. Ali; Mastroberardino, Antonio

2014-01-01

The purpose of this article is to present an analytical method, namely the improved F-expansion method combined with the Riccati equation, for finding exact solutions of nonlinear evolution equations. The present method is capable of calculating all branches of solutions simultaneously, even if multiple solutions are very close and thus difficult to distinguish with numerical techniques. To verify the computational efficiency, we consider the modified Benjamin–Bona–Mahony equation and the modified Korteweg-de Vries equation. Our results reveal that the method is a very effective and straightforward way of formulating the exact travelling wave solutions of nonlinear wave equations arising in mathematical physics and engineering. PMID:26064530

NUMERICAL MODELING OF THE COAGULATION AND POROSITY EVOLUTION OF DUST AGGREGATES

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

Okuzumi, Satoshi; Sakagami, Masa-aki; Tanaka, Hidekazu, E-mail: satoshi.okuzumi@ax2.ecs.kyoto-u.ac.j

2009-12-20

Porosity evolution of dust aggregates is crucial in understanding dust evolution in protoplanetary disks. In this study, we present useful tools to study the coagulation and porosity evolution of dust aggregates. First, we present a new numerical method for simulating dust coagulation and porosity evolution as an extension of the conventional Smoluchowski equation. This method follows the evolution of the mean porosity for each aggregate mass simultaneously with the evolution of the mass distribution function. This method reproduces the results of previous Monte Carlo simulations with much less computational expense. Second, we propose a new collision model for porous dustmore » aggregates on the basis of our N-body experiments on aggregate collisions. As the first step, we focus on 'hit-and-stick' collisions, which involve neither compression nor fragmentation of aggregates. We first obtain empirical data on porosity changes between the classical limits of ballistic cluster-cluster and particle-cluster aggregation. Using the data, we construct a recipe for the porosity change due to general hit-and-stick collisions as well as formulae for the aerodynamical and collisional cross sections. Our collision model is thus more realistic than a previous model of Ormel et al. based on the classical aggregation limits only. Simple coagulation simulations using the extended Smoluchowski method show that our collision model explains the fractal dimensions of porous aggregates observed in a full N-body simulation and a laboratory experiment. By contrast, similar simulations using the collision model of Ormel et al. result in much less porous aggregates, meaning that this model underestimates the porosity increase upon unequal-sized collisions. Besides, we discover that aggregates at the high-mass end of the distribution can have a considerably small aerodynamical cross section per unit mass compared with aggregates of lower masses. This occurs when aggregates drift under uniform acceleration (e.g., gravity) and their collision is induced by the difference in their terminal velocities. We point out an important implication of this discovery for dust growth in protoplanetary disks.« less

The orbital evolution of the AMOR asteroidal group during 11,550 years

NASA Astrophysics Data System (ADS)

Babadzhanov, P. B.; Zausaev, A. F.; Pushkaryov, A. N.

The orbital evolution of twenty seven Amor asteroids was determined by the Everhart method for the time interval from 2250 AD to 9300 BC. Closest encounters with terrestrial planets are calculated in the evolution process. Stable resonances with Venus, Earth and Jupiter over the period from 2250 AD to 9300 BC have been obtained. Theoretical coordinates of radiants on initial and final moments of integrating were calculated.

Accelerating pathway evolution by increasing the gene dosage of chromosomal segments.

PubMed

Tumen-Velasquez, Melissa; Johnson, Christopher W; Ahmed, Alaa; Dominick, Graham; Fulk, Emily M; Khanna, Payal; Lee, Sarah A; Schmidt, Alicia L; Linger, Jeffrey G; Eiteman, Mark A; Beckham, Gregg T; Neidle, Ellen L

2018-06-18

Experimental evolution is a critical tool in many disciplines, including metabolic engineering and synthetic biology. However, current methods rely on the chance occurrence of a key step that can dramatically accelerate evolution in natural systems, namely increased gene dosage. Our studies sought to induce the targeted amplification of chromosomal segments to facilitate rapid evolution. Since increased gene dosage confers novel phenotypes and genetic redundancy, we developed a method, Evolution by Amplification and Synthetic Biology (EASy), to create tandem arrays of chromosomal regions. In Acinetobacter baylyi , EASy was demonstrated on an important bioenergy problem, the catabolism of lignin-derived aromatic compounds. The initial focus on guaiacol (2-methoxyphenol), a common lignin degradation product, led to the discovery of Amycolatopsis genes ( gcoAB ) encoding a cytochrome P450 enzyme that converts guaiacol to catechol. However, chromosomal integration of gcoAB in Pseudomonas putida or A. baylyi did not enable guaiacol to be used as the sole carbon source despite catechol being a growth substrate. In ∼1,000 generations, EASy yielded alleles that in single chromosomal copy confer growth on guaiacol. Different variants emerged, including fusions between GcoA and CatA (catechol 1,2-dioxygenase). This study illustrates the power of harnessing chromosomal gene amplification to accelerate the evolution of desirable traits.

Dynamic imaging in electrical impedance tomography of the human chest with online transition matrix identification.

PubMed

Moura, Fernando Silva; Aya, Julio Cesar Ceballos; Fleury, Agenor Toledo; Amato, Marcelo Britto Passos; Lima, Raul Gonzalez

2010-02-01

One of the electrical impedance tomography objectives is to estimate the electrical resistivity distribution in a domain based only on electrical potential measurements at its boundary generated by an imposed electrical current distribution into the boundary. One of the methods used in dynamic estimation is the Kalman filter. In biomedical applications, the random walk model is frequently used as evolution model and, under this conditions, poor tracking ability of the extended Kalman filter (EKF) is achieved. An analytically developed evolution model is not feasible at this moment. The paper investigates the identification of the evolution model in parallel to the EKF and updating the evolution model with certain periodicity. The evolution model transition matrix is identified using the history of the estimated resistivity distribution obtained by a sensitivity matrix based algorithm and a Newton-Raphson algorithm. To numerically identify the linear evolution model, the Ibrahim time-domain method is used. The investigation is performed by numerical simulations of a domain with time-varying resistivity and by experimental data collected from the boundary of a human chest during normal breathing. The obtained dynamic resistivity values lie within the expected values for the tissues of a human chest. The EKF results suggest that the tracking ability is significantly improved with this approach.

New extended (G'/G)-expansion method to solve nonlinear evolution equation: the (3 + 1)-dimensional potential-YTSF equation.

PubMed

Roshid, Harun-Or-; Akbar, M Ali; Alam, Md Nur; Hoque, Md Fazlul; Rahman, Nizhum

2014-01-01

In this article, a new extended (G'/G) -expansion method has been proposed for constructing more general exact traveling wave solutions of nonlinear evolution equations with the aid of symbolic computation. In order to illustrate the validity and effectiveness of the method, we pick the (3 + 1)-dimensional potential-YTSF equation. As a result, abundant new and more general exact solutions have been achieved of this equation. It has been shown that the proposed method provides a powerful mathematical tool for solving nonlinear wave equations in applied mathematics, engineering and mathematical physics.

Evolution of Query Optimization Methods

NASA Astrophysics Data System (ADS)

Hameurlain, Abdelkader; Morvan, Franck

Query optimization is the most critical phase in query processing. In this paper, we try to describe synthetically the evolution of query optimization methods from uniprocessor relational database systems to data Grid systems through parallel, distributed and data integration systems. We point out a set of parameters to characterize and compare query optimization methods, mainly: (i) size of the search space, (ii) type of method (static or dynamic), (iii) modification types of execution plans (re-optimization or re-scheduling), (iv) level of modification (intra-operator and/or inter-operator), (v) type of event (estimation errors, delay, user preferences), and (vi) nature of decision-making (centralized or decentralized control).

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

Mechanical and Microstructural Effects of Thermal Aging on Cast Duplex Stainless Steels by Experiment and Finite Element Method

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

Schwarm, Samuel C.; Mburu, Sarah N.; Kolli, Ratna P.

Cast duplex stainless steel piping in light water nuclear reactors expe- rience thermal aging embrittlement during operational service. Interest in extending the operational life to 80 years requires an increased understanding of the microstructural evolution and corresponding changes in mechanical behavior. We analyze the evolution of the microstructure during thermal aging of cast CF-3 and CF-8 stainless steels using electron microscopy and atom probe tomography. The evolution of the mechanical properties is measured concurrently by mechanical methods such as tensile tests, Charpy V-notch tests, and instrumented nanoinden- tation. A microstructure-based finite element method model is developed and uti- lized inmore » conjunction with the characterization results in order to correlate the local stress-strain effects in the microstructure with the bulk measurements. This work is supported by the DOE Nuclear Energy University Programs (NEUP), contract number DE-NE0000724.« less

Evolving neural networks through augmenting topologies.

PubMed

Stanley, Kenneth O; Miikkulainen, Risto

2002-01-01

An important question in neuroevolution is how to gain an advantage from evolving neural network topologies along with weights. We present a method, NeuroEvolution of Augmenting Topologies (NEAT), which outperforms the best fixed-topology method on a challenging benchmark reinforcement learning task. We claim that the increased efficiency is due to (1) employing a principled method of crossover of different topologies, (2) protecting structural innovation using speciation, and (3) incrementally growing from minimal structure. We test this claim through a series of ablation studies that demonstrate that each component is necessary to the system as a whole and to each other. What results is significantly faster learning. NEAT is also an important contribution to GAs because it shows how it is possible for evolution to both optimize and complexify solutions simultaneously, offering the possibility of evolving increasingly complex solutions over generations, and strengthening the analogy with biological evolution.

CONTINUOUS, AUTOMATED AND SIMULTANEOUS MEASUREMENT OF OXYGEN UPTAKE AND CARBON DIOXIDE EVOLUTION IN BIOLOGICAL SYSTEMS

EPA Science Inventory

Commercial respirometers are capable of continuously and automatically measuring oxygen uptake in bioreactors. A method for continuously and automatically measuring carbon dioxide evolution can be retrofitted to commercial respirometers. Continuous and automatic measurements of...

The Evolution of Thought

ERIC Educational Resources Information Center

Shadrikov, V. D.

2017-01-01

We investigate the evolution of thought using the method of historical reconstruction, the theory of the cultural and historical determinism of psychological development, data on the relationship between morphological studies, modern findings about child development, and the scientific understanding of neural morphogenesis. We argue for…

Infrared contrast data analysis method for quantitative measurement and monitoring in flash infrared thermography

NASA Astrophysics Data System (ADS)

Koshti, Ajay M.

2015-04-01

The paper provides information on a new infrared (IR) image contrast data post-processing method that involves converting raw data to normalized contrast versus time evolutions from the flash infrared thermography inspection video data. Thermal measurement features such as peak contrast, peak contrast time, persistence time, and persistence energy are calculated from the contrast evolutions. In addition, simulation of the contrast evolution is achieved through calibration on measured contrast evolutions from many flat bottom holes in a test plate of the subject material. The measurement features are used to monitor growth of anomalies and to characterize the void-like anomalies. The method was developed to monitor and analyze void-like anomalies in reinforced carbon-carbon (RCC) materials used on the wing leading edge of the NASA Space Shuttle Orbiters, but the method is equally applicable to other materials. The thermal measurement features relate to the anomaly characteristics such as depth and size. Calibration of the contrast is used to provide an assessment of the anomaly depth and width which correspond to the depth and diameter of the equivalent flat bottom hole (EFBH) from the calibration data. An edge detection technique called the half-max is used to measure width and length of the anomaly. Results of the half-max width and the EFBH diameter are compared with actual widths to evaluate utility of IR Contrast method. Some thermal measurements relate to gap thickness of the delaminations. Results of IR Contrast method on RCC hardware are provided. Keywords: normalized contrast, flash infrared thermography.

Approximate analytic method for high-apogee twelve-hour orbits of artificial Earth's satellites

NASA Astrophysics Data System (ADS)

Vashkovyaka, M. A.; Zaslavskii, G. S.

2016-09-01

We propose an approach to the study of the evolution of high-apogee twelve-hour orbits of artificial Earth's satellites. We describe parameters of the motion model used for the artificial Earth's satellite such that the principal gravitational perturbations of the Moon and Sun, nonsphericity of the Earth, and perturbations from the light pressure force are approximately taken into account. To solve the system of averaged equations describing the evolution of the orbit parameters of an artificial satellite, we use both numeric and analytic methods. To select initial parameters of the twelve-hour orbit, we assume that the path of the satellite along the surface of the Earth is stable. Results obtained by the analytic method and by the numerical integration of the evolving system are compared. For intervals of several years, we obtain estimates of oscillation periods and amplitudes for orbital elements. To verify the results and estimate the precision of the method, we use the numerical integration of rigorous (not averaged) equations of motion of the artificial satellite: they take into account forces acting on the satellite substantially more completely and precisely. The described method can be applied not only to the investigation of orbit evolutions of artificial satellites of the Earth; it can be applied to the investigation of the orbit evolution for other planets of the Solar system provided that the corresponding research problem will arise in the future and the considered special class of resonance orbits of satellites will be used for that purpose.

The polarization evolution of electromagnetic waves as a diagnostic method for a motional plasma

NASA Astrophysics Data System (ADS)

Shahrokhi, Alireza; Mehdian, Hassan; Hajisharifi, Kamal; Hasanbeigi, Ali

2017-12-01

The polarization evolution of electromagnetic (EM) radiation propagating through an electron beam-ion channel system is studied in the presence of self-magnetic field. Solving the fluid-Maxwell equations to obtain the medium dielectric tensor, the Stokes vector-Mueller matrix approach is employed to determine the polarization of the launched EM wave at any point in the propagation direction, applying the space-dependent Mueller matrix on the initial polarization vector of the wave at the plasma-vacuum interface. Results show that the polarization evolution of the wave is periodic in space along the beam axis with the specified polarization wavelength. Using the obtained results, a novel diagnostic method based on the polarization evolution of the EM waves is proposed to evaluate the electron beam density and velocity. Moreover, to use the mentioned plasma system as a polarizer, the fraction of the output radiation power transmitted through a motional plasma crossed with the input polarization is calculated. The results of the present investigation will greatly contribute to design a new EM amplifier with fixed polarization or EM polarizer, as well as a new diagnostic approach for the electron beam system where the polarimetric method is employed.

Efficient Nondomination Level Update Method for Steady-State Evolutionary Multiobjective Optimization.

PubMed

Li, Ke; Deb, Kalyanmoy; Zhang, Qingfu; Zhang, Qiang

2017-09-01

Nondominated sorting (NDS), which divides a population into several nondomination levels (NDLs), is a basic step in many evolutionary multiobjective optimization (EMO) algorithms. It has been widely studied in a generational evolution model, where the environmental selection is performed after generating a whole population of offspring. However, in a steady-state evolution model, where a population is updated right after the generation of a new candidate, the NDS can be extremely time consuming. This is especially severe when the number of objectives and population size become large. In this paper, we propose an efficient NDL update method to reduce the cost for maintaining the NDL structure in steady-state EMO. Instead of performing the NDS from scratch, our method only updates the NDLs of a limited number of solutions by extracting the knowledge from the current NDL structure. Notice that our NDL update method is performed twice at each iteration. One is after the reproduction, the other is after the environmental selection. Extensive experiments fully demonstrate that, comparing to the other five state-of-the-art NDS methods, our proposed method avoids a significant amount of unnecessary comparisons, not only in the synthetic data sets, but also in some real optimization scenarios. Last but not least, we find that our proposed method is also useful for the generational evolution model.

Applicability of transfer tensor method for open quantum system dynamics.

PubMed

Gelzinis, Andrius; Rybakovas, Edvardas; Valkunas, Leonas

2017-12-21

Accurate simulations of open quantum system dynamics is a long standing issue in the field of chemical physics. Exact methods exist, but are costly, while perturbative methods are limited in their applicability. Recently a new black-box type method, called transfer tensor method (TTM), was proposed [J. Cerrillo and J. Cao, Phys. Rev. Lett. 112, 110401 (2014)]. It allows one to accurately simulate long time dynamics with a numerical cost of solving a time-convolution master equation, provided many initial system evolution trajectories are obtained from some exact method beforehand. The possible time-savings thus strongly depend on the ratio of total versus initial evolution lengths. In this work, we investigate the parameter regimes where an application of TTM would be most beneficial in terms of computational time. We identify several promising parameter regimes. Although some of them correspond to cases when perturbative theories could be expected to perform well, we find that the accuracy of such approaches depends on system parameters in a more complex way than it is commonly thought. We propose that the TTM should be applied whenever system evolution is expected to be long and accuracy of perturbative methods cannot be ensured or in cases when the system under consideration does not correspond to any single perturbative regime.

The orbital evolution of the Apollo asteroid group over 11,550 years

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Pushkarev, A. N.

1992-08-01

The Everhard method was used to monitor the orbital evolution of 20 Apollo asteroids in the time interval from 2250 A.D. to 9300 B.C. The closest encounters with large planets in the evolution process are calculated. Stable resonances with Venus and Earth over the period from 2250 A.D. to 9300 B.C. are obtained. Theoretical coordinates of radiants on initial and final moments of integration are calculated.

[The evolution of vacuum extraction in obstetrics].

PubMed

Nikolov, A

2010-01-01

Vacuum extraction is one of the methods for assisted vaginal delivery. In this article the evolution of vacuum extraction in obstetrics is been discussed. Historical facts and data from the invention up to state-of-the-art vacuum systems in modern obstetrics are presented.

An experimental and computational evolution-based method to study a mode of co-evolution of overlapping open reading frames in the AAV2 viral genome.

PubMed

Kawano, Yasuhiro; Neeley, Shane; Adachi, Kei; Nakai, Hiroyuki

2013-01-01

Overlapping open reading frames (ORFs) in viral genomes undergo co-evolution; however, how individual amino acids coded by overlapping ORFs are structurally, functionally, and co-evolutionarily constrained remains difficult to address by conventional homologous sequence alignment approaches. We report here a new experimental and computational evolution-based methodology to address this question and report its preliminary application to elucidating a mode of co-evolution of the frame-shifted overlapping ORFs in the adeno-associated virus (AAV) serotype 2 viral genome. These ORFs encode both capsid VP protein and non-structural assembly-activating protein (AAP). To show proof of principle of the new method, we focused on the evolutionarily conserved QVKEVTQ and KSKRSRR motifs, a pair of overlapping heptapeptides in VP and AAP, respectively. In the new method, we first identified a large number of capsid-forming VP3 mutants and functionally competent AAP mutants of these motifs from mutant libraries by experimental directed evolution under no co-evolutionary constraints. We used Illumina sequencing to obtain a large dataset and then statistically assessed the viability of VP and AAP heptapeptide mutants. The obtained heptapeptide information was then integrated into an evolutionary algorithm, with which VP and AAP were co-evolved from random or native nucleotide sequences in silico. As a result, we demonstrate that these two heptapeptide motifs could exhibit high degeneracy if coded by separate nucleotide sequences, and elucidate how overlap-evoked co-evolutionary constraints play a role in making the VP and AAP heptapeptide sequences into the present shape. Specifically, we demonstrate that two valine (V) residues and β-strand propensity in QVKEVTQ are structurally important, the strongly negative and hydrophilic nature of KSKRSRR is functionally important, and overlap-evoked co-evolution imposes strong constraints on serine (S) residues in KSKRSRR, despite high degeneracy of the motifs in the absence of co-evolutionary constraints.

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.

A Differential Evolution Algorithm Based on Nikaido-Isoda Function for Solving Nash Equilibrium in Nonlinear Continuous Games

PubMed Central

He, Feng; Zhang, Wei; Zhang, Guoqiang

2016-01-01

A differential evolution algorithm for solving Nash equilibrium in nonlinear continuous games is presented in this paper, called NIDE (Nikaido-Isoda differential evolution). At each generation, parent and child strategy profiles are compared one by one pairwisely, adapting Nikaido-Isoda function as fitness function. In practice, the NE of nonlinear game model with cubic cost function and quadratic demand function is solved, and this method could also be applied to non-concave payoff functions. Moreover, the NIDE is compared with the existing Nash Domination Evolutionary Multiplayer Optimization (NDEMO), the result showed that NIDE was significantly better than NDEMO with less iterations and shorter running time. These numerical examples suggested that the NIDE method is potentially useful. PMID:27589229

Fast wavelet based algorithms for linear evolution equations

NASA Technical Reports Server (NTRS)

Engquist, Bjorn; Osher, Stanley; Zhong, Sifen

1992-01-01

A class was devised of fast wavelet based algorithms for linear evolution equations whose coefficients are time independent. The method draws on the work of Beylkin, Coifman, and Rokhlin which they applied to general Calderon-Zygmund type integral operators. A modification of their idea is applied to linear hyperbolic and parabolic equations, with spatially varying coefficients. A significant speedup over standard methods is obtained when applied to hyperbolic equations in one space dimension and parabolic equations in multidimensions.

A probabilistic-entropy approach of finding thematically similar documents with creating context-semantic graph for investigating evolution of society opinion

NASA Astrophysics Data System (ADS)

Moloshnikov, I. A.; Sboev, A. G.; Rybka, R. B.; Gydovskikh, D. V.

2016-02-01

The composite algorithm integrating, on one hand, the algorithm of finding documents on a given topic, and, on the other hand, the method of emotiveness evaluation of topical texts is presented. This method is convenient for analysis of people opinions expressed in social media and, as a result, for automated analysis of event evolutions in social media. Some examples of such analysing are demonstrated and discussed.

Evolution of monitoring for Giardia and Cryptosporidium in water.

PubMed

Efstratiou, Artemis; Ongerth, Jerry; Karanis, Panagiotis

2017-10-15

This review describes the evolution of monitoring methodology for Cryptosporidium and Giardia in water since the 1970's. Methods in current use for Giardia and Cryptosporidium in water are highlighted, though attention is given to all available published methods by country and continent. The review is intended to stimulate research leading to future improvements and further developments in monitoring methodology for Giardia, Cryptosporidium and other waterborne protozoan parasites in water. Copyright © 2017. Published by Elsevier Ltd.

Research of the orbital evolution of asteroid 2012 DA14 (in Russian)

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Denisov, S. S.; Derevyanka, A. E.

Research of the orbital evolution of asteroid 2012 DA14 on the time interval from 1800 to 2206 is made, an object close approaches with Earth and the Moon are detected, the probability of impact with Earth is calculated. The used mathematical model is consistent with the DE405, the integration was performed using a modified Everhart's method of 27th order, the probability of collision is calculated using the Monte Carlo method.

Neonatal peripheral facial paralysis' evaluation with photogrammetry: A case report.

PubMed

da Fonseca Filho, Gentil Gomes; de Medeiros Cirne, Gabriele Natane; Cacho, Roberta Oliveira; de Souza, Jane Carla; Nagem, Danilo; Cacho, Enio Walker Azevedo; Moran, Cristiane Aparecida; Abreu, Bruna; Pereira, Silvana Alves

2015-12-01

Facial paralysis in newborns can leave functional sequelae. Determining the evolution and amount of functional losses requires consistent evaluation methods that measure, quantitatively, the evolution of clinical functionality. This paper reports an innovative method of facial assessment for the case of a child 28 days of age with unilateral facial paralysis. The child had difficulty breast feeding, and quickly responded to the physical therapy treatment. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

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.

Estimating the time evolution of NMR systems via a quantum-speed-limit-like expression

NASA Astrophysics Data System (ADS)

Villamizar, D. V.; Duzzioni, E. I.; Leal, A. C. S.; Auccaise, R.

2018-05-01

Finding the solutions of the equations that describe the dynamics of a given physical system is crucial in order to obtain important information about its evolution. However, by using estimation theory, it is possible to obtain, under certain limitations, some information on its dynamics. The quantum-speed-limit (QSL) theory was originally used to estimate the shortest time in which a Hamiltonian drives an initial state to a final one for a given fidelity. Using the QSL theory in a slightly different way, we are able to estimate the running time of a given quantum process. For that purpose, we impose the saturation of the Anandan-Aharonov bound in a rotating frame of reference where the state of the system travels slower than in the original frame (laboratory frame). Through this procedure it is possible to estimate the actual evolution time in the laboratory frame of reference with good accuracy when compared to previous methods. Our method is tested successfully to predict the time spent in the evolution of nuclear spins 1/2 and 3/2 in NMR systems. We find that the estimated time according to our method is better than previous approaches by up to four orders of magnitude. One disadvantage of our method is that we need to solve a number of transcendental equations, which increases with the system dimension and parameter discretization used to solve such equations numerically.

The method of projected characteristics for the evolution of magnetic arches

NASA Technical Reports Server (NTRS)

Nakagawa, Y.; Hu, Y. Q.; Wu, S. T.

1987-01-01

A numerical method of solving fully nonlinear MHD equation is described. In particular, the formulation based on the newly developed method of projected characteristics (Nakagawa, 1981) suitable to study the evolution of magnetic arches due to motions of their foot-points is presented. The final formulation is given in the form of difference equations; therefore, the analysis of numerical stability is also presented. Further, the most important derivation of physically self-consistent, time-dependent boundary conditions (i.e. the evolving boundary equations) is given in detail, and some results obtained with such boundary equations are reported.

Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

PubMed Central

Currin, Andrew; Swainston, Neil; Day, Philip J.

2015-01-01

The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the ‘search space’ of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (K d) and catalytic (k cat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving k cat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the ‘best’ amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust. PMID:25503938

New solitary wave and multiple soliton solutions for fifth order nonlinear evolution equation with time variable coefficients

NASA Astrophysics Data System (ADS)

Jaradat, H. M.; Syam, Muhammed; Jaradat, M. M. M.; Mustafa, Zead; Moman, S.

2018-03-01

In this paper, we investigate the multiple soliton solutions and multiple singular soliton solutions of a class of the fifth order nonlinear evolution equation with variable coefficients of t using the simplified bilinear method based on a transformation method combined with the Hirota's bilinear sense. In addition, we present analysis for some parameters such as the soliton amplitude and the characteristic line. Several equation in the literature are special cases of the class which we discuss such as Caudrey-Dodd-Gibbon equation and Sawada-Kotera. Comparison with several methods in the literature, such as Helmholtz solution of the inverse variational problem, rational exponential function method, tanh method, homotopy perturbation method, exp-function method, and coth method, are made. From these comparisons, we conclude that the proposed method is efficient and our solutions are correct. It is worth mention that the proposed solution can solve many physical problems.

Phylogenetic analyses of mode of larval development.

PubMed

Hart, M

2000-12-01

Phylogenies based on morphological or molecular characters have been used to provide an evolutionary context for analysis of larval evolution. Studies of gastropods, bivalves, tunicates, sea stars, sea urchins, and polychaetes have revealed massive parallel evolution of similar larval forms. Some of these studies were designed to test, and have rejected, the species selection hypothesis for evolutionary trends in the frequency of derived larvae or life history traits. However, the lack of well supported models of larval character evolution leave some doubt about the quality of inferences of larval evolution from phylogenies of living taxa. Better models based on maximum likelihood methods and known prior probabilities of larval character state changes will improve our understanding of the history of larval evolution. Copyright 2000 Academic Press.

Biophysics of protein evolution and evolutionary protein biophysics

PubMed Central

Sikosek, Tobias; Chan, Hue Sun

2014-01-01

The study of molecular evolution at the level of protein-coding genes often entails comparing large datasets of sequences to infer their evolutionary relationships. Despite the importance of a protein's structure and conformational dynamics to its function and thus its fitness, common phylogenetic methods embody minimal biophysical knowledge of proteins. To underscore the biophysical constraints on natural selection, we survey effects of protein mutations, highlighting the physical basis for marginal stability of natural globular proteins and how requirement for kinetic stability and avoidance of misfolding and misinteractions might have affected protein evolution. The biophysical underpinnings of these effects have been addressed by models with an explicit coarse-grained spatial representation of the polypeptide chain. Sequence–structure mappings based on such models are powerful conceptual tools that rationalize mutational robustness, evolvability, epistasis, promiscuous function performed by ‘hidden’ conformational states, resolution of adaptive conflicts and conformational switches in the evolution from one protein fold to another. Recently, protein biophysics has been applied to derive more accurate evolutionary accounts of sequence data. Methods have also been developed to exploit sequence-based evolutionary information to predict biophysical behaviours of proteins. The success of these approaches demonstrates a deep synergy between the fields of protein biophysics and protein evolution. PMID:25165599

The evolution of the Quarantid meteoroid shower

NASA Astrophysics Data System (ADS)

Babadzhanov, P. B.; Obrubov, Iu. V.; Pushkarev, A. N.

1991-02-01

The Everhart method is used to trace the orbital evolution of 36 model Quadrantid meteoroids over a 5750 yr period. It is found that the Quadrantid shower is responsible for eight related showers. These include the Ursids, the Northern and Southern delta-Aquarids, and the Carinids.

Reduction of Large Dynamical Systems by Minimization of Evolution Rate

NASA Technical Reports Server (NTRS)

Girimaji, Sharath S.

1999-01-01

Reduction of a large system of equations to a lower-dimensional system of similar dynamics is investigated. For dynamical systems with disparate timescales, a criterion for determining redundant dimensions and a general reduction method based on the minimization of evolution rate are proposed.

Complete chloroplast and ribosomal sequences for 30 accessions elucidate evolution of Oryza AA genome species

PubMed Central

Kim, Kyunghee; Lee, Sang-Choon; Lee, Junki; Yu, Yeisoo; Yang, Kiwoung; Choi, Beom-Soon; Koh, Hee-Jong; Waminal, Nomar Espinosa; Choi, Hong-Il; Kim, Nam-Hoon; Jang, Woojong; Park, Hyun-Seung; Lee, Jonghoon; Lee, Hyun Oh; Joh, Ho Jun; Lee, Hyeon Ju; Park, Jee Young; Perumal, Sampath; Jayakodi, Murukarthick; Lee, Yun Sun; Kim, Backki; Copetti, Dario; Kim, Soonok; Kim, Sunggil; Lim, Ki-Byung; Kim, Young-Dong; Lee, Jungho; Cho, Kwang-Su; Park, Beom-Seok; Wing, Rod A.; Yang, Tae-Jin

2015-01-01

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis. PMID:26506948

Observation on the transformation domains of super-elastic NiTi shape memory alloy and their evolutions during cyclic loading

NASA Astrophysics Data System (ADS)

Xie, Xi; Kan, Qianhua; Kang, Guozheng; Li, Jian; Qiu, Bo; Yu, Chao

2016-04-01

The strain field of a super-elastic NiTi shape memory alloy (SMA) and its variation during uniaxial cyclic tension-unloading were observed by a non-contact digital image correlation method, and then the transformation domains and their evolutions were indirectly investigated and discussed. It is seen that the super-elastic NiTi (SMA) exhibits a remarkable localized deformation and the transformation domains evolve periodically with the repeated cyclic tension-unloading within the first several cycles. However, the evolutions of transformation domains at the stage of stable cyclic transformation depend on applied peak stress: when the peak stress is low, no obvious transformation band is observed and the strain field is nearly uniform; when the peak stress is large enough, obvious transformation bands occur due to the residual martensite caused by the prevention of enriched dislocations to the reverse transformation from induced martensite to austenite. Temperature variations measured by an infrared thermal imaging method further verifies the formation and evolution of transformation domains.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software.

PubMed

Nakano, Shogo; Asano, Yasuhisa

2015-02-03

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

Protein evolution analysis of S-hydroxynitrile lyase by complete sequence design utilizing the INTMSAlign software

NASA Astrophysics Data System (ADS)

Nakano, Shogo; Asano, Yasuhisa

2015-02-01

Development of software and methods for design of complete sequences of functional proteins could contribute to studies of protein engineering and protein evolution. To this end, we developed the INTMSAlign software, and used it to design functional proteins and evaluate their usefulness. The software could assign both consensus and correlation residues of target proteins. We generated three protein sequences with S-selective hydroxynitrile lyase (S-HNL) activity, which we call designed S-HNLs; these proteins folded as efficiently as the native S-HNL. Sequence and biochemical analysis of the designed S-HNLs suggested that accumulation of neutral mutations occurs during the process of S-HNLs evolution from a low-activity form to a high-activity (native) form. Taken together, our results demonstrate that our software and the associated methods could be applied not only to design of complete sequences, but also to predictions of protein evolution, especially within families such as esterases and S-HNLs.

Measuring and Estimating Normalized Contrast in Infrared Flash Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M.

2013-01-01

Infrared flash thermography (IRFT) is used to detect void-like flaws in a test object. The IRFT technique involves heating up the part surface using a flash of flash lamps. The post-flash evolution of the part surface temperature is sensed by an IR camera in terms of pixel intensity of image pixels. The IR technique involves recording of the IR video image data and analysis of the data using the normalized pixel intensity and temperature contrast analysis method for characterization of void-like flaws for depth and width. This work introduces a new definition of the normalized IR pixel intensity contrast and normalized surface temperature contrast. A procedure is provided to compute the pixel intensity contrast from the camera pixel intensity evolution data. The pixel intensity contrast and the corresponding surface temperature contrast differ but are related. This work provides a method to estimate the temperature evolution and the normalized temperature contrast from the measured pixel intensity evolution data and some additional measurements during data acquisition.

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

PubMed Central

McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae).

PubMed

McCann, Jamie; Schneeweiss, Gerald M; Stuessy, Tod F; Villaseñor, Jose L; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction.

Reconstructing the origin and elaboration of insect-trapping inflorescences in the Araceae1

PubMed Central

Bröderbauer, David; Diaz, Anita; Weber, Anton

2016-01-01

Premise of the study Floral traps are among the most sophisticated devices that have evolved in angiosperms in the context of pollination, but the evolution of trap pollination has not yet been studied in a phylogenetic context. We aim to determine the evolutionary history of morphological traits that facilitate trap pollination and to elucidate the impact of pollinators on the evolution of inflorescence traps in the family Araceae. Methods Inflorescence morphology was investigated to determine the presence of trapping devices and to classify functional types of traps. We inferred phylogenetic relationships in the family using maximum likelihood and Bayesian methods. Character evolution of trapping devices, trap types, and pollinator types was then assessed with maximum parsimony and Bayesian methods. We also tested for an association of trap pollination with specific pollinator types. Key results Inflorescence traps have evolved independently at least 10 times within the Araceae. Trapping devices were found in 27 genera. On the basis of different combinations of trapping devices, six functional types of traps were identified. Trap pollination in Araceae is correlated with pollination by flies. Conclusions Trap pollination in the Araceae is more common than was previously thought. Preadaptations such as papillate cells or elongated sterile flowers facilitated the evolution of inflorescence traps. In some clades, imperfect traps served as a precursor for the evolution of more elaborate traps. Traps that evolved in association with fly pollination were most probably derived from mutualistic ancestors, offering a brood-site to their pollinators. PMID:22965851

A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.

PubMed

Belsare, Ketaki D; Andorfer, Mary C; Cardenas, Frida S; Chael, Julia R; Park, Hyun June; Lewis, Jared C

2017-03-17

Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450 BM3 , pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.

Fully Bayesian tests of neutrality using genealogical summary statistics.

PubMed

Drummond, Alexei J; Suchard, Marc A

2008-10-31

Many data summary statistics have been developed to detect departures from neutral expectations of evolutionary models. However questions about the neutrality of the evolution of genetic loci within natural populations remain difficult to assess. One critical cause of this difficulty is that most methods for testing neutrality make simplifying assumptions simultaneously about the mutational model and the population size model. Consequentially, rejecting the null hypothesis of neutrality under these methods could result from violations of either or both assumptions, making interpretation troublesome. Here we harness posterior predictive simulation to exploit summary statistics of both the data and model parameters to test the goodness-of-fit of standard models of evolution. We apply the method to test the selective neutrality of molecular evolution in non-recombining gene genealogies and we demonstrate the utility of our method on four real data sets, identifying significant departures of neutrality in human influenza A virus, even after controlling for variation in population size. Importantly, by employing a full model-based Bayesian analysis, our method separates the effects of demography from the effects of selection. The method also allows multiple summary statistics to be used in concert, thus potentially increasing sensitivity. Furthermore, our method remains useful in situations where analytical expectations and variances of summary statistics are not available. This aspect has great potential for the analysis of temporally spaced data, an expanding area previously ignored for limited availability of theory and methods.

Gamma-ray luminosity and photon index evolution of FSRQ blazars and contribution to the gamma-ray background

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

Singal, J.; Ko, A.; Petrosian, V., E-mail: jsingal@richmond.edu

We present the redshift evolutions and distributions of the gamma-ray luminosity and photon spectral index of flat spectrum radio quasar (FSRQ) type blazars, using non-parametric methods to obtain the evolutions and distributions directly from the data. The sample we use for analysis consists of almost all FSRQs observed with a greater than approximately 7σ detection threshold in the first-year catalog of the Fermi Gamma-ray Space Telescope's Large Area Telescope, with redshifts as determined from optical spectroscopy by Shaw et al. We find that FSQRs undergo rapid gamma-ray luminosity evolution, but negligible photon index evolution, with redshift. With these evolutions accountedmore » for we determine the density evolution and luminosity function of FSRQs and calculate their total contribution to the extragalactic gamma-ray background radiation, resolved and unresolved, which is found to be 16(+10/–4)%, in agreement with previous studies.« less

Correlating hydrogen oxidation and evolution activity on platinum at different pH with measured hydrogen binding energy

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

Sheng, WC; Zhuang, ZB; Gao, MR

2015-01-08

The hydrogen oxidation/evolution reactions are two of the most fundamental reactions in distributed renewable electrochemical energy conversion and storage systems. The identification of the reaction descriptor is therefore of critical importance for the rational catalyst design and development. Here we report the correlation between hydrogen oxidation/evolution activity and experimentally measured hydrogen binding energy for polycrystalline platinum examined in several buffer solutions in a wide range of electrolyte pH from 0 to 13. The hydrogen oxidation/evolution activity obtained using the rotating disk electrode method is found to decrease with the pH, while the hydrogen binding energy, obtained from cyclic voltammograms, linearlymore » increases with the pH. Correlating the hydrogen oxidation/evolution activity to the hydrogen binding energy renders a monotonic decreasing hydrogen oxidation/evolution activity with the hydrogen binding energy, strongly supporting the hypothesis that hydrogen binding energy is the sole reaction descriptor for the hydrogen oxidation/evolution activity on monometallic platinum.« less

Time evolution of a Gaussian class of quasi-distribution functions under quadratic Hamiltonian.

PubMed

Ginzburg, D; Mann, A

2014-03-10

A Lie algebraic method for propagation of the Wigner quasi-distribution function (QDF) under quadratic Hamiltonian was presented by Zoubi and Ben-Aryeh. We show that the same method can be used in order to propagate a rather general class of QDFs, which we call the "Gaussian class." This class contains as special cases the well-known Wigner, Husimi, Glauber, and Kirkwood-Rihaczek QDFs. We present some examples of the calculation of the time evolution of those functions.

Biomass transition metal hydrogen-evolution electrocatalysts and electrodes

DOEpatents

Chen, Wei-Fu; Iyer, Shweta; Iyer, Shilpa; Sasaki, Kotaro; Muckerman, James T.; Fujita, Etsuko

2017-02-28

A catalytic composition from earth-abundant transition metal salts and biomass is disclosed. A calcined catalytic composition formed from soybean powder and ammonium molybdate is specifically exemplified herein. Methods for making the catalytic composition are disclosed as are electrodes for hydrogen evolution reactions comprising the catalytic composition.

Multi Groups Cooperation based Symbiotic Evolution for TSK-type Neuro-Fuzzy Systems Design

PubMed Central

Cheng, Yi-Chang; Hsu, Yung-Chi

2010-01-01

In this paper, a TSK-type neuro-fuzzy system with multi groups cooperation based symbiotic evolution method (TNFS-MGCSE) is proposed. The TNFS-MGCSE is developed from symbiotic evolution. The symbiotic evolution is different from traditional GAs (genetic algorithms) that each chromosome in symbiotic evolution represents a rule of fuzzy model. The MGCSE is different from the traditional symbiotic evolution; with a population in MGCSE is divided to several groups. Each group formed by a set of chromosomes represents a fuzzy rule and cooperate with other groups to generate the better chromosomes by using the proposed cooperation based crossover strategy (CCS). In this paper, the proposed TNFS-MGCSE is used to evaluate by numerical examples (Mackey-Glass chaotic time series and sunspot number forecasting). The performance of the TNFS-MGCSE achieves excellently with other existing models in the simulations. PMID:21709856

Inferring explicit weighted consensus networks to represent alternative evolutionary histories

PubMed Central

2013-01-01

Background The advent of molecular biology techniques and constant increase in availability of genetic material have triggered the development of many phylogenetic tree inference methods. However, several reticulate evolution processes, such as horizontal gene transfer and hybridization, have been shown to blur the species evolutionary history by causing discordance among phylogenies inferred from different genes. Methods To tackle this problem, we hereby describe a new method for inferring and representing alternative (reticulate) evolutionary histories of species as an explicit weighted consensus network which can be constructed from a collection of gene trees with or without prior knowledge of the species phylogeny. Results We provide a way of building a weighted phylogenetic network for each of the following reticulation mechanisms: diploid hybridization, intragenic recombination and complete or partial horizontal gene transfer. We successfully tested our method on some synthetic and real datasets to infer the above-mentioned evolutionary events which may have influenced the evolution of many species. Conclusions Our weighted consensus network inference method allows one to infer, visualize and validate statistically major conflicting signals induced by the mechanisms of reticulate evolution. The results provided by the new method can be used to represent the inferred conflicting signals by means of explicit and easy-to-interpret phylogenetic networks. PMID:24359207

Evolution in Stage-Structured Populations

PubMed Central

Barfield, Michael; Holt, Robert D.; Gomulkiewicz, Richard

2016-01-01

For many organisms, stage is a better predictor of demographic rates than age. Yet no general theoretical framework exists for understanding or predicting evolution in stage-structured populations. Here, we provide a general modeling approach that can be used to predict evolution and demography of stage-structured populations. This advances our ability to understand evolution in stage-structured populations to a level previously available only for populations structured by age. We use this framework to provide the first rigorous proof that Lande’s theorem, which relates adaptive evolution to population growth, applies to stage-classified populations, assuming only normality and that evolution is slow relative to population dynamics. We extend this theorem to allow for different means or variances among stages. Our next major result is the formulation of Price’s theorem, a fundamental law of evolution, for stage-structured populations. In addition, we use data from Trillium grandiflorum to demonstrate how our models can be applied to a real-world population and thereby show their practical potential to generate accurate projections of evolutionary and population dynamics. Finally, we use our framework to compare rates of evolution in age- versus stage-structured populations, which shows how our methods can yield biological insights about evolution in stage-structured populations. PMID:21460563

Iterated learning and the evolution of language.

PubMed

Kirby, Simon; Griffiths, Tom; Smith, Kenny

2014-10-01

Iterated learning describes the process whereby an individual learns their behaviour by exposure to another individual's behaviour, who themselves learnt it in the same way. It can be seen as a key mechanism of cultural evolution. We review various methods for understanding how behaviour is shaped by the iterated learning process: computational agent-based simulations; mathematical modelling; and laboratory experiments in humans and non-human animals. We show how this framework has been used to explain the origins of structure in language, and argue that cultural evolution must be considered alongside biological evolution in explanations of language origins. Copyright © 2014 Elsevier Ltd. All rights reserved.

[Identification and phylogenetic analysis of one strain of Lactobacillus delbrueckii subsp. bulgaricus separated from yoghourt].

PubMed

Wang, Chuan; Zhang, Chaowu; Pei, Xiaofang; Liu, Hengchuan

2007-11-01

For being further applied and studied, one strain of Lactobacillus delbrueckii subsp. bulgaricus (wch9901) separated from yoghourt which had been identified by phenotype characteristic analysis was identified by 16S rDNA and phylogenetic analyzed. The 16S rDNA of wch9901 was amplified with the genomic DNA of wch9901 as template, and the conservative sequences of the 16S rDNA as primers. Inserted 16S rDNA amplified into clonal vector pGEM-T under the function of T4 DNA ligase to construct recombined plasmid pGEM-wch9901 16S rDNA. The recombined plasmid was identified by restriction enzyme digestion, and the eligible plasmid was presented to sequencing company for DNA sequencing. Nucleic acid sequence was blast in GenBank and phylogenetic tree was constructed using neighbor-joining method of distance methods by Mega3.1 soft. Results of blastn showed that the homology of 16S rDNA of wch9901 with the 16S rDNA of Lactobacillus delbrueckii subsp. bulgaricus strains was higher than 96%. On the phylogenetic tree, wch9901 formed a separate branch and located between Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch and another evolution branch which was composed of Lactobacillus delbrueckii subsp. bulgaricus DL2 evolution cluster and Lactobacillus delbrueckii subsp. bulgaricus JSQ evolution cluster. The distance between wch9901 evolution branch and Lactobacillus delbrueckii subsp. bulgaricus LGM2 evolution branch was the closest. wch9901 belonged to Lactobacillus delbrueckii subsp. bulgaricus. wch9901 showed the closest evolution relationship to Lactobacillus delbrueckii subsp. bulgaricus LGM2.

Semiautomatic segmentation and follow-up of multicomponent low-grade tumors in longitudinal brain MRI studies

PubMed Central

Weizman, Lior; Sira, Liat Ben; Joskowicz, Leo; Rubin, Daniel L.; Yeom, Kristen W.; Constantini, Shlomi; Shofty, Ben; Bashat, Dafna Ben

2014-01-01

Purpose: Tracking the progression of low grade tumors (LGTs) is a challenging task, due to their slow growth rate and associated complex internal tumor components, such as heterogeneous enhancement, hemorrhage, and cysts. In this paper, the authors show a semiautomatic method to reliably track the volume of LGTs and the evolution of their internal components in longitudinal MRI scans. Methods: The authors' method utilizes a spatiotemporal evolution modeling of the tumor and its internal components. Tumor components gray level parameters are estimated from the follow-up scan itself, obviating temporal normalization of gray levels. The tumor delineation procedure effectively incorporates internal classification of the baseline scan in the time-series as prior data to segment and classify a series of follow-up scans. The authors applied their method to 40 MRI scans of ten patients, acquired at two different institutions. Two types of LGTs were included: Optic pathway gliomas and thalamic astrocytomas. For each scan, a “gold standard” was obtained manually by experienced radiologists. The method is evaluated versus the gold standard with three measures: gross total volume error, total surface distance, and reliability of tracking tumor components evolution. Results: Compared to the gold standard the authors' method exhibits a mean Dice similarity volumetric measure of 86.58% and a mean surface distance error of 0.25 mm. In terms of its reliability in tracking the evolution of the internal components, the method exhibits strong positive correlation with the gold standard. Conclusions: The authors' method provides accurate and repeatable delineation of the tumor and its internal components, which is essential for therapy assessment of LGTs. Reliable tracking of internal tumor components over time is novel and potentially will be useful to streamline and improve follow-up of brain tumors, with indolent growth and behavior. PMID:24784396

Decoupling the NLO-coupled QED⊗QCD, DGLAP evolution equations, using Laplace transform method

NASA Astrophysics Data System (ADS)

Mottaghizadeh, Marzieh; Eslami, Parvin; Taghavi-Shahri, Fatemeh

2017-05-01

We analytically solved the QED⊗QCD-coupled DGLAP evolution equations at leading order (LO) quantum electrodynamics (QED) and next-to-leading order (NLO) quantum chromodynamics (QCD) approximations, using the Laplace transform method and then computed the proton structure function in terms of the unpolarized parton distribution functions. Our analytical solutions for parton densities are in good agreement with those from CT14QED (1.2952 < Q2 < 1010) (Ref. 6) global parametrizations and APFEL (A PDF Evolution Library) (2 < Q2 < 108) (Ref. 4). We also compared the proton structure function, F2p(x,Q2), with the experimental data released by the ZEUS and H1 collaborations at HERA. There is a nice agreement between them in the range of low and high x and Q2.

SCM: A method to improve network service layout efficiency with network evolution.

PubMed

Zhao, Qi; Zhang, Chuanhao; Zhao, Zheng

2017-01-01

Network services are an important component of the Internet, which are used to expand network functions for third-party developers. Network function virtualization (NFV) can improve the speed and flexibility of network service deployment. However, with the evolution of the network, network service layout may become inefficient. Regarding this problem, this paper proposes a service chain migration (SCM) method with the framework of "software defined network + network function virtualization" (SDN+NFV), which migrates service chains to adapt to network evolution and improves the efficiency of the network service layout. SCM is modeled as an integer linear programming problem and resolved via particle swarm optimization. An SCM prototype system is designed based on an SDN controller. Experiments demonstrate that SCM could reduce the network traffic cost and energy consumption efficiently.

Principal Component Relaxation Mode Analysis of an All-Atom Molecular Dynamics Simulation of Human Lysozyme

NASA Astrophysics Data System (ADS)

Nagai, Toshiki; Mitsutake, Ayori; Takano, Hiroshi

2013-02-01

A new relaxation mode analysis method, which is referred to as the principal component relaxation mode analysis method, has been proposed to handle a large number of degrees of freedom of protein systems. In this method, principal component analysis is carried out first and then relaxation mode analysis is applied to a small number of principal components with large fluctuations. To reduce the contribution of fast relaxation modes in these principal components efficiently, we have also proposed a relaxation mode analysis method using multiple evolution times. The principal component relaxation mode analysis method using two evolution times has been applied to an all-atom molecular dynamics simulation of human lysozyme in aqueous solution. Slow relaxation modes and corresponding relaxation times have been appropriately estimated, demonstrating that the method is applicable to protein systems.

Methods to estimate effective population size using pedigree data: Examples in dog, sheep, cattle and horse

PubMed Central

2013-01-01

Background Effective population sizes of 140 populations (including 60 dog breeds, 40 sheep breeds, 20 cattle breeds and 20 horse breeds) were computed using pedigree information and six different computation methods. Simple demographical information (number of breeding males and females), variance of progeny size, or evolution of identity by descent probabilities based on coancestry or inbreeding were used as well as identity by descent rate between two successive generations or individual identity by descent rate. Results Depending on breed and method, effective population sizes ranged from 15 to 133 056, computation method and interaction between computation method and species showing a significant effect on effective population size (P < 0.0001). On average, methods based on number of breeding males and females and variance of progeny size produced larger values (4425 and 356, respectively), than those based on identity by descent probabilities (average values between 93 and 203). Since breeding practices and genetic substructure within dog breeds increased inbreeding, methods taking into account the evolution of inbreeding produced lower effective population sizes than those taking into account evolution of coancestry. The correlation level between the simplest method (number of breeding males and females, requiring no genealogical information) and the most sophisticated one ranged from 0.44 to 0.60 according to species. Conclusions When choosing a method to compute effective population size, particular attention should be paid to the species and the specific genetic structure of the population studied. PMID:23281913

Evolution of Medication Administration Workflow in Implementing Electronic Health Record System

ERIC Educational Resources Information Center

Huang, Yuan-Han

2013-01-01

This study focused on the clinical workflow evolutions when implementing the health information technology (HIT). The study especially emphasized on administrating medication when the electronic health record (EHR) systems were adopted at rural healthcare facilities. Mixed-mode research methods, such as survey, observation, and focus group, were…

Evolution of Observation: Implementing Programmatic Change

ERIC Educational Resources Information Center

Bender-Slack, Delane A.; Young, Teresa

2013-01-01

In the study reported, we examine the evolution of preservice teacher observation, focusing on the essential nature of observation to preservice teachers' learning about teaching while in the field. The study was 3 years long, and it involved 79 preservice teachers during semester-long language arts methods courses in early childhood and…

Comparison of νμ->νe Oscillation calculations with matter effects

NASA Astrophysics Data System (ADS)

Gordon, Michael; Toki, Walter

2013-04-01

An introduction to neutrino oscillations in vacuum is presented, followed by a survey of various techniques for obtaining either exact or approximate expressions for νμ->νe oscillations in matter. The method devised by Mann, Kafka, Schneps, and Altinok produces an exact expression for the oscillation by determining explicitely the evolution operator. The method used by Freund yields an approximate oscillation probability by diagonalizing the Hamiltonian, finding the eigenvalues and eigenvectors, and then using those to find modified mixing angles with the matter effect taken into account. The method developed by Arafune, Koike, and Sato uses an alternate method to find an approximation of the evolution operator. These methods are compared to each other using parameters from both the T2K and LBNE experiments.

Study regarding the density evolution of messages and the characteristic functions associated of a LDPC code

NASA Astrophysics Data System (ADS)

Drăghici, S.; Proştean, O.; Răduca, E.; Haţiegan, C.; Hălălae, I.; Pădureanu, I.; Nedeloni, M.; (Barboni Haţiegan, L.

2017-01-01

In this paper a method with which a set of characteristic functions are associated to a LDPC code is shown and also functions that represent the evolution density of messages that go along the edges of a Tanner graph. Graphic representations of the density evolution are shown respectively the study and simulation of likelihood threshold that render asymptotic boundaries between which there are decodable codes were made using MathCad V14 software.

Evolution of orbits of the Apollo group asteroids over 11550 years.

NASA Astrophysics Data System (ADS)

Zausaev, A. F.; Pushkarev, A. N.

The Everhart method is used to study the evolution of the orbits of 20 asteroids of the Apollo group over the time period from 9300 B.C. to 2250 A.D. Minimum distances of the asteroids to the major planets over the evolution process are calculated. The stability of resonances with Venus and Earth over the 9300 B.C.to 2250 A.D. time period is shown. Theoretical coordinates of radiants for the initial and final integration times are presented.

Some simple solutions of Schrödinger's equation for a free particle or for an oscillator

NASA Astrophysics Data System (ADS)

Andrews, Mark

2018-05-01

For a non-relativistic free particle, we show that the evolution of some simple initial wave functions made up of linear segments can be expressed in terms of Fresnel integrals. Examples include the square wave function and the triangular wave function. The method is then extended to wave functions made from quadratic elements. The evolution of all these initial wave functions can also be found for the harmonic oscillator by a transformation of the free evolutions.

Pseudospectral method for gravitational wave collapse

NASA Astrophysics Data System (ADS)

Hilditch, David; Weyhausen, Andreas; Brügmann, Bernd

2016-03-01

We present a new pseudospectral code, bamps, for numerical relativity written with the evolution of collapsing gravitational waves in mind. We employ the first-order generalized harmonic gauge formulation. The relevant theory is reviewed, and the numerical method is critically examined and specialized for the task at hand. In particular, we investigate formulation parameters—gauge- and constraint-preserving boundary conditions well suited to nonvanishing gauge source functions. Different types of axisymmetric twist-free moment-of-time-symmetry gravitational wave initial data are discussed. A treatment of the axisymmetric apparent horizon condition is presented with careful attention to regularity on axis. Our apparent horizon finder is then evaluated in a number of test cases. Moving on to evolutions, we investigate modifications to the generalized harmonic gauge constraint damping scheme to improve conservation in the strong-field regime. We demonstrate strong-scaling of our pseudospectral penalty code. We employ the Cartoon method to efficiently evolve axisymmetric data in our 3 +1 -dimensional code. We perform test evolutions of the Schwarzschild spacetime perturbed by gravitational waves and by gauge pulses, both to demonstrate the use of our black-hole excision scheme and for comparison with earlier results. Finally, numerical evolutions of supercritical Brill waves are presented to demonstrate durability of the excision scheme for the dynamical formation of a black hole.

[Gene method for inconsistent hydrological frequency calculation. I: Inheritance, variability and evolution principles of hydrological genes].

PubMed

Xie, Ping; Wu, Zi Yi; Zhao, Jiang Yan; Sang, Yan Fang; Chen, Jie

2018-04-01

A stochastic hydrological process is influenced by both stochastic and deterministic factors. A hydrological time series contains not only pure random components reflecting its inheri-tance characteristics, but also deterministic components reflecting variability characteristics, such as jump, trend, period, and stochastic dependence. As a result, the stochastic hydrological process presents complicated evolution phenomena and rules. To better understand these complicated phenomena and rules, this study described the inheritance and variability characteristics of an inconsistent hydrological series from two aspects: stochastic process simulation and time series analysis. In addition, several frequency analysis approaches for inconsistent time series were compared to reveal the main problems in inconsistency study. Then, we proposed a new concept of hydrological genes origined from biological genes to describe the inconsistent hydrolocal processes. The hydrologi-cal genes were constructed using moments methods, such as general moments, weight function moments, probability weight moments and L-moments. Meanwhile, the five components, including jump, trend, periodic, dependence and pure random components, of a stochastic hydrological process were defined as five hydrological bases. With this method, the inheritance and variability of inconsistent hydrological time series were synthetically considered and the inheritance, variability and evolution principles were fully described. Our study would contribute to reveal the inheritance, variability and evolution principles in probability distribution of hydrological elements.

Differential evolution-based multi-objective optimization for the definition of a health indicator for fault diagnostics and prognostics

NASA Astrophysics Data System (ADS)

Baraldi, P.; Bonfanti, G.; Zio, E.

2018-03-01

The identification of the current degradation state of an industrial component and the prediction of its future evolution is a fundamental step for the development of condition-based and predictive maintenance approaches. The objective of the present work is to propose a general method for extracting a health indicator to measure the amount of component degradation from a set of signals measured during operation. The proposed method is based on the combined use of feature extraction techniques, such as Empirical Mode Decomposition and Auto-Associative Kernel Regression, and a multi-objective Binary Differential Evolution (BDE) algorithm for selecting the subset of features optimal for the definition of the health indicator. The objectives of the optimization are desired characteristics of the health indicator, such as monotonicity, trendability and prognosability. A case study is considered, concerning the prediction of the remaining useful life of turbofan engines. The obtained results confirm that the method is capable of extracting health indicators suitable for accurate prognostics.

Cross-cultural dataset for the evolution of religion and morality project.

PubMed

Purzycki, Benjamin Grant; Apicella, Coren; Atkinson, Quentin D; Cohen, Emma; McNamara, Rita Anne; Willard, Aiyana K; Xygalatas, Dimitris; Norenzayan, Ara; Henrich, Joseph

2016-11-08

A considerable body of research cross-culturally examines the evolution of religious traditions, beliefs and behaviors. The bulk of this research, however, draws from coded qualitative ethnographies rather than from standardized methods specifically designed to measure religious beliefs and behaviors. Psychological data sets that examine religious thought and behavior in controlled conditions tend to be disproportionately sampled from student populations. Some cross-national databases employ standardized methods at the individual level, but are primarily focused on fully market integrated, state-level societies. The Evolution of Religion and Morality Project sought to generate a data set that systematically probed individual level measures sampling across a wider range of human populations. The set includes data from behavioral economic experiments and detailed surveys of demographics, religious beliefs and practices, material security, and intergroup perceptions. This paper describes the methods and variables, briefly introduces the sites and sampling techniques, notes inconsistencies across sites, and provides some basic reporting for the data set.

Ultra-high-throughput screening method for the directed evolution of glucose oxidase.

PubMed

Ostafe, Raluca; Prodanovic, Radivoje; Nazor, Jovana; Fischer, Rainer

2014-03-20

Glucose oxidase (GOx) is used in many industrial processes that could benefit from improved versions of the enzyme. Some improvements like higher activity under physiological conditions and thermal stability could be useful for GOx applications in biosensors and biofuel cells. Directed evolution is one of the currently available methods to engineer improved GOx variants. Here, we describe an ultra-high-throughput screening system for sorting the best enzyme variants generated by directed evolution that incorporates several methodological refinements: flow cytometry, in vitro compartmentalization, yeast surface display, fluorescent labeling of the expressed enzyme, delivery of glucose substrate to the reaction mixture through the oil phase, and covalent labeling of the cells with fluorescein-tyramide. The method enables quantitative screening of gene libraries to identify clones with improved activity and it also allows cells to be selected based not only on the overall activity but also on the specific activity of the enzyme. Copyright © 2014 Elsevier Ltd. All rights reserved.

Cross-cultural dataset for the evolution of religion and morality project

PubMed Central

Purzycki, Benjamin Grant; Apicella, Coren; Atkinson, Quentin D.; Cohen, Emma; McNamara, Rita Anne; Willard, Aiyana K.; Xygalatas, Dimitris; Norenzayan, Ara; Henrich, Joseph

2016-01-01

A considerable body of research cross-culturally examines the evolution of religious traditions, beliefs and behaviors. The bulk of this research, however, draws from coded qualitative ethnographies rather than from standardized methods specifically designed to measure religious beliefs and behaviors. Psychological data sets that examine religious thought and behavior in controlled conditions tend to be disproportionately sampled from student populations. Some cross-national databases employ standardized methods at the individual level, but are primarily focused on fully market integrated, state-level societies. The Evolution of Religion and Morality Project sought to generate a data set that systematically probed individual level measures sampling across a wider range of human populations. The set includes data from behavioral economic experiments and detailed surveys of demographics, religious beliefs and practices, material security, and intergroup perceptions. This paper describes the methods and variables, briefly introduces the sites and sampling techniques, notes inconsistencies across sites, and provides some basic reporting for the data set. PMID:27824332

Evolution of inviscid Kelvin-Helmholtz instability from a piecewise linear shear layer

NASA Astrophysics Data System (ADS)

Guha, Anirban; Rahmani, Mona; Lawrence, Gregory

2012-11-01

Here we study the evolution of 2D, inviscid Kelvin-Helmholtz instability (KH) ensuing from a piecewise linear shear layer. Although KH pertaining to smooth shear layers (eg. Hyperbolic tangent profile) has been thorough investigated in the past, very little is known about KH resulting from sharp shear layers. Pozrikidis and Higdon (1985) have shown that piecewise shear layer evolves into elliptical vortex patches. This non-linear state is dramatically different from the well known spiral-billow structure of KH. In fact, there is a little acknowledgement that elliptical vortex patches can represent non-linear KH. In this work, we show how such patches evolve through the interaction of vorticity waves. Our work is based on two types of computational methods (i) Contour Dynamics: a boundary-element method which tracks the evolution of the contour of a vortex patch using Lagrangian marker points, and (ii) Direct Numerical Simulation (DNS): an Eulerian pseudo-spectral method heavily used in studying hydrodynamic instability and turbulence.

Study on probability distributions for evolution in modified extremal optimization

NASA Astrophysics Data System (ADS)

Zeng, Guo-Qiang; Lu, Yong-Zai; Mao, Wei-Jie; Chu, Jian

2010-05-01

It is widely believed that the power-law is a proper probability distribution being effectively applied for evolution in τ-EO (extremal optimization), a general-purpose stochastic local-search approach inspired by self-organized criticality, and its applications in some NP-hard problems, e.g., graph partitioning, graph coloring, spin glass, etc. In this study, we discover that the exponential distributions or hybrid ones (e.g., power-laws with exponential cutoff) being popularly used in the research of network sciences may replace the original power-laws in a modified τ-EO method called self-organized algorithm (SOA), and provide better performances than other statistical physics oriented methods, such as simulated annealing, τ-EO and SOA etc., from the experimental results on random Euclidean traveling salesman problems (TSP) and non-uniform instances. From the perspective of optimization, our results appear to demonstrate that the power-law is not the only proper probability distribution for evolution in EO-similar methods at least for TSP, the exponential and hybrid distributions may be other choices.

Enhanced differential evolution to combine optical mouse sensor with image structural patches for robust endoscopic navigation.

PubMed

Luo, Xiongbiao; Jayarathne, Uditha L; McLeod, A Jonathan; Mori, Kensaku

2014-01-01

Endoscopic navigation generally integrates different modalities of sensory information in order to continuously locate an endoscope relative to suspicious tissues in the body during interventions. Current electromagnetic tracking techniques for endoscopic navigation have limited accuracy due to tissue deformation and magnetic field distortion. To avoid these limitations and improve the endoscopic localization accuracy, this paper proposes a new endoscopic navigation framework that uses an optical mouse sensor to measure the endoscope movements along its viewing direction. We then enhance the differential evolution algorithm by modifying its mutation operation. Based on the enhanced differential evolution method, these movement measurements and image structural patches in endoscopic videos are fused to accurately determine the endoscope position. An evaluation on a dynamic phantom demonstrated that our method provides a more accurate navigation framework. Compared to state-of-the-art methods, it improved the navigation accuracy from 2.4 to 1.6 mm and reduced the processing time from 2.8 to 0.9 seconds.

New exact solutions of the Tzitzéica-type equations in non-linear optics using the expa function method

NASA Astrophysics Data System (ADS)

Hosseini, K.; Ayati, Z.; Ansari, R.

2018-04-01

One specific class of non-linear evolution equations, known as the Tzitzéica-type equations, has received great attention from a group of researchers involved in non-linear science. In this article, new exact solutions of the Tzitzéica-type equations arising in non-linear optics, including the Tzitzéica, Dodd-Bullough-Mikhailov and Tzitzéica-Dodd-Bullough equations, are obtained using the expa function method. The integration technique actually suggests a useful and reliable method to extract new exact solutions of a wide range of non-linear evolution equations.

Artificial evolution by viability rather than competition.

PubMed

Maesani, Andrea; Fernando, Pradeep Ruben; Floreano, Dario

2014-01-01

Evolutionary algorithms are widespread heuristic methods inspired by natural evolution to solve difficult problems for which analytical approaches are not suitable. In many domains experimenters are not only interested in discovering optimal solutions, but also in finding the largest number of different solutions satisfying minimal requirements. However, the formulation of an effective performance measure describing these requirements, also known as fitness function, represents a major challenge. The difficulty of combining and weighting multiple problem objectives and constraints of possibly varying nature and scale into a single fitness function often leads to unsatisfactory solutions. Furthermore, selective reproduction of the fittest solutions, which is inspired by competition-based selection in nature, leads to loss of diversity within the evolving population and premature convergence of the algorithm, hindering the discovery of many different solutions. Here we present an alternative abstraction of artificial evolution, which does not require the formulation of a composite fitness function. Inspired from viability theory in dynamical systems, natural evolution and ethology, the proposed method puts emphasis on the elimination of individuals that do not meet a set of changing criteria, which are defined on the problem objectives and constraints. Experimental results show that the proposed method maintains higher diversity in the evolving population and generates more unique solutions when compared to classical competition-based evolutionary algorithms. Our findings suggest that incorporating viability principles into evolutionary algorithms can significantly improve the applicability and effectiveness of evolutionary methods to numerous complex problems of science and engineering, ranging from protein structure prediction to aircraft wing design.

The Evolution of Nondestructive Evaluation Methods for the Space Shuttle External Tank Thermal Protection System

NASA Technical Reports Server (NTRS)

Walker, James L.; Richter, Joel D.

2006-01-01

Three nondestructive evaluation methods are being developed to identify defects in the foam thermal protection system (TPS) of the Space Shuttle External Tank (ET). Shearography is being developed to identify shallow delaminations, shallow voids and crush damage in the foam while terahertz imaging and backscatter radiography are being developed to identify voids and cracks in thick foam regions. The basic theory of operation along with factors affecting the results of these methods will be described. Also, the evolution of these methods from lab tools to implementation on the ET will be discussed. Results from both test panels and flight tank inspections will be provided to show the range in defect sizes and types that can be readily detected.

Voids in cosmological simulations over cosmic time

NASA Astrophysics Data System (ADS)

Wojtak, Radosław; Powell, Devon; Abel, Tom

2016-06-01

We study evolution of voids in cosmological simulations using a new method for tracing voids over cosmic time. The method is based on tracking watershed basins (contiguous regions around density minima) of well-developed voids at low redshift, on a regular grid of density field. It enables us to construct a robust and continuous mapping between voids at different redshifts, from initial conditions to the present time. We discuss how the new approach eliminates strong spurious effects of numerical origin when voids' evolution is traced by matching voids between successive snapshots (by analogy to halo merger trees). We apply the new method to a cosmological simulation of a standard Λ-cold-dark-matter cosmological model and study evolution of basic properties of typical voids (with effective radii 6 h-1 Mpc < Rv < 20 h-1 Mpc at redshift z = 0) such as volumes, shapes, matter density distributions and relative alignments. The final voids at low redshifts appear to retain a significant part of the configuration acquired in initial conditions. Shapes of voids evolve in a collective way which barely modifies the overall distribution of the axial ratios. The evolution appears to have a weak impact on mutual alignments of voids implying that the present state is in large part set up by the primordial density field. We present evolution of dark matter density profiles computed on isodensity surfaces which comply with the actual shapes of voids. Unlike spherical density profiles, this approach enables us to demonstrate development of theoretically predicted bucket-like shape of the final density profiles indicating a wide flat core and a sharp transition to high-density void walls.

Dynamic evolution of nearby galaxy clusters

NASA Astrophysics Data System (ADS)

Biernacka, M.; Flin, P.

2011-06-01

A study of the evolution of 377 rich ACO clusters with redshift z<0.2 is presented. The data concerning galaxies in the investigated clusters were obtained using FOCAS packages applied to Digital Sky Survey I. The 377 galaxy clusters constitute a statistically uniform sample to which visual galaxy/star reclassifications were applied. Cluster shape within 2.0 h-1 Mpc from the adopted cluster centre (the mean and the median of all galaxy coordinates, the position of the brightest and of the third brightest galaxy in the cluster) was determined through its ellipticity calculated using two methods: the covariance ellipse method (hereafter CEM) and the method based on Minkowski functionals (hereafter MFM). We investigated ellipticity dependence on the radius of circular annuli, in which ellipticity was calculated. This was realized by varying the radius from 0.5 to 2 Mpc in steps of 0.25 Mpc. By performing Monte Carlo simulations, we generated clusters to which the two ellipticity methods were applied. We found that the covariance ellipse method works better than the method based on Minkowski functionals. We also found that ellipticity distributions are different for different methods used. Using the ellipticity-redshift relation, we investigated the possibility of cluster evolution in the low-redshift Universe. The correlation of cluster ellipticities with redshifts is undoubtly an indicator of structural evolution. Using the t-Student statistics, we found a statistically significant correlation between ellipticity and redshift at the significance level of α = 0.95. In one of the two shape determination methods we found that ellipticity grew with redshift, while the other method gave opposite results. Monte Carlo simulations showed that only ellipticities calculated at the distance of 1.5 Mpc from cluster centre in the Minkowski functional method are robust enough to be taken into account, but for that radius we did not find any relation between e and z. Since CEM pointed towards the existence of the e(z) relation, we conclude that such an effect is real though rather weak. A detailed study of the e(z) relation showed that the observed relation is nonlinear, and the number of elongated structures grows rapidly for z>0.14.

Evolution of opercle shape in cichlid fishes from Lake Tanganyika - adaptive trait interactions in extant and extinct species flocks.

PubMed

Wilson, Laura A B; Colombo, Marco; Sánchez-Villagra, Marcelo R; Salzburger, Walter

2015-11-20

Phenotype-environment correlations and the evolution of trait interactions in adaptive radiations have been widely studied to gain insight into the dynamics underpinning rapid species diversification. In this study we explore the phenotype-environment correlation and evolution of operculum shape in cichlid fishes using an outline-based geometric morphometric approach combined with stable isotope indicators of macrohabitat and trophic niche. We then apply our method to a sample of extinct saurichthyid fishes, a highly diverse and near globally distributed group of actinopterygians occurring throughout the Triassic, to assess the utility of extant data to inform our understanding of ecomorphological evolution in extinct species flocks. A series of comparative methods were used to analyze shape data for 54 extant species of cichlids (N = 416), and 6 extinct species of saurichthyids (N = 44). Results provide evidence for a relationship between operculum shape and feeding ecology, a concentration in shape evolution towards present along with evidence for convergence in form, and significant correlation between the major axes of shape change and measures of gut length and body elongation. The operculum is one of few features that can be compared in extant and extinct groups, enabling reconstruction of phenotype-environment interactions and modes of evolutionary diversification in deep time.

Programming cells by multiplex genome engineering and accelerated evolution.

PubMed

Wang, Harris H; Isaacs, Farren J; Carr, Peter A; Sun, Zachary Z; Xu, George; Forest, Craig R; Church, George M

2009-08-13

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales. Although in vitro and directed evolution methods have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-D-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

Evolution of the degree of substructures in simulated galaxy clusters

NASA Astrophysics Data System (ADS)

De Boni, Cristiano; Böhringer, Hans; Chon, Gayoung; Dolag, Klaus

2018-05-01

We study the evolution of substructure in the mass distribution with mass, redshift and radius in a sample of simulated galaxy clusters. The sample, containing 1226 objects, spans the mass range M200 = 1014 - 1.74 × 1015 M⊙ h-1 in six redshift bins from z = 0 to z = 1.179. We consider three different diagnostics: 1) subhalos identified with SUBFIND; 2) overdense regions localized by dividing the cluster into octants; 3) offset between the potential minimum and the center of mass. The octant analysis is a new method that we introduce in this work. We find that none of the diagnostics indicate a correlation between the mass of the cluster and the fraction of substructures. On the other hand, all the diagnostics suggest an evolution of substructures with redshift. For SUBFIND halos, the mass fraction is constant with redshift at Rvir, but shows a mild evolution at R200 and R500. Also, the fraction of clusters with at least a subhalo more massive than one thirtieth of the total mass is less than 20%. Our new method based on the octants returns a mass fraction in substructures which has a strong evolution with redshift at all radii. The offsets also evolve strongly with redshift. We also find a strong correlation for individual clusters between the offset and the fraction of substructures identified with the octant analysis. Our work puts strong constraints on the amount of substructures we expect to find in galaxy clusters and on their evolution with redshift.

Robust and fast-converging level set method for side-scan sonar image segmentation

NASA Astrophysics Data System (ADS)

Liu, Yan; Li, Qingwu; Huo, Guanying

2017-11-01

A robust and fast-converging level set method is proposed for side-scan sonar (SSS) image segmentation. First, the noise in each sonar image is removed using the adaptive nonlinear complex diffusion filter. Second, k-means clustering is used to obtain the initial presegmentation image from the denoised image, and then the distance maps of the initial contours are reinitialized to guarantee the accuracy of the numerical calculation used in the level set evolution. Finally, the satisfactory segmentation is achieved using a robust variational level set model, where the evolution control parameters are generated by the presegmentation. The proposed method is successfully applied to both synthetic image with speckle noise and real SSS images. Experimental results show that the proposed method needs much less iteration and therefore is much faster than the fuzzy local information c-means clustering method, the level set method using a gamma observation model, and the enhanced region-scalable fitting method. Moreover, the proposed method can usually obtain more accurate segmentation results compared with other methods.

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.

Chemical element transport in stellar evolution models

PubMed Central

Cassisi, Santi

2017-01-01

Stellar evolution computations provide the foundation of several methods applied to study the evolutionary properties of stars and stellar populations, both Galactic and extragalactic. The accuracy of the results obtained with these techniques is linked to the accuracy of the stellar models, and in this context the correct treatment of the transport of chemical elements is crucial. Unfortunately, in many respects calculations of the evolution of the chemical abundance profiles in stars are still affected by sometimes sizable uncertainties. Here, we review the various mechanisms of element transport included in the current generation of stellar evolution calculations, how they are implemented, the free parameters and uncertainties involved, the impact on the models and the observational constraints. PMID:28878972

Chemical element transport in stellar evolution models.

PubMed

Salaris, Maurizio; Cassisi, Santi

2017-08-01

Stellar evolution computations provide the foundation of several methods applied to study the evolutionary properties of stars and stellar populations, both Galactic and extragalactic. The accuracy of the results obtained with these techniques is linked to the accuracy of the stellar models, and in this context the correct treatment of the transport of chemical elements is crucial. Unfortunately, in many respects calculations of the evolution of the chemical abundance profiles in stars are still affected by sometimes sizable uncertainties. Here, we review the various mechanisms of element transport included in the current generation of stellar evolution calculations, how they are implemented, the free parameters and uncertainties involved, the impact on the models and the observational constraints.

Phase-field Model for Interstitial Loop Growth Kinetics and Thermodynamic and Kinetic Models of Irradiated Fe-Cr Alloys

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

Li, Yulan; Hu, Shenyang Y.; Sun, Xin

2011-06-15

Microstructure evolution kinetics in irradiated materials has strongly spatial correlation. For example, void and second phases prefer to nucleate and grow at pre-existing defects such as dislocations, grain boundaries, and cracks. Inhomogeneous microstructure evolution results in inhomogeneity of microstructure and thermo-mechanical properties. Therefore, the simulation capability for predicting three dimensional (3-D) microstructure evolution kinetics and its subsequent impact on material properties and performance is crucial for scientific design of advanced nuclear materials and optimal operation conditions in order to reduce uncertainty in operational and safety margins. Very recently the meso-scale phase-field (PF) method has been used to predict gas bubblemore » evolution, void swelling, void lattice formation and void migration in irradiated materials,. Although most results of phase-field simulations are qualitative due to the lake of accurate thermodynamic and kinetic properties of defects, possible missing of important kinetic properties and processes, and the capability of current codes and computers for large time and length scale modeling, the simulations demonstrate that PF method is a promising simulation tool for predicting 3-D heterogeneous microstructure and property evolution, and providing microstructure evolution kinetics for higher scale level simulations of microstructure and property evolution such as mean field methods. This report consists of two parts. In part I, we will present a new phase-field model for predicting interstitial loop growth kinetics in irradiated materials. The effect of defect (vacancy/interstitial) generation, diffusion and recombination, sink strength, long-range elastic interaction, inhomogeneous and anisotropic mobility on microstructure evolution kinetics is taken into account in the model. The model is used to study the effect of elastic interaction on interstitial loop growth kinetics, the interstitial flux, and sink strength of interstitial loop for interstitials. In part II, we present a generic phase field model and discuss the thermodynamic and kinetic properties in phase-field models including the reaction kinetics of radiation defects and local free energy of irradiated materials. In particular, a two-sublattice thermodynamic model is suggested to describe the local free energy of alloys with irradiated defects. Fe-Cr alloy is taken as an example to explain the required thermodynamic and kinetic properties for quantitative phase-field modeling. Finally the great challenges in phase-field modeling will be discussed.« less

A Socratic Method for Surveying Students' Readiness to Study Evolution

ERIC Educational Resources Information Center

Stansfield, William D.

2013-01-01

Before beginning a series of presentations on evolution, it would be prudent to survey the general level of students' understanding of prerequisite basic concepts of reproduction, heredity, ontology, and phenotypic diversity so that teachers can avoid devoting time to well-known subjects of general knowledge and can spend more time on subjects…

Evaluating the Discrete Element Method as a Tool for Predicting the Seasonal Evolution of the MIZ

DTIC Science & Technology

2015-09-30

wave-ice interaction (Hopkins & Shen 2001), and the mesoscale evolution of the floe size distribution (Hopkins & Thorndike 2006). This modeling effort...33(1), 355-360. Hopkins, M. A., & Thorndike , A. S. (2006) Floe formation in Arctic sea ice. Journal of Geophysical Research: Oceans (1978–2012), 111

A method for observing gas evolution during plastic laminate cure

NASA Technical Reports Server (NTRS)

Nicholls, A. H.

1969-01-01

Polyimide, phenolic, and other resins which develop volatiles during laminating or molding cure are studied using optimum cure cycles. The specimen is placed on a platen and sealed in a plastic bag, then heated and observed for gas evolution using a binocular microscope. A cover plate is added to sumulate an autoclave.

Designing a Resource Evolution Support System for Open Knowledge Communities

ERIC Educational Resources Information Center

Yang, Xianmin; Yu, Shengquan

2015-01-01

The continuous generation and evolution of digital learning resources is important for promoting open learning and meeting the personalized needs of learners. In the Web 2.0 era, open and collaborative authoring is becoming a popular method by which to create vast personalized learning resources in open knowledge communities (OKCs). However, the…

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…

Polyallylamine-Rh nanosheet nanoassemblies-carbon nanotubes organic-inorganic nanohybrids: A electrocatalyst superior to Pt for the hydrogen evolution reaction

NASA Astrophysics Data System (ADS)

Bai, Juan; Xing, Shi-Hui; Zhu, Ying-Ying; Jiang, Jia-Xing; Zeng, Jing-Hui; Chen, Yu

2018-05-01

Rationally tailoring the surface/interface structures of noble metal nanostructures emerges as a highly efficient method for improving their electrocatalytic activity, selectivity, and long-term stability. Recently, hydrogen evolution reaction is attracting more and more attention due to the energy crisis and environment pollution. Herein, we successfully synthesize polyallylamine-functionalized rhodium nanosheet nanoassemblies-carbon nanotube nanohybrids via a facile one-pot hydrothermal method. Three-dimensionally branched rhodium nanosheet nanoassemblies are consisted of two dimensionally atomically thick ultrathin rhodium nanosheets. The as-prepared polyallylamine-functionalized rhodium nanosheet nanoassemblies-carbon nanotube nanohybrids show the excellent electrocatalytic activity for the hydrogen evolution reaction in acidic media, with a low onset reduction potential of -1 mV, a small overpotential of 5 mV at 10 mA cm-2, which is much superior to commercial platinum nanocrystals. Two dimensionally ultrathin morphology of rhodium nanosheet, particular rhodium-polyallylamine interface, and three-dimensionally networks induced by carbon nanotube are the key factors for the excellent hydrogen evolution reaction activity in acidic media.

3D Studies of the Solar Corona and its Evolution with SOHO/EIT

NASA Astrophysics Data System (ADS)

Portier-Fozzani, F.

This thesis deals with 3D evolution of coronal structures based upon the ultraviolet telescope of SOHO : EIT. Anaglyphs and incertainties on a complete stereovision reconstruction are described. Stereoscopic methods for loop reconstruction were successfully made to find 3D parameters. With dynamical stereoscopy, physical conditions were derived for 30 loops of temperature around 1MK. A method which is able to derive twist variation were also built. Emerging loops were found highly twisted and they detwist as they grow. According to helicity conservation, this correspond to a transfert of twist into expansion. Long time twist evolution of magnetic flux tubes are followed in relation with flares as relaxation. Interaction between magnetic field lines were analysed. An example of reconnection between open and closed field line were observed. Other interactions were found with multi-wavelength observations : coronal holes borders (and thus CH) are better defined when an active region nearby is growing. Other imaging techniques were used to better take profit as possible of SOHO/EIT. A multiscale vision model (MVM) was applied with success to show small coronal structures evolutions hidden by the noise level.

Evolution method and ``differential hierarchy'' of colored knot polynomials

NASA Astrophysics Data System (ADS)

Mironov, A.; Morozov, A.; Morozov, And.

2013-10-01

We consider braids with repeating patterns inside arbitrary knots which provides a multi-parametric family of knots, depending on the "evolution" parameter, which controls the number of repetitions. The dependence of knot (super)polynomials on such evolution parameters is very easy to find. We apply this evolution method to study of the families of knots and links which include the cases with just two parallel and anti-parallel strands in the braid, like the ordinary twist and 2-strand torus knots/links and counter-oriented 2-strand links. When the answers were available before, they are immediately reproduced, and an essentially new example is added of the "double braid", which is a combination of parallel and anti-parallel 2-strand braids. This study helps us to reveal with the full clarity and partly investigate a mysterious hierarchical structure of the colored HOMFLY polynomials, at least, in (anti)symmetric representations, which extends the original observation for the figure-eight knot to many (presumably all) knots. We demonstrate that this structure is typically respected by the t-deformation to the superpolynomials.

Detection of timescales in evolving complex systems

PubMed Central

Darst, Richard K.; Granell, Clara; Arenas, Alex; Gómez, Sergio; Saramäki, Jari; Fortunato, Santo

2016-01-01

Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant of time. This is often done by using constant intervals but a better approach would be to define dynamic intervals that match the evolution of the system’s configuration. To this end, we propose a method that aims at detecting evolutionary changes in the configuration of a complex system, and generates intervals accordingly. We show that evolutionary timescales can be identified by looking for peaks in the similarity between the sets of events on consecutive time intervals of data. Tests on simple toy models reveal that the technique is able to detect evolutionary timescales of time-varying data both when the evolution is smooth as well as when it changes sharply. This is further corroborated by analyses of several real datasets. Our method is scalable to extremely large datasets and is computationally efficient. This allows a quick, parameter-free detection of multiple timescales in the evolution of a complex system. PMID:28004820

Battery parameterisation based on differential evolution via a boundary evolution strategy

NASA Astrophysics Data System (ADS)

Yang, Guangya

2014-01-01

Attention has been given to the battery modelling in the electric engineering field following the current development of renewable energy and electrification of transportation. The establishment of the equivalent circuit model of the battery requires data preparation and parameterisation. Besides, as the equivalent circuit model is an abstract map of the battery electric characteristics, the determination of the possible ranges of parameters can be a challenging task. In this paper, an efficient yet easy to implement method is proposed to parameterise the equivalent circuit model of batteries utilising the advances of evolutionary algorithms (EAs). Differential evolution (DE) is selected and modified to parameterise an equivalent circuit model of lithium-ion batteries. A boundary evolution strategy (BES) is developed and incorporated into the DE to update the parameter boundaries during the parameterisation. The method can parameterise the model without extensive data preparation. In addition, the approach can also estimate the initial SOC and the available capacity. The efficiency of the approach is verified through two battery packs, one is an 8-cell battery module and one from an electrical vehicle.

A behavioral perspective on fishing-induced evolution.

PubMed

Uusi-Heikkilä, Silva; Wolter, Christian; Klefoth, Thomas; Arlinghaus, Robert

2008-08-01

The potential for excessive and/or selective fishing to act as an evolutionary force has been emphasized recently. However, most studies have focused on evolution of life-history traits in response to size-selective harvesting. Here we draw attention to fishing-induced evolution of behavioral and underlying physiological traits. We contend that fishing-induced selection directly acting on behavioral rather than on life-history traits per se can be expected in all fisheries that operate with passive gears such as trapping, angling and gill-netting. Recent artificial selection experiments in the nest-guarding largemouth bass Micropterus salmoides suggest that fishing-induced evolution of behavioral traits that reduce exposure to fishing gear might be maladaptive, potentially reducing natural recruitment. To improve understanding and management of fisheries-induced evolution, we encourage greater application of methods from behavioral ecology, physiological ecology and behavioral genetics.

Life span in online communities

NASA Astrophysics Data System (ADS)

Grabowski, A.; Kosiński, R. A.

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users’ activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users’ lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

Life span in online communities.

PubMed

Grabowski, A; Kosiński, R A

2010-12-01

Recently online communities have attracted great interest and have become an important medium of information exchange between users. The aim of this work is to introduce a simple model of the evolution of online communities. This model describes (a) the time evolution of users' activity in a web service, e.g., the time evolution of the number of online friends or written posts, (b) the time evolution of the degree distribution of a social network, and (c) the time evolution of the number of active users of a web service. In the second part of the paper we investigate the influence of the users' lifespan (i.e., the total time in which they are active in an online community) on the process of rumor propagation in evolving social networks. Viral marketing is an important application of such method of information propagation.

Modeling the evolution space of breakage fusion bridge cycles with a stochastic folding process.

PubMed

Greenman, C D; Cooke, S L; Marshall, J; Stratton, M R; Campbell, P J

2016-01-01

Breakage-fusion-bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then 'unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the localised amplicons observed in cancer genome data. Here we study the evolution space of breakage-fusion-bridge structures in detail. We firstly consider discrete representations of this space with 2-d trees to demonstrate that there are [Formula: see text] qualitatively distinct evolutions involving [Formula: see text] breakage-fusion-bridge cycles. Secondly we consider the stochastic nature of the process to show these evolutions are not equally likely, and also describe how amplicons become localized. Finally we highlight these methods by inferring the evolution of breakage-fusion-bridge cycles with data from primary tissue cancer samples.

Markovian Monte Carlo program EvolFMC v.2 for solving QCD evolution equations

NASA Astrophysics Data System (ADS)

Jadach, S.; Płaczek, W.; Skrzypek, M.; Stokłosa, P.

2010-02-01

We present the program EvolFMC v.2 that solves the evolution equations in QCD for the parton momentum distributions by means of the Monte Carlo technique based on the Markovian process. The program solves the DGLAP-type evolution as well as modified-DGLAP ones. In both cases the evolution can be performed in the LO or NLO approximation. The quarks are treated as massless. The overall technical precision of the code has been established at 5×10. This way, for the first time ever, we demonstrate that with the Monte Carlo method one can solve the evolution equations with precision comparable to the other numerical methods. New version program summaryProgram title: EvolFMC v.2 Catalogue identifier: AEFN_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFN_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including binary test data, etc.: 66 456 (7407 lines of C++ code) No. of bytes in distributed program, including test data, etc.: 412 752 Distribution format: tar.gz Programming language: C++ Computer: PC, Mac Operating system: Linux, Mac OS X RAM: Less than 256 MB Classification: 11.5 External routines: ROOT ( http://root.cern.ch/drupal/) Nature of problem: Solution of the QCD evolution equations for the parton momentum distributions of the DGLAP- and modified-DGLAP-type in the LO and NLO approximations. Solution method: Monte Carlo simulation of the Markovian process of a multiple emission of partons. Restrictions:Limited to the case of massless partons. Implemented in the LO and NLO approximations only. Weighted events only. Unusual features: Modified-DGLAP evolutions included up to the NLO level. Additional comments: Technical precision established at 5×10. Running time: For the 10 6 events at 100 GeV: DGLAP NLO: 27s; C-type modified DGLAP NLO: 150s (MacBook Pro with Mac OS X v.10.5.5, 2.4 GHz Intel Core 2 Duo, gcc 4.2.4, single thread).

Nature vs Nurture: Effects of Learning on Evolution

NASA Astrophysics Data System (ADS)

Nagrani, Nagina

In the field of Evolutionary Robotics, the design, development and application of artificial neural networks as controllers have derived their inspiration from biology. Biologists and artificial intelligence researchers are trying to understand the effects of neural network learning during the lifetime of the individuals on evolution of these individuals by qualitative and quantitative analyses. The conclusion of these analyses can help develop optimized artificial neural networks to perform any given task. The purpose of this thesis is to study the effects of learning on evolution. This has been done by applying Temporal Difference Reinforcement Learning methods to the evolution of Artificial Neural Tissue controller. The controller has been assigned the task to collect resources in a designated area in a simulated environment. The performance of the individuals is measured by the amount of resources collected. A comparison has been made between the results obtained by incorporating learning in evolution and evolution alone. The effects of learning parameters: learning rate, training period, discount rate, and policy on evolution have also been studied. It was observed that learning delays the performance of the evolving individuals over the generations. However, the non zero learning rate throughout the evolution process signifies natural selection preferring individuals possessing plasticity.

Turbomachinery Airfoil Design Optimization Using Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.; Biegel, Bryan A. (Technical Monitor)

2002-01-01

An aerodynamic design optimization procedure that is based on a evolutionary algorithm known at Differential Evolution is described. Differential Evolution is a simple, fast, and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems, including highly nonlinear systems with discontinuities and multiple local optima. The method is combined with a Navier-Stokes solver that evaluates the various intermediate designs and provides inputs to the optimization procedure. An efficient constraint handling mechanism is also incorporated. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated. Substantial reductions in the overall computing time requirements are achieved by using the algorithm in conjunction with neural networks.

Differential Evolution algorithm applied to FSW model calibration

NASA Astrophysics Data System (ADS)

Idagawa, H. S.; Santos, T. F. A.; Ramirez, A. J.

2014-03-01

Friction Stir Welding (FSW) is a solid state welding process that can be modelled using a Computational Fluid Dynamics (CFD) approach. These models use adjustable parameters to control the heat transfer and the heat input to the weld. These parameters are used to calibrate the model and they are generally determined using the conventional trial and error approach. Since this method is not very efficient, we used the Differential Evolution (DE) algorithm to successfully determine these parameters. In order to improve the success rate and to reduce the computational cost of the method, this work studied different characteristics of the DE algorithm, such as the evolution strategy, the objective function, the mutation scaling factor and the crossover rate. The DE algorithm was tested using a friction stir weld performed on a UNS S32205 Duplex Stainless Steel.

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.

SCM: A method to improve network service layout efficiency with network evolution

PubMed Central

Zhao, Qi; Zhang, Chuanhao

2017-01-01

Network services are an important component of the Internet, which are used to expand network functions for third-party developers. Network function virtualization (NFV) can improve the speed and flexibility of network service deployment. However, with the evolution of the network, network service layout may become inefficient. Regarding this problem, this paper proposes a service chain migration (SCM) method with the framework of “software defined network + network function virtualization” (SDN+NFV), which migrates service chains to adapt to network evolution and improves the efficiency of the network service layout. SCM is modeled as an integer linear programming problem and resolved via particle swarm optimization. An SCM prototype system is designed based on an SDN controller. Experiments demonstrate that SCM could reduce the network traffic cost and energy consumption efficiently. PMID:29267299

Soliton evolution and radiation loss for the sine-Gordon equation.

PubMed

Smyth, N F; Worthy, A L

1999-08-01

An approximate method for describing the evolution of solitonlike initial conditions to solitons for the sine-Gordon equation is developed. This method is based on using a solitonlike pulse with variable parameters in an averaged Lagrangian for the sine-Gordon equation. This averaged Lagrangian is then used to determine ordinary differential equations governing the evolution of the pulse parameters. The pulse evolves to a steady soliton by shedding dispersive radiation. The effect of this radiation is determined by examining the linearized sine-Gordon equation and loss terms are added to the variational equations derived from the averaged Lagrangian by using the momentum and energy conservation equations for the sine-Gordon equation. Solutions of the resulting approximate equations, which include loss, are found to be in good agreement with full numerical solutions of the sine-Gordon equation.

Microbial detection method based on sensing molecular hydrogen

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Stoner, G. E.; Boykin, E. H.

1974-01-01

An approach involving the measurement of hydrogen evolution by test organisms was used to detect and enumerate various members of the Enterobacteriaceae group. The experimental setup for measuring hydrogen evolution consisted of a test tube containing two electrodes plus broth and organisms. The test tube was kept in a water bath at a temperature of 35 C. It is pointed out that the hydrogen-sensing method, coupled with the pressure transducer technique reported by Wilkins (1974) could be used in various experiments in which gas production by microorganisms is being measured.

Bridging Inter- and Intraspecific Trait Evolution with a Hierarchical Bayesian Approach.

PubMed

Kostikova, Anna; Silvestro, Daniele; Pearman, Peter B; Salamin, Nicolas

2016-05-01

The evolution of organisms is crucially dependent on the evolution of intraspecific variation. Its interactions with selective agents in the biotic and abiotic environments underlie many processes, such as intraspecific competition, resource partitioning and, eventually, species formation. Nevertheless, comparative models of trait evolution neither allow explicit testing of hypotheses related to the evolution of intraspecific variation nor do they simultaneously estimate rates of trait evolution by accounting for both trait mean and variance. Here, we present a model of phenotypic trait evolution using a hierarchical Bayesian approach that simultaneously incorporates interspecific and intraspecific variation. We assume that species-specific trait means evolve under a simple Brownian motion process, whereas species-specific trait variances are modeled with Brownian or Ornstein-Uhlenbeck processes. After evaluating the power of the method through simulations, we examine whether life-history traits impact evolution of intraspecific variation in the Eriogonoideae (buckwheat family, Polygonaceae). Our model is readily extendible to more complex scenarios of the evolution of inter- and intraspecific variation and presents a step toward more comprehensive comparative models for macroevolutionary studies. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evidence of Repeated and Independent Saltational Evolution in a Peculiar Genus of Sphinx Moths (Proserpinus: Sphingidae)

PubMed Central

Rubinoff, Daniel; Le Roux, Johannes J.

2008-01-01

Background Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species. Methodology/Principal Findings Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide. Conclusions/Significance Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated—even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated. PMID:19107205

Evidence of repeated and independent saltational evolution in a peculiar genus of sphinx moths (Proserpinus: Sphingidae).

PubMed

Rubinoff, Daniel; Le Roux, Johannes J

2008-01-01

Saltational evolution in which a particular lineage undergoes relatively rapid, significant, and unparalleled change as compared with its closest relatives is rarely invoked as an alternative model to the dominant paradigm of gradualistic evolution. Identifying saltational events is an important first-step in assessing the importance of this discontinuous model in generating evolutionary novelty. We offer evidence for three independent instances of saltational evolution in a charismatic moth genus with only eight species. Maximum parsimony, maximum likelihood and Bayesian search criteria offered congruent, well supported phylogenies based on 1,965 base pairs of DNA sequence using the mitochondrial gene cytochrome oxidase subunit I, and the nuclear genes elongation factor-1 alpha and wingless. Using a comparative methods approach, we examined three taxa exhibiting novelty in the form of Batesian mimicry, host plant shift, and dramatic physiological differences in light of the phylogenetic data. All three traits appear to have evolved relatively rapidly and independently in three different species of Proserpinus. Each saltational species exhibits a markedly different and discrete example of discontinuous trait evolution while remaining canalized for other typical traits shared by the rest of the genus. All three saltational taxa show insignificantly different levels of overall genetic change as compared with their congeners, implying that their divergence is targeted to particular traits and not genome-wide. Such rapid evolution of novel traits in individual species suggests that the pace of evolution can be quick, dramatic, and isolated--even on the species level. These results may be applicable to other groups in which specific taxa have generated pronounced evolutionary novelty. Genetic mechanisms and methods for assessing such relatively rapid changes are postulated.

CD4+ T-cell recovery with suppressive ART-induced rapid sequence evolution in hepatitis C virus envelope but not NS3.

PubMed

Liu, Lin; Nardo, David; Li, Eric; Wang, Gary P

2016-03-13

CD4 T-cell depletion from HIV infection leads to a global decline in anti-hepatitis C virus (HCV) envelope neutralizing antibody (nAb) response, which may play a role in accelerating liver fibrosis. An increase in anti-HCV nAb titers has been reported during antiretroviral therapy (ART) but its impact on HCV remains poorly understood. The objective of this study is to determine the effects of ART on long-term HCV evolution. We examined HCV quasispecies structure and long-term evolution in HIV/HCV coinfected patients with ART-induced CD4 T-cell recovery, and compared with patients with CD4 T-cell depletion from delayed ART. We applied a single-variant sequencing (SVS) method to construct authentic viral quasispecies and compared sequence evolution in HCV envelope, the primary target for humoral immune responses, and NS3, a target for cellular immunity, between the two cohorts. The SVS method corrected biases known to skew the proportions of viral variants, revealing authentic HCV quasispeices structures. We observed higher rates of HCV envelope sequence evolution in patients with ART-induced CD4 T-cell recovery, compared with patients with CD4 T-cell depletion from delayed ART (P = 0.03). Evolutionary rates for NS3 were considerably lower than the rates for envelope (P < 0.01), with no significant difference observed between the two groups. ART-induced CD4 T-cell recovery results in rapid sequence evolution in HCV envelope, but not in NS3. These results suggest that suppressive ART disproportionally enhances HCV-specific humoral responses more than cellular responses, resulting in rapid sequence evolution in HCV envelope but not NS3.

Identifying hidden rate changes in the evolution of a binary morphological character: the evolution of plant habit in campanulid angiosperms.

PubMed

Beaulieu, Jeremy M; O'Meara, Brian C; Donoghue, Michael J

2013-09-01

The growth of phylogenetic trees in scope and in size is promising from the standpoint of understanding a wide variety of evolutionary patterns and processes. With trees comprised of larger, older, and globally distributed clades, it is likely that the lability of a binary character will differ significantly among lineages, which could lead to errors in estimating transition rates and the associated inference of ancestral states. Here we develop and implement a new method for identifying different rates of evolution in a binary character along different branches of a phylogeny. We illustrate this approach by exploring the evolution of growth habit in Campanulidae, a flowering plant clade containing some 35,000 species. The distribution of woody versus herbaceous species calls into question the use of traditional models of binary character evolution. The recognition and accommodation of changes in the rate of growth form evolution in different lineages demonstrates, for the first time, a robust picture of growth form evolution across a very large, very old, and very widespread flowering plant clade.

High-temperature morphological evolution of lithographically introduced cavities in silicon carbide

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

Narushima, Takayuki; Glaeser, Andreas M.

2000-12-01

Internal cavities of controlled geometry and crystallography were introduced in 6H silicon carbide single crystals by combining lithographic methods, ion beam etching, and solid-state diffusion bonding. The morphological evolution of these internal cavities (negative crystals) in response to anneals of up to 128 h duration at 1900 degrees C was examined using optical microscopy. Surface energy anisotropy and faceting have a strong influence on both the geometric and kinetic characteristics of evolution. Decomposition of 12{bar 1}0 cavity edges into 101{bar 0} facets was observed after 16 h anneals, indicating that 12{bar 1}0 faces are not components of the Wulff shape.more » The shape evolution kinetics of penny-shaped cavities were also investigated. Experimentally observed evolution rates decreased much more rapidly with those predicted by a model in which surface diffusion is assumed to be rate-limiting. This suggests that the development of facets, and the associated loss of ledges and terraces during the initial stages of evolution results in an evolution process limited by the nucleation rate of attachment/detachment sites (ledges) on the facets.« less

Computational modeling of bedform evolution in rivers with implications for predictions of flood stage and bed evolution

USGS Publications Warehouse

Nelson, Jonathan M.; Shimizu, Yasuyuki; Giri, Sanjay; McDonald, Richard R.

2010-01-01

Uncertainties in flood stage prediction and bed evolution in rivers are frequently associated with the evolution of bedforms over a hydrograph. For the case of flood prediction, the evolution of the bedforms may alter the effective bed roughness, so predictions of stage and velocity based on assuming bedforms retain the same size and shape over a hydrograph will be incorrect. These same effects will produce errors in the prediction of the sediment transport and bed evolution, but in this latter case the errors are typically larger, as even small errors in the prediction of bedform form drag can make very large errors in predicting the rates of sediment motion and the associated erosion and deposition. In situations where flows change slowly, it may be possible to use empirical results that relate bedform morphology to roughness and effective form drag to avoid these errors; but in many cases where the bedforms evolve rapidly and are in disequilibrium with the instantaneous flow, these empirical methods cannot be accurately applied. Over the past few years, computational models for bedform development, migration, and adjustment to varying flows have been developed and tested with a variety of laboratory and field data. These models, which are based on detailed multidimensional flow modeling incorporating large eddy simulation, appear to be capable of predicting bedform dimensions during steady flows as well as their time dependence during discharge variations. In the work presented here, models of this type are used to investigate the impacts of bedform on stage and bed evolution in rivers during flood hydrographs. The method is shown to reproduce hysteresis in rating curves as well as other more subtle effects in the shape of flood waves. Techniques for combining the bedform evolution models with larger-scale models for river reach flow, sediment transport, and bed evolution are described and used to show the importance of including dynamic bedform effects in river modeling. For example calculations for a flood on the Kootenai River, errors of almost 1m in predicted stage and errors of about a factor of two in the predicted maximum depths of erosion can be attributed to bedform evolution. Thus, treating bedforms explicitly in flood and bed evolution models can decrease uncertainty and increase the accuracy of predictions.

A Numerical Method for Simulating the Microscopic Damage Evolution in Composites Under Uniaxial Transverse Tension

NASA Astrophysics Data System (ADS)

Zhi, Jie; Zhao, Libin; Zhang, Jianyu; Liu, Zhanli

2016-06-01

In this paper, a new numerical method that combines a surface-based cohesive model and extended finite element method (XFEM) without predefining the crack paths is presented to simulate the microscopic damage evolution in composites under uniaxial transverse tension. The proposed method is verified to accurately capture the crack kinking into the matrix after fiber/matrix debonding. A statistical representative volume element (SRVE) under periodic boundary conditions is used to approximate the microstructure of the composites. The interface parameters of the cohesive models are investigated, in which the initial interface stiffness has a great effect on the predictions of the fiber/matrix debonding. The detailed debonding states of SRVE with strong and weak interfaces are compared based on the surface-based and element-based cohesive models. The mechanism of damage in composites under transverse tension is described as the appearance of the interface cracks and their induced matrix micro-cracking, both of which coalesce into transversal macro-cracks. Good agreement is found between the predictions of the model and the in situ experimental observations, demonstrating the efficiency of the presented model for simulating the microscopic damage evolution in composites.

Adaptive laboratory evolution -- principles and applications for biotechnology.

PubMed

Dragosits, Martin; Mattanovich, Diethard

2013-07-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering.

Facile Synthesis of Single Crystal Vanadium Disulfide Nanosheets by Chemical Vapor Deposition for Efficient Hydrogen Evolution Reaction.

PubMed

Yuan, Jiangtan; Wu, Jingjie; Hardy, Will J; Loya, Philip; Lou, Minhan; Yang, Yingchao; Najmaei, Sina; Jiang, Menglei; Qin, Fan; Keyshar, Kunttal; Ji, Heng; Gao, Weilu; Bao, Jiming; Kono, Junichiro; Natelson, Douglas; Ajayan, Pulickel M; Lou, Jun

2015-10-07

A facile chemical vapor deposition method to prepare single-crystalline VS2 nanosheets for the hydrogen evolution reaction is reported. The electrocatalytic hydrogen evolution reaction (HER) activities of VS2 show an extremely low overpotential of -68 mV at 10 mA cm(-2), small Tafel slopes of ≈34 mV decade(-1), as well as high stability, demonstrating its potential as a candidate non-noble-metal catalyst for the HER. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Methylome evolution in plants.

PubMed

Vidalis, Amaryllis; Živković, Daniel; Wardenaar, René; Roquis, David; Tellier, Aurélien; Johannes, Frank

2016-12-20

Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.

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 .

Modeling of the Orbital Evolution of 2060 Chiron

NASA Astrophysics Data System (ADS)

Kovalenko, Nataliya S.; Babenko, Yury G.; Churyumov, Klim I.

2002-03-01

The origin of Centaurs is one of the most interesting problems of Solar system science, and it has not yet been solved. To shed light on this problem one can investigate Centaurs' past and future orbital evolution. In this paper we discuss the results of Chiron's orbital evolution modeling. It was the first discovered Centaur and is the brightest one. Numerical integration was produced for 1 Myr forward and backward from the present time. A program based on the Everhart single sequence method for integrating orbits was used.

Evolutional Optimization on Material Ordering and Inventory Control of Supply Chain through Incentive Scheme

NASA Astrophysics Data System (ADS)

Prasertwattana, Kanit; Shimizu, Yoshiaki; Chiadamrong, Navee

This paper studied the material ordering and inventory control of supply chain systems. The effect of controlling policies is analyzed under three different configurations of the supply chain systems, and the formulated problem has been solved by using an evolutional optimization method known as Differential Evolution (DE). The numerical results show that the coordinating policy with the incentive scheme outperforms the other policies and can improve the performance of the overall system as well as all members under the concept of supply chain management.

The early evolution of Jean Piaget's clinical method.

PubMed

Mayer, Susan Jean

2005-11-01

This article analyzes the early evolution of Jean Piaget's renowned "clinical method" in order to investigate the method's strikingly original and generative character. Throughout his 1st decade in the field, Piaget frequently discussed and justified the many different approaches to data collection he used. Analysis of his methodological progression during this period reveals that Piaget's determination to access the genuine convictions of children eventually led him to combine 3 distinct traditions in which he had been trained-naturalistic observation, psychometrics, and the psychiatric clinical examination. It was in this amalgam, first evident in his 4th text, that Piaget discovered the clinical dynamic that would drive the classic experiments for which he is most well known.

The contribution of statistical physics to evolutionary biology.

PubMed

de Vladar, Harold P; Barton, Nicholas H

2011-08-01

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. Here, we discuss aspects of population genetics that have embraced methods from physics: non-equilibrium statistical mechanics, travelling waves and Monte-Carlo methods, among others, have been used to study polygenic evolution, rates of adaptation and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics; for example, by following the distribution of paths taken by a population through time. Copyright © 2011 Elsevier Ltd. All rights reserved.

[Feature extraction for breast cancer data based on geometric algebra theory and feature selection using differential evolution].

PubMed

Li, Jing; Hong, Wenxue

2014-12-01

The feature extraction and feature selection are the important issues in pattern recognition. Based on the geometric algebra representation of vector, a new feature extraction method using blade coefficient of geometric algebra was proposed in this study. At the same time, an improved differential evolution (DE) feature selection method was proposed to solve the elevated high dimension issue. The simple linear discriminant analysis was used as the classifier. The result of the 10-fold cross-validation (10 CV) classification of public breast cancer biomedical dataset was more than 96% and proved superior to that of the original features and traditional feature extraction method.

On the upscaling of process-based models in deltaic applications

NASA Astrophysics Data System (ADS)

Li, L.; Storms, J. E. A.; Walstra, D. J. R.

2018-03-01

Process-based numerical models are increasingly used to study the evolution of marine and terrestrial depositional environments. Whilst a detailed description of small-scale processes provides an accurate representation of reality, application on geological timescales is restrained by the associated increase in computational time. In order to reduce the computational time, a number of acceleration methods are combined and evaluated for a schematic supply-driven delta (static base level) and an accommodation-driven delta (variable base level). The performance of the combined acceleration methods is evaluated by comparing the morphological indicators such as distributary channel networking and delta volumes derived from the model predictions for various levels of acceleration. The results of the accelerated models are compared to the outcomes from a series of simulations to capture autogenic variability. Autogenic variability is quantified by re-running identical models on an initial bathymetry with 1 cm added noise. The overall results show that the variability of the accelerated models fall within the autogenic variability range, suggesting that the application of acceleration methods does not significantly affect the simulated delta evolution. The Time-scale compression method (the acceleration method introduced in this paper) results in an increased computational efficiency of 75% without adversely affecting the simulated delta evolution compared to a base case. The combination of the Time-scale compression method with the existing acceleration methods has the potential to extend the application range of process-based models towards geologic timescales.

Elliptical optical solitary waves in a finite nematic liquid crystal cell

NASA Astrophysics Data System (ADS)

Minzoni, Antonmaria A.; Sciberras, Luke W.; Smyth, Noel F.; Worthy, Annette L.

2015-05-01

The addition of orbital angular momentum has been previously shown to stabilise beams of elliptic cross-section. In this article the evolution of such elliptical beams is explored through the use of an approximate methodology based on modulation theory. An approximate method is used as the equations that govern the optical system have no known exact solitary wave solution. This study brings to light two distinct phases in the evolution of a beam carrying orbital angular momentum. The two phases are determined by the shedding of radiation in the form of mass loss and angular momentum loss. The first phase is dominated by the shedding of angular momentum loss through spiral waves. The second phase is dominated by diffractive radiation loss which drives the elliptical solitary wave to a steady state. In addition to modulation theory, the "chirp" variational method is also used to study this evolution. Due to the significant role radiation loss plays in the evolution of an elliptical solitary wave, an attempt is made to couple radiation loss to the chirp variational method. This attempt furthers understanding as to why radiation loss cannot be coupled to the chirp method. The basic reason for this is that there is no consistent manner to match the chirp trial function to the generated radiating waves which is uniformly valid in time. Finally, full numerical solutions of the governing equations are compared with solutions obtained using the various variational approximations, with the best agreement achieved with modulation theory due to its ability to include both mass and angular momentum losses to shed diffractive radiation.

Discovering significant evolution patterns from satellite image time series.

PubMed

Petitjean, François; Masseglia, Florent; Gançarski, Pierre; Forestier, Germain

2011-12-01

Satellite Image Time Series (SITS) provide us with precious information on land cover evolution. By studying these series of images we can both understand the changes of specific areas and discover global phenomena that spread over larger areas. Changes that can occur throughout the sensing time can spread over very long periods and may have different start time and end time depending on the location, which complicates the mining and the analysis of series of images. This work focuses on frequent sequential pattern mining (FSPM) methods, since this family of methods fits the above-mentioned issues. This family of methods consists of finding the most frequent evolution behaviors, and is actually able to extract long-term changes as well as short term ones, whenever the change may start and end. However, applying FSPM methods to SITS implies confronting two main challenges, related to the characteristics of SITS and the domain's constraints. First, satellite images associate multiple measures with a single pixel (the radiometric levels of different wavelengths corresponding to infra-red, red, etc.), which makes the search space multi-dimensional and thus requires specific mining algorithms. Furthermore, the non evolving regions, which are the vast majority and overwhelm the evolving ones, challenge the discovery of these patterns. We propose a SITS mining framework that enables discovery of these patterns despite these constraints and characteristics. Our proposal is inspired from FSPM and provides a relevant visualization principle. Experiments carried out on 35 images sensed over 20 years show the proposed approach makes it possible to extract relevant evolution behaviors.

Evolution of Humans: Understanding the Nature and Methods of Science through Cooperative Learning

ERIC Educational Resources Information Center

Lee, Yeung Chung

2011-01-01

This article describes the use of an enquiry-based approach to the study of human evolution in a practical context, integrating role-playing, jigsaw cooperative learning and scientific argumentation. The activity seeks to unravel the evolutionary relationships of five hominids and one ape from rather "messy" evidence. This approach enhanced the…

Evolution of Policy Leading to the 2006 General Dental Service Contract and Some Possible Outcomes

ERIC Educational Resources Information Center

Downer, Martin C.; Drugan, Caroline S.

2007-01-01

Background and objective: This paper was designed to rehearse the evolution of policy for the UK NHS General Dental Service (and related services) since its inception in 1948, culminating in the establishment of a new contract for general dental practitioners in 2006. Methods: Information was abstracted from the literature, historical records,…

Teaching Evolution through the Hardy-Weinberg Principle: A Real-Time, Active-Learning Exercise Using Classroom Response Devices

ERIC Educational Resources Information Center

Brewer, Michael S.; Gardner, Grant E.

2013-01-01

Teaching population genetics provides a bridge between genetics and evolution by using examples of the mechanisms that underlie changes in allele frequencies over time. Existing methods of teaching these concepts often rely on computer simulations or hand calculations, which distract students from the material and are problematic for those with…

Cooperative Office Education: Its Evolution in the Secondary Schools of the United States from 1900-1969.

ERIC Educational Resources Information Center

Donley, Audrey Bell

Using the historical, documentary analysis, and questionnaire methods of research, this study traces the development and evolution of cooperative office education in the secondary schools of the United States from 1900 through 1969. The study was organized under the following topical divisions: (1) Original of Vocational Education, (2) Development…

Volcanoes: Where and Why? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Which Way is North? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Quake Estate (board game). Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

SEDIMENT TOXICITY ASSESSMENT: COMPARISON OF STANDARD AND NEW TESTING DESIGNS

EPA Science Inventory

Standard methods of sediment toxicity testing are fairly well accepted; however, as with all else, evolution of these methods is inevitable. We compared a standard ASTM 10-day amphipod toxicity testing method with smaller, 48- and 96-h test methods using very toxic and reference ...

Robust regression and posterior predictive simulation increase power to detect early bursts of trait evolution.

PubMed

Slater, Graham J; Pennell, Matthew W

2014-05-01

A central prediction of much theory on adaptive radiations is that traits should evolve rapidly during the early stages of a clade's history and subsequently slowdown in rate as niches become saturated--a so-called "Early Burst." Although a common pattern in the fossil record, evidence for early bursts of trait evolution in phylogenetic comparative data has been equivocal at best. We show here that this may not necessarily be due to the absence of this pattern in nature. Rather, commonly used methods to infer its presence perform poorly when when the strength of the burst--the rate at which phenotypic evolution declines--is small, and when some morphological convergence is present within the clade. We present two modifications to existing comparative methods that allow greater power to detect early bursts in simulated datasets. First, we develop posterior predictive simulation approaches and show that they outperform maximum likelihood approaches at identifying early bursts at moderate strength. Second, we use a robust regression procedure that allows for the identification and down-weighting of convergent taxa, leading to moderate increases in method performance. We demonstrate the utility and power of these approach by investigating the evolution of body size in cetaceans. Model fitting using maximum likelihood is equivocal with regards the mode of cetacean body size evolution. However, posterior predictive simulation combined with a robust node height test return low support for Brownian motion or rate shift models, but not the early burst model. While the jury is still out on whether early bursts are actually common in nature, our approach will hopefully facilitate more robust testing of this hypothesis. We advocate the adoption of similar posterior predictive approaches to improve the fit and to assess the adequacy of macroevolutionary models in general.

Coronal hole evolution from multi-viewpoint data as input for a STEREO solar wind speed persistence model

NASA Astrophysics Data System (ADS)

Temmer, Manuela; Hinterreiter, Jürgen; Reiss, Martin A.

2018-03-01

We present a concept study of a solar wind forecasting method for Earth, based on persistence modeling from STEREO in situ measurements combined with multi-viewpoint EUV observational data. By comparing the fractional areas of coronal holes (CHs) extracted from EUV data of STEREO and SoHO/SDO, we perform an uncertainty assessment derived from changes in the CHs and apply those changes to the predicted solar wind speed profile at 1 AU. We evaluate the method for the time period 2008-2012, and compare the results to a persistence model based on ACE in situ measurements and to the STEREO persistence model without implementing the information on CH evolution. Compared to an ACE based persistence model, the performance of the STEREO persistence model which takes into account the evolution of CHs, is able to increase the number of correctly predicted high-speed streams by about 12%, and to decrease the number of missed streams by about 23%, and the number of false alarms by about 19%. However, the added information on CH evolution is not able to deliver more accurate speed values for the forecast than using the STEREO persistence model without CH information which performs better than an ACE based persistence model. Investigating the CH evolution between STEREO and Earth view for varying separation angles over ˜25-140° East of Earth, we derive some relation between expanding CHs and increasing solar wind speed, but a less clear relation for decaying CHs and decreasing solar wind speed. This fact most likely prevents the method from making more precise forecasts. The obtained results support a future L5 mission and show the importance and valuable contribution using multi-viewpoint data.

A Preliminary Analysis of Correlated Evolution in Mammalian Chewing Motor Patterns

PubMed Central

Williams, Susan H.; Vinyard, Christopher J.; Wall, Christine E.; Doherty, Alison H.; Crompton, Alfred W.; Hylander, William L.

2011-01-01

Descriptive and quantitative analyses of electromyograms (EMG) from the jaw adductors during feeding in mammals have demonstrated both similarities and differences among species in chewing motor patterns. These observations have led to a number of hypotheses of the evolution of motor patterns, the most comprehensive of which was proposed by Weijs in 1994. Since then, new data have been collected and additional hypotheses for the evolution of motor patterns have been proposed. Here, we take advantage of these new data and a well-resolved species-level phylogeny for mammals to test for the correlated evolution of specific components of mammalian chewing motor patterns. We focus on the evolution of the coordination of working-side (WS) and balancing-side (BS) jaw adductors (i.e., Weijs’ Triplets I and II), the evolution of WS and BS muscle recruitment levels, and the evolution of asynchrony between pairs of muscles. We converted existing chewing EMG data into binary traits to incorporate as much data as possible and facilitate robust phylogenetic analyses. We then tested hypotheses of correlated evolution of these traits across our phylogeny using a maximum likelihood method and the Bayesian Markov Chain Monte Carlo method. Both sets of analyses yielded similar results highlighting the evolutionary changes that have occurred across mammals in chewing motor patterns. We find support for the correlated evolution of (1) Triplets I and II, (2) BS deep masseter asynchrony and Triplets I and II, (3) a relative delay in the activity of the BS deep masseter and a decrease in the ratio of WS to BS muscle recruitment levels, and (4) a relative delay in the activity of the BS deep masseter and a delay in the activity of the BS posterior temporalis. In contrast, changes in relative WS and BS activity levels across mammals are not correlated with Triplets I and II. Results from this work can be integrated with dietary and morphological data to better understand how feeding and the masticatory apparatus have evolved across mammals in the context of new masticatory demands. PMID:21719433

A preliminary analysis of correlated evolution in Mammalian chewing motor patterns.

PubMed

Williams, Susan H; Vinyard, Christopher J; Wall, Christine E; Doherty, Alison H; Crompton, Alfred W; Hylander, William L

2011-08-01

Descriptive and quantitative analyses of electromyograms (EMG) from the jaw adductors during feeding in mammals have demonstrated both similarities and differences among species in chewing motor patterns. These observations have led to a number of hypotheses of the evolution of motor patterns, the most comprehensive of which was proposed by Weijs in 1994. Since then, new data have been collected and additional hypotheses for the evolution of motor patterns have been proposed. Here, we take advantage of these new data and a well-resolved species-level phylogeny for mammals to test for the correlated evolution of specific components of mammalian chewing motor patterns. We focus on the evolution of the coordination of working-side (WS) and balancing-side (BS) jaw adductors (i.e., Weijs' Triplets I and II), the evolution of WS and BS muscle recruitment levels, and the evolution of asynchrony between pairs of muscles. We converted existing chewing EMG data into binary traits to incorporate as much data as possible and facilitate robust phylogenetic analyses. We then tested hypotheses of correlated evolution of these traits across our phylogeny using a maximum likelihood method and the Bayesian Markov Chain Monte Carlo method. Both sets of analyses yielded similar results highlighting the evolutionary changes that have occurred across mammals in chewing motor patterns. We find support for the correlated evolution of (1) Triplets I and II, (2) BS deep masseter asynchrony and Triplets I and II, (3) a relative delay in the activity of the BS deep masseter and a decrease in the ratio of WS to BS muscle recruitment levels, and (4) a relative delay in the activity of the BS deep masseter and a delay in the activity of the BS posterior temporalis. In contrast, changes in relative WS and BS activity levels across mammals are not correlated with Triplets I and II. Results from this work can be integrated with dietary and morphological data to better understand how feeding and the masticatory apparatus have evolved across mammals in the context of new masticatory demands.

Ludwig von Bertalanffy's organismic view on the theory of evolution.

PubMed

Drack, Manfred

2015-03-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. © 2015 Wiley Periodicals, Inc.

Evolution of heteromorphic sex chromosomes in the order Aulopiformes.

PubMed

Ota, K; Kobayashi, T; Ueno, K; Gojobori, T

2000-12-23

The fish order Aulopiformes contains both synchronously hermaphroditic and gonochoristic species. From the cytogenetic viewpoint, few reports show that gonochoristic Aulopiformes have heteromorphic sex chromosomes. Because fish in this order give us a unique opportunity to elucidate the evolution of sex chromosomes, it is important to examine a phylogenetic relationship in Aulopiformes by both molecular evolutionary and cytogenetic methods. Thus, we conducted molecular phylogenetic and cytogenetic studies of six Aulopiform species. Our results suggested that hermaphroditic species were evolutionarily derived from gonochoristic species. It follows that the hermaphroditic species might have lost the heteromorphic sex chromosomes during evolution. Here, we suggest a possibility that heteromorphic sex chromosomes can disappear from the genome, even if they have appeared once in evolution. Taking into account Ohno's hypothesis that heteromorphic sex chromosomes might have emerged from autosomes, we propose the hypothesis that heteromorphic sex chromosomes may have undergone repeated events of appearance and disappearance during the course of fish evolution.

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

Bradonjic, Milan; Hagberg, Aric; Hengartner, Nick

We analyze component evolution in general random intersection graphs (RIGs) and give conditions on existence and uniqueness of the giant component. Our techniques generalize the existing methods for analysis on component evolution in RIGs. That is, we analyze survival and extinction properties of a dependent, inhomogeneous Galton-Watson branching process on general RIGs. Our analysis relies on bounding the branching processes and inherits the fundamental concepts from the study on component evolution in Erdos-Renyi graphs. The main challenge becomes from the underlying structure of RIGs, when the number of offsprings follows a binomial distribution with a different number of nodes andmore » different rate at each step during the evolution. RIGs can be interpreted as a model for large randomly formed non-metric data sets. Besides the mathematical analysis on component evolution, which we provide in this work, we perceive RIGs as an important random structure which has already found applications in social networks, epidemic networks, blog readership, or wireless sensor networks.« less

Multidisciplinary design optimisation of a recurve bow based on applications of the autogenetic design theory and distributed computing

NASA Astrophysics Data System (ADS)

Fritzsche, Matthias; Kittel, Konstantin; Blankenburg, Alexander; Vajna, Sándor

2012-08-01

The focus of this paper is to present a method of multidisciplinary design optimisation based on the autogenetic design theory (ADT) that provides methods, which are partially implemented in the optimisation software described here. The main thesis of the ADT is that biological evolution and the process of developing products are mainly similar, i.e. procedures from biological evolution can be transferred into product development. In order to fulfil requirements and boundary conditions of any kind (that may change at any time), both biological evolution and product development look for appropriate solution possibilities in a certain area, and try to optimise those that are actually promising by varying parameters and combinations of these solutions. As the time necessary for multidisciplinary design optimisations is a critical aspect in product development, ways to distribute the optimisation process with the effective use of unused calculating capacity, can reduce the optimisation time drastically. Finally, a practical example shows how ADT methods and distributed optimising are applied to improve a product.

Darwinian perspectives on the evolution of human languages.

PubMed

Pagel, Mark

2017-02-01

Human languages evolve by a process of descent with modification in which parent languages give rise to daughter languages over time and in a manner that mimics the evolution of biological species. Descent with modification is just one of many parallels between biological and linguistic evolution that, taken together, offer up a Darwinian perspective on how languages evolve. Combined with statistical methods borrowed from evolutionary biology, this Darwinian perspective has brought new opportunities to the study of the evolution of human languages. These include the statistical inference of phylogenetic trees of languages, the study of how linguistic traits evolve over thousands of years of language change, the reconstruction of ancestral or proto-languages, and using language change to date historical events.

A theoretical model and phase field simulation on the evolution of interface roughness in the oxidation process

NASA Astrophysics Data System (ADS)

Yang, Fan; Fang, Dai-Ning; Liu, Bin

2012-01-01

An oxidation kinetics model is developed to account for the effects of the oxidation interface curvature and the oxidation-induced volume change or Pilling-Bedworth ratio. For the oxidation of Fe-Cr-Al-Y alloy fiber, the predictions agree well with experimental results. By considering the influence of the oxidation interface curvature on oxidation rates, the evolution of fluctuant oxidation interface is predicted. We also developed the phase field method (PFM) to simulate the evolution of the interface roughness. Both the theoretical model and the PFM results show that the interface will become smooth during high temperature oxidation. Stress distribution and evolution are calculated by PFM, which indicates that the stress level decreases as the interface morphology evolves.

Investigation of crystallization kinetics of sodium bicarbonate in a continuous stirred tank crystallizer

NASA Astrophysics Data System (ADS)

Zhu, Yi; Haut, Benoît; Halloin, Veronique; Delplancke-Ogletree, Marie-Paule

2005-08-01

In our previous work [J. Crystal Growth 263 (2004) 459], a supersaturation determination method using a high-precision densimeter was designed and developed for monitoring sodium bicarbonate supersaturation in the sodium carbonate-bicarbonate system, a two-component solution in equilibrium. In the present paper, we apply this method to the study of sodium bicarbonate continuous crystallization. It gives us access to the sodium bicarbonate supersaturation evolution. The sodium bicarbonate supersaturation evolution and their crystallization kinetics obtained in a continuous stirred tank crystallizer are investigated under different operational conditions, such as residence time, initial supersaturation and seeding. The induction time determined by density measurements is discussed. Mathematical modeling is used to interpret the supersaturation evolution. It is shown that measuring the density gives satisfying performances for studying the crystallization of a two-component solution in equilibrium, such as the sodium carbonate-bicarbonate system.

Using surface segregation to design stable Ru-Ir oxides for the oxygen evolution reaction in acidic environments.

DOE PAGES

Danilovic, N.; Subbaraman, R.; Chang, K-C.; ...

2014-10-08

The methods used to improve catalytic activity are well-established, however elucidating the factors that simultaneously control activity and stability is still lacking, especially for oxygen evolution reaction (OER) catalysts. Here, by studying fundamental links between the activity and stability of well-characterized monometallic and bimetallic oxides, we found that there is generally an inverse relationship between activity and stability. To overcome this limitation, we developed a new synthesis strategy that is based on tuning the near-surface composition of Ru and Ir elements by surface segregation, thereby resulting in the formation of a nanosegregated domain that balances the stability and activity ofmore » surface atoms. We demonstrate that a Ru0.5Ir0.5 alloy synthesized by using this method exhibits four-times higher stability than the best Ru-Ir oxygen evolution reaction materials, while still preserving the same activity.« less

Methods and Systems for Characterization of an Anomaly Using Infrared Flash Thermography

NASA Technical Reports Server (NTRS)

Koshti, Ajay M. (Inventor)

2013-01-01

A method for characterizing an anomaly in a material comprises (a) extracting contrast data; (b) measuring a contrast evolution; (c) filtering the contrast evolution; (d) measuring a peak amplitude of the contrast evolution; (d) determining a diameter and a depth of the anomaly, and (e) repeating the step of determining the diameter and the depth of the anomaly until a change in the estimate of the depth is less than a set value. The step of determining the diameter and the depth of the anomaly comprises estimating the depth using a diameter constant C.sub.D equal to one for the first iteration of determining the diameter and the depth; estimating the diameter; and comparing the estimate of the depth of the anomaly after each iteration of estimating to the prior estimate of the depth to calculate the change in the estimate of the depth of the anomaly.

Evolution of instruments for harvest of the skin grafts

PubMed Central

Ameer, Faisal; Singh, Arun Kumar; Kumar, Sandeep

2013-01-01

Background: The harvest of autologous skin graft is considered to be a fundamental skill of the plastic surgeon. The objective of this article is to provide an interesting account of the development of skin grafting instruments as we use them today in various plastic surgical procedures. Materials and Methods: The authors present the chronological evolution and modifications of the skin grafting knife, including those contributions not often cited in the literature, using articles sourced from MEDLINE, ancient manuscripts, original quotes, techniques and illustrations. Results: This article traces the evolution of instrumentation for harvest of skin grafts from free hand techniques to precise modern automated methods. Conclusions: Although skin grafting is one of the basic techniques used in reconstructive surgery yet harvest of a uniform graft of desired thickness poses a challenge. This article is dedicated to innovators who have devoted their lives and work to the advancement of the field of plastic surgery. PMID:23960303

Rise and fall of political complexity in island South-East Asia and the Pacific.

PubMed

Currie, Thomas E; Greenhill, Simon J; Gray, Russell D; Hasegawa, Toshikazu; Mace, Ruth

2010-10-14

There is disagreement about whether human political evolution has proceeded through a sequence of incremental increases in complexity, or whether larger, non-sequential increases have occurred. The extent to which societies have decreased in complexity is also unclear. These debates have continued largely in the absence of rigorous, quantitative tests. We evaluated six competing models of political evolution in Austronesian-speaking societies using phylogenetic methods. Here we show that in the best-fitting model political complexity rises and falls in a sequence of small steps. This is closely followed by another model in which increases are sequential but decreases can be either sequential or in bigger drops. The results indicate that large, non-sequential jumps in political complexity have not occurred during the evolutionary history of these societies. This suggests that, despite the numerous contingent pathways of human history, there are regularities in cultural evolution that can be detected using computational phylogenetic methods.

The modern temperature-accelerated dynamics approach

DOE PAGES

Zamora, Richard J.; Uberuaga, Blas P.; Perez, Danny; ...

2016-06-01

Accelerated molecular dynamics (AMD) is a class of MD-based methods used to simulate atomistic systems in which the metastable state-to-state evolution is slow compared with thermal vibrations. Temperature-accelerated dynamics (TAD) is a particularly efficient AMD procedure in which the predicted evolution is hastened by elevating the temperature of the system and then recovering the correct state-to-state dynamics at the temperature of interest. TAD has been used to study various materials applications, often revealing surprising behavior beyond the reach of direct MD. This success has inspired several algorithmic performance enhancements, as well as the analysis of its mathematical framework. Recently, thesemore » enhancements have leveraged parallel programming techniques to enhance both the spatial and temporal scaling of the traditional approach. Here, we review the ongoing evolution of the modern TAD method and introduce the latest development: speculatively parallel TAD.« less

High-resolution method for evolving complex interface networks

NASA Astrophysics Data System (ADS)

Pan, Shucheng; Hu, Xiangyu Y.; Adams, Nikolaus A.

2018-04-01

In this paper we describe a high-resolution transport formulation of the regional level-set approach for an improved prediction of the evolution of complex interface networks. The novelty of this method is twofold: (i) construction of local level sets and reconstruction of a global level set, (ii) local transport of the interface network by employing high-order spatial discretization schemes for improved representation of complex topologies. Various numerical test cases of multi-region flow problems, including triple-point advection, single vortex flow, mean curvature flow, normal driven flow, dry foam dynamics and shock-bubble interaction show that the method is accurate and suitable for a wide range of complex interface-network evolutions. Its overall computational cost is comparable to the Semi-Lagrangian regional level-set method while the prediction accuracy is significantly improved. The approach thus offers a viable alternative to previous interface-network level-set method.

Probabilistic modeling of the evolution of gene synteny within reconciled phylogenies

PubMed Central

2015-01-01

Background Most models of genome evolution concern either genetic sequences, gene content or gene order. They sometimes integrate two of the three levels, but rarely the three of them. Probabilistic models of gene order evolution usually have to assume constant gene content or adopt a presence/absence coding of gene neighborhoods which is blind to complex events modifying gene content. Results We propose a probabilistic evolutionary model for gene neighborhoods, allowing genes to be inserted, duplicated or lost. It uses reconciled phylogenies, which integrate sequence and gene content evolution. We are then able to optimize parameters such as phylogeny branch lengths, or probabilistic laws depicting the diversity of susceptibility of syntenic regions to rearrangements. We reconstruct a structure for ancestral genomes by optimizing a likelihood, keeping track of all evolutionary events at the level of gene content and gene synteny. Ancestral syntenies are associated with a probability of presence. We implemented the model with the restriction that at most one gene duplication separates two gene speciations in reconciled gene trees. We reconstruct ancestral syntenies on a set of 12 drosophila genomes, and compare the evolutionary rates along the branches and along the sites. We compare with a parsimony method and find a significant number of results not supported by the posterior probability. The model is implemented in the Bio++ library. It thus benefits from and enriches the classical models and methods for molecular evolution. PMID:26452018

Testing the Role of Multicopy Plasmids in the Evolution of Antibiotic Resistance.

PubMed

Escudero, Jose Antonio; MacLean, R Craig; San Millan, Alvaro

2018-05-02

Multicopy plasmids are extremely abundant in prokaryotes but their role in bacterial evolution remains poorly understood. We recently showed that the increase in gene copy number per cell provided by multicopy plasmids could accelerate the evolution of plasmid-encoded genes. In this work, we present an experimental system to test the ability of multicopy plasmids to promote gene evolution. Using simple molecular biology methods, we constructed a model system where an antibiotic resistance gene can be inserted into Escherichia coli MG1655, either in the chromosome or on a multicopy plasmid. We use an experimental evolution approach to propagate the different strains under increasing concentrations of antibiotics and we measure survival of bacterial populations over time. The choice of the antibiotic molecule and the resistance gene is so that the gene can only confer resistance through the acquisition of mutations. This "evolutionary rescue" approach provides a simple method to test the potential of multicopy plasmids to promote the acquisition of antibiotic resistance. In the next step of the experimental system, the molecular bases of antibiotic resistance are characterized. To identify mutations responsible for the acquisition of antibiotic resistance we use deep DNA sequencing of samples obtained from whole populations and clones. Finally, to confirm the role of the mutations in the gene under study, we reconstruct them in the parental background and test the resistance phenotype of the resulting strains.

Correlated evolution of body and fin morphology in the cichlid fishes.

PubMed

Feilich, Kara L

2016-10-01

Body and fin shapes are chief determinants of swimming performance in fishes. Different configurations of body and fin shapes can suit different locomotor specializations. The success of any configuration is dependent upon the hydrodynamic interactions between body and fins. Despite the importance of body-fin interactions for swimming, there are few data indicating whether body and fin configurations evolve in concert, or whether these structures vary independently. The cichlid fishes are a diverse family whose well-studied phylogenetic relationships make them ideal for the study of macroevolution of ecomorphology. This study measured body, and caudal and median fin morphology from radiographs of 131 cichlid genera, using morphometrics and phylogenetic comparative methods to determine whether these traits exhibit correlated evolution. Partial least squares canonical analysis revealed that body, caudal fin, dorsal fin, and anal fin shapes all exhibited strong correlated evolution consistent with locomotor ecomorphology. Major patterns included the evolution of deep body profiles with long fins, suggestive of maneuvering specialization; and the evolution of narrow, elongate caudal peduncles with concave tails, a combination that characterizes economical cruisers. These results demonstrate that body shape evolution does not occur independently of other traits, but among a suite of other morphological changes that augment locomotor specialization. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Computing and visualizing time-varying merge trees for high-dimensional data

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

Oesterling, Patrick; Heine, Christian; Weber, Gunther H.

2017-06-03

We introduce a new method that identifies and tracks features in arbitrary dimensions using the merge tree -- a structure for identifying topological features based on thresholding in scalar fields. This method analyzes the evolution of features of the function by tracking changes in the merge tree and relates features by matching subtrees between consecutive time steps. Using the time-varying merge tree, we present a structural visualization of the changing function that illustrates both features and their temporal evolution. We demonstrate the utility of our approach by applying it to temporal cluster analysis of high-dimensional point clouds.

[TRAUMATIC INTRAORGANIC HEPATIC AND SPLENIC HEMATOMAS].

PubMed

Timerbulatov, V M; Khalikov, A A; Timerbulatov, Sh V; Verzakova, I V; Amirova, A M; Smyr, R A

2015-01-01

An analysis of application results of complex research methods of diagnostics of intraorganic hepatic and splenic hematomas was made. At the same time, options of these methods were used for determination of prescription of injury. The ultrasound, CT, MR-imaging, videolaparoscopy, angiography, Doppler ultrasonics, impedometry, biochemical, laboratory and cytological study of punctate sample from hematomas were applied for this purpose in 33 patients. According to authors, an evolution of hematomas happened in 3 stages, each of this stage was characterized by specified data associated with investigation results. The staging procedure of hematomas or their evolution allowed setting the prescription of injury.

The theoretical and experimental study of a material structure evolution in gigacyclic fatigue regime

NASA Astrophysics Data System (ADS)

Plekhov, Oleg; Naimark, Oleg; Narykova, Maria; Kadomtsev, Andrey; Betekhtin, Vladimir

2015-10-01

The work is devoted to the study of the metal structure evolution under gigacyclic fatigue (VHCF) regime. The study of the mechanical properties of the samples (Armco iron) with different state of life time existing was carried out on the base of the acoustic resonance method. The damage accumulation (porosity of the samples) was studied by the hydrostatic weighing method. A statistical model of damage accumulation was proposed in order to describe the damage accumulation process. The model describes the influence of the sample surface on the location of fatigue crack initiation.

Computing Nash equilibria through computational intelligence methods

NASA Astrophysics Data System (ADS)

Pavlidis, N. G.; Parsopoulos, K. E.; Vrahatis, M. N.

2005-03-01

Nash equilibrium constitutes a central solution concept in game theory. The task of detecting the Nash equilibria of a finite strategic game remains a challenging problem up-to-date. This paper investigates the effectiveness of three computational intelligence techniques, namely, covariance matrix adaptation evolution strategies, particle swarm optimization, as well as, differential evolution, to compute Nash equilibria of finite strategic games, as global minima of a real-valued, nonnegative function. An issue of particular interest is to detect more than one Nash equilibria of a game. The performance of the considered computational intelligence methods on this problem is investigated using multistart and deflection.

Tempo and mode of climatic niche evolution in Primates.

PubMed

Duran, Andressa; Pie, Marcio R

2015-09-01

Climatic niches have increasingly become a nexus in our understanding of a variety of ecological and evolutionary phenomena, from species distributions to latitudinal diversity gradients. Despite the increasing availability of comprehensive datasets on species ranges, phylogenetic histories, and georeferenced environmental conditions, studies on the evolution of climate niches have only begun to understand how niches evolve over evolutionary timescales. Here, using primates as a model system, we integrate recently developed phylogenetic comparative methods, species distribution patterns, and climatic data to explore primate climatic niche evolution, both among clades and over time. In general, we found that simple, constant-rate models provide a poor representation of how climatic niches evolve. For instance, there have been shifts in the rate of climatic niche evolution in several independent clades, particularly in response to the increasingly cooler climates of the past 10 My. Interestingly, rate accelerations greatly outnumbered rate decelerations. These results highlight the importance of considering more realistic evolutionary models that allow for the detection of heterogeneity in the tempo and mode of climatic niche evolution, as well as to infer possible constraining factors for species distributions in geographical space. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Discrete maximal regularity of time-stepping schemes for fractional evolution equations.

PubMed

Jin, Bangti; Li, Buyang; Zhou, Zhi

2018-01-01

In this work, we establish the maximal [Formula: see text]-regularity for several time stepping schemes for a fractional evolution model, which involves a fractional derivative of order [Formula: see text], [Formula: see text], in time. These schemes include convolution quadratures generated by backward Euler method and second-order backward difference formula, the L1 scheme, explicit Euler method and a fractional variant of the Crank-Nicolson method. The main tools for the analysis include operator-valued Fourier multiplier theorem due to Weis (Math Ann 319:735-758, 2001. doi:10.1007/PL00004457) and its discrete analogue due to Blunck (Stud Math 146:157-176, 2001. doi:10.4064/sm146-2-3). These results generalize the corresponding results for parabolic problems.

Molybdenum and tungsten nanostructures and methods for making and using same

DOEpatents

Kotaro, Sasaki; Chen, Wei-Fu; Muckerman, James T; Adzic, Radoslav R

2015-01-06

The present invention provides molybdenum and tungsten nanostructures, for example, nanosheets and nanoparticles, and methods of making and using same, including using such nanostructures as catlysts for hydrogen evolution reactions.

A robust and fast method of sampling and analysis of delta13C of dissolved inorganic carbon in ground waters.

PubMed

Spötl, Christoph

2005-09-01

The stable carbon isotopic composition of dissolved inorganic carbon (delta13C(DIC)) is traditionally determined using either direct precipitation or gas evolution methods in conjunction with offline gas preparation and measurement in a dual-inlet isotope ratio mass spectrometer. A gas evolution method based on continuous-flow technology is described here, which is easy to use and robust. Water samples (100-1500 microl depending on the carbonate alkalinity) are injected into He-filled autosampler vials in the field and analysed on an automated continuous-flow gas preparation system interfaced to an isotope ratio mass spectrometer. Sample analysis time including online preparation is 10 min and overall precision is 0.1 per thousand. This method is thus fast and can easily be automated for handling large sample batches.

ALARIC: An algorithm for constructing arbitrarily complex initial density distributions with low particle noise for SPH/SPMHD applications

NASA Astrophysics Data System (ADS)

Vela Vela, Luis; Sanchez, Raul; Geiger, Joachim

2018-03-01

A method is presented to obtain initial conditions for Smoothed Particle Hydrodynamic (SPH) scenarios where arbitrarily complex density distributions and low particle noise are needed. Our method, named ALARIC, tampers with the evolution of the internal variables to obtain a fast and efficient profile evolution towards the desired goal. The result has very low levels of particle noise and constitutes a perfect candidate to study the equilibrium and stability properties of SPH/SPMHD systems. The method uses the iso-thermal SPH equations to calculate hydrodynamical forces under the presence of an external fictitious potential and evolves them in time with a 2nd-order symplectic integrator. The proposed method generates tailored initial conditions that perform better in many cases than those based on purely crystalline lattices, since it prevents the appearance of anisotropies.

Random mutagenesis by error-prone pol plasmid replication in Escherichia coli.

PubMed

Alexander, David L; Lilly, Joshua; Hernandez, Jaime; Romsdahl, Jillian; Troll, Christopher J; Camps, Manel

2014-01-01

Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail, and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available.

Continents and Ocean Basins: Floaters and Sinkers. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Deep Sea Trenches and Radioactive Water. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Revisiting the School of the Future: The Evolution of a School-Based Services Project.

ERIC Educational Resources Information Center

Iscoe, Louise K.; Keir, Scott S.

The Hogg Foundation for Mental Health created the School of the Future (SoF) project to enable selected Texas schools to coordinate and implement school-based social and health services on their campuses and to demonstrate the effectiveness of this method of service delivery by evaluating the project. This report documents the evolution of the SoF…

The Evolution of Art and Design Pedagogies in England: Influences of the Past, Challenges for the Future

ERIC Educational Resources Information Center

Souleles, Nicos

2013-01-01

This article traces the historical evolution of instructional methods in art and design education in Britain to identify the influences that inform current practices and compare the latter against recent debates on what are design education and designer in the context of the global economy and the widespread use of information and communication…

When a Piece of a Continent Breaks Off. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Measuring Continental Drift: The Laser Ranging Experiment. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Drifting Continents and Wandering Poles. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

A Sea-Floor Mystery: Mapping Polarity Reversals. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Movement of the Pacific Ocean Floor. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Hot Spots in the Earth's Crust. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Iceland: The Case of the Splitting Personality. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Plate Boundaries and Earthquake Prediction. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Plotting the Shape of the Ocean Floor. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Online Learning from Input versus Offline Memory Evolution in Adult Word Learning: Effects of Neighborhood Density and Phonologically Related Practice

ERIC Educational Resources Information Center

Storkel, Holly L.; Bontempo, Daniel E.; Pak, Natalie S.

2014-01-01

Purpose: In this study, the authors investigated adult word learning to determine how neighborhood density and practice across phonologically related training sets influence online learning from input during training versus offline memory evolution during no-training gaps. Method: Sixty-one adults were randomly assigned to learn low- or…

Drifting Continents and Magnetic Fields. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Why Does Sea Level Change? Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

The Evolution of Work Values during the School-to-Work Transition: The Case of Young Adults in the "Missing Middle"

ERIC Educational Resources Information Center

Masdonati, Jonas; Fournier, Geneviève; Pinault, Mathieu; Lahrizi, Imane Z.

2016-01-01

Adopting a mixed method design, this paper explores the configuration and evolution of work values of 64 young adults in transition from education to employment. Qualitative analyses point out the existence of four categories of work values: interesting tasks, good relationships, self-fulfillment, and attractive work conditions. Quantitative…

Wavelet transform analysis of dynamic speckle patterns texture

NASA Astrophysics Data System (ADS)

Limia, Margarita Fernandez; Nunez, Adriana Mavilio; Rabal, Hector; Trivi, Marcelo

2002-11-01

We propose the use of the wavelet transform to characterize the time evolution of dynamic speckle patterns. We describe it by using as an example a method used for the assessment of the drying of paint. Optimal texture features are determined and the time evolution is described in terms of the Mahalanobis distance to the final (dry) state. From the behavior of this distance function, two parameters are defined that characterize the evolution. Because detailed knowledge of the involved dynamics is not required, the methodology could be implemented for other complex or poorly understood dynamic phenomena.

Polishing the craft of genetic diversity creation in directed evolution.

PubMed

Tee, Kang Lan; Wong, Tuck Seng

2013-12-01

Genetic diversity creation is a core technology in directed evolution where a high quality mutant library is crucial to its success. Owing to its importance, the technology in genetic diversity creation has seen rapid development over the years and its application has diversified into other fields of scientific research. The advances in molecular cloning and mutagenesis since 2008 were reviewed. Specifically, new cloning techniques were classified based on their principles of complementary overhangs, homologous sequences, overlapping PCR and megaprimers and the advantages, drawbacks and performances of these methods were highlighted. New mutagenesis methods developed for random mutagenesis, focused mutagenesis and DNA recombination were surveyed. The technical requirements of these methods and the mutational spectra were compared and discussed with references to commonly used techniques. The trends of mutant library preparation were summarised. Challenges in genetic diversity creation were discussed with emphases on creating "smart" libraries, controlling the mutagenesis spectrum and specific challenges in each group of mutagenesis methods. An outline of the wider applications of genetic diversity creation includes genome engineering, viral evolution, metagenomics and a study of protein functions. The review ends with an outlook for genetic diversity creation and the prospective developments that can have future impact in this field. © 2013. Published by Elsevier Inc. All rights reserved.

Ludwig von Bertalanffy's Organismic View on the Theory of Evolution

PubMed Central

Drack, Manfred

2015-01-01

Ludwig von Bertalanffy was a key figure in the advancement of theoretical biology. His early considerations already led him to recognize the necessity of considering the organism as a system, as an organization of parts and processes. He termed the resulting research program organismic biology, which he extended to all basic questions of biology and almost all areas of biology, hence also to the theory of evolution. This article begins by outlining the rather unknown (because often written in German) research of Bertalanffy in the field of theoretical biology. The basics of the organismic approach are then described. This is followed by Bertalanffy's considerations on the theory of evolution, in which he used methods from theoretical biology and then introduced his own, organismic, view on evolution, leading to the demand for finding laws of evolution. Finally, his view on the concept of homology is presented. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 77–90, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:25727202

Experimental implementation of local adiabatic evolution algorithms by an NMR quantum information processor.

PubMed

Mitra, Avik; Ghosh, Arindam; Das, Ranabir; Patel, Apoorva; Kumar, Anil

2005-12-01

Quantum adiabatic algorithm is a method of solving computational problems by evolving the ground state of a slowly varying Hamiltonian. The technique uses evolution of the ground state of a slowly varying Hamiltonian to reach the required output state. In some cases, such as the adiabatic versions of Grover's search algorithm and Deutsch-Jozsa algorithm, applying the global adiabatic evolution yields a complexity similar to their classical algorithms. However, using the local adiabatic evolution, the algorithms given by J. Roland and N.J. Cerf for Grover's search [J. Roland, N.J. Cerf, Quantum search by local adiabatic evolution, Phys. Rev. A 65 (2002) 042308] and by Saurya Das, Randy Kobes, and Gabor Kunstatter for the Deutsch-Jozsa algorithm [S. Das, R. Kobes, G. Kunstatter, Adiabatic quantum computation and Deutsh's algorithm, Phys. Rev. A 65 (2002) 062301], yield a complexity of order N (where N=2(n) and n is the number of qubits). In this paper, we report the experimental implementation of these local adiabatic evolution algorithms on a 2-qubit quantum information processor, by Nuclear Magnetic Resonance.

Evolution families of conformal mappings with fixed points and the Löwner-Kufarev equation

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

Goryainov, V V

2015-01-31

The paper is concerned with evolution families of conformal mappings of the unit disc to itself that fix an interior point and a boundary point. Conditions are obtained for the evolution families to be differentiable, and an existence and uniqueness theorem for an evolution equation is proved. A convergence theorem is established which describes the topology of locally uniform convergence of evolution families in terms of infinitesimal generating functions. The main result in this paper is the embedding theorem which shows that any conformal mapping of the unit disc to itself with two fixed points can be embedded into a differentiable evolution familymore » of such mappings. This result extends the range of the parametric method in the theory of univalent functions. In this way the problem of the mutual change of the derivative at an interior point and the angular derivative at a fixed point on the boundary is solved for a class of mappings of the unit disc to itself. In particular, the rotation theorem is established for this class of mappings. Bibliography: 27 titles.« less

Adaptive laboratory evolution – principles and applications for biotechnology

PubMed Central

2013-01-01

Adaptive laboratory evolution is a frequent method in biological studies to gain insights into the basic mechanisms of molecular evolution and adaptive changes that accumulate in microbial populations during long term selection under specified growth conditions. Although regularly performed for more than 25 years, the advent of transcript and cheap next-generation sequencing technologies has resulted in many recent studies, which successfully applied this technique in order to engineer microbial cells for biotechnological applications. Adaptive laboratory evolution has some major benefits as compared with classical genetic engineering but also some inherent limitations. However, recent studies show how some of the limitations may be overcome in order to successfully incorporate adaptive laboratory evolution in microbial cell factory design. Over the last two decades important insights into nutrient and stress metabolism of relevant model species were acquired, whereas some other aspects such as niche-specific differences of non-conventional cell factories are not completely understood. Altogether the current status and its future perspectives highlight the importance and potential of adaptive laboratory evolution as approach in biotechnological engineering. PMID:23815749

2D Transition-Metal-Dichalcogenide-Nanosheet-Based Composites for Photocatalytic and Electrocatalytic Hydrogen Evolution Reactions.

PubMed

Lu, Qipeng; Yu, Yifu; Ma, Qinglang; Chen, Bo; Zhang, Hua

2016-03-09

Hydrogen (H2) is one of the most important clean and renewable energy sources for future energy sustainability. Nowadays, photocatalytic and electrocatalytic hydrogen evolution reactions (HERs) from water splitting are considered as two of the most efficient methods to convert sustainable energy to the clean energy carrier, H2. Catalysts based on transition metal dichalcogenides (TMDs) are recognized as greatly promising substitutes for noble-metal-based catalysts for HER. The photocatalytic and electrocatalytic activities of TMD nanosheets for the HER can be further improved after hybridization with many kinds of nanomaterials, such as metals, oxides, sulfides, and carbon materials, through different methods including the in situ reduction method, the hot-injection method, the heating-up method, the hydro(solvo)thermal method, chemical vapor deposition (CVD), and thermal annealing. Here, recent progress in photocatalytic and electrocatalytic HERs using 2D TMD-based composites as catalysts is discussed. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

Inferring the photometric and size evolution of galaxies from image simulations. I. Method

NASA Astrophysics Data System (ADS)

Carassou, Sébastien; de Lapparent, Valérie; Bertin, Emmanuel; Le Borgne, Damien

2017-09-01

Context. Current constraints on models of galaxy evolution rely on morphometric catalogs extracted from multi-band photometric surveys. However, these catalogs are altered by selection effects that are difficult to model, that correlate in non trivial ways, and that can lead to contradictory predictions if not taken into account carefully. Aims: To address this issue, we have developed a new approach combining parametric Bayesian indirect likelihood (pBIL) techniques and empirical modeling with realistic image simulations that reproduce a large fraction of these selection effects. This allows us to perform a direct comparison between observed and simulated images and to infer robust constraints on model parameters. Methods: We use a semi-empirical forward model to generate a distribution of mock galaxies from a set of physical parameters. These galaxies are passed through an image simulator reproducing the instrumental characteristics of any survey and are then extracted in the same way as the observed data. The discrepancy between the simulated and observed data is quantified, and minimized with a custom sampling process based on adaptive Markov chain Monte Carlo methods. Results: Using synthetic data matching most of the properties of a Canada-France-Hawaii Telescope Legacy Survey Deep field, we demonstrate the robustness and internal consistency of our approach by inferring the parameters governing the size and luminosity functions and their evolutions for different realistic populations of galaxies. We also compare the results of our approach with those obtained from the classical spectral energy distribution fitting and photometric redshift approach. Conclusions: Our pipeline infers efficiently the luminosity and size distribution and evolution parameters with a very limited number of observables (three photometric bands). When compared to SED fitting based on the same set of observables, our method yields results that are more accurate and free from systematic biases.

Multi-locus analysis of genomic time series data from experimental evolution.

PubMed

Terhorst, Jonathan; Schlötterer, Christian; Song, Yun S

2015-04-01

Genomic time series data generated by evolve-and-resequence (E&R) experiments offer a powerful window into the mechanisms that drive evolution. However, standard population genetic inference procedures do not account for sampling serially over time, and new methods are needed to make full use of modern experimental evolution data. To address this problem, we develop a Gaussian process approximation to the multi-locus Wright-Fisher process with selection over a time course of tens of generations. The mean and covariance structure of the Gaussian process are obtained by computing the corresponding moments in discrete-time Wright-Fisher models conditioned on the presence of a linked selected site. This enables our method to account for the effects of linkage and selection, both along the genome and across sampled time points, in an approximate but principled manner. We first use simulated data to demonstrate the power of our method to correctly detect, locate and estimate the fitness of a selected allele from among several linked sites. We study how this power changes for different values of selection strength, initial haplotypic diversity, population size, sampling frequency, experimental duration, number of replicates, and sequencing coverage depth. In addition to providing quantitative estimates of selection parameters from experimental evolution data, our model can be used by practitioners to design E&R experiments with requisite power. We also explore how our likelihood-based approach can be used to infer other model parameters, including effective population size and recombination rate. Then, we apply our method to analyze genome-wide data from a real E&R experiment designed to study the adaptation of D. melanogaster to a new laboratory environment with alternating cold and hot temperatures.

Accurate detection of hierarchical communities in complex networks based on nonlinear dynamical evolution

NASA Astrophysics Data System (ADS)

Zhuo, Zhao; Cai, Shi-Min; Tang, Ming; Lai, Ying-Cheng

2018-04-01

One of the most challenging problems in network science is to accurately detect communities at distinct hierarchical scales. Most existing methods are based on structural analysis and manipulation, which are NP-hard. We articulate an alternative, dynamical evolution-based approach to the problem. The basic principle is to computationally implement a nonlinear dynamical process on all nodes in the network with a general coupling scheme, creating a networked dynamical system. Under a proper system setting and with an adjustable control parameter, the community structure of the network would "come out" or emerge naturally from the dynamical evolution of the system. As the control parameter is systematically varied, the community hierarchies at different scales can be revealed. As a concrete example of this general principle, we exploit clustered synchronization as a dynamical mechanism through which the hierarchical community structure can be uncovered. In particular, for quite arbitrary choices of the nonlinear nodal dynamics and coupling scheme, decreasing the coupling parameter from the global synchronization regime, in which the dynamical states of all nodes are perfectly synchronized, can lead to a weaker type of synchronization organized as clusters. We demonstrate the existence of optimal choices of the coupling parameter for which the synchronization clusters encode accurate information about the hierarchical community structure of the network. We test and validate our method using a standard class of benchmark modular networks with two distinct hierarchies of communities and a number of empirical networks arising from the real world. Our method is computationally extremely efficient, eliminating completely the NP-hard difficulty associated with previous methods. The basic principle of exploiting dynamical evolution to uncover hidden community organizations at different scales represents a "game-change" type of approach to addressing the problem of community detection in complex networks.

Corolla morphology influences diversification rates in bifid toadflaxes (Linaria sect. Versicolores)

PubMed Central

Fernández-Mazuecos, Mario; Blanco-Pastor, José Luis; Gómez, José M.; Vargas, Pablo

2013-01-01

Background and Aims The role of flower specialization in plant speciation and evolution remains controversial. In this study the evolution of flower traits restricting access to pollinators was analysed in the bifid toadflaxes (Linaria sect. Versicolores), a monophyletic group of ∼30 species and subspecies with highly specialized corollas. Methods A time-calibrated phylogeny based on both nuclear and plastid DNA sequences was obtained using a coalescent-based method, and flower morphology was characterized by means of morphometric analyses. Directional trends in flower shape evolution and trait-dependent diversification rates were jointly analysed using recently developed methods, and morphological shifts were reconstructed along the phylogeny. Pollinator surveys were conducted for a representative sample of species. Key Results A restrictive character state (narrow corolla tube) was reconstructed in the most recent common ancestor of Linaria sect. Versicolores. After its early loss in the most species-rich clade, this character state has been convergently reacquired in multiple lineages of this clade in recent times, yet it seems to have exerted a negative influence on diversification rates. Comparative analyses and pollinator surveys suggest that the narrow- and broad-tubed flowers are evolutionary optima representing divergent strategies of pollen placement on nectar-feeding insects. Conclusions The results confirm that different forms of floral specialization can lead to dissimilar evolutionary success in terms of diversification. It is additionally suggested that opposing individual-level and species-level selection pressures may have driven the evolution of pollinator-restrictive traits in bifid toadflaxes. PMID:24142920

The Evolution of Campylobacter jejuni and Campylobacter coli

PubMed Central

Sheppard, Samuel K.; Maiden, Martin C.J.

2015-01-01

The global significance of Campylobacter jejuni and Campylobacter coli as gastrointestinal human pathogens has motivated numerous studies to characterize their population biology and evolution. These bacteria are a common component of the intestinal microbiota of numerous bird and mammal species and cause disease in humans, typically via consumption of contaminated meat products, especially poultry meat. Sequence-based molecular typing methods, such as multilocus sequence typing (MLST) and whole genome sequencing (WGS), have been instructive for understanding the epidemiology and evolution of these bacteria and how phenotypic variation relates to the high degree of genetic structuring in C. coli and C. jejuni populations. Here, we describe aspects of the relatively short history of coevolution between humans and pathogenic Campylobacter, by reviewing research investigating how mutation and lateral or horizontal gene transfer (LGT or HGT, respectively) interact to create the observed population structure. These genetic changes occur in a complex fitness landscape with divergent ecologies, including multiple host species, which can lead to rapid adaptation, for example, through frame-shift mutations that alter gene expression or the acquisition of novel genetic elements by HGT. Recombination is a particularly strong evolutionary force in Campylobacter, leading to the emergence of new lineages and even large-scale genome-wide interspecies introgression between C. jejuni and C. coli. The increasing availability of large genome datasets is enhancing understanding of Campylobacter evolution through the application of methods, such as genome-wide association studies, but MLST-derived clonal complex designations remain a useful method for describing population structure. PMID:26101080

Evolution of Self-Reporting Methods for Identifying Discrete Emotions in Science Classrooms

ERIC Educational Resources Information Center

Ritchie, Stephen M.; Hudson, Peter; Bellocchi, Alberto; Henderson, Senka; King, Donna; Tobin, Kenneth

2016-01-01

Emotion researchers have grappled with challenging methodological issues in capturing emotions of participants in naturalistic settings such as school or university classrooms. Self-reporting methods have been used frequently, yet these methods are inadequate when used alone. We argue that the self-reporting methods of emotion diaries and…

Microsporidians as evolution-proof agents of malaria control?

PubMed

Koella, Jacob C; Lorenz, Lena; Bargielowski, Irka

2009-01-01

Despite our efforts at malaria control, malaria remains one of our most serious and deadly diseases. The failure of control stems in part from the parasite's intense transmission in many areas and from the emergence and spread of resistance of the malaria parasites and their mosquito vectors against most of the chemicals used to attack them. New methods for control are desperately needed. However, new methods will be useful only if they are effective (i.e., decrease transmission substantially) and evolutionarily sustainable (i.e., evolution-proof, in that they prevent evolution from eroding efficacy). We suggest microsporidian parasites that infect mosquitoes could be potentially effective and sustainable agents for malaria control. They may be effective because they target several epidemiologically important traits: survival of larvae (and thus number of adult mosquitoes), adult longevity, biting rate and the development of malaria within the mosquitoes. Even if each trait is affected only moderately, the intensity of transmission can be reduced considerably. They may be evolution-proof, for the evolutionarily most important trait is juvenile survival, whereas the two epidemiologically most important factors are traits of the adult mosquito: biting rate and longevity. Under the intense microsporidian pressure of a control programme, it is likely (if not inevitable) that the larvae evolve to survive microsporidian infection. However, if this larval tolerance to microsporidians is genetically correlated with the adult traits, tolerant mosquitoes may not live as long and bite less frequently than microsporidian-sensitive ones. While such a trade-off has not been measured, combining several studies suggests indirectly a negative genetic correlation between larval tolerance and adult longevity. Therefore, evolution might not undermine control; rather it might increase its effectiveness. While the evolution of resistance may be inevitable, the failure of control need not be.

Size Evolution and Stochastic Models: Explaining Ostracod Size through Probabilistic Distributions

NASA Astrophysics Data System (ADS)

Krawczyk, M.; Decker, S.; Heim, N. A.; Payne, J.

2014-12-01

The biovolume of animals has functioned as an important benchmark for measuring evolution throughout geologic time. In our project, we examined the observed average body size of ostracods over time in order to understand the mechanism of size evolution in these marine organisms. The body size of ostracods has varied since the beginning of the Ordovician, where the first true ostracods appeared. We created a stochastic branching model to create possible evolutionary trees of ostracod size. Using stratigraphic ranges for ostracods compiled from over 750 genera in the Treatise on Invertebrate Paleontology, we calculated overall speciation and extinction rates for our model. At each timestep in our model, new lineages can evolve or existing lineages can become extinct. Newly evolved lineages are assigned sizes based on their parent genera. We parameterized our model to generate neutral and directional changes in ostracod size to compare with the observed data. New sizes were chosen via a normal distribution, and the neutral model selected new sizes differentials centered on zero, allowing for an equal chance of larger or smaller ostracods at each speciation. Conversely, the directional model centered the distribution on a negative value, giving a larger chance of smaller ostracods. Our data strongly suggests that the overall direction of ostracod evolution has been following a model that directionally pushes mean ostracod size down, shying away from a neutral model. Our model was able to match the magnitude of size decrease. Our models had a constant linear decrease while the actual data had a much more rapid initial rate followed by a constant size. The nuance of the observed trends ultimately suggests a more complex method of size evolution. In conclusion, probabilistic methods can provide valuable insight into possible evolutionary mechanisms determining size evolution in ostracods.

Case studies in teaching evolution: The intersection of dilemmas in practice

NASA Astrophysics Data System (ADS)

Fisher, Rachel

Despite recent science education reform documents citing evolution as a core concept to be taught in grades K-12, research shows problems with how it is currently taught. Evolution is often avoided, teachers minimize its importance within biology, infuse misconceptions, and/or interject non-scientific ideologies into lessons. My research focused on how teachers in two geographically and culturally distinct school districts in the southwestern U.S. negotiate dilemmas during an evolution unit. One school district was rural and had a large population of Mormon students, while the other district was urban, with a large majority Mexican/Mexican-American students. Using a case study approach, I observed three biology teachers during their evolution lessons, interviewed them throughout the unit, co-planned lessons with them, and collected artifacts from this unit, including anonymous student work. I also included data from four genetics lessons for each teacher to determine if the issues that arose during the evolution unit were a result of the general practice of the teacher, or if they were unique to evolution. Findings showed teachers' backgrounds and comfort levels with evolution, in addition to their perceptions of community context, affected how they negotiated pedagogical, conceptual, political, and cultural dilemmas. This study's findings will inform in-service teachers' future practice and professional development tools to aid with their teaching---this may include methods to negotiate some of the political (e.g. state standards) or cultural (e.g. religious resistance) issues inherent to teaching evolution.

Evolution of the SCS curve number method and its applications to continuous runoff simulation

USDA-ARS?s Scientific Manuscript database

The Natural Resources Conservation Service (NRCS) [previously Soil Conservation Service (SCS)] developed the SCS runoff curve-number (CN) method for estimating direct runoff from storm rainfall. The NRCS uses the CN method for designing structures and for evaluating their effectiveness. Structural...

EVOLUTION OF AN ANALYTICAL METHOD FOR HALOGENATED FURANONES IN DRINKING WATER

EPA Science Inventory

A unified method of detection for seven halogenated furanones present in drinking waters at the ng/L level has been developed. The use of GC/ECD makes this method amenable to manyenvironmental laboratories and water treatment plants in the United States. Detection limits observe...

Application of the pulsed fast/thermal neutron method for soil elemental analysis

USDA-ARS?s Scientific Manuscript database

Soil science is a research field where physic concepts and experimental methods are widely used, particularly in agro-chemistry and soil elemental analysis. Different methods of analysis are currently available. The evolution of nuclear physics (methodology and instrumentation) combined with the ava...

Curriculum Evolution at Air Command and Staff College in the Post-Cold War Era

ERIC Educational Resources Information Center

Donovan, William Robert, II.

2010-01-01

This qualitative study used a historical research method to eliminate the gap in the historical knowledge of Air Command and Staff College (ACSC) curriculum evolution in the post-Cold War era. This study is the only known analysis of the forces that influenced the ACSC curriculum and the rationale behind curricular change at ACSC in the post-Cold…

The Rise and Fall of the Bering Land Bridge. Crustal Evolution Education Project. Teacher's Guide [and] Student Investigation.

ERIC Educational Resources Information Center

Stoever, Edward C., Jr.

Crustal Evolution Education Project (CEEP) modules were designed to: (1) provide students with the methods and results of continuing investigations into the composition, history, and processes of the earth's crust and the application of this knowledge to man's activities and (2) to be used by teachers with little or no previous background in the…

Of woods and webs: possible alternatives to the tree of life for studying genomic fluidity in E. coli.

PubMed

Beauregard-Racine, Julie; Bicep, Cédric; Schliep, Klaus; Lopez, Philippe; Lapointe, François-Joseph; Bapteste, Eric

2011-07-20

We introduce several forest-based and network-based methods for exploring microbial evolution, and apply them to the study of thousands of genes from 30 strains of E. coli. This case study illustrates how additional analyses could offer fast heuristic alternatives to standard tree of life (TOL) approaches. We use gene networks to identify genes with atypical modes of evolution, and genome networks to characterize the evolution of genetic partnerships between E. coli and mobile genetic elements. We develop a novel polychromatic quartet method to capture patterns of recombination within E. coli, to update the clanistic toolkit, and to search for the impact of lateral gene transfer and of pathogenicity on gene evolution in two large forests of trees bearing E. coli. We unravel high rates of lateral gene transfer involving E. coli (about 40% of the trees under study), and show that both core genes and shell genes of E. coli are affected by non-tree-like evolutionary processes. We show that pathogenic lifestyle impacted the structure of 30% of the gene trees, and that pathogenic strains are more likely to transfer genes with one another than with non-pathogenic strains. In addition, we propose five groups of genes as candidate mobile modules of pathogenicity. We also present strong evidence for recent lateral gene transfer between E. coli and mobile genetic elements. Depending on which evolutionary questions biologists want to address (i.e. the identification of modules, genetic partnerships, recombination, lateral gene transfer, or genes with atypical evolutionary modes, etc.), forest-based and network-based methods are preferable to the reconstruction of a single tree, because they provide insights and produce hypotheses about the dynamics of genome evolution, rather than the relative branching order of species and lineages. Such a methodological pluralism - the use of woods and webs - is to be encouraged to analyse the evolutionary processes at play in microbial evolution.This manuscript was reviewed by: Ford Doolittle, Tal Pupko, Richard Burian, James McInerney, Didier Raoult, and Yan Boucher.

Contextualising primate origins--an ecomorphological framework.

PubMed

Soligo, Christophe; Smaers, Jeroen B

2016-04-01

Ecomorphology - the characterisation of the adaptive relationship between an organism's morphology and its ecological role - has long been central to theories of the origin and early evolution of the primate order. This is exemplified by two of the most influential theories of primate origins: Matt Cartmill's Visual Predation Hypothesis, and Bob Sussman's Angiosperm Co-Evolution Hypothesis. However, the study of primate origins is constrained by the absence of data directly documenting the events under investigation, and has to rely instead on a fragmentary fossil record and the methodological assumptions inherent in phylogenetic comparative analyses of extant species. These constraints introduce particular challenges for inferring the ecomorphology of primate origins, as morphology and environmental context must first be inferred before the relationship between the two can be considered. Fossils can be integrated in comparative analyses and observations of extant model species and laboratory experiments of form-function relationships are critical for the functional interpretation of the morphology of extinct species. Recent developments have led to important advancements, including phylogenetic comparative methods based on more realistic models of evolution, and improved methods for the inference of clade divergence times, as well as an improved fossil record. This contribution will review current perspectives on the origin and early evolution of primates, paying particular attention to their phylogenetic (including cladistic relationships and character evolution) and environmental (including chronology, geography, and physical environments) contextualisation, before attempting an up-to-date ecomorphological synthesis of primate origins. © 2016 Anatomical Society.

Solar Energy Evolution and Diffusion Studies | Solar Research | NREL

Science.gov Websites

industry-wide studies that use data-driven and evidence-based methods to identify characteristics developed models of U.S. household PV adoption. The project also conducted two market pilots to test methods

Pulmonary lung surfactant synthetic peptide concentration-dependent modulation of DPPC and POPG acyl chain order in a DPPC:POPG:palmitic acid lipid mixture.

PubMed

Krill, S L; Gupta, S L; Smith, T

1994-05-06

Lung surfactant-associated protein interaction with lipid matrices and the effects on lipid thermotropic phase behavior are areas of active research. Many studies limit the lipids to a single or two-component system. The current investigation utilizes a three-lipid component matrix (DPPC:POPG:palmitic acid) to investigate the impact of a synthetic surfactant protein B fragment (SP-B 53-78 DiACM) on the dynamic surface activity of the lipid admixture as measured by a Wilhelmy surface balance. Also, the modulation of the individual lipid acyl chain order by the peptide within the lipid matrix is studied through the use of thermal perturbation FTIR spectroscopy. The data clearly demonstrate a concentration-dependent effect of the peptide on the surface activity with an improvement in the dynamic surface tension diagram characteristics (decreased surface tension and increased collapse plateau) especially at low, 0.36 M%, peptide concentrations. These effects are diminished upon further addition of the peptide. FTIR spectral data demonstrate that the peptide addition results in a significant increase in the acyl chain order of the DPPC and POPG components as measured by the position of the methylene stretching vibrational bands. DPPC is most sensitive to the peptide presence, while the palmitic acid is least affected. The transition temperatures of the individual lipids are also increased with the addition of the peptide. The presence of POPG in the matrix achieves the surface activity similarly seen with natural lung surfactant relative to a DPPC/palmitic acid lipid matrix alone. Its presence increases the sensitivity of the DPPC acyl chains to the presence of the peptide. These effects on the chain order are most probably related to the increased acyl chain fluidity which POPG imparts to the lipid matrix because of the presence of the cis double bond. The phosphatidylglycerol headgroup also adds a negative charge to the lipid matrix which enhances the peptide-lipid interaction. Although the palmitic acid is minimally affected by the peptide, its presence, as suggested by surface balance measurements, results in the establishment of a stable lipid film with DPPC, capable of achieving low surface tension values.

Daymet: Daily Surface Weather Data on a 1-km Grid for North America, Version 2.

NASA Astrophysics Data System (ADS)

Devarakonda, R.

2014-12-01

Daymet: Daily Surface Weather Data and Climatological Summaries provides gridded estimates of daily weather parameters for North America, including daily continuous surfaces of minimum and maximum temperature, precipitation occurrence and amount, humidity, shortwave radiation, snow water equivalent, and day length. The current data product (Version 2) covers the period January 1, 1980 to December 31, 2013 [1]. Data are available on a daily time step at a 1-km x 1-km spatial resolution in Lambert Conformal Conic projection with a spatial extent that covers the North America as meteorological station density allows. Daymet data can be downloaded from 1) the ORNL Distributed Active Archive Center (DAAC) search and order tools (http://daac.ornl.gov/cgi-bin/cart/add2cart.pl?add=1219) or directly from the DAAC FTP site (http://daac.ornl.gov/cgi-bin/dsviewer.pl?ds_id=1219) and 2) the Single Pixel Tool (http://daymet.ornl.gov/singlepixel.html) and THREDDS (Thematic Real-time Environmental Data Services) Data Server (TDS) (http://daymet.ornl.gov/thredds_mosaics.html). The Single Pixel Data Extraction Tool [2] allows users to enter a single geographic point by latitude and longitude in decimal degrees. A routine is executed that translates the (lon, lat) coordinates into projected Daymet (x,y) coordinates. These coordinates are used to access the Daymet database of daily-interpolated surface weather variables. The Single Pixel Data Extraction Tool also provides the option to download multiple coordinates programmatically. The ORNL DAAC's TDS provides customized visualization and access to Daymet time series of North American mosaics. Users can subset and download Daymet data via a variety of community standards, including OPeNDAP, NetCDF Subset service, and Open Geospatial Consortium (OGC) Web Map/Coverage Service. References: [1] Thornton, P. E., Thornton, M. M., Mayer, B. W., Wilhelmi, N., Wei, Y., Devarakonda, R., & Cook, R. (2012). "Daymet: Daily surface weather on a 1 km grid for North America, 1980-2008". Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center for Biogeochemical Dynamics (DAAC), 1. [2] Devarakonda R., et al. 2012. Daymet: Single Pixel Data Extraction Tool. Available [http://daymet.ornl.go/singlepixel.html].

Coupled molybdenum carbide and reduced graphene oxide electrocatalysts for efficient hydrogen evolution.

PubMed

Li, Ji-Sen; Wang, Yu; Liu, Chun-Hui; Li, Shun-Li; Wang, Yu-Guang; Dong, Long-Zhang; Dai, Zhi-Hui; Li, Ya-Fei; Lan, Ya-Qian

2016-04-01

Electrochemical water splitting is one of the most economical and sustainable methods for large-scale hydrogen production. However, the development of low-cost and earth-abundant non-noble-metal catalysts for the hydrogen evolution reaction remains a challenge. Here we report a two-dimensional coupled hybrid of molybdenum carbide and reduced graphene oxide with a ternary polyoxometalate-polypyrrole/reduced graphene oxide nanocomposite as a precursor. The hybrid exhibits outstanding electrocatalytic activity for the hydrogen evolution reaction and excellent stability in acidic media, which is, to the best of our knowledge, the best among these reported non-noble-metal catalysts. Theoretical calculations on the basis of density functional theory reveal that the active sites for hydrogen evolution stem from the pyridinic nitrogens, as well as the carbon atoms, in the graphene. In a proof-of-concept trial, an electrocatalyst for hydrogen evolution is fabricated, which may open new avenues for the design of nanomaterials utilizing POMs/conducting polymer/reduced-graphene oxide nanocomposites.

Coupled molybdenum carbide and reduced graphene oxide electrocatalysts for efficient hydrogen evolution

NASA Astrophysics Data System (ADS)

Li, Ji-Sen; Wang, Yu; Liu, Chun-Hui; Li, Shun-Li; Wang, Yu-Guang; Dong, Long-Zhang; Dai, Zhi-Hui; Li, Ya-Fei; Lan, Ya-Qian

2016-04-01

Electrochemical water splitting is one of the most economical and sustainable methods for large-scale hydrogen production. However, the development of low-cost and earth-abundant non-noble-metal catalysts for the hydrogen evolution reaction remains a challenge. Here we report a two-dimensional coupled hybrid of molybdenum carbide and reduced graphene oxide with a ternary polyoxometalate-polypyrrole/reduced graphene oxide nanocomposite as a precursor. The hybrid exhibits outstanding electrocatalytic activity for the hydrogen evolution reaction and excellent stability in acidic media, which is, to the best of our knowledge, the best among these reported non-noble-metal catalysts. Theoretical calculations on the basis of density functional theory reveal that the active sites for hydrogen evolution stem from the pyridinic nitrogens, as well as the carbon atoms, in the graphene. In a proof-of-concept trial, an electrocatalyst for hydrogen evolution is fabricated, which may open new avenues for the design of nanomaterials utilizing POMs/conducting polymer/reduced-graphene oxide nanocomposites.

Microstructural evolution of type 304 and 316 stainless steels under neutron irradiation at LWR relevant conditions

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

Tan, Lizhen; Stoller, Roger E.; Field, Kevin G.

Extension of light water reactors' useful life will expose austenitic internal core components to irradiation damage levels beyond 100 displacements per atom (dpa), which will lead to profound microstructural evolution and consequent degradation of macroscopic properties. Microstructural evolution, including Frank loops, cavities, precipitates, and segregation at boundaries and the resultant radiation hardening in type 304 and 316 stainless steel (SS) variants, were studied in this work via experimental characterization and multiple simulation methods. Experimental data for up to 40 heats of type 304SS and 316SS variants irradiated in different reactors to 0.6–120 dpa at 275–375°C were either generated from thismore » work or collected from literature reports. These experimental data were then combined with models of Frank loop and cavity evolution, computational thermodynamics and precipitation, and ab initio and rate theory integrated radiation-induced segregation models to provide insights into microstructural evolution and degradation at higher radiation doses.« less

Unscrambling the lead model ages

NASA Astrophysics Data System (ADS)

Albarede, Francis; Martine, Juteau

1984-01-01

A linear relation is derived for the secular evolution of 206Pb/204Pb, 207Pb/204Pb and 208Pb/204Pb ratios, that permits tests to be made for open system evolution on each system independently. Application of the method to conformable ore bodies of various geological age indicates that the available data do not demand an open system evolution for the last 3.8 b.y. 238U/204Pb and 232Th/204Pb of 9.66 ± 0.15 and 37.65 ± 1.14 respectively fit best the data for this time interval. A single stage evolution since 4.5 b.y. is unlikely, however, and the major events of continent formation postdate the Earth accretion by at least 400 m.y. The larger scatter of 207Pb/204Pb data about the evolution line relative to the other isotopic ratios is also interpreted as resulting from a series of continental differentiation events taking place at 3.85 ± 0.15 b.y.

Microstructural evolution of type 304 and 316 stainless steels under neutron irradiation at LWR relevant conditions

DOE PAGES

Tan, Lizhen; Stoller, Roger E.; Field, Kevin G.; ...

2015-12-11

Extension of light water reactors' useful life will expose austenitic internal core components to irradiation damage levels beyond 100 displacements per atom (dpa), which will lead to profound microstructural evolution and consequent degradation of macroscopic properties. Microstructural evolution, including Frank loops, cavities, precipitates, and segregation at boundaries and the resultant radiation hardening in type 304 and 316 stainless steel (SS) variants, were studied in this work via experimental characterization and multiple simulation methods. Experimental data for up to 40 heats of type 304SS and 316SS variants irradiated in different reactors to 0.6–120 dpa at 275–375°C were either generated from thismore » work or collected from literature reports. These experimental data were then combined with models of Frank loop and cavity evolution, computational thermodynamics and precipitation, and ab initio and rate theory integrated radiation-induced segregation models to provide insights into microstructural evolution and degradation at higher radiation doses.« less

Differential-Evolution Control Parameter Optimization for Unmanned Aerial Vehicle Path Planning

PubMed Central

Kok, Kai Yit; Rajendran, Parvathy

2016-01-01

The differential evolution algorithm has been widely applied on unmanned aerial vehicle (UAV) path planning. At present, four random tuning parameters exist for differential evolution algorithm, namely, population size, differential weight, crossover, and generation number. These tuning parameters are required, together with user setting on path and computational cost weightage. However, the optimum settings of these tuning parameters vary according to application. Instead of trial and error, this paper presents an optimization method of differential evolution algorithm for tuning the parameters of UAV path planning. The parameters that this research focuses on are population size, differential weight, crossover, and generation number. The developed algorithm enables the user to simply define the weightage desired between the path and computational cost to converge with the minimum generation required based on user requirement. In conclusion, the proposed optimization of tuning parameters in differential evolution algorithm for UAV path planning expedites and improves the final output path and computational cost. PMID:26943630

Reversible adapting layer produces robust single-crystal electrocatalyst for oxygen evolution.

PubMed

Tung, Ching-Wei; Hsu, Ying-Ya; Shen, Yen-Ping; Zheng, Yixin; Chan, Ting-Shan; Sheu, Hwo-Shuenn; Cheng, Yuan-Chung; Chen, Hao Ming

2015-08-28

Electrochemically converting water into oxygen/hydrogen gas is ideal for high-density renewable energy storage in which robust electrocatalysts for efficient oxygen evolution play crucial roles. To date, however, electrocatalysts with long-term stability have remained elusive. Here we report that single-crystal Co3O4 nanocube underlay with a thin CoO layer results in a high-performance and high-stability electrocatalyst in oxygen evolution reaction. An in situ X-ray diffraction method is developed to observe a strong correlation between the initialization of the oxygen evolution and the formation of active metal oxyhydroxide phase. The lattice of skin layer adapts to the structure of the active phase, which enables a reversible facile structural change that facilitates the chemical reactions without breaking the scaffold of the electrocatalysts. The single-crystal nanocube electrode exhibits stable, continuous oxygen evolution for >1,000 h. This robust stability is attributed to the complementary nature of defect-free single-crystal electrocatalyst and the reversible adapting layer.

Designing non-Hermitian dynamics for conservative state evolution on the Bloch sphere

NASA Astrophysics Data System (ADS)

Yu, Sunkyu; Piao, Xianji; Park, Namkyoo

2018-03-01

An evolution on the Bloch sphere is the fundamental state transition, including optical polarization controls and qubit operations. Conventional evolution of a polarization state or qubit is implemented within a closed system that automatically satisfies energy conservation from the Hermitian formalism. Although particular forms of static non-Hermitian Hamiltonians, such as parity-time-symmetric Hamiltonians, allow conservative states in an open system, the criteria for the energy conservation in a dynamical open system have not been fully explored. Here, we derive the condition of conservative state evolution in open-system dynamics and its inverse design method, by developing the non-Hermitian modification of the Larmor precession equation. We show that the geometrically designed locus on the Bloch sphere can be realized by different forms of dynamics, leading to the isolocus family of non-Hermitian dynamics. This increased degree of freedom allows the complementary phenomena of error-robust and highly sensitive evolutions on the Bloch sphere, which could be applicable to stable polarizers, quantum gates, and optimized sensors in dynamical open systems.

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

NASA Technical Reports Server (NTRS)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

A parametric finite element method for solid-state dewetting problems with anisotropic surface energies

NASA Astrophysics Data System (ADS)

Bao, Weizhu; Jiang, Wei; Wang, Yan; Zhao, Quan

2017-02-01

We propose an efficient and accurate parametric finite element method (PFEM) for solving sharp-interface continuum models for solid-state dewetting of thin films with anisotropic surface energies. The governing equations of the sharp-interface models belong to a new type of high-order (4th- or 6th-order) geometric evolution partial differential equations about open curve/surface interface tracking problems which include anisotropic surface diffusion flow and contact line migration. Compared to the traditional methods (e.g., marker-particle methods), the proposed PFEM not only has very good accuracy, but also poses very mild restrictions on the numerical stability, and thus it has significant advantages for solving this type of open curve evolution problems with applications in the simulation of solid-state dewetting. Extensive numerical results are reported to demonstrate the accuracy and high efficiency of the proposed PFEM.

Numerical simulations of electrohydrodynamic evolution of thin polymer films

NASA Astrophysics Data System (ADS)

Borglum, Joshua Christopher

Recently developed needleless electrospinning and electrolithography are two successful techniques that have been utilized extensively for low-cost, scalable, and continuous nano-fabrication. Rational understanding of the electrohydrodynamic principles underneath these nano-manufacturing methods is crucial to fabrication of continuous nanofibers and patterned thin films. This research project is to formulate robust, high-efficiency finite-difference Fourier spectral methods to simulate the electrohydrodynamic evolution of thin polymer films. Two thin-film models were considered and refined. The first was based on reduced lubrication theory; the second further took into account the effect of solvent drying and dewetting of the substrate. Fast Fourier Transform (FFT) based spectral method was integrated into the finite-difference algorithms for fast, accurately solving the governing nonlinear partial differential equations. The present methods have been used to examine the dependencies of the evolving surface features of the thin films upon the model parameters. The present study can be used for fast, controllable nanofabrication.

Fast hydrological model calibration based on the heterogeneous parallel computing accelerated shuffled complex evolution method

NASA Astrophysics Data System (ADS)

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Hong, Yang; Zuo, Depeng; Ren, Minglei; Lei, Tianjie; Liang, Ke

2018-01-01

Hydrological model calibration has been a hot issue for decades. The shuffled complex evolution method developed at the University of Arizona (SCE-UA) has been proved to be an effective and robust optimization approach. However, its computational efficiency deteriorates significantly when the amount of hydrometeorological data increases. In recent years, the rise of heterogeneous parallel computing has brought hope for the acceleration of hydrological model calibration. This study proposed a parallel SCE-UA method and applied it to the calibration of a watershed rainfall-runoff model, the Xinanjiang model. The parallel method was implemented on heterogeneous computing systems using OpenMP and CUDA. Performance testing and sensitivity analysis were carried out to verify its correctness and efficiency. Comparison results indicated that heterogeneous parallel computing-accelerated SCE-UA converged much more quickly than the original serial version and possessed satisfactory accuracy and stability for the task of fast hydrological model calibration.

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

Chen, Chuchu, E-mail: chenchuchu@lsec.cc.ac.cn; Hong, Jialin, E-mail: hjl@lsec.cc.ac.cn; Zhang, Liying, E-mail: lyzhang@lsec.cc.ac.cn

Stochastic Maxwell equations with additive noise are a system of stochastic Hamiltonian partial differential equations intrinsically, possessing the stochastic multi-symplectic conservation law. It is shown that the averaged energy increases linearly with respect to the evolution of time and the flow of stochastic Maxwell equations with additive noise preserves the divergence in the sense of expectation. Moreover, we propose three novel stochastic multi-symplectic methods to discretize stochastic Maxwell equations in order to investigate the preservation of these properties numerically. We make theoretical discussions and comparisons on all of the three methods to observe that all of them preserve the correspondingmore » discrete version of the averaged divergence. Meanwhile, we obtain the corresponding dissipative property of the discrete averaged energy satisfied by each method. Especially, the evolution rates of the averaged energies for all of the three methods are derived which are in accordance with the continuous case. Numerical experiments are performed to verify our theoretical results.« less

Adaptive characterization of recrystallization kinetics in IF steel by electron backscatter diffraction.

PubMed

Kim, Dong-Kyu; Park, Won-Woong; Lee, Ho Won; Kang, Seong-Hoon; Im, Yong-Taek

2013-12-01

In this study, a rigorous methodology for quantifying recrystallization kinetics by electron backscatter diffraction is proposed in order to reduce errors associated with the operator's skill. An adaptive criterion to determine adjustable grain orientation spread depending on the recrystallization stage is proposed to better identify the recrystallized grains in the partially recrystallized microstructure. The proposed method was applied in characterizing the microstructure evolution during annealing of interstitial-free steel cold rolled to low and high true strain levels of 0.7 and 1.6, respectively. The recrystallization kinetics determined by the proposed method was found to be consistent with the standard method of Vickers microhardness. The application of the proposed method to the overall recrystallization stages showed that it can be used for the rigorous characterization of progressive microstructure evolution, especially for the severely deformed material. © 2013 The Authors Journal of Microscopy © 2013 Royal Microscopical Society.

Computational model, method, and system for kinetically-tailoring multi-drug chemotherapy for individuals

DOEpatents

Gardner, Shea Nicole

2007-10-23

A method and system for tailoring treatment regimens to individual patients with diseased cells exhibiting evolution of resistance to such treatments. A mathematical model is provided which models rates of population change of proliferating and quiescent diseased cells using cell kinetics and evolution of resistance of the diseased cells, and pharmacokinetic and pharmacodynamic models. Cell kinetic parameters are obtained from an individual patient and applied to the mathematical model to solve for a plurality of treatment regimens, each having a quantitative efficacy value associated therewith. A treatment regimen may then be selected from the plurlaity of treatment options based on the efficacy value.

Numerical time evolution of ETH spin chains by means of matrix product density operators

NASA Astrophysics Data System (ADS)

White, Christopher; Zaletel, Michael; Mong, Roger; Refael, Gil

We introduce a method for approximating density operators of 1D systems that, when combined with a standard framework for time evolution (TEBD), makes possible simulation of the dynamics of strongly thermalizing systems to arbitrary times. We demonstrate that the method works on both near-equilibrium initial states (Gibbs states with spatially varying temperatures) and far-from-equilibrium initial states, including quenches across phase transitions and pure states. This work was supported by the National Science Foundation Graduate Research Fellowship under Grant No. DGE \\x901144469 and by the Caltech IQIM, an NSF Physics Frontiers Center with support of the Gordon and Betty Moore.

The digital language of amino acids.

PubMed

Kurić, L

2007-11-01

The subject of this paper is a digital approach to the investigation of the biochemical basis of genetic processes. The digital mechanism of nucleic acid and protein bio-syntheses, the evolution of biomacromolecules and, especially, the biochemical evolution of genetic language have been analyzed by the application of cybernetic methods, information theory and system theory, respectively. This paper reports the discovery of new methods for developing the new technologies in genetics. It is about the most advanced digital technology which is based on program, cybernetics and informational systems and laws. The results in the practical application of the new technology could be useful in bioinformatics, genetics, biochemistry, medicine and other natural sciences.

Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

NASA Astrophysics Data System (ADS)

Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

2017-11-01

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

Evolution of learning strategies in temporally and spatially variable environments: A review of theory

PubMed Central

Aoki, Kenichi; Feldman, Marcus W.

2013-01-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change – coevolutionary, two-timescale, and information decay – are compared and shown to sometimes yield contradictory results. The so-called Rogers’ paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers’ paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. PMID:24211681

Evolution of learning strategies in temporally and spatially variable environments: a review of theory.

PubMed

Aoki, Kenichi; Feldman, Marcus W

2014-02-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change--coevolutionary, two-timescale, and information decay--are compared and shown to sometimes yield contradictory results. The so-called Rogers' paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers' paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. Copyright © 2013 Elsevier Inc. All rights reserved.

The spatial distribution and evolution characteristics of North Atlantic cyclones

NASA Astrophysics Data System (ADS)

Dacre, H.; Gray, S.

2009-09-01

Mid-latitude cyclones play a large role in determining the day-to-day weather conditions in western Europe through their associated wind and precipitation patterns. Thus, their typical spatial and evolution characteristics are of great interest to meteorologists, insurance and risk management companies. In this study a feature tracking algorithm is applied to a cyclone database produced using the Hewson-method of cyclone identification, based on low-level gradients of wet-bulb potential temperature, to produce a climatology of mid-latitude cyclones. The aim of this work is to compare the cyclone track and density statistics found in this study with previous climatologies and to determine reasons for any differences. This method is found to compare well with other cyclone identification methods; the north Atlantic storm track is reproduced along with the major regions of genesis. Differences are attributed to cyclone lifetime and strength thresholds, dataset resolution and cyclone identification and tracking methods. Previous work on cyclone development has been largely limited to case studies as opposed to analysis of climatological data, and does not distinguish between the different stages of cyclone evolution. The cyclone database used in this study allows cyclone characteristics to be tracked throughout the cyclone lifecycle. This enables the evaluation of the characteristics of cyclone evolution for systems forming in different genesis regions and a calculation of the spatial distribution and evolution of these characteristics in composite cyclones. It was found that most of the cyclones that cross western Europe originate in the east Atlantic where the baroclinicity and sea surface temperature gradients are weak compared to the west Atlantic. East Atlantic cyclones also have higher low-level relative vorticity and lower mean sea level pressure at their genesis point than west Atlantic cyclones. This is consistent with the hypothesis that they are secondary cyclones developing on the trailing fronts of pre-existing 'parent' cyclones. Furthermore, it was found that a higher proportion of east Atlantic cyclones are type C cyclones with strong upper-level forcing but weak low-level forcing suggesting that latent energy plays a more important role in their intensification than for west Atlantic cyclones.

The spatial distribution and evolution characteristics of North Atlantic cyclones

NASA Astrophysics Data System (ADS)

Dacre, H.; Gray, S.

2009-04-01

Mid-latitude cyclones play a large role in determining the day-to-day weather conditions in western Europe through their associated wind and precipitation patterns. Thus, their typical spatial and evolution characteristics are of great interest to meteorologists, insurance and risk management companies. In this study a feature tracking algorithm is applied to a cyclone database produced using the Hewson-method of cyclone identification, based on low-level gradients of wet-bulb potential temperature, to produce a climatology of mid-latitude cyclones. The aim of this work is to compare the cyclone track and density statistics found in this study with previous climatologies. This method is found to compare well with other cyclone identification methods; the north Atlantic storm track is reproduced along with the major regions of genesis. Differences are attributed to cyclone lifetime and strength thresholds, dataset resolution and cyclone identification and tracking methods. Previous work on cyclone development has been largely limited to case studies as opposed to analysis of climatological data, and does not distinguish between the different stages of cyclone evolution. The cyclone database used in this study allows cyclone characteristics to be tracked throughout the cyclone lifecycle. This enables the evaluation of the characteristics of cyclone evolution for systems forming in different genesis regions and a calculation of the spatial distribution and evolution of these characteristics in composite cyclones. It was found that most of the cyclones that cross western Europe originate in the east Atlantic where the baroclinicity and sea surface temperature gradients are weak compared to the west Atlantic. East Atlantic cyclones also have higher low-level relative vorticity and lower mean sea level pressure at their genesis point than west Atlantic cyclones. This is consistent with the hypothesis that they are secondary cyclones developing on the trailing fronts of pre-existing 'parent' cyclones. Furthermore, it was found that a higher proportion of east Atlantic cyclones are type C cyclones with strong upper-level forcing but weak low-level forcing suggesting that latent energy plays a more important role in their intensification than for west Atlantic cyclones.

Nuclear shape evolution based on microscopic level densities

DOE PAGES

Ward, D. E.; Carlsson, B. G.; Døssing, T.; ...

2017-02-27

Here, by combining microscopically calculated level densities with the Metropolis walk method, we develop a consistent framework for treating the energy and angular-momentum dependence of the nuclear shape evolution in the fission process. For each nucleus under consideration, the level density is calculated microscopically for each of more than five million shapes with a recently developed combinatorial method. The method employs the same single-particle levels as those used for the extraction of the pairing and shell contributions to the macroscopic-microscopic deformation-energy surface. Containing no new parameters, the treatment is suitable for elucidating the energy dependence of the dynamics of warmmore » nuclei on pairing and shell effects. It is illustrated for the fission fragment mass distribution for several uranium and plutonium isotopes of particular interest.« less

Curious parallels and curious connections--phylogenetic thinking in biology and historical linguistics.

PubMed

Atkinson, Quentin D; Gray, Russell D

2005-08-01

In The Descent of Man (1871), Darwin observed "curious parallels" between the processes of biological and linguistic evolution. These parallels mean that evolutionary biologists and historical linguists seek answers to similar questions and face similar problems. As a result, the theory and methodology of the two disciplines have evolved in remarkably similar ways. In addition to Darwin's curious parallels of process, there are a number of equally curious parallels and connections between the development of methods in biology and historical linguistics. Here we briefly review the parallels between biological and linguistic evolution and contrast the historical development of phylogenetic methods in the two disciplines. We then look at a number of recent studies that have applied phylogenetic methods to language data and outline some current problems shared by the two fields.

A norm knockout method on indirect reciprocity to reveal indispensable norms

PubMed Central

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-01-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out. PMID:28276485

A norm knockout method on indirect reciprocity to reveal indispensable norms

NASA Astrophysics Data System (ADS)

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-03-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out.

Microscopic morphology evolution during ion beam smoothing of Zerodur® surfaces.

PubMed

Liao, Wenlin; Dai, Yifan; Xie, Xuhui; Zhou, Lin

2014-01-13

Ion sputtering of Zerodur material often results in the formation of nanoscale microstructures on the surfaces, which seriously influences optical surface quality. In this paper, we describe the microscopic morphology evolution during ion sputtering of Zerodur surfaces through experimental researches and theoretical analysis, which shows that preferential sputtering together with curvature-dependent sputtering overcomes ion-induced smoothing mechanisms leading to granular nanopatterns formation in morphology and the coarsening of the surface. Consequently, we propose a new method for ion beam smoothing (IBS) of Zerodur optics assisted by deterministic ion beam material adding (IBA) technology. With this method, Zerodur optics with surface roughness down to 0.15 nm root mean square (RMS) level is obtained through the experimental investigation, which demonstrates the feasibility of our proposed method.

Method and System for Hydrogen Evolution and Storage

DOEpatents

Thorn, David L.; Tumas, William; Hay, P. Jeffrey; Schwarz, Daniel E.; Cameron, Thomas M.

2008-10-21

A method and system for storing and evolving hydrogen employ chemical compounds that can be hydrogenated to store hydrogen and dehydrogenated to evolve hydrogen. A catalyst lowers the energy required for storing and evolving hydrogen. The method and system can provide hydrogen for devices that consume hydrogen as fuel.

Stability of the IMEX Methods, CNLF and BDF2-AB2, for Uncoupling Systems of Evolution Equations

DTIC Science & Technology

2011-02-01

Implicit-Explicit linear multistep methods, Tech. rep., Centrum Wiskunde and Informatica (CWI) (1996). [14] W. Hundsdorfer, J. Verwer, Numerical...component splitting for the Crank-Nicolson Leap- Frog integration method, Tech. rep., Centrum Wiskunde and Informatica (CWI) (2009). [23] J. Verwer

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution.

PubMed

Hopkins, Melanie J; Smith, Andrew B

2015-03-24

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.

Study of deformation evolution during failure of rock specimens using laser-based vibration measurements

NASA Astrophysics Data System (ADS)

Smolin, I. Yu.; Kulkov, A. S.; Makarov, P. V.; Tunda, V. A.; Krasnoveikin, V. A.; Eremin, M. O.; Bakeev, R. A.

2017-12-01

The aim of the paper is to analyze experimental data on the dynamic response of the marble specimen in uniaxial compression. To make it we use the methods of mathematical statistics. The lateral surface velocity evolution obtained by the laser Doppler vibrometer represents the data for analysis. The registered data were regarded as a time series that reflects deformation evolution of the specimen loaded up to failure. The revealed changes in statistical parameters were considered as precursors of failure. It is shown that before failure the deformation response is autocorrelated and reflects the states of dynamic chaos and self-organized criticality.

Research and Development for Technology Evolution Potential Forecasting System

NASA Astrophysics Data System (ADS)

Gao, Changqing; Cao, Shukun; Wang, Yuzeng; Ai, Changsheng; Ze, Xiangbo

Technology forecasting is a powerful weapon for many enterprises to gain an animate future. Evolutionary potential radar plot is a necessary step of some valuable methods to help the technology managers with right technical strategy. A software system for Technology Evolution Potential Forecasting (TEPF) with automatic radar plot drawing is introduced in this paper. The framework of the system and the date structure describing the concrete evolution pattern are illustrated in details. And the algorithm for radar plot drawing is researched. It is proved that the TEPF system is an effective tool during the technology strategy analyzing process with a referenced case study.

Automatic Clustering Using FSDE-Forced Strategy Differential Evolution

NASA Astrophysics Data System (ADS)

Yasid, A.

2018-01-01

Clustering analysis is important in datamining for unsupervised data, cause no adequate prior knowledge. One of the important tasks is defining the number of clusters without user involvement that is known as automatic clustering. This study intends on acquiring cluster number automatically utilizing forced strategy differential evolution (AC-FSDE). Two mutation parameters, namely: constant parameter and variable parameter are employed to boost differential evolution performance. Four well-known benchmark datasets were used to evaluate the algorithm. Moreover, the result is compared with other state of the art automatic clustering methods. The experiment results evidence that AC-FSDE is better or competitive with other existing automatic clustering algorithm.

Brain Evolution and Human Neuropsychology: The Inferential Brain Hypothesis

PubMed Central

Koscik, Timothy R.; Tranel, Daniel

2013-01-01

Collaboration between human neuropsychology and comparative neuroscience has generated invaluable contributions to our understanding of human brain evolution and function. Further cross-talk between these disciplines has the potential to continue to revolutionize these fields. Modern neuroimaging methods could be applied in a comparative context, yielding exciting new data with the potential of providing insight into brain evolution. Conversely, incorporating an evolutionary base into the theoretical perspectives from which we approach human neuropsychology could lead to novel hypotheses and testable predictions. In the spirit of these objectives, we present here a new theoretical proposal, the Inferential Brain Hypothesis, whereby the human brain is thought to be characterized by a shift from perceptual processing to inferential computation, particularly within the social realm. This shift is believed to be a driving force for the evolution of the large human cortex. PMID:22459075

In situ/Operando studies of electrocatalysts using hard X-ray spectroscopy

DOE PAGES

Lassalle-Kaiser, Benedikt; Gul, Sheraz; Kern, Jan; ...

2017-05-02

This review focuses on the use of X-ray absorption and emission spectroscopy techniques using hard X-rays to study electrocatalysts under in situ/operando conditions. The importance and the versatility of methods in the study of electrodes in contact with the electrolytes are described, when they are being cycled through the catalytic potentials during the progress of the oxygen-evolution, oxygen reduction and hydrogen evolution reactions. The catalytic oxygen evolution reaction is illustrated with examples using three oxides, Co, Ni and Mn, and two sulfides, Mo and Co. These are used as examples for the hydrogen evolution reaction. A bimetallic, bifunctional oxygen evolvingmore » and oxygen reducing Ni/Mn oxide is also presented. The various advantages and constraints in the use of these techniques and the future outlook are discussed.« less

Biological evolution and statistical physics

NASA Astrophysics Data System (ADS)

Drossel, Barbara

2001-03-01

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. Throughout the review, attention is paid to giving the necessary biological information, and to pointing out the assumptions underlying the models, and their limits of validity.

Boundary-Layer Receptivity and Integrated Transition Prediction

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Choudhari, Meelan

2005-01-01

The adjoint parabold stability equations (PSE) formulation is used to calculate the boundary layer receptivity to localized surface roughness and suction for compressible boundary layers. Receptivity efficiency functions predicted by the adjoint PSE approach agree well with results based on other nonparallel methods including linearized Navier-Stokes equations for both Tollmien-Schlichting waves and crossflow instability in swept wing boundary layers. The receptivity efficiency function can be regarded as the Green's function to the disturbance amplitude evolution in a nonparallel (growing) boundary layer. Given the Fourier transformed geometry factor distribution along the chordwise direction, the linear disturbance amplitude evolution for a finite size, distributed nonuniformity can be computed by evaluating the integral effects of both disturbance generation and linear amplification. The synergistic approach via the linear adjoint PSE for receptivity and nonlinear PSE for disturbance evolution downstream of the leading edge forms the basis for an integrated transition prediction tool. Eventually, such physics-based, high fidelity prediction methods could simulate the transition process from the disturbance generation through the nonlinear breakdown in a holistic manner.

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning.

PubMed

Davatzikos, Christos

2016-10-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. Copyright © 2016. Published by Elsevier B.V.

Automatic method for evaluating the activity of sourdough strains based on gas pressure measurements.

PubMed

Wick, M; Vanhoutte, J J; Adhemard, A; Turini, G; Lebeault, J M

2001-04-01

A new method is proposed for the evaluation of the activity of sourdough strains, based on gas pressure measurements in closed air-tight reactors. Gas pressure and pH were monitored on-line during the cultivation of commercial yeasts and heterofermentative lactic acid bacteria on a semi-synthetic medium with glucose as the major carbon source. Relative gas pressure evolution was compared both to glucose consumption and to acidification and growth. It became obvious that gas pressure evolution is related to glucose consumption kinetics. For each strain, a correlation was made between maximum gas pressure variation and amount of glucose consumed. The mass balance of CO2 in both liquid and gas phase demonstrated that around 90% of CO2 was recovered. Concerning biomass production, a linear relationship was found between log colony-forming units/ml and log pressure for both yeasts and bacteria during the exponential phase; and for yeasts, relative gas pressure evolution also followed optical density variation.

Calibration of a stochastic health evolution model using NHIS data

NASA Astrophysics Data System (ADS)

Gupta, Aparna; Li, Zhisheng

2011-10-01

This paper presents and calibrates an individual's stochastic health evolution model. In this health evolution model, the uncertainty of health incidents is described by a stochastic process with a finite number of possible outcomes. We construct a comprehensive health status index (HSI) to describe an individual's health status, as well as a health risk factor system (RFS) to classify individuals into different risk groups. Based on the maximum likelihood estimation (MLE) method and the method of nonlinear least squares fitting, model calibration is formulated in terms of two mixed-integer nonlinear optimization problems. Using the National Health Interview Survey (NHIS) data, the model is calibrated for specific risk groups. Longitudinal data from the Health and Retirement Study (HRS) is used to validate the calibrated model, which displays good validation properties. The end goal of this paper is to provide a model and methodology, whose output can serve as a crucial component of decision support for strategic planning of health related financing and risk management.

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning

PubMed Central

Davatzikos, Christos

2017-01-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. PMID:27514582

Discriminative motif discovery via simulated evolution and random under-sampling.

PubMed

Song, Tao; Gu, Hong

2014-01-01

Conserved motifs in biological sequences are closely related to their structure and functions. Recently, discriminative motif discovery methods have attracted more and more attention. However, little attention has been devoted to the data imbalance problem, which is one of the main reasons affecting the performance of the discriminative models. In this article, a simulated evolution method is applied to solve the multi-class imbalance problem at the stage of data preprocessing, and at the stage of Hidden Markov Models (HMMs) training, a random under-sampling method is introduced for the imbalance between the positive and negative datasets. It is shown that, in the task of discovering targeting motifs of nine subcellular compartments, the motifs found by our method are more conserved than the methods without considering data imbalance problem and recover the most known targeting motifs from Minimotif Miner and InterPro. Meanwhile, we use the found motifs to predict protein subcellular localization and achieve higher prediction precision and recall for the minority classes.

Nonparametric Determination of Redshift Evolution Index of Dark Energy

NASA Astrophysics Data System (ADS)

Ziaeepour, Houri

We propose a nonparametric method to determine the sign of γ — the redshift evolution index of dark energy. This is important for distinguishing between positive energy models, a cosmological constant, and what is generally called ghost models. Our method is based on geometrical properties and is more tolerant to uncertainties of other cosmological parameters than fitting methods in what concerns the sign of γ. The same parametrization can also be used for determining γ and its redshift dependence by fitting. We apply this method to SNLS supernovae and to gold sample of re-analyzed supernovae data from Riess et al. Both datasets show strong indication of a negative γ. If this result is confirmed by more extended and precise data, many of the dark energy models, including simple cosmological constant, standard quintessence models without interaction between quintessence scalar field(s) and matter, and scaling models are ruled out. We have also applied this method to Gurzadyan-Xue models with varying fundamental constants to demonstrate the possibility of using it to test other cosmologies.

Spatio-temporal evolutions of non-orthogonal equatorial wave modes derived from observations

NASA Astrophysics Data System (ADS)

Barton, Cory

Equatorial waves have been studied extensively due to their importance to the tropical climate and weather systems. Historically, their activity is diagnosed mainly in the wavenumber-frequency domain. Recently, many studies have projected observational data onto parabolic cylinder functions (PCFs), which represent the meridional structure of individual wave modes, to attain time-dependent spatial wave structures. The non-orthogonality of wave modes has yet posed a problem when attempting to separate data into wave fields where the waves project onto the same structure functions. We propose the development and application of a new methodology for equatorial wave expansion of instantaneous flows using the full equatorial wave spectrum. By creating a mapping from the meridional structure function amplitudes to the equatorial wave class amplitudes, we are able to diagnose instantaneous wave fields and determine their evolution. Because all meridional modes are shared by some subset of the wave classes, we require constraints on the wave class amplitudes to yield a closed system with a unique solution for all waves' spatial structures, including IG waves. A synthetic field is analyzed using this method to determine its accuracy for data of a single vertical mode. The wave class spectra diagnosed using this method successfully match the correct dispersion curves even if the incorrect depth is chosen for the spatial decomposition. In the case of more than one depth scale, waves with varying equivalent depth may be similarly identified using the dispersion curves. The primary vertical mode is the 200 m equivalent depth mode, which is that of the peak projection response. A distinct spectral power peak along the Kelvin wave dispersion curve for this value validates our choice of equivalent depth, although the possibility of depth varying with time and height is explored. The wave class spectra diagnosed assuming this depth scale mostly match their expected dispersion curves, showing that this method successfully partitions the wave spectra by calculating wave amplitudes in physical space. This is particularly striking because the time evolution, and therefore the frequency characteristics, is determined simply by a timeseries of independently-diagnosed instantaneous horizontal fields. We use the wave fields diagnosed by this method to study wave evolution in the context of the stratospheric QBO of zonal wind, confirming the continuous evolution of the selection mechanism for equatorial waves in the middle atmosphere. The amplitude cycle synchronized with the background zonal wind as predicted by QBO theory is present in the wave class fields even though the dynamics are not forced by the method itself. We have additionally identified a time-evolution of the zonal wavenumber spectrum responsible for the amplitude variability in physical space. Similar to the temporal characteristics, the vertical structures are also the result of a simple height cross-section through multiple independently-diagnosed levels.

A comparison of two methods for quantifying parasitic nematode fecundity

USDA-ARS?s Scientific Manuscript database

Accurate measures of nematode fecundity can provide important information for investigating parasite life history evolution, transmission potential, and effects on host health. Understanding differences among fecundity assessment protocols and standardizing methods, where possible, will enable compa...

Fast and robust brain tumor segmentation using level set method with multiple image information.

PubMed

Lok, Ka Hei; Shi, Lin; Zhu, Xianlun; Wang, Defeng

2017-01-01

Brain tumor segmentation is a challenging task for its variation in intensity. The phenomenon is caused by the inhomogeneous content of tumor tissue and the choice of imaging modality. In 2010 Zhang developed the Selective Binary Gaussian Filtering Regularizing Level Set (SBGFRLS) model that combined the merits of edge-based and region-based segmentation. To improve the SBGFRLS method by modifying the singed pressure force (SPF) term with multiple image information and demonstrate effectiveness of proposed method on clinical images. In original SBGFRLS model, the contour evolution direction mainly depends on the SPF. By introducing a directional term in SPF, the metric could control the evolution direction. The SPF is altered by statistic values enclosed by the contour. This concept can be extended to jointly incorporate multiple image information. The new SPF term is expected to bring a solution for blur edge problem in brain tumor segmentation. The proposed method is validated with clinical images including pre- and post-contrast magnetic resonance images. The accuracy and robustness is compared with sensitivity, specificity, DICE similarity coefficient and Jaccard similarity index. Experimental results show improvement, in particular the increase of sensitivity at the same specificity, in segmenting all types of tumors except for the diffused tumor. The novel brain tumor segmentation method is clinical-oriented with fast, robust and accurate implementation and a minimal user interaction. The method effectively segmented homogeneously enhanced, non-enhanced, heterogeneously-enhanced, and ring-enhanced tumor under MR imaging. Though the method is limited by identifying edema and diffuse tumor, several possible solutions are suggested to turn the curve evolution into a fully functional clinical diagnosis tool.

Spin-dependent evolution of collectivity in 112Te

NASA Astrophysics Data System (ADS)

Doncel, M.; Bäck, T.; Qi, C.; Cullen, D. M.; Hodge, D.; Cederwall, B.; Taylor, M. J.; Procter, M.; Giles, M.; Auranen, K.; Grahn, T.; Greenlees, P. T.; Jakobsson, U.; Julin, R.; Juutinen, S.; HerzáÅ, A.; Konki, J.; Pakarinen, J.; Partanen, J.; Peura, P.; Rahkila, P.; Ruotsalainen, P.; Sandzelius, M.; Sarén, J.; Scholey, C.; Sorri, J.; Stolze, S.; Uusitalo, J.

2017-11-01

The evolution of collectivity with spin along the yrast line in the neutron-deficient nucleus 112Te has been studied by measuring the reduced transition probability of excited states in the yrast band. In particular, the lifetimes of the 4+ and 6+ excited states have been determined by using the recoil distance Doppler-shift method. The results are discussed using both large-scale shell-model and total Routhian surface calculations.

Shape evolution with angular momentum in Lu isotopes

NASA Astrophysics Data System (ADS)

Kardan, Azam; Sayyah, Sepideh

2016-06-01

The nuclear potential energies of Lu isotopes with neutron number N = 90 - 98 up to high spins are computed within the framework of the unpaired cranked Nilsson-Strutinsky method. The potential and the macroscopic Lublin-Strasbourg drop (LSD) energy-surface diagrams are analyzed in terms of quadrupole deformation and triaxiality parameter. The shape evolution of these isotopes with respect to angular momentum, as well as the neutron number is studied.

Cauchy-Jost function and hierarchy of integrable equations

NASA Astrophysics Data System (ADS)

Boiti, M.; Pempinelli, F.; Pogrebkov, A. K.

2015-11-01

We describe the properties of the Cauchy-Jost (also known as Cauchy-Baker-Akhiezer) function of the Kadomtsev-Petviashvili-II equation. Using the bar partial -method, we show that for this function, all equations of the Kadomtsev-Petviashvili-II hierarchy are given in a compact and explicit form, including equations for the Cauchy-Jost function itself, time evolutions of the Jost solutions, and evolutions of the potential of the heat equation.

Structure functions in decomposing Au-Pt systems

NASA Astrophysics Data System (ADS)

Glas, R.; Blaschko, O.; Rosta, L.

1992-09-01

The evolution of Au-Pt alloys quenched within the miscibility gap is investigated by small-angle neutron-scattering techniques. Moreover, in the vicinity of fundamental Bragg reflections the evolution of ``sideband'' satellites induced by a lattice-parameter modulation connected with the precipitation pattern is investigated by diffuse scattering methods. Structure functions are evaluated for a series of concentrations within the miscibility gap and compared to recent results of the literature.

Optimal Control of Evolution Mixed Variational Inclusions

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

Alduncin, Gonzalo, E-mail: alduncin@geofisica.unam.mx

2013-12-15

Optimal control problems of primal and dual evolution mixed variational inclusions, in reflexive Banach spaces, are studied. The solvability analysis of the mixed state systems is established via duality principles. The optimality analysis is performed in terms of perturbation conjugate duality methods, and proximation penalty-duality algorithms to mixed optimality conditions are further presented. Applications to nonlinear diffusion constrained problems as well as quasistatic elastoviscoplastic bilateral contact problems exemplify the theory.

TTLEM: Open access tool for building numerically accurate landscape evolution models in MATLAB

NASA Astrophysics Data System (ADS)

Campforts, Benjamin; Schwanghart, Wolfgang; Govers, Gerard

2017-04-01

Despite a growing interest in LEMs, accuracy assessment of the numerical methods they are based on has received little attention. Here, we present TTLEM which is an open access landscape evolution package designed to develop and test your own scenarios and hypothesises. TTLEM uses a higher order flux-limiting finite-volume method to simulate river incision and tectonic displacement. We show that this scheme significantly influences the evolution of simulated landscapes and the spatial and temporal variability of erosion rates. Moreover, it allows the simulation of lateral tectonic displacement on a fixed grid. Through the use of a simple GUI the software produces visible output of evolving landscapes through model run time. In this contribution, we illustrate numerical landscape evolution through a set of movies spanning different spatial and temporal scales. We focus on the erosional domain and use both spatially constant and variable input values for uplift, lateral tectonic shortening, erodibility and precipitation. Moreover, we illustrate the relevance of a stochastic approach for realistic hillslope response modelling. TTLEM is a fully open source software package, written in MATLAB and based on the TopoToolbox platform (topotoolbox.wordpress.com). Installation instructions can be found on this website and the therefore designed GitHub repository.

Phylogeny-based comparative methods question the adaptive nature of sporophytic specializations in mosses.

PubMed

Huttunen, Sanna; Olsson, Sanna; Buchbender, Volker; Enroth, Johannes; Hedenäs, Lars; Quandt, Dietmar

2012-01-01

Adaptive evolution has often been proposed to explain correlations between habitats and certain phenotypes. In mosses, a high frequency of species with specialized sporophytic traits in exposed or epiphytic habitats was, already 100 years ago, suggested as due to adaptation. We tested this hypothesis by contrasting phylogenetic and morphological data from two moss families, Neckeraceae and Lembophyllaceae, both of which show parallel shifts to a specialized morphology and to exposed epiphytic or epilithic habitats. Phylogeny-based tests for correlated evolution revealed that evolution of four sporophytic traits is correlated with a habitat shift. For three of them, evolutionary rates of dual character-state changes suggest that habitat shifts appear prior to changes in morphology. This suggests that they could have evolved as adaptations to new habitats. Regarding the fourth correlated trait the specialized morphology had already evolved before the habitat shift. In addition, several other specialized "epiphytic" traits show no correlation with a habitat shift. Besides adaptive diversification, other processes thus also affect the match between phenotype and environment. Several potential factors such as complex genetic and developmental pathways yielding the same phenotypes, differences in strength of selection, or constraints in phenotypic evolution may lead to an inability of phylogeny-based comparative methods to detect potential adaptations.

Large-scale and Long-duration Simulation of a Multi-stage Eruptive Solar Event

NASA Astrophysics Data System (ADS)

Jiang, chaowei; Hu, Qiang; Wu, S. T.

2015-04-01

We employ a data-driven 3D MHD active region evolution model by using the Conservation Element and Solution Element (CESE) numerical method. This newly developed model retains the full MHD effects, allowing time-dependent boundary conditions and time evolution studies. The time-dependent simulation is driven by measured vector magnetograms and the method of MHD characteristics on the bottom boundary. We have applied the model to investigate the coronal magnetic field evolution of AR11283 which was characterized by a pre-existing sigmoid structure in the core region and multiple eruptions, both in relatively small and large scales. We have succeeded in producing the core magnetic field structure and the subsequent eruptions of flux-rope structures (see https://dl.dropboxusercontent.com/u/96898685/large.mp4 for an animation) as the measured vector magnetograms on the bottom boundary evolve in time with constant flux emergence. The whole process, lasting for about an hour in real time, compares well with the corresponding SDO/AIA and coronagraph imaging observations. From these results, we show the capability of the model, largely data-driven, that is able to simulate complex, topological, and highly dynamic active region evolutions. (We acknowledge partial support of NSF grants AGS 1153323 and AGS 1062050, and data support from SDO/HMI and AIA teams).

GIS and paleoanthropology: incorporating new approaches from the geospatial sciences in the analysis of primate and human evolution.

PubMed

Anemone, R L; Conroy, G C; Emerson, C W

2011-01-01

The incorporation of research tools and analytical approaches from the geospatial sciences is a welcome trend for the study of primate and human evolution. The use of remote sensing (RS) imagery and geographic information systems (GIS) allows vertebrate paleontologists, paleoanthropologists, and functional morphologists to study fossil localities, landscapes, and individual specimens in new and innovative ways that recognize and analyze the spatial nature of much paleoanthropological data. Whether one is interested in locating and mapping fossiliferous rock units in the field, creating a searchable and georeferenced database to catalog fossil localities and specimens, or studying the functional morphology of fossil teeth, bones, or artifacts, the new geospatial sciences provide an essential element in modern paleoanthropological inquiry. In this article we review recent successful applications of RS and GIS within paleoanthropology and related fields and argue for the importance of these methods for the study of human evolution in the twenty first century. We argue that the time has come for inclusion of geospatial specialists in all interdisciplinary field research in paleoanthropology, and suggest some promising areas of development and application of the methods of geospatial science to the science of human evolution. Copyright © 2011 Wiley Periodicals, Inc.

Parallel and Divergent Evolutionary Solutions for the Optimization of an Engineered Central Metabolism in Methylobacterium extorquens AM1

PubMed Central

Carroll, Sean Michael; Chubiz, Lon M.; Agashe, Deepa; Marx, Christopher J.

2015-01-01

Bioengineering holds great promise to provide fast and efficient biocatalysts for methanol-based biotechnology, but necessitates proven methods to optimize physiology in engineered strains. Here, we highlight experimental evolution as an effective means for optimizing an engineered Methylobacterium extorquens AM1. Replacement of the native formaldehyde oxidation pathway with a functional analog substantially decreased growth in an engineered Methylobacterium, but growth rapidly recovered after six hundred generations of evolution on methanol. We used whole-genome sequencing to identify the basis of adaptation in eight replicate evolved strains, and examined genomic changes in light of other growth and physiological data. We observed great variety in the numbers and types of mutations that occurred, including instances of parallel mutations at targets that may have been “rationalized” by the bioengineer, plus other “illogical” mutations that demonstrate the ability of evolution to expose unforeseen optimization solutions. Notably, we investigated mutations to RNA polymerase, which provided a massive growth benefit but are linked to highly aberrant transcriptional profiles. Overall, we highlight the power of experimental evolution to present genetic and physiological solutions for strain optimization, particularly in systems where the challenges of engineering are too many or too difficult to overcome via traditional engineering methods. PMID:27682084

DyKOSMap: A framework for mapping adaptation between biomedical knowledge organization systems.

PubMed

Dos Reis, Julio Cesar; Pruski, Cédric; Da Silveira, Marcos; Reynaud-Delaître, Chantal

2015-06-01

Knowledge Organization Systems (KOS) and their associated mappings play a central role in several decision support systems. However, by virtue of knowledge evolution, KOS entities are modified over time, impacting mappings and potentially turning them invalid. This requires semi-automatic methods to maintain such semantic correspondences up-to-date at KOS evolution time. We define a complete and original framework based on formal heuristics that drives the adaptation of KOS mappings. Our approach takes into account the definition of established mappings, the evolution of KOS and the possible changes that can be applied to mappings. This study experimentally evaluates the proposed heuristics and the entire framework on realistic case studies borrowed from the biomedical domain, using official mappings between several biomedical KOSs. We demonstrate the overall performance of the approach over biomedical datasets of different characteristics and sizes. Our findings reveal the effectiveness in terms of precision, recall and F-measure of the suggested heuristics and methods defining the framework to adapt mappings affected by KOS evolution. The obtained results contribute and improve the quality of mappings over time. The proposed framework can adapt mappings largely automatically, facilitating thus the maintenance task. The implemented algorithms and tools support and minimize the work of users in charge of KOS mapping maintenance. Copyright © 2015 Elsevier Inc. All rights reserved.

Inferring the Limit Behavior of Some Elementary Cellular Automata

NASA Astrophysics Data System (ADS)

Ruivo, Eurico L. P.; de Oliveira, Pedro P. B.

Cellular automata locally define dynamical systems, discrete in space, time and in the state variables, capable of displaying arbitrarily complex global emergent behavior. One core question in the study of cellular automata refers to their limit behavior, that is, to the global dynamical features in an infinite time evolution. Previous works have shown that for finite time evolutions, the dynamics of one-dimensional cellular automata can be described by regular languages and, therefore, by finite automata. Such studies have shown the existence of growth patterns in the evolution of such finite automata for some elementary cellular automata rules and also inferred the limit behavior of such rules based upon the growth patterns; however, the results on the limit behavior were obtained manually, by direct inspection of the structures that arise during the time evolution. Here we present the formalization of an automatic method to compute such structures. Based on this, the rules of the elementary cellular automata space were classified according to the existence of a growth pattern in their finite automata. Also, we present a method to infer the limit graph of some elementary cellular automata rules, derived from the analysis of the regular expressions that describe their behavior in finite time. Finally, we analyze some attractors of two rules for which we could not compute the whole limit set.

Predicting knee replacement damage in a simulator machine using a computational model with a consistent wear factor.

PubMed

Zhao, Dong; Sakoda, Hideyuki; Sawyer, W Gregory; Banks, Scott A; Fregly, Benjamin J

2008-02-01

Wear of ultrahigh molecular weight polyethylene remains a primary factor limiting the longevity of total knee replacements (TKRs). However, wear testing on a simulator machine is time consuming and expensive, making it impractical for iterative design purposes. The objectives of this paper were first, to evaluate whether a computational model using a wear factor consistent with the TKR material pair can predict accurate TKR damage measured in a simulator machine, and second, to investigate how choice of surface evolution method (fixed or variable step) and material model (linear or nonlinear) affect the prediction. An iterative computational damage model was constructed for a commercial knee implant in an AMTI simulator machine. The damage model combined a dynamic contact model with a surface evolution model to predict how wear plus creep progressively alter tibial insert geometry over multiple simulations. The computational framework was validated by predicting wear in a cylinder-on-plate system for which an analytical solution was derived. The implant damage model was evaluated for 5 million cycles of simulated gait using damage measurements made on the same implant in an AMTI machine. Using a pin-on-plate wear factor for the same material pair as the implant, the model predicted tibial insert wear volume to within 2% error and damage depths and areas to within 18% and 10% error, respectively. Choice of material model had little influence, while inclusion of surface evolution affected damage depth and area but not wear volume predictions. Surface evolution method was important only during the initial cycles, where variable step was needed to capture rapid geometry changes due to the creep. Overall, our results indicate that accurate TKR damage predictions can be made with a computational model using a constant wear factor obtained from pin-on-plate tests for the same material pair, and furthermore, that surface evolution method matters only during the initial "break in" period of the simulation.

Natural and Chemotherapy-Induced Clonal Evolution of Tumors.

PubMed

Ibragimova, M K; Tsyganov, M M; Litviakov, N V

2017-04-01

Evolution and natural selection of tumoral clones in the process of transformation and the following carcinogenesis can be called natural clonal evolution. Its main driving factors are internal: genetic instability initiated by driver mutations and microenvironment, which enables selective pressure while forming the environment for cell transformation and their survival. We present our overview of contemporary research dealing with mechanisms of carcinogenesis in different localizations from precancerous pathologies to metastasis and relapse. It shows that natural clonal evolution establishes intratumoral heterogeneity and enables tumor progression. Tumors of monoclonal origin are of low-level intratumoral heterogeneity in the initial stages, and this increases with the size of the tumor. Tumors of polyclonal origin are of extremely high-level intratumoral heterogeneity in the initial stages and become more homogeneous when larger due to clonal expansion. In cases of chemotherapy-induced clonal evolution of a tumor, chemotherapy becomes the leading factor in treatment. The latest research shows that the impact of chemotherapy can radically increase the speed of clonal evolution and lead to new malignant and resistant clones that cause tumor metastasis. Another option of chemotherapy-induced clonal evolution is formation of a new dominant clone from a clone that was minor in the initial tumor and obtained free space due to elimination of sensitive clones by chemotherapy. As a result, in ~20% of cases, chemotherapy can stimulate metastasis and relapse of tumors due to clonal evolution. The conclusion of the overview formulates approaches to tumor treatment based on clonal evolution: in particular, precision therapy, prediction of metastasis stimulation in patients treated with chemotherapy, methods of genetic evaluation of chemotherapy efficiency and clonal-oriented treatment, and approaches to manipulating the clonal evolution of tumors are presented.

Recovery of evolution of Grad-Shafranov equilibria from single-spacecraft data: Benchmarking and application to a flux transfer event

NASA Astrophysics Data System (ADS)

Sonnerup, B. U.; Hasegawa, H.; Nakamura, T.

2010-12-01

Even after the advent of multi-spacecraft missions such as Cluster and THEMIS, it has been difficult to distinguish between time evolution of, and spatial variation within, a space plasma structure on the basis of in situ measurements. We present a method for analyzing time evolution of two-dimensional (2D) and magnetohydrostatic, namely Grad-Shafranov equilibria, using data recorded by an observing probe as it traverses a quasi-static, 2D magnetic-field/plasma structure. The method recovers spatial initial values used in the classical Grad-Shafranov (GS) reconstruction [Sonnerup et al., JGR, 2006] for an interval before and after the time of actual measurements, by advancing them backward and forward in time based on a set of equation for an incompressible plasma; the consequence is generation of multiple GS maps or a movie of the 2D field structure. The method is successfully benchmarked by use of a 2D magnetohydrodynamic simulation of time-dependent magnetic reconnection, and then is applied to a magnetic flux transfer event (FTE) seen by Cluster at the dayside high-latitude magnetopause, which has been analyzed with the GS method [Hasegawa et al., Ann. Geophys., 2006]. The application shows that the field lines constituting the FTE flux rope were contracting toward its center as a result of modest convective flow in the region around the core of the flux rope.

Reticulate evolution and the human past: an anthropological perspective.

PubMed

Winder, Isabelle C; Winder, Nick P

2014-01-01

The evidence is mounting that reticulate (web-like) evolution has shaped the biological histories of many macroscopic plants and animals, including non-human primates closely related to Homo sapiens, but the implications of this non-hierarchical evolution for anthropological enquiry are not yet fully understood. When they are understood, the result may be a paradigm shift in evolutionary anthropology. This paper reviews the evidence for reticulated evolution in the non-human primates and human lineage. Then it makes the case for extrapolating this sort of patterning to Homo sapiens and other hominins and explores the implications this would have for research design, method and understandings of evolution in anthropology. Reticulation was significant in human evolutionary history and continues to influence societies today. Anthropologists and human scientists-whether working on ancient or modern populations-thus need to consider the implications of non-hierarchic evolution, particularly where molecular clocks, mathematical models and simplifying assumptions about evolutionary processes are used. This is not just a problem for palaeoanthropology. The simple fact of different mating systems among modern human groups, for example, may demand that more attention is paid to the potential for complexity in human genetic and cultural histories.

Tempo and Mode of the Evolution of Venom and Poison in Tetrapods.

PubMed

Harris, Richard J; Arbuckle, Kevin

2016-06-23

Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods.

Tempo and Mode of the Evolution of Venom and Poison in Tetrapods

PubMed Central

Harris, Richard J.; Arbuckle, Kevin

2016-01-01

Toxic weaponry in the form of venom and poison has evolved in most groups of animals, including all four major lineages of tetrapods. Moreover, the evolution of such traits has been linked to several key aspects of the biology of toxic animals including life-history and diversification. Despite this, attempts to investigate the macroevolutionary patterns underlying such weaponry are lacking. In this study we analyse patterns of venom and poison evolution across reptiles, amphibians, mammals, and birds using a suite of phylogenetic comparative methods. We find that each major lineage has a characteristic pattern of trait evolution, but mammals and reptiles evolve under a surprisingly similar regime, whilst that of amphibians appears to be particularly distinct and highly contrasting compared to other groups. Our results also suggest that the mechanism of toxin acquisition may be an important distinction in such evolutionary patterns; the evolution of biosynthesis is far less dynamic than that of sequestration of toxins from the diet. Finally, contrary to the situation in amphibians, other tetrapod groups show an association between the evolution of toxic weaponry and higher diversification rates. Taken together, our study provides the first broad-scale analysis of macroevolutionary patterns of venom and poison throughout tetrapods. PMID:27348001

Testing of some assumptions about biodegradability in soil as measured by carbon dioxide evolution

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

El-Din Sharabi, N.; Bartha, R.

1993-04-01

The Toxic Substance Control Act calls for a premanufacturing review of novel chemical substances including their biodegradability. Carbon dioxide evolution, using non-labeled carbon or [sup 14]C, is a common method of testing. This study examines assumptions of carbon dioxide evolution testing. Test substances used included: glucose, adipic acid, benzoic acid, and n-hexadecane. Chemical composition other than carbon content appears to influence minimally the percentages conversion to CO[sub 2]. However, that although CO[sub 2] evolution seemed proportional to the carbon content and concentration of the test substance, at least one-half of the evolved net CO[sub 2] did not come directly frommore » the test substance. Conversion to CO[sub 2] in the soil appeared to depend on carbon content only. In experiments of 1 month or longer, the net CO[sub 2] evolution in response to substrate may be above 100% of the added substrate carbon. Whether this applies to all substrate additions remains to be studied. The authors conclude that net CO[sub 2] and [sup 14]CO[sub 2] evolution measurements are useful as a first-tier tests for assessing biodegradability in soil. 11 refs., 6 figs.« less

New thinking: the evolution of human cognition

PubMed Central

Heyes, Cecilia

2012-01-01

Humans are animals that specialize in thinking and knowing, and our extraordinary cognitive abilities have transformed every aspect of our lives. In contrast to our chimpanzee cousins and Stone Age ancestors, we are complex political, economic, scientific and artistic creatures, living in a vast range of habitats, many of which are our own creation. Research on the evolution of human cognition asks what types of thinking make us such peculiar animals, and how they have been generated by evolutionary processes. New research in this field looks deeper into the evolutionary history of human cognition, and adopts a more multi-disciplinary approach than earlier ‘Evolutionary Psychology’. It is informed by comparisons between humans and a range of primate and non-primate species, and integrates findings from anthropology, archaeology, economics, evolutionary biology, neuroscience, philosophy and psychology. Using these methods, recent research reveals profound commonalities, as well striking differences, between human and non-human minds, and suggests that the evolution of human cognition has been much more gradual and incremental than previously assumed. It accords crucial roles to cultural evolution, techno-social co-evolution and gene–culture co-evolution. These have produced domain-general developmental processes with extraordinary power—power that makes human cognition, and human lives, unique. PMID:22734052

New thinking: the evolution of human cognition.

PubMed

Heyes, Cecilia

2012-08-05

Humans are animals that specialize in thinking and knowing, and our extraordinary cognitive abilities have transformed every aspect of our lives. In contrast to our chimpanzee cousins and Stone Age ancestors, we are complex political, economic, scientific and artistic creatures, living in a vast range of habitats, many of which are our own creation. Research on the evolution of human cognition asks what types of thinking make us such peculiar animals, and how they have been generated by evolutionary processes. New research in this field looks deeper into the evolutionary history of human cognition, and adopts a more multi-disciplinary approach than earlier 'Evolutionary Psychology'. It is informed by comparisons between humans and a range of primate and non-primate species, and integrates findings from anthropology, archaeology, economics, evolutionary biology, neuroscience, philosophy and psychology. Using these methods, recent research reveals profound commonalities, as well striking differences, between human and non-human minds, and suggests that the evolution of human cognition has been much more gradual and incremental than previously assumed. It accords crucial roles to cultural evolution, techno-social co-evolution and gene-culture co-evolution. These have produced domain-general developmental processes with extraordinary power-power that makes human cognition, and human lives, unique.

Deciphering Late-Pleistocence landscape evolution: linking proxies by combining pedo-stratigraphy and luminescence dating

NASA Astrophysics Data System (ADS)

Kreutzer, Sebastian; Meszner, Sascha; Faust, Dominik; Fuchs, Markus

2014-05-01

Interpreting former landscape evolution asks for understanding the processes that sculpt such landforms by means of deciphering complex systems. For reconstructing terrestrial Quaternary environments based on loess archives this might be considered, at least, as a three step process: (1) Identifying valuable records in appropriate morphological positions in a previously defined research area, (2) analysing the profiles by field work and laboratory methods and finally (3) linking the previously considered pseudo-isolated systems to set up a comprehensive picture. Especially the first and the last step might bring some pitfalls, as it is tempting to specify single records as pseudo-isolated, closed systems. They might be, with regard to their preservation in their specific morphological position, but in fact they are part of a complex, open system. Between 2008 and 2013, Late-Pleistocene loess archives in Saxony have been intensively investigated by field and laboratory methods. Linking pedo- and luminescence dating based chronostratigraphies, a composite profile for the entire Saxonian Loess Region has been established. With this, at least, two-fold approach we tried to avoid misinterpretations that might appear when focussing on one standard profile in an open morphological system. Our contribution focuses on this multi-proxy approach to decipher the Late-Pleistocene landscape evolution in the Saxonian Loess Region. Highlighting the challenges and advantages of combining different methods, we believe that (1) this multi-proxy approach is without alternative, (2) the combination of different profiles may simplify the more complex reality, but it may be a useful generalisation to understand and reveal the stratigraphical significance of the landscape evolution in this region.

Evolutionary dynamics on graphs: Efficient method for weak selection

NASA Astrophysics Data System (ADS)

Fu, Feng; Wang, Long; Nowak, Martin A.; Hauert, Christoph

2009-04-01

Investigating the evolutionary dynamics of game theoretical interactions in populations where individuals are arranged on a graph can be challenging in terms of computation time. Here, we propose an efficient method to study any type of game on arbitrary graph structures for weak selection. In this limit, evolutionary game dynamics represents a first-order correction to neutral evolution. Spatial correlations can be empirically determined under neutral evolution and provide the basis for formulating the game dynamics as a discrete Markov process by incorporating a detailed description of the microscopic dynamics based on the neutral correlations. This framework is then applied to one of the most intriguing questions in evolutionary biology: the evolution of cooperation. We demonstrate that the degree heterogeneity of a graph impedes cooperation and that the success of tit for tat depends not only on the number of rounds but also on the degree of the graph. Moreover, considering the mutation-selection equilibrium shows that the symmetry of the stationary distribution of states under weak selection is skewed in favor of defectors for larger selection strengths. In particular, degree heterogeneity—a prominent feature of scale-free networks—generally results in a more pronounced increase in the critical benefit-to-cost ratio required for evolution to favor cooperation as compared to regular graphs. This conclusion is corroborated by an analysis of the effects of population structures on the fixation probabilities of strategies in general 2×2 games for different types of graphs. Computer simulations confirm the predictive power of our method and illustrate the improved accuracy as compared to previous studies.

Machine Learning Biogeographic Processes from Biotic Patterns: A New Trait-Dependent Dispersal and Diversification Model with Model Choice By Simulation-Trained Discriminant Analysis.

PubMed

Sukumaran, Jeet; Economo, Evan P; Lacey Knowles, L

2016-05-01

Current statistical biogeographical analysis methods are limited in the ways ecology can be related to the processes of diversification and geographical range evolution, requiring conflation of geography and ecology, and/or assuming ecologies that are uniform across all lineages and invariant in time. This precludes the possibility of studying a broad class of macroevolutionary biogeographical theories that relate geographical and species histories through lineage-specific ecological and evolutionary dynamics, such as taxon cycle theory. Here we present a new model that generates phylogenies under a complex of superpositioned geographical range evolution, trait evolution, and diversification processes that can communicate with each other. We present a likelihood-free method of inference under our model using discriminant analysis of principal components of summary statistics calculated on phylogenies, with the discriminant functions trained on data generated by simulations under our model. This approach of model selection by classification of empirical data with respect to data generated under training models is shown to be efficient, robust, and performs well over a broad range of parameter space defined by the relative rates of dispersal, trait evolution, and diversification processes. We apply our method to a case study of the taxon cycle, that is testing for habitat and trophic level constraints in the dispersal regimes of the Wallacean avifaunal radiation. ©The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Dislocation density evolution of AA 7020-T6 investigated by in-situ synchrotron diffraction under tensile load

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

Zhong, Z.Y., E-mail: zhengye.zhong@hzg.de; Helmholtz-Zentrum Geesthacht, Max-Planck-Straße 1, D-21502 Geesthacht; Brokmeier, H.-G.

2015-10-15

The dislocation density evolution along the loading axis of a textured AA 7020-T6 aluminum alloy during uniaxial tension was investigated by in-situ synchrotron diffraction. The highly parallel synchrotron beam at the High Energy Materials Science beamline P07 in PETRA III, DESY, offers excellent conditions to separate different influences for line broadening from which micro-strains are obtained using the modified Williamson–Hall method which is also for defect density investigations. During tensile loading the dislocation density evolution was documented from the as-received material (initial micro-strain state) to the relaxation of the strains during elastic deformation. After yield, the increasing rate of dislocationmore » density growth was relatively fast till half-way between yield and UTS. After that, the rate started to decrease and the dislocation density fluctuated as the elongation increased due to the generation and annihilation of dislocations. When dislocation generation is dominant, the correlation between the flow stress and dislocation density satisfies the Taylor equation. Besides, a method to correct the thickness effect on peak broadening is developed in the present study. - Highlights: • In-situ synchrotron diffraction was applied to characterize peak broadening. • Dislocation evolution along the loading axis during uniaxial tension was investigated. • A method to correct the sample thickness effect on peak broadening was developed. • Dislocation density and flow stress satisfy the Taylor equation at a certain range. • The texture before load and after sample fracture was analyzed.« less

Method and system for hydrogen evolution and storage

DOEpatents

Thorn, David L.; Tumas, William; Hay, P. Jeffrey; Schwarz, Daniel E.; Cameron, Thomas M.

2012-12-11

A method and system for storing and evolving hydrogen (H.sub.2) employ chemical compounds that can be hydrogenated to store hydrogen and dehydrogenated to evolve hydrogen. A catalyst lowers the energy required for storing and evolving hydrogen. The method and system can provide hydrogen for devices that consume hydrogen as fuel.

Pursuing Darwin’s curious parallel: Prospects for a science of cultural evolution

PubMed Central

2017-01-01

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities. PMID:28739929

Pursuing Darwin's curious parallel: Prospects for a science of cultural evolution.

PubMed

Mesoudi, Alex

2017-07-24

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities.

An Equation-Free Reduced-Order Modeling Approach to Tropical Pacific Simulation

NASA Astrophysics Data System (ADS)

Wang, Ruiwen; Zhu, Jiang; Luo, Zhendong; Navon, I. M.

2009-03-01

The “equation-free” (EF) method is often used in complex, multi-scale problems. In such cases it is necessary to know the closed form of the required evolution equations about oscopic variables within some applied fields. Conceptually such equations exist, however, they are not available in closed form. The EF method can bypass this difficulty. This method can obtain oscopic information by implementing models at a microscopic level. Given an initial oscopic variable, through lifting we can obtain the associated microscopic variable, which may be evolved using Direct Numerical Simulations (DNS) and by restriction, we can obtain the necessary oscopic information and the projective integration to obtain the desired quantities. In this paper we apply the EF POD-assisted method to the reduced modeling of a large-scale upper ocean circulation in the tropical Pacific domain. The computation cost is reduced dramatically. Compared with the POD method, the method provided more accurate results and it did not require the availability of any explicit equations or the right-hand side (RHS) of the evolution equation.

ComplexContact: a web server for inter-protein contact prediction using deep learning.

PubMed

Zeng, Hong; Wang, Sheng; Zhou, Tianming; Zhao, Feifeng; Li, Xiufeng; Wu, Qing; Xu, Jinbo

2018-05-22

ComplexContact (http://raptorx2.uchicago.edu/ComplexContact/) is a web server for sequence-based interfacial residue-residue contact prediction of a putative protein complex. Interfacial residue-residue contacts are critical for understanding how proteins form complex and interact at residue level. When receiving a pair of protein sequences, ComplexContact first searches for their sequence homologs and builds two paired multiple sequence alignments (MSA), then it applies co-evolution analysis and a CASP-winning deep learning (DL) method to predict interfacial contacts from paired MSAs and visualizes the prediction as an image. The DL method was originally developed for intra-protein contact prediction and performed the best in CASP12. Our large-scale experimental test further shows that ComplexContact greatly outperforms pure co-evolution methods for inter-protein contact prediction, regardless of the species.

Dynamics of the human brain network revealed by time-frequency effective connectivity in fNIRS

PubMed Central

Vergotte, Grégoire; Torre, Kjerstin; Chirumamilla, Venkata Chaitanya; Anwar, Abdul Rauf; Groppa, Sergiu; Perrey, Stéphane; Muthuraman, Muthuraman

2017-01-01

Functional near infrared spectroscopy (fNIRS) is a promising neuroimaging method for investigating networks of cortical regions over time. We propose a directed effective connectivity method (TPDC) allowing the capture of both time and frequency evolution of the brain’s networks using fNIRS data acquired from healthy subjects performing a continuous finger-tapping task. Using this method we show the directed connectivity patterns among cortical motor regions involved in the task and their significant variations in the strength of information flow exchanges. Intra and inter-hemispheric connections during the motor task with their temporal evolution are also provided. Characterisation of the fluctuations in brain connectivity opens up a new way to assess the organisation of the brain to adapt to changing task constraints, or under pathological conditions. PMID:29188123

Simulations of Fluvial Landscapes

NASA Astrophysics Data System (ADS)

Cattan, D.; Birnir, B.

2013-12-01

The Smith-Bretherton-Birnir (SBB) model for fluvial landsurfaces consists of a pair of partial differential equations, one governing water flow and one governing the sediment flow. Numerical solutions of these equations have been shown to provide realistic models in the evolution of fluvial landscapes. Further analysis of these equations shows that they possess scaling laws (Hack's Law) that are known to exist in nature. However, the simulations are highly dependent on the numerical methods used; with implicit methods exhibiting the correct scaling laws, but the explicit methods fail to do so. These equations, and the resulting models, help to bridge the gap between the deterministic and the stochastic theories of landscape evolution. Slight modifications of the SBB equations make the results of the model more realistic. By modifying the sediment flow equation, the model obtains more pronounced meandering rivers. Typical landsurface with rivers.

Extremal Optimization: Methods Derived from Co-Evolution

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

Boettcher, S.; Percus, A.G.

1999-07-13

We describe a general-purpose method for finding high-quality solutions to hard optimization problems, inspired by self-organized critical models of co-evolution such as the Bak-Sneppen model. The method, called Extremal Optimization, successively eliminates extremely undesirable components of sub-optimal solutions, rather than ''breeding'' better components. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, Extremal Optimization improves on a single candidate solution by treating each of its components as species co-evolving according to Darwinian principles. Unlike Simulated Annealing, its non-equilibrium approach effects an algorithm requiring few parameters to tune. With only one adjustable parameter, its performance provesmore » competitive with, and often superior to, more elaborate stochastic optimization procedures. We demonstrate it here on two classic hard optimization problems: graph partitioning and the traveling salesman problem.« less

A comparative study of the evolution of the geographical ideas and measurements until the time of Eratosthenes

NASA Astrophysics Data System (ADS)

Pinotsis, Antonios D.

2005-04-01

We perform a comparative study of the evolution of the most important methods for geographical, carto-graphical and astronomical measurements developed by ancient Greek scientists and philosophers until the time of Eratosthenes. It seems that the novel geometrical method invented by Eratosthenes for the measurement of the size of the Earth did not appear suddenly but was the final outcome of long-lasting intellectual activity. It is shown that Anaximander, Pytheas, Eudoxus of Cnidus, Dicaearchus, Aristotle and Archimedes, the most famous ancient Greek philosopher astronomers and geographers before Eratosthenes, affected his thinking and contributed to his discovery. Furthermore, we briefly describe and explain the method of Eratosthenes, its significance, new errors that intruded into Eratosthenes’ measurement, as well as its application for the determination of the shape and the size of the Earth.

Detecting and Analyzing Genetic Recombination Using RDP4.

PubMed

Martin, Darren P; Murrell, Ben; Khoosal, Arjun; Muhire, Brejnev

2017-01-01

Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. The evolutionary value of recombination has been widely debated and so too has its influence on evolutionary analysis methods that assume nucleotide sequences replicate without recombining. When nucleic acids recombine, the evolution of the daughter or recombinant molecule cannot be accurately described by a single phylogeny. This simple fact can seriously undermine the accuracy of any phylogenetics-based analytical approach which assumes that the evolutionary history of a set of recombining sequences can be adequately described by a single phylogenetic tree. There are presently a large number of available methods and associated computer programs for analyzing and characterizing recombination in various classes of nucleotide sequence datasets. Here we examine the use of some of these methods to derive and test recombination hypotheses using multiple sequence alignments.

Niche-tracking migrants and niche-switching residents: evolution of climatic niches in New World warblers (Parulidae)

PubMed Central

Gómez, Camila; Tenorio, Elkin A.; Montoya, Paola; Cadena, Carlos Daniel

2016-01-01

Differences in life-history traits between tropical and temperate lineages are often attributed to differences in their climatic niche dynamics. For example, the more frequent appearance of migratory behaviour in temperate-breeding species than in species originally breeding in the tropics is believed to have resulted partly from tropical climatic stability and niche conservatism constraining tropical species from shifting their ranges. However, little is known about the patterns and processes underlying climatic niche evolution in migrant and resident animals. We evaluated the evolution of overlap in climatic niches between seasons and its relationship to migratory behaviour in the Parulidae, a family of New World passerine birds. We used ordination methods to measure seasonal niche overlap and niche breadth of 54 resident and 49 migrant species and used phylogenetic comparative methods to assess patterns of climatic niche evolution. We found that despite travelling thousands of kilometres, migrants tracked climatic conditions across the year to a greater extent than tropical residents. Migrant species had wider niches than resident species, although residents as a group occupied a wider climatic space and niches of migrants and residents overlapped extensively. Neither breeding latitude nor migratory distance explained variation among species in climatic niche overlap between seasons. Our findings support the notion that tropical species have narrower niches than temperate-breeders, but does not necessarily constrain their ability to shift or expand their geographical ranges and become migratory. Overall, the tropics may have been historically less likely to experience the suite of components that generate strong selection pressures for the evolution of migratory behaviour. PMID:26865303

Single-virion sequencing of lamivudine-treated HBV populations reveal population evolution dynamics and demographic history.

PubMed

Zhu, Yuan O; Aw, Pauline P K; de Sessions, Paola Florez; Hong, Shuzhen; See, Lee Xian; Hong, Lewis Z; Wilm, Andreas; Li, Chen Hao; Hue, Stephane; Lim, Seng Gee; Nagarajan, Niranjan; Burkholder, William F; Hibberd, Martin

2017-10-27

Viral populations are complex, dynamic, and fast evolving. The evolution of groups of closely related viruses in a competitive environment is termed quasispecies. To fully understand the role that quasispecies play in viral evolution, characterizing the trajectories of viral genotypes in an evolving population is the key. In particular, long-range haplotype information for thousands of individual viruses is critical; yet generating this information is non-trivial. Popular deep sequencing methods generate relatively short reads that do not preserve linkage information, while third generation sequencing methods have higher error rates that make detection of low frequency mutations a bioinformatics challenge. Here we applied BAsE-Seq, an Illumina-based single-virion sequencing technology, to eight samples from four chronic hepatitis B (CHB) patients - once before antiviral treatment and once after viral rebound due to resistance. With single-virion sequencing, we obtained 248-8796 single-virion sequences per sample, which allowed us to find evidence for both hard and soft selective sweeps. We were able to reconstruct population demographic history that was independently verified by clinically collected data. We further verified four of the samples independently through PacBio SMRT and Illumina Pooled deep sequencing. Overall, we showed that single-virion sequencing yields insight into viral evolution and population dynamics in an efficient and high throughput manner. We believe that single-virion sequencing is widely applicable to the study of viral evolution in the context of drug resistance and host adaptation, allows differentiation between soft or hard selective sweeps, and may be useful in the reconstruction of intra-host viral population demographic history.

Evolution of Geometric Sensitivity Derivatives from Computer Aided Design Models

NASA Technical Reports Server (NTRS)

Jones, William T.; Lazzara, David; Haimes, Robert

2010-01-01

The generation of design parameter sensitivity derivatives is required for gradient-based optimization. Such sensitivity derivatives are elusive at best when working with geometry defined within the solid modeling context of Computer-Aided Design (CAD) systems. Solid modeling CAD systems are often proprietary and always complex, thereby necessitating ad hoc procedures to infer parameter sensitivity. A new perspective is presented that makes direct use of the hierarchical associativity of CAD features to trace their evolution and thereby track design parameter sensitivity. In contrast to ad hoc methods, this method provides a more concise procedure following the model design intent and determining the sensitivity of CAD geometry directly to its respective defining parameters.

Three-dimensional microstructure simulation of Ni-based superalloy investment castings

NASA Astrophysics Data System (ADS)

Pan, Dong; Xu, Qingyan; Liu, Baicheng

2011-05-01

An integrated macro and micro multi-scale model for the three-dimensional microstructure simulation of Ni-based superalloy investment castings was developed, and applied to industrial castings to investigate grain evolution during solidification. A ray tracing method was used to deal with the complex heat radiation transfer. The microstructure evolution was simulated based on the Modified Cellular Automaton method, which was coupled with three-dimensional nested macro and micro grids. Experiments for Ni-based superalloy turbine wheel investment casting were carried out, which showed a good correspondence with the simulated results. It is indicated that the proposed model is able to predict the microstructure of the casting precisely, which provides a tool for the optimizing process.

Finding intrinsic rewards by embodied evolution and constrained reinforcement learning.

PubMed

Uchibe, Eiji; Doya, Kenji

2008-12-01

Understanding the design principle of reward functions is a substantial challenge both in artificial intelligence and neuroscience. Successful acquisition of a task usually requires not only rewards for goals, but also for intermediate states to promote effective exploration. This paper proposes a method for designing 'intrinsic' rewards of autonomous agents by combining constrained policy gradient reinforcement learning and embodied evolution. To validate the method, we use Cyber Rodent robots, in which collision avoidance, recharging from battery packs, and 'mating' by software reproduction are three major 'extrinsic' rewards. We show in hardware experiments that the robots can find appropriate 'intrinsic' rewards for the vision of battery packs and other robots to promote approach behaviors.

Computing element evolution towards Exascale and its impact on legacy simulation codes

NASA Astrophysics Data System (ADS)

Colin de Verdière, Guillaume J. L.

2015-12-01

In the light of the current race towards the Exascale, this article highlights the main features of the forthcoming computing elements that will be at the core of next generations of supercomputers. The market analysis, underlying this work, shows that computers are facing a major evolution in terms of architecture. As a consequence, it is important to understand the impacts of those evolutions on legacy codes or programming methods. The problems of dissipated power and memory access are discussed and will lead to a vision of what should be an exascale system. To survive, programming languages had to respond to the hardware evolutions either by evolving or with the creation of new ones. From the previous elements, we elaborate why vectorization, multithreading, data locality awareness and hybrid programming will be the key to reach the exascale, implying that it is time to start rewriting codes.

[Prediction method of rural landscape pattern evolution based on life cycle: a case study of Jinjing Town, Hunan Province, China].

PubMed

Ji, Xiang; Liu, Li-Ming; Li, Hong-Qing

2014-11-01

Taking Jinjing Town in Dongting Lake area as a case, this paper analyzed the evolution of rural landscape patterns by means of life cycle theory, simulated the evolution cycle curve, and calculated its evolution period, then combining CA-Markov model, a complete prediction model was built based on the rule of rural landscape change. The results showed that rural settlement and paddy landscapes of Jinjing Town would change most in 2020, with the rural settlement landscape increased to 1194.01 hm2 and paddy landscape greatly reduced to 3090.24 hm2. The quantitative and spatial prediction accuracies of the model were up to 99.3% and 96.4%, respectively, being more explicit than single CA-Markov model. The prediction model of rural landscape patterns change proposed in this paper would be helpful for rural landscape planning in future.

Quantum gates by periodic driving.

PubMed

Shi, Z C; Wang, W; Yi, X X

2016-02-25

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions-it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation.

Structural evolution and properties of small-size thiol-protected gold nanoclusters

NASA Astrophysics Data System (ADS)

Ma, Miaomiao; Liu, Liren; Zhu, Hengjiang; Lu, Junzhe; Tan, Guiping

2018-07-01

Ligand-protected gold clusters are widely used in biosensors and catalysis. Understanding the structural evolution of these kinds of nanoclusters is important for experimental synthesis. Herein, based on the particle swarm optimisation algorithm and density functional theory method, we use [Au1(SH)2]n, [Au2(SH)3]n, [Au3(SH)4]n (n = 1-3) as basic units to research the structural evolution relationships from building blocks to the final whole structures. Results show that there is a 'line-ring-core' structural evolution pattern in the growth process of the nanoclusters. The core structures of the ligand-protected gold clusters consist of Au3, Au4, Au6 and Au7 atoms. The electronics and optics analysis reflects that stability and optical properties gradually enhance with increase in size. These results can be used to understand the initial growth stage and design new ligand-protected nanoclusters.

Unitary evolution of the quantum Universe with a Brown-Kuchař dust

NASA Astrophysics Data System (ADS)

Maeda, Hideki

2015-12-01

We study the time evolution of a wave function for the spatially flat Friedmann-Lemaître-Robertson-Walker Universe governed by the Wheeler-DeWitt equation in both analytical and numerical methods. We consider a Brown-Kuchař dust as a matter field in order to introduce a ‘clock’ in quantum cosmology and adopt the Laplace-Beltrami operator-ordering. The Hamiltonian operator admits an infinite number of self-adjoint extensions corresponding to a one-parameter family of boundary conditions at the origin in the minisuperspace. For any value of the extension parameter in the boundary condition, the evolution of a wave function is unitary and the classical initial singularity is avoided and replaced by the big bounce in the quantum system. Exact wave functions show that the expectation value of the spatial volume of the Universe obeys the classical-time evolution in the late time but its variance diverges.

Transfer of electrical space charge from corona between ground and thundercloud: Measurements and modeling

NASA Technical Reports Server (NTRS)

Soula, Serge

1994-01-01

The evolution of the vertical electric field profile deduced from simultaneous field measurements at several levels below a thundercloud shows the development of a space charge layer at least up to 600 m. The average charge density in the whole layer from 0 m to 600 m can reach about 1 nC m(exp -3). The ions are generated at the ground by corona effect and the production rate is evaluated with a new method from the comparison of field evolutions at the ground and at altitude after a lightning flash. The modeling of the relevant processes shows tht ground corona accounts for the observed field evolutions and that the aerosol particles concentration has a very large effect on the evolution of corona ions. However, with a realistic value for this concentration a large amount of ground corona ions reach the level of 600 m.

Phylomemetic patterns in science evolution--the rise and fall of scientific fields.

PubMed

Chavalarias, David; Cointet, Jean-Philippe

2013-01-01

We introduce an automated method for the bottom-up reconstruction of the cognitive evolution of science, based on big-data issued from digital libraries, and modeled as lineage relationships between scientific fields. We refer to these dynamic structures as phylomemetic networks or phylomemies, by analogy with biological evolution; and we show that they exhibit strong regularities, with clearly identifiable phylomemetic patterns. Some structural properties of the scientific fields - in particular their density -, which are defined independently of the phylomemy reconstruction, are clearly correlated with their status and their fate in the phylomemy (like their age or their short term survival). Within the framework of a quantitative epistemology, this approach raises the question of predictibility for science evolution, and sketches a prototypical life cycle of the scientific fields: an increase of their cohesion after their emergence, the renewal of their conceptual background through branching or merging events, before decaying when their density is getting too low.

Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

PubMed Central

Tsuboi, Masahito; Gonzalez-Voyer, Alejandro; Kolm, Niclas

2015-01-01

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution. PMID:25948565

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae

PubMed Central

Chaguza, Chrispin; Cornick, Jennifer E.; Everett, Dean B.

2015-01-01

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus. PMID:25904996

Mechanisms and impact of genetic recombination in the evolution of Streptococcus pneumoniae.

PubMed

Chaguza, Chrispin; Cornick, Jennifer E; Everett, Dean B

2015-01-01

Streptococcus pneumoniae (the pneumococcus) is a highly recombinogenic bacterium responsible for a high burden of human disease globally. Genetic recombination, a process in which exogenous DNA is acquired and incorporated into its genome, is a key evolutionary mechanism employed by the pneumococcus to rapidly adapt to selective pressures. The rate at which the pneumococcus acquires genetic variation through recombination is much higher than the rate at which the organism acquires variation through spontaneous mutations. This higher rate of variation allows the pneumococcus to circumvent the host innate and adaptive immune responses, escape clinical interventions, including antibiotic therapy and vaccine introduction. The rapid influx of whole genome sequence (WGS) data and the advent of novel analysis methods and powerful computational tools for population genetics and evolution studies has transformed our understanding of how genetic recombination drives pneumococcal adaptation and evolution. Here we discuss how genetic recombination has impacted upon the evolution of the pneumococcus.

Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids.

PubMed

Tsuboi, Masahito; Gonzalez-Voyer, Alejandro; Kolm, Niclas

2015-05-01

Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using a combination of geometric morphometrics and a recently developed phylogenetic comparative method, we found that head morphology evolution was 43% faster in substrate guarding species than in mouthbrooding species. Furthermore, for species in which females were solely responsible for mouthbrooding the males had a higher rate of head morphology evolution than in those with bi-parental mouthbrooding. Our results support the hypothesis that adaptations resulting in functional coupling constrain phenotypic evolution.

Gradual plasmon evolution and huge infrared near-field enhancement of metallic bridged nanoparticle dimers.

PubMed

Huang, Yu; Ma, Lingwei; Hou, Mengjing; Xie, Zheng; Zhang, Zhengjun

2016-01-28

By three-dimensional (3D) finite element method (FEM) plasmon mapping, gradual plasmon evolutions of both bonding dipole plasmon (BDP) and charge transfer plasmon (CTP) modes are visualized. In particular, the evolved BDP mode provides a physical insight into the rapid degeneration of electromagnetic hot spots in practical applications, while the rising CTP mode enables a huge near-field enhancement for potential plasmonic devices at infrared wavelengths.

Gravitational field calculations on a dynamic lattice by distributed computing.

NASA Astrophysics Data System (ADS)

Mähönen, P.; Punkka, V.

A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing

NASA Astrophysics Data System (ADS)

Mähönen, Petri; Punkka, Veikko

A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.

Modeling the hydrogeophysical response of lake talik evolution

USGS Publications Warehouse

Minsley, Burke J.; Wellman, Tristan; Walvoord, Michelle Ann; Revil, Andre

2014-01-01

Geophysical methods provide valuable information about subsurface permafrost and its relation to dynamic hydrologic systems. Airborne electromagnetic data from interior Alaska are used to map the distribution of permafrost, geological features, surface water, and groundwater. To validate and gain further insight into these field datasets, we also explore the geophysical response to hydrologic simulations of permafrost evolution by implementing a physical property relationship that connects geology, temperature, and ice saturation to changes in electrical properties.

Textural Evolution During Micro Direct Metal Deposition of NiTi Alloy

NASA Astrophysics Data System (ADS)

Khademzadeh, Saeed; Bariani, Paolo F.; Bruschi, Stefania

2018-03-01

In this research, a micro direct metal deposition process, newly developed as a potential method for micro additive manufacturing was used to fabricate NiTi builds. The effect of scanning strategy on grain growth and textural evolution was investigated using scanning electron microscope equipped with electron backscattered diffraction detector. Investigations showed that, the angle between the successive single tracks has an important role in grain size distribution and textural evolution of NiTi phase. Unidirectional laser beam scanning pattern developed a fiber texture; conversely, a backward and forward scanning pattern developed a strong < {100} > ‖‖ RD texture on the surface of NiTi cubic samples produced by micro direct metal deposition.

Bioprosthetic Mesh in Abdominal Wall Reconstruction

PubMed Central

Baumann, Donald P.; Butler, Charles E.

2012-01-01

Mesh materials have undergone a considerable evolution over the last several decades. There has been enhancement of biomechanical properties, improvement in manufacturing processes, and development of antiadhesive laminate synthetic meshes. The evolution of bioprosthetic mesh materials has markedly changed our indications and methods for complex abdominal wall reconstruction. The authors review the optimal properties of bioprosthetic mesh materials, their evolution over time, and their indications for use. The techniques to optimize outcomes are described using bioprosthetic mesh for complex abdominal wall reconstruction. Bioprosthetic mesh materials clearly have certain advantages over other implantable mesh materials in select indications. Appropriate patient selection and surgical technique are critical to the successful use of bioprosthetic materials for abdominal wall repair. PMID:23372454

Textural Evolution During Micro Direct Metal Deposition of NiTi Alloy

NASA Astrophysics Data System (ADS)

Khademzadeh, Saeed; Bariani, Paolo F.; Bruschi, Stefania

2018-07-01

In this research, a micro direct metal deposition process, newly developed as a potential method for micro additive manufacturing was used to fabricate NiTi builds. The effect of scanning strategy on grain growth and textural evolution was investigated using scanning electron microscope equipped with electron backscattered diffraction detector. Investigations showed that, the angle between the successive single tracks has an important role in grain size distribution and textural evolution of NiTi phase. Unidirectional laser beam scanning pattern developed a fiber texture; conversely, a backward and forward scanning pattern developed a strong < {100} > ‖‖ RD texture on the surface of NiTi cubic samples produced by micro direct metal deposition.

Dynamics of entanglement between two atomic samples with spontaneous scattering

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

Di Lisi, Antonio; De Siena, Silvio; Illuminati, Fabrizio

2004-07-01

We investigate the effects of spontaneous scattering on the evolution of entanglement of two atomic samples, probed by phase-shift measurements on optical beams interacting with both samples. We develop a formalism of conditional quantum evolutions and present a wave function analysis implemented in numerical simulations of the state vector dynamics. This method allows us to track the evolution of entanglement and to compare it with the predictions obtained when spontaneous scattering is neglected. We provide numerical evidence that the interferometric scheme to entangle atomic samples is only marginally affected by the presence of spontaneous scattering and should thus be robustmore » even in more realistic situations.« less

Engineering microbes for efficient production of chemicals

DOEpatents

Gong, Wei; Dole, Sudhanshu; Grabar, Tammy; Collard, Andrew Christopher; Pero, Janice G; Yocum, R Rogers

2015-04-28

This present invention relates to production of chemicals from microorganisms that have been genetically engineered and metabolically evolved. Improvements in chemical production have been established, and particular mutations that lead to those improvements have been identified. Specific examples are given in the identification of mutations that occurred during the metabolic evolution of a bacterial strain genetically engineered to produce succinic acid. This present invention also provides a method for evaluating the industrial applicability of mutations that were selected during the metabolic evolution for increased succinic acid production. This present invention further provides microorganisms engineered to have mutations that are selected during metabolic evolution and contribute to improved production of succinic acid, other organic acids and other chemicals of commercial interest.

Optimizing romanian maritime coastline using mathematical model Litpack

NASA Astrophysics Data System (ADS)

Anton, I. A.; Panaitescu, M.; Panaitescu, F. V.

2017-08-01

There are many methods and tools to study shoreline change in coastal engineering. LITPACK is a numerical model included in MIKE software developed by DHI (Danish Hydraulic Institute). With this matehematical model we can simulate coastline evolution and profile along beach. Research and methodology: the paper contents location of the study area, the current status of Midia-Mangalia shoreline, protection objectives, the changes of shoreline after having protected constructions. In this paper are presented numerical and graphycal results obtained with this model for studying the romanian maritime coastline in area MIDIA-MANGALIA: non-cohesive sediment transport, long-shore current and littoral drift, coastline evolution, crossshore profile evolution, the development of the coastline position in time.

Formation Stellaire Aux Échelles Des Galaxies

NASA Astrophysics Data System (ADS)

Boissier, S.

2012-12-01

Star Formation is at the very core of the evolution of galaxies. From their gas reservoir (filled by infall or fusions), stars form at the "Star Formation Rate" (SFR), with an enormous impact on many aspects of the evolution of galaxies. This HDR presents first the formalism concerning star formation (SFR, IMF), some theoretical suggestions on physical processes that may affect star formation on various galactic scales, and the methods used to determine the SFR from observations. A large part is dedicated to the "Star Formation Laws" (e.g. Schmidt law) on various scales (local, radial, and global law). Finally, the last part concerns the largest scales (evolution of the "cosmic" SFR and effect of the environment).

Modeling of Microstructure Evolution During Alloy Solidification

NASA Astrophysics Data System (ADS)

Zhu, Mingfang; Pan, Shiyan; Sun, Dongke

In recent years, considerable advances have been achieved in the numerical modeling of microstructure evolution during solidification. This paper presents the models based on the cellular automaton (CA) technique and lattice Boltzmann method (LBM), which can reproduce a wide variety of solidification microstructure features observed experimentally with an acceptable computational efficiency. The capabilities of the models are addressed by presenting representative examples encompassing a broad variety of issues, such as the evolution of dendritic structure and microsegregation in two and three dimensions, dendritic growth in the presence of convection, divorced eutectic solidification of spheroidal graphite irons, and gas porosity formation. The simulations offer insights into the underlying physics of microstructure formation during alloy solidification.

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.

Spectral evolution of weakly nonlinear random waves: kinetic description vs direct numerical simulations

NASA Astrophysics Data System (ADS)

Annenkov, Sergei; Shrira, Victor

2016-04-01

We study numerically the long-term evolution of water wave spectra without wind forcing, using three different models, aiming at understanding the role of different sets of assumptions. The first model is the classical Hasselmann kinetic equation (KE). We employ the WRT code kindly provided by G. van Vledder. Two other models are new. As the second model, we use the generalised kinetic equation (gKE), derived without the assumption of quasi-stationarity. Thus, unlike the KE, the gKE is valid in the cases when a wave spectrum is changing rapidly (e.g. at the initial stage of evolution of a narrow spectrum). However, the gKE employs the same statistical closure as the KE. The third model is based on the Zakharov integrodifferential equation for water waves and does not depend on any statistical assumptions. Since the Zakharov equation plays the role of the primitive equation of the theory of wave turbulence, we refer to this model as direct numerical simulation of spectral evolution (DNS-ZE). For initial conditions, we choose two narrow-banded spectra with the same frequency distribution (a JONSWAP spectrum with high peakedness γ = 6) and different degrees of directionality. These spectra are from the set of observations collected in a directional wave tank by Onorato et al (2009). Spectrum A is very narrow in angle (corresponding to N = 840 in the cosN directional model). Spectrum B is initially wider in angle (corresponds to N = 24). Short-term evolution of both spectra (O(102) wave periods) has been studied numerically by Xiao et al (2013) using two other approaches (broad-band modified nonlinear Schrödinger equation and direct numerical simulation based on the high-order spectral method). We use these results to verify the initial stage of our DNS-ZE simulations. However, the advantage of the DNS-ZE method is that it allows to study long-term spectral evolution (up to O(104) periods), which was previously possible only with the KE. In the short-term evolution, we find a good agreement between our DNS-ZE results and simulations by Xiao et al (2013), both for the evolution of frequency spectra and for the directional spreading. In the long term, all three approaches demonstrate very close evolution of integral characteristics of spectra, approaching for large time the theoretical asymptotes of the self-similar stage of evolution. However, the detailed comparison of the spectral evolution shows certain notable differences. Both kinetic equations give virtually identical evolution of spectrum B, but in the case of initially nearly one-dimensional spectrum A the KE overestimates the amplitude of the spectral peak. Meanwhile, the DNS-ZE results show considerably wider spectra with less pronounced peak. There is a striking difference for the rate of spectral broadening, which is much larger for the gKE and especially for the KE, than for the DNS-ZE. We show that the rates of change of the spectra obtained with the DNS-ZE are proportional to the fourth power of nonlinearity, corresponding to the dynamical timescale of evolution, rather than the statistical timescale of both kinetic equations.

Dynamic evolutionary change in post-Paleozoic echinoids and the importance of scale when interpreting changes in rates of evolution

PubMed Central

Hopkins, Melanie J.; Smith, Andrew B.

2015-01-01

How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with “early bursts” of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today’s oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis. PMID:25713369

Is sociality required for the evolution of communicative complexity? Evidence weighed against alternative hypotheses in diverse taxonomic groups

PubMed Central

Ord, Terry J.; Garcia-Porta, Joan

2012-01-01

Complex social communication is expected to evolve whenever animals engage in many and varied social interactions; that is, sociality should promote communicative complexity. Yet, informal comparisons among phylogenetically independent taxonomic groups seem to cast doubt on the putative role of social factors in the evolution of complex communication. Here, we provide a formal test of the sociality hypothesis alongside alternative explanations for the evolution of communicative complexity. We compiled data documenting variations in signal complexity among closely related species for several case study groups—ants, frogs, lizards and birds—and used new phylogenetic methods to investigate the factors underlying communication evolution. Social factors were only implicated in the evolution of complex visual signals in lizards. Ecology, and to some degree allometry, were most likely explanations for complexity in the vocal signals of frogs (ecology) and birds (ecology and allometry). There was some evidence for adaptive evolution in the pheromone complexity of ants, although no compelling selection pressure was identified. For most taxa, phylogenetic null models were consistently ranked above adaptive models and, for some taxa, signal complexity seems to have accumulated in species via incremental or random changes over long periods of evolutionary time. Becoming social presumably leads to the origin of social communication in animals, but its subsequent influence on the trajectory of signal evolution has been neither clear-cut nor general among taxonomic groups. PMID:22641820

Flashback: Comparing Two Approaches to Teaching World History.

ERIC Educational Resources Information Center

Khazzaka, Joseph

1997-01-01

Discusses the "flashback" method of history instruction that begins with analyzing specific, current conditions and then traces their historical evolution. This method allows students to feel connected to the subject while participating in its historical investigation. Compares the "flashback" and the traditional chronological…

Launch window analysis of satellites in high eccentricity or large circular orbits

NASA Technical Reports Server (NTRS)

Renard, M. L.; Bhate, S. K.; Sridharan, R.

1973-01-01

Numerical methods and computer programs for studying the stability and evolution of orbits of large eccentricity are presented. Methods for determining launch windows and target dates are developed. Mathematical models are prepared to analyze the characteristics of specific missions.

An analysis of factors influencing the teaching of biological evolution in Louisiana public secondary schools

NASA Astrophysics Data System (ADS)

Aguillard, Donald Wayne

Louisiana public school biology teachers were surveyed to investigate their attitudes toward biological evolution. A mixed method investigation was employed using a questionnaire and open-ended interviews. Results obtained from 64 percent of the sample receiving the questionnaire indicate that although teachers endorse the study of evolution as important, instructional time allocated to evolution is disproportionate with its status as a unifying concept of science. Two variables, number of college courses specifically devoted to evolution and number of semester credit hours in biology, produced a significant correlation with emphasis placed on evolution. The data suggest that teachers' knowledge base emerged as the most significant factor in determining degree of classroom emphasis on evolution. The data suggest a need for substantive changes in the training of biology teachers. Thirty-five percent of teachers reported pursuing fewer than 20 semester credit hours in biology and 68 percent reported fewer than three college courses in which evolution was specifically discussed. Fifty percent reported a willingness to undergo additional training about evolution. In spite of the fact that evolution has been identified as a major conceptual theme across all of the sciences, there is strong evidence that Louisiana biology teachers de-emphasize evolutionary theory. Even when biology teachers allocate instructional time to evolutionary theory, many avoid discussion of human evolution. The research data show that only ten percent of teachers reported allocating more than sixty minutes of instructional time to human evolution. Louisiana biology teachers were found to hold extreme views on the subject of creationism as a component of the biology curriculum. Twenty-nine percent indicated that creationism should be taught in high school biology and 25--35 percent allocated instructional time to discussions of creationism. Contributing to the de-emphasis of evolutionary theory, as a unifying theme of biology, is the courtesy extended to classroom teachers to determine what topics are emphasized. The inclusion of evolution in curriculum documents is not sufficient to ensure that evolutionary theory is regarded as a unifying theme of biology. School administrators, science supervisors, and local school boards have a clear responsibility to articulate strong support for requiring classroom discussions of evolutionary theory.

Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test.

PubMed

Berlin, Sofia; Smith, Nick G C

2005-11-10

Adaptive evolution appears to be a common feature of reproductive proteins across a very wide range of organisms. A promising way of addressing the evolutionary forces responsible for this general phenomenon is to test for adaptive evolution in the same gene but among groups of species, which differ in their reproductive biology. One can then test evolutionary hypotheses by asking whether the variation in adaptive evolution is consistent with the variation in reproductive biology. We have attempted to apply this approach to the study of a female reproductive protein, zona pellucida C (ZPC), which has been previously shown by the use of likelihood ratio tests (LRTs) to be under positive selection in mammals. We tested for evidence of adaptive evolution of ZPC in 15 mammalian species, in 11 avian species and in six fish species using three different LRTs (M1a-M2a, M7-M8, and M8a-M8). The only significant findings of adaptive evolution came from the M7-M8 test in mammals and fishes. Since LRTs of adaptive evolution may yield false positives in some situations, we examined the properties of the LRTs by several different simulation methods. When we simulated data to test the robustness of the LRTs, we found that the pattern of evolution in ZPC generates an excess of false positives for the M7-M8 LRT but not for the M1a-M2a or M8a-M8 LRTs. This bias is strong enough to have generated the significant M7-M8 results for mammals and fishes. We conclude that there is no strong evidence for adaptive evolution of ZPC in any of the vertebrate groups we studied, and that the M7-M8 LRT can be biased towards false inference of adaptive evolution by certain patterns of non-adaptive evolution.

Adapting clinical paradigms to the challenges of cancer clonal evolution.

PubMed

Murugaesu, Nirupa; Chew, Su Kit; Swanton, Charles

2013-06-01

Emerging evidence suggests that cancer branched evolution may affect biomarker validation, clinical outcome, and emergence of drug resistance. The changing spatial and temporal nature of cancer subclonal architecture during the disease course suggests the need for longitudinal prospective studies of cancer evolution and robust and clinically implementable pathologic definitions of intratumor heterogeneity, genetic diversity, and chromosomal instability. Furthermore, subclonal heterogeneous events in tumors may evade detection through conventional biomarker strategies and influence clinical outcome. Minimally invasive methods for the study of cancer evolution and new approaches to clinical study design, incorporating understanding of the dynamics of tumor clonal architectures through treatment and during acquisition of drug resistance, have been suggested as important areas for development. Coordinated efforts will be required by the scientific and clinical trial communities to adapt to the challenges of detecting infrequently occurring somatic events that may influence clinical outcome and to understand the dynamics of cancer evolution and the waxing and waning of tumor subclones over time in advanced metastatic epithelial malignancies. Copyright © 2013 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.

Spatiotemporal evolution of the chlorophyll a trend in the North Atlantic Ocean.

PubMed

Zhang, Min; Zhang, Yuanling; Shu, Qi; Zhao, Chang; Wang, Gang; Wu, Zhaohua; Qiao, Fangli

2018-01-15

Analyses of the chlorophyll a concentration (chla) from satellite ocean color products have suggested the decadal-scale variability of chla linked to the climate change. The decadal-scale variability in chla is both spatially and temporally non-uniform. We need to understand the spatiotemporal evolution of chla in decadal or multi-decadal timescales to better evaluate its linkage to climate variability. Here, the spatiotemporal evolution of the chla trend in the North Atlantic Ocean for the period 1997-2016 is analyzed using the multidimensional ensemble empirical mode decomposition method. We find that this variable trend signal of chla shows a dipole pattern between the subpolar gyre and along the Gulf Stream path, and propagation along the opposite direction of the North Atlantic Current. This propagation signal has an overlapping variability of approximately twenty years. Our findings suggest that the spatiotemporal evolution of chla during the two most recent decades is part of the multidecadal variations and possibly regulated by the changes of Atlantic Meridional Overturning Circulation, whereas the mechanisms of such evolution patterns still need to be explored. Copyright © 2017 Elsevier B.V. All rights reserved.

Atomic scale modeling of defect production and microstructure evolution in irradiated metals

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

Diaz de la Rubia, T.; Soneda, N.; Shimomura, Y.

1997-04-01

Irradiation effects in materials depend in a complex way on the form of the as-produced primary damage state and its spatial and temporal evolution. Thus, while collision cascades produce defects on a time scale of tens of picosecond, diffusion occurs over much longer time scales, of the order of seconds, and microstructure evolution over even longer time scales. In this report the authors present work aimed at describing damage production and evolution in metals across all the relevant time and length scales. They discuss results of molecular dynamics simulations of displacement cascades in Fe and V. They show that interstitialmore » clusters are produced in cascades above 5 keV, but not vacancy clusters. Next, they discuss the development of a kinetic Monte Carlo model that enables calculations of damage evolution over much longer time scales (1000`s of s) than the picosecond lifetime of the cascade. They demonstrate the applicability of the method by presenting predictions on the fraction of freely migrating defects in {alpha}Fe during irradiation at 600 K.« less

Prereduction of Metal Oxides via Carbon Plasma Treatment for Efficient and Stable Electrocatalytic Hydrogen Evolution.

PubMed

Zhang, Yongqi; Ouyang, Bo; Xu, Kun; Xia, Xinhui; Zhang, Zheng; Rawat, Rajdeep Singh; Fan, Hong Jin

2018-04-01

Prereduction of transition metal oxides is a feasible and efficient strategy to enhance their catalytic activity for hydrogen evolution. Unfortunately, the prereduction via the common H 2 annealing method is unstable for nanomaterials during the hydrogen evolution process. Here, using NiMoO 4 nanowire arrays as the example, it is demonstrated that carbon plasma (C-plasma) treatment can greatly enhance both the catalytic activity and the long-term stability of transition metal oxides for hydrogen evolution. The C-plasma treatment has two functions at the same time: it induces partial surface reduction of the NiMoO 4 nanowire to form Ni 4 Mo nanoclusters, and simultaneously deposits a thin graphitic carbon shell. As a result, the C-plasma treated NiMoO 4 can maintain its array morphology, chemical composition, and catalytic activity during long-term intermittent hydrogen evolution process. This work may pave a new way for simultaneous activation and stabilization of transition metal oxide-based electrocatalysts. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Tracking the origin and divergence of cholinesterases and neuroligins: the evolution of synaptic proteins.

PubMed

Lenfant, Nicolas; Hotelier, Thierry; Bourne, Yves; Marchot, Pascale; Chatonnet, Arnaud

2014-07-01

A cholinesterase activity can be found in all kingdoms of living organism, yet cholinesterases involved in cholinergic transmission appeared only recently in the animal phylum. Among various proteins homologous to cholinesterases, one finds neuroligins. These proteins, with an altered catalytic triad and no known hydrolytic activity, display well-identified cell adhesion properties. The availability of complete genomes of a few metazoans provides opportunities to evaluate when these two protein families emerged during evolution. In bilaterian animals, acetylcholinesterase co-localizes with proteins of cholinergic synapses while neuroligins co-localize and may interact with proteins of excitatory glutamatergic or inhibitory GABAergic/glycinergic synapses. To compare evolution of the cholinesterases and neuroligins with other proteins involved in the architecture and functioning of synapses, we devised a method to search for orthologs of these partners in genomes of model organisms representing distinct stages of metazoan evolution. Our data point to a progressive recruitment of synaptic components during evolution. This finding may shed light on the common or divergent developmental regulation events involved into the setting and maintenance of the cholinergic versus glutamatergic and GABAergic/glycinergic synapses.