evolution code comparison: Topics by Science.gov

Sample records for evolution code comparison

MOCCA code for star cluster simulation: comparison with optical observations using COCOA

NASA Astrophysics Data System (ADS)

Askar, Abbas; Giersz, Mirek; Pych, Wojciech; Olech, Arkadiusz; Hypki, Arkadiusz

2016-02-01

We introduce and present preliminary results from COCOA (Cluster simulatiOn Comparison with ObservAtions) code for a star cluster after 12 Gyr of evolution simulated using the MOCCA code. The COCOA code is being developed to quickly compare results of numerical simulations of star clusters with observational data. We use COCOA to obtain parameters of the projected cluster model. For comparison, a FITS file of the projected cluster was provided to observers so that they could use their observational methods and techniques to obtain cluster parameters. The results show that the similarity of cluster parameters obtained through numerical simulations and observations depends significantly on the quality of observational data and photometric accuracy.
A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

DOE PAGES

Motl, Patrick M.; Frank, Juhan; Staff, Jan; ...

2017-03-29

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume "grid" code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code aremore » chosen to match as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. Here, we also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less
A Comparison of Three Elliptical Galaxy Photochemical Evolution Codes

NASA Astrophysics Data System (ADS)

Gibson, Brad K.

1996-09-01

Working within the classic supernovae-driven wind framework for elliptical galaxy evolution, We perform a systematic investigation into the discrepancies between the predictions of three contemporary codes (by Arimoto & Yoshii, Bressan et al., and Gibson). By being primarily concerned with reproducing the present-day color-metallicity-luminosity (CML) relations among elliptical galaxies, the approaches taken in the theoretical modeling have managed to obscure many of the hidden differences between the codes. Targeting the timescale for the onset of the initial galactic wind, t_GW_, as a primary "difference" indicator, We demonstrate exactly how and why each code is able to claim successful reproduction of the CML relations, despite possessing apparently incompatible input ingredients.
The Evolution and Expression Pattern of Human Overlapping lncRNA and Protein-coding Gene Pairs.

PubMed

Ning, Qianqian; Li, Yixue; Wang, Zhen; Zhou, Songwen; Sun, Hong; Yu, Guangjun

2017-03-27

Long non-coding RNA overlapping with protein-coding gene (lncRNA-coding pair) is a special type of overlapping genes. Protein-coding overlapping genes have been well studied and increasing attention has been paid to lncRNAs. By studying lncRNA-coding pairs in human genome, we showed that lncRNA-coding pairs were more likely to be generated by overprinting and retaining genes in lncRNA-coding pairs were given higher priority than non-overlapping genes. Besides, the preference of overlapping configurations preserved during evolution was based on the origin of lncRNA-coding pairs. Further investigations showed that lncRNAs promoting the splicing of their embedded protein-coding partners was a unilateral interaction, but the existence of overlapping partners improving the gene expression was bidirectional and the effect was decreased with the increased evolutionary age of genes. Additionally, the expression of lncRNA-coding pairs showed an overall positive correlation and the expression correlation was associated with their overlapping configurations, local genomic environment and evolutionary age of genes. Comparison of the expression correlation of lncRNA-coding pairs between normal and cancer samples found that the lineage-specific pairs including old protein-coding genes may play an important role in tumorigenesis. This work presents a systematically comprehensive understanding of the evolution and the expression pattern of human lncRNA-coding pairs.
A Comparison of Grid-based and SPH Binary Mass-transfer and Merger Simulations

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

Motl, Patrick M.; Frank, Juhan; Clayton, Geoffrey C.

2017-04-01

There is currently a great amount of interest in the outcomes and astrophysical implications of mergers of double degenerate binaries. In a commonly adopted approximation, the components of such binaries are represented by polytropes with an index of n = 3/2. We present detailed comparisons of stellar mass-transfer and merger simulations of polytropic binaries that have been carried out using two very different numerical algorithms—a finite-volume “grid” code and a smoothed-particle hydrodynamics (SPH) code. We find that there is agreement in both the ultimate outcomes of the evolutions and the intermediate stages if the initial conditions for each code are chosen to matchmore » as closely as possible. We find that even with closely matching initial setups, the time it takes to reach a concordant evolution differs between the two codes because the initial depth of contact cannot be matched exactly. There is a general tendency for SPH to yield higher mass transfer rates and faster evolution to the final outcome. We also present comparisons of simulations calculated from two different energy equations: in one series, we assume a polytropic equation of state and in the other series an ideal gas equation of state. In the latter series of simulations, an atmosphere forms around the accretor, which can exchange angular momentum and cause a more rapid loss of orbital angular momentum. In the simulations presented here, the effect of the ideal equation of state is to de-stabilize the binary in both SPH and grid simulations, but the effect is more pronounced in the grid code.« less
Million-body star cluster simulations: comparisons between Monte Carlo and direct N-body

NASA Astrophysics Data System (ADS)

Rodriguez, Carl L.; Morscher, Meagan; Wang, Long; Chatterjee, Sourav; Rasio, Frederic A.; Spurzem, Rainer

2016-12-01

We present the first detailed comparison between million-body globular cluster simulations computed with a Hénon-type Monte Carlo code, CMC, and a direct N-body code, NBODY6++GPU. Both simulations start from an identical cluster model with 106 particles, and include all of the relevant physics needed to treat the system in a highly realistic way. With the two codes `frozen' (no fine-tuning of any free parameters or internal algorithms of the codes) we find good agreement in the overall evolution of the two models. Furthermore, we find that in both models, large numbers of stellar-mass black holes (>1000) are retained for 12 Gyr. Thus, the very accurate direct N-body approach confirms recent predictions that black holes can be retained in present-day, old globular clusters. We find only minor disagreements between the two models and attribute these to the small-N dynamics driving the evolution of the cluster core for which the Monte Carlo assumptions are less ideal. Based on the overwhelming general agreement between the two models computed using these vastly different techniques, we conclude that our Monte Carlo approach, which is more approximate, but dramatically faster compared to the direct N-body, is capable of producing an accurate description of the long-term evolution of massive globular clusters even when the clusters contain large populations of stellar-mass black holes.
Comparisons between stellar models and reliability of the theoretical models

NASA Astrophysics Data System (ADS)

Lebreton, Yveline; Montalbán, Josefina

2010-07-01

The high quality of the asteroseismic data provided by space missions such as CoRoT (Michel et al. in The CoRoT Mission, ESA Spec. Publ. vol. 1306, p. 39, 2006) or expected from new operating missions such as Kepler (Christensen-Dalsgaard et al. in Commun. Asteroseismol. 150:350, 2007) requires the capacity of stellar evolution codes to provide accurate models whose numerical precision is better than the expected observational errors (i.e. below 0.1 μHz on the frequencies in the case of CoRoT). We present a review of some thorough comparisons of stellar models produced by different evolution codes, involved in the CoRoT/ESTA activities (Monteiro in Evolution and Seismic Tools for Stellar Astrophysics, 2009). We examine the numerical aspects of the computations as well as the effects of different implementations of the same physics on the global quantities, physical structure and oscillations properties of the stellar models. We also discuss a few aspects of the input physics.
Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes.

PubMed

Seligmann, Hervé

2018-05-01

Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections. Copyright © 2018 Elsevier B.V. All rights reserved.
Modeling carbon production and transport during ELMs in DIII-D

NASA Astrophysics Data System (ADS)

Hogan, J.; Wade, M.; Coster, D.; Lasnier, C.

2004-11-01

Large-scale Type I ELM events could provide a significant C source in ITER, and C production rates depend on incident D flux density and surface temperature, quantities which can vary significantly during an ELM event. Recent progress on DIII-D has improved opportunities for code comparison. Fast time-scale measurements of divertor CIII evolution [1] and fast edge CER measurements of C profile evolution during low-density DIII-D LSN ELMy H-modes (type I) [2] have been modeled using the solps5.0/Eirene99 coupled edge code and time dependent thermal analysis codes. An ELM model based on characteristics of MHD peeling-ballooning modes reproduces the pedestal evolution. Qualitative agreement for the CIII evolution during an ELM event is found using the Roth et al annealing model for chemical sputtering and the sensitivity to other models is described. Significant ELM-to-ELM variations in observed maximum divertor target IR temperature during nominally identical ELMs are investigated with models for C emission from micron-scale dust particles. [1] M Groth, M Fenstermacher et al J Nucl Mater 2003, [2] M Wade, K Burrell et al PSI-16
A comparison of models for supernova remnants including cosmic rays

NASA Astrophysics Data System (ADS)

Kang, Hyesung; Drury, L. O'C.

1992-11-01

A simplified model which can follow the dynamical evolution of a supernova remnant including the acceleration of cosmic rays without carrying out full numerical simulations has been proposed by Drury, Markiewicz, & Voelk in 1989. To explore the accuracy and the merits of using such a model, we have recalculated with the simplified code the evolution of the supernova remnants considered in Jones & Kang, in which more detailed and accurate numerical simulations were done using a full hydrodynamic code based on the two-fluid approximation. For the total energy transferred to cosmic rays the two codes are in good agreement, the acceleration efficiency being the same within a factor of 2 or so. The dependence of the results of the two codes on the closure parameters for the two-fluid approximation is also qualitatively similar. The agreement is somewhat degraded in those cases where the shock is smoothed out by the cosmic rays.
Position specific variation in the rate of evolution in transcription factor binding sites

PubMed Central

Moses, Alan M; Chiang, Derek Y; Kellis, Manolis; Lander, Eric S; Eisen, Michael B

2003-01-01

Background The binding sites of sequence specific transcription factors are an important and relatively well-understood class of functional non-coding DNAs. Although a wide variety of experimental and computational methods have been developed to characterize transcription factor binding sites, they remain difficult to identify. Comparison of non-coding DNA from related species has shown considerable promise in identifying these functional non-coding sequences, even though relatively little is known about their evolution. Results Here we analyse the genome sequences of the budding yeasts Saccharomyces cerevisiae, S. bayanus, S. paradoxus and S. mikatae to study the evolution of transcription factor binding sites. As expected, we find that both experimentally characterized and computationally predicted binding sites evolve slower than surrounding sequence, consistent with the hypothesis that they are under purifying selection. We also observe position-specific variation in the rate of evolution within binding sites. We find that the position-specific rate of evolution is positively correlated with degeneracy among binding sites within S. cerevisiae. We test theoretical predictions for the rate of evolution at positions where the base frequencies deviate from background due to purifying selection and find reasonable agreement with the observed rates of evolution. Finally, we show how the evolutionary characteristics of real binding motifs can be used to distinguish them from artefacts of computational motif finding algorithms. Conclusion As has been observed for protein sequences, the rate of evolution in transcription factor binding sites varies with position, suggesting that some regions are under stronger functional constraint than others. This variation likely reflects the varying importance of different positions in the formation of the protein-DNA complex. The characterization of the pattern of evolution in known binding sites will likely contribute to the effective use of comparative sequence data in the identification of transcription factor binding sites and is an important step toward understanding the evolution of functional non-coding DNA. PMID:12946282
The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape.

PubMed

Yousaf, Aisha; Sohail Raza, Muhammad; Ali Abbasi, Amir

2015-08-06

Enhancers lie at the heart of transcriptional and developmental gene regulation. Therefore, changes in enhancer sequences usually disrupt the target gene expression and result in disease phenotypes. Despite the well-established role of enhancers in development and disease, evolutionary sequence studies are lacking. The current study attempts to unravel the puzzle of bony vertebrates' conserved noncoding elements (CNE) enhancer evolution. Bayesian phylogenetics of enhancer sequences spotlights promising interordinal relationships among placental mammals, proposing a closer relationship between humans and laurasiatherians while placing rodents at the basal position. Clock-based estimates of enhancer evolution provided a dynamic picture of interspecific rate changes across the bony vertebrate lineage. Moreover, coelacanth in the study augmented our appreciation of the vertebrate cis-regulatory evolution during water-land transition. Intriguingly, we observed a pronounced upsurge in enhancer evolution in land-dwelling vertebrates. These novel findings triggered us to further investigate the evolutionary trend of coding as well as CNE nonenhancer repertoires, to highlight the relative evolutionary dynamics of diverse genomic landscapes. Surprisingly, the evolutionary rates of enhancer sequences were clearly at odds with those of the coding and the CNE nonenhancer sequences during vertebrate adaptation to land, with land vertebrates exhibiting significantly reduced rates of coding sequence evolution in comparison to their fast evolving regulatory landscape. The observed variation in tetrapod cis-regulatory elements caused the fine-tuning of associated gene regulatory networks. Therefore, the increased evolutionary rate of tetrapods' enhancer sequences might be responsible for the variation in developmental regulatory circuits during the process of vertebrate adaptation to land. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Computational methods for coupling microstructural and micromechanical materials response simulations

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

HOLM,ELIZABETH A.; BATTAILE,CORBETT C.; BUCHHEIT,THOMAS E.

2000-04-01

Computational materials simulations have traditionally focused on individual phenomena: grain growth, crack propagation, plastic flow, etc. However, real materials behavior results from a complex interplay between phenomena. In this project, the authors explored methods for coupling mesoscale simulations of microstructural evolution and micromechanical response. In one case, massively parallel (MP) simulations for grain evolution and microcracking in alumina stronglink materials were dynamically coupled. In the other, codes for domain coarsening and plastic deformation in CuSi braze alloys were iteratively linked. this program provided the first comparison of two promising ways to integrate mesoscale computer codes. Coupled microstructural/micromechanical codes were appliedmore » to experimentally observed microstructures for the first time. In addition to the coupled codes, this project developed a suite of new computational capabilities (PARGRAIN, GLAD, OOF, MPM, polycrystal plasticity, front tracking). The problem of plasticity length scale in continuum calculations was recognized and a solution strategy was developed. The simulations were experimentally validated on stockpile materials.« less
Independent evolution of genomic characters during major metazoan transitions.

PubMed

Simakov, Oleg; Kawashima, Takeshi

2017-07-15

Metazoan evolution encompasses a vast evolutionary time scale spanning over 600 million years. Our ability to infer ancestral metazoan characters, both morphological and functional, is limited by our understanding of the nature and evolutionary dynamics of the underlying regulatory networks. Increasing coverage of metazoan genomes enables us to identify the evolutionary changes of the relevant genomic characters such as the loss or gain of coding sequences, gene duplications, micro- and macro-synteny, and non-coding element evolution in different lineages. In this review we describe recent advances in our understanding of ancestral metazoan coding and non-coding features, as deduced from genomic comparisons. Some genomic changes such as innovations in gene and linkage content occur at different rates across metazoan clades, suggesting some level of independence among genomic characters. While their contribution to biological innovation remains largely unclear, we review recent literature about certain genomic changes that do correlate with changes to specific developmental pathways and metazoan innovations. In particular, we discuss the origins of the recently described pharyngeal cluster which is conserved across deuterostome genomes, and highlight different genomic features that have contributed to the evolution of this group. We also assess our current capacity to infer ancestral metazoan states from gene models and comparative genomics tools and elaborate on the future directions of metazoan comparative genomics relevant to evo-devo studies. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.
CoRoT/ESTA TASK 1 and TASK 3 comparison of the internal structure and seismic properties of representative stellar models. Comparisons between the ASTEC, CESAM, CLES, GARSTEC and STAROX codes

NASA Astrophysics Data System (ADS)

Lebreton, Yveline; Montalbán, Josefina; Christensen-Dalsgaard, Jørgen; Roxburgh, Ian W.; Weiss, Achim

2008-08-01

We compare stellar models produced by different stellar evolution codes for the CoRoT/ESTA project, comparing their global quantities, their physical structure, and their oscillation properties. We discuss the differences between models and identify the underlying reasons for these differences. The stellar models are representative of potential CoRoT targets. Overall we find very good agreement between the five different codes, but with some significant deviations. We find noticeable discrepancies (though still at the per cent level) that result from the handling of the equation of state, of the opacities and of the convective boundaries. The results of our work will be helpful in interpreting future asteroseismology results from CoRoT.
Metal-poor stars. IV - The evolution of red giants.

NASA Technical Reports Server (NTRS)

Rood, R. T.

1972-01-01

Detailed evolutionary calculations for six Population-II red giants are presented. The first five of these models are followed from the zero age main sequence to the onset of the helium flash. The sixth model allows the effect of direct electron-neutrino interactions to be estimated. The updated input physics and evolutionary code are described briefly. The results of the calculations are presented in a manner pertinent to later stages of evolutions and suitable for comparison with observations.
COCOA: Simulating Observations of Star Cluster Simulations

NASA Astrophysics Data System (ADS)

Askar, Abbas; Giersz, Mirek; Pych, Wojciech; Dalessandro, Emanuele

2017-03-01

COCOA (Cluster simulatiOn Comparison with ObservAtions) creates idealized mock photometric observations using results from numerical simulations of star cluster evolution. COCOA is able to present the output of realistic numerical simulations of star clusters carried out using Monte Carlo or N-body codes in a way that is useful for direct comparison with photometric observations. The code can simulate optical observations from simulation snapshots in which positions and magnitudes of objects are known. The parameters for simulating the observations can be adjusted to mimic telescopes of various sizes. COCOA also has a photometry pipeline that can use standalone versions of DAOPHOT (ascl:1104.011) and ALLSTAR to produce photometric catalogs for all observed stars.
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.
The application of CFD for military aircraft design at transonic speeds

NASA Technical Reports Server (NTRS)

Smith, C. W.; Braymen, W. W.; Bhateley, I. C.; Londenberg, W. K.

1989-01-01

Numerous computational fluid dynamics (CFD) codes are available that solve any of several variations of the transonic flow equations from small disturbance to full Navier-Stokes. The design philosophy at General Dynamics Fort Worth Division involves use of all these levels of codes, depending on the stage of configuration development. Throughout this process, drag calculation is a central issue. An overview is provided for several transonic codes and representative test-to-theory comparisons for fighter-type configurations are presented. Correlations are shown for lift, drag, pitching moment, and pressure distributions. The future of applied CFD is also discussed, including the important task of code validation. With the progress being made in code development and the continued evolution in computer hardware, the routine application of these codes for increasingly more complex geometries and flow conditions seems apparent.
Numerical modeling of the Madison Dynamo Experiment.

NASA Astrophysics Data System (ADS)

Bayliss, R. A.; Wright, J. C.; Forest, C. B.; O'Connell, R.

2002-11-01

Growth, saturation and turbulent evolution of the Madison dynamo experiment is investigated numerically using a 3-D pseudo-spectral simulation of the MHD equations; results of the simulations will be compared to results obtained from the experiment. The code, Dynamo (Fortran90), allows for full evolution of the magnetic and velocity fields. The induction equation governing B and the curl of the momentum equation governing V are separately or simultaneously solved. The code uses a spectral representation via spherical harmonic basis functions of the vector fields in longitude and latitude, and fourth order finite differences in the radial direction. The magnetic field evolution has been benchmarked against the laminar kinematic dynamo predicted by M.L. Dudley and R.W. James (M.L. Dudley and R.W. James, Time-dependent kinematic dynamos with stationary flows, Proc. R. Soc. Lond. A 425, p. 407 (1989)). Power balance in the system has been verified in both mechanically driven and perturbed hydrodynamic, kinematic, and dynamic cases. Evolution of the vacuum magnetic field has been added to facilitate comparison with the experiment. Modeling of the Madison Dynamo eXperiment will be presented.

Neutral helium beam probe

NASA Astrophysics Data System (ADS)

Karim, Rezwanul

1999-10-01

This article discusses the development of a code where diagnostic neutral helium beam can be used as a probe. The code solves numerically the evolution of the population densities of helium atoms at their several different energy levels as the beam propagates through the plasma. The collisional radiative model has been utilized in this numerical calculation. The spatial dependence of the metastable states of neutral helium atom, as obtained in this numerical analysis, offers a possible diagnostic tool for tokamak plasma. The spatial evolution for several hypothetical plasma conditions was tested. Simulation routines were also run with the plasma parameters (density and temperature profiles) similar to a shot in the Princeton beta experiment modified (PBX-M) tokamak and a shot in Tokamak Fusion Test Reactor tokamak. A comparison between the simulation result and the experimentally obtained data (for each of these two shots) is presented. A good correlation in such comparisons for a number of such shots can establish the accurateness and usefulness of this probe. The result can possibly be extended for other plasma machines and for various plasma conditions in those machines.
Regional tectonic analysis of Venus equatorial highlands and comparison with Earth-based Magellan radar images

NASA Technical Reports Server (NTRS)

Williams, David R.; Wetherill, George

1993-01-01

Research on regional tectonic analysis of Venus equatorial highlands and comparison with earth-based and Magellan radar images is presented. Over the past two years, the tectonic analysis of Venus performed centered on global properties of the planet, in order to understand fundamental aspects of the dynamics of the mantle and lithosphere of Venus. These include studies pertaining to the original constitutive and thermal character of the planet, as well as the evolution of Venus through time, and the present day tectonics. Parameterized convection models of the Earth and Venus were developed. The parameterized convection code was reformulated to model Venus with an initially hydrous mantle to determine how the cold-trap could affect the evolution of the planet.
Parallel evolution of the glycogen synthase 1 (muscle) gene Gys1 between Old World and New World fruit bats (Order: Chiroptera).

PubMed

Fang, Lu; Shen, Bin; Irwin, David M; Zhang, Shuyi

2014-10-01

Glycogen synthase, which catalyzes the synthesis of glycogen, is especially important for Old World (Pteropodidae) and New World (Phyllostomidae) fruit bats that ingest high-carbohydrate diets. Glycogen synthase 1, encoded by the Gys1 gene, is the glycogen synthase isozyme that functions in muscles. To determine whether Gys1 has undergone adaptive evolution in bats with carbohydrate-rich diets, in comparison to insect-eating sister bat taxa, we sequenced the coding region of the Gys1 gene from 10 species of bats, including two Old World fruit bats (Pteropodidae) and a New World fruit bat (Phyllostomidae). Our results show no evidence for positive selection in the Gys1 coding sequence on the ancestral Old World and the New World Artibeus lituratus branches. Tests for convergent evolution indicated convergence of the sequences and one parallel amino acid substitution (T395A) was detected on these branches, which was likely driven by natural selection.
The Scylla Multi-Code Comparison Project

NASA Astrophysics Data System (ADS)

Maller, Ariyeh; Stewart, Kyle; Bullock, James; Oñorbe, Jose; Scylla Team

2016-01-01

Cosmological hydrodynamical simulations are one of the main techniques used to understand galaxy formation and evolution. However, it is far from clear to what extent different numerical techniques and different implementations of feedback yield different results. The Scylla Multi-Code Comparison Project seeks to address this issue by running idenitical initial condition simulations with different popular hydrodynamic galaxy formation codes. Here we compare simulations of a Milky Way mass halo using the codes enzo, ramses, art, arepo and gizmo-psph. The different runs produce galaxies with a variety of properties. There are many differences, but also many similarities. For example we find that in all runs cold flow disks exist; extended gas structures, far beyond the galactic disk, that show signs of rotation. Also, the angular momentum of warm gas in the halo is much larger than the angular momentum of the dark matter. We also find notable differences between runs. The temperature and density distribution of hot gas can differ by over an order of magnitude between codes and the stellar mass to halo mass relation also varies widely. These results suggest that observations of galaxy gas halos and the stellar mass to halo mass relation can be used to constarin the correct model of feedback.
CSTminer: a web tool for the identification of coding and noncoding conserved sequence tags through cross-species genome comparison

PubMed Central

Castrignanò, Tiziana; Canali, Alessandro; Grillo, Giorgio; Liuni, Sabino; Mignone, Flavio; Pesole, Graziano

2004-01-01

The identification and characterization of genome tracts that are highly conserved across species during evolution may contribute significantly to the functional annotation of whole-genome sequences. Indeed, such sequences are likely to correspond to known or unknown coding exons or regulatory motifs. Here, we present a web server implementing a previously developed algorithm that, by comparing user-submitted genome sequences, is able to identify statistically significant conserved blocks and assess their coding or noncoding nature through the measure of a coding potential score. The web tool, available at http://www.caspur.it/CSTminer/, is dynamically interconnected with the Ensembl genome resources and produces a graphical output showing a map of detected conserved sequences and annotated gene features. PMID:15215464
COCOA code for creating mock observations of star cluster models

NASA Astrophysics Data System (ADS)

Askar, Abbas; Giersz, Mirek; Pych, Wojciech; Dalessandro, Emanuele

2018-04-01

We introduce and present results from the COCOA (Cluster simulatiOn Comparison with ObservAtions) code that has been developed to create idealized mock photometric observations using results from numerical simulations of star cluster evolution. COCOA is able to present the output of realistic numerical simulations of star clusters carried out using Monte Carlo or N-body codes in a way that is useful for direct comparison with photometric observations. In this paper, we describe the COCOA code and demonstrate its different applications by utilizing globular cluster (GC) models simulated with the MOCCA (MOnte Carlo Cluster simulAtor) code. COCOA is used to synthetically observe these different GC models with optical telescopes, perform point spread function photometry, and subsequently produce observed colour-magnitude diagrams. We also use COCOA to compare the results from synthetic observations of a cluster model that has the same age and metallicity as the Galactic GC NGC 2808 with observations of the same cluster carried out with a 2.2 m optical telescope. We find that COCOA can effectively simulate realistic observations and recover photometric data. COCOA has numerous scientific applications that maybe be helpful for both theoreticians and observers that work on star clusters. Plans for further improving and developing the code are also discussed in this paper.
Insights into hominid evolution from the gorilla genome sequence

PubMed Central

Scally, Aylwyn; Dutheil, Julien Y.; Hillier, LaDeana W.; Jordan, Greg E.; Goodhead, Ian; Herrero, Javier; Hobolth, Asger; Lappalainen, Tuuli; Mailund, Thomas; Marques-Bonet, Tomas; McCarthy, Shane; Montgomery, Stephen H.; Schwalie, Petra C.; Tang, Y. Amy; Ward, Michelle C.; Xue, Yali; Yngvadottir, Bryndis; Alkan, Can; Andersen, Lars N.; Ayub, Qasim; Ball, Edward V.; Beal, Kathryn; Bradley, Brenda J.; Chen, Yuan; Clee, Chris M.; Fitzgerald, Stephen; Graves, Tina A.; Gu, Yong; Heath, Paul; Heger, Andreas; Karakoc, Emre; Kolb-Kokocinski, Anja; Laird, Gavin K.; Lunter, Gerton; Meader, Stephen; Mort, Matthew; Mullikin, James C.; Munch, Kasper; O’Connor, Timothy D.; Phillips, Andrew D.; Prado-Martinez, Javier; Rogers, Anthony S.; Sajjadian, Saba; Schmidt, Dominic; Shaw, Katy; Simpson, Jared T.; Stenson, Peter D.; Turner, Daniel J.; Vigilant, Linda; Vilella, Albert J.; Whitener, Weldon; Zhu, Baoli; Cooper, David N.; de Jong, Pieter; Dermitzakis, Emmanouil T.; Eichler, Evan E.; Flicek, Paul; Goldman, Nick; Mundy, Nicholas I.; Ning, Zemin; Odom, Duncan T.; Ponting, Chris P.; Quail, Michael A.; Ryder, Oliver A.; Searle, Stephen M.; Warren, Wesley C.; Wilson, Richard K.; Schierup, Mikkel H.; Rogers, Jane; Tyler-Smith, Chris; Durbin, Richard

2012-01-01

Summary Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human-chimpanzee and human-chimpanzee-gorilla speciation events at approximately 6 and 10 million years ago (Mya). In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution. PMID:22398555
Nucleotide sequence determination of guinea-pig casein B mRNA reveals homology with bovine and rat alpha s1 caseins and conservation of the non-coding regions of the mRNA.

PubMed Central

Hall, L; Laird, J E; Craig, R K

1984-01-01

Nucleotide sequence analysis of cloned guinea-pig casein B cDNA sequences has identified two casein B variants related to the bovine and rat alpha s1 caseins. Amino acid homology was largely confined to the known bovine or predicted rat phosphorylation sites and within the 'signal' precursor sequence. Comparison of the deduced nucleotide sequence of the guinea-pig and rat alpha s1 casein mRNA species showed greater sequence conservation in the non-coding than in the coding regions, suggesting a functional and possibly regulatory role for the non-coding regions of casein mRNA. The results provide insight into the evolution of the casein genes, and raise questions as to the role of conserved nucleotide sequences within the non-coding regions of mRNA species. Images Fig. 1. PMID:6548375
The spotted gar genome illuminates vertebrate evolution and facilitates human-to-teleost comparisons

PubMed Central

Braasch, Ingo; Gehrke, Andrew R.; Smith, Jeramiah J.; Kawasaki, Kazuhiko; Manousaki, Tereza; Pasquier, Jeremy; Amores, Angel; Desvignes, Thomas; Batzel, Peter; Catchen, Julian; Berlin, Aaron M.; Campbell, Michael S.; Barrell, Daniel; Martin, Kyle J.; Mulley, John F.; Ravi, Vydianathan; Lee, Alison P.; Nakamura, Tetsuya; Chalopin, Domitille; Fan, Shaohua; Wcisel, Dustin; Cañestro, Cristian; Sydes, Jason; Beaudry, Felix E. G.; Sun, Yi; Hertel, Jana; Beam, Michael J.; Fasold, Mario; Ishiyama, Mikio; Johnson, Jeremy; Kehr, Steffi; Lara, Marcia; Letaw, John H.; Litman, Gary W.; Litman, Ronda T.; Mikami, Masato; Ota, Tatsuya; Saha, Nil Ratan; Williams, Louise; Stadler, Peter F.; Wang, Han; Taylor, John S.; Fontenot, Quenton; Ferrara, Allyse; Searle, Stephen M. J.; Aken, Bronwen; Yandell, Mark; Schneider, Igor; Yoder, Jeffrey A.; Volff, Jean-Nicolas; Meyer, Axel; Amemiya, Chris T.; Venkatesh, Byrappa; Holland, Peter W. H.; Guiguen, Yann; Bobe, Julien; Shubin, Neil H.; Di Palma, Federica; Alföldi, Jessica; Lindblad-Toh, Kerstin; Postlethwait, John H.

2016-01-01

To connect human biology to fish biomedical models, we sequenced the genome of spotted gar (Lepisosteus oculatus), whose lineage diverged from teleosts before the teleost genome duplication (TGD). The slowly evolving gar genome conserved in content and size many entire chromosomes from bony vertebrate ancestors. Gar bridges teleosts to tetrapods by illuminating the evolution of immunity, mineralization, and development (e.g., Hox, ParaHox, and miRNA genes). Numerous conserved non-coding elements (CNEs, often cis-regulatory) undetectable in direct human-teleost comparisons become apparent using gar: functional studies uncovered conserved roles of such cryptic CNEs, facilitating annotation of sequences identified in human genome-wide association studies. Transcriptomic analyses revealed that the sum of expression domains and levels from duplicated teleost genes often approximate patterns and levels of gar genes, consistent with subfunctionalization. The gar genome provides a resource for understanding evolution after genome duplication, the origin of vertebrate genomes, and the function of human regulatory sequences. PMID:26950095
Parallel evolution of chordate cis-regulatory code for development.

PubMed

Doglio, Laura; Goode, Debbie K; Pelleri, Maria C; Pauls, Stefan; Frabetti, Flavia; Shimeld, Sebastian M; Vavouri, Tanya; Elgar, Greg

2013-11-01

Urochordates are the closest relatives of vertebrates and at the larval stage, possess a characteristic bilateral chordate body plan. In vertebrates, the genes that orchestrate embryonic patterning are in part regulated by highly conserved non-coding elements (CNEs), yet these elements have not been identified in urochordate genomes. Consequently the evolution of the cis-regulatory code for urochordate development remains largely uncharacterised. Here, we use genome-wide comparisons between C. intestinalis and C. savignyi to identify putative urochordate cis-regulatory sequences. Ciona conserved non-coding elements (ciCNEs) are associated with largely the same key regulatory genes as vertebrate CNEs. Furthermore, some of the tested ciCNEs are able to activate reporter gene expression in both zebrafish and Ciona embryos, in a pattern that at least partially overlaps that of the gene they associate with, despite the absence of sequence identity. We also show that the ability of a ciCNE to up-regulate gene expression in vertebrate embryos can in some cases be localised to short sub-sequences, suggesting that functional cross-talk may be defined by small regions of ancestral regulatory logic, although functional sub-sequences may also be dispersed across the whole element. We conclude that the structure and organisation of cis-regulatory modules is very different between vertebrates and urochordates, reflecting their separate evolutionary histories. However, functional cross-talk still exists because the same repertoire of transcription factors has likely guided their parallel evolution, exploiting similar sets of binding sites but in different combinations.
Rooted tRNAomes and evolution of the genetic code

PubMed Central

Pak, Daewoo; Du, Nan; Kim, Yunsoo; Sun, Yanni

2018-01-01

ABSTRACT We advocate for a tRNA- rather than an mRNA-centric model for evolution of the genetic code. The mechanism for evolution of cloverleaf tRNA provides a root sequence for radiation of tRNAs and suggests a simplified understanding of code evolution. To analyze code sectoring, rooted tRNAomes were compared for several archaeal and one bacterial species. Rooting of tRNAome trees reveals conserved structures, indicating how the code was shaped during evolution and suggesting a model for evolution of a LUCA tRNAome tree. We propose the polyglycine hypothesis that the initial product of the genetic code may have been short chain polyglycine to stabilize protocells. In order to describe how anticodons were allotted in evolution, the sectoring-degeneracy hypothesis is proposed. Based on sectoring, a simple stepwise model is developed, in which the code sectors from a 1→4→8→∼16 letter code. At initial stages of code evolution, we posit strong positive selection for wobble base ambiguity, supporting convergence to 4-codon sectors and ∼16 letters. In a later stage, ∼5–6 letters, including stops, were added through innovating at the anticodon wobble position. In archaea and bacteria, tRNA wobble adenine is negatively selected, shrinking the maximum size of the primordial genetic code to 48 anticodons. Because 64 codons are recognized in mRNA, tRNA-mRNA coevolution requires tRNA wobble position ambiguity leading to degeneracy of the code. PMID:29372672
Design of orbital debris shields for oblique hypervelocity impact

NASA Technical Reports Server (NTRS)

Fahrenthold, Eric P.

1994-01-01

A new impact debris propagation code was written to link CTH simulations of space debris shield perforation to the Lagrangian finite element code DYNA3D, for space structure wall impact simulations. This software (DC3D) simulates debris cloud evolution using a nonlinear elastic-plastic deformable particle dynamics model, and renders computationally tractable the supercomputer simulation of oblique impacts on Whipple shield protected structures. Comparison of three dimensional, oblique impact simulations with experimental data shows good agreement over a range of velocities of interest in the design of orbital debris shielding. Source code developed during this research is provided on the enclosed floppy disk. An abstract based on the work described was submitted to the 1994 Hypervelocity Impact Symposium.
GrowYourIC: an open access Python code to facilitate comparison between kinematic models of inner core evolution and seismic observations

NASA Astrophysics Data System (ADS)

Lasbleis, M.; Day, E. A.; Waszek, L.

2017-12-01

The complex nature of inner core structure has been well-established from seismic studies, with heterogeneities at various length scales, both radially and laterally. Despite this, no geodynamic model has successfully explained all of the observed seismic features. To facilitate comparisons between seismic observations and geodynamic models of inner core growth we have developed a new, open access Python tool - GrowYourIC - that allows users to compare models of inner core structure. The code allows users to simulate different evolution models of the inner core, with user-defined rates of inner core growth, translation and rotation. Once the user has "grown" an inner core with their preferred parameters they can then explore the effect of "their" inner core's evolution on the relative age and growth rate in different regions of the inner core. The code will convert these parameters into seismic properties using either built-in mineral physics models, or user-supplied ones that calculate these seismic properties with users' own preferred mineralogical models. The 3D model of isotropic inner core properties can then be used to calculate the predicted seismic travel time anomalies for a random, or user-specified, set of seismic ray paths through the inner core. A real dataset of inner core body-wave differential travel times is included for the purpose of comparing user-generated models of inner core growth to actual observed travel time anomalies in the top 100km of the inner core. Here, we explore some of the possibilities of our code. We investigate the effect of the limited illumination of the inner core by seismic waves on the robustness of kinematic model interpretation. We test the impact on seismic differential travel time observations of several kinematic models of inner core growth: fast lateral translation; slow differential growth; and inner core super-rotation. We find that a model of inner core evolution incorporating both differential growth and slow super-rotation is able to recreate some of the more intricate details of the seismic observations. Specifically we are able to "grow" an inner core that has an asymmetric shift in isotropic hemisphere boundaries with increasing depth in the inner core.
BayeSED: A General Approach to Fitting the Spectral Energy Distribution of Galaxies

NASA Astrophysics Data System (ADS)

Han, Yunkun; Han, Zhanwen

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large Ks -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has been performed for the first time. We found that the 2003 model by Bruzual & Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the Ks -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.
BayeSED: A GENERAL APPROACH TO FITTING THE SPECTRAL ENERGY DISTRIBUTION OF GALAXIES

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

Han, Yunkun; Han, Zhanwen, E-mail: hanyk@ynao.ac.cn, E-mail: zhanwenhan@ynao.ac.cn

2014-11-01

We present a newly developed version of BayeSED, a general Bayesian approach to the spectral energy distribution (SED) fitting of galaxies. The new BayeSED code has been systematically tested on a mock sample of galaxies. The comparison between the estimated and input values of the parameters shows that BayeSED can recover the physical parameters of galaxies reasonably well. We then applied BayeSED to interpret the SEDs of a large K{sub s} -selected sample of galaxies in the COSMOS/UltraVISTA field with stellar population synthesis models. Using the new BayeSED code, a Bayesian model comparison of stellar population synthesis models has beenmore » performed for the first time. We found that the 2003 model by Bruzual and Charlot, statistically speaking, has greater Bayesian evidence than the 2005 model by Maraston for the K{sub s} -selected sample. In addition, while setting the stellar metallicity as a free parameter obviously increases the Bayesian evidence of both models, varying the initial mass function has a notable effect only on the Maraston model. Meanwhile, the physical parameters estimated with BayeSED are found to be generally consistent with those obtained using the popular grid-based FAST code, while the former parameters exhibit more natural distributions. Based on the estimated physical parameters of the galaxies in the sample, we qualitatively classified the galaxies in the sample into five populations that may represent galaxies at different evolution stages or in different environments. We conclude that BayeSED could be a reliable and powerful tool for investigating the formation and evolution of galaxies from the rich multi-wavelength observations currently available. A binary version of the BayeSED code parallelized with Message Passing Interface is publicly available at https://bitbucket.org/hanyk/bayesed.« less
Analysis of adaptive evolution in Lyssavirus genomes reveals pervasive diversifying selection during species diversification.

PubMed

Voloch, Carolina M; Capellão, Renata T; Mello, Beatriz; Schrago, Carlos G

2014-11-19

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups.
Analysis of Adaptive Evolution in Lyssavirus Genomes Reveals Pervasive Diversifying Selection during Species Diversification

PubMed Central

Voloch, Carolina M.; Capellão, Renata T.; Mello, Beatriz; Schrago, Carlos G.

2014-01-01

Lyssavirus is a diverse genus of viruses that infect a variety of mammalian hosts, typically causing encephalitis. The evolution of this lineage, particularly the rabies virus, has been a focus of research because of the extensive occurrence of cross-species transmission, and the distinctive geographical patterns present throughout the diversification of these viruses. Although numerous studies have examined pattern-related questions concerning Lyssavirus evolution, analyses of the evolutionary processes acting on Lyssavirus diversification are scarce. To clarify the relevance of positive natural selection in Lyssavirus diversification, we conducted a comprehensive scan for episodic diversifying selection across all lineages and codon sites of the five coding regions in lyssavirus genomes. Although the genomes of these viruses are generally conserved, the glycoprotein (G), RNA-dependent RNA polymerase (L) and polymerase (P) genes were frequently targets of adaptive evolution during the diversification of the genus. Adaptive evolution is particularly manifest in the glycoprotein gene, which was inferred to have experienced the highest density of positively selected codon sites along branches. Substitutions in the L gene were found to be associated with the early diversification of phylogroups. A comparison between the number of positively selected sites inferred along the branches of RABV population branches and Lyssavirus intespecies branches suggested that the occurrence of positive selection was similar on the five coding regions of the genome in both groups. PMID:25415197
Calculation of electromagnetic fields induced on a geostationary satellite by an electrostatic discharge

NASA Astrophysics Data System (ADS)

Froger, E.; Marque, J. P.

The electromagnetic response of an orbiting satellite to an electrostatic discharge is compared to that of the same object subjected (in a susceptibility test) to an injection current. In the absence of actual data, the comparison was performed on the basis of two numerical simulations: one using the GEODE particle code for the orbiting case, and the other using the ALICE code for a representative injection configuration. It is found that the evolution of the electromagnetic fields is controlled in particular by the particle emission rhythm, giving rise to an ejection flux 'slit' whose rise time is about several tens of nanoseconds.
FIRST NEW SOLAR MODELS WITH OPAS OPACITY TABLES

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

Le Pennec, M.; Turck-Chièze, S.; Salmon, S.

Stellar seismology appears more and more as a powerful tool for a better determination of the fundamental properties of solar-type stars. However, the particular case of the Sun is still challenging. For about a decade now, the helioseismic sound-speed determination has continued to disagree with the standard solar model (SSM) prediction, questioning the reliability of this model. One of the sources of uncertainty could be in the treatment of the transport of radiation from the solar core to the surface. In this Letter, we use the new OPAS opacity tables, recently available for solar modeling, to address this issue. Wemore » discuss first the peculiarities of these tables, then we quantify their impact on the solar sound-speed and density profiles using the reduced OPAS tables taken on the grids of the OPAL ones. We use the two evolution codes, Modules for Experiments in Stellar Astrophysics and Code Liégeois d’Evolution Stellaire, that led to similar conclusions in the solar radiative zone. In comparison to commonly used OPAL opacity tables, the new solar models are computed for the most recent photospheric composition with OPAS tables and present improvements to the location of the base of the convective zone and to the description of the solar radiative zone in comparison to the helioseismic observations, even if the differences in the Rosseland mean opacity do not exceed 6%. We finally carry out a comparison to a solar model computed with the OP opacity tables.« less
Code dependencies of pre-supernova evolution and nucleosynthesis in massive stars: evolution to the end of core helium burning

DOE PAGES

Jones, S.; Hirschi, R.; Pignatari, M.; ...

2015-01-15

We present a comparison of 15M ⊙ , 20M ⊙ and 25M ⊙ stellar models from three different codes|GENEC, KEPLER and MESA|and their nucleosynthetic yields. The models are calculated from the main sequence up to the pre-supernova (pre-SN) stage and do not include rotation. The GENEC and KEPLER models hold physics assumptions that are characteristic of the two codes. The MESA code is generally more flexible; overshooting of the convective core during the hydrogen and helium burning phases in MESA is chosen such that the CO core masses are consistent with those in the GENEC models. Full nucleosynthesis calculations aremore » performed for all models using the NuGrid post-processing tool MPPNP and the key energy-generating nuclear reaction rates are the same for all codes. We are thus able to highlight the key diferences between the models that are caused by the contrasting physics assumptions and numerical implementations of the three codes. A reasonable agreement is found between the surface abundances predicted by the models computed using the different codes, with GENEC exhibiting the strongest enrichment of H-burning products and KEPLER exhibiting the weakest. There are large variations in both the structure and composition of the models—the 15M ⊙ and 20M ⊙ in particular—at the pre-SN stage from code to code caused primarily by convective shell merging during the advanced stages. For example the C-shell abundances of O, Ne and Mg predicted by the three codes span one order of magnitude in the 15M ⊙ models. For the alpha elements between Si and Fe the differences are even larger. The s-process abundances in the C shell are modified by the merging of convective shells; the modification is strongest in the 15M ⊙ model in which the C-shell material is exposed to O-burning temperatures and the γ -process is activated. The variation in the s-process abundances across the codes is smallest in the 25M ⊙ models, where it is comparable to the impact of nuclear reaction rate uncertainties. In general the differences in the results from the three codes are due to their contrasting physics assumptions (e.g. prescriptions for mass loss and convection). The broadly similar evolution of the 25M ⊙ models gives us reassurance that different stellar evolution codes do produce similar results. For the 15M ⊙ and 20M ⊙ models, however, the different input physics and the interplay between the various convective zones lead to important differences in both the pre-supernova structure and nucleosynthesis predicted by the three codes. For the KEPLER models the core masses are different and therefore an exact match could not be expected.« less

Differential expression of non-coding RNAs and continuous evolution of the X chromosome in testicular transcriptome of two mouse species.

PubMed

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-02-14

Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition.
Comparing models of star formation simulating observed interacting galaxies

NASA Astrophysics Data System (ADS)

Quiroga, L. F.; Muñoz-Cuartas, J. C.; Rodrigues, I.

2017-07-01

In this work, we make a comparison between different models of star formation to reproduce observed interacting galaxies. We use observational data to model the evolution of a pair of galaxies undergoing a minor merger. Minor mergers represent situations weakly deviated from the equilibrium configuration but significant changes in star fomation (SF) efficiency can take place, then, minor mergers provide an unique scene to study SF in galaxies in a realistic but yet simple way. Reproducing observed systems also give us the opportunity to compare the results of the simulations with observations, which at the end can be used as probes to characterize the models of SF implemented in the comparison. In this work we compare two different star formation recipes implemented in Gadget3 and GIZMO codes. Both codes share the same numerical background, and differences arise mainly in the star formation recipe they use. We use observations from Pico dos Días and GEMINI telescopes and show how we use observational data of the interacting pair in AM2229-735 to characterize the interacting pair. Later we use this information to simulate the evolution of the system to finally reproduce the observations: Mass distribution, morphology and main features of the merger-induced star formation burst. We show that both methods manage to reproduce roughly the star formation activity. We show, through a careful study, that resolution plays a major role in the reproducibility of the system. In that sense, star formation recipe implemented in GIZMO code has shown a more robust performance. Acknowledgements: This work is supported by Colciencias, Doctorado Nacional - 617 program.
Comparing nonlinear MHD simulations of low-aspect-ratio RFPs to RELAX experiments

NASA Astrophysics Data System (ADS)

McCollam, K. J.; den Hartog, D. J.; Jacobson, C. M.; Sovinec, C. R.; Masamune, S.; Sanpei, A.

2016-10-01

Standard reversed-field pinch (RFP) plasmas provide a nonlinear dynamical system as a validation domain for numerical MHD simulation codes, with applications in general toroidal confinement scenarios including tokamaks. Using the NIMROD code, we simulate the nonlinear evolution of RFP plasmas similar to those in the RELAX experiment. The experiment's modest Lundquist numbers S (as low as a few times 104) make closely matching MHD simulations tractable given present computing resources. Its low aspect ratio ( 2) motivates a comparison study using cylindrical and toroidal geometries in NIMROD. We present initial results from nonlinear single-fluid runs at S =104 for both geometries and a range of equilibrium parameters, which preliminarily show that the magnetic fluctuations are roughly similar between the two geometries and between simulation and experiment, though there appear to be some qualitative differences in their temporal evolution. Runs at higher S are planned. This work is supported by the U.S. DOE and by the Japan Society for the Promotion of Science.
On the Maximum Mass of Accreting Primordial Supermassive Stars

NASA Astrophysics Data System (ADS)

Woods, T. E.; Heger, Alexander; Whalen, Daniel J.; Haemmerlé, Lionel; Klessen, Ralf S.

2017-06-01

Supermassive primordial stars are suspected to be the progenitors of the most massive quasars at z ˜ 6. Previous studies of such stars were either unable to resolve hydrodynamical timescales or considered stars in isolation, not in the extreme accretion flows in which they actually form. Therefore, they could not self-consistently predict their final masses at collapse, or those of the resulting supermassive black hole seeds, but rather invoked comparison to simple polytropic models. Here, we systematically examine the birth, evolution, and collapse of accreting, non-rotating supermassive stars under accretion rates of 0.01-10 M ⊙ yr-1 using the stellar evolution code Kepler. Our approach includes post-Newtonian corrections to the stellar structure and an adaptive nuclear network and can transition to following the hydrodynamic evolution of supermassive stars after they encounter the general relativistic instability. We find that this instability triggers the collapse of the star at masses of 150,000-330,000 M ⊙ for accretion rates of 0.1-10 M ⊙ yr-1, and that the final mass of the star scales roughly logarithmically with the rate. The structure of the star, and thus its stability against collapse, is sensitive to the treatment of convection and the heat content of the outer accreted envelope. Comparison with other codes suggests differences here may lead to small deviations in the evolutionary state of the star as a function of time, that worsen with accretion rate. Since the general relativistic instability leads to the immediate death of these stars, our models place an upper limit on the masses of the first quasars at birth.
Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids.

PubMed

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia , which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla ), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase ( ndh ) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci- ndhA intron, matK-5'trnK , clpP-psbB , rps8-rpl14 , trnT-trnL , 3'trnK-matK , clpP intron , psbK-trnK , trnS-psbC , and ndhF-rpl32 -that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed.
Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

PubMed Central

Niu, Zhitao; Pan, Jiajia; Zhu, Shuying; Li, Ludan; Xue, Qingyun; Liu, Wei; Ding, Xiaoyu

2017-01-01

Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids. Unlike many orchid plastomes (e.g., Paphiopedilum and Vanilla), the plastomes of Apostasioideae contain a full set of 11 functional NADH dehydrogenase (ndh) genes. The distribution of repeat sequences and simple sequence repeat elements enhanced the view that the mutation rate of non-coding regions was higher than that of coding regions. The 10 loci—ndhA intron, matK-5′trnK, clpP-psbB, rps8-rpl14, trnT-trnL, 3′trnK-matK, clpP intron, psbK-trnK, trnS-psbC, and ndhF-rpl32—that had the highest degrees of sequence variability were identified as mutational hotspots for the Apostasia plastome. Furthermore, our results revealed that plastid genes exhibited a variable evolution rate within and among different orchid genus. Considering the diversified evolution of both coding and non-coding regions, we suggested that the plastome-wide evolution of orchid species was disproportional. Additionally, the sequences flanking the inverted repeat/small single copy (IR/SSC) junctions of photosynthetic orchid plastomes were categorized into three types according to the presence/absence of ndh genes. Different evolutionary dynamics for each of the three IR/SSC types of photosynthetic orchid plastomes were also proposed. PMID:29046685
Helioseismic Constraints on New Solar Models from the MoSEC Code

NASA Technical Reports Server (NTRS)

Elliott, J. R.

1998-01-01

Evolutionary solar models are computed using a new stellar evolution code, MOSEC (Modular Stellar Evolution Code). This code has been designed with carefully controlled truncation errors in order to achieve a precision which reflects the increasingly accurate determination of solar interior structure by helioseismology. A series of models is constructed to investigate the effects of the choice of equation of state (OPAL or MHD-E, the latter being a version of the MHD equation of state recalculated by the author), the inclusion of helium and heavy-element settling and diffusion, and the inclusion of a simple model of mixing associated with the solar tachocline. The neutrino flux predictions are discussed, while the sound speed of the computed models is compared to that of the sun via the latest inversion of SOI-NMI p-mode frequency data. The comparison between models calculated with the OPAL and MHD-E equations of state is particularly interesting because the MHD-E equation of state includes relativistic effects for the electrons, whereas neither MHD nor OPAL do. This has a significant effect on the sound speed of the computed model, worsening the agreement with the solar sound speed. Using the OPAL equation of state and including the settling and diffusion of helium and heavy elements produces agreement in sound speed with the helioseismic results to within about +.-0.2%; the inclusion of mixing slightly improves the agreement.
Energy loss of argon in a laser-generated carbon plasma.

PubMed

Frank, A; Blazević, A; Grande, P L; Harres, K; Hessling, T; Hoffmann, D H H; Knobloch-Maas, R; Kuznetsov, P G; Nürnberg, F; Pelka, A; Schaumann, G; Schiwietz, G; Schökel, A; Schollmeier, M; Schumacher, D; Schütrumpf, J; Vatulin, V V; Vinokurov, O A; Roth, M

2010-02-01

The experimental data presented in this paper address the energy loss determination for argon at 4 MeV/u projectile energy in laser-generated carbon plasma covering a huge parameter range in density and temperature. Furthermore, a consistent theoretical description of the projectile charge state evolution via a Monte Carlo code is combined with an improved version of the CasP code that allows us to calculate the contributions to the stopping power of bound and free electrons for each projectile charge state. This approach gets rid of any effective charge description of the stopping power. Comparison of experimental data and theoretical results allows us to judge the influence of different plasma parameters.
Evolution of the snake body form reveals homoplasy in amniote Hox gene function.

PubMed

Head, Jason J; Polly, P David

2015-04-02

Hox genes regulate regionalization of the axial skeleton in vertebrates, and changes in their expression have been proposed to be a fundamental mechanism driving the evolution of new body forms. The origin of the snake-like body form, with its deregionalized pre-cloacal axial skeleton, has been explained as either homogenization of Hox gene expression domains, or retention of standard vertebrate Hox domains with alteration of downstream expression that suppresses development of distinct regions. Both models assume a highly regionalized ancestor, but the extent of deregionalization of the primaxial domain (vertebrae, dorsal ribs) of the skeleton in snake-like body forms has never been analysed. Here we combine geometric morphometrics and maximum-likelihood analysis to show that the pre-cloacal primaxial domain of elongate, limb-reduced lizards and snakes is not deregionalized compared with limbed taxa, and that the phylogenetic structure of primaxial morphology in reptiles does not support a loss of regionalization in the evolution of snakes. We demonstrate that morphometric regional boundaries correspond to mapped gene expression domains in snakes, suggesting that their primaxial domain is patterned by a normally functional Hox code. Comparison of primaxial osteology in fossil and modern amniotes with Hox gene distributions within Amniota indicates that a functional, sequentially expressed Hox code patterned a subtle morphological gradient along the anterior-posterior axis in stem members of amniote clades and extant lizards, including snakes. The highly regionalized skeletons of extant archosaurs and mammals result from independent evolution in the Hox code and do not represent ancestral conditions for clades with snake-like body forms. The developmental origin of snakes is best explained by decoupling of the primaxial and abaxial domains and by increases in somite number, not by changes in the function of primaxial Hox genes.
Natural selection in avian protein-coding genes expressed in brain.

PubMed

Axelsson, Erik; Hultin-Rosenberg, Lina; Brandström, Mikael; Zwahlén, Martin; Clayton, David F; Ellegren, Hans

2008-06-01

The evolution of birds from theropod dinosaurs took place approximately 150 million years ago, and was associated with a number of specific adaptations that are still evident among extant birds, including feathers, song and extravagant secondary sexual characteristics. Knowledge about the molecular evolutionary background to such adaptations is lacking. Here, we analyse the evolution of > 5000 protein-coding gene sequences expressed in zebra finch brain by comparison to orthologous sequences in chicken. Mean d(N)/d(S) is 0.085 and genes with their maximal expression in the eye and central nervous system have the lowest mean d(N)/d(S) value, while those expressed in digestive and reproductive tissues exhibit the highest. We find that fast-evolving genes (those which have higher than expected rate of nonsynonymous substitution, indicative of adaptive evolution) are enriched for biological functions such as fertilization, muscle contraction, defence response, response to stress, wounding and endogenous stimulus, and cell death. After alignment to mammalian orthologues, we identify a catalogue of 228 genes that show a significantly higher rate of protein evolution in the two bird lineages than in mammals. These accelerated bird genes, representing candidates for avian-specific adaptations, include genes implicated in vocal learning and other cognitive processes. Moreover, colouration genes evolve faster in birds than in mammals, which may have been driven by sexual selection for extravagant plumage characteristics.
The Formation of a Milky Way-sized Disk Galaxy. I. A Comparison of Numerical Methods

NASA Astrophysics Data System (ADS)

Zhu, Qirong; Li, Yuexing

2016-11-01

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellar evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.
THE FORMATION OF A MILKY WAY-SIZED DISK GALAXY. I. A COMPARISON OF NUMERICAL METHODS

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

Zhu, Qirong; Li, Yuexing, E-mail: qxz125@psu.edu

The long-standing challenge of creating a Milky Way- (MW-) like disk galaxy from cosmological simulations has motivated significant developments in both numerical methods and physical models. We investigate these two fundamental aspects in a new comparison project using a set of cosmological hydrodynamic simulations of an MW-sized galaxy. In this study, we focus on the comparison of two particle-based hydrodynamics methods: an improved smoothed particle hydrodynamics (SPH) code Gadget, and a Lagrangian Meshless Finite-Mass (MFM) code Gizmo. All the simulations in this paper use the same initial conditions and physical models, which include star formation, “energy-driven” outflows, metal-dependent cooling, stellarmore » evolution, and metal enrichment. We find that both numerical schemes produce a late-type galaxy with extended gaseous and stellar disks. However, notable differences are present in a wide range of galaxy properties and their evolution, including star-formation history, gas content, disk structure, and kinematics. Compared to Gizmo, the Gadget simulation produced a larger fraction of cold, dense gas at high redshift which fuels rapid star formation and results in a higher stellar mass by 20% and a lower gas fraction by 10% at z = 0, and the resulting gas disk is smoother and more coherent in rotation due to damping of turbulent motion by the numerical viscosity in SPH, in contrast to the Gizmo simulation, which shows a more prominent spiral structure. Given its better convergence properties and lower computational cost, we argue that the MFM method is a promising alternative to SPH in cosmological hydrodynamic simulations.« less
Interpreting Mammalian Evolution using Fugu Genome Comparisons

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

Stubbs, L; Ovcharenko, I; Loots, G G

2004-04-02

Comparative sequence analysis of the human and the pufferfish Fugu rubripes (fugu) genomes has revealed several novel functional coding and noncoding regions in the human genome. In particular, the fugu genome has been extremely valuable for identifying transcriptional regulatory elements in human loci harboring unusually high levels of evolutionary conservation to rodent genomes. In such regions, the large evolutionary distance between human and fishes provides an additional filter through which functional noncoding elements can be detected with high efficiency.
CoCoNuT: General relativistic hydrodynamics code with dynamical space-time evolution

NASA Astrophysics Data System (ADS)

Dimmelmeier, Harald; Novak, Jérôme; Cerdá-Durán, Pablo

2012-02-01

CoCoNuT is a general relativistic hydrodynamics code with dynamical space-time evolution. The main aim of this numerical code is the study of several astrophysical scenarios in which general relativity can play an important role, namely the collapse of rapidly rotating stellar cores and the evolution of isolated neutron stars. The code has two flavors: CoCoA, the axisymmetric (2D) magnetized version, and CoCoNuT, the 3D non-magnetized version.
Simulation of profile evolution from ramp-up to ramp-down and optimization of tokamak plasma termination with the RAPTOR code

NASA Astrophysics Data System (ADS)

Teplukhina, A. A.; Sauter, O.; Felici, F.; Merle, A.; Kim, D.; the TCV Team; the ASDEX Upgrade Team; the EUROfusion MST1 Team

2017-12-01

The present work demonstrates the capabilities of the transport code RAPTOR as a fast and reliable simulator of plasma profiles for the entire plasma discharge, i.e. from ramp-up to ramp-down. This code focuses, at this stage, on the simulation of electron temperature and poloidal flux profiles using prescribed equilibrium and some kinetic profiles. In this work we extend the RAPTOR transport model to include a time-varying plasma equilibrium geometry and verify the changes via comparison with ATSRA code simulations. In addition a new ad hoc transport model based on constant gradients and suitable for simulations of L-H and H-L mode transitions has been incorporated into the RAPTOR code and validated with rapid simulations of the time evolution of the safety factor and the electron temperature over the entire AUG and TCV discharges. An optimization procedure for the plasma termination phase has also been developed during this work. We define the goal of the optimization as ramping down the plasma current as fast as possible while avoiding any disruptions caused by reaching physical or technical limits. Our numerical study of this problem shows that a fast decrease of plasma elongation during current ramp-down can help in reducing plasma internal inductance. An early transition from H- to L-mode allows us to reduce the drop in poloidal beta, which is also important for plasma MHD stability and control. This work shows how these complex nonlinear interactions can be optimized automatically using relevant cost functions and constraints. Preliminary experimental results for TCV are demonstrated.
Evolution at the tips: Asclepias phylogenomics and new perspectives on leaf surfaces.

PubMed

Fishbein, Mark; Straub, Shannon C K; Boutte, Julien; Hansen, Kimberly; Cronn, Richard C; Liston, Aaron

2018-03-01

Leaf surface traits, such as trichome density and wax production, mediate important ecological processes such as anti-herbivory defense and water-use efficiency. We present a phylogenetic analysis of Asclepias plastomes as a framework for analyzing the evolution of trichome density and presence of epicuticular waxes. We produced a maximum-likelihood phylogeny using plastomes of 103 species of Asclepias. We reconstructed ancestral states and used model comparisons in a likelihood framework to analyze character evolution across Asclepias. We resolved the backbone of Asclepias, placing the Sonoran Desert clade and Incarnatae clade as successive sisters to the remaining species. We present novel findings about leaf surface evolution of Asclepias-the ancestor is reconstructed as waxless and sparsely hairy, a macroevolutionary optimal trichome density is supported, and the rate of evolution of trichome density has accelerated. Increased sampling and selection of best-fitting models of evolution provide more resolved and robust estimates of phylogeny and character evolution than obtained in previous studies. Evolutionary inferences are more sensitive to character coding than model selection. © 2018 The Authors. American Journal of Botany is published by Wiley Periodicals, Inc. on behalf of the Botanical Society of America.
GATA: A graphic alignment tool for comparative sequenceanalysis

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

Nix, David A.; Eisen, Michael B.

2005-01-01

Several problems exist with current methods used to align DNA sequences for comparative sequence analysis. Most dynamic programming algorithms assume that conserved sequence elements are collinear. This assumption appears valid when comparing orthologous protein coding sequences. Functional constraints on proteins provide strong selective pressure against sequence inversions, and minimize sequence duplications and feature shuffling. For non-coding sequences this collinearity assumption is often invalid. For example, enhancers contain clusters of transcription factor binding sites that change in number, orientation, and spacing during evolution yet the enhancer retains its activity. Dotplot analysis is often used to estimate non-coding sequence relatedness. Yet dotmore » plots do not actually align sequences and thus cannot account well for base insertions or deletions. Moreover, they lack an adequate statistical framework for comparing sequence relatedness and are limited to pairwise comparisons. Lastly, dot plots and dynamic programming text outputs fail to provide an intuitive means for visualizing DNA alignments.« less
On the Maximum Mass of Accreting Primordial Supermassive Stars

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

Woods, T. E.; Heger, Alexander; Whalen, Daniel J.

Supermassive primordial stars are suspected to be the progenitors of the most massive quasars at z ∼ 6. Previous studies of such stars were either unable to resolve hydrodynamical timescales or considered stars in isolation, not in the extreme accretion flows in which they actually form. Therefore, they could not self-consistently predict their final masses at collapse, or those of the resulting supermassive black hole seeds, but rather invoked comparison to simple polytropic models. Here, we systematically examine the birth, evolution, and collapse of accreting, non-rotating supermassive stars under accretion rates of 0.01–10 M {sub ⊙} yr{sup −1} using themore » stellar evolution code Kepler . Our approach includes post-Newtonian corrections to the stellar structure and an adaptive nuclear network and can transition to following the hydrodynamic evolution of supermassive stars after they encounter the general relativistic instability. We find that this instability triggers the collapse of the star at masses of 150,000–330,000 M {sub ⊙} for accretion rates of 0.1–10 M {sub ⊙} yr{sup −1}, and that the final mass of the star scales roughly logarithmically with the rate. The structure of the star, and thus its stability against collapse, is sensitive to the treatment of convection and the heat content of the outer accreted envelope. Comparison with other codes suggests differences here may lead to small deviations in the evolutionary state of the star as a function of time, that worsen with accretion rate. Since the general relativistic instability leads to the immediate death of these stars, our models place an upper limit on the masses of the first quasars at birth.« less
Differential Expression of Non-Coding RNAs and Continuous Evolution of the X Chromosome in Testicular Transcriptome of Two Mouse Species

PubMed Central

Homolka, David; Ivanek, Robert; Forejt, Jiri; Jansa, Petr

2011-01-01

Background Tight regulation of testicular gene expression is a prerequisite for male reproductive success, while differentiation of gene activity in spermatogenesis is important during speciation. Thus, comparison of testicular transcriptomes between closely related species can reveal unique regulatory patterns and shed light on evolutionary constraints separating the species. Methodology/Principal Findings Here, we compared testicular transcriptomes of two closely related mouse species, Mus musculus and Mus spretus, which diverged more than one million years ago. We analyzed testicular expression using tiling arrays overlapping Chromosomes 2, X, Y and mitochondrial genome. An excess of differentially regulated non-coding RNAs was found on Chromosome 2 including the intronic antisense RNAs, intergenic RNAs and premature forms of Piwi-interacting RNAs (piRNAs). Moreover, striking difference was found in the expression of X-linked G6pdx gene, the parental gene of the autosomal retrogene G6pd2. Conclusions/Significance The prevalence of non-coding RNAs among differentially expressed transcripts indicates their role in species-specific regulation of spermatogenesis. The postmeiotic expression of G6pdx in Mus spretus points towards the continuous evolution of X-chromosome silencing and provides an example of expression change accompanying the out-of-the X-chromosomal retroposition. PMID:21347268
TIME-DEPENDENT MULTI-GROUP MULTI-DIMENSIONAL RELATIVISTIC RADIATIVE TRANSFER CODE BASED ON SPHERICAL HARMONIC DISCRETE ORDINATE METHOD

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

Tominaga, Nozomu; Shibata, Sanshiro; Blinnikov, Sergei I., E-mail: tominaga@konan-u.ac.jp, E-mail: sshibata@post.kek.jp, E-mail: Sergei.Blinnikov@itep.ru

We develop a time-dependent, multi-group, multi-dimensional relativistic radiative transfer code, which is required to numerically investigate radiation from relativistic fluids that are involved in, e.g., gamma-ray bursts and active galactic nuclei. The code is based on the spherical harmonic discrete ordinate method (SHDOM) which evaluates a source function including anisotropic scattering in spherical harmonics and implicitly solves the static radiative transfer equation with ray tracing in discrete ordinates. We implement treatments of time dependence, multi-frequency bins, Lorentz transformation, and elastic Thomson and inelastic Compton scattering to the publicly available SHDOM code. Our code adopts a mixed-frame approach; the source functionmore » is evaluated in the comoving frame, whereas the radiative transfer equation is solved in the laboratory frame. This implementation is validated using various test problems and comparisons with the results from a relativistic Monte Carlo code. These validations confirm that the code correctly calculates the intensity and its evolution in the computational domain. The code enables us to obtain an Eddington tensor that relates the first and third moments of intensity (energy density and radiation pressure) and is frequently used as a closure relation in radiation hydrodynamics calculations.« less

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.
Current Status of Post-combustor Trace Chemistry Modeling and Simulation at NASA Glenn Research Center

NASA Technical Reports Server (NTRS)

Wey, Thomas; Liu, Nan-Suey

2003-01-01

The overall objective of the current effort at NASA GRC is to evaluate, develop, and apply methodologies suitable for modeling intra-engine trace chemical changes over post combustor flow path relevant to the pollutant emissions from aircraft engines. At the present time, the focus is the high pressure turbine environment. At first, the trace chemistry model of CNEWT were implemented into GLENN-HT as well as NCC. Then, CNEWT, CGLENN-HT, and NCC were applied to the trace species evolution in a cascade of Cambridge University's No. 2 rotor and in a turbine vane passage. In general, the results from these different codes provide similar features. However, the details of some of the quantities of interest can be sensitive to the differences of these codes. This report summaries the implementation effort and presents the comparison of the No. 2 rotor results obtained from these different codes. The comparison of the turbine vane passage results is reported elsewhere. In addition to the implementation of trace chemistry model into existing CFD codes, several pre/post-processing tools that can handle the manipulations of the geometry, the unstructured and structured grids as well as the CFD solutions also have been enhanced and seamlessly tied with NCC, CGLENN-HT, and CNEWT. Thus, a complete CFD package consisting of pre/post-processing tools and flow solvers suitable for post-combustor intra-engine trace chemistry study is assembled.
A Comparison of the CHILD and Landlab Computational Landscape Evolution Models and Examples of Best Practices in Numerical Modeling of Surface Processes

NASA Astrophysics Data System (ADS)

Gasparini, N. M.; Hobley, D. E. J.; Tucker, G. E.; Istanbulluoglu, E.; Adams, J. M.; Nudurupati, S. S.; Hutton, E. W. H.

2014-12-01

Computational models are important tools that can be used to quantitatively understand the evolution of real landscapes. Commonalities exist among most landscape evolution models, although they are also idiosyncratic, in that they are coded in different languages, require different input values, and are designed to tackle a unique set of questions. These differences can make applying a landscape evolution model challenging, especially for novice programmers. In this study, we compare and contrast two landscape evolution models that are designed to tackle similar questions, but the actual model designs are quite different. The first model, CHILD, is over a decade-old and is relatively well-tested, well-developed and well-used. It is coded in C++, operates on an irregular grid and was designed more with function rather than user-experience in mind. In contrast, the second model, Landlab, is relatively new and was designed to be accessible to a wide range of scientists, including those who have not previously used or developed a numerical model. Landlab is coded in Python, a relatively easy language for the non-proficient programmer, and has the ability to model landscapes described on both regular and irregular grids. We present landscape simulations from both modeling platforms. Our goal is to illustrate best practices for implementing a new process module in a landscape evolution model, and therefore the simulations are applicable regardless of the modeling platform. We contrast differences and highlight similarities between the use of the two models, including setting-up the model and input file for different evolutionary scenarios, computational time, and model output. Whenever possible, we compare model output with analytical solutions and illustrate the effects, or lack thereof, of a uniform vs. non-uniform grid. Our simulations focus on implementing a single process, including detachment-limited or transport-limited fluvial bedrock incision and linear or non-linear diffusion of material on hillslopes. We also illustrate the steps necessary to couple processes together, for example, detachment-limited fluvial bedrock incision with linear diffusion on hillslopes. Trade-offs exist between the two modeling platforms, and these are primarily in speed and ease-of-use.
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes

PubMed Central

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-01-01

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution. PMID:25523484
Decelerated genome evolution in modern vertebrates revealed by analysis of multiple lancelet genomes.

PubMed

Huang, Shengfeng; Chen, Zelin; Yan, Xinyu; Yu, Ting; Huang, Guangrui; Yan, Qingyu; Pontarotti, Pierre Antoine; Zhao, Hongchen; Li, Jie; Yang, Ping; Wang, Ruihua; Li, Rui; Tao, Xin; Deng, Ting; Wang, Yiquan; Li, Guang; Zhang, Qiujin; Zhou, Sisi; You, Leiming; Yuan, Shaochun; Fu, Yonggui; Wu, Fenfang; Dong, Meiling; Chen, Shangwu; Xu, Anlong

2014-12-19

Vertebrates diverged from other chordates ~500 Myr ago and experienced successful innovations and adaptations, but the genomic basis underlying vertebrate origins are not fully understood. Here we suggest, through comparison with multiple lancelet (amphioxus) genomes, that ancient vertebrates experienced high rates of protein evolution, genome rearrangement and domain shuffling and that these rates greatly slowed down after the divergence of jawed and jawless vertebrates. Compared with lancelets, modern vertebrates retain, at least relatively, less protein diversity, fewer nucleotide polymorphisms, domain combinations and conserved non-coding elements (CNE). Modern vertebrates also lost substantial transposable element (TE) diversity, whereas lancelets preserve high TE diversity that includes even the long-sought RAG transposon. Lancelets also exhibit rapid gene turnover, pervasive transcription, fastest exon shuffling in metazoans and substantial TE methylation not observed in other invertebrates. These new lancelet genome sequences provide new insights into the chordate ancestral state and the vertebrate evolution.
Evaluation of fusion-evaporation cross-section calculations

NASA Astrophysics Data System (ADS)

Blank, B.; Canchel, G.; Seis, F.; Delahaye, P.

2018-02-01

Calculated fusion-evaporation cross sections from five different codes are compared to experimental data. The present comparison extents over a large range of nuclei and isotopic chains to investigate the evolution of experimental and calculated cross sections. All models more or less overestimate the experimental cross sections. We found reasonable agreement by using the geometrical average of the five model calculations and dividing the average by a factor of 11.2. More refined analyses are made for example for the 100Sn region.
Overview of Recent Radiation Transport Code Comparisons for Space Applications

NASA Astrophysics Data System (ADS)

Townsend, Lawrence

Recent advances in radiation transport code development for space applications have resulted in various comparisons of code predictions for a variety of scenarios and codes. Comparisons among both Monte Carlo and deterministic codes have been made and published by vari-ous groups and collaborations, including comparisons involving, but not limited to HZETRN, HETC-HEDS, FLUKA, GEANT, PHITS, and MCNPX. In this work, an overview of recent code prediction inter-comparisons, including comparisons to available experimental data, is presented and discussed, with emphases on those areas of agreement and disagreement among the various code predictions and published data.
Possibilities for the evolution of the genetic code from a preceding form

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1973-01-01

Analysis of the interaction between mRNA codons and tRNA anticodons suggests a model for the evolution of the genetic code. Modification of the nucleic acid following the anticodon is at present essential in both eukaryotes and prokaryotes to ensure fidelity of translation of codons starting with A, and the amino acids which could be coded for before the evolution of the modifying enzymes can be deduced.
Characteristic Evolution and Matching

NASA Astrophysics Data System (ADS)

Winicour, Jeffrey

2012-01-01

I review the development of numerical evolution codes for general relativity based upon the characteristic initial-value problem. Progress in characteristic evolution is traced from the early stage of 1D feasibility studies to 2D-axisymmetric codes that accurately simulate the oscillations and gravitational collapse of relativistic stars and to current 3D codes that provide pieces of a binary black-hole spacetime. Cauchy codes have now been successful at simulating all aspects of the binary black-hole problem inside an artificially constructed outer boundary. A prime application of characteristic evolution is to extend such simulations to null infinity where the waveform from the binary inspiral and merger can be unambiguously computed. This has now been accomplished by Cauchy-characteristic extraction, where data for the characteristic evolution is supplied by Cauchy data on an extraction worldtube inside the artificial outer boundary. The ultimate application of characteristic evolution is to eliminate the role of this outer boundary by constructing a global solution via Cauchy-characteristic matching. Progress in this direction is discussed.
Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches.

PubMed

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code enzo-2.4 and the smoothed particle hydrodynamics (SPH)/ N -body code gadget-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in gadget-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H 2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ∼ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, gadget-3 requires significantly larger computational resources than enzo-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.
Direct collapse to supermassive black hole seeds: comparing the AMR and SPH approaches

NASA Astrophysics Data System (ADS)

Luo, Yang; Nagamine, Kentaro; Shlosman, Isaac

2016-07-01

We provide detailed comparison between the adaptive mesh refinement (AMR) code ENZO-2.4 and the smoothed particle hydrodynamics (SPH)/N-body code GADGET-3 in the context of isolated or cosmological direct baryonic collapse within dark matter (DM) haloes to form supermassive black holes. Gas flow is examined by following evolution of basic parameters of accretion flows. Both codes show an overall agreement in the general features of the collapse; however, many subtle differences exist. For isolated models, the codes increase their spatial and mass resolutions at different pace, which leads to substantially earlier collapse in SPH than in AMR cases due to higher gravitational resolution in GADGET-3. In cosmological runs, the AMR develops a slightly higher baryonic resolution than SPH during halo growth via cold accretion permeated by mergers. Still, both codes agree in the build-up of DM and baryonic structures. However, with the onset of collapse, this difference in mass and spatial resolution is amplified, so evolution of SPH models begins to lag behind. Such a delay can have effect on formation/destruction rate of H2 due to UV background, and on basic properties of host haloes. Finally, isolated non-cosmological models in spinning haloes, with spin parameter λ ˜ 0.01-0.07, show delayed collapse for greater λ, but pace of this increase is faster for AMR. Within our simulation set-up, GADGET-3 requires significantly larger computational resources than ENZO-2.4 during collapse, and needs similar resources, during the pre-collapse, cosmological structure formation phase. Yet it benefits from substantially higher gravitational force and hydrodynamic resolutions, except at the end of collapse.
Inclusion of the fitness sharing technique in an evolutionary algorithm to analyze the fitness landscape of the genetic code adaptability.

PubMed

Santos, José; Monteagudo, Ángel

2017-03-27

The canonical code, although prevailing in complex genomes, is not universal. It was shown the canonical genetic code superior robustness compared to random codes, but it is not clearly determined how it evolved towards its current form. The error minimization theory considers the minimization of point mutation adverse effect as the main selection factor in the evolution of the code. We have used simulated evolution in a computer to search for optimized codes, which helps to obtain information about the optimization level of the canonical code in its evolution. A genetic algorithm searches for efficient codes in a fitness landscape that corresponds with the adaptability of possible hypothetical genetic codes. The lower the effects of errors or mutations in the codon bases of a hypothetical code, the more efficient or optimal is that code. The inclusion of the fitness sharing technique in the evolutionary algorithm allows the extent to which the canonical genetic code is in an area corresponding to a deep local minimum to be easily determined, even in the high dimensional spaces considered. The analyses show that the canonical code is not in a deep local minimum and that the fitness landscape is not a multimodal fitness landscape with deep and separated peaks. Moreover, the canonical code is clearly far away from the areas of higher fitness in the landscape. Given the non-presence of deep local minima in the landscape, although the code could evolve and different forces could shape its structure, the fitness landscape nature considered in the error minimization theory does not explain why the canonical code ended its evolution in a location which is not an area of a localized deep minimum of the huge fitness landscape.
Phenotypic Graphs and Evolution Unfold the Standard Genetic Code as the Optimal

NASA Astrophysics Data System (ADS)

Zamudio, Gabriel S.; José, Marco V.

2018-03-01

In this work, we explicitly consider the evolution of the Standard Genetic Code (SGC) by assuming two evolutionary stages, to wit, the primeval RNY code and two intermediate codes in between. We used network theory and graph theory to measure the connectivity of each phenotypic graph. The connectivity values are compared to the values of the codes under different randomization scenarios. An error-correcting optimal code is one in which the algebraic connectivity is minimized. We show that the SGC is optimal in regard to its robustness and error-tolerance when compared to all random codes under different assumptions.
Mechanistic prediction of fission-gas behavior during in-cell transient heating tests on LWR fuel using the GRASS-SST and FASTGRASS computer codes

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

Rest, J; Gehl, S M

1979-01-01

GRASS-SST and FASTGRASS are mechanistic computer codes for predicting fission-gas behavior in UO/sub 2/-base fuels during steady-state and transient conditions. FASTGRASS was developed in order to satisfy the need for a fast-running alternative to GRASS-SST. Althrough based on GRASS-SST, FASTGRASS is approximately an order of magnitude quicker in execution. The GRASS-SST transient analysis has evolved through comparisons of code predictions with the fission-gas release and physical phenomena that occur during reactor operation and transient direct-electrical-heating (DEH) testing of irradiated light-water reactor fuel. The FASTGRASS calculational procedure is described in this paper, along with models of key physical processes included inmore » both FASTGRASS and GRASS-SST. Predictions of fission-gas release obtained from GRASS-SST and FASTGRASS analyses are compared with experimental observations from a series of DEH tests. The major conclusions is that the computer codes should include an improved model for the evolution of the grain-edge porosity.« less
Cross-verification of the GENE and XGC codes in preparation for their coupling

NASA Astrophysics Data System (ADS)

Jenko, Frank; Merlo, Gabriele; Bhattacharjee, Amitava; Chang, Cs; Dominski, Julien; Ku, Seunghoe; Parker, Scott; Lanti, Emmanuel

2017-10-01

A high-fidelity Whole Device Model (WDM) of a magnetically confined plasma is a crucial tool for planning and optimizing the design of future fusion reactors, including ITER. Aiming at building such a tool, in the framework of the Exascale Computing Project (ECP) the two existing gyrokinetic codes GENE (Eulerian delta-f) and XGC (PIC full-f) will be coupled, thus enabling to carry out first principle kinetic WDM simulations. In preparation for this ultimate goal, a benchmark between the two codes is carried out looking at ITG modes in the adiabatic electron limit. This verification exercise is also joined by the global Lagrangian PIC code ORB5. Linear and nonlinear comparisons have been carried out, neglecting for simplicity collisions and sources. A very good agreement is recovered on frequency, growth rate and mode structure of linear modes. A similarly excellent agreement is also observed comparing the evolution of the heat flux and of the background temperature profile during nonlinear simulations. Work supported by the US DOE under the Exascale Computing Project (17-SC-20-SC).
Comparative Mitogenomic Analysis of Damsel Bugs Representing Three Tribes in the Family Nabidae (Insecta: Hemiptera)

PubMed Central

Song, Fan; Shi, Aimin; Zhou, Xuguo; Cai, Wanzhi

2012-01-01

Background Nabidae, a family of predatory heteropterans, includes two subfamilies and five tribes. We previously reported the complete mitogenome of Alloeorhynchus bakeri, a representative of the tribe Prostemmatini in the subfamily Prostemmatinae. To gain a better understanding of architecture and evolution of mitogenome in Nabidae, mitogenomes of five species representing two tribes (Gorpini and Nabini) in the subfamily Nabinae were sequenced, and a comparative mitogenomic analysis of three nabid tribes in two subfamilies was carried out. Methodology/Principal Findings Nabid mitogenomes share a similar nucleotide composition and base bias, except for the control region, where differences are observed at the subfamily level. In addition, the pattern of codon usage is influenced by the GC content and consistent with the standard invertebrate mitochondrial genetic code and the preference for A+T-rich codons. The comparison among orthologous protein-coding genes shows that different genes have been subject to different rates of molecular evolution correlated with the GC content. The stems and anticodon loops of tRNAs are extremely conserved, and the nucleotide substitutions are largely restricted to TψC and DHU loops and extra arms, with insertion-deletion polymorphisms. Comparative analysis shows similar rates of substitution between the two rRNAs. Long non-coding regions are observed in most Gorpini and Nabini mtDNAs in-between trnI-trnQ and/or trnS2-nad1. The lone exception, Nabis apicalis, however, has lost three tRNAs. Overall, phylogenetic analysis using mitogenomic data is consistent with phylogenies constructed mainly form morphological traits. Conclusions/Significance This comparative mitogenomic analysis sheds light on the architecture and evolution of mitogenomes in the family Nabidae. Nucleotide diversity and mitogenomic traits are phylogenetically informative at subfamily level. Furthermore, inclusion of a broader range of samples representing various taxonomic levels is critical for the understanding of mitogenomic evolution in damsel bugs. PMID:23029320
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.
Comparison of ACCENT 2000 Shuttle Plume Data with SIMPLE Model Predictions

NASA Astrophysics Data System (ADS)

Swaminathan, P. K.; Taylor, J. C.; Ross, M. N.; Zittel, P. F.; Lloyd, S. A.

2001-12-01

The JHU/APL Stratospheric IMpact of PLume Effluents (SIMPLE)model was employed to analyze the trace species in situ composition data collected during the ACCENT 2000 intercepts of the space shuttle Space Transportation Launch System (STS) rocket plume as a function of time and radial location within the cold plume. The SIMPLE model is initialized using predictions for species depositions calculated using an afterburning model based on standard TDK/SPP nozzle and SPF plume flowfield codes with an expanded chemical kinetic scheme. The time dependent ambient stratospheric chemistry is fully coupled to the plume species evolution whose transport is based on empirically derived diffusion. Model/data comparisons are encouraging through capturing observed local ozone recovery times as well as overall morphology of chlorine chemistry.
Implications of the plastid genome sequence of typha (typhaceae, poales) for understanding genome evolution in poaceae.

PubMed

Guisinger, Mary M; Chumley, Timothy W; Kuehl, Jennifer V; Boore, Jeffrey L; Jansen, Robert K

2010-02-01

Plastid genomes of the grasses (Poaceae) are unusual in their organization and rates of sequence evolution. There has been a recent surge in the availability of grass plastid genome sequences, but a comprehensive comparative analysis of genome evolution has not been performed that includes any related families in the Poales. We report on the plastid genome of Typha latifolia, the first non-grass Poales sequenced to date, and we present comparisons of genome organization and sequence evolution within Poales. Our results confirm that grass plastid genomes exhibit acceleration in both genomic rearrangements and nucleotide substitutions. Poaceae have multiple structural rearrangements, including three inversions, three genes losses (accD, ycf1, ycf2), intron losses in two genes (clpP, rpoC1), and expansion of the inverted repeat (IR) into both large and small single-copy regions. These rearrangements are restricted to the Poaceae, and IR expansion into the small single-copy region correlates with the phylogeny of the family. Comparisons of 73 protein-coding genes for 47 angiosperms including nine Poaceae genera confirm that the branch leading to Poaceae has significantly accelerated rates of change relative to other monocots and angiosperms. Furthermore, rates of sequence evolution within grasses are lower, indicating a deceleration during diversification of the family. Overall there is a strong correlation between accelerated rates of genomic rearrangements and nucleotide substitutions in Poaceae, a phenomenon that has been noted recently throughout angiosperms. The cause of the correlation is unknown, but faulty DNA repair has been suggested in other systems including bacterial and animal mitochondrial genomes.
Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India.

PubMed

Subramaniam, Saravanan; Mohapatra, Jajati K; Das, Biswajit; Sharma, Gaurav K; Biswal, Jitendra K; Mahajan, Sonalika; Misri, Jyoti; Dash, Bana B; Pattnaik, Bramhadev

2015-07-01

Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.

Hardware-efficient bosonic quantum error-correcting codes based on symmetry operators

NASA Astrophysics Data System (ADS)

Niu, Murphy Yuezhen; Chuang, Isaac L.; Shapiro, Jeffrey H.

2018-03-01

We establish a symmetry-operator framework for designing quantum error-correcting (QEC) codes based on fundamental properties of the underlying system dynamics. Based on this framework, we propose three hardware-efficient bosonic QEC codes that are suitable for χ(2 )-interaction based quantum computation in multimode Fock bases: the χ(2 ) parity-check code, the χ(2 ) embedded error-correcting code, and the χ(2 ) binomial code. All of these QEC codes detect photon-loss or photon-gain errors by means of photon-number parity measurements, and then correct them via χ(2 ) Hamiltonian evolutions and linear-optics transformations. Our symmetry-operator framework provides a systematic procedure for finding QEC codes that are not stabilizer codes, and it enables convenient extension of a given encoding to higher-dimensional qudit bases. The χ(2 ) binomial code is of special interest because, with m ≤N identified from channel monitoring, it can correct m -photon-loss errors, or m -photon-gain errors, or (m -1 )th -order dephasing errors using logical qudits that are encoded in O (N ) photons. In comparison, other bosonic QEC codes require O (N2) photons to correct the same degree of bosonic errors. Such improved photon efficiency underscores the additional error-correction power that can be provided by channel monitoring. We develop quantum Hamming bounds for photon-loss errors in the code subspaces associated with the χ(2 ) parity-check code and the χ(2 ) embedded error-correcting code, and we prove that these codes saturate their respective bounds. Our χ(2 ) QEC codes exhibit hardware efficiency in that they address the principal error mechanisms and exploit the available physical interactions of the underlying hardware, thus reducing the physical resources required for implementing their encoding, decoding, and error-correction operations, and their universal encoded-basis gate sets.
Direct modeling of coda wave interferometry: comparison of numerical and experimental approaches

NASA Astrophysics Data System (ADS)

Azzola, Jérôme; Masson, Frédéric; Schmittbuhl, Jean

2017-04-01

The sensitivity of coda waves to small changes of the propagation medium is the principle of the coda waves interferometry, a technique which has been found to have a large range of applications over the past years. It exploits the evolution of strongly scattered waves in a limited region of space, to estimate slight changes like the wave velocity of the medium but also the location of scatterer positions or the stress field. Because of the sensitivity of the method, it is of a great value for the monitoring of geothermal EGS reservoir in order to detect fine changes. The aim of this work is thus to monitor the impact of different scatterer distributions and of the loading condition evolution using coda wave interferometry in the laboratory and numerically by modelling the scatter wavefield. In the laboratory, we analyze the scattering of an acoustic wave through a perforated loaded plate of DURAL. Indeed, the localized damages introduced behave as a scatter source. Coda wave interferometry is performed computing correlations of waveforms under different loading conditions, for different scatter distributions. Numerically, we used SPECFEM2D (a 2D spectral element code, (Komatitsch and Vilotte (1998)) to perform 2D simulations of acoustic and elastic seismic wave propagation and enables a direct comparison with laboratory and field results. An unstructured mesh is thus used to simulate the propagation of a wavelet in a loaded plate, before and after introduction of localized damages. The linear elastic deformation of the plate is simulated using Code Aster. The coda wave interferometry is performed similarly to experimental measurements. The accuracy of the comparison of the numerically and laboratory obtained results is strongly depending on the capacity to adapt the laboratory and numerical simulation conditions. In laboratory, the capacity to illuminate the medium in a similar way to that used in the numerical simulation deeply conditions among others the comparison. In the simulation, the gesture of the mesh and its dispersion also influences the rightness of the comparison and interpretation. Moreover, the spectral elements distribution of the mesh and its relative refinement could also be considered as an interesting scatter source.
Mitochondrial genome evolution in the Saccharomyces sensu stricto complex.

PubMed

Ruan, Jiangxing; Cheng, Jian; Zhang, Tongcun; Jiang, Huifeng

2017-01-01

Exploring the evolutionary patterns of mitochondrial genomes is important for our understanding of the Saccharomyces sensu stricto (SSS) group, which is a model system for genomic evolution and ecological analysis. In this study, we first obtained the complete mitochondrial sequences of two important species, Saccharomyces mikatae and Saccharomyces kudriavzevii. We then compared the mitochondrial genomes in the SSS group with those of close relatives, and found that the non-coding regions evolved rapidly, including dramatic expansion of intergenic regions, fast evolution of introns and almost 20-fold higher rearrangement rates than those of the nuclear genomes. However, the coding regions, and especially the protein-coding genes, are more conserved than those in the nuclear genomes of the SSS group. The different evolutionary patterns of coding and non-coding regions in the mitochondrial and nuclear genomes may be related to the origin of the aerobic fermentation lifestyle in this group. Our analysis thus provides novel insights into the evolution of mitochondrial genomes.
GPU accelerated manifold correction method for spinning compact binaries

NASA Astrophysics Data System (ADS)

Ran, Chong-xi; Liu, Song; Zhong, Shuang-ying

2018-04-01

The graphics processing unit (GPU) acceleration of the manifold correction algorithm based on the compute unified device architecture (CUDA) technology is designed to simulate the dynamic evolution of the Post-Newtonian (PN) Hamiltonian formulation of spinning compact binaries. The feasibility and the efficiency of parallel computation on GPU have been confirmed by various numerical experiments. The numerical comparisons show that the accuracy on GPU execution of manifold corrections method has a good agreement with the execution of codes on merely central processing unit (CPU-based) method. The acceleration ability when the codes are implemented on GPU can increase enormously through the use of shared memory and register optimization techniques without additional hardware costs, implying that the speedup is nearly 13 times as compared with the codes executed on CPU for phase space scan (including 314 × 314 orbits). In addition, GPU-accelerated manifold correction method is used to numerically study how dynamics are affected by the spin-induced quadrupole-monopole interaction for black hole binary system.
Evolutionary Dynamics of Microsatellite Distribution in Plants: Insight from the Comparison of Sequenced Brassica, Arabidopsis and Other Angiosperm Species

PubMed Central

Shi, Jiaqin; Huang, Shunmou; Fu, Donghui; Yu, Jinyin; Wang, Xinfa; Hua, Wei; Liu, Shengyi; Liu, Guihua; Wang, Hanzhong

2013-01-01

Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences). The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number) of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type) the angiosperm species (aside from a few species) all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite distribution with respect to motif length, type and repeat number. Interestingly, several microsatellite characteristics seemed to be constant in plant evolution, which can be well explained by the general biological rules. PMID:23555856
An Analysis of the Changes in Communication Techniques in the Italian Codes of Medical Deontology.

PubMed

Conti, Andrea Alberto

2017-04-28

The code of deontology of the Italian National Federation of the Colleges of Physicians, Surgeons and Dentists (FNOMCeO) contains the principles and rules to which the professional medical practitioner must adhere. This work identifies and analyzes the medical-linguistic choices and the expressive techniques present in the different editions of the code, and evaluates their purpose and function, focusing on the first appearance and the subsequent frequency of key terms. Various aspects of the formal and expressive revisions of the eight editions of the Codes of Medical Deontology published after the Second World War (from 1947/48 to 2014) are here presented, starting from a brief comparison with the first edition of 1903. Formal characteristics, choices of medical terminology and the introduction of new concepts and communicative attitudes are here identified and evaluated. This paper, in presenting a quantitative and epistemological analysis of variations, modifications and confirmations in the different editions of the Italian code of medical deontology over the last century, enucleates and demonstrates the dynamic paradigm of changing attitudes in the medical profession. This analysis shows the evolution in medical-scientific communication as embodied in the Italian code of medical deontology. This code, in its adoption, changes and adaptations, as evidenced in its successive editions, bears witness to the expressions and attitudes pertinent to and characteristic of the deontological stance of the medical profession during the twentieth century.
Snake mitochondrial genomes: phylogenetic relationships and implications of extended taxon sampling for interpretations of mitogenomic evolution

PubMed Central

2010-01-01

Background Snake mitochondrial genomes are of great interest in understanding mitogenomic evolution because of gene duplications and rearrangements and the fast evolutionary rate of their genes compared to other vertebrates. Mitochondrial gene sequences have also played an important role in attempts to resolve the contentious phylogenetic relationships of especially the early divergences among alethinophidian snakes. Two recent innovative studies found dramatic gene- and branch-specific relative acceleration in snake protein-coding gene evolution, particularly along internal branches leading to Serpentes and Alethinophidia. It has been hypothesized that some of these rate shifts are temporally (and possibly causally) associated with control region duplication and/or major changes in ecology and anatomy. Results The near-complete mitochondrial (mt) genomes of three henophidian snakes were sequenced: Anilius scytale, Rhinophis philippinus, and Charina trivirgata. All three genomes share a duplicated control region and translocated tRNALEU, derived features found in all alethinophidian snakes studied to date. The new sequence data were aligned with mt genome data for 21 other species of snakes and used in phylogenetic analyses. Phylogenetic results agreed with many other studies in recovering several robust clades, including Colubroidea, Caenophidia, and Cylindrophiidae+Uropeltidae. Nodes within Henophidia that have been difficult to resolve robustly in previous analyses remained uncompellingly resolved here. Comparisons of relative rates of evolution of rRNA vs. protein-coding genes were conducted by estimating branch lengths across the tree. Our expanded sampling revealed dramatic acceleration along the branch leading to Typhlopidae, particularly long rRNA terminal branches within Scolecophidia, and that most of the dramatic acceleration in protein-coding gene rate along Serpentes and Alethinophidia branches occurred before Anilius diverged from other alethinophidians. Conclusions Mitochondrial gene sequence data alone may not be able to robustly resolve basal divergences among alethinophidian snakes. Taxon sampling plays an important role in identifying mitogenomic evolutionary events within snakes, and in testing hypotheses explaining their origin. Dramatic rate shifts in mitogenomic evolution occur within Scolecophidia as well as Alethinophidia, thus falsifying the hypothesis that these shifts in snakes are associated exclusively with evolution of a non-burrowing lifestyle, macrostomatan feeding ecology and/or duplication of the control region, both restricted to alethinophidians among living snakes. PMID:20055998
Genome sequences of two closely related strains of Escherichia coli K-12 GM4792.

PubMed

Zhang, Yan-Cong; Zhang, Yan; Zhu, Bi-Ru; Zhang, Bo-Wen; Ni, Chuan; Zhang, Da-Yong; Huang, Ying; Pang, Erli; Lin, Kui

2015-01-01

Escherichia coli lab strains K-12 GM4792 Lac(+) and GM4792 Lac(-) carry opposite lactose markers, which are useful for distinguishing evolved lines as they produce different colored colonies. The two closely related strains are chosen as ancestors for our ongoing studies of experimental evolution. Here, we describe the genome sequences, annotation, and features of GM4792 Lac(+) and GM4792 Lac(-). GM4792 Lac(+) has a 4,622,342-bp long chromosome with 4,061 protein-coding genes and 83 RNA genes. Similarly, the genome of GM4792 Lac(-) consists of a 4,621,656-bp chromosome containing 4,043 protein-coding genes and 74 RNA genes. Genome comparison analysis reveals that the differences between GM4792 Lac(+) and GM4792 Lac(-) are minimal and limited to only the targeted lac region. Moreover, a previous study on competitive experimentation indicates the two strains are identical or nearly identical in survivability except for lactose utilization in a nitrogen-limited environment. Therefore, at both a genetic and a phenotypic level, GM4792 Lac(+) and GM4792 Lac(-), with opposite neutral markers, are ideal systems for future experimental evolution studies.
Sputtering, Plasma Chemistry, and RF Sheath Effects in Low-Temperature and Fusion Plasma Modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Kruger, Scott E.; McGugan, James M.; Pankin, Alexei Y.; Roark, Christine M.; Smithe, David N.; Stoltz, Peter H.

2016-09-01

A new sheath boundary condition has been implemented in VSim, a plasma modeling code which makes use of both PIC/MCC and fluid FDTD representations. It enables physics effects associated with DC and RF sheath formation - local sheath potential evolution, heat/particle fluxes, and sputtering effects on complex plasma-facing components - to be included in macroscopic-scale plasma simulations that need not resolve sheath scale lengths. We model these effects in typical ICRF antenna operation scenarios on the Alcator C-Mod fusion device, and present comparisons of our simulation results with experimental data together with detailed 3D animations of antenna operation. Complex low-temperature plasma chemistry modeling in VSim is facilitated by MUNCHKIN, a standalone python/C++/SQL code that identifies possible reaction paths for a given set of input species, solves 1D rate equations for the ensuing system's chemical evolution, and generates VSim input blocks with appropriate cross-sections/reaction rates. These features, as well as principal path analysis (to reduce the number of simulated chemical reactions while retaining accuracy) and reaction rate calculations from user-specified distribution functions, will also be demonstrated. Supported by the U.S. Department of Energy's SBIR program, Award DE-SC0009501.
Nonlinear wave vacillation in the atmosphere

NASA Technical Reports Server (NTRS)

Antar, Basil N.

1987-01-01

The problem of vacillation in a baroclinically unstable flow field is studied through the time evolution of a single nonlinearly unstable wave. To this end a computer code is being developed to solve numerically for the time evolution of the amplitude of such a wave. The final working code will be the end product resulting from the development of a heirarchy of codes with increasing complexity. The first code in this series was completed and is undergoing several diagnostic analyses to verify its validity. The development of this code is detailed.
Three-dimensional inviscid analysis of radial-turbine flow and a limited comparison with experimental data

NASA Technical Reports Server (NTRS)

Choo, Y. K.; Civinskas, K. C.

1985-01-01

The three-dimensional inviscid DENTON code is used to analyze flow through a radial-inflow turbine rotor. Experimental data from the rotor are compared with analytical results obtained by using the code. The experimental data available for comparison are the radial distributions of circumferentially averaged values of absolute flow angle and total pressure downstream of the rotor exit. The computed rotor-exit flow angles are generally underturned relative to the experimental values, which reflect the boundary-layer separation at the trailing edge and the development of wakes downstream of the rotor. The experimental rotor is designed for a higher-than-optimum work factor of 1.126 resulting in a nonoptimum positive incidence and causing a region of rapid flow adjustment and large velocity gradients. For this experimental rotor, the computed radial distribution of rotor-exit to turbine-inlet total pressure ratios are underpredicted due to the errors in the finite-difference approximations in the regions of rapid flow adjustment, and due to using the relatively coarser grids in the middle of the blade region where the flow passage is highly three-dimensional. Additional results obtained from the three-dimensional inviscid computation are also presented, but without comparison due to the lack of experimental data. These include quasi-secondary velocity vectors on cross-channel surfaces, velocity components on the meridional and blade-to-blade surfaces, and blade surface loading diagrams. Computed results show the evolution of a passage vortex and large streamline deviations from the computational streamwise grid lines. Experience gained from applying the code to a radial turbine geometry is also discussed.
Three-dimensional inviscid analysis of radial turbine flow and a limited comparison with experimental data

NASA Technical Reports Server (NTRS)

Choo, Y. K.; Civinskas, K. C.

1985-01-01

The three-dimensional inviscid DENTON code is used to analyze flow through a radial-inflow turbine rotor. Experimental data from the rotor are compared with analytical results obtained by using the code. The experimental data available for comparison are the radial distributions of circumferentially averaged values of absolute flow angle and total pressure downstream of the rotor exit. The computed rotor-exit flow angles are generally underturned relative to the experimental values, which reflect the boundary-layer separation at the trailing edge and the development of wakes downstream of the rotor. The experimental rotor is designed for a higher-than-optimum work factor of 1.126 resulting in a nonoptimum positive incidence and causing a region of rapid flow adjustment and large velocity gradients. For this experimental rotor, the computed radial distribution of rotor-exit to turbine-inlet total pressure ratios are underpredicted due to the errors in the finite-difference approximations in the regions of rapid flow adjustment, and due to using the relatively coarser grids in the middle of the blade region where the flow passage is highly three-dimensional. Additional results obtained from the three-dimensional inviscid computation are also presented, but without comparison due to the lack of experimental data. These include quasi-secondary velocity vectors on cross-channel surfaces, velocity components on the meridional and blade-to-blade surfaces, and blade surface loading diagrams. Computed results show the evolution of a passage vortex and large streamline deviations from the computational streamwise grid lines. Experience gained from applying the code to a radial turbine geometry is also discussed.
Studying the laws of software evolution in a long-lived FLOSS project.

PubMed

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-07-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd.
Studying the laws of software evolution in a long-lived FLOSS project

PubMed Central

Gonzalez-Barahona, Jesus M; Robles, Gregorio; Herraiz, Israel; Ortega, Felipe

2014-01-01

Some free, open-source software projects have been around for quite a long time, the longest living ones dating from the early 1980s. For some of them, detailed information about their evolution is available in source code management systems tracking all their code changes for periods of more than 15 years. This paper examines in detail the evolution of one of such projects, glibc, with the main aim of understanding how it evolved and how it matched Lehman's laws of software evolution. As a result, we have developed a methodology for studying the evolution of such long-lived projects based on the information in their source code management repository, described in detail several aspects of the history of glibc, including some activity and size metrics, and found how some of the laws of software evolution may not hold in this case. © 2013 The Authors. Journal of Software: Evolution and Process published by John Wiley & Sons Ltd. PMID:25893093
A validated non-linear Kelvin-Helmholtz benchmark for numerical hydrodynamics

NASA Astrophysics Data System (ADS)

Lecoanet, D.; McCourt, M.; Quataert, E.; Burns, K. J.; Vasil, G. M.; Oishi, J. S.; Brown, B. P.; Stone, J. M.; O'Leary, R. M.

2016-02-01

The non-linear evolution of the Kelvin-Helmholtz instability is a popular test for code verification. To date, most Kelvin-Helmholtz problems discussed in the literature are ill-posed: they do not converge to any single solution with increasing resolution. This precludes comparisons among different codes and severely limits the utility of the Kelvin-Helmholtz instability as a test problem. The lack of a reference solution has led various authors to assert the accuracy of their simulations based on ad hoc proxies, e.g. the existence of small-scale structures. This paper proposes well-posed two-dimensional Kelvin-Helmholtz problems with smooth initial conditions and explicit diffusion. We show that in many cases numerical errors/noise can seed spurious small-scale structure in Kelvin-Helmholtz problems. We demonstrate convergence to a reference solution using both ATHENA, a Godunov code, and DEDALUS, a pseudo-spectral code. Problems with constant initial density throughout the domain are relatively straightforward for both codes. However, problems with an initial density jump (which are the norm in astrophysical systems) exhibit rich behaviour and are more computationally challenging. In the latter case, ATHENA simulations are prone to an instability of the inner rolled-up vortex; this instability is seeded by grid-scale errors introduced by the algorithm, and disappears as resolution increases. Both ATHENA and DEDALUS exhibit late-time chaos. Inviscid simulations are riddled with extremely vigorous secondary instabilities which induce more mixing than simulations with explicit diffusion. Our results highlight the importance of running well-posed test problems with demonstrated convergence to a reference solution. To facilitate future comparisons, we include as supplementary material the resolved, converged solutions to the Kelvin-Helmholtz problems in this paper in machine-readable form.
Physical Model for the Evolution of the Genetic Code

NASA Astrophysics Data System (ADS)

Yamashita, Tatsuro; Narikiyo, Osamu

2011-12-01

Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our description, a physical quantity, codon level is introduced. In terms of the codon levels two scenarios are typically classified into two different routes of the evolutional process. In the case of the ambiguous intermediate scenario we perform an evolutional simulation implemented cost selection of amino acids and confirm a rapid transition of the code change. Such rapidness reduces uncomfortableness of the non-unique translation of the code at intermediate state that is the weakness of the scenario. In the case of the codon capture scenario the survival against mutations under the mutational pressure minimizing GC content in genomes is simulated and it is demonstrated that cells which experience only neutral mutations survive.
The Evolution of a Coding Schema in a Paced Program of Research

ERIC Educational Resources Information Center

Winters, Charlene A.; Cudney, Shirley; Sullivan, Therese

2010-01-01

A major task involved in the management, analysis, and integration of qualitative data is the development of a coding schema to facilitate the analytic process. Described in this paper is the evolution of a coding schema that was used in the analysis of qualitative data generated from online forums of middle-aged women with chronic conditions who…
The Spectroscopic Evolution of Nova Cygni 1992

NASA Astrophysics Data System (ADS)

Moro-Martin, A.; Garnavich, P. M.; Noriega-Crespo, A.; Alpert, A.

1996-12-01

Optical spectroscopic observations of Nova Cygni 1992 spanning 4 years are modeled in this study. The data were obtained primarily with the DAO 1.8m telescope and cover a wavelength range from ~ 3200 - 8000 Angstroms. The observations begin on May 92 (85 days after the outburst) and end on June 1996, i.e. during most of the optically thin evolutionary phase. The spectra were modeled in a relatively straightforward way by using the flux predicted by a photoionization code [1] for most of the emission lines (down to 0.1% of Hβ ) and transforming these numbers into a synthetic spectrum. There are, however, significant differences in the detailed procedure in comparison with similar works [2]. First, the photoionization models were run at a fixed abundance value for the most prominent elements (i.e. H, He, C, O, N, Ne, Fe, etc) over the entire time sequence. Second, the brightest lines, e.g. [Ne V], [Ne III], [O III] and the Balmer lines, were initially used as guide to match the observations. The rest of the spectra, which includes the fainter lines, were then directly predicted by the photoionization code. Considering the complicated structure of the shell [3], the lack of well defined values of its gas density and our limited knowledge of the time evolution of the surface temperature of the photoionization source, the comparison between models and observations agrees remarkably well. It was found that the time evolution of some of the Iron coronal lines, [Fe VII] 6087 Angstroms and [Fe X] 6374 Angstroms, closely follows that of the X-rays [4]. [1] Ferland, G.J 1993, CLOUDY, U. of Kentucky Dept. Phys & Astr. Internal Report. [2] Austin et al. 1992, AJ, 111, 869 [3] Paresce, Livio, Hack & Korista (1995) A&A, 299, 823 [4] Krautter et al. (1996), ApJ, 456, 788
Modelling of LOCA Tests with the BISON Fuel Performance Code

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

Williamson, Richard L; Pastore, Giovanni; Novascone, Stephen Rhead

2016-05-01

BISON is a modern finite-element based, multidimensional nuclear fuel performance code that is under development at Idaho National Laboratory (USA). Recent advances of BISON include the extension of the code to the analysis of LWR fuel rod behaviour during loss-of-coolant accidents (LOCAs). In this work, BISON models for the phenomena relevant to LWR cladding behaviour during LOCAs are described, followed by presentation of code results for the simulation of LOCA tests. Analysed experiments include separate effects tests of cladding ballooning and burst, as well as the Halden IFA-650.2 fuel rod test. Two-dimensional modelling of the experiments is performed, and calculationsmore » are compared to available experimental data. Comparisons include cladding burst pressure and temperature in separate effects tests, as well as the evolution of fuel rod inner pressure during ballooning and time to cladding burst. Furthermore, BISON three-dimensional simulations of separate effects tests are performed, which demonstrate the capability to reproduce the effect of azimuthal temperature variations in the cladding. The work has been carried out in the frame of the collaboration between Idaho National Laboratory and Halden Reactor Project, and the IAEA Coordinated Research Project FUMAC.« less
Pretest aerosol code comparisons for LWR aerosol containment tests LA1 and LA2

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

Wright, A.L.; Wilson, J.H.; Arwood, P.C.

The Light-Water-Reactor (LWR) Aerosol Containment Experiments (LACE) are being performed in Richland, Washington, at the Hanford Engineering Development Laboratory (HEDL) under the leadership of an international project board and the Electric Power Research Institute. These tests have two objectives: (1) to investigate, at large scale, the inherent aerosol retention behavior in LWR containments under simulated severe accident conditions, and (2) to provide an experimental data base for validating aerosol behavior and thermal-hydraulic computer codes. Aerosol computer-code comparison activities are being coordinated at the Oak Ridge National Laboratory. For each of the six LACE tests, ''pretest'' calculations (for code-to-code comparisons) andmore » ''posttest'' calculations (for code-to-test data comparisons) are being performed. The overall goals of the comparison effort are (1) to provide code users with experience in applying their codes to LWR accident-sequence conditions and (2) to evaluate and improve the code models.« less

Gene network polymorphism is the raw material of natural selection: the selfish gene network hypothesis.

PubMed

Boldogköi, Zsolt

2004-09-01

Population genetics, the mathematical theory of modern evolutionary biology, defines evolution as the alteration of the frequency of distinct gene variants (alleles) differing in fitness over the time. The major problem with this view is that in gene and protein sequences we can find little evidence concerning the molecular basis of phenotypic variance, especially those that would confer adaptive benefit to the bearers. Some novel data, however, suggest that a large amount of genetic variation exists in the regulatory region of genes within populations. In addition, comparison of homologous DNA sequences of various species shows that evolution appears to depend more strongly on gene expression than on the genes themselves. Furthermore, it has been demonstrated in several systems that genes form functional networks, whose products exhibit interrelated expression profiles. Finally, it has been found that regulatory circuits of development behave as evolutionary units. These data demonstrate that our view of evolution calls for a new synthesis. In this article I propose a novel concept, termed the selfish gene network hypothesis, which is based on an overall consideration of the above findings. The major statements of this hypothesis are as follows. (1) Instead of individual genes, gene networks (GNs) are responsible for the determination of traits and behaviors. (2) The primary source of microevolution is the intraspecific polymorphism in GNs and not the allelic variation in either the coding or the regulatory sequences of individual genes. (3) GN polymorphism is generated by the variation in the regulatory regions of the component genes and not by the variance in their coding sequences. (4) Evolution proceeds through continuous restructuring of the composition of GNs rather than fixing of specific alleles or GN variants.
Genomics, evolution and development of amphioxus and tunicates: The Goldilocks principle.

PubMed

Holland, Linda Z

2015-06-01

Morphological comparisons among extant animals have long been used to infer their long-extinct ancestors for which the fossil record is poor or non-existent. For evolution of the vertebrates, the comparison has typically involved amphioxus and vertebrates. Both groups are evolving relatively slowly, and their genomes share a high level of synteny. Both vertebrates and amphioxus have regulative development in which cell fates become fixed only gradually during embryogenesis. Thus, their development fits a modified hourglass model in which constraints are greatest at the phylotypic stage (i.e., the late neurula/early larva), but are somewhat greater on earlier development than on later development. In contrast, the third group of chordates, the tunicates, which are sister group to vertebrates, are evolving rapidly. Constraints on evolution of tunicate genomes are relaxed, and they have discarded key developmental genes and organized much of their coding sequences into operons, which are transcribed as a single mRNA that undergoes trans-splicing. This contrasts with vertebrates and amphioxus, whose genomes are not organized into operons. Concomitantly, tunicates have switched to determinant development with very early fixation of cell fates. Thus, tunicate development more closely fits a progressive divergence model (shaped more like a wine glass than an hourglass) in which the constraints on the zygote and very early development are greatest. This model can help explain why tunicate body plans are so very diverse. The relaxed constraints on development after early cleavage stages are correlated with relaxed constraints on genome evolution. The question remains: which came first? © 2014 Wiley Periodicals, Inc.
The mitochondrial genome of Paraspadella gotoi is highly reduced and reveals that chaetognaths are a sister-group to protostomes

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

Helfenbein, Kevin G.; Fourcade, H. Matthew; Vanjani, Rohit G.

2004-05-01

We report the first complete mitochondrial (mt) DNA sequence from a member of the phylum Chaetognatha (arrow worms). The Paraspadella gotoi mtDNA is highly unusual, missing 23 of the genes commonly found in animal mtDNAs, including atp6, which has otherwise been found universally to be present. Its 14 genes are unusually arranged into two groups, one on each strand. One group is punctuated by numerous non-coding intergenic nucleotides, while the other group is tightly packed, having no non-coding nucleotides, leading to speculation that there are two transcription units with differing modes of expression. The phylogenetic position of the Chaetognatha withinmore » the Metazoa has long been uncertain, with conflicting or equivocal results from various morphological analyses and rRNA sequence comparisons. Comparisons here of amino acid sequences from mitochondrially encoded proteins gives a single most parsimonious tree that supports a position of Chaetognatha as sister to the protostomes studied here. From this, one can more clearly interpret the patterns of evolution of various developmental features, especially regarding the embryological fate of the blastopore.« less
Computer modeling of pulsed CO2 lasers for lidar applications

NASA Technical Reports Server (NTRS)

Spiers, Gary D.

1993-01-01

The object of this effort is to develop code to enable the accurate prediction of the performance of pulsed transversely excited (TE) CO2 lasers prior to their construction. This is of particular benefit to the NASA Laser Atmospheric Wind Sounder (LAWS) project. A benefit of the completed code is that although developed specifically for the pulsed CO2 laser much of the code can be modified to model other laser systems of interest to the lidar community. A Boltzmann equation solver has been developed which enables the electron excitation rates for the vibrational levels of CO2 and N2, together with the electron ionization and attachment coefficients to be determined for any CO2 laser gas mixture consisting of a combination of CO2, N2, CO, He and CO. The validity of the model has been verified by comparison with published material. The results from the Boltzmann equation solver have been used as input to the laser kinetics code which is currently under development. A numerical code to model the laser induced medium perturbation (LIMP) arising from the relaxation of the lower laser level has been developed and used to determine the effect of LIMP on the frequency spectrum of the LAWS laser output pulse. The enclosed figures show representative results for a laser operating at 0.5 atm. with a discharge cross-section of 4.5 cm to produce a 20 J pulse with aFWHM of 3.1 microns. The first four plots show the temporal evolution of the laser pulse power, energy evolution, LIMP frequency chirp and electric field magnitude. The electric field magnitude is taken by beating the calculated complex electric field and beating it with a local oscillator signal. The remaining two figures show the power spectrum and energy distribution in the pulse as a function of the varying pulse frequency. The LIMP theory has been compared with experimental data from the NOAA Windvan Lidar and has been found to be in good agreement.
The eukaryotic genome is structurally and functionally more like a social insect colony than a book.

PubMed

Qiu, Guo-Hua; Yang, Xiaoyan; Zheng, Xintian; Huang, Cuiqin

2017-11-01

Traditionally, the genome has been described as the 'book of life'. However, the metaphor of a book may not reflect the dynamic nature of the structure and function of the genome. In the eukaryotic genome, the number of centrally located protein-coding sequences is relatively constant across species, but the amount of noncoding DNA increases considerably with the increase of organismal evolutional complexity. Therefore, it has been hypothesized that the abundant peripheral noncoding DNA protects the genome and the central protein-coding sequences in the eukaryotic genome. Upon comparison with the habitation, sociality and defense mechanisms of a social insect colony, it is found that the genome is similar to a social insect colony in various aspects. A social insect colony may thus be a better metaphor than a book to describe the spatial organization and physical functions of the genome. The potential implications of the metaphor are also discussed.
The Complete Mitochondrial Genome of Mindarus keteleerifoliae (Insecta: Hemiptera: Aphididae) and Comparison with Other Aphididae Insects.

PubMed

Wang, Yuan; Chen, Jing; Jiang, Li-Yun; Qiao, Ge-Xia

2015-12-17

The mitogenome of Mindarus keteleerifoliae Zhang (Hemiptera: Aphididae) is a 15,199 bp circular molecule. The gene order and orientation of M. keteleerifoliae is similarly arranged to that of the ancestral insect of other aphid mitogenomes, and, a tRNA isomerism event maybe identified in the mitogenome of M. keteleerifoliae. The tRNA-Trp gene is coded in the J-strand and the same sequence in the N-strand codes for the tRNA-Ser gene. A similar phenomenon was also found in the mitogenome of Eriosoma lanigerum. However, whether tRNA isomers in aphids exist requires further study. Phylogenetic analyses, using all available protein-coding genes, support Mindarinae as the basal position of Aphididae. Two tribes of Aphidinae were recovered with high statistical significance. Characteristics of the M. keteleerifoliae mitogenome revealed distinct mitogenome structures and provided abundant phylogenetic signals, thus advancing our understanding of insect mitogenomic architecture and evolution. But, because only eight complete aphid mitogenomes, including M. keteleerifoliae, were published, future studies with larger taxon sampling sizes are necessary.
Testing Feedback Models with Nearby Star Forming Regions

NASA Astrophysics Data System (ADS)

Doran, E.; Crowther, P.

2012-12-01

The feedback from massive stars plays a crucial role in the evolution of galaxies. Accurate modelling of this feedback is essential in understanding distant star forming regions. Young nearby, high mass (> 104 M⊙) clusters such as R136 (in the 30 Doradus region) are ideal test beds for population synthesis since they host large numbers of spatially resolved massive stars at a pre-supernovae stage. We present a quantitative comparison of empirical calibrations of radiative and mechanical feedback from individual stars in R136, with instantaneous burst predictions from the popular Starburst99 evolution synthesis code. We find that empirical results exceed predictions by factors of ˜3-9, as a result of limiting simulations to an upper limit of 100 M⊙. 100-300 M⊙ stars should to be incorporated in population synthesis models for high mass clusters to bring predictions into close agreement with empirical results.
The Genome of Naegleria gruberi Illuminates Early Eukaryotic Versatility

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

Fritz-Laylin, Lillian K.; Prochnik, Simon E.; Ginger, Michael L.

2010-03-01

Genome sequences of diverse free-living protists are essential for understanding eukaryotic evolution and molecular and cell biology. The free-living amoeboflagellate Naegleria gruberi belongs to a varied and ubiquitous protist clade (Heterolobosea) that diverged from other eukaryotic lineages over a billion years ago. Analysis of the 15,727 protein-coding genes encoded by Naegleria's 41 Mb nuclear genome indicates a capacity for both aerobic respiration and anaerobic metabolism with concomitant hydrogen production, with fundamental implications for the evolution of organelle metabolism. The Naegleria genome facilitates substantially broader phylogenomic comparisons of free-living eukaryotes than previously possible, allowing us to identify thousands of genes likelymore » present in the pan-eukaryotic ancestor, with 40% likely eukaryotic inventions. Moreover, we construct a comprehensive catalog of amoeboid-motility genes. The Naegleria genome, analyzed in the context of other protists, reveals a remarkably complex ancestral eukaryote with a rich repertoire of cytoskeletal, sexual, signaling, and metabolic modules.« less
The draft genome of the parasitic nematode Trichinella spiralis

PubMed Central

Mitreva, Makedonka; Jasmer, Douglas P.; Zarlenga, Dante S.; Wang, Zhengyuan; Abubucker, Sahar; Martin, John; Taylor, Christina M.; Yin, Yong; Fulton, Lucinda; Minx, Pat; Yang, Shiaw-Pyng; Warren, Wesley C.; Fulton, Robert S.; Bhonagiri, Veena; Zhang, Xu; Hallsworth-Pepin, Kym; Clifton, Sandra W.; McCarter, James P.; Appleton, Judith; Mardis, Elaine R.; Wilson, Richard K.

2011-01-01

Genome-based studies of metazoan evolution are most informative when phylogenetically diverse species are incorporated in the analysis. As such, evolutionary trends within and outside the phylum Nematoda have been less revealing by focusing only on comparisons involving Caenorhabditis elegans. Herein, we present a draft of the 64 megabase nuclear genome of Trichinella spiralis, containing 15,808 protein coding genes. This parasitic nematode is an extant member of a clade that diverged early in the evolution of the phylum enabling identification of archetypical genes and molecular signatures exclusive to nematodes. Comparative analyses support intrachromosomal rearrangements across the phylum, disproportionate numbers of protein family deaths over births in parasitic vs. a non-parasitic nematode, and a preponderance of gene loss and gain events in nematodes relative to Drosophila melanogaster. This sequence and the panphylum characteristics identified herein will advance evolutionary studies and strategies to combat global parasites of humans, food animals and crops. PMID:21336279
Experiments and simulations of single shock Richtmeyer-Meshkov Instability with measured, volumetric initial conditions

NASA Astrophysics Data System (ADS)

Sewell, Everest; Ferguson, Kevin; Greenough, Jeffrey; Jacobs, Jeffrey

2014-11-01

We describe new experiments of single shock Richtmeyer-Meshkov Instability (RMI) performed on the shock tube apparatus at the University of Arizona in which the initial conditions are volumetrically imaged prior to shock wave arrival. Initial perturbation plays a major role in the evolution of RMI, and previous experimental efforts only capture a narrow slice of the initial condition. The method presented uses a rastered laser sheet to capture additional images in the depth of the initial condition shortly before the experimental start time. These images are then used to reconstruct a volumetric approximation of the experimental perturbation, which is simulated using the hydrodynamics code ARES, developed at Lawrence Livermore National Laboratory (LLNL). Comparison is made between the time evolution of the interface width and the mixedness ratio measured from the experiments against the predictions from the numerical simulations.
Supporting Source Code Comprehension during Software Evolution and Maintenance

ERIC Educational Resources Information Center

Alhindawi, Nouh

2013-01-01

This dissertation addresses the problems of program comprehension to support the evolution of large-scale software systems. The research concerns how software engineers locate features and concepts along with categorizing changes within very large bodies of source code along with their versioned histories. More specifically, advanced Information…
Secondary School Students' Reasoning about Evolution

ERIC Educational Resources Information Center

To, Cheryl; Tenenbaum, Harriet R.; Hogh, Henriette

2017-01-01

This study examined age differences in young people's understanding of evolution theory in secondary school. A second aim of this study was to propose a new coding scheme that more accurately described students' conceptual understanding about evolutionary theory. We argue that coding schemes adopted in previous research may have overestimated…
Nada: A new code for studying self-gravitating tori around black holes

NASA Astrophysics Data System (ADS)

Montero, Pedro J.; Font, José A.; Shibata, Masaru

2008-09-01

We present a new two-dimensional numerical code called Nada designed to solve the full Einstein equations coupled to the general relativistic hydrodynamics equations. The code is mainly intended for studies of self-gravitating accretion disks (or tori) around black holes, although it is also suitable for regular spacetimes. Concerning technical aspects the Einstein equations are formulated and solved in the code using a formulation of the standard 3+1 Arnowitt-Deser-Misner canonical formalism system, the so-called Baumgarte-Shapiro Shibata-Nakamura approach. A key feature of the code is that derivative terms in the spacetime evolution equations are computed using a fourth-order centered finite difference approximation in conjunction with the Cartoon method to impose the axisymmetry condition under Cartesian coordinates (the choice in Nada), and the puncture/moving puncture approach to carry out black hole evolutions. Correspondingly, the general relativistic hydrodynamics equations are written in flux-conservative form and solved with high-resolution, shock-capturing schemes. We perform and discuss a number of tests to assess the accuracy and expected convergence of the code, namely, (single) black hole evolutions, shock tubes, and evolutions of both spherical and rotating relativistic stars in equilibrium, the gravitational collapse of a spherical relativistic star leading to the formation of a black hole. In addition, paving the way for specific applications of the code, we also present results from fully general relativistic numerical simulations of a system formed by a black hole surrounded by a self-gravitating torus in equilibrium.
A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate

PubMed Central

Samuels, David C.; Boys, Richard J.; Henderson, Daniel A.; Chinnery, Patrick F.

2003-01-01

We applied a hidden Markov model segmentation method to the human mitochondrial genome to identify patterns in the sequence, to compare these patterns to the gene structure of mtDNA and to see whether these patterns reveal additional characteristics important for our understanding of genome evolution, structure and function. Our analysis identified three segmentation categories based upon the sequence transition probabilities. Category 2 segments corresponded to the tRNA and rRNA genes, with a greater strand-symmetry in these segments. Category 1 and 3 segments covered the protein- coding genes and almost all of the non-coding D-loop. Compared to category 1, the mtDNA segments assigned to category 3 had much lower guanine abundance. A comparison to two independent databases of mitochondrial mutations and polymorphisms showed that the high substitution rate of guanine in human mtDNA is largest in the category 3 segments. Analysis of synonymous mutations showed the same pattern. This suggests that this heterogeneity in the mutation rate is partly independent of respiratory chain function and is a direct property of the genome sequence itself. This has important implications for our understanding of mtDNA evolution and its use as a ‘molecular clock’ to determine the rate of population and species divergence. PMID:14530452
Characterization and Evolution of Conserved MicroRNA through Duplication Events in Date Palm (Phoenix dactylifera)

PubMed Central

Yang, Yaodong; Mason, Annaliese S.; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events. PMID:23951162
Characterization and evolution of conserved MicroRNA through duplication events in date palm (Phoenix dactylifera).

PubMed

Xiao, Yong; Xia, Wei; Yang, Yaodong; Mason, Annaliese S; Lei, Xintao; Ma, Zilong

2013-01-01

MicroRNAs (miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of species. Highly conserved miRNAs regulate ancestral transcription factors common to all plants, and control important basic processes such as cell division and meristem function. We selected 21 conserved miRNA families to analyze the distribution and maintenance of miRNAs. Recently, the first genome sequence in Palmaceae was released: date palm (Phoenix dactylifera). We conducted a systematic miRNA analysis in date palm, computationally identifying and characterizing the distribution and duplication of conserved miRNAs in this species compared to other published plant genomes. A total of 81 miRNAs belonging to 18 miRNA families were identified in date palm. The majority of miRNAs in date palm and seven other well-studied plant species were located in intergenic regions and located 4 to 5 kb away from the nearest protein-coding genes. Sequence comparison showed that 67% of date palm miRNA members were present in duplicated segments, and that 135 pairs of miRNA-containing segments were duplicated in Arabidopsis, tomato, orange, rice, apple, poplar and soybean with a high similarity of non coding sequences between duplicated segments, indicating genomic duplication was a major force for expansion of conserved miRNAs. Duplicated miRNA pairs in date palm showed divergence in pre-miRNA sequence and in number of promoters, implying that these duplicated pairs may have undergone divergent evolution. Comparisons between date palm and the seven other plant species for the gain/loss of miR167 loci in an ancient segment shared between monocots and dicots suggested that these conserved miRNAs were highly influenced by and diverged as a result of genomic duplication events.
Tracing the evolution of the Galactic bulge with chemodynamical modelling of alpha-elements

NASA Astrophysics Data System (ADS)

Friaça, A. C. S.; Barbuy, B.

2017-02-01

Context. Galactic bulge abundances can be best understood as indicators of bulge formation and nucleosynthesis processes by comparing them with chemo-dynamical evolution models. Aims: The aim of this work is to study the abundances of alpha-elements in the Galactic bulge, including a revision of the oxygen abundance in a sample of 56 bulge red giants. Methods: Literature abundances for O, Mg, Si, Ca and Ti in Galactic bulge stars are compared with chemical evolution models. For oxygen in particular, we reanalysed high-resolution spectra obtained using FLAMES+UVES on the Very Large Telescope, now taking each star's carbon abundances, derived from CI and C2 lines, into account simultaneously. Results: We present a chemical evolution model of alpha-element enrichment in a massive spheroid that represents a typical classical bulge evolution. The code includes multi-zone chemical evolution coupled with hydrodynamics of the gas. Comparisons between the model predictions and the abundance data suggest a typical bulge formation timescale of 1-2 Gyr. The main constraint on the bulge evolution is provided by the O data from analyses that have taken the C abundance and dissociative equilibrium into account. Mg, Si, Ca and Ti trends are well reproduced, whereas the level of overabundance critically depends on the adopted nucleosynthesis prescriptions. Observations collected both at the European Southern Observatory, Paranal, Chile (ESO programmes 71.B-0617A, 73.B0074A, and GTO 71.B-0196)
Non-local gravity and comparison with observational datasets. II. Updated results and Bayesian model comparison with ΛCDM

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

Dirian, Yves; Foffa, Stefano; Kunz, Martin

We present a comprehensive and updated comparison with cosmological observations of two non-local modifications of gravity previously introduced by our group, the so called RR and RT models. We implement the background evolution and the cosmological perturbations of the models in a modified Boltzmann code, using CLASS. We then test the non-local models against the Planck 2015 TT, TE, EE and Cosmic Microwave Background (CMB) lensing data, isotropic and anisotropic Baryonic Acoustic Oscillations (BAO) data, JLA supernovae, H {sub 0} measurements and growth rate data, and we perform Bayesian parameter estimation. We then compare the RR, RT and ΛCDM models,more » using the Savage-Dickey method. We find that the RT model and ΛCDM perform equally well, while the performance of the RR model with respect to ΛCDM depends on whether or not we include a prior on H {sub 0} based on local measurements.« less
Simulation of the hybrid and steady state advanced operating modes in ITER

NASA Astrophysics Data System (ADS)

Kessel, C. E.; Giruzzi, G.; Sips, A. C. C.; Budny, R. V.; Artaud, J. F.; Basiuk, V.; Imbeaux, F.; Joffrin, E.; Schneider, M.; Murakami, M.; Luce, T.; St. John, Holger; Oikawa, T.; Hayashi, N.; Takizuka, T.; Ozeki, T.; Na, Y.-S.; Park, J. M.; Garcia, J.; Tucillo, A. A.

2007-09-01

Integrated simulations are performed to establish a physics basis, in conjunction with present tokamak experiments, for the operating modes in the International Thermonuclear Experimental Reactor (ITER). Simulations of the hybrid mode are done using both fixed and free-boundary 1.5D transport evolution codes including CRONOS, ONETWO, TSC/TRANSP, TOPICS and ASTRA. The hybrid operating mode is simulated using the GLF23 and CDBM05 energy transport models. The injected powers are limited to the negative ion neutral beam, ion cyclotron and electron cyclotron heating systems. Several plasma parameters and source parameters are specified for the hybrid cases to provide a comparison of 1.5D core transport modelling assumptions, source physics modelling assumptions, as well as numerous peripheral physics modelling. Initial results indicate that very strict guidelines will need to be imposed on the application of GLF23, for example, to make useful comparisons. Some of the variations among the simulations are due to source models which vary widely among the codes used. In addition, there are a number of peripheral physics models that should be examined, some of which include fusion power production, bootstrap current, treatment of fast particles and treatment of impurities. The hybrid simulations project to fusion gains of 5.6-8.3, βN values of 2.1-2.6 and fusion powers ranging from 350 to 500 MW, under the assumptions outlined in section 3. Simulations of the steady state operating mode are done with the same 1.5D transport evolution codes cited above, except the ASTRA code. In these cases the energy transport model is more difficult to prescribe, so that energy confinement models will range from theory based to empirically based. The injected powers include the same sources as used for the hybrid with the possible addition of lower hybrid. The simulations of the steady state mode project to fusion gains of 3.5-7, βN values of 2.3-3.0 and fusion powers of 290 to 415 MW, under the assumptions described in section 4. These simulations will be presented and compared with particular focus on the resulting temperature profiles, source profiles and peripheral physics profiles. The steady state simulations are at an early stage and are focused on developing a range of safety factor profiles with 100% non-inductive current.
The Prediction of Microstructure Evolution of 6005A Aluminum Alloy in a P-ECAP Extrusion Study

NASA Astrophysics Data System (ADS)

Lei, Shi; Jiu-Ba, Wen; Chang, Ren

2018-05-01

Finite element modeling (FEM) was applied for predicting the recrystallized structure in extruded 6005 aluminum alloy, and simulated results were experimentally validated. First, microstructure evolution of 6005 aluminum alloy during deformation was studied by means of isothermal compression test, where the processing parameters were chosen to reproduce the typical industrial conditions. Second, microstructure evolution was analyzed, and the obtained information was used to fit a dynamic recrystallization model implementing inside the DEFORM-3D FEM code environment. FEM of deformation of 6005 aluminum has been established and validated by microstructure comparison. Finally, the obtained dynamic recrystallization model was applied to tube extrusion by using a portholes-equal channel angular pressing die. The finite element analysis results showed that coarse DRX grains occur in the extruded tube at higher temperature and in the extruded tube at the faster speed of the stem. The test results showed material from the front end of the extruded tube has coarse grains (60 μm) and other extruded tube has finer grains (20 μm).

The Prediction of Microstructure Evolution of 6005A Aluminum Alloy in a P-ECAP Extrusion Study

NASA Astrophysics Data System (ADS)

Lei, Shi; Jiu-Ba, Wen; Chang, Ren

2018-04-01

Finite element modeling (FEM) was applied for predicting the recrystallized structure in extruded 6005 aluminum alloy, and simulated results were experimentally validated. First, microstructure evolution of 6005 aluminum alloy during deformation was studied by means of isothermal compression test, where the processing parameters were chosen to reproduce the typical industrial conditions. Second, microstructure evolution was analyzed, and the obtained information was used to fit a dynamic recrystallization model implementing inside the DEFORM-3D FEM code environment. FEM of deformation of 6005 aluminum has been established and validated by microstructure comparison. Finally, the obtained dynamic recrystallization model was applied to tube extrusion by using a portholes-equal channel angular pressing die. The finite element analysis results showed that coarse DRX grains occur in the extruded tube at higher temperature and in the extruded tube at the faster speed of the stem. The test results showed material from the front end of the extruded tube has coarse grains (60 μm) and other extruded tube has finer grains (20 μm).
Reference results for time-like evolution up to

NASA Astrophysics Data System (ADS)

Bertone, Valerio; Carrazza, Stefano; Nocera, Emanuele R.

2015-03-01

We present high-precision numerical results for time-like Dokshitzer-Gribov-Lipatov-Altarelli-Parisi evolution in the factorisation scheme, for the first time up to next-to-next-to-leading order accuracy in quantum chromodynamics. First, we scrutinise the analytical expressions of the splitting functions available in the literature, in both x and N space, and check their mutual consistency. Second, we implement time-like evolution in two publicly available, entirely independent and conceptually different numerical codes, in x and N space respectively: the already existing APFEL code, which has been updated with time-like evolution, and the new MELA code, which has been specifically developed to perform the study in this work. Third, by means of a model for fragmentation functions, we provide results for the evolution in different factorisation schemes, for different ratios between renormalisation and factorisation scales and at different final scales. Our results are collected in the format of benchmark tables, which could be used as a reference for global determinations of fragmentation functions in the future.
CHEMICAL EVOLUTION LIBRARY FOR GALAXY FORMATION SIMULATION

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

Saitoh, Takayuki R., E-mail: saitoh@elsi.jp

We have developed a software library for chemical evolution simulations of galaxy formation under the simple stellar population (SSP) approximation. In this library, all of the necessary components concerning chemical evolution, such as initial mass functions, stellar lifetimes, yields from Type II and Type Ia supernovae, asymptotic giant branch stars, and neutron star mergers, are compiled from the literature. Various models are pre-implemented in this library so that users can choose their favorite combination of models. Subroutines of this library return released energy and masses of individual elements depending on a given event type. Since the redistribution manner of thesemore » quantities depends on the implementation of users’ simulation codes, this library leaves it up to the simulation code. As demonstrations, we carry out both one-zone, closed-box simulations and 3D simulations of a collapsing gas and dark matter system using this library. In these simulations, we can easily compare the impact of individual models on the chemical evolution of galaxies, just by changing the control flags and parameters of the library. Since this library only deals with the part of chemical evolution under the SSP approximation, any simulation codes that use the SSP approximation—namely, particle-base and mesh codes, as well as semianalytical models—can use it. This library is named “CELib” after the term “Chemical Evolution Library” and is made available to the community.« less
A Phylogenomic Assessment of Ancient Polyploidy and Genome Evolution across the Poales

PubMed Central

McKain, Michael R.; Tang, Haibao; McNeal, Joel R.; Ayyampalayam, Saravanaraj; Davis, Jerrold I.; dePamphilis, Claude W.; Givnish, Thomas J.; Pires, J. Chris; Stevenson, Dennis Wm.; Leebens-Mack, James H.

2016-01-01

Comparisons of flowering plant genomes reveal multiple rounds of ancient polyploidy characterized by large intragenomic syntenic blocks. Three such whole-genome duplication (WGD) events, designated as rho (ρ), sigma (σ), and tau (τ), have been identified in the genomes of cereal grasses. Precise dating of these WGD events is necessary to investigate how they have influenced diversification rates, evolutionary innovations, and genomic characteristics such as the GC profile of protein-coding sequences. The timing of these events has remained uncertain due to the paucity of monocot genome sequence data outside the grass family (Poaceae). Phylogenomic analysis of protein-coding genes from sequenced genomes and transcriptome assemblies from 35 species, including representatives of all families within the Poales, has resolved the timing of rho and sigma relative to speciation events and placed tau prior to divergence of Asparagales and the commelinids but after divergence with eudicots. Examination of gene family phylogenies indicates that rho occurred just prior to the diversification of Poaceae and sigma occurred before early diversification of Poales lineages but after the Poales-commelinid split. Additional lineage-specific WGD events were identified on the basis of the transcriptome data. Gene families exhibiting high GC content are underrepresented among those with duplicate genes that persisted following these genome duplications. However, genome duplications had little overall influence on lineage-specific changes in the GC content of coding genes. Improved resolution of the timing of WGD events in monocot history provides evidence for the influence of polyploidization on functional evolution and species diversification. PMID:26988252
Drosophila muller f elements maintain a distinct set of genomic properties over 40 million years of evolution.

PubMed

Leung, Wilson; Shaffer, Christopher D; Reed, Laura K; Smith, Sheryl T; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E J; Machone, Joshua F; Patterson, Seantay D; Price, Amber L; Turner, Bryce A; Robic, Srebrenka; Luippold, Erin K; McCartha, Shannon R; Walji, Tezin A; Walker, Chelsea A; Saville, Kenneth; Abrams, Marita K; Armstrong, Andrew R; Armstrong, William; Bailey, Robert J; Barberi, Chelsea R; Beck, Lauren R; Blaker, Amanda L; Blunden, Christopher E; Brand, Jordan P; Brock, Ethan J; Brooks, Dana W; Brown, Marie; Butzler, Sarah C; Clark, Eric M; Clark, Nicole B; Collins, Ashley A; Cotteleer, Rebecca J; Cullimore, Peterson R; Dawson, Seth G; Docking, Carter T; Dorsett, Sasha L; Dougherty, Grace A; Downey, Kaitlyn A; Drake, Andrew P; Earl, Erica K; Floyd, Trevor G; Forsyth, Joshua D; Foust, Jonathan D; Franchi, Spencer L; Geary, James F; Hanson, Cynthia K; Harding, Taylor S; Harris, Cameron B; Heckman, Jonathan M; Holderness, Heather L; Howey, Nicole A; Jacobs, Dontae A; Jewell, Elizabeth S; Kaisler, Maria; Karaska, Elizabeth A; Kehoe, James L; Koaches, Hannah C; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J; Kus, Jordan E; Lammers, Jennifer A; Leads, Rachel R; Leatherman, Emily C; Lippert, Rachel N; Messenger, Gregory S; Morrow, Adam T; Newcomb, Victoria; Plasman, Haley J; Potocny, Stephanie J; Powers, Michelle K; Reem, Rachel M; Rennhack, Jonathan P; Reynolds, Katherine R; Reynolds, Lyndsey A; Rhee, Dong K; Rivard, Allyson B; Ronk, Adam J; Rooney, Meghan B; Rubin, Lainey S; Salbert, Luke R; Saluja, Rasleen K; Schauder, Taylor; Schneiter, Allison R; Schulz, Robert W; Smith, Karl E; Spencer, Sarah; Swanson, Bryant R; Tache, Melissa A; Tewilliager, Ashley A; Tilot, Amanda K; VanEck, Eve; Villerot, Matthew M; Vylonis, Megan B; Watson, David T; Wurzler, Juliana A; Wysocki, Lauren M; Yalamanchili, Monica; Zaborowicz, Matthew A; Emerson, Julia A; Ortiz, Carlos; Deuschle, Frederic J; DiLorenzo, Lauren A; Goeller, Katie L; Macchi, Christopher R; Muller, Sarah E; Pasierb, Brittany D; Sable, Joseph E; Tucci, Jessica M; Tynon, Marykathryn; Dunbar, David A; Beken, Levent H; Conturso, Alaina C; Danner, Benjamin L; DeMichele, Gabriella A; Gonzales, Justin A; Hammond, Maureen S; Kelley, Colleen V; Kelly, Elisabeth A; Kulich, Danielle; Mageeney, Catherine M; McCabe, Nikie L; Newman, Alyssa M; Spaeder, Lindsay A; Tumminello, Richard A; Revie, Dennis; Benson, Jonathon M; Cristostomo, Michael C; DaSilva, Paolo A; Harker, Katherine S; Jarrell, Jenifer N; Jimenez, Luis A; Katz, Brandon M; Kennedy, William R; Kolibas, Kimberly S; LeBlanc, Mark T; Nguyen, Trung T; Nicolas, Daniel S; Patao, Melissa D; Patao, Shane M; Rupley, Bryan J; Sessions, Bridget J; Weaver, Jennifer A; Goodman, Anya L; Alvendia, Erica L; Baldassari, Shana M; Brown, Ashley S; Chase, Ian O; Chen, Maida; Chiang, Scott; Cromwell, Avery B; Custer, Ashley F; DiTommaso, Tia M; El-Adaimi, Jad; Goscinski, Nora C; Grove, Ryan A; Gutierrez, Nestor; Harnoto, Raechel S; Hedeen, Heather; Hong, Emily L; Hopkins, Barbara L; Huerta, Vilma F; Khoshabian, Colin; LaForge, Kristin M; Lee, Cassidy T; Lewis, Benjamin M; Lydon, Anniken M; Maniaci, Brian J; Mitchell, Ryan D; Morlock, Elaine V; Morris, William M; Naik, Priyanka; Olson, Nicole C; Osterloh, Jeannette M; Perez, Marcos A; Presley, Jonathan D; Randazzo, Matt J; Regan, Melanie K; Rossi, Franca G; Smith, Melanie A; Soliterman, Eugenia A; Sparks, Ciani J; Tran, Danny L; Wan, Tiffany; Welker, Anne A; Wong, Jeremy N; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J; Hoogewerf, Arlene J; Ackerman, Cheri M; Armistead, Isaac O; Baatenburg, Lara; Borr, Matthew J; Brouwer, Lindsay K; Burkhart, Brandon J; Bushhouse, Kelsey T; Cesko, Lejla; Choi, Tiffany Y Y; Cohen, Heather; Damsteegt, Amanda M; Darusz, Jess M; Dauphin, Cory M; Davis, Yelena P; Diekema, Emily J; Drewry, Melissa; Eisen, Michelle E M; Faber, Hayley M; Faber, Katherine J; Feenstra, Elizabeth; Felzer-Kim, Isabella T; Hammond, Brandy L; Hendriksma, Jesse; Herrold, Milton R; Hilbrands, Julia A; Howell, Emily J; Jelgerhuis, Sarah A; Jelsema, Timothy R; Johnson, Benjamin K; Jones, Kelly K; Kim, Anna; Kooienga, Ross D; Menyes, Erika E; Nollet, Eric A; Plescher, Brittany E; Rios, Lindsay; Rose, Jenny L; Schepers, Allison J; Scott, Geoff; Smith, Joshua R; Sterling, Allison M; Tenney, Jenna C; Uitvlugt, Chris; VanDyken, Rachel E; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P; Agbley, Kwabea; Boham, Sampson K; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S; Banker, Roxanne; Bartling, Justina R; Bhatiya, Chinmoy I; Boudoures, Anna L; Christiansen, Lena; Fosselman, Daniel S; French, Kristin M; Gill, Ishwar S; Havill, Jessen T; Johnson, Jaelyn L; Keny, Lauren J; Kerber, John M; Klett, Bethany M; Kufel, Christina N; May, Francis J; Mecoli, Jonathan P; Merry, Callie R; Meyer, Lauren R; Miller, Emily G; Mullen, Gregory J; Palozola, Katherine C; Pfeil, Jacob J; Thomas, Jessica G; Verbofsky, Evan M; Spana, Eric P; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I N; Fitzgibbons, John D; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J; Knouse, Kristin A; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S; Norton, Diana; Pham, Philip; Polk, Jessica W; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D; Scala, Victoria; Schwartz, Nicholas U; Shuen, Jessica A; Xu, Amy; Xu, Thomas Q; Zhang, Yi; Rosenwald, Anne G; Burg, Martin G; Adams, Stephanie J; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J; Robertson, Gregory M; Smith, Samuel I; DiAngelo, Justin R; Sassu, Eric D; Bhalla, Satish C; Sharif, Karim A; Choeying, Tenzin; Macias, Jason S; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E; Alvarez, Consuelo J; Davis, Kristen C; Dunham, Carrie A; Grantham, Alaina J; Hare, Amber N; Schottler, Jennifer; Scott, Zackary W; Kuleck, Gary A; Yu, Nicole S; Kaehler, Marian M; Jipp, Jacob; Overvoorde, Paul J; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques Dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T; Poet, Jeffrey L; Allen, Alica B; Anderson, John E; Barnett, Jason M; Baumgardner, Jordan S; Brown, Adam D; Carney, Jordan E; Chavez, Ramiro A; Christgen, Shelbi L; Christie, Jordan S; Clary, Andrea N; Conn, Michel A; Cooper, Kristen M; Crowley, Matt J; Crowley, Samuel T; Doty, Jennifer S; Dow, Brian A; Edwards, Curtis R; Elder, Darcie D; Fanning, John P; Janssen, Bridget M; Lambright, Anthony K; Lane, Curtiss E; Limle, Austin B; Mazur, Tammy; McCracken, Marly R; McDonough, Alexa M; Melton, Amy D; Minnick, Phillip J; Musick, Adam E; Newhart, William H; Noynaert, Joseph W; Ogden, Bradley J; Sandusky, Michael W; Schmuecker, Samantha M; Shipman, Anna L; Smith, Anna L; Thomsen, Kristen M; Unzicker, Matthew R; Vernon, William B; Winn, Wesley W; Woyski, Dustin S; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J; Aronhalt, Todd; Bellush, James M; Burke, Christa; DeFazio, Steve; Does, Benjamin R; Johnson, Todd D; Keysock, Nicholas; Knudsen, Nelson H; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S; Stagaard, Erica; Starcher, Justin R; Waggoner, Andrew W; Yemelyanova, Anastasia K; Hark, Amy T; Bertolet, Anne; Kuschner, Cyrus E; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E; Smith, Mary A; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S Catherine Silver; Henry, Tyneshia C P; Johnson, Ashlee G; White, Jackie X; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L M; Chau, Kim M; Ward, Alyssa; Regisford, E Gloria C; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M; Bahr, Thomas J; Caesar, Nicole M; Campana, Christopher; Cassidy, Daniel W; Cognetti, Peter A; English, Johnathan D; Fadus, Matthew C; Fick, Cameron N; Freda, Philip J; Hennessy, Bryan M; Hockenberger, Kelsey; Jones, Jennifer K; King, Jessica E; Knob, Christopher R; Kraftmann, Karen J; Li, Linghui; Lupey, Lena N; Minniti, Carl J; Minton, Thomas F; Moran, Joseph V; Mudumbi, Krishna; Nordman, Elizabeth C; Puetz, William J; Robinson, Lauren M; Rose, Thomas J; Sweeney, Edward P; Timko, Ashley S; Paetkau, Don W; Eisler, Heather L; Aldrup, Megan E; Bodenberg, Jessica M; Cole, Mara G; Deranek, Kelly M; DeShetler, Megan; Dowd, Rose M; Eckardt, Alexandra K; Ehret, Sharon C; Fese, Jessica; Garrett, Amanda D; Kammrath, Anna; Kappes, Michelle L; Light, Morgan R; Meier, Anne C; O'Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R; Reilly, Mary T; Robinett, Deirdre; Rossi, Nadine L; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R; Herrick, Douglas A; Khoury, Christopher B; Lea, Charlotte; Louie, Christopher A; Lowell, Shannon M; Reynolds, Thomas J; Schibler, Jeanine; Scoma, Alexandra H; Smith-Gee, Maxwell T; Tuberty, Sarah; Smith, Christopher D; Lopilato, Jane E; Hauke, Jeanette; Roecklein-Canfield, Jennifer A; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R; Flohr, Sarah; Flores, Amanda H; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B; Smith, Jonathan E; Unruh, Anna K; Velasquez, Vicente; Wolski, Matthew W; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T; Moore, Zachary D; Savell, Christopher D; Watson, Reece; Mel, Stephanie F; Anilkumar, Arjun A; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M; Dai, Tiffany; Garbagnati, Giancarlo F; Horton, Lanor S; Kim, Dongyeon; Lau, Joyce H; Liu, James Z; Mach, Sandy D; Phan, Thu A; Ren, Yi; Stapleton, Kenneth E; Strelitz, Jean M; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J; Fafara-Thompson, Antoinette E; Gross, Meleah J; Gygi, Amber M; Jackson, Lesley E; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L; Neely, Jessica; Ogawa, Emmy E; Rich, Ashley; Rogers, Anna; Spencer, J Devin; Stemler, Kristina M; Throm, Allison A; Van Camp, Matt; Weihbrecht, Katie; Wiles, T Aaron; Williams, Mallory A; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M; Bashiri, Azita; Bower, Mindy E; Florian, Kayla A; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S; Karim, Helmet; Mullen, Victor W; Pelchen, Carly E; Yenerall, Paul M; Zhang, Jiayu; Rubin, Michael R; Arias-Mejias, Suzette M; Bermudez-Capo, Armando G; Bernal-Vega, Gabriela V; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G; Martinez-Rodriguez, Javier O; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J; Santiago-Sanabria, Arnaldo J; Senquiz-Gonzalez, Andrea M; delValle, Frank R Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I; Zambrana-Burgos, Joan D; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P; Collado-Méndez, Xavier A; Colón-Cruz, Luis R; Correa-Muller, Ana I; Crooke-Rosado, Jonathan L; Cruz-García, José M; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M; Feliciano-Cancela, Alex J; Gónzalez-Pérez, Valerie M; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N; Laboy-Corales, Ángel L; Llaurador-Caraballo, Gabriela A; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A; Martínez-Traverso, Idaliz M; Medina-Ortega, Kiara N; Méndez-Castellanos, Sonya G; Menéndez-Serrano, Krizia C; Morales-Caraballo, Carol I; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M; Ramírez-Aponte, Edwin G; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S; Rivera-Pagán, Ingrid T; Rivera-Vicéns, Ramón E; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O; Rodríguez-García, Priscila M; Rodríguez-Laboy, Abneris E; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L; Rubio-Marrero, Eva N; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L; Santos-Ramos, Carlos E; Serrano-González, Joseline; Tamayo-Figueroa, Alina M; Tascón-Peñaranda, Edna P; Torres-Castillo, José L; Valentín-Feliciano, Nelson A; Valentín-Feliciano, Yashira M; Vargas-Barreto, Nadyan M; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L; Molleston, Jerome M; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y; Zheng, Yin; Preuss, Mary L; Garcia, Angelica; Juergens, Matt; Morris, Robert W; Nagengast, Alexis A; Azarewicz, Julie; Carr, Thomas J; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L; Adams, Ashley L; Barnard, Brianna K; Cheramie, Martin N; Eime, Anne M; Golden, Kathryn L; Hawkins, Allyson P; Hill, Jessica E; Kampmeier, Jessica A; Kern, Cody D; Magnuson, Emily E; Miller, Ashley R; Morrow, Cody M; Peairs, Julia C; Pickett, Gentry L; Popelka, Sarah A; Scott, Alexis J; Teepe, Emily J; TerMeer, Katie A; Watchinski, Carmen A; Watson, Lucas A; Weber, Rachel E; Woodard, Kate A; Barnard, Daron C; Appiah, Isaac; Giddens, Michelle M; McNeil, Gerard P; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C; Buhler, Jeremy; Mardis, Elaine R; Elgin, Sarah C R

2015-03-04

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25-50%) than euchromatic reference regions (3-11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11-27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4-3.6 vs. 8.4-8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. Copyright © 2015 Leung et al.
Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant

PubMed Central

Hawkins, Angela K; Garza, Elyssa R; Dietz, Valerie A; Hernandez, Oscar J; Hawkins, W Daryl; Burrell, A Millie

2017-01-01

Abstract Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation. PMID:29220486
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.
A comparison of theoretical and experimental pressure distributions for two advanced fighter wings

NASA Technical Reports Server (NTRS)

Haney, H. P.; Hicks, R. M.

1981-01-01

A comparison was made between experimental pressure distributions measured during testing of the Vought A-7 fighter and the theoretical predictions of four transonic potential flow codes. Isolated wind and three wing-body codes were used for comparison. All comparisons are for transonic Mach numbers and include both attached and separate flows. In general, the wing-body codes gave better agreement with the experiment than did the isolated wing code but, because of the greater complexity of the geometry, were found to be considerably more expensive and less reliable.
Development of a GPU-Accelerated 3-D Full-Wave Code for Electromagnetic Wave Propagation in a Cold Plasma

NASA Astrophysics Data System (ADS)

Woodbury, D.; Kubota, S.; Johnson, I.

2014-10-01

Computer simulations of electromagnetic wave propagation in magnetized plasmas are an important tool for both plasma heating and diagnostics. For active millimeter-wave and microwave diagnostics, accurately modeling the evolution of the beam parameters for launched, reflected or scattered waves in a toroidal plasma requires that calculations be done using the full 3-D geometry. Previously, we reported on the application of GPGPU (General-Purpose computing on Graphics Processing Units) to a 3-D vacuum Maxwell code using the FDTD (Finite-Difference Time-Domain) method. Tests were done for Gaussian beam propagation with a hard source antenna, utilizing the parallel processing capabilities of the NVIDIA K20M. In the current study, we have modified the 3-D code to include a soft source antenna and an induced current density based on the cold plasma approximation. Results from Gaussian beam propagation in an inhomogeneous anisotropic plasma, along with comparisons to ray- and beam-tracing calculations will be presented. Additional enhancements, such as advanced coding techniques for improved speedup, will also be investigated. Supported by U.S. DoE Grant DE-FG02-99-ER54527 and in part by the U.S. DoE, Office of Science, WDTS under the Science Undergraduate Laboratory Internship program.
Metrics for comparing dynamic earthquake rupture simulations

USGS Publications Warehouse

Barall, Michael; Harris, Ruth A.

2014-01-01

Earthquakes are complex events that involve a myriad of interactions among multiple geologic features and processes. One of the tools that is available to assist with their study is computer simulation, particularly dynamic rupture simulation. A dynamic rupture simulation is a numerical model of the physical processes that occur during an earthquake. Starting with the fault geometry, friction constitutive law, initial stress conditions, and assumptions about the condition and response of the near‐fault rocks, a dynamic earthquake rupture simulation calculates the evolution of fault slip and stress over time as part of the elastodynamic numerical solution (Ⓔ see the simulation description in the electronic supplement to this article). The complexity of the computations in a dynamic rupture simulation make it challenging to verify that the computer code is operating as intended, because there are no exact analytic solutions against which these codes’ results can be directly compared. One approach for checking if dynamic rupture computer codes are working satisfactorily is to compare each code’s results with the results of other dynamic rupture codes running the same earthquake simulation benchmark. To perform such a comparison consistently, it is necessary to have quantitative metrics. In this paper, we present a new method for quantitatively comparing the results of dynamic earthquake rupture computer simulation codes.
Compression performance of HEVC and its format range and screen content coding extensions

NASA Astrophysics Data System (ADS)

Li, Bin; Xu, Jizheng; Sullivan, Gary J.

2015-09-01

This paper presents a comparison-based test of the objective compression performance of the High Efficiency Video Coding (HEVC) standard, its format range extensions (RExt), and its draft screen content coding extensions (SCC). The current dominant standard, H.264/MPEG-4 AVC, is used as an anchor reference in the comparison. The conditions used for the comparison tests were designed to reflect relevant application scenarios and to enable a fair comparison to the maximum extent feasible - i.e., using comparable quantization settings, reference frame buffering, intra refresh periods, rate-distortion optimization decision processing, etc. It is noted that such PSNR-based objective comparisons generally provide more conservative estimates of HEVC benefit than are found in subjective studies. The experimental results show that, when compared with H.264/MPEG-4 AVC, HEVC version 1 provides a bit rate savings for equal PSNR of about 23% for all-intra coding, 34% for random access coding, and 38% for low-delay coding. This is consistent with prior studies and the general characterization that HEVC can provide about a bit rate savings of about 50% for equal subjective quality for most applications. The HEVC format range extensions provide a similar bit rate savings of about 13-25% for all-intra coding, 28-33% for random access coding, and 32-38% for low-delay coding at different bit rate ranges. For lossy coding of screen content, the HEVC screen content coding extensions achieve a bit rate savings of about 66%, 63%, and 61% for all-intra coding, random access coding, and low-delay coding, respectively. For lossless coding, the corresponding bit rate savings are about 40%, 33%, and 32%, respectively.
Dual Coding, Reasoning and Fallacies.

ERIC Educational Resources Information Center

Hample, Dale

1982-01-01

Develops the theory that a fallacy is not a comparison of a rhetorical text to a set of definitions but a comparison of one person's cognition with another's. Reviews Paivio's dual coding theory, relates nonverbal coding to reasoning processes, and generates a limited fallacy theory based on dual coding theory. (PD)
Different evolutionary patterns of SNPs between domains and unassigned regions in human protein-coding sequences.

PubMed

Pang, Erli; Wu, Xiaomei; Lin, Kui

2016-06-01

Protein evolution plays an important role in the evolution of each genome. Because of their functional nature, in general, most of their parts or sites are differently constrained selectively, particularly by purifying selection. Most previous studies on protein evolution considered individual proteins in their entirety or compared protein-coding sequences with non-coding sequences. Less attention has been paid to the evolution of different parts within each protein of a given genome. To this end, based on PfamA annotation of all human proteins, each protein sequence can be split into two parts: domains or unassigned regions. Using this rationale, single nucleotide polymorphisms (SNPs) in protein-coding sequences from the 1000 Genomes Project were mapped according to two classifications: SNPs occurring within protein domains and those within unassigned regions. With these classifications, we found: the density of synonymous SNPs within domains is significantly greater than that of synonymous SNPs within unassigned regions; however, the density of non-synonymous SNPs shows the opposite pattern. We also found there are signatures of purifying selection on both the domain and unassigned regions. Furthermore, the selective strength on domains is significantly greater than that on unassigned regions. In addition, among all of the human protein sequences, there are 117 PfamA domains in which no SNPs are found. Our results highlight an important aspect of protein domains and may contribute to our understanding of protein evolution.
Improving 1D Stellar Models with 3D Atmospheres

NASA Astrophysics Data System (ADS)

Mosumgaard, Jakob Rørsted; Silva Aguirre, Víctor; Weiss, Achim; Christensen-Dalsgaard, Jørgen; Trampedach, Regner

2017-10-01

Stellar evolution codes play a major role in present-day astrophysics, yet they share common issues. In this work we seek to remedy some of those by the use of results from realistic and highly detailed 3D hydrodynamical simulations of stellar atmospheres. We have implemented a new temperature stratification extracted directly from the 3D simulations into the Garching Stellar Evolution Code to replace the simplified atmosphere normally used. Secondly, we have implemented the use of a variable mixing-length parameter, which changes as a function of the stellar surface gravity and temperature - also derived from the 3D simulations. Furthermore, to make our models consistent, we have calculated new opacity tables to match the atmospheric simulations. Here, we present the modified code and initial results on stellar evolution using it.
A 2D and 3D Code Comparison of Turbulent Mixing in Spherical Implosions

NASA Astrophysics Data System (ADS)

Flaig, Markus; Thornber, Ben; Grieves, Brian; Youngs, David; Williams, Robin; Clark, Dan; Weber, Chris

2016-10-01

Turbulent mixing due to Richtmyer-Meshkov and Rayleigh-Taylor instabilities has proven to be a major obstacle on the way to achieving ignition in inertial confinement fusion (ICF) implosions. Numerical simulations are an important tool for understanding the mixing process, however, the results of such simulations depend on the choice of grid geometry and the numerical scheme used. In order to clarify this issue, we compare the simulation codes FLASH, TURMOIL, HYDRA, MIRANDA and FLAMENCO for the problem of the growth of single- and multi-mode perturbations on the inner interface of a dense imploding shell. We consider two setups: A single-shock setup with a convergence ratio of 4, as well as a higher convergence multi-shock setup that mimics a typical NIF mixcap experiment. We employ both singlemode and ICF-like broadband perturbations. We find good agreement between all codes concerning the evolution of the mix layer width, however, the are differences in the small scale mixing. We also develop a Bell-Plesset model that is able to predict the mix layer width and find excellent agreement with the simulation results. This work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government.
On the evolution of primitive genetic codes.

PubMed

Weberndorfer, Günter; Hofacker, Ivo L; Stadler, Peter F

2003-10-01

The primordial genetic code probably has been a drastically simplified ancestor of the canonical code that is used by contemporary cells. In order to understand how the present-day code came about we first need to explain how the language of the building plan can change without destroying the encoded information. In this work we introduce a minimal organism model that is based on biophysically reasonable descriptions of RNA and protein, namely secondary structure folding and knowledge based potentials. The evolution of a population of such organism under competition for a common resource is simulated explicitly at the level of individual replication events. Starting with very simple codes, and hence greatly reduced amino acid alphabets, we observe a diversification of the codes in most simulation runs. The driving force behind this effect is the possibility to produce fitter proteins when the repertoire of amino acids is enlarged.
Gas and dust from solar metallicity AGB stars

NASA Astrophysics Data System (ADS)

Ventura, P.; Karakas, A.; Dell'Agli, F.; García-Hernández, D. A.; Guzman-Ramirez, L.

2018-04-01

We study the asymptotic giant branch (AGB) evolution of stars with masses between 1 M⊙and8.5 M⊙. We focus on stars with a solar chemical composition, which allows us to interpret evolved stars in the Galaxy. We present a detailed comparison with models of the same chemistry, calculated with a different evolution code and based on a different set of physical assumptions. We find that stars of mass ≥3.5 M⊙ experience hot bottom burning at the base of the envelope. They have AGB lifetimes shorter than ˜3 × 105 yr and eject into their surroundings gas contaminated by proton-capture nucleosynthesis, at an extent sensitive to the treatment of convection. Low-mass stars with 1.5 M⊙ ≤ M ≤ 3 M⊙ become carbon stars. During the final phases, the C/O ratio grows to ˜3. We find a remarkable agreement between the two codes for the low-mass models and conclude that predictions for the physical and chemical properties of these stars, and the AGB lifetime, are not that sensitive to the modelling of the AGB phase. The dust produced is also dependent on the mass: low-mass stars produce mainly solid carbon and silicon carbide dust, whereas higher mass stars produce silicates and alumina dust. Possible future observations potentially able to add more robustness to the present results are also discussed.
Quaternionic representation of the genetic code.

PubMed

Carlevaro, C Manuel; Irastorza, Ramiro M; Vericat, Fernando

2016-03-01

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearance of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.
When Genomics Is Not Enough: Experimental Evidence for a Decrease in LINE-1 Activity During the Evolution of Australian Marsupials

PubMed Central

Gallus, Susanne; Lammers, Fritjof

2016-01-01

The autonomous transposable element LINE-1 is a highly abundant element that makes up between 15% and 20% of therian mammal genomes. Since their origin before the divergence of marsupials and placental mammals, LINE-1 elements have contributed actively to the genome landscape. A previous in silico screen of the Tasmanian devil genome revealed a lack of functional coding LINE-1 sequences. In this study we present the results of an in vitro analysis from a partial LINE-1 reverse transcriptase coding sequence in five marsupial species. Our experimental screen supports the in silico findings of the genome-wide degradation of LINE-1 sequences in the Tasmanian devil, and identifies a high frequency of degraded LINE-1 sequences in other Australian marsupials. The comparison between the experimentally obtained LINE-1 sequences and reference genome assemblies suggests that conclusions from in silico analyses of retrotransposition activity can be influenced by incomplete genome assemblies from short reads. PMID:27389686
Comparison of Computed and Measured Vortex Evolution for a UH-60A Rotor in Forward Flight

NASA Technical Reports Server (NTRS)

Ahmad, Jasim Uddin; Yamauchi, Gloria K.; Kao, David L.

2013-01-01

A Computational Fluid Dynamics (CFD) simulation using the Navier-Stokes equations was performed to determine the evolutionary and dynamical characteristics of the vortex flowfield for a highly flexible aeroelastic UH-60A rotor in forward flight. The experimental wake data were acquired using Particle Image Velocimetry (PIV) during a test of the fullscale UH-60A rotor in the National Full-Scale Aerodynamics Complex 40- by 80-Foot Wind Tunnel. The PIV measurements were made in a stationary cross-flow plane at 90 deg rotor azimuth. The CFD simulation was performed using the OVERFLOW CFD solver loosely coupled with the rotorcraft comprehensive code CAMRAD II. Characteristics of vortices captured in the PIV plane from different blades are compared with CFD calculations. The blade airloads were calculated using two different turbulence models. A limited spatial, temporal, and CFD/comprehensive-code coupling sensitivity analysis was performed in order to verify the unsteady helicopter simulations with a moving rotor grid system.

De Novo ORFs in Drosophila Are Important to Organismal Fitness and Evolved Rapidly from Previously Non-coding Sequences

PubMed Central

Reinhardt, Josephine A.; Wanjiru, Betty M.; Brant, Alicia T.; Saelao, Perot; Begun, David J.; Jones, Corbin D.

2013-01-01

How non-coding DNA gives rise to new protein-coding genes (de novo genes) is not well understood. Recent work has revealed the origins and functions of a few de novo genes, but common principles governing the evolution or biological roles of these genes are unknown. To better define these principles, we performed a parallel analysis of the evolution and function of six putatively protein-coding de novo genes described in Drosophila melanogaster. Reconstruction of the transcriptional history of de novo genes shows that two de novo genes emerged from novel long non-coding RNAs that arose at least 5 MY prior to evolution of an open reading frame. In contrast, four other de novo genes evolved a translated open reading frame and transcription within the same evolutionary interval suggesting that nascent open reading frames (proto-ORFs), while not required, can contribute to the emergence of a new de novo gene. However, none of the genes arose from proto-ORFs that existed long before expression evolved. Sequence and structural evolution of de novo genes was rapid compared to nearby genes and the structural complexity of de novo genes steadily increases over evolutionary time. Despite the fact that these genes are transcribed at a higher level in males than females, and are most strongly expressed in testes, RNAi experiments show that most of these genes are essential in both sexes during metamorphosis. This lethality suggests that protein coding de novo genes in Drosophila quickly become functionally important. PMID:24146629
Dynamic Monte Carlo simulations of radiatively accelerated GRB fireballs

NASA Astrophysics Data System (ADS)

Chhotray, Atul; Lazzati, Davide

2018-05-01

We present a novel Dynamic Monte Carlo code (DynaMo code) that self-consistently simulates the Compton-scattering-driven dynamic evolution of a plasma. We use the DynaMo code to investigate the time-dependent expansion and acceleration of dissipationless gamma-ray burst fireballs by varying their initial opacities and baryonic content. We study the opacity and energy density evolution of an initially optically thick, radiation-dominated fireball across its entire phase space - in particular during the Rph < Rsat regime. Our results reveal new phases of fireball evolution: a transition phase with a radial extent of several orders of magnitude - the fireball transitions from Γ ∝ R to Γ ∝ R0, a post-photospheric acceleration phase - where fireballs accelerate beyond the photosphere and a Thomson-dominated acceleration phase - characterized by slow acceleration of optically thick, matter-dominated fireballs due to Thomson scattering. We quantify the new phases by providing analytical expressions of Lorentz factor evolution, which will be useful for deriving jet parameters.
Drosophila Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

PubMed Central

Leung, Wilson; Shaffer, Christopher D.; Reed, Laura K.; Smith, Sheryl T.; Barshop, William; Dirkes, William; Dothager, Matthew; Lee, Paul; Wong, Jeannette; Xiong, David; Yuan, Han; Bedard, James E. J.; Machone, Joshua F.; Patterson, Seantay D.; Price, Amber L.; Turner, Bryce A.; Robic, Srebrenka; Luippold, Erin K.; McCartha, Shannon R.; Walji, Tezin A.; Walker, Chelsea A.; Saville, Kenneth; Abrams, Marita K.; Armstrong, Andrew R.; Armstrong, William; Bailey, Robert J.; Barberi, Chelsea R.; Beck, Lauren R.; Blaker, Amanda L.; Blunden, Christopher E.; Brand, Jordan P.; Brock, Ethan J.; Brooks, Dana W.; Brown, Marie; Butzler, Sarah C.; Clark, Eric M.; Clark, Nicole B.; Collins, Ashley A.; Cotteleer, Rebecca J.; Cullimore, Peterson R.; Dawson, Seth G.; Docking, Carter T.; Dorsett, Sasha L.; Dougherty, Grace A.; Downey, Kaitlyn A.; Drake, Andrew P.; Earl, Erica K.; Floyd, Trevor G.; Forsyth, Joshua D.; Foust, Jonathan D.; Franchi, Spencer L.; Geary, James F.; Hanson, Cynthia K.; Harding, Taylor S.; Harris, Cameron B.; Heckman, Jonathan M.; Holderness, Heather L.; Howey, Nicole A.; Jacobs, Dontae A.; Jewell, Elizabeth S.; Kaisler, Maria; Karaska, Elizabeth A.; Kehoe, James L.; Koaches, Hannah C.; Koehler, Jessica; Koenig, Dana; Kujawski, Alexander J.; Kus, Jordan E.; Lammers, Jennifer A.; Leads, Rachel R.; Leatherman, Emily C.; Lippert, Rachel N.; Messenger, Gregory S.; Morrow, Adam T.; Newcomb, Victoria; Plasman, Haley J.; Potocny, Stephanie J.; Powers, Michelle K.; Reem, Rachel M.; Rennhack, Jonathan P.; Reynolds, Katherine R.; Reynolds, Lyndsey A.; Rhee, Dong K.; Rivard, Allyson B.; Ronk, Adam J.; Rooney, Meghan B.; Rubin, Lainey S.; Salbert, Luke R.; Saluja, Rasleen K.; Schauder, Taylor; Schneiter, Allison R.; Schulz, Robert W.; Smith, Karl E.; Spencer, Sarah; Swanson, Bryant R.; Tache, Melissa A.; Tewilliager, Ashley A.; Tilot, Amanda K.; VanEck, Eve; Villerot, Matthew M.; Vylonis, Megan B.; Watson, David T.; Wurzler, Juliana A.; Wysocki, Lauren M.; Yalamanchili, Monica; Zaborowicz, Matthew A.; Emerson, Julia A.; Ortiz, Carlos; Deuschle, Frederic J.; DiLorenzo, Lauren A.; Goeller, Katie L.; Macchi, Christopher R.; Muller, Sarah E.; Pasierb, Brittany D.; Sable, Joseph E.; Tucci, Jessica M.; Tynon, Marykathryn; Dunbar, David A.; Beken, Levent H.; Conturso, Alaina C.; Danner, Benjamin L.; DeMichele, Gabriella A.; Gonzales, Justin A.; Hammond, Maureen S.; Kelley, Colleen V.; Kelly, Elisabeth A.; Kulich, Danielle; Mageeney, Catherine M.; McCabe, Nikie L.; Newman, Alyssa M.; Spaeder, Lindsay A.; Tumminello, Richard A.; Revie, Dennis; Benson, Jonathon M.; Cristostomo, Michael C.; DaSilva, Paolo A.; Harker, Katherine S.; Jarrell, Jenifer N.; Jimenez, Luis A.; Katz, Brandon M.; Kennedy, William R.; Kolibas, Kimberly S.; LeBlanc, Mark T.; Nguyen, Trung T.; Nicolas, Daniel S.; Patao, Melissa D.; Patao, Shane M.; Rupley, Bryan J.; Sessions, Bridget J.; Weaver, Jennifer A.; Goodman, Anya L.; Alvendia, Erica L.; Baldassari, Shana M.; Brown, Ashley S.; Chase, Ian O.; Chen, Maida; Chiang, Scott; Cromwell, Avery B.; Custer, Ashley F.; DiTommaso, Tia M.; El-Adaimi, Jad; Goscinski, Nora C.; Grove, Ryan A.; Gutierrez, Nestor; Harnoto, Raechel S.; Hedeen, Heather; Hong, Emily L.; Hopkins, Barbara L.; Huerta, Vilma F.; Khoshabian, Colin; LaForge, Kristin M.; Lee, Cassidy T.; Lewis, Benjamin M.; Lydon, Anniken M.; Maniaci, Brian J.; Mitchell, Ryan D.; Morlock, Elaine V.; Morris, William M.; Naik, Priyanka; Olson, Nicole C.; Osterloh, Jeannette M.; Perez, Marcos A.; Presley, Jonathan D.; Randazzo, Matt J.; Regan, Melanie K.; Rossi, Franca G.; Smith, Melanie A.; Soliterman, Eugenia A.; Sparks, Ciani J.; Tran, Danny L.; Wan, Tiffany; Welker, Anne A.; Wong, Jeremy N.; Sreenivasan, Aparna; Youngblom, Jim; Adams, Andrew; Alldredge, Justin; Bryant, Ashley; Carranza, David; Cifelli, Alyssa; Coulson, Kevin; Debow, Calise; Delacruz, Noelle; Emerson, Charlene; Farrar, Cassandra; Foret, Don; Garibay, Edgar; Gooch, John; Heslop, Michelle; Kaur, Sukhjit; Khan, Ambreen; Kim, Van; Lamb, Travis; Lindbeck, Peter; Lucas, Gabi; Macias, Elizabeth; Martiniuc, Daniela; Mayorga, Lissett; Medina, Joseph; Membreno, Nelson; Messiah, Shady; Neufeld, Lacey; Nguyen, San Francisco; Nichols, Zachary; Odisho, George; Peterson, Daymon; Rodela, Laura; Rodriguez, Priscilla; Rodriguez, Vanessa; Ruiz, Jorge; Sherrill, Will; Silva, Valeria; Sparks, Jeri; Statton, Geeta; Townsend, Ashley; Valdez, Isabel; Waters, Mary; Westphal, Kyle; Winkler, Stacey; Zumkehr, Joannee; DeJong, Randall J.; Hoogewerf, Arlene J.; Ackerman, Cheri M.; Armistead, Isaac O.; Baatenburg, Lara; Borr, Matthew J.; Brouwer, Lindsay K.; Burkhart, Brandon J.; Bushhouse, Kelsey T.; Cesko, Lejla; Choi, Tiffany Y. Y.; Cohen, Heather; Damsteegt, Amanda M.; Darusz, Jess M.; Dauphin, Cory M.; Davis, Yelena P.; Diekema, Emily J.; Drewry, Melissa; Eisen, Michelle E. M.; Faber, Hayley M.; Faber, Katherine J.; Feenstra, Elizabeth; Felzer-Kim, Isabella T.; Hammond, Brandy L.; Hendriksma, Jesse; Herrold, Milton R.; Hilbrands, Julia A.; Howell, Emily J.; Jelgerhuis, Sarah A.; Jelsema, Timothy R.; Johnson, Benjamin K.; Jones, Kelly K.; Kim, Anna; Kooienga, Ross D.; Menyes, Erika E.; Nollet, Eric A.; Plescher, Brittany E.; Rios, Lindsay; Rose, Jenny L.; Schepers, Allison J.; Scott, Geoff; Smith, Joshua R.; Sterling, Allison M.; Tenney, Jenna C.; Uitvlugt, Chris; VanDyken, Rachel E.; VanderVennen, Marielle; Vue, Samantha; Kokan, Nighat P.; Agbley, Kwabea; Boham, Sampson K.; Broomfield, Daniel; Chapman, Kayla; Dobbe, Ali; Dobbe, Ian; Harrington, William; Ibrahem, Marwan; Kennedy, Andre; Koplinsky, Chad A.; Kubricky, Cassandra; Ladzekpo, Danielle; Pattison, Claire; Ramirez, Roman E.; Wande, Lucia; Woehlke, Sarah; Wawersik, Matthew; Kiernan, Elizabeth; Thompson, Jeffrey S.; Banker, Roxanne; Bartling, Justina R.; Bhatiya, Chinmoy I.; Boudoures, Anna L.; Christiansen, Lena; Fosselman, Daniel S.; French, Kristin M.; Gill, Ishwar S.; Havill, Jessen T.; Johnson, Jaelyn L.; Keny, Lauren J.; Kerber, John M.; Klett, Bethany M.; Kufel, Christina N.; May, Francis J.; Mecoli, Jonathan P.; Merry, Callie R.; Meyer, Lauren R.; Miller, Emily G.; Mullen, Gregory J.; Palozola, Katherine C.; Pfeil, Jacob J.; Thomas, Jessica G.; Verbofsky, Evan M.; Spana, Eric P.; Agarwalla, Anant; Chapman, Julia; Chlebina, Ben; Chong, Insun; Falk, I.N.; Fitzgibbons, John D.; Friedman, Harrison; Ighile, Osagie; Kim, Andrew J.; Knouse, Kristin A.; Kung, Faith; Mammo, Danny; Ng, Chun Leung; Nikam, Vinayak S.; Norton, Diana; Pham, Philip; Polk, Jessica W.; Prasad, Shreya; Rankin, Helen; Ratliff, Camille D.; Scala, Victoria; Schwartz, Nicholas U.; Shuen, Jessica A.; Xu, Amy; Xu, Thomas Q.; Zhang, Yi; Rosenwald, Anne G.; Burg, Martin G.; Adams, Stephanie J.; Baker, Morgan; Botsford, Bobbi; Brinkley, Briana; Brown, Carter; Emiah, Shadie; Enoch, Erica; Gier, Chad; Greenwell, Alyson; Hoogenboom, Lindsay; Matthews, Jordan E.; McDonald, Mitchell; Mercer, Amanda; Monsma, Nicholaus; Ostby, Kristine; Ramic, Alen; Shallman, Devon; Simon, Matthew; Spencer, Eric; Tomkins, Trisha; Wendland, Pete; Wylie, Anna; Wolyniak, Michael J.; Robertson, Gregory M.; Smith, Samuel I.; DiAngelo, Justin R.; Sassu, Eric D.; Bhalla, Satish C.; Sharif, Karim A.; Choeying, Tenzin; Macias, Jason S.; Sanusi, Fareed; Torchon, Karvyn; Bednarski, April E.; Alvarez, Consuelo J.; Davis, Kristen C.; Dunham, Carrie A.; Grantham, Alaina J.; Hare, Amber N.; Schottler, Jennifer; Scott, Zackary W.; Kuleck, Gary A.; Yu, Nicole S.; Kaehler, Marian M.; Jipp, Jacob; Overvoorde, Paul J.; Shoop, Elizabeth; Cyrankowski, Olivia; Hoover, Betsy; Kusner, Matt; Lin, Devry; Martinov, Tijana; Misch, Jonathan; Salzman, Garrett; Schiedermayer, Holly; Snavely, Michael; Zarrasola, Stephanie; Parrish, Susan; Baker, Atlee; Beckett, Alissa; Belella, Carissa; Bryant, Julie; Conrad, Turner; Fearnow, Adam; Gomez, Carolina; Herbstsomer, Robert A.; Hirsch, Sarah; Johnson, Christen; Jones, Melissa; Kabaso, Rita; Lemmon, Eric; Vieira, Carolina Marques dos Santos; McFarland, Darryl; McLaughlin, Christopher; Morgan, Abbie; Musokotwane, Sepo; Neutzling, William; Nietmann, Jana; Paluskievicz, Christina; Penn, Jessica; Peoples, Emily; Pozmanter, Caitlin; Reed, Emily; Rigby, Nichole; Schmidt, Lasse; Shelton, Micah; Shuford, Rebecca; Tirasawasdichai, Tiara; Undem, Blair; Urick, Damian; Vondy, Kayla; Yarrington, Bryan; Eckdahl, Todd T.; Poet, Jeffrey L.; Allen, Alica B.; Anderson, John E.; Barnett, Jason M.; Baumgardner, Jordan S.; Brown, Adam D.; Carney, Jordan E.; Chavez, Ramiro A.; Christgen, Shelbi L.; Christie, Jordan S.; Clary, Andrea N.; Conn, Michel A.; Cooper, Kristen M.; Crowley, Matt J.; Crowley, Samuel T.; Doty, Jennifer S.; Dow, Brian A.; Edwards, Curtis R.; Elder, Darcie D.; Fanning, John P.; Janssen, Bridget M.; Lambright, Anthony K.; Lane, Curtiss E.; Limle, Austin B.; Mazur, Tammy; McCracken, Marly R.; McDonough, Alexa M.; Melton, Amy D.; Minnick, Phillip J.; Musick, Adam E.; Newhart, William H.; Noynaert, Joseph W.; Ogden, Bradley J.; Sandusky, Michael W.; Schmuecker, Samantha M.; Shipman, Anna L.; Smith, Anna L.; Thomsen, Kristen M.; Unzicker, Matthew R.; Vernon, William B.; Winn, Wesley W.; Woyski, Dustin S.; Zhu, Xiao; Du, Chunguang; Ament, Caitlin; Aso, Soham; Bisogno, Laura Simone; Caronna, Jason; Fefelova, Nadezhda; Lopez, Lenin; Malkowitz, Lorraine; Marra, Jonathan; Menillo, Daniella; Obiorah, Ifeanyi; Onsarigo, Eric Nyabeta; Primus, Shekerah; Soos, Mahdi; Tare, Archana; Zidan, Ameer; Jones, Christopher J.; Aronhalt, Todd; Bellush, James M.; Burke, Christa; DeFazio, Steve; Does, Benjamin R.; Johnson, Todd D.; Keysock, Nicholas; Knudsen, Nelson H.; Messler, James; Myirski, Kevin; Rekai, Jade Lea; Rempe, Ryan Michael; Salgado, Michael S.; Stagaard, Erica; Starcher, Justin R.; Waggoner, Andrew W.; Yemelyanova, Anastasia K.; Hark, Amy T.; Bertolet, Anne; Kuschner, Cyrus E.; Parry, Kesley; Quach, Michael; Shantzer, Lindsey; Shaw, Mary E.; Smith, Mary A.; Glenn, Omolara; Mason, Portia; Williams, Charlotte; Key, S. Catherine Silver; Henry, Tyneshia C. P.; Johnson, Ashlee G.; White, Jackie X.; Haberman, Adam; Asinof, Sam; Drumm, Kelly; Freeburg, Trip; Safa, Nadia; Schultz, Darrin; Shevin, Yakov; Svoronos, Petros; Vuong, Tam; Wellinghoff, Jules; Hoopes, Laura L. M.; Chau, Kim M.; Ward, Alyssa; Regisford, E. Gloria C.; Augustine, LaJerald; Davis-Reyes, Brionna; Echendu, Vivienne; Hales, Jasmine; Ibarra, Sharon; Johnson, Lauriaun; Ovu, Steven; Braverman, John M.; Bahr, Thomas J.; Caesar, Nicole M.; Campana, Christopher; Cassidy, Daniel W.; Cognetti, Peter A.; English, Johnathan D.; Fadus, Matthew C.; Fick, Cameron N.; Freda, Philip J.; Hennessy, Bryan M.; Hockenberger, Kelsey; Jones, Jennifer K.; King, Jessica E.; Knob, Christopher R.; Kraftmann, Karen J.; Li, Linghui; Lupey, Lena N.; Minniti, Carl J.; Minton, Thomas F.; Moran, Joseph V.; Mudumbi, Krishna; Nordman, Elizabeth C.; Puetz, William J.; Robinson, Lauren M.; Rose, Thomas J.; Sweeney, Edward P.; Timko, Ashley S.; Paetkau, Don W.; Eisler, Heather L.; Aldrup, Megan E.; Bodenberg, Jessica M.; Cole, Mara G.; Deranek, Kelly M.; DeShetler, Megan; Dowd, Rose M.; Eckardt, Alexandra K.; Ehret, Sharon C.; Fese, Jessica; Garrett, Amanda D.; Kammrath, Anna; Kappes, Michelle L.; Light, Morgan R.; Meier, Anne C.; O’Rouke, Allison; Perella, Mallory; Ramsey, Kimberley; Ramthun, Jennifer R.; Reilly, Mary T.; Robinett, Deirdre; Rossi, Nadine L.; Schueler, Mary Grace; Shoemaker, Emma; Starkey, Kristin M.; Vetor, Ashley; Vrable, Abby; Chandrasekaran, Vidya; Beck, Christopher; Hatfield, Kristen R.; Herrick, Douglas A.; Khoury, Christopher B.; Lea, Charlotte; Louie, Christopher A.; Lowell, Shannon M.; Reynolds, Thomas J.; Schibler, Jeanine; Scoma, Alexandra H.; Smith-Gee, Maxwell T.; Tuberty, Sarah; Smith, Christopher D.; Lopilato, Jane E.; Hauke, Jeanette; Roecklein-Canfield, Jennifer A.; Corrielus, Maureen; Gilman, Hannah; Intriago, Stephanie; Maffa, Amanda; Rauf, Sabya A.; Thistle, Katrina; Trieu, Melissa; Winters, Jenifer; Yang, Bib; Hauser, Charles R.; Abusheikh, Tariq; Ashrawi, Yara; Benitez, Pedro; Boudreaux, Lauren R.; Bourland, Megan; Chavez, Miranda; Cruz, Samantha; Elliott, GiNell; Farek, Jesse R.; Flohr, Sarah; Flores, Amanda H.; Friedrichs, Chelsey; Fusco, Zach; Goodwin, Zane; Helmreich, Eric; Kiley, John; Knepper, John Mark; Langner, Christine; Martinez, Megan; Mendoza, Carlos; Naik, Monal; Ochoa, Andrea; Ragland, Nicolas; Raimey, England; Rathore, Sunil; Reza, Evangelina; Sadovsky, Griffin; Seydoux, Marie-Isabelle B.; Smith, Jonathan E.; Unruh, Anna K.; Velasquez, Vicente; Wolski, Matthew W.; Gosser, Yuying; Govind, Shubha; Clarke-Medley, Nicole; Guadron, Leslie; Lau, Dawn; Lu, Alvin; Mazzeo, Cheryl; Meghdari, Mariam; Ng, Simon; Pamnani, Brad; Plante, Olivia; Shum, Yuki Kwan Wa; Song, Roy; Johnson, Diana E.; Abdelnabi, Mai; Archambault, Alexi; Chamma, Norma; Gaur, Shailly; Hammett, Deborah; Kandahari, Adrese; Khayrullina, Guzal; Kumar, Sonali; Lawrence, Samantha; Madden, Nigel; Mandelbaum, Max; Milnthorp, Heather; Mohini, Shiv; Patel, Roshni; Peacock, Sarah J.; Perling, Emily; Quintana, Amber; Rahimi, Michael; Ramirez, Kristen; Singhal, Rishi; Weeks, Corinne; Wong, Tiffany; Gillis, Aubree T.; Moore, Zachary D.; Savell, Christopher D.; Watson, Reece; Mel, Stephanie F.; Anilkumar, Arjun A.; Bilinski, Paul; Castillo, Rostislav; Closser, Michael; Cruz, Nathalia M.; Dai, Tiffany; Garbagnati, Giancarlo F.; Horton, Lanor S.; Kim, Dongyeon; Lau, Joyce H.; Liu, James Z.; Mach, Sandy D.; Phan, Thu A.; Ren, Yi; Stapleton, Kenneth E.; Strelitz, Jean M.; Sunjed, Ray; Stamm, Joyce; Anderson, Morgan C.; Bonifield, Bethany Grace; Coomes, Daniel; Dillman, Adam; Durchholz, Elaine J.; Fafara-Thompson, Antoinette E.; Gross, Meleah J.; Gygi, Amber M.; Jackson, Lesley E.; Johnson, Amy; Kocsisova, Zuzana; Manghelli, Joshua L.; McNeil, Kylie; Murillo, Michael; Naylor, Kierstin L.; Neely, Jessica; Ogawa, Emmy E.; Rich, Ashley; Rogers, Anna; Spencer, J. Devin; Stemler, Kristina M.; Throm, Allison A.; Van Camp, Matt; Weihbrecht, Katie; Wiles, T. Aaron; Williams, Mallory A.; Williams, Matthew; Zoll, Kyle; Bailey, Cheryl; Zhou, Leming; Balthaser, Darla M.; Bashiri, Azita; Bower, Mindy E.; Florian, Kayla A.; Ghavam, Nazanin; Greiner-Sosanko, Elizabeth S.; Karim, Helmet; Mullen, Victor W.; Pelchen, Carly E.; Yenerall, Paul M.; Zhang, Jiayu; Rubin, Michael R.; Arias-Mejias, Suzette M.; Bermudez-Capo, Armando G.; Bernal-Vega, Gabriela V.; Colon-Vazquez, Mariela; Flores-Vazquez, Arelys; Gines-Rosario, Mariela; Llavona-Cartagena, Ivan G.; Martinez-Rodriguez, Javier O.; Ortiz-Fuentes, Lionel; Perez-Colomba, Eliezer O.; Perez-Otero, Joseph; Rivera, Elisandra; Rodriguez-Giron, Luke J.; Santiago-Sanabria, Arnaldo J.; Senquiz-Gonzalez, Andrea M.; delValle, Frank R. Soto; Vargas-Franco, Dorianmarie; Velázquez-Soto, Karla I.; Zambrana-Burgos, Joan D.; Martinez-Cruzado, Juan Carlos; Asencio-Zayas, Lillyann; Babilonia-Figueroa, Kevin; Beauchamp-Pérez, Francis D.; Belén-Rodríguez, Juliana; Bracero-Quiñones, Luciann; Burgos-Bula, Andrea P.; Collado-Méndez, Xavier A.; Colón-Cruz, Luis R.; Correa-Muller, Ana I.; Crooke-Rosado, Jonathan L.; Cruz-García, José M.; Defendini-Ávila, Marianna; Delgado-Peraza, Francheska M.; Feliciano-Cancela, Alex J.; Gónzalez-Pérez, Valerie M.; Guiblet, Wilfried; Heredia-Negrón, Aldo; Hernández-Muñiz, Jennifer; Irizarry-González, Lourdes N.; Laboy-Corales, Ángel L.; Llaurador-Caraballo, Gabriela A.; Marín-Maldonado, Frances; Marrero-Llerena, Ulises; Martell-Martínez, Héctor A.; Martínez-Traverso, Idaliz M.; Medina-Ortega, Kiara N.; Méndez-Castellanos, Sonya G.; Menéndez-Serrano, Krizia C.; Morales-Caraballo, Carol I.; Ortiz-DeChoudens, Saryleine; Ortiz-Ortiz, Patricia; Pagán-Torres, Hendrick; Pérez-Afanador, Diana; Quintana-Torres, Enid M.; Ramírez-Aponte, Edwin G.; Riascos-Cuero, Carolina; Rivera-Llovet, Michelle S.; Rivera-Pagán, Ingrid T.; Rivera-Vicéns, Ramón E.; Robles-Juarbe, Fabiola; Rodríguez-Bonilla, Lorraine; Rodríguez-Echevarría, Brian O.; Rodríguez-García, Priscila M.; Rodríguez-Laboy, Abneris E.; Rodríguez-Santiago, Susana; Rojas-Vargas, Michael L.; Rubio-Marrero, Eva N.; Santiago-Colón, Albeliz; Santiago-Ortiz, Jorge L.; Santos-Ramos, Carlos E.; Serrano-González, Joseline; Tamayo-Figueroa, Alina M.; Tascón-Peñaranda, Edna P.; Torres-Castillo, José L.; Valentín-Feliciano, Nelson A.; Valentín-Feliciano, Yashira M.; Vargas-Barreto, Nadyan M.; Vélez-Vázquez, Miguel; Vilanova-Vélez, Luis R.; Zambrana-Echevarría, Cristina; MacKinnon, Christy; Chung, Hui-Min; Kay, Chris; Pinto, Anthony; Kopp, Olga R.; Burkhardt, Joshua; Harward, Chris; Allen, Robert; Bhat, Pavan; Chang, Jimmy Hsiang-Chun; Chen, York; Chesley, Christopher; Cohn, Dara; DuPuis, David; Fasano, Michael; Fazzio, Nicholas; Gavinski, Katherine; Gebreyesus, Heran; Giarla, Thomas; Gostelow, Marcus; Greenstein, Rachel; Gunasinghe, Hashini; Hanson, Casey; Hay, Amanda; He, Tao Jian; Homa, Katie; Howe, Ruth; Howenstein, Jeff; Huang, Henry; Khatri, Aaditya; Kim, Young Lu; Knowles, Olivia; Kong, Sarah; Krock, Rebecca; Kroll, Matt; Kuhn, Julia; Kwong, Matthew; Lee, Brandon; Lee, Ryan; Levine, Kevin; Li, Yedda; Liu, Bo; Liu, Lucy; Liu, Max; Lousararian, Adam; Ma, Jimmy; Mallya, Allyson; Manchee, Charlie; Marcus, Joseph; McDaniel, Stephen; Miller, Michelle L.; Molleston, Jerome M.; Diez, Cristina Montero; Ng, Patrick; Ngai, Natalie; Nguyen, Hien; Nylander, Andrew; Pollack, Jason; Rastogi, Suchita; Reddy, Himabindu; Regenold, Nathaniel; Sarezky, Jon; Schultz, Michael; Shim, Jien; Skorupa, Tara; Smith, Kenneth; Spencer, Sarah J.; Srikanth, Priya; Stancu, Gabriel; Stein, Andrew P.; Strother, Marshall; Sudmeier, Lisa; Sun, Mengyang; Sundaram, Varun; Tazudeen, Noor; Tseng, Alan; Tzeng, Albert; Venkat, Rohit; Venkataram, Sandeep; Waldman, Leah; Wang, Tracy; Yang, Hao; Yu, Jack Y.; Zheng, Yin; Preuss, Mary L.; Garcia, Angelica; Juergens, Matt; Morris, Robert W.; Nagengast, Alexis A.; Azarewicz, Julie; Carr, Thomas J.; Chichearo, Nicole; Colgan, Mike; Donegan, Megan; Gardner, Bob; Kolba, Nik; Krumm, Janice L.; Lytle, Stacey; MacMillian, Laurell; Miller, Mary; Montgomery, Andrew; Moretti, Alysha; Offenbacker, Brittney; Polen, Mike; Toth, John; Woytanowski, John; Kadlec, Lisa; Crawford, Justin; Spratt, Mary L.; Adams, Ashley L.; Barnard, Brianna K.; Cheramie, Martin N.; Eime, Anne M.; Golden, Kathryn L.; Hawkins, Allyson P.; Hill, Jessica E.; Kampmeier, Jessica A.; Kern, Cody D.; Magnuson, Emily E.; Miller, Ashley R.; Morrow, Cody M.; Peairs, Julia C.; Pickett, Gentry L.; Popelka, Sarah A.; Scott, Alexis J.; Teepe, Emily J.; TerMeer, Katie A.; Watchinski, Carmen A.; Watson, Lucas A.; Weber, Rachel E.; Woodard, Kate A.; Barnard, Daron C.; Appiah, Isaac; Giddens, Michelle M.; McNeil, Gerard P.; Adebayo, Adeola; Bagaeva, Kate; Chinwong, Justina; Dol, Chrystel; George, Eunice; Haltaufderhyde, Kirk; Haye, Joanna; Kaur, Manpreet; Semon, Max; Serjanov, Dmitri; Toorie, Anika; Wilson, Christopher; Riddle, Nicole C.; Buhler, Jeremy; Mardis, Elaine R.

2015-01-01

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu. PMID:25740935
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes

PubMed Central

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-01-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including “codon capture,” “genome streamlining,” and “ambiguous intermediate” theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNAAla containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. PMID:27197221
Was Wright Right? The Canonical Genetic Code is an Empirical Example of an Adaptive Peak in Nature; Deviant Genetic Codes Evolved Using Adaptive Bridges

PubMed Central

2010-01-01

The canonical genetic code is on a sub-optimal adaptive peak with respect to its ability to minimize errors, and is close to, but not quite, optimal. This is demonstrated by the near-total adjacency of synonymous codons, the similarity of adjacent codons, and comparisons of frequency of amino acid usage with number of codons in the code for each amino acid. As a rare empirical example of an adaptive peak in nature, it shows adaptive peaks are real, not merely theoretical. The evolution of deviant genetic codes illustrates how populations move from a lower to a higher adaptive peak. This is done by the use of “adaptive bridges,” neutral pathways that cross over maladaptive valleys by virtue of masking of the phenotypic expression of some maladaptive aspects in the genotype. This appears to be the general mechanism by which populations travel from one adaptive peak to another. There are multiple routes a population can follow to cross from one adaptive peak to another. These routes vary in the probability that they will be used, and this probability is determined by the number and nature of the mutations that happen along each of the routes. A modification of the depiction of adaptive landscapes showing genetic distances and probabilities of travel along their multiple possible routes would throw light on this important concept. PMID:20711776
Tracking Energetics of a CME Core in the Low Solar Corona

NASA Astrophysics Data System (ADS)

Kocher, M.; Landi, E.; Lepri, S. T.

2017-12-01

In order to understand the processes that generate CMEs, and develop the ability to predict their evolution and geoeffectiveness, it is very important to determine how the plasma properties within coronal mass ejections (CME) evolve through their journey from the low corona through the solar environment. This study uses a combination of remote-sensing and in-situ observations of a filament eruption (that later formed the core of the CME) that left the Sun on August 4th, 2011 - shortly after an M-class flare. Separate absorption and emission diagnostic techniques are utilized to compute time-evolution estimates of the density and temperature of multiple plasma parcels within the filament using SDO/AIA EUV images. Twin STEREO spacecraft observations are used to estimate the height, speed, and acceleration of the CME at corresponding times. These observation-based densities, temperatures, and speeds allowed us to use the Michigan Ionization Code to compute the ionization history of this CME in the low solar corona. Along with the thermal and kinetic properties of this CME, we present a comparison with existing CME evolution models and draw inferences on its heating and acceleration.
A process model for the heat-affected zone microstructure evolution in duplex stainless steel weldments: Part II. Application to electron beam welding

NASA Astrophysics Data System (ADS)

Hemmer, H.; Grong, Ø.; Klokkehaug, S.

2000-03-01

In the present investigation, a process model for electron beam (EB) welding of different grades of duplex stainless steels (i.e. SAF 2205 and 2507) has been developed. A number of attractive features are built into the original finite element code, including (1) a separate module for prediction of the penetration depth and distribution of the heat source into the plate, (2) adaptive refinement of the three-dimensional (3-D) element mesh for quick and reliable solution of the differential heat flow equation, and (3) special subroutines for calculation of the heat-affected zone (HAZ) microstructure evolution. The process model has been validated by comparison with experimental data obtained from in situ thermocouple measurements and optical microscope examinations. Subsequently, its aptness to alloy design and optimization of welding conditions for duplex stainless steels is illustrated in different numerical examples and case studies pertaining to EB welding of tubular joints.
Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.

PubMed

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-11-24

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci.
Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication

PubMed Central

Dong, Heng; Liu, Dandan; Han, Tianyu; Zhao, Yuxue; Sun, Ji; Lin, Sue; Cao, Jiashu; Chen, Zhong-Hua; Huang, Li

2015-01-01

Histone lysine methylation, controlled by the SET Domain Group (SDG) gene family, is part of the histone code that regulates chromatin function and epigenetic control of gene expression. Analyzing the SDG gene family in Brassica rapa for their gene structure, domain architecture, subcellular localization, rate of molecular evolution and gene expression pattern revealed common occurrences of subfunctionalization and neofunctionalization in BrSDGs. In comparison with Arabidopsis thaliana, the BrSDG gene family was found to be more divergent than AtSDGs, which might partly explain the rich variety of morphotypes in B. rapa. In addition, a new evolutionary pattern of the four main groups of SDGs was presented, in which the Trx group and the SUVR subgroup evolved faster than the E(z), Ash groups and the SUVH subgroup. These differences in evolutionary rate among the four main groups of SDGs are perhaps due to the complexity and variability of the regions that bind with biomacromolecules, which guide SDGs to their target loci. PMID:26596461
HARD X-RAY ASYMMETRY LIMITS IN SOLAR FLARE CONJUGATE FOOTPOINTS

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

Daou, Antoun G.; Alexander, David, E-mail: agdaou@rice.edu, E-mail: dalex@rice.edu

2016-11-20

The transport of energetic electrons in a solar flare is modeled using a time-dependent one-dimensional Fokker–Planck code that incorporates asymmetric magnetic convergence. We derive the temporal and spectral evolution of the resulting hard X-ray (HXR) emission in the conjugate chromospheric footpoints, assuming thick target photon production, and characterize the time evolution of the numerically simulated footpoint asymmetry and its relationship to the photospheric magnetic configuration. The thick target HXR asymmetry in the conjugate footpoints is found to increase with magnetic field ratio as expected. However, we find that the footpoint HXR asymmetry saturates for conjugate footpoint magnetic field ratios ≥4.more » This result is borne out in a direct comparison with observations of 44 double-footpoint flares. The presence of such a limit has not been reported before, and may serve as both a theoretical and observational benchmark for testing a range of particle transport and flare morphology constraints, particularly as a means to differentiate between isotropic and anisotropic particle injection.« less
Ram Pressure Stripping of Galaxy JO201

NASA Astrophysics Data System (ADS)

Zhong, Greta; Tonnesen, Stephanie; Jaffé, Yara; Bellhouse, Callum; Bianca Poggianti

2017-01-01

Despite the discovery of the morphology-density relation more than 30 years ago, the process driving the evolution of spiral galaxies into S0s in clusters is still widely debated. Ram pressure stripping--the removal of a galaxy's interstellar medium by the pressure of the intracluster medium through which it orbits--may help explain galactic evolution and quenching in clusters. MUSE (Multi Unit Spectroscopic Explorer) observational data of galaxy JO201 in cluster Abell 85 reveal it to be a jellyfish galaxy--one with an H-alpha emitting gas tail on only one side. We model the possible orbits for this galaxy, constrained by the cluster mass profile, line of sight velocity, and projected distance from the cluster center. Using Enzo, an adaptive mesh refinement hydrodynamics code, we simulate effects of ram pressure on this galaxy for a range of possible orbits. We present comparisons of both the morphology and velocity structure of our simulated galaxy to the observations of H-alpha emission.
Comparison of equilibrium ohmic and nonequilibrium swarm models for monitoring conduction electron evolution in high-altitude EMP calculations

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

Pusateri, Elise N.; Morris, Heidi E.; Nelson, Eric

2016-10-17

Here, atmospheric electromagnetic pulse (EMP) events are important physical phenomena that occur through both man-made and natural processes. Radiation-induced currents and voltages in EMP can couple with electrical systems, such as those found in satellites, and cause significant damage. Due to the disruptive nature of EMP, it is important to accurately predict EMP evolution and propagation with computational models. CHAP-LA (Compton High Altitude Pulse-Los Alamos) is a state-of-the-art EMP code that solves Maxwell inline images equations for gamma source-induced electromagnetic fields in the atmosphere. In EMP, low-energy, conduction electrons constitute a conduction current that limits the EMP by opposing themore » Compton current. CHAP-LA calculates the conduction current using an equilibrium ohmic model. The equilibrium model works well at low altitudes, where the electron energy equilibration time is short compared to the rise time or duration of the EMP. At high altitudes, the equilibration time increases beyond the EMP rise time and the predicted equilibrium ionization rate becomes very large. The ohmic model predicts an unphysically large production of conduction electrons which prematurely and abruptly shorts the EMP in the simulation code. An electron swarm model, which implicitly accounts for the time evolution of the conduction electron energy distribution, can be used to overcome the limitations exhibited by the equilibrium ohmic model. We have developed and validated an electron swarm model previously in Pusateri et al. (2015). Here we demonstrate EMP damping behavior caused by the ohmic model at high altitudes and show improvements on high-altitude, upward EMP modeling obtained by integrating a swarm model into CHAP-LA.« less
Comparison of equilibrium ohmic and nonequilibrium swarm models for monitoring conduction electron evolution in high-altitude EMP calculations

NASA Astrophysics Data System (ADS)

Pusateri, Elise N.; Morris, Heidi E.; Nelson, Eric; Ji, Wei

2016-10-01

Atmospheric electromagnetic pulse (EMP) events are important physical phenomena that occur through both man-made and natural processes. Radiation-induced currents and voltages in EMP can couple with electrical systems, such as those found in satellites, and cause significant damage. Due to the disruptive nature of EMP, it is important to accurately predict EMP evolution and propagation with computational models. CHAP-LA (Compton High Altitude Pulse-Los Alamos) is a state-of-the-art EMP code that solves Maxwell's equations for gamma source-induced electromagnetic fields in the atmosphere. In EMP, low-energy, conduction electrons constitute a conduction current that limits the EMP by opposing the Compton current. CHAP-LA calculates the conduction current using an equilibrium ohmic model. The equilibrium model works well at low altitudes, where the electron energy equilibration time is short compared to the rise time or duration of the EMP. At high altitudes, the equilibration time increases beyond the EMP rise time and the predicted equilibrium ionization rate becomes very large. The ohmic model predicts an unphysically large production of conduction electrons which prematurely and abruptly shorts the EMP in the simulation code. An electron swarm model, which implicitly accounts for the time evolution of the conduction electron energy distribution, can be used to overcome the limitations exhibited by the equilibrium ohmic model. We have developed and validated an electron swarm model previously in Pusateri et al. (2015). Here we demonstrate EMP damping behavior caused by the ohmic model at high altitudes and show improvements on high-altitude, upward EMP modeling obtained by integrating a swarm model into CHAP-LA.
Orthopoxvirus Genome Evolution: The Role of Gene Loss

PubMed Central

Hendrickson, Robert Curtis; Wang, Chunlin; Hatcher, Eneida L.; Lefkowitz, Elliot J.

2010-01-01

Poxviruses are highly successful pathogens, known to infect a variety of hosts. The family Poxviridae includes Variola virus, the causative agent of smallpox, which has been eradicated as a public health threat but could potentially reemerge as a bioterrorist threat. The risk scenario includes other animal poxviruses and genetically engineered manipulations of poxviruses. Studies of orthologous gene sets have established the evolutionary relationships of members within the Poxviridae family. It is not clear, however, how variations between family members arose in the past, an important issue in understanding how these viruses may vary and possibly produce future threats. Using a newly developed poxvirus-specific tool, we predicted accurate gene sets for viruses with completely sequenced genomes in the genus Orthopoxvirus. Employing sensitive sequence comparison techniques together with comparison of syntenic gene maps, we established the relationships between all viral gene sets. These techniques allowed us to unambiguously identify the gene loss/gain events that have occurred over the course of orthopoxvirus evolution. It is clear that for all existing Orthopoxvirus species, no individual species has acquired protein-coding genes unique to that species. All existing species contain genes that are all present in members of the species Cowpox virus and that cowpox virus strains contain every gene present in any other orthopoxvirus strain. These results support a theory of reductive evolution in which the reduction in size of the core gene set of a putative ancestral virus played a critical role in speciation and confining any newly emerging virus species to a particular environmental (host or tissue) niche. PMID:21994715
The physics of symbols: bridging the epistemic cut.

PubMed

Pattee, H H

2001-01-01

Evolution requires the genotype-phenotype distinction, a primeval epistemic cut that separates energy-degenerate, rate-independent genetic symbols from the rate-dependent dynamics of construction that they control. This symbol-matter or subject-object distinction occurs at all higher levels where symbols are related to a referent by an arbitrary code. The converse of control is measurement in which a rate-dependent dynamical state is coded into quiescent symbols. Non-integrable constraints are one necessary condition for bridging the epistemic cut by measurement, control, and coding. Additional properties of heteropolymer constraints are necessary for biological evolution.
Comparing Different Strategies in Directed Evolution of Enzyme Stereoselectivity: Single- versus Double-Code Saturation Mutagenesis.

PubMed

Sun, Zhoutong; Lonsdale, Richard; Li, Guangyue; Reetz, Manfred T

2016-10-04

Saturation mutagenesis at sites lining the binding pockets of enzymes constitutes a viable protein engineering technique for enhancing or inverting stereoselectivity. Statistical analysis shows that oversampling in the screening step (the bottleneck) increases astronomically as the number of residues in the randomization site increases, which is the reason why reduced amino acid alphabets have been employed, in addition to splitting large sites into smaller ones. Limonene epoxide hydrolase (LEH) has previously served as the experimental platform in these methodological efforts, enabling comparisons between single-code saturation mutagenesis (SCSM) and triple-code saturation mutagenesis (TCSM); these employ either only one or three amino acids, respectively, as building blocks. In this study the comparative platform is extended by exploring the efficacy of double-code saturation mutagenesis (DCSM), in which the reduced amino acid alphabet consists of two members, chosen according to the principles of rational design on the basis of structural information. The hydrolytic desymmetrization of cyclohexene oxide is used as the model reaction, with formation of either (R,R)- or (S,S)-cyclohexane-1,2-diol. DCSM proves to be clearly superior to the likewise tested SCSM, affording both R,R- and S,S-selective mutants. These variants are also good catalysts in reactions of further substrates. Docking computations reveal the basis of enantioselectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Yunnan-III models for evolutionary population synthesis

NASA Astrophysics Data System (ADS)

Zhang, F.; Li, L.; Han, Z.; Zhuang, Y.; Kang, X.

2013-02-01

We build the Yunnan-III evolutionary population synthesis (EPS) models by using the mesa stellar evolution code, BaSeL stellar spectra library and the initial mass functions (IMFs) of Kroupa and Salpeter, and present colours and integrated spectral energy distributions (ISEDs) of solar-metallicity stellar populations (SPs) in the range of 1 Myr to 15 Gyr. The main characteristic of the Yunnan-III EPS models is the usage of a set of self-consistent solar-metallicity stellar evolutionary tracks (the masses of stars are from 0.1 to 100 M⊙). This set of tracks is obtained by using the state-of-the-art mesa code. mesa code can evolve stellar models through thermally pulsing asymptotic giant branch (TP-AGB) phase for low- and intermediate-mass stars. By comparisons, we confirm that the inclusion of TP-AGB stars makes the V - K, V - J and V - R colours of SPs redder and the infrared flux larger at ages log(t/yr) ≳ 7.6 [the differences reach the maximum at log(t/yr) ˜ 8.6, ˜0.5-0.2 mag for colours, approximately two times for K-band flux]. We also find that the colour-evolution trends of Model with-TPAGB at intermediate and large ages are similar to those from the starburst99 code, which employs the Padova-AGB stellar library, BaSeL spectral library and the Kroupa IMF. At last, we compare the colours with the other EPS models comprising TP-AGB stars (such as CB07, M05, V10 and POPSTAR), and find that the B - V colour agrees with each other but the V-K colour shows a larger discrepancy among these EPS models [˜1 mag when 8 ≲ log(t/yr) ≲ 9]. The stellar evolutionary tracks, isochrones, colours and ISEDs can be obtained on request from the first author or from our website (http://www1.ynao.ac.cn/~zhangfh/). Using the isochrones, you can build your EPS models. Now the format of stellar evolutionary tracks is the same as that in the starburst99 code; you can put them into the starburst99 code and get the SP's results. Moreover, the colours involving other passbands or on other systems (e.g. HST F439W - F555W colour on AB system) can also be obtained on request.
Automated UMLS-Based Comparison of Medical Forms

PubMed Central

Dugas, Martin; Fritz, Fleur; Krumm, Rainer; Breil, Bernhard

2013-01-01

Medical forms are very heterogeneous: on a European scale there are thousands of data items in several hundred different systems. To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture. A prerequisite in this harmonization process is comparison of forms. So far – to our knowledge – an automated method for comparison of medical forms is not available. A form contains a list of data items with corresponding medical concepts. An automatic comparison needs data types, item names and especially item with these unique concept codes from medical terminologies. The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain. Two items are called identical, if item name, concept code and value domain are the same. Two items are called matching, if only concept code and value domain are the same. Two items are called similar, if their concept codes are the same, but the value domains are different. Based on these definitions an open-source implementation for automated comparison of medical forms in ODM format with UMLS-based semantic annotations was developed. It is available as package compareODM from http://cran.r-project.org. To evaluate this method, it was applied to a set of 7 real medical forms with 285 data items from a large public ODM repository with forms for different medical purposes (research, quality management, routine care). Comparison results were visualized with grid images and dendrograms. Automated comparison of semantically annotated medical forms is feasible. Dendrograms allow a view on clustered similar forms. The approach is scalable for a large set of real medical forms. PMID:23861827
Codon Usage Selection Can Bias Estimation of the Fraction of Adaptive Amino Acid Fixations.

PubMed

Matsumoto, Tomotaka; John, Anoop; Baeza-Centurion, Pablo; Li, Boyang; Akashi, Hiroshi

2016-06-01

A growing number of molecular evolutionary studies are estimating the proportion of adaptive amino acid substitutions (α) from comparisons of ratios of polymorphic and fixed DNA mutations. Here, we examine how violations of two of the model assumptions, neutral evolution of synonymous mutations and stationary base composition, affect α estimation. We simulated the evolution of coding sequences assuming weak selection on synonymous codon usage bias and neutral protein evolution, α = 0. We show that weak selection on synonymous mutations can give polymorphism/divergence ratios that yield α-hat (estimated α) considerably larger than its true value. Nonstationary evolution (changes in population size, selection, or mutation) can exacerbate such biases or, in some scenarios, give biases in the opposite direction, α-hat < α. These results demonstrate that two factors that appear to be prevalent among taxa, weak selection on synonymous mutations and non-steady-state nucleotide composition, should be considered when estimating α. Estimates of the proportion of adaptive amino acid fixations from large-scale analyses of Drosophila melanogaster polymorphism and divergence data are positively correlated with codon usage bias. Such patterns are consistent with α-hat inflation from weak selection on synonymous mutations and/or mutational changes within the examined gene trees. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Progenitors of Core-Collapse Supernovae

NASA Astrophysics Data System (ADS)

Hirschi, R.; Arnett, D.; Cristini, A.; Georgy, C.; Meakin, C.; Walkington, I.

2017-02-01

Massive stars have a strong impact on their surroundings, in particular when they produce a core-collapse supernova at the end of their evolution. In these proceedings, we review the general evolution of massive stars and their properties at collapse as well as the transition between massive and intermediate-mass stars. We also summarise the effects of metallicity and rotation. We then discuss some of the major uncertainties in the modelling of massive stars, with a particular emphasis on the treatment of convection in 1D stellar evolution codes. Finally, we present new 3D hydrodynamic simulations of convection in carbon burning and list key points to take from 3D hydrodynamic studies for the development of new prescriptions for convective boundary mixing in 1D stellar evolution codes.

Explanatory Parent-Child Conversation Predominates at an Evolution Exhibit

ERIC Educational Resources Information Center

Tare, Medha; French, Jason; Frazier, Brandy N.; Diamond, Judy; Evans, E. Margaret

2011-01-01

To investigate how parents support children's learning at an exhibit on evolution, the conversations of 12 families were recorded, transcribed, and coded (6,263 utterances). Children (mean age 9.6 years) and parents visited Explore Evolution, which conveyed current research about the evolution of seven organisms. Families were engaged with the…
General practitioners’ justifications for therapeutic inertia in cardiovascular prevention: an empirically grounded typology

PubMed Central

Lebeau, Jean-Pierre; Cadwallader, Jean-Sébastien; Vaillant-Roussel, Hélène; Pouchain, Denis; Yaouanc, Virginie; Aubin-Auger, Isabelle; Mercier, Alain; Rusch, Emmanuel; Remmen, Roy; Vermeire, Etienne; Hendrickx, Kristin

2016-01-01

Objective To construct a typology of general practitioners’ (GPs) responses regarding their justification of therapeutic inertia in cardiovascular primary prevention for high-risk patients with hypertension. Design Empirically grounded construction of typology. Types were defined by attributes derived from the qualitative analysis of GPs’ reported reasons for inaction. Participants 256 GPs randomised in the intervention group of a cluster randomised controlled trial. Setting GPs members of 23 French Regional Colleges of Teachers in General Practice, included in the EffectS of a multifaceted intervention on CArdiovascular risk factors in high-risk hyPErtensive patients (ESCAPE) trial. Data collection and analysis The database consisted of 2638 written responses given by the GPs to an open-ended question asking for the reasons why drug treatment was not changed as suggested by the national guidelines. All answers were coded using constant comparison analysis. A matrix analysis of codes per GP allowed the construction of a response typology, where types were defined by codes as attributes. Initial coding and definition of types were performed independently by two teams. Results Initial coding resulted in a list of 69 codes in the final codebook, representing 4764 coded references in the question responses. A typology including seven types was constructed. 100 GPs were allocated to one and only one of these types, while 25 GPs did not provide enough data to allow classification. Types (numbers of GPs allocated) were: ‘optimists’ (28), ‘negotiators’ (20), ‘checkers’ (15), ‘contextualisers’ (13), ‘cautious’ (11), ‘rounders’ (8) and ‘scientists’ (5). For the 36 GPs that provided 50 or more coded references, analysis of the code evolution over time and across patients showed a consistent belonging to the initial type for any given GP. Conclusion This typology could provide GPs with some insight into their general ways of considering changes in the treatment/management of cardiovascular risk factors and guide design of specific physician-centred interventions to reduce inappropriate inaction. Trial registration number NCT00348855. PMID:27178974
Micromechanics and constitutive models for soft active materials with phase evolution

NASA Astrophysics Data System (ADS)

Wang, Binglian

Soft active materials, such as shape memory polymers, liquid crystal elastomers, soft tissues, gels etc., are materials that can deform largely in response to external stimuli. Micromechanics analysis of heterogeneous materials based on finite element method is a typically numerical way to study the thermal-mechanical behaviors of soft active materials with phase evolution. While the constitutive models that can precisely describe the stress and strain fields of materials in the process of phase evolution can not be found in the databases of some commercial finite element analysis (FEA) tools such as ANSYS or Abaqus, even the specific constitutive behavior for each individual phase either the new formed one or the original one has already been well-known. So developing a computationally efficient and general three dimensional (3D) thermal-mechanical constitutive model for soft active materials with phase evolution which can be implemented into FEA is eagerly demanded. This paper first solved this problem theoretically by recording the deformation history of each individual phase in the phase evolution process, and adopted the idea of effectiveness by regarding all the new formed phase as an effective phase with an effective deformation to make this theory computationally efficient. A user material subroutine (UMAT) code based on this theoretical constitutive model has been finished in this work which can be added into the material database in Abaqus or ANSYS and can be easily used for most soft active materials with phase evolution. Model validation also has been done through comparison between micromechanical FEA and experiments on a particular composite material, shape memory elastomeric composite (SMEC) which consisted of an elastomeric matrix and the crystallizable fibre. Results show that the micromechanics and the constitutive models developed in this paper for soft active materials with phase evolution are completely relied on.
Evidence of a Conserved Molecular Response to Selection for Increased Brain Size in Primates

PubMed Central

Harrison, Peter W.; Caravas, Jason A.; Raghanti, Mary Ann; Phillips, Kimberley A.; Mundy, Nicholas I.

2017-01-01

The adaptive significance of human brain evolution has been frequently studied through comparisons with other primates. However, the evolution of increased brain size is not restricted to the human lineage but is a general characteristic of primate evolution. Whether or not these independent episodes of increased brain size share a common genetic basis is unclear. We sequenced and de novo assembled the transcriptome from the neocortical tissue of the most highly encephalized nonhuman primate, the tufted capuchin monkey (Cebus apella). Using this novel data set, we conducted a genome-wide analysis of orthologous brain-expressed protein coding genes to identify evidence of conserved gene–phenotype associations and species-specific adaptations during three independent episodes of brain size increase. We identify a greater number of genes associated with either total brain mass or relative brain size across these six species than show species-specific accelerated rates of evolution in individual large-brained lineages. We test the robustness of these associations in an expanded data set of 13 species, through permutation tests and by analyzing how genome-wide patterns of substitution co-vary with brain size. Many of the genes targeted by selection during brain expansion have glutamatergic functions or roles in cell cycle dynamics. We also identify accelerated evolution in a number of individual capuchin genes whose human orthologs are associated with human neuropsychiatric disorders. These findings demonstrate the value of phenotypically informed genome analyses, and suggest at least some aspects of human brain evolution have occurred through conserved gene–phenotype associations. Understanding these commonalities is essential for distinguishing human-specific selection events from general trends in brain evolution. PMID:28391320
Adaptive Precoded MIMO for LTE Wireless Communication

NASA Astrophysics Data System (ADS)

Nabilla, A. F.; Tiong, T. C.

2015-04-01

Long-Term Evolution (LTE) and Long Term Evolution-Advanced (ATE-A) have provided a major step forward in mobile communication capability. The objectives to be achieved are high peak data rates in high spectrum bandwidth and high spectral efficiencies. Technically, pre-coding means that multiple data streams are emitted from the transmit antenna with independent and appropriate weightings such that the link throughput is maximized at the receiver output thus increasing or equalizing the received signal to interference and noise (SINR) across the multiple receiver terminals. However, it is not reliable enough to fully utilize the information transfer rate to fit the condition of channel according to the bandwidth size. Thus, adaptive pre-coding is proposed. It applies pre-coding matrix indicator (PMI) channel state making it possible to change the pre-coding codebook accordingly thus improving the data rate higher than fixed pre-coding.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Vassilevska, Tanya

This is the first code, designed to run on a desktop, which models the intracellular replication and the cell-to-cell infection and demonstrates virus evolution at the molecular level. This code simulates the infection of a population of "idealized biological cells" (represented as objects that do not divide or have metabolism) with "virus" (represented by its genetic sequence), the replication and simultaneous mutation of the virus which leads to evolution of the population of genetically diverse viruses. The code is built to simulate single-stranded RNA viruses. The input for the code is 1. the number of biological cells in the culture,more » 2. the initial composition of the virus population, 3. the reference genome of the RNA virus, 4. the coordinates of the genome regions and their significance and, 5. parameters determining the dynamics of virus replication, such as the mutation rate. The simulation ends when all cells have been infected or when no more infections occurs after a given number of attempts. The code has the ability to simulate the evolution of the virus in serial passage of cell "cultures", i.e. after the end of a simulation, a new one is immediately scheduled with a new culture of infected cells. The code outputs characteristics of the resulting virus population dynamics and genetic composition of the virus population, such as the top dominant genomes, percentage of a genome with specific characteristics.« less
Critical roles for a genetic code alteration in the evolution of the genus Candida.

PubMed

Silva, Raquel M; Paredes, João A; Moura, Gabriela R; Manadas, Bruno; Lima-Costa, Tatiana; Rocha, Rita; Miranda, Isabel; Gomes, Ana C; Koerkamp, Marian J G; Perrot, Michel; Holstege, Frank C P; Boucherie, Hélian; Santos, Manuel A S

2007-10-31

During the last 30 years, several alterations to the standard genetic code have been discovered in various bacterial and eukaryotic species. Sense and nonsense codons have been reassigned or reprogrammed to expand the genetic code to selenocysteine and pyrrolysine. These discoveries highlight unexpected flexibility in the genetic code, but do not elucidate how the organisms survived the proteome chaos generated by codon identity redefinition. In order to shed new light on this question, we have reconstructed a Candida genetic code alteration in Saccharomyces cerevisiae and used a combination of DNA microarrays, proteomics and genetics approaches to evaluate its impact on gene expression, adaptation and sexual reproduction. This genetic manipulation blocked mating, locked yeast in a diploid state, remodelled gene expression and created stress cross-protection that generated adaptive advantages under environmental challenging conditions. This study highlights unanticipated roles for codon identity redefinition during the evolution of the genus Candida, and strongly suggests that genetic code alterations create genetic barriers that speed up speciation.
Comparison of SAND-II and FERRET

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

Wootan, D.W.; Schmittroth, F.

1981-01-01

A comparison was made of the advantages and disadvantages of two codes, SAND-II and FERRET, for determining the neutron flux spectrum and uncertainty from experimental dosimeter measurements as anticipated in the FFTF Reactor Characterization Program. This comparison involved an examination of the methodology and the operational performance of each code. The merits of each code were identified with respect to theoretical basis, directness of method, solution uniqueness, subjective influences, and sensitivity to various input parameters.
An engineer's view on genetic information and biological evolution.

PubMed

Battail, Gérard

2004-01-01

We develop ideas on genome replication introduced in Battail [Europhys. Lett. 40 (1997) 343]. Starting with the hypothesis that the genome replication process uses error-correcting means, and the auxiliary one that nested codes are used to this end, we first review the concepts of redundancy and error-correcting codes. Then we show that these hypotheses imply that: distinct species exist with a hierarchical taxonomy, there is a trend of evolution towards complexity, and evolution proceeds by discrete jumps. At least the first two features above may be considered as biological facts so, in the absence of direct evidence, they provide an indirect proof in favour of the hypothesized error-correction system. The very high redundancy of genomes makes it possible. In order to explain how it is implemented, we suggest that soft codes and replication decoding, to be briefly described, are plausible candidates. Experimentally proven properties of long-range correlation of the DNA message substantiate this claim.
The evolution of transcriptional regulation in eukaryotes

NASA Technical Reports Server (NTRS)

Wray, Gregory A.; Hahn, Matthew W.; Abouheif, Ehab; Balhoff, James P.; Pizer, Margaret; Rockman, Matthew V.; Romano, Laura A.

2003-01-01

Gene expression is central to the genotype-phenotype relationship in all organisms, and it is an important component of the genetic basis for evolutionary change in diverse aspects of phenotype. However, the evolution of transcriptional regulation remains understudied and poorly understood. Here we review the evolutionary dynamics of promoter, or cis-regulatory, sequences and the evolutionary mechanisms that shape them. Existing evidence indicates that populations harbor extensive genetic variation in promoter sequences, that a substantial fraction of this variation has consequences for both biochemical and organismal phenotype, and that some of this functional variation is sorted by selection. As with protein-coding sequences, rates and patterns of promoter sequence evolution differ considerably among loci and among clades for reasons that are not well understood. Studying the evolution of transcriptional regulation poses empirical and conceptual challenges beyond those typically encountered in analyses of coding sequence evolution: promoter organization is much less regular than that of coding sequences, and sequences required for the transcription of each locus reside at multiple other loci in the genome. Because of the strong context-dependence of transcriptional regulation, sequence inspection alone provides limited information about promoter function. Understanding the functional consequences of sequence differences among promoters generally requires biochemical and in vivo functional assays. Despite these challenges, important insights have already been gained into the evolution of transcriptional regulation, and the pace of discovery is accelerating.
Evolution of Structure and Composition in Saturn's Rings Due to Ballistic Transport of Micrometeoroid Impact Ejecta

NASA Astrophysics Data System (ADS)

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

2014-04-01

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

NASA Technical Reports Server (NTRS)

Rappaport, S.; Joss, P. C.; Verbunt, F.

1983-01-01

The development of appropriate computer programs has made it possible to conduct studies of stellar evolution which are more detailed and accurate than the investigations previously feasible. However, the use of such programs can also entail some serious drawbacks which are related to the time and expense required for the work. One approach for overcoming these drawbacks involves the employment of simplified stellar evolution codes which incorporate the essential physics of the problem of interest without attempting either great generality or maximal accuracy. Rappaport et al. (1982) have developed a simplified code to study the evolution of close binary stellar systems composed of a collapsed object and a low-mass secondary. The present investigation is concerned with a more general, but still simplified, technique for calculating the evolution of close binary systems with collapsed binaries and mass-losing secondaries.
Long-time efficacy of the surface code in the presence of a super-Ohmic environment

NASA Astrophysics Data System (ADS)

López-Delgado, D. A.; Novais, E.; Mucciolo, E. R.; Caldeira, A. O.

2017-06-01

We study the long-time evolution of a quantum memory coupled to a bosonic environment on which quantum error correction (QEC) is performed using the surface code. The memory's evolution encompasses N QEC cycles, each of them yielding a nonerror syndrome. This assumption makes our analysis independent of the recovery process. We map the expression for the time evolution of the memory onto the partition function of an equivalent statistical-mechanical spin system. In the super-Ohmic dissipation case the long-time evolution of the memory has the same behavior as the time evolution for just one QEC cycle. For this case we find analytical expressions for the critical parameters of the order-disorder phase transition of an equivalent spin system. These critical parameters determine the threshold value for the system-environment coupling below which it is possible to preserve the memory's state.
Description of Transport Codes for Space Radiation Shielding

NASA Technical Reports Server (NTRS)

Kim, Myung-Hee Y.; Wilson, John W.; Cucinotta, Francis A.

2011-01-01

This slide presentation describes transport codes and their use for studying and designing space radiation shielding. When combined with risk projection models radiation transport codes serve as the main tool for study radiation and designing shielding. There are three criteria for assessing the accuracy of transport codes: (1) Ground-based studies with defined beams and material layouts, (2) Inter-comparison of transport code results for matched boundary conditions and (3) Comparisons to flight measurements. These three criteria have a very high degree with NASA's HZETRN/QMSFRG.
Comparison of laser anemometer measurements and theory in an annular turbine cascade with experimental accuracy determined by parameter estimation

NASA Technical Reports Server (NTRS)

Goldman, L. J.; Seasholtz, R. G.

1982-01-01

Experimental measurements of the velocity components in the blade to blade (axial tangential) plane were obtained with an axial flow turbine stator passage and were compared with calculations from three turbomachinery computer programs. The theoretical results were calculated from a quasi three dimensional inviscid code, a three dimensional inviscid code, and a three dimensional viscous code. Parameter estimation techniques and a particle dynamics calculation were used to assess the accuracy of the laser measurements, which allow a rational basis for comparison of the experimenal and theoretical results. The general agreement of the experimental data with the results from the two inviscid computer codes indicates the usefulness of these calculation procedures for turbomachinery blading. The comparison with the viscous code, while generally reasonable, was not as good as for the inviscid codes.
A comparison of native GPU computing versus OpenACC for implementing flow-routing algorithms in hydrological applications

NASA Astrophysics Data System (ADS)

Rueda, Antonio J.; Noguera, José M.; Luque, Adrián

2016-02-01

In recent years GPU computing has gained wide acceptance as a simple low-cost solution for speeding up computationally expensive processing in many scientific and engineering applications. However, in most cases accelerating a traditional CPU implementation for a GPU is a non-trivial task that requires a thorough refactorization of the code and specific optimizations that depend on the architecture of the device. OpenACC is a promising technology that aims at reducing the effort required to accelerate C/C++/Fortran code on an attached multicore device. Virtually with this technology the CPU code only has to be augmented with a few compiler directives to identify the areas to be accelerated and the way in which data has to be moved between the CPU and GPU. Its potential benefits are multiple: better code readability, less development time, lower risk of errors and less dependency on the underlying architecture and future evolution of the GPU technology. Our aim with this work is to evaluate the pros and cons of using OpenACC against native GPU implementations in computationally expensive hydrological applications, using the classic D8 algorithm of O'Callaghan and Mark for river network extraction as case-study. We implemented the flow accumulation step of this algorithm in CPU, using OpenACC and two different CUDA versions, comparing the length and complexity of the code and its performance with different datasets. We advance that although OpenACC can not match the performance of a CUDA optimized implementation (×3.5 slower in average), it provides a significant performance improvement against a CPU implementation (×2-6) with by far a simpler code and less implementation effort.
Comparative Mitogenomics of Plant Bugs (Hemiptera: Miridae): Identifying the AGG Codon Reassignments between Serine and Lysine

PubMed Central

Wang, Pei; Song, Fan; Cai, Wanzhi

2014-01-01

Insect mitochondrial genomes are very important to understand the molecular evolution as well as for phylogenetic and phylogeographic studies of the insects. The Miridae are the largest family of Heteroptera encompassing more than 11,000 described species and of great economic importance. For better understanding the diversity and the evolution of plant bugs, we sequence five new mitochondrial genomes and present the first comparative analysis of nine mitochondrial genomes of mirids available to date. Our result showed that gene content, gene arrangement, base composition and sequences of mitochondrial transcription termination factor were conserved in plant bugs. Intra-genus species shared more conserved genomic characteristics, such as nucleotide and amino acid composition of protein-coding genes, secondary structure and anticodon mutations of tRNAs, and non-coding sequences. Control region possessed several distinct characteristics, including: variable size, abundant tandem repetitions, and intra-genus conservation; and was useful in evolutionary and population genetic studies. The AGG codon reassignments were investigated between serine and lysine in the genera Adelphocoris and other cimicomorphans. Our analysis revealed correlated evolution between reassignments of the AGG codon and specific point mutations at the antidocons of tRNALys and tRNASer(AGN). Phylogenetic analysis indicated that mitochondrial genome sequences were useful in resolving family level relationship of Cimicomorpha. Comparative evolutionary analysis of plant bug mitochondrial genomes allowed the identification of previously neglected coding genes or non-coding regions as potential molecular markers. The finding of the AGG codon reassignments between serine and lysine indicated the parallel evolution of the genetic code in Hemiptera mitochondrial genomes. PMID:24988409
Comparison of Transport Codes, HZETRN, HETC and FLUKA, Using 1977 GCR Solar Minimum Spectra

NASA Technical Reports Server (NTRS)

Heinbockel, John H.; Slaba, Tony C.; Tripathi, Ram K.; Blattnig, Steve R.; Norbury, John W.; Badavi, Francis F.; Townsend, Lawrence W.; Handler, Thomas; Gabriel, Tony A.; Pinsky, Lawrence S.;

2009-01-01

The HZETRN deterministic radiation transport code is one of several tools developed to analyze the effects of harmful galactic cosmic rays (GCR) and solar particle events (SPE) on mission planning, astronaut shielding and instrumentation. This paper is a comparison study involving the two Monte Carlo transport codes, HETC-HEDS and FLUKA, and the deterministic transport code, HZETRN. Each code is used to transport ions from the 1977 solar minimum GCR spectrum impinging upon a 20 g/cm2 Aluminum slab followed by a 30 g/cm2 water slab. This research is part of a systematic effort of verification and validation to quantify the accuracy of HZETRN and determine areas where it can be improved. Comparisons of dose and dose equivalent values at various depths in the water slab are presented in this report. This is followed by a comparison of the proton fluxes, and the forward, backward and total neutron fluxes at various depths in the water slab. Comparisons of the secondary light ion 2H, 3H, 3He and 4He fluxes are also examined.

SIGNUM: A Matlab, TIN-based landscape evolution model

NASA Astrophysics Data System (ADS)

Refice, A.; Giachetta, E.; Capolongo, D.

2012-08-01

Several numerical landscape evolution models (LEMs) have been developed to date, and many are available as open source codes. Most are written in efficient programming languages such as Fortran or C, but often require additional code efforts to plug in to more user-friendly data analysis and/or visualization tools to ease interpretation and scientific insight. In this paper, we present an effort to port a common core of accepted physical principles governing landscape evolution directly into a high-level language and data analysis environment such as Matlab. SIGNUM (acronym for Simple Integrated Geomorphological Numerical Model) is an independent and self-contained Matlab, TIN-based landscape evolution model, built to simulate topography development at various space and time scales. SIGNUM is presently capable of simulating hillslope processes such as linear and nonlinear diffusion, fluvial incision into bedrock, spatially varying surface uplift which can be used to simulate changes in base level, thrust and faulting, as well as effects of climate changes. Although based on accepted and well-known processes and algorithms in its present version, it is built with a modular structure, which allows to easily modify and upgrade the simulated physical processes to suite virtually any user needs. The code is conceived as an open-source project, and is thus an ideal tool for both research and didactic purposes, thanks to the high-level nature of the Matlab environment and its popularity among the scientific community. In this paper the simulation code is presented together with some simple examples of surface evolution, and guidelines for development of new modules and algorithms are proposed.
A novel nuclear genetic code alteration in yeasts and the evolution of codon reassignment in eukaryotes.

PubMed

Mühlhausen, Stefanie; Findeisen, Peggy; Plessmann, Uwe; Urlaub, Henning; Kollmar, Martin

2016-07-01

The genetic code is the cellular translation table for the conversion of nucleotide sequences into amino acid sequences. Changes to the meaning of sense codons would introduce errors into almost every translated message and are expected to be highly detrimental. However, reassignment of single or multiple codons in mitochondria and nuclear genomes, although extremely rare, demonstrates that the code can evolve. Several models for the mechanism of alteration of nuclear genetic codes have been proposed (including "codon capture," "genome streamlining," and "ambiguous intermediate" theories), but with little resolution. Here, we report a novel sense codon reassignment in Pachysolen tannophilus, a yeast related to the Pichiaceae. By generating proteomics data and using tRNA sequence comparisons, we show that Pachysolen translates CUG codons as alanine and not as the more usual leucine. The Pachysolen tRNACAG is an anticodon-mutated tRNA(Ala) containing all major alanine tRNA recognition sites. The polyphyly of the CUG-decoding tRNAs in yeasts is best explained by a tRNA loss driven codon reassignment mechanism. Loss of the CUG-tRNA in the ancient yeast is followed by gradual decrease of respective codons and subsequent codon capture by tRNAs whose anticodon is not part of the aminoacyl-tRNA synthetase recognition region. Our hypothesis applies to all nuclear genetic code alterations and provides several testable predictions. We anticipate more codon reassignments to be uncovered in existing and upcoming genome projects. © 2016 Mühlhausen et al.; Published by Cold Spring Harbor Laboratory Press.

Bayesian Atmospheric Radiative Transfer (BART): Model, Statistics Driver, and Application to HD 209458b

NASA Astrophysics Data System (ADS)

Cubillos, Patricio; Harrington, Joseph; Blecic, Jasmina; Stemm, Madison M.; Lust, Nate B.; Foster, Andrew S.; Rojo, Patricio M.; Loredo, Thomas J.

2014-11-01

Multi-wavelength secondary-eclipse and transit depths probe the thermo-chemical properties of exoplanets. In recent years, several research groups have developed retrieval codes to analyze the existing data and study the prospects of future facilities. However, the scientific community has limited access to these packages. Here we premiere the open-source Bayesian Atmospheric Radiative Transfer (BART) code. We discuss the key aspects of the radiative-transfer algorithm and the statistical package. The radiation code includes line databases for all HITRAN molecules, high-temperature H2O, TiO, and VO, and includes a preprocessor for adding additional line databases without recompiling the radiation code. Collision-induced absorption lines are available for H2-H2 and H2-He. The parameterized thermal and molecular abundance profiles can be modified arbitrarily without recompilation. The generated spectra are integrated over arbitrary bandpasses for comparison to data. BART's statistical package, Multi-core Markov-chain Monte Carlo (MC3), is a general-purpose MCMC module. MC3 implements the Differental-evolution Markov-chain Monte Carlo algorithm (ter Braak 2006, 2009). MC3 converges 20-400 times faster than the usual Metropolis-Hastings MCMC algorithm, and in addition uses the Message Passing Interface (MPI) to parallelize the MCMC chains. We apply the BART retrieval code to the HD 209458b data set to estimate the planet's temperature profile and molecular abundances. This work was supported by NASA Planetary Atmospheres grant NNX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G. JB holds a NASA Earth and Space Science Fellowship.
Nothing in Evolution Makes Sense Except in the Light of Genomics: Read-Write Genome Evolution as an Active Biological Process.

PubMed

Shapiro, James A

2016-06-08

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess "Read-Write Genomes" they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification.
Nothing in Evolution Makes Sense Except in the Light of Genomics: Read–Write Genome Evolution as an Active Biological Process

PubMed Central

Shapiro, James A.

2016-01-01

The 21st century genomics-based analysis of evolutionary variation reveals a number of novel features impossible to predict when Dobzhansky and other evolutionary biologists formulated the neo-Darwinian Modern Synthesis in the middle of the last century. These include three distinct realms of cell evolution; symbiogenetic fusions forming eukaryotic cells with multiple genome compartments; horizontal organelle, virus and DNA transfers; functional organization of proteins as systems of interacting domains subject to rapid evolution by exon shuffling and exonization; distributed genome networks integrated by mobile repetitive regulatory signals; and regulation of multicellular development by non-coding lncRNAs containing repetitive sequence components. Rather than single gene traits, all phenotypes involve coordinated activity by multiple interacting cell molecules. Genomes contain abundant and functional repetitive components in addition to the unique coding sequences envisaged in the early days of molecular biology. Combinatorial coding, plus the biochemical abilities cells possess to rearrange DNA molecules, constitute a powerful toolbox for adaptive genome rewriting. That is, cells possess “Read–Write Genomes” they alter by numerous biochemical processes capable of rapidly restructuring cellular DNA molecules. Rather than viewing genome evolution as a series of accidental modifications, we can now study it as a complex biological process of active self-modification. PMID:27338490
Coupled thermal–hydrological–mechanical modeling of CO 2 -enhanced coalbed methane recovery

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

Ma, Tianran; Rutqvist, Jonny; Oldenburg, Curtis M.

CO 2 -enhanced coalbed methane recovery, also known as CO 2 -ECBM, is a potential win-win approach for enhanced methane production while simultaneously sequestering injected anthropogenic CO 2 to decrease CO 2 emissions into the atmosphere. Here, CO 2 -ECBM is simulated using a coupled thermal–hydrological–mechanical (THM) numerical model that considers multiphase (gas and water) flow and solubility, multicomponent (CO 2 and CH 4 ) diffusion and adsorption, heat transfer and coal deformation. The coupled model is based on the TOUGH-FLAC simulator, which is applied here for the first time to model CO 2 -ECBM. The capacity of the simulatormore » for modeling methane production is verified by a code-to-code comparison with the general-purpose finite-element solver COMSOL. Then, the TOUGH-FLAC simulator is applied in an isothermal simulation to study the variations in permeability evolution during a CO 2 -ECBM operation while considering four different stress-dependent permeability models that have been implemented into the simulator. Finally, the TOUGH-FLAC simulator is applied in non-isothermal simulations to model THM responses during a CO 2 -ECBM operation.Our simulations show that the permeability evolution, mechanical stress, and deformation are all affected by changes in pressure, temperature and adsorption swelling, with adsorption swelling having the largest effect. The calculated stress changes do not induce any mechanical failure in the coal seam, except near the injection well in one case of a very unfavorable stress field.« less
Coupled thermal–hydrological–mechanical modeling of CO 2 -enhanced coalbed methane recovery

DOE PAGES

Ma, Tianran; Rutqvist, Jonny; Oldenburg, Curtis M.; ...

2017-05-22

CO 2 -enhanced coalbed methane recovery, also known as CO 2 -ECBM, is a potential win-win approach for enhanced methane production while simultaneously sequestering injected anthropogenic CO 2 to decrease CO 2 emissions into the atmosphere. Here, CO 2 -ECBM is simulated using a coupled thermal–hydrological–mechanical (THM) numerical model that considers multiphase (gas and water) flow and solubility, multicomponent (CO 2 and CH 4 ) diffusion and adsorption, heat transfer and coal deformation. The coupled model is based on the TOUGH-FLAC simulator, which is applied here for the first time to model CO 2 -ECBM. The capacity of the simulatormore » for modeling methane production is verified by a code-to-code comparison with the general-purpose finite-element solver COMSOL. Then, the TOUGH-FLAC simulator is applied in an isothermal simulation to study the variations in permeability evolution during a CO 2 -ECBM operation while considering four different stress-dependent permeability models that have been implemented into the simulator. Finally, the TOUGH-FLAC simulator is applied in non-isothermal simulations to model THM responses during a CO 2 -ECBM operation.Our simulations show that the permeability evolution, mechanical stress, and deformation are all affected by changes in pressure, temperature and adsorption swelling, with adsorption swelling having the largest effect. The calculated stress changes do not induce any mechanical failure in the coal seam, except near the injection well in one case of a very unfavorable stress field.« less
JavaGenes Molecular Evolution

NASA Technical Reports Server (NTRS)

Lohn, Jason; Smith, David; Frank, Jeremy; Globus, Al; Crawford, James

2007-01-01

JavaGenes is a general-purpose, evolutionary software system written in Java. It implements several versions of a genetic algorithm, simulated annealing, stochastic hill climbing, and other search techniques. This software has been used to evolve molecules, atomic force field parameters, digital circuits, Earth Observing Satellite schedules, and antennas. This version differs from version 0.7.28 in that it includes the molecule evolution code and other improvements. Except for the antenna code, JaveGenes is available for NASA Open Source distribution.
Validation of CESAR Thermal-hydraulic Module of ASTEC V1.2 Code on BETHSY Experiments

NASA Astrophysics Data System (ADS)

Tregoures, Nicolas; Bandini, Giacomino; Foucher, Laurent; Fleurot, Joëlle; Meloni, Paride

The ASTEC V1 system code is being jointly developed by the French Institut de Radioprotection et Sûreté Nucléaire (IRSN) and the German Gesellschaft für Anlagen und ReaktorSicherheit (GRS) to address severe accident sequences in a nuclear power plant. Thermal-hydraulics in primary and secondary system is addressed by the CESAR module. The aim of this paper is to present the validation of the CESAR module, from the ASTEC V1.2 version, on the basis of well instrumented and qualified integral experiments carried out in the BETHSY facility (CEA, France), which simulates a French 900 MWe PWR reactor. Three tests have been thoroughly investigated with CESAR: the loss of coolant 9.1b test (OECD ISP N° 27), the loss of feedwater 5.2e test, and the multiple steam generator tube rupture 4.3b test. In the present paper, the results of the code for the three analyzed tests are presented in comparison with the experimental data. The thermal-hydraulic behavior of the BETHSY facility during the transient phase is well reproduced by CESAR: the occurrence of major events and the time evolution of main thermal-hydraulic parameters of both primary and secondary circuits are well predicted.
Unified Models of Turbulence and Nonlinear Wave Evolution in the Extended Solar Corona and Solar Wind

NASA Technical Reports Server (NTRS)

Wagner, William (Technical Monitor); Cranmer, Steven R.

2005-01-01

The paper discusses the following: 1. No-cost Extension. The no-cost extension is required to complete the work on the unified model codes (both hydrodynamic and kinetic Monte Carlo) as described in the initial proposal and previous annual reports. 2. Scientific Accomplishments during the Report Period. We completed a comprehensive model of Alfvtn wave reflection that spans the full distance from the photosphere to the distant heliosphere. 3. Comparison of Accomplishments with Proposed Goals. The proposal contained two specific objectives for Year 3: (1) to complete the unified model code, and (2) to apply it to various kinds of coronal holes (and polar plumes within coronal holes). Although the anticipated route toward these two final goals has changed (see accomplishments 2a and 2b above), they remain the major milestones for the extended period of performance. Accomplishments la and IC were necessary prerequisites for the derivation of "physically relevant transport and mode-coupling terms" for the unified model codes (as stated in the proposal Year 3 goals). We have fulfilled the proposed "core work" to study 4 general types of physical processes; in previous years we studied turbulence, mode coupling (Le., non-WKB reflection), and kinetic wave damping, and accomplishment lb provides the fourth topic: nonlinear steepening.
GEOtop, a model with coupled water and energy budgets and non linear hydrological interactions. (Invited)

NASA Astrophysics Data System (ADS)

Endrizzi, S.; Gruber, S.; Dall'Amico, M.; Rigon, R.

2013-12-01

This contribution describes the new version of GEOtop which emerges after almost eight years of development from the original version. GEOtop now integrate the 3D Richards equation with a new numerical method; improvements were made on the treatment of surface waters by using the shallow water equation. The freezing-soil module was greatly improved, and the evapotranspiration -vegetation modelling is now based on a double layer scheme. Here we discuss the rational of each choice that was made, and we compare the differences between the actual solutions and the old solutions. In doing we highlight the issues that we faced during the development, including the trade-off between complexity and simplicity of the code, the requirements of a shared development, the different branches that were opened during the evolution of the code, and why we think that a code like GEOtop is indeed necessary. Models where the hydrological cycle is simplified can be built on the base of perceptual models that neglects some fundamental aspects of the hydrological processes, of which some examples are presented. At the same time, also process-based models like GEOtop can indeed neglect some fundamental process: but this is made evident with the comparison with measurements, especially when data are imposed ex-ante, instead than calibrated.
A New Cell-Centered Implicit Numerical Scheme for Ions in the 2-D Axisymmetric Code Hall2de

NASA Technical Reports Server (NTRS)

Lopez Ortega, Alejandro; Mikellides, Ioannis G.

2014-01-01

We present a new algorithm in the Hall2De code to simulate the ion hydrodynamics in the acceleration channel and near plume regions of Hall-effect thrusters. This implementation constitutes an upgrade of the capabilities built in the Hall2De code. The equations of mass conservation and momentum for unmagnetized ions are solved using a conservative, finite-volume, cell-centered scheme on a magnetic-field-aligned grid. Major computational savings are achieved by making use of an implicit predictor/multi-corrector algorithm for time evolution. Inaccuracies in the prediction of the motion of low-energy ions in the near plume in hydrodynamics approaches are addressed by implementing a multi-fluid algorithm that tracks ions of different energies separately. A wide range of comparisons with measurements are performed to validate the new ion algorithms. Several numerical experiments with the location and value of the anomalous collision frequency are also presented. Differences in the plasma properties in the near-plume between the single fluid and multi-fluid approaches are discussed. We complete our validation by comparing predicted erosion rates at the channel walls of the thruster with measurements. Erosion rates predicted by the plasma properties obtained from simulations replicate accurately measured rates of erosion within the uncertainty range of the sputtering models employed.
Electric dipole moment planning with a resurrected BNL Alternating Gradient Synchrotron electron analog ring

NASA Astrophysics Data System (ADS)

Talman, Richard M.; Talman, John D.

2015-07-01

There has been much recent interest in directly measuring the electric dipole moments (EDM) of the proton and the electron, because of their possible importance in the present day observed matter/antimatter imbalance in the Universe. Such a measurement will require storing a polarized beam of "frozen spin" particles, 15 MeV electrons or 230 MeV protons, in an all-electric storage ring. Only one such relativistic electric accelerator has ever been built—the 10 MeV "electron analog" ring at Brookhaven National Laboratory in 1954; it can also be referred to as the "AGS analog" ring to make clear it was a prototype for the Alternating Gradient Synchrotron (AGS) proton ring under construction at that time at BNL. (Its purpose was to investigate nonlinear resonances as well as passage through "transition" with the newly invented alternating gradient proton ring design.) By chance this electron ring, long since dismantled and its engineering drawings disappeared, would have been appropriate both for measuring the electron EDM and to serve as an inexpensive prototype for the arguably more promising, but 10 times more expensive, proton EDM measurement. Today it is cheaper yet to "resurrect" the electron analog ring by simulating its performance computationally. This is one purpose for the present paper. Most existing accelerator simulation codes cannot be used for this purpose because they implicitly assume magnetic bending. The new ual/eteapot code, described in detail in an accompanying paper, has been developed for modeling storage ring performance, including spin evolution, in electric rings. Illustrating its use, comparing its predictions with the old observations, and describing new expectations concerning spin evolution and code performance, are other goals of the paper. To set up some of these calculations has required a kind of "archeological physics" to reconstitute the detailed electron analog lattice design from a 1991 retrospective report by Plotkin as well as unpublished notes of Courant describing machine studies performed in 1954-1955. This paper describes the practical application of the eteapot code and provides sample results, with emphasis on emulating lattice optics in the AGS analog ring for comparison with the historical machine studies and to predict the electron spin evolution they would have measured if they had polarized electrons and electron polarimetry. Of greater present day interest is the performance to be expected for a proton storage ring experiment. To exhibit the eteapot code performance and confirm its symplecticity, results are also given for 30 million turn proton spin tracking in an all-electric lattice that would be appropriate for a present day measurement of the proton EDM. The accompanying paper "Symplectic orbit and spin tracking code for all-electric storage rings" documents in detail the theoretical formulation implemented in eteapot, which is a new module in the Unified Accelerator Libraries (ual) environment.
Quasi-Static Evolution, Catastrophe, and Failed Eruption of Solar Flux Ropes

DTIC Science & Technology

2016-12-30

Naval Research Laboratory Washington, DC 20375-5320 NRL/MR/6794--16-9710 Quasi -Static Evolution, Catastrophe, and “Failed” Eruption of Solar Flux...TELEPHONE NUMBER (include area code) b. ABSTRACT c. THIS PAGE 18. NUMBER OF PAGES 17. LIMITATION OF ABSTRACT Quasi -Static Evolution, Catastrophe...evolution of solar flux ropes subject to slowly increasing magnetic energy, encompassing quasi -static evolution, “catastrophic” transition to an eruptive
New progress in snake mitochondrial gene rearrangement.

PubMed

Chen, Nian; Zhao, Shujin

2009-08-01

To further understand the evolution of snake mitochondrial genomes, the complete mitochondrial DNA (mtDNA) sequences were determined for representative species from two snake families: the Many-banded krait, the Banded krait, the Chinese cobra, the King cobra, the Hundred-pace viper, the Short-tailed mamushi, and the Chain viper. Thirteen protein-coding genes, 22-23 tRNA genes, 2 rRNA genes, and 2 control regions were identified in these mtDNAs. Duplication of the control region and translocation of the tRNAPro gene were two notable features of the snake mtDNAs. These results from the gene rearrangement comparisons confirm the correctness of traditional classification schemes and validate the utility of comparing complete mtDNA sequences for snake phylogeny reconstruction.
Comparison of evolutionary algorithms for LPDA antenna optimization

NASA Astrophysics Data System (ADS)

Lazaridis, Pavlos I.; Tziris, Emmanouil N.; Zaharis, Zaharias D.; Xenos, Thomas D.; Cosmas, John P.; Gallion, Philippe B.; Holmes, Violeta; Glover, Ian A.

2016-08-01

A novel approach to broadband log-periodic antenna design is presented, where some of the most powerful evolutionary algorithms are applied and compared for the optimal design of wire log-periodic dipole arrays (LPDA) using Numerical Electromagnetics Code. The target is to achieve an optimal antenna design with respect to maximum gain, gain flatness, front-to-rear ratio (F/R) and standing wave ratio. The parameters of the LPDA optimized are the dipole lengths, the spacing between the dipoles, and the dipole wire diameters. The evolutionary algorithms compared are the Differential Evolution (DE), Particle Swarm (PSO), Taguchi, Invasive Weed (IWO), and Adaptive Invasive Weed Optimization (ADIWO). Superior performance is achieved by the IWO (best results) and PSO (fast convergence) algorithms.
Chromaticity calculations and code comparisons for x-ray lithography source XLS and SXLS rings

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

Parsa, Z.

1988-06-16

This note presents the chromaticity calculations and code comparison results for the (x-ray lithography source) XLS (Chasman Green, XUV Cosy lattice) and (2 magnet 4T) SXLS lattices, with the standard beam optic codes, including programs SYNCH88.5, MAD6, PATRICIA88.4, PATPET88.2, DIMAD, BETA, and MARYLIE. This analysis is a part of our ongoing accelerator physics code studies. 4 figs., 10 tabs.
Comparison of two computer codes for crack growth analysis: NASCRAC Versus NASA/FLAGRO

NASA Technical Reports Server (NTRS)

Stallworth, R.; Meyers, C. A.; Stinson, H. C.

1989-01-01

Results are presented from the comparison study of two computer codes for crack growth analysis - NASCRAC and NASA/FLAGRO. The two computer codes gave compatible conservative results when the part through crack analysis solutions were analyzed versus experimental test data. Results showed good correlation between the codes for the through crack at a lug solution. For the through crack at a lug solution, NASA/FLAGRO gave the most conservative results.
SNAP dendrimers: multivalent protein display on dendrimer-like DNA for directed evolution.

PubMed

Kaltenbach, Miriam; Stein, Viktor; Hollfelder, Florian

2011-09-19

Display systems connect a protein with the DNA encoding it. Such systems (e.g., phage or ribosome display) have found widespread application in the directed evolution of protein binders and constitute a key element of the biotechnological toolkit. In this proof-of-concept study we describe the construction of a system that allows the display of multiple copies of a protein of interest in order to take advantage of avidity effects during affinity panning. To this end, dendrimer-like DNA is used as a scaffold with docking points that can join the coding DNA with multiple protein copies. Each DNA construct is compartmentalised in water-in-oil emulsion droplets. The corresponding protein is expressed, in vitro, inside the droplets as a SNAP-tag fusion. The covalent bond between DNA and the SNAP-tag is created by reaction with dendrimer-bound benzylguanine (BG). The ability to form dendrimer-like DNA straightforwardly from oligonucleotides bearing BG allowed the comparison of a series of templates differing in size, valency and position of BG. In model selections the most efficient constructs show recoveries of up to 0.86 % and up to 400-fold enrichments. The comparison of mono- and multivalent constructs suggests that the avidity effect enhances enrichment by up to fivefold and recovery by up to 25-fold. Our data establish a multivalent format for SNAP-display based on dendrimer-like DNA as the first in vitro display system with defined tailor-made valencies and explore a new application for DNA nanostructures. These data suggest that multivalent SNAP dendrimers have the potential to facilitate the selection of protein binders especially during early rounds of directed evolution, allowing a larger diversity of candidate binders to be recovered. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Changes in base composition bias of nuclear and mitochondrial genes in lice (Insecta: Psocodea).

PubMed

Yoshizawa, Kazunori; Johnson, Kevin P

2013-12-01

While it is well known that changes in the general processes of molecular evolution have occurred on a variety of timescales, the mechanisms underlying these changes are less well understood. Parasitic lice ("Phthiraptera") and their close relatives (infraorder Nanopsocetae of the insect order Psocodea) are a group of insects well known for their unusual features of molecular evolution. We examined changes in base composition across parasitic lice and bark lice. We identified substantial differences in percent GC content between the clade comprising parasitic lice plus closely related bark lice (=Nanopsocetae) versus all other bark lice. These changes occurred for both nuclear and mitochondrial protein coding and ribosomal RNA genes, often in the same direction. To evaluate whether correlations in base composition change also occurred within lineages, we used phylogenetically controlled comparisons, and in this case few significant correlations were identified. Examining more constrained sites (first/second codon positions and rRNA) revealed that, in comparison to the other bark lice, the GC content of parasitic lice and close relatives tended towards 50 % either up from less than 50 % GC or down from greater than 50 % GC. In contrast, less constrained sites (third codon positions) in both nuclear and mitochondrial genes showed less of a consistent change of base composition in parasitic lice and very close relatives. We conclude that relaxed selection on this group of insects is a potential explanation of the change in base composition for both mitochondrial and nuclear genes, which could lead to nucleotide frequencies closer to random expectation (i.e., 50 % GC) in the absence of any mutation bias. Evidence suggests this relaxed selection arose once in the non-parasitic common ancestor of Phthiraptera + Nanopsocetae and is not directly related to the evolution of the parasitism in lice.
Computerized Dental Comparison: A Critical Review of Dental Coding and Ranking Algorithms Used in Victim Identification.

PubMed

Adams, Bradley J; Aschheim, Kenneth W

2016-01-01

Comparison of antemortem and postmortem dental records is a leading method of victim identification, especially for incidents involving a large number of decedents. This process may be expedited with computer software that provides a ranked list of best possible matches. This study provides a comparison of the most commonly used conventional coding and sorting algorithms used in the United States (WinID3) with a simplified coding format that utilizes an optimized sorting algorithm. The simplified system consists of seven basic codes and utilizes an optimized algorithm based largely on the percentage of matches. To perform this research, a large reference database of approximately 50,000 antemortem and postmortem records was created. For most disaster scenarios, the proposed simplified codes, paired with the optimized algorithm, performed better than WinID3 which uses more complex codes. The detailed coding system does show better performance with extremely large numbers of records and/or significant body fragmentation. © 2015 American Academy of Forensic Sciences.
Low-Density Parity-Check (LDPC) Codes Constructed from Protographs

NASA Astrophysics Data System (ADS)

Thorpe, J.

2003-08-01

We introduce a new class of low-density parity-check (LDPC) codes constructed from a template called a protograph. The protograph serves as a blueprint for constructing LDPC codes of arbitrary size whose performance can be predicted by analyzing the protograph. We apply standard density evolution techniques to predict the performance of large protograph codes. Finally, we use a randomized search algorithm to find good protographs.

The Evolution of Random Number Generation in MUVES

DTIC Science & Technology

2017-01-01

mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results identical to the current...MUVES, includ- ing the mathematical basis and statistical justification for algorithms used in the code. The working code provided produces results...questionable numerical and statistical properties. The development of the modern system is traced through software change requests, resulting in a random number
Code-to-Code Comparison, and Material Response Modeling of Stardust and MSL using PATO and FIAT

NASA Technical Reports Server (NTRS)

Omidy, Ali D.; Panerai, Francesco; Martin, Alexandre; Lachaud, Jean R.; Cozmuta, Ioana; Mansour, Nagi N.

2015-01-01

This report provides a code-to-code comparison between PATO, a recently developed high fidelity material response code, and FIAT, NASA's legacy code for ablation response modeling. The goal is to demonstrates that FIAT and PATO generate the same results when using the same models. Test cases of increasing complexity are used, from both arc-jet testing and flight experiment. When using the exact same physical models, material properties and boundary conditions, the two codes give results that are within 2% of errors. The minor discrepancy is attributed to the inclusion of the gas phase heat capacity (cp) in the energy equation in PATO, and not in FIAT.
LIDT-DD: A New Self-Consistent Debris Disc Model Including Radiation Pressure and Coupling Dynamical and Collisional Evolution

NASA Astrophysics Data System (ADS)

Kral, Q.; Thebault, P.; Charnoz, S.

2014-01-01

The first attempt at developing a fully self-consistent code coupling dynamics and collisions to study debris discs (Kral et al. 2013) is presented. So far, these two crucial mechanisms were studied separately, with N-body and statistical collisional codes respectively, because of stringent computational constraints. We present a new model named LIDT-DD which is able to follow over long timescales the coupled evolution of dynamics (including radiation forces) and collisions in a self-consistent way.
CHOLLA: A New Massively Parallel Hydrodynamics Code for Astrophysical Simulation

NASA Astrophysics Data System (ADS)

Schneider, Evan E.; Robertson, Brant E.

2015-04-01

We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳2563) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.
Non-local electron transport validation using 2D DRACO simulations

NASA Astrophysics Data System (ADS)

Cao, Duc; Chenhall, Jeff; Moll, Eli; Prochaska, Alex; Moses, Gregory; Delettrez, Jacques; Collins, Tim

2012-10-01

Comparison of 2D DRACO simulations, using a modified versionfootnotetextprivate communications with M. Marinak and G. Zimmerman, LLNL. of the Schurtz, Nicolai and Busquet (SNB) algorithmfootnotetextSchurtz, Nicolai and Busquet, ``A nonlocal electron conduction model for multidimensional radiation hydrodynamics codes,'' Phys. Plasmas 7, 4238(2000). for non-local electron transport, with direct drive shock timing experimentsfootnotetextT. Boehly, et. al., ``Multiple spherically converging shock waves in liquid deuterium,'' Phys. Plasmas 18, 092706(2011). and with the Goncharov non-local modelfootnotetextV. Goncharov, et. al., ``Early stage of implosion in inertial confinement fusion: Shock timing and perturbation evolution,'' Phys. Plasmas 13, 012702(2006). in 1D LILAC will be presented. Addition of an improved SNB non-local electron transport algorithm in DRACO allows direct drive simulations with no need for an electron conduction flux limiter. Validation with shock timing experiments that mimic the laser pulse profile of direct drive ignition targets gives a higher confidence level in the predictive capability of the DRACO code. This research was supported by the University of Rochester Laboratory for Laser Energetics.
Hydrodynamic Modeling of the Deep Impact Mission into Comet Tempel 1

NASA Astrophysics Data System (ADS)

Sorli, Kya; Remington, Tané; Bruck Syal, Megan

2018-01-01

Kinetic impact is one of the primary strategies to deflect hazardous objects off of an Earth-impacting trajectory. The only test of a small-body impact is the 2005 Deep Impact mission into comet Tempel 1, where a 366-kg mass impactor collided at ~10 km/s into the comet, liberating an enormous amount of vapor and ejecta. Code comparisons with observations of the event represent an important source of new information about the initial conditions of small bodies and an extraordinary opportunity to test our simulation capabilities on a rare, full-scale experiment. Using the Adaptive Smoothed Particle Hydrodynamics (ASPH) code, Spheral, we explore how variations in target material properties such as strength, composition, porosity, and layering affect impact results, in order to best match the observed crater size and ejecta evolution. Benchmarking against this unique small-body experiment provides an enhanced understanding of our ability to simulate asteroid or comet response to future deflection missions. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344. LLNL-ABS-739336-DRAFT.
MOCCA-SURVEY Database I: Is NGC 6535 a dark star cluster harbouring an IMBH?

NASA Astrophysics Data System (ADS)

Askar, Abbas; Bianchini, Paolo; de Vita, Ruggero; Giersz, Mirek; Hypki, Arkadiusz; Kamann, Sebastian

2017-01-01

We describe the dynamical evolution of a unique type of dark star cluster model in which the majority of the cluster mass at Hubble time is dominated by an intermediate-mass black hole (IMBH). We analysed results from about 2000 star cluster models (Survey Database I) simulated using the Monte Carlo code MOnte Carlo Cluster simulAtor and identified these dark star cluster models. Taking one of these models, we apply the method of simulating realistic `mock observations' by utilizing the Cluster simulatiOn Comparison with ObservAtions (COCOA) and Simulating Stellar Cluster Observation (SISCO) codes to obtain the photometric and kinematic observational properties of the dark star cluster model at 12 Gyr. We find that the perplexing Galactic globular cluster NGC 6535 closely matches the observational photometric and kinematic properties of the dark star cluster model presented in this paper. Based on our analysis and currently observed properties of NGC 6535, we suggest that this globular cluster could potentially harbour an IMBH. If it exists, the presence of this IMBH can be detected robustly with proposed kinematic observations of NGC 6535.
Turbulent AGN tori .

NASA Astrophysics Data System (ADS)

Schartmann, M.; Meisenheimer, K.; Klahr, H.; Camenzind, M.; Wolf, S.; Henning, Th.

Recently, the MID-infrared Interferometric instrument (MIDI) at the VLTI has shown that dust tori in the two nearby Seyfert galaxies NGC 1068 and the Circinus galaxy are geometrically thick and can be well described by a thin, warm central disk, surrounded by a colder and fluffy torus component. By carrying out hydrodynamical simulations with the help of the TRAMP code \\citep{schartmann_Klahr_99}, we follow the evolution of a young nuclear star cluster in terms of discrete mass-loss and energy injection from stellar processes. This naturally leads to a filamentary large scale torus component, where cold gas is able to flow radially inwards. The filaments open out into a dense and very turbulent disk structure. In a post-processing step, we calculate observable quantities like spectral energy distributions or images with the help of the 3D radiative transfer code MC3D \\citep{schartmann_Wolf_03}. Good agreement is found in comparisons with data due to the existence of almost dust-free lines of sight through the large scale component and the large column densities caused by the dense disk.
Cardiac ultrasonography over 4G wireless networks using a tele-operated robot

PubMed Central

Panayides, Andreas S.; Jossif, Antonis P.; Christoforou, Eftychios G.; Vieyres, Pierre; Novales, Cyril; Voskarides, Sotos; Pattichis, Constantinos S.

2016-01-01

This Letter proposes an end-to-end mobile tele-echography platform using a portable robot for remote cardiac ultrasonography. Performance evaluation investigates the capacity of long-term evolution (LTE) wireless networks to facilitate responsive robot tele-manipulation and real-time ultrasound video streaming that qualifies for clinical practice. Within this context, a thorough video coding standards comparison for cardiac ultrasound applications is performed, using a data set of ten ultrasound videos. Both objective and subjective (clinical) video quality assessment demonstrate that H.264/AVC and high efficiency video coding standards can achieve diagnostically-lossless video quality at bitrates well within the LTE supported data rates. Most importantly, reduced latencies experienced throughout the live tele-echography sessions allow the medical expert to remotely operate the robot in a responsive manner, using the wirelessly communicated cardiac ultrasound video to reach a diagnosis. Based on preliminary results documented in this Letter, the proposed robotised tele-echography platform can provide for reliable, remote diagnosis, achieving comparable quality of experience levels with in-hospital ultrasound examinations. PMID:27733929
Modeling the effect of subgrain rotation recrystallization on the evolution of olivine crystal preferred orientations in simple shear

NASA Astrophysics Data System (ADS)

Signorelli, Javier; Tommasi, Andréa

2015-11-01

Homogenization models are widely used to predict the evolution of texture (crystal preferred orientations) and resulting anisotropy of physical properties in metals, rocks, and ice. They fail, however, in predicting two main features of texture evolution in simple shear (the dominant deformation regime on Earth) for highly anisotropic crystals, like olivine: (1) the fast rotation of the CPO towards a stable position characterized by parallelism of the dominant slip system and the macroscopic shear and (2) the asymptotical evolution towards a constant intensity. To better predict CPO-induced anisotropy in the mantle, but limiting computational costs and use of poorly-constrained physical parameters, we modified a viscoplastic self-consistent code to simulate the effects of subgrain rotation recrystallization. To each crystal is associated a finite number of fragments (possible subgrains). Formation of a subgrain corresponds to introduction of a disorientation (relative to the parent) and resetting of the fragment strain and internal energy. The probability of formation of a subgrain is controlled by comparison between the local internal energy and the average value in the polycrystal. A two-level mechanical interaction scheme is applied for simulating the intracrystalline strain heterogeneity allowed by the formation of low-angle grain boundaries. Within a crystal, interactions between subgrains follow a constant stress scheme. The interactions between grains are simulated by a tangent viscoplastic self-consistent approach. This two-level approach better reproduces the evolution of olivine CPO in simple shear in experiments and nature. It also predicts a marked weakening at low shear strains, consistently with experimental data.
Comparative genomics of 28 Salmonella enterica isolates: evidence for CRISPR-mediated adaptive sublineage evolution.

PubMed

Fricke, W Florian; Mammel, Mark K; McDermott, Patrick F; Tartera, Carmen; White, David G; Leclerc, J Eugene; Ravel, Jacques; Cebula, Thomas A

2011-07-01

Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks.
Comparative Genomics of 28 Salmonella enterica Isolates: Evidence for CRISPR-Mediated Adaptive Sublineage Evolution ▿†

PubMed Central

Fricke, W. Florian; Mammel, Mark K.; McDermott, Patrick F.; Tartera, Carmen; White, David G.; LeClerc, J. Eugene; Ravel, Jacques; Cebula, Thomas A.

2011-01-01

Despite extensive surveillance, food-borne Salmonella enterica infections continue to be a significant burden on public health systems worldwide. As the S. enterica species comprises sublineages that differ greatly in antigenic representation, virulence, and antimicrobial resistance phenotypes, a better understanding of the species' evolution is critical for the prediction and prevention of future outbreaks. The roles that virulence and resistance phenotype acquisition, exchange, and loss play in the evolution of S. enterica sublineages, which to a certain extent are represented by serotypes, remains mostly uncharacterized. Here, we compare 17 newly sequenced and phenotypically characterized nontyphoidal S. enterica strains to 11 previously sequenced S. enterica genomes to carry out the most comprehensive comparative analysis of this species so far. These phenotypic and genotypic data comparisons in the phylogenetic species context suggest that the evolution of known S. enterica sublineages is mediated mostly by two mechanisms, (i) the loss of coding sequences with known metabolic functions, which leads to functional reduction, and (ii) the acquisition of horizontally transferred phage and plasmid DNA, which provides virulence and resistance functions and leads to increasing specialization. Matches between S. enterica clustered regularly interspaced short palindromic repeats (CRISPR), part of a defense mechanism against invading plasmid and phage DNA, and plasmid and prophage regions suggest that CRISPR-mediated immunity could control short-term phenotype changes and mediate long-term sublineage evolution. CRISPR analysis could therefore be critical in assessing the evolutionary potential of S. enterica sublineages and aid in the prediction and prevention of future S. enterica outbreaks. PMID:21602358
A NEW HYBRID N-BODY-COAGULATION CODE FOR THE FORMATION OF GAS GIANT PLANETS

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

Bromley, Benjamin C.; Kenyon, Scott J., E-mail: bromley@physics.utah.edu, E-mail: skenyon@cfa.harvard.edu

2011-04-20

We describe an updated version of our hybrid N-body-coagulation code for planet formation. In addition to the features of our 2006-2008 code, our treatment now includes algorithms for the one-dimensional evolution of the viscous disk, the accretion of small particles in planetary atmospheres, gas accretion onto massive cores, and the response of N-bodies to the gravitational potential of the gaseous disk and the swarm of planetesimals. To validate the N-body portion of the algorithm, we use a battery of tests in planetary dynamics. As a first application of the complete code, we consider the evolution of Pluto-mass planetesimals in amore » swarm of 0.1-1 cm pebbles. In a typical evolution time of 1-3 Myr, our calculations transform 0.01-0.1 M{sub sun} disks of gas and dust into planetary systems containing super-Earths, Saturns, and Jupiters. Low-mass planets form more often than massive planets; disks with smaller {alpha} form more massive planets than disks with larger {alpha}. For Jupiter-mass planets, masses of solid cores are 10-100 M{sub +}.« less
Two fundamental questions about protein evolution.

PubMed

Penny, David; Zhong, Bojian

2015-12-01

Two basic questions are considered that approach protein evolution from different directions; the problems arising from using Markov models for the deeper divergences, and then the origin of proteins themselves. The real problem for the first question (going backwards in time) is that at deeper phylogenies the Markov models of sequence evolution must lose information exponentially at deeper divergences, and several testable methods are suggested that should help resolve these deeper divergences. For the second question (coming forwards in time) a problem is that most models for the origin of protein synthesis do not give a role for the very earliest stages of the process. From our knowledge of the importance of replication accuracy in limiting the length of a coding molecule, a testable hypothesis is proposed. The length of the code, the code itself, and tRNAs would all have prior roles in increasing the accuracy of RNA replication; thus proteins would have been formed only after the tRNAs and the length of the triplet code are already formed. Both questions lead to testable predictions. Copyright © 2014 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.
Combinatorial neural codes from a mathematical coding theory perspective.

PubMed

Curto, Carina; Itskov, Vladimir; Morrison, Katherine; Roth, Zachary; Walker, Judy L

2013-07-01

Shannon's seminal 1948 work gave rise to two distinct areas of research: information theory and mathematical coding theory. While information theory has had a strong influence on theoretical neuroscience, ideas from mathematical coding theory have received considerably less attention. Here we take a new look at combinatorial neural codes from a mathematical coding theory perspective, examining the error correction capabilities of familiar receptive field codes (RF codes). We find, perhaps surprisingly, that the high levels of redundancy present in these codes do not support accurate error correction, although the error-correcting performance of receptive field codes catches up to that of random comparison codes when a small tolerance to error is introduced. However, receptive field codes are good at reflecting distances between represented stimuli, while the random comparison codes are not. We suggest that a compromise in error-correcting capability may be a necessary price to pay for a neural code whose structure serves not only error correction, but must also reflect relationships between stimuli.
On the possible origin and evolution of the genetic code

NASA Technical Reports Server (NTRS)

Jukes, T. H.

1974-01-01

The genetic code is examined for indications of possible preceding codes that existed during early evolution. Eight of the 20 amino acids are coded by 'quartets' of codons with fourfold degeneracy, and 16 such quartets can exist, so that an earlier code could have provided for 15 or 16 amino acids, rather than 20. If twofold degeneracy is postulated for the first position of the codon, there could have been ten amino acids in the code. It is speculated that these may have been phenylalanine, valine, proline, alanine, histidine, glutamine, glutanic acid, aspartic acid, cysteine and glycine. There is a notable deficiency of arginine in proteins, despite the fact that it has six codons. Simultaneously, there is more lysine in proteins than would be expected from its two codons, if the four bases in mRNA are equiprobable and are arranged randomly. It is speculated that arginine is an 'intruder' into the genetic code, and that it may have displayed another amino acid such as ornithine, or may even have displayed lysine from some of its previous codon assignments. As a result, natural selection has favored lysine against the fact that it has only two codons.
Planned Comparisons as Better Alternatives to ANOVA Omnibus Tests.

ERIC Educational Resources Information Center

Benton, Roberta L.

Analyses of data are presented to illustrate the advantages of using a priori or planned comparisons rather than omnibus analysis of variance (ANOVA) tests followed by post hoc or posteriori testing. The two types of planned comparisons considered are planned orthogonal non-trend coding contrasts and orthogonal polynomial or trend contrast coding.…
The complete mitochondrial genome of the stomatopod crustacean Squilla mantis

PubMed Central

Cook, Charles E

2005-01-01

Background Animal mitochondrial genomes are physically separate from the much larger nuclear genomes and have proven useful both for phylogenetic studies and for understanding genome evolution. Within the phylum Arthropoda the subphylum Crustacea includes over 50,000 named species with immense variation in body plans and habitats, yet only 23 complete mitochondrial genomes are available from this subphylum. Results I describe here the complete mitochondrial genome of the crustacean Squilla mantis (Crustacea: Malacostraca: Stomatopoda). This 15994-nucleotide genome, the first described from a hoplocarid, contains the standard complement of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a non-coding AT-rich region that is found in most other metazoans. The gene order is identical to that considered ancestral for hexapods and crustaceans. The 70% AT base composition is within the range described for other arthropods. A single unusual feature of the genome is a 230 nucleotide non-coding region between a serine transfer RNA and the nad1 gene, which has no apparent function. I also compare gene order, nucleotide composition, and codon usage of the S. mantis genome and eight other malacostracan crustaceans. A translocation of the histidine transfer RNA gene is shared by three taxa in the order Decapoda, infraorder Brachyura; Callinectes sapidus, Portunus trituberculatus and Pseudocarcinus gigas. This translocation may be diagnostic for the Brachyura. For all nine taxa nucleotide composition is biased towards AT-richness, as expected for arthropods, and is within the range reported for other arthropods. Codon usage is biased, and much of this bias is probably due to the skew in nucleotide composition towards AT-richness. Conclusion The mitochondrial genome of Squilla mantis contains one unusual feature, a 230 base pair non-coding region has so far not been described in any other malacostracan. Comparisons with other Malacostraca show that all nine genomes, like most other mitochondrial genomes, share a bias toward AT-richness and a related bias in codon usage. The nine malacostracans included in this analysis are not representative of the diversity of the class Malacostraca, and additional malacostracan sequences would surely reveal other unusual genomic features that could be useful in understanding mitochondrial evolution in this taxon. PMID:16091132
Partial sequence homogenization in the 5S multigene families may generate sequence chimeras and spurious results in phylogenetic reconstructions.

PubMed

Galián, José A; Rosato, Marcela; Rosselló, Josep A

2014-03-01

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.
MCNP and GADRAS Comparisons

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

Klasky, Marc Louis; Myers, Steven Charles; James, Michael R.

To facilitate the timely execution of System Threat Reviews (STRs) for DNDO, and also to develop a methodology for performing STRs, LANL performed comparisons of several radiation transport codes (MCNP, GADRAS, and Gamma-Designer) that have been previously utilized to compute radiation signatures. While each of these codes has strengths, it is of paramount interest to determine the limitations of each of the respective codes and also to identify the most time efficient means by which to produce computational results, given the large number of parametric cases that are anticipated in performing STR's. These comparisons serve to identify regions of applicabilitymore » for each code and provide estimates of uncertainty that may be anticipated. Furthermore, while performing these comparisons, examination of the sensitivity of the results to modeling assumptions was also examined. These investigations serve to enable the creation of the LANL methodology for performing STRs. Given the wide variety of radiation test sources, scenarios, and detectors, LANL calculated comparisons of the following parameters: decay data, multiplicity, device (n,γ) leakages, and radiation transport through representative scenes and shielding. This investigation was performed to understand potential limitations utilizing specific codes for different aspects of the STR challenges.« less

A Cross-disciplinary Framework for the Description of Contextually Mediated Change

NASA Astrophysics Data System (ADS)

Gabora, Liane; Aerts, Diederik

We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of entities studied in different disciplines. Processes are seen to differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. Our analysis suggests that the dynamical evolution of a quantum entity described by the Schrödinger equation is not fundamentally different from change provoked by a measurement often referred to as collapse but a limiting case, with only one way to collapse. The biological transition to coded replication is seen as a means of preserving structure in the face of context, and sexual replication as a means of increasing potentiality thus enhancing diversity through interaction with context. The framework sheds light on concepts like selection and fitness, reveals how exceptional Darwinian evolution is as a means of 'change of state', and clarifies in what sense culture (and the creative process underlying it) are Darwinian.
Archaebacterial rhodopsin sequences: Implications for evolution

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1991-01-01

It was proposed over 10 years ago that the archaebacteria represent a separate kingdom which diverged very early from the eubacteria and eukaryotes. It follows that investigations of archaebacterial characteristics might reveal features of early evolution. So far, two genes, one for bacteriorhodopsin and another for halorhodopsin, both from Halobacterium halobium, have been sequenced. We cloned and sequenced the gene coding for the polypeptide of another one of these rhodopsins, a halorhodopsin in Natronobacterium pharaonis. Peptide sequencing of cyanogen bromide fragments, and immuno-reactions of the protein and synthetic peptides derived from the C-terminal gene sequence, confirmed that the open reading frame was the structural gene for the pharaonis halorhodopsin polypeptide. The flanking DNA sequences of this gene, as well as those of other bacterial rhodopsins, were compared to previously proposed archaebacterial consensus sequences. In pairwise comparisons of the open reading frame with DNA sequences for bacterio-opsin and halo-opsin from Halobacterium halobium, silent divergences were calculated. These indicate very considerable evolutionary distance between each pair of genes, even in the dame organism. In spite of this, three protein sequences show extensive similarities, indicating strong selective pressures.
Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops.

PubMed

Murat, Florent; Zhang, Rongzhi; Guizard, Sébastien; Gavranović, Haris; Flores, Raphael; Steinbach, Delphine; Quesneville, Hadi; Tannier, Eric; Salse, Jérôme

2015-01-29

We used nine complete genome sequences, from grape, poplar, Arabidopsis, soybean, lotus, apple, strawberry, cacao, and papaya, to investigate the paleohistory of rosid crops. We characterized an ancestral rosid karyotype, structured into 7/21 protochomosomes, with a minimal set of 6,250 ordered protogenes and a minimum physical coding gene space of 50 megabases. We also proposed ancestral karyotypes for the Caricaceae, Brassicaceae, Malvaceae, Fabaceae, Rosaceae, Salicaceae, and Vitaceae families with 9, 8, 10, 6, 12, 9, 12, and 19 protochromosomes, respectively. On the basis of these ancestral karyotypes and present-day species comparisons, we proposed a two-step evolutionary scenario based on allohexaploidization involving the newly characterized A, B, and C diploid progenitors leading to dominant (stable) and sensitive (plastic) genomic compartments in any modern rosid crops. Finally, a new user-friendly online tool, "DicotSyntenyViewer" (available from http://urgi.versailles.inra.fr/synteny-dicot), has been made available for accurate translational genomics in rosids. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
Status and future of MUSE

NASA Astrophysics Data System (ADS)

Harfst, S.; Portegies Zwart, S.; McMillan, S.

2008-12-01

We present MUSE, a software framework for combining existing computational tools from different astrophysical domains into a single multi-physics, multi-scale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a ``Noah's Ark'' milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multi-scale and multi-physics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe two examples calculated using MUSE: the merger of two galaxies and an N-body simulation with live stellar evolution. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.
Calculation of inviscid flow over shuttle-like vehicles at high angles of attack and comparisons with experimental data

NASA Technical Reports Server (NTRS)

Weilmuenster, K. J.; Hamilton, H. H., II

1983-01-01

A computer code HALIS, designed to compute the three dimensional flow about shuttle like configurations at angles of attack greater than 25 deg, is described. Results from HALIS are compared where possible with an existing flow field code; such comparisons show excellent agreement. Also, HALIS results are compared with experimental pressure distributions on shuttle models over a wide range of angle of attack. These comparisons are excellent. It is demonstrated that the HALIS code can incorporate equilibrium air chemistry in flow field computations.
Validation of the NCC Code for Staged Transverse Injection and Computations for a RBCC Combustor

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Liu, Nan-Suey

2005-01-01

The NCC code was validated for a case involving staged transverse injection into Mach 2 flow behind a rearward facing step. Comparisons with experimental data and with solutions from the FPVortex code was then used to perform computations to study fuel-air mixing for the combustor of a candidate rocket based combined cycle engine geometry. Comparisons with a one-dimensional analysis and a three-dimensional code (VULCAN) were performed to assess the qualitative and quantitative performance of the NCC solver.
Calculations of Helium Bubble Evolution in the PISCES Experiments with Cluster Dynamics

NASA Astrophysics Data System (ADS)

Blondel, Sophie; Younkin, Timothy; Wirth, Brian; Lasa, Ane; Green, David; Canik, John; Drobny, Jon; Curreli, Davide

2017-10-01

Plasma surface interactions in fusion tokamak reactors involve an inherently multiscale, highly non-equilibrium set of phenomena, for which current models are inadequate to predict the divertor response to and feedback on the plasma. In this presentation, we describe the latest code developments of Xolotl, a spatially-dependent reaction diffusion cluster dynamics code to simulate the divertor surface response to fusion-relevant plasma exposure. Xolotl is part of a code-coupling effort to model both plasma and material simultaneously; the first benchmark for this effort is the series of PISCES linear device experiments. We will discuss the processes leading to surface morphology changes, which further affect erosion, as well as how Xolotl has been updated in order to communicate with other codes. Furthermore, we will show results of the sub-surface evolution of helium bubbles in tungsten as well as the material surface displacement under these conditions.
The Evolution of Human Cells in Terms of Protein Innovation

PubMed Central

Sardar, Adam J.; Oates, Matt E.; Fang, Hai; Forrest, Alistair R.R.; Kawaji, Hideya; Gough, Julian; Rackham, Owen J.L.

2014-01-01

Humans are composed of hundreds of cell types. As the genomic DNA of each somatic cell is identical, cell type is determined by what is expressed and when. Until recently, little has been reported about the determinants of human cell identity, particularly from the joint perspective of gene evolution and expression. Here, we chart the evolutionary past of all documented human cell types via the collective histories of proteins, the principal product of gene expression. FANTOM5 data provide cell-type–specific digital expression of human protein-coding genes and the SUPERFAMILY resource is used to provide protein domain annotation. The evolutionary epoch in which each protein was created is inferred by comparison with domain annotation of all other completely sequenced genomes. Studying the distribution across epochs of genes expressed in each cell type reveals insights into human cellular evolution in terms of protein innovation. For each cell type, its history of protein innovation is charted based on the genes it expresses. Combining the histories of all cell types enables us to create a timeline of cell evolution. This timeline identifies the possibility that our common ancestor Coelomata (cavity-forming animals) provided the innovation required for the innate immune system, whereas cells which now form the brain of human have followed a trajectory of continually accumulating novel proteins since Opisthokonta (boundary of animals and fungi). We conclude that exaptation of existing domain architectures into new contexts is the dominant source of cell-type–specific domain architectures. PMID:24692656
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms.

PubMed

Buschiazzo, Emmanuel; Ritland, Carol; Bohlmann, Jörg; Ritland, Kermit

2012-01-20

Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10(-9) synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations.
Historical Roots and Future Perspectives Related to Nursing Ethics.

ERIC Educational Resources Information Center

Freitas, Lorraine

1990-01-01

This article traces the evolution of the development and refinement of the professional code from concerns about the ethical conduct of nurses to its present state as a professional code for all nurses. The relationship of the Ethics Committee of the American Nurses' Association to the development of the code is also discussed. (Author/MLW)
Wolf-Rayet stars, black holes and the first detected gravitational wave source

NASA Astrophysics Data System (ADS)

Bogomazov, A. I.; Cherepashchuk, A. M.; Lipunov, V. M.; Tutukov, A. V.

2018-01-01

The recently discovered burst of gravitational waves GW150914 provides a good new chance to verify the current view on the evolution of close binary stars. Modern population synthesis codes help to study this evolution from two main sequence stars up to the formation of two final remnant degenerate dwarfs, neutron stars or black holes (Masevich and Tutukov, 1988). To study the evolution of the GW150914 predecessor we use the ;Scenario Machine; code presented by Lipunov et al. (1996). The scenario modeling conducted in this study allowed to describe the evolution of systems for which the final stage is a massive BH+BH merger. We find that the initial mass of the primary component can be 100÷140M⊙ and the initial separation of the components can be 50÷350R⊙. Our calculations show the plausibility of modern evolutionary scenarios for binary stars and the population synthesis modeling based on it.
Unraveling the Complexity of the Evolution of the Sun's Photospheric Magnetic Field

NASA Astrophysics Data System (ADS)

Hathaway, David H.

2016-10-01

Given the emergence of tilted, bipolar active regions, surface flux transport has been shown to reproduce much of the complex evolution of the Sun's photospheric magnetic field. Surface flux is transported by flows in the surface shear layer - the axisymmetric differential rotation and meridional flow and the non-axisymmetric convective motions (granules, supergranules, and giant cells). We have measured these flows by correlation tracking of the magnetic elements themselves, correlation tracking of the Doppler features (supergranules), and by direct Doppler measurements using SDO/HMI data. These measurements fully constrain (with no free parameters) the flows used in our surface flux transport code - the Advective Flux Transport or AFT code. Here we show the up-to-date evolution of these flows, their impact on the detailed evolution of the Sun's photospheric magnetic field, and predictions for what the polar fields will be at the next minimum in 2020.
Biosemiotics: a new understanding of life.

PubMed

Barbieri, Marcello

2008-07-01

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes--copying and coding--and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.
Comparisons of time explicit hybrid kinetic-fluid code Architect for Plasma Wakefield Acceleration with a full PIC code

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

Massimo, F., E-mail: francesco.massimo@ensta-paristech.fr; Dipartimento SBAI, Università di Roma “La Sapienza“, Via A. Scarpa 14, 00161 Roma; Atzeni, S.

Architect, a time explicit hybrid code designed to perform quick simulations for electron driven plasma wakefield acceleration, is described. In order to obtain beam quality acceptable for applications, control of the beam-plasma-dynamics is necessary. Particle in Cell (PIC) codes represent the state-of-the-art technique to investigate the underlying physics and possible experimental scenarios; however PIC codes demand the necessity of heavy computational resources. Architect code substantially reduces the need for computational resources by using a hybrid approach: relativistic electron bunches are treated kinetically as in a PIC code and the background plasma as a fluid. Cylindrical symmetry is assumed for themore » solution of the electromagnetic fields and fluid equations. In this paper both the underlying algorithms as well as a comparison with a fully three dimensional particle in cell code are reported. The comparison highlights the good agreement between the two models up to the weakly non-linear regimes. In highly non-linear regimes the two models only disagree in a localized region, where the plasma electrons expelled by the bunch close up at the end of the first plasma oscillation.« less
X-ray clusters from a high-resolution hydrodynamic PPM simulation of the cold dark matter universe

NASA Technical Reports Server (NTRS)

Bryan, Greg L.; Cen, Renyue; Norman, Michael L.; Ostriker, Jermemiah P.; Stone, James M.

1994-01-01

A new three-dimensional hydrodynamic code based on the piecewise parabolic method (PPM) is utilized to compute the distribution of hot gas in the standard Cosmic Background Explorer (COBE)-normalized cold dark matter (CDM) universe. Utilizing periodic boundary conditions, a box with size 85 h(exp-1) Mpc, having cell size 0.31 h(exp-1) Mpc, is followed in a simulation with 270(exp 3)=10(exp 7.3) cells. Adopting standard parameters determined from COBE and light-element nucleosynthesis, Sigma(sub 8)=1.05, Omega(sub b)=0.06, we find the X-ray-emitting clusters, compute the luminosity function at several wavelengths, the temperature distribution, and estimated sizes, as well as the evolution of these quantities with redshift. The results, which are compared with those obtained in the preceding paper (Kang et al. 1994a), may be used in conjuction with ROSAT and other observational data sets. Overall, the results of the two computations are qualitatively very similar with regard to the trends of cluster properties, i.e., how the number density, radius, and temeprature depend on luminosity and redshift. The total luminosity from clusters is approximately a factor of 2 higher using the PPM code (as compared to the 'total variation diminishing' (TVD) code used in the previous paper) with the number of bright clusters higher by a similar factor. The primary conclusions of the prior paper, with regard to the power spectrum of the primeval density perturbations, are strengthened: the standard CDM model, normalized to the COBE microwave detection, predicts too many bright X-ray emitting clusters, by a factor probably in excess of 5. The comparison between observations and theoretical predictions for the evolution of cluster properties, luminosity functions, and size and temperature distributions should provide an important discriminator among competing scenarios for the development of structure in the universe.
Piece2.0: an update for the pant gene structure comparison and evolution database

USDA-ARS?s Scientific Manuscript database

PIECE (Plant Intron Exon Comparison and Evolution) is a web-accessible database that houses intron and exon information of plant genes. PIECE serves as a resource for biologists interested in comparing intron–exon organization and provides valuable insights into the evolution of gene structure in pl...
General practitioners' justifications for therapeutic inertia in cardiovascular prevention: an empirically grounded typology.

PubMed

Lebeau, Jean-Pierre; Cadwallader, Jean-Sébastien; Vaillant-Roussel, Hélène; Pouchain, Denis; Yaouanc, Virginie; Aubin-Auger, Isabelle; Mercier, Alain; Rusch, Emmanuel; Remmen, Roy; Vermeire, Etienne; Hendrickx, Kristin

2016-05-13

To construct a typology of general practitioners' (GPs) responses regarding their justification of therapeutic inertia in cardiovascular primary prevention for high-risk patients with hypertension. Empirically grounded construction of typology. Types were defined by attributes derived from the qualitative analysis of GPs' reported reasons for inaction. 256 GPs randomised in the intervention group of a cluster randomised controlled trial. GPs members of 23 French Regional Colleges of Teachers in General Practice, included in the EffectS of a multifaceted intervention on CArdiovascular risk factors in high-risk hyPErtensive patients (ESCAPE) trial. The database consisted of 2638 written responses given by the GPs to an open-ended question asking for the reasons why drug treatment was not changed as suggested by the national guidelines. All answers were coded using constant comparison analysis. A matrix analysis of codes per GP allowed the construction of a response typology, where types were defined by codes as attributes. Initial coding and definition of types were performed independently by two teams. Initial coding resulted in a list of 69 codes in the final codebook, representing 4764 coded references in the question responses. A typology including seven types was constructed. 100 GPs were allocated to one and only one of these types, while 25 GPs did not provide enough data to allow classification. Types (numbers of GPs allocated) were: 'optimists' (28), 'negotiators' (20), 'checkers' (15), 'contextualisers' (13), 'cautious' (11), 'rounders' (8) and 'scientists' (5). For the 36 GPs that provided 50 or more coded references, analysis of the code evolution over time and across patients showed a consistent belonging to the initial type for any given GP. This typology could provide GPs with some insight into their general ways of considering changes in the treatment/management of cardiovascular risk factors and guide design of specific physician-centred interventions to reduce inappropriate inaction. NCT00348855. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/
Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat

USDA-ARS?s Scientific Manuscript database

Cycles of whole genome duplication (WGD) and diploidization are hallmarks of eukaryotic genome evolution and speciation. Polyploid wheat (Triticum aestivum) has had a massive increase in genome size largely due to recent WGDs. How these processes may impact the dynamics of gene evolution was studied...
The Nature of the Arguments for Creationism, Intelligent Design, and Evolution

ERIC Educational Resources Information Center

Barnes, Ralph M.; Church, Rebecca A.; Draznin-Nagy, Samuel

2017-01-01

Seventy-two Internet documents promoting creationism, intelligent design (I.D.), or evolution were selected for analysis. The primary goal of each of the 72 documents was to present arguments for creationism, I.D., or evolution. We first identified all arguments in these documents. Each argument was then coded in terms of both argument type…
Wind turbine design codes: A comparison of the structural response

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

Buhl, M.L. Jr.; Wright, A.D.; Pierce, K.G.

2000-03-01

The National Wind Technology Center (NWTC) of the National Renewable Energy Laboratory is continuing a comparison of several computer codes used in the design and analysis of wind turbines. The second part of this comparison determined how well the programs predict the structural response of wind turbines. In this paper, the authors compare the structural response for four programs: ADAMS, BLADED, FAST{_}AD, and YawDyn. ADAMS is a commercial, multibody-dynamics code from Mechanical Dynamics, Inc. BLADED is a commercial, performance and structural-response code from Garrad Hassan and Partners Limited. FAST{_}AD is a structural-response code developed by Oregon State University and themore » University of Utah for the NWTC. YawDyn is a structural-response code developed by the University of Utah for the NWTC. ADAMS, FAST{_}AD, and YawDyn use the University of Utah's AeroDyn subroutine package for calculating aerodynamic forces. Although errors were found in all the codes during this study, once they were fixed, the codes agreed surprisingly well for most of the cases and configurations that were evaluated. One unresolved discrepancy between BLADED and the AeroDyn-based codes was when there was blade and/or teeter motion in addition to a large yaw error.« less

Directed Chemical Evolution with an Outsized Genetic Code

PubMed Central

Krusemark, Casey J.; Tilmans, Nicolas P.; Brown, Patrick O.; Harbury, Pehr B.

2016-01-01

The first demonstration that macromolecules could be evolved in a test tube was reported twenty-five years ago. That breakthrough meant that billions of years of chance discovery and refinement could be compressed into a few weeks, and provided a powerful tool that now dominates all aspects of protein engineering. A challenge has been to extend this scientific advance into synthetic chemical space: to enable the directed evolution of abiotic molecules. The problem has been tackled in many ways. These include expanding the natural genetic code to include unnatural amino acids, engineering polyketide and polypeptide synthases to produce novel products, and tagging combinatorial chemistry libraries with DNA. Importantly, there is still no small-molecule analog of directed protein evolution, i.e. a substantiated approach for optimizing complex (≥ 10^9 diversity) populations of synthetic small molecules over successive generations. We present a key advance towards this goal: a tool for genetically-programmed synthesis of small-molecule libraries from large chemical alphabets. The approach accommodates alphabets that are one to two orders of magnitude larger than any in Nature, and facilitates evolution within the chemical spaces they create. This is critical for small molecules, which are built up from numerous and highly varied chemical fragments. We report a proof-of-concept chemical evolution experiment utilizing an outsized genetic code, and demonstrate that fitness traits can be passed from an initial small-molecule population through to the great-grandchildren of that population. The results establish the practical feasibility of engineering synthetic small molecules through accelerated evolution. PMID:27508294
DOE Office of Scientific and Technical Information (OSTI.GOV)

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less
Advanced LIGO constraints on neutron star mergers and r-process sites

DOE PAGES

Côté, Benoit; Belczynski, Krzysztof; Fryer, Chris L.; ...

2017-02-20

The role of compact binary mergers as the main production site of r-process elements is investigated by combining stellar abundances of Eu observed in the Milky Way, galactic chemical evolution (GCE) simulations, and binary population synthesis models, and gravitational wave measurements from Advanced LIGO. We compiled and reviewed seven recent GCE studies to extract the frequency of neutron star–neutron star (NS–NS) mergers that is needed in order to reproduce the observed [Eu/Fe] versus [Fe/H] relationship. We used our simple chemical evolution code to explore the impact of different analytical delay-time distribution functions for NS–NS mergers. We then combined our metallicity-dependent population synthesis models with our chemical evolution code to bring their predictions, for both NS–NS mergers and black hole–neutron star mergers, into a GCE context. Finally, we convolved our results with the cosmic star formation history to provide a direct comparison with current and upcoming Advanced LIGO measurements. When assuming that NS–NS mergers are the exclusive r-process sites, and that the ejected r-process mass per merger event is 0.01 Mmore » $${}_{\\odot }$$, the number of NS–NS mergers needed in GCE studies is about 10 times larger than what is predicted by standard population synthesis models. Here, these two distinct fields can only be consistent with each other when assuming optimistic rates, massive NS–NS merger ejecta, and low Fe yields for massive stars. For now, population synthesis models and GCE simulations are in agreement with the current upper limit (O1) established by Advanced LIGO during their first run of observations. Upcoming measurements will provide an important constraint on the actual local NS–NS merger rate, will provide valuable insights on the plausibility of the GCE requirement, and will help to define whether or not compact binary mergers can be the dominant source of r-process elements in the universe.« less
Conference on Early Mars: Geologic and Hydrologic Evolution, Physical and Chemical Environments, and the Implications for Life

NASA Technical Reports Server (NTRS)

Clifford, S. M. (Editor); Treiman, A. H. (Editor); Newsom, H. E. (Editor); Farmer, J. D. (Editor)

1997-01-01

Topics considered include: Geology alteration and life in an extreme environment; developing a chemical code to identify magnetic biominerals; effect of impacts on early Martin geologic evolution; spectroscopic identification of minerals in Hematite-bearing soils and sediments; exopaleontology and the search for a Fossil record on Mars; geochemical evolution of the crust of Mars; geological evolution of the early earth;solar-wind-induced erosion of the Mars atmosphere. Also included geological evolution of the crust of Mars.
Closed coronal structures. V - Gasdynamic models of flaring loops and comparison with SMM observations

NASA Technical Reports Server (NTRS)

Peres, G.; Serio, S.; Vaiana, G.; Acton, L.; Leibacher, J.; Rosner, R.; Pallavicini, R.

1983-01-01

A time-dependent one-dimensional code incorporating energy, momentum and mass conservation equations, and taking the entire solar atmospheric structure into account, is used to investigate the hydrodynamic response of confined magnetic structures to strong heating perturbations. Model calculation results are compared with flare observations which include the light curves of spectral lines formed over a wide range of coronal flare temperatures, as well as determinations of Doppler shifts for the high temperature plasma. It is shown that the numerical simulation predictions are in good overall agreement with the observed flare coronal plasma evolution, correctly reproducing the temporal profile of X-ray spectral lines and their relative intensities. The predicted upflow velocities support the interpretation of the blueshifts as due to evaporation of chromospheric material.
The complete mitochondrial genome of domestic sheep, Ovis aries.

PubMed

Hu, Xiao-di; Gao, Li-zhi

2016-01-01

In this study, we report a complete mitochondrial (mt) genome sequence of the Texel ewe, Ovis aries. The total genome is 16,615 bp in length and its overall base composition was estimated to be 33.68% for A, 27.36% for T, 25.86% for C, and 13.10% for G indicating an AT-rich (61.04%) feature in the O. aries mtgenome. It contains a total of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and a control region (D-loop region). Comparisons with other publicly available sheep mitogenomes revealed a bunch of nucleotide diversity. This complete mitgenome sequence would enlarge useful genomic information for further studies on sheep evolution and domestication that will enhance germplasm conservation and breeding programs of O. aries.
Biosemiotics: a new understanding of life

NASA Astrophysics Data System (ADS)

Barbieri, Marcello

2008-07-01

Biosemiotics is the idea that life is based on semiosis, i.e., on signs and codes. This idea has been strongly suggested by the discovery of the genetic code, but so far it has made little impact in the scientific world and is largely regarded as a philosophy rather than a science. The main reason for this is that modern biology assumes that signs and meanings do not exist at the molecular level, and that the genetic code was not followed by any other organic code for almost four billion years, which implies that it was an utterly isolated exception in the history of life. These ideas have effectively ruled out the existence of semiosis in the organic world, and yet there are experimental facts against all of them. If we look at the evidence of life without the preconditions of the present paradigm, we discover that semiosis is there, in every single cell, and that it has been there since the very beginning. This is what biosemiotics is really about. It is not a philosophy. It is a new scientific paradigm that is rigorously based on experimental facts. Biosemiotics claims that the genetic code (1) is a real code and (2) has been the first of a long series of organic codes that have shaped the history of life on our planet. The reality of the genetic code and the existence of other organic codes imply that life is based on two fundamental processes—copying and coding—and this in turn implies that evolution took place by two distinct mechanisms, i.e., by natural selection (based on copying) and by natural conventions (based on coding). It also implies that the copying of genes works on individual molecules, whereas the coding of proteins operates on collections of molecules, which means that different mechanisms of evolution exist at different levels of organization. This review intends to underline the scientific nature of biosemiotics, and to this purpose, it aims to prove (1) that the cell is a real semiotic system, (2) that the genetic code is a real code, (3) that evolution took place by natural selection and by natural conventions, and (4) that it was natural conventions, i.e., organic codes, that gave origin to the great novelties of macroevolution. Biological semiosis, in other words, is a scientific reality because the codes of life are experimental realities. The time has come, therefore, to acknowledge this fact of life, even if that means abandoning the present theoretical framework in favor of a more general one where biology and semiotics finally come together and become biosemiotics.
De novo insertion of an intron into the mammalian sex determining gene, SRY

PubMed Central

O’Neill, Rachel J. Waugh; Brennan, Francine E.; Delbridge, Margaret L.; Crozier, Ross H.; Graves, Jennifer A. Marshall

1998-01-01

Two theories have been proposed to explain the evolution of introns within eukaryotic genes. The introns early theory, or “exon theory of genes,” proposes that introns are ancient and that recombination within introns provided new exon structure, and thus new genes. The introns late theory, or “insertional theory of introns,” proposes that ancient genes existed as uninterrupted exons and that introns have been introduced during the course of evolution. There is still controversy as to how intron–exon structure evolved and whether the majority of introns are ancient or novel. Although there is extensive evidence in support of the introns early theory, phylogenetic comparisons of several genes indicate recent gain and loss of introns within these genes. However, no example has been shown of a protein coding gene, intronless in its ancestral form, which has acquired an intron in a derived form. The mammalian sex determining gene, SRY, is intronless in all mammals studied to date, as is the gene from which it recently evolved. However, we report here comparisons of genomic and cDNA sequences that now provide evidence of a de novo insertion of an intron into the SRY gene of dasyurid marsupials. This recently (approximately 45 million years ago) inserted sequence is not homologous with known transposable elements. Our data demonstrate that introns may be inserted as spliced units within a developmentally crucial gene without disrupting its function. PMID:9465071
Retroposed SNOfall--a mammalian-wide comparison of platypus snoRNAs.

PubMed

Schmitz, Jürgen; Zemann, Anja; Churakov, Gennady; Kuhl, Heiner; Grützner, Frank; Reinhardt, Richard; Brosius, Jürgen

2008-06-01

Diversification of mammalian species began more than 160 million years ago when the egg-laying monotremes diverged from live bearing mammals. The duck-billed platypus (Ornithorhynchus anatinus) and echidnas are the only potential contemporary witnesses of this period and, thereby, provide a unique insight into mammalian genome evolution. It has become clear that small RNAs are major regulatory agents in eukaryotic cells, and the significant role of non-protein-coding (npc) RNAs in transcription, processing, and translation is now well accepted. Here we show that the platypus genome contains more than 200 small nucleolar (sno) RNAs among hundreds of other diverse npcRNAs. Their comparison among key mammalian groups and other vertebrates enabled us to reconstruct a complete temporal pathway of acquisition and loss of these snoRNAs. In platypus we found cis- and trans-duplication distribution patterns for snoRNAs, which have not been described in any other vertebrates but are known to occur in nematodes. An exciting novelty in platypus is a snoRNA-derived retroposon (termed snoRTE) that facilitates a very effective dispersal of an H/ACA snoRNA via RTE-mediated retroposition. From more than 40,000 detected full-length and truncated genomic copies of this snoRTE, at least 21 are processed into mature snoRNAs. High-copy retroposition via multiple host gene-promoted transcription units is a novel pathway for combining housekeeping function and SINE-like dispersal and reveals a new dimension in the evolution of novel snoRNA function.
Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs

PubMed Central

Schmitz, Jürgen; Zemann, Anja; Churakov, Gennady; Kuhl, Heiner; Grützner, Frank; Reinhardt, Richard; Brosius, Jürgen

2008-01-01

Diversification of mammalian species began more than 160 million years ago when the egg-laying monotremes diverged from live bearing mammals. The duck-billed platypus (Ornithorhynchus anatinus) and echidnas are the only potential contemporary witnesses of this period and, thereby, provide a unique insight into mammalian genome evolution. It has become clear that small RNAs are major regulatory agents in eukaryotic cells, and the significant role of non-protein-coding (npc) RNAs in transcription, processing, and translation is now well accepted. Here we show that the platypus genome contains more than 200 small nucleolar (sno) RNAs among hundreds of other diverse npcRNAs. Their comparison among key mammalian groups and other vertebrates enabled us to reconstruct a complete temporal pathway of acquisition and loss of these snoRNAs. In platypus we found cis- and trans-duplication distribution patterns for snoRNAs, which have not been described in any other vertebrates but are known to occur in nematodes. An exciting novelty in platypus is a snoRNA-derived retroposon (termed snoRTE) that facilitates a very effective dispersal of an H/ACA snoRNA via RTE-mediated retroposition. From more than 40,000 detected full-length and truncated genomic copies of this snoRTE, at least 21 are processed into mature snoRNAs. High-copy retroposition via multiple host gene-promoted transcription units is a novel pathway for combining housekeeping function and SINE-like dispersal and reveals a new dimension in the evolution of novel snoRNA function. PMID:18463303
Analysis of Complete Nucleotide Sequences of 12 Gossypium Chloroplast Genomes: Origin and Evolution of Allotetraploids

PubMed Central

Xu, Qin; Xiong, Guanjun; Li, Pengbo; He, Fei; Huang, Yi; Wang, Kunbo; Li, Zhaohu; Hua, Jinping

2012-01-01

Background Cotton (Gossypium spp.) is a model system for the analysis of polyploidization. Although ascertaining the donor species of allotetraploid cotton has been intensively studied, sequence comparison of Gossypium chloroplast genomes is still of interest to understand the mechanisms underlining the evolution of Gossypium allotetraploids, while it is generally accepted that the parents were A- and D-genome containing species. Here we performed a comparative analysis of 13 Gossypium chloroplast genomes, twelve of which are presented here for the first time. Methodology/Principal Findings The size of 12 chloroplast genomes under study varied from 159,959 bp to 160,433 bp. The chromosomes were highly similar having >98% sequence identity. They encoded the same set of 112 unique genes which occurred in a uniform order with only slightly different boundary junctions. Divergence due to indels as well as substitutions was examined separately for genome, coding and noncoding sequences. The genome divergence was estimated as 0.374% to 0.583% between allotetraploid species and A-genome, and 0.159% to 0.454% within allotetraploids. Forty protein-coding genes were completely identical at the protein level, and 20 intergenic sequences were completely conserved. The 9 allotetraploids shared 5 insertions and 9 deletions in whole genome, and 7-bp substitutions in protein-coding genes. The phylogenetic tree confirmed a close relationship between allotetraploids and the ancestor of A-genome, and the allotetraploids were divided into four separate groups. Progenitor allotetraploid cotton originated 0.43–0.68 million years ago (MYA). Conclusion Despite high degree of conservation between the Gossypium chloroplast genomes, sequence variations among species could still be detected. Gossypium chloroplast genomes preferred for 5-bp indels and 1–3-bp indels are mainly attributed to the SSR polymorphisms. This study supports that the common ancestor of diploid A-genome species in Gossypium is the maternal source of extant allotetraploid species and allotetraploids have a monophyletic origin. G. hirsutum AD1 lineages have experienced more sequence variations than other allotetraploids in intergenic regions. The available complete nucleotide sequences of 12 Gossypium chloroplast genomes should facilitate studies to uncover the molecular mechanisms of compartmental co-evolution and speciation of Gossypium allotetraploids. PMID:22876273
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence.

PubMed

Kim, Dong Seon; Hahn, Yoonsoo

2012-11-13

Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution.
The Coding of Biological Information: From Nucleotide Sequence to Protein Recognition

NASA Astrophysics Data System (ADS)

Štambuk, Nikola

The paper reviews the classic results of Swanson, Dayhoff, Grantham, Blalock and Root-Bernstein, which link genetic code nucleotide patterns to the protein structure, evolution and molecular recognition. Symbolic representation of the binary addresses defining particular nucleotide and amino acid properties is discussed, with consideration of: structure and metric of the code, direct correspondence between amino acid and nucleotide information, and molecular recognition of the interacting protein motifs coded by the complementary DNA and RNA strands.
Comparison of Measured and Block Structured Simulations for the F-16XL Aircraft

NASA Technical Reports Server (NTRS)

Boelens, O. J.; Badcock, K. J.; Elmilgui, A.; Abdol-Hamid, K. S.; Massey, S. J.

2008-01-01

This article presents a comparison of the predictions of three RANS codes for flight conditions of the F-16XL aircraft which feature vortical flow. The three codes, ENSOLV, PMB and PAB3D, solve on structured multi-block grids. Flight data for comparison was available in the form of surface pressures, skin friction, boundary layer data and photographs of tufts. The three codes provided predictions which were consistent with expectations based on the turbulence modelling used, which was k- , k- with vortex corrections and an Algebraic Stress Model. The agreement with flight data was good, with the exception of the outer wing primary vortex strength. The confidence in the application of the CFD codes to complex fighter configurations increased significantly through this study.
Saturation of recognition elements blocks evolution of new tRNA identities

PubMed Central

Saint-Léger, Adélaïde; Bello, Carla; Dans, Pablo D.; Torres, Adrian Gabriel; Novoa, Eva Maria; Camacho, Noelia; Orozco, Modesto; Kondrashov, Fyodor A.; Ribas de Pouplana, Lluís

2016-01-01

Understanding the principles that led to the current complexity of the genetic code is a central question in evolution. Expansion of the genetic code required the selection of new transfer RNAs (tRNAs) with specific recognition signals that allowed them to be matured, modified, aminoacylated, and processed by the ribosome without compromising the fidelity or efficiency of protein synthesis. We show that saturation of recognition signals blocks the emergence of new tRNA identities and that the rate of nucleotide substitutions in tRNAs is higher in species with fewer tRNA genes. We propose that the growth of the genetic code stalled because a limit was reached in the number of identity elements that can be effectively used in the tRNA structure. PMID:27386510
History of the Nuclei Important for Cosmochemistry

NASA Technical Reports Server (NTRS)

Meyer, Bradley S.

2004-01-01

An essential aspect of studying the nuclei important for cosmochemistry is their production in stars. Over the grant period, we have further developed the Clemson/American University of Beirut stellar evolution code. Through use of a biconjugate-gradient matrix solver, we now routinely solve l0(exp 6) x l0(exp 6) sparse matrices on our desktop computers. This has allowed us to couple nucleosynthesis and convection fully in the 1-D star, which, in turn, provides better estimates of nuclear yields when the mixing and nuclear burning timescales are comparable. We also have incorporated radiation transport into our 1-D supernova explosion code. We used the stellar evolution and explosion codes to compute iron abundances in a 25 Solar mass star and compared the results to data from RIMS.
Post-Newtonian Dynamical Modeling of Supermassive Black Holes in Galactic-scale Simulations

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

Rantala, Antti; Pihajoki, Pauli; Johansson, Peter H.

We present KETJU, a new extension of the widely used smoothed particle hydrodynamics simulation code GADGET-3. The key feature of the code is the inclusion of algorithmically regularized regions around every supermassive black hole (SMBH). This allows for simultaneously following global galactic-scale dynamical and astrophysical processes, while solving the dynamics of SMBHs, SMBH binaries, and surrounding stellar systems at subparsec scales. The KETJU code includes post-Newtonian terms in the equations of motions of the SMBHs, which enables a new SMBH merger criterion based on the gravitational wave coalescence timescale, pushing the merger separation of SMBHs down to ∼0.005 pc. Wemore » test the performance of our code by comparison to NBODY7 and rVINE. We set up dynamically stable multicomponent merger progenitor galaxies to study the SMBH binary evolution during galaxy mergers. In our simulation sample the SMBH binaries do not suffer from the final-parsec problem, which we attribute to the nonspherical shape of the merger remnants. For bulge-only models, the hardening rate decreases with increasing resolution, whereas for models that in addition include massive dark matter halos, the SMBH binary hardening rate becomes practically independent of the mass resolution of the stellar bulge. The SMBHs coalesce on average 200 Myr after the formation of the SMBH binary. However, small differences in the initial SMBH binary eccentricities can result in large differences in the SMBH coalescence times. Finally, we discuss the future prospects of KETJU, which allows for a straightforward inclusion of gas physics in the simulations.« less
When Homoplasy Is Not Homoplasy: Dissecting Trait Evolution by Contrasting Composite and Reductive Coding.

PubMed

Torres-Montúfar, Alejandro; Borsch, Thomas; Ochoterena, Helga

2018-05-01

The conceptualization and coding of characters is a difficult issue in phylogenetic systematics, no matter which inference method is used when reconstructing phylogenetic trees or if the characters are just mapped onto a specific tree. Complex characters are groups of features that can be divided into simpler hierarchical characters (reductive coding), although the implied hierarchical relational information may change depending on the type of coding (composite vs. reductive). Up to now, there is no common agreement to either code characters as complex or simple. Phylogeneticists have discussed which coding method is best but have not incorporated the heuristic process of reciprocal illumination to evaluate the coding. Composite coding allows to test whether 1) several characters were linked resulting in a structure described as a complex character or trait or 2) independently evolving characters resulted in the configuration incorrectly interpreted as a complex character. We propose that complex characters or character states should be decomposed iteratively into simpler characters when the original homology hypothesis is not corroborated by a phylogenetic analysis, and the character or character state is retrieved as homoplastic. We tested this approach using the case of fruit types within subfamily Cinchonoideae (Rubiaceae). The iterative reductive coding of characters associated with drupes allowed us to unthread fruit evolution within Cinchonoideae. Our results show that drupes and berries are not homologous. As a consequence, a more precise ontology for the Cinchonoideae drupes is required.
The trellis complexity of convolutional codes

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Lin, W.

1995-01-01

It has long been known that convolutional codes have a natural, regular trellis structure that facilitates the implementation of Viterbi's algorithm. It has gradually become apparent that linear block codes also have a natural, though not in general a regular, 'minimal' trellis structure, which allows them to be decoded with a Viterbi-like algorithm. In both cases, the complexity of the Viterbi decoding algorithm can be accurately estimated by the number of trellis edges per encoded bit. It would, therefore, appear that we are in a good position to make a fair comparison of the Viterbi decoding complexity of block and convolutional codes. Unfortunately, however, this comparison is somewhat muddled by the fact that some convolutional codes, the punctured convolutional codes, are known to have trellis representations that are significantly less complex than the conventional trellis. In other words, the conventional trellis representation for a convolutional code may not be the minimal trellis representation. Thus, ironically, at present we seem to know more about the minimal trellis representation for block than for convolutional codes. In this article, we provide a remedy, by developing a theory of minimal trellises for convolutional codes. (A similar theory has recently been given by Sidorenko and Zyablov). This allows us to make a direct performance-complexity comparison for block and convolutional codes. A by-product of our work is an algorithm for choosing, from among all generator matrices for a given convolutional code, what we call a trellis-minimal generator matrix, from which the minimal trellis for the code can be directly constructed. Another by-product is that, in the new theory, punctured convolutional codes no longer appear as a special class, but simply as high-rate convolutional codes whose trellis complexity is unexpectedly small.
An Efficient Method for Verifying Gyrokinetic Microstability Codes

NASA Astrophysics Data System (ADS)

Bravenec, R.; Candy, J.; Dorland, W.; Holland, C.

2009-11-01

Benchmarks for gyrokinetic microstability codes can be developed through successful ``apples-to-apples'' comparisons among them. Unlike previous efforts, we perform the comparisons for actual discharges, rendering the verification efforts relevant to existing experiments and future devices (ITER). The process requires i) assembling the experimental analyses at multiple times, radii, discharges, and devices, ii) creating the input files ensuring that the input parameters are faithfully translated code-to-code, iii) running the codes, and iv) comparing the results, all in an organized fashion. The purpose of this work is to automate this process as much as possible: At present, a python routine is used to generate and organize GYRO input files from TRANSP or ONETWO analyses. Another routine translates the GYRO input files into GS2 input files. (Translation software for other codes has not yet been written.) Other python codes submit the multiple GYRO and GS2 jobs, organize the results, and collect them into a table suitable for plotting. (These separate python routines could easily be consolidated.) An example of the process -- a linear comparison between GYRO and GS2 for a DIII-D discharge at multiple radii -- will be presented.

Exploring the read-write genome: mobile DNA and mammalian adaptation.

PubMed

Shapiro, James A

2017-02-01

The read-write genome idea predicts that mobile DNA elements will act in evolution to generate adaptive changes in organismal DNA. This prediction was examined in the context of mammalian adaptations involving regulatory non-coding RNAs, viviparous reproduction, early embryonic and stem cell development, the nervous system, and innate immunity. The evidence shows that mobile elements have played specific and sometimes major roles in mammalian adaptive evolution by generating regulatory sites in the DNA and providing interaction motifs in non-coding RNA. Endogenous retroviruses and retrotransposons have been the predominant mobile elements in mammalian adaptive evolution, with the notable exception of bats, where DNA transposons are the major agents of RW genome inscriptions. A few examples of independent but convergent exaptation of mobile DNA elements for similar regulatory rewiring functions are noted.
Comparison of DAC and MONACO DSMC Codes with Flat Plate Simulation

NASA Technical Reports Server (NTRS)

Padilla, Jose F.

2010-01-01

Various implementations of the direct simulation Monte Carlo (DSMC) method exist in academia, government and industry. By comparing implementations, deficiencies and merits of each can be discovered. This document reports comparisons between DSMC Analysis Code (DAC) and MONACO. DAC is NASA's standard DSMC production code and MONACO is a research DSMC code developed in academia. These codes have various differences; in particular, they employ distinct computational grid definitions. In this study, DAC and MONACO are compared by having each simulate a blunted flat plate wind tunnel test, using an identical volume mesh. Simulation expense and DSMC metrics are compared. In addition, flow results are compared with available laboratory data. Overall, this study revealed that both codes, excluding grid adaptation, performed similarly. For parallel processing, DAC was generally more efficient. As expected, code accuracy was mainly dependent on physical models employed.
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.
Genomic suppression subtractive hybridization as a tool to identify differences in mycorrhizal fungal genomes.

PubMed

Murat, Claude; Zampieri, Elisa; Vallino, Marta; Daghino, Stefania; Perotto, Silvia; Bonfante, Paola

2011-05-01

Characterization of genomic variation among different microbial species, or different strains of the same species, is a field of significant interest with a wide range of potential applications. We have investigated the genomic variation in mycorrhizal fungal genomes through genomic suppressive subtractive hybridization. The comparison was between phylogenetically distant and close truffle species (Tuber spp.), and between isolates of the ericoid mycorrhizal fungus Oidiodendron maius featuring different degrees of metal tolerance. In the interspecies experiment, almost all the sequences that were identified in the Tuber melanosporum genome and absent in Tuber borchii and Tuber indicum corresponded to transposable elements. In the intraspecies comparison, some specific sequences corresponded to regions coding for enzymes, among them a glutathione synthetase known to be involved in metal tolerance. This approach is a quick and rather inexpensive tool to develop molecular markers for mycorrhizal fungi tracking and barcoding, to identify functional genes and to investigate the genome plasticity, adaptation and evolution. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.
First light with Trident: multi-platform synthetic quasar spectra

NASA Astrophysics Data System (ADS)

Silvia, Devin W.; Hummels, Cameron B.; Smith, Britton

2017-01-01

Observational efforts to better understand the nature of the intergalactic and circumgalactic media have relied heavily on the information encoded in the absorption line systems of quasar spectra. Numerical simulations of large-scale structure and galaxy evolution are well-suited to explore the properties of those same media owing to the relative ease with which one can access physical quantities from complex, three-dimensional data. However, a difficulty arises when one tries to make direct “apple-to-apples” comparisons between observed spectra and simulated data. In an effort to provide a common language capable of linking theory and observation, we announce the release of Trident. Trident is a publicly available software tool that enables the creation of realistic synthetic absorption spectra from virtually all widely-used hydrodynamics simulation codes. Through user-controlled levels of spectral realism, direct comparisons between simulated and observed data become not only possible, but greatly simplified. We present the methods for extracting artificial quasar sightlines and generating spectra as well as early-stage applications of those spectra to intergalactic and circumgalactic absorption line studies.
Comparisons of 'Identical' Simulations by the Eulerian Gyrokinetic Codes GS2 and GYRO

NASA Astrophysics Data System (ADS)

Bravenec, R. V.; Ross, D. W.; Candy, J.; Dorland, W.; McKee, G. R.

2003-10-01

A major goal of the fusion program is to be able to predict tokamak transport from first-principles theory. To this end, the Eulerian gyrokinetic code GS2 was developed years ago and continues to be improved [1]. Recently, the Eulerian code GYRO was developed [2]. These codes are not subject to the statistical noise inherent to particle-in-cell (PIC) codes, and have been very successful in treating electromagnetic fluctuations. GS2 is fully spectral in the radial coordinate while GYRO uses finite-differences and ``banded" spectral schemes. To gain confidence in nonlinear simulations of experiment with these codes, ``apples-to-apples" comparisons (identical profile inputs, flux-tube geometry, two species, etc.) are first performed. We report on a series of linear and nonlinear comparisons (with overall agreement) including kinetic electrons, collisions, and shaped flux surfaces. We also compare nonlinear simulations of a DIII-D discharge to measurements of not only the fluxes but also the turbulence parameters. [1] F. Jenko, et al., Phys. Plasmas 7, 1904 (2000) and refs. therein. [2] J. Candy, J. Comput. Phys. 186, 545 (2003).
THE EVOLUTION OF SOLAR FLUX FROM 0.1 nm TO 160 {mu}m: QUANTITATIVE ESTIMATES FOR PLANETARY STUDIES

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

Claire, Mark W.; Sheets, John; Meadows, Victoria S.

2012-09-20

Understanding changes in the solar flux over geologic time is vital for understanding the evolution of planetary atmospheres because it affects atmospheric escape and chemistry, as well as climate. We describe a numerical parameterization for wavelength-dependent changes to the non-attenuated solar flux appropriate for most times and places in the solar system. We combine data from the Sun and solar analogs to estimate enhanced UV and X-ray fluxes for the young Sun and use standard solar models to estimate changing visible and infrared fluxes. The parameterization, a series of multipliers relative to the modern top of the atmosphere flux atmore » Earth, is valid from 0.1 nm through the infrared, and from 0.6 Gyr through 6.7 Gyr, and is extended from the solar zero-age main sequence to 8.0 Gyr subject to additional uncertainties. The parameterization is applied to a representative modern day flux, providing quantitative estimates of the wavelength dependence of solar flux for paleodates relevant to the evolution of atmospheres in the solar system (or around other G-type stars). We validate the code by Monte Carlo analysis of uncertainties in stellar age and flux, and with comparisons to the solar proxies {kappa}{sup 1} Cet and EK Dra. The model is applied to the computation of photolysis rates on the Archean Earth.« less
Contamination of RR Lyrae stars from Binary Evolution Pulsators

NASA Astrophysics Data System (ADS)

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

2016-06-01

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

ERIC Educational Resources Information Center

Almquist, Alan J.; Cronin, John E.

This Chautauqua-type short course in human evolution is divided into two parts: The Biochemical Evidence for Human Evolution, and the Fossil Evidence for Human Evolution. The first part covers the comparison of macromolecular differences between species. This includes comparison of DNA base-ratios and amino acid substitution in enzymes and other…
A validation of LTRAN2 with high frequency extensions by comparisons with experimental measurements of unsteady transonic flows

NASA Technical Reports Server (NTRS)

Hessenius, K. A.; Goorjian, P. M.

1981-01-01

A high frequency extension of the unsteady, transonic code LTRAN2 was created and is evaluated by comparisons with experimental results. The experimental test case is a NACA 64A010 airfoil in pitching motion at a Mach number of 0.8 over a range of reduced frequencies. Comparisons indicate that the modified code is an improvement of the original LTRAN2 and provides closer agreement with experimental lift and moment coefficients. A discussion of the code modifications, which involve the addition of high frequency terms of the boundary conditions of the numerical algorithm, is included.
Comparison of two- and three-dimensional flow computations with laser anemometer measurements in a transonic compressor rotor

NASA Technical Reports Server (NTRS)

Chima, R. V.; Strazisar, A. J.

1982-01-01

Two and three dimensional inviscid solutions for the flow in a transonic axial compressor rotor at design speed are compared with probe and laser anemometers measurements at near-stall and maximum-flow operating points. Experimental details of the laser anemometer system and computational details of the two dimensional axisymmetric code and three dimensional Euler code are described. Comparisons are made between relative Mach number and flow angle contours, shock location, and shock strength. A procedure for using an efficient axisymmetric code to generate downstream pressure input for computationally expensive Euler codes is discussed. A film supplement shows the calculations of the two operating points with the time-marching Euler code.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.

PubMed

2004-12-09

We present here a draft genome sequence of the red jungle fowl, Gallus gallus. Because the chicken is a modern descendant of the dinosaurs and the first non-mammalian amniote to have its genome sequenced, the draft sequence of its genome--composed of approximately one billion base pairs of sequence and an estimated 20,000-23,000 genes--provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes. For example, the evolutionary distance between chicken and human provides high specificity in detecting functional elements, both non-coding and coding. Notably, many conserved non-coding sequences are far from genes and cannot be assigned to defined functional classes. In coding regions the evolutionary dynamics of protein domains and orthologous groups illustrate processes that distinguish the lineages leading to birds and mammals. The distinctive properties of avian microchromosomes, together with the inferred patterns of conserved synteny, provide additional insights into vertebrate chromosome architecture.
Complete genome sequencing of the luminescent bacterium, Vibrio qinghaiensis sp. Q67 using PacBio technology

NASA Astrophysics Data System (ADS)

Gong, Liang; Wu, Yu; Jian, Qijie; Yin, Chunxiao; Li, Taotao; Gupta, Vijai Kumar; Duan, Xuewu; Jiang, Yueming

2018-01-01

Vibrio qinghaiensis sp.-Q67 (Vqin-Q67) is a freshwater luminescent bacterium that continuously emits blue-green light (485 nm). The bacterium has been widely used for detecting toxic contaminants. Here, we report the complete genome sequence of Vqin-Q67, obtained using third-generation PacBio sequencing technology. Continuous long reads were attained from three PacBio sequencing runs and reads >500 bp with a quality value of >0.75 were merged together into a single dataset. This resultant highly-contiguous de novo assembly has no genome gaps, and comprises two chromosomes with substantial genetic information, including protein-coding genes, non-coding RNA, transposon and gene islands. Our dataset can be useful as a comparative genome for evolution and speciation studies, as well as for the analysis of protein-coding gene families, the pathogenicity of different Vibrio species in fish, the evolution of non-coding RNA and transposon, and the regulation of gene expression in relation to the bioluminescence of Vqin-Q67.
Studies of Planet Formation Using a Hybrid N-Body + Planetesimal Code

NASA Technical Reports Server (NTRS)

Kenyon, Scott J.

2004-01-01

The goal of our proposal was to use a hybrid multi-annulus planetesimal/n-body code to examine the planetesimal theory, one of the two main theories of planet formation. We developed this code to follow the evolution of numerous 1 m to 1 km planetesimals as they collide, merge, and grow into full-fledged planets. Our goal was to apply the code to several well-posed, topical problems in planet formation and to derive observational consequences of the models. We planned to construct detailed models to address two fundamental issues: (1) icy planets: models for icy planet formation will demonstrate how the physical properties of debris disks - including the Kuiper Belt in our solar system - depend on initial conditions and input physics; and (2) terrestrial planets: calculations following the evolution of 1-10 km planetesimals into Earth-mass planets and rings of dust will provide a better understanding of how terrestrial planets form and interact with their environment.
There is no MacWilliams identity for convolutional codes. [transmission gain comparison

NASA Technical Reports Server (NTRS)

Shearer, J. B.; Mceliece, R. J.

1977-01-01

An example is provided of two convolutional codes that have the same transmission gain but whose dual codes do not. This shows that no analog of the MacWilliams identity for block codes can exist relating the transmission gains of a convolutional code and its dual.
Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1991-01-01

Shannon's capacity bound shows that coding can achieve large reductions in the required signal to noise ratio per information bit (E sub b/N sub 0 where E sub b is the energy per bit and (N sub 0)/2 is the double sided noise density) in comparison to uncoded schemes. For bandwidth efficiencies of 2 bit/sym or greater, these improvements were obtained through the use of Trellis Coded Modulation and Block Coded Modulation. A method of obtaining these high efficiencies using multidimensional Multiple Phase Shift Keying (MPSK) and Quadrature Amplitude Modulation (QAM) signal sets with trellis coding is described. These schemes have advantages in decoding speed, phase transparency, and coding gain in comparison to other trellis coding schemes. Finally, a general parity check equation for rotationally invariant trellis codes is introduced from which non-linear codes for two dimensional MPSK and QAM signal sets are found. These codes are fully transparent to all rotations of the signal set.
PFLOTRAN-RepoTREND Source Term Comparison Summary.

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

Frederick, Jennifer M.

Code inter-comparison studies are useful exercises to verify and benchmark independently developed software to ensure proper function, especially when the software is used to model high-consequence systems which cannot be physically tested in a fully representative environment. This summary describes the results of the first portion of the code inter-comparison between PFLOTRAN and RepoTREND, which compares the radionuclide source term used in a typical performance assessment.
Process and metaphors in the evolutionary paradigm

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

Ho, M.; Fox, S

1988-01-01

Presents thinking on the processes and interpretation of biological evolution, emphasizing the study of biological processes as they occur in living organisms and their communities, rather than through mechanical or statistical models. Contributors explore processes and metaphors in evolution, the origin of the genetic code, new genetic mechanisms and their implications for the formation of new species, panbiogeography, the active role of behavior in evolution, sociobiology, and more.
Targeted Sequencing of Venom Genes from Cone Snail Genomes Improves Understanding of Conotoxin Molecular Evolution

PubMed Central

Mahardika, Gusti N

2018-01-01

Abstract To expand our capacity to discover venom sequences from the genomes of venomous organisms, we applied targeted sequencing techniques to selectively recover venom gene superfamilies and nontoxin loci from the genomes of 32 cone snail species (family, Conidae), a diverse group of marine gastropods that capture their prey using a cocktail of neurotoxic peptides (conotoxins). We were able to successfully recover conotoxin gene superfamilies across all species with high confidence (> 100× coverage) and used these data to provide new insights into conotoxin evolution. First, we found that conotoxin gene superfamilies are composed of one to six exons and are typically short in length (mean = ∼85 bp). Second, we expanded our understanding of the following genetic features of conotoxin evolution: 1) positive selection, where exons coding the mature toxin region were often three times more divergent than their adjacent noncoding regions, 2) expression regulation, with comparisons to transcriptome data showing that cone snails only express a fraction of the genes available in their genome (24–63%), and 3) extensive gene turnover, where Conidae species varied from 120 to 859 conotoxin gene copies. Finally, using comparative phylogenetic methods, we found that while diet specificity did not predict patterns of conotoxin evolution, dietary breadth was positively correlated with total conotoxin gene diversity. Overall, the targeted sequencing technique demonstrated here has the potential to radically increase the pace at which venom gene families are sequenced and studied, reshaping our ability to understand the impact of genetic changes on ecologically relevant phenotypes and subsequent diversification. PMID:29514313

No cataclysmic variables missing: higher merger rate brings into agreement observed and predicted space densities

NASA Astrophysics Data System (ADS)

Belloni, Diogo; Schreiber, Matthias R.; Zorotovic, Mónica; Iłkiewicz, Krystian; Hurley, Jarrod R.; Giersz, Mirek; Lagos, Felipe

2018-06-01

The predicted and observed space density of cataclysmic variables (CVs) have been for a long time discrepant by at least an order of magnitude. The standard model of CV evolution predicts that the vast majority of CVs should be period bouncers, whose space density has been recently measured to be ρ ≲ 2 × 10-5 pc-3. We performed population synthesis of CVs using an updated version of the Binary Stellar Evolution (BSE) code for single and binary star evolution. We find that the recently suggested empirical prescription of consequential angular momentum loss (CAML) brings into agreement predicted and observed space densities of CVs and period bouncers. To progress with our understanding of CV evolution it is crucial to understand the physical mechanism behind empirical CAML. Our changes to the BSE code are also provided in details, which will allow the community to accurately model mass transfer in interacting binaries in which degenerate objects accrete from low-mass main-sequence donor stars.
Numerical modelling of the Madison Dynamo Experiment.

NASA Astrophysics Data System (ADS)

Bayliss, R. A.; Wright, J. C.; Forest, C. B.; O'Connell, R.; Truitt, J. L.

2000-10-01

Growth, saturation and turbulent evolution of the Madison dynamo experiment is investigated numerically using a newly developed 3-D pseudo-spectral simulation of the MHD equations; results of the simulations will be compared to the experimental results obtained from the experiment. The code, Dynamo, is in Fortran90 and allows for full evolution of the magnetic and velocity fields. The induction equation governing B and the Navier-Stokes equation governing V are solved. The code uses a spectral representation via spherical harmonic basis functions of the vector fields in longitude and latitude, and finite differences in the radial direction. The magnetic field evolution has been benchmarked against the laminar kinematic dynamo predicted by M.L. Dudley and R.W. James (M.L. Dudley and R.W. James, Time-dependant kinematic dynamos with stationary flows, Proc. R. Soc. Lond. A 425, p. 407 (1989)). Initial results on magnetic field saturation, generated by the simultaneous evolution of magnetic and velocity fields be presented using a variety of mechanical forcing terms.
Validation of the analytical methods in the LWR code BOXER for gadolinium-loaded fuel pins

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

Paratte, J.M.; Arkuszewski, J.J.; Kamboj, B.K.

1990-01-01

Due to the very high absorption occurring in gadolinium-loaded fuel pins, calculations of lattices with such pins present are a demanding test of the analysis methods in light water reactor (LWR) cell and assembly codes. Considerable effort has, therefore, been devoted to the validation of code methods for gadolinia fuel. The goal of the work reported in this paper is to check the analysis methods in the LWR cell/assembly code BOXER and its associated cross-section processing code ETOBOX, by comparison of BOXER results with those from a very accurate Monte Carlo calculation for a gadolinium benchmark problem. Initial results ofmore » such a comparison have been previously reported. However, the Monte Carlo calculations, done with the MCNP code, were performed at Los Alamos National Laboratory using ENDF/B-V data, while the BOXER calculations were performed at the Paul Scherrer Institute using JEF-1 nuclear data. This difference in the basic nuclear data used for the two calculations, caused by the restricted nature of these evaluated data files, led to associated uncertainties in a comparison of the results for methods validation. In the joint investigations at the Georgia Institute of Technology and PSI, such uncertainty in this comparison was eliminated by using ENDF/B-V data for BOXER calculations at Georgia Tech.« less
Wavelet subband coding of computer simulation output using the A++ array class library

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

Bradley, J.N.; Brislawn, C.M.; Quinlan, D.J.

1995-07-01

The goal of the project is to produce utility software for off-line compression of existing data and library code that can be called from a simulation program for on-line compression of data dumps as the simulation proceeds. Naturally, we would like the amount of CPU time required by the compression algorithm to be small in comparison to the requirements of typical simulation codes. We also want the algorithm to accomodate a wide variety of smooth, multidimensional data types. For these reasons, the subband vector quantization (VQ) approach employed in has been replaced by a scalar quantization (SQ) strategy using amore » bank of almost-uniform scalar subband quantizers in a scheme similar to that used in the FBI fingerprint image compression standard. This eliminates the considerable computational burdens of training VQ codebooks for each new type of data and performing nearest-vector searches to encode the data. The comparison of subband VQ and SQ algorithms in indicated that, in practice, there is relatively little additional gain from using vector as opposed to scalar quantization on DWT subbands, even when the source imagery is from a very homogeneous population, and our subjective experience with synthetic computer-generated data supports this stance. It appears that a careful study is needed of the tradeoffs involved in selecting scalar vs. vector subband quantization, but such an analysis is beyond the scope of this paper. Our present work is focused on the problem of generating wavelet transform/scalar quantization (WSQ) implementations that can be ported easily between different hardware environments. This is an extremely important consideration given the great profusion of different high-performance computing architectures available, the high cost associated with learning how to map algorithms effectively onto a new architecture, and the rapid rate of evolution in the world of high-performance computing.« less
Comparison of 2-3D convection models with parameterized thermal evolution models: Application to Mars

NASA Astrophysics Data System (ADS)

Thiriet, M.; Plesa, A. C.; Breuer, D.; Michaut, C.

2017-12-01

To model the thermal evolution of terrestrial planets, 1D parametrized models are often used as 2 or 3D mantle convection codes are very time-consuming. In these parameterized models, scaling laws that describe the convective heat transfer rate as a function of the convective parameters are derived from 2-3D steady state convection models. However, so far there has been no comprehensive comparison whether they can be applied to model the thermal evolution of a cooling planet. Here we compare 2D and 3D thermal evolution models in the stagnant lid regime with 1D parametrized models and use parameters representing the cooling of the Martian mantle. For the 1D parameterized models, we use the approach of Grasset and Parmentier (1998) and treat the stagnant lid and the convecting layer separately. In the convecting layer, the scaling law for a fluid with constant viscosity is valid with Nu (Ra/Rac) ?, with Rac the critical Rayleigh number at which the thermal boundary layers (TBL) - top or bottom - destabilize. ? varies between 1/3 and 1/4 depending on the heating mode and previous studies have proposed intermediate values of b 0.28-0.32 according to their model set-up. The base of the stagnant lid is defined by the temperature at which the mantle viscosity has increased by a factor of 10; it thus depends on the rate of viscosity change with temperature multiplied by a factor? , whose value appears to vary depending on the geometry and convection conditions. In applying Monte Carlo simulations, we search for the best fit to temperature profiles and heat flux using three free parameters, i.e. ? of the upper TBL, ? and the Rac of the lower TBL. We find that depending on the definition of the stagnant lid thickness in the 2-3D models several combinations of ? and ? for the upper TBL can retrieve suitable fits. E.g. combinations of ? = 0.329 and ? = 2.19 but also ? = 0.295 and ? = 2.97 are possible; Rac of the lower TBL is 10 for all best fits. The results show that although the heating conditions change from bottom to mainly internally heating as a function of time, the thermal evolution can be represented by one set of parameters.
GRABGAM Analysis of Ultra-Low-Level HPGe Gamma Spectra

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

Winn, W.G.

The GRABGAM code has been used successfully for ultra-low level HPGe gamma spectrometry analysis since its development in 1985 at Savannah River Technology Center (SRTC). Although numerous gamma analysis codes existed at that time, reviews of institutional and commercial codes indicated that none addressed all features that were desired by SRTC. Furthermore, it was recognized that development of an in-house code would better facilitate future evolution of the code to address SRTC needs based on experience with low-level spectra. GRABGAM derives its name from Gamma Ray Analysis BASIC Generated At MCA/PC.
Utilitarianism and the evolution of ecological ethics.

PubMed

Varner, Gary

2008-12-01

R.M. Hare's two-level utilitarianism provides a useful framework for understanding the evolution of codes of professional ethics. From a Harean perspective, the codes reflect both the fact that members of various professions face special kinds of ethically charged situations in the normal course of their work, and the need for people in special roles to acquire various habits of thought and action. This highlights the role of virtue in professional ethics and provides guidance to professional societies when considering modifications to their codes. From a Harean perspective, a professional society should ask both "Are there kinds of situations that members of this profession will normally encounter which members of other professions and/or the general public will not?" and "What habits of thought and action would it be good for individuals encountering such situations to have?"
A Dancing Black Hole

NASA Astrophysics Data System (ADS)

Shoemaker, Deirdre; Smith, Kenneth; Schnetter, Erik; Fiske, David; Laguna, Pablo; Pullin, Jorge

2002-04-01

Recently, stationary black holes have been successfully simulated for up to times of approximately 600-1000M, where M is the mass of the black hole. Considering that the expected burst of gravitational radiation from a binary black hole merger would last approximately 200-500M, black hole codes are approaching the point where simulations of mergers may be feasible. We will present two types of simulations of single black holes obtained with a code based on the Baumgarte-Shapiro-Shibata-Nakamura formulation of the Einstein evolution equations. One type of simulations addresses the stability properties of stationary black hole evolutions. The second type of simulations demonstrates the ability of our code to move a black hole through the computational domain. This is accomplished by shifting the stationary black hole solution to a coordinate system in which the location of the black hole is time dependent.
ASTEC—the Aarhus STellar Evolution Code

NASA Astrophysics Data System (ADS)

Christensen-Dalsgaard, Jørgen

2008-08-01

The Aarhus code is the result of a long development, starting in 1974, and still ongoing. A novel feature is the integration of the computation of adiabatic oscillations for specified models as part of the code. It offers substantial flexibility in terms of microphysics and has been carefully tested for the computation of solar models. However, considerable development is still required in the treatment of nuclear reactions, diffusion and convective mixing.
The origins and evolutionary history of human non-coding RNA regulatory networks.

PubMed

Sherafatian, Masih; Mowla, Seyed Javad

2017-04-01

The evolutionary history and origin of the regulatory function of animal non-coding RNAs are not well understood. Lack of conservation of long non-coding RNAs and small sizes of microRNAs has been major obstacles in their phylogenetic analysis. In this study, we tried to shed more light on the evolution of ncRNA regulatory networks by changing our phylogenetic strategy to focus on the evolutionary pattern of their protein coding targets. We used available target databases of miRNAs and lncRNAs to find their protein coding targets in human. We were able to recognize evolutionary hallmarks of ncRNA targets by phylostratigraphic analysis. We found the conventional 3'-UTR and lesser known 5'-UTR targets of miRNAs to be enriched at three consecutive phylostrata. Firstly, in eukaryata phylostratum corresponding to the emergence of miRNAs, our study revealed that miRNA targets function primarily in cell cycle processes. Moreover, the same overrepresentation of the targets observed in the next two consecutive phylostrata, opisthokonta and eumetazoa, corresponded to the expansion periods of miRNAs in animals evolution. Coding sequence targets of miRNAs showed a delayed rise at opisthokonta phylostratum, compared to the 3' and 5' UTR targets of miRNAs. LncRNA regulatory network was the latest to evolve at eumetazoa.
Xenomicrobiology: a roadmap for genetic code engineering.

PubMed

Acevedo-Rocha, Carlos G; Budisa, Nediljko

2016-09-01

Biology is an analytical and informational science that is becoming increasingly dependent on chemical synthesis. One example is the high-throughput and low-cost synthesis of DNA, which is a foundation for the research field of synthetic biology (SB). The aim of SB is to provide biotechnological solutions to health, energy and environmental issues as well as unsustainable manufacturing processes in the frame of naturally existing chemical building blocks. Xenobiology (XB) goes a step further by implementing non-natural building blocks in living cells. In this context, genetic code engineering respectively enables the re-design of genes/genomes and proteins/proteomes with non-canonical nucleic (XNAs) and amino (ncAAs) acids. Besides studying information flow and evolutionary innovation in living systems, XB allows the development of new-to-nature therapeutic proteins/peptides, new biocatalysts for potential applications in synthetic organic chemistry and biocontainment strategies for enhanced biosafety. In this perspective, we provide a brief history and evolution of the genetic code in the context of XB. We then discuss the latest efforts and challenges ahead for engineering the genetic code with focus on substitutions and additions of ncAAs as well as standard amino acid reductions. Finally, we present a roadmap for the directed evolution of artificial microbes for emancipating rare sense codons that could be used to introduce novel building blocks. The development of such xenomicroorganisms endowed with a 'genetic firewall' will also allow to study and understand the relation between code evolution and horizontal gene transfer. © 2016 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
Chemical and physical characterization of the first stages of protoplanetary disk formation

NASA Astrophysics Data System (ADS)

Hincelin, Ugo

2012-12-01

Low mass stars, like our Sun, are born from the collapse of a molecular cloud. The matter falls in the center of the cloud, creating a protoplanetary disk surrounding a protostar. Planets and other Solar System bodies will be formed in the disk. The chemical composition of the interstellar matter and its evolution during the formation of the disk are important to better understand the formation process of these objects. I studied the chemical and physical evolution of this matter, from the cloud to the disk, using the chemical gas-grain code Nautilus. A sensitivity study to some parameters of the code (such as elemental abundances and parameters of grain surface chemistry) has been done. More particularly, the updates of rate coefficients and branching ratios of the reactions of our chemical network showed their importance, such as on the abundances of some chemical species, and on the code sensitivity to others parameters. Several physical models of collapsing dense core have also been considered. The more complex and solid approach has been to interface our chemical code with the radiation-magneto-hydrodynamic model of stellar formation RAMSES, in order to model in three dimensions the physical and chemical evolution of a young disk formation. Our study showed that the disk keeps imprints of the past history of the matter, and so its chemical composition is sensitive to the initial conditions.
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization

PubMed Central

Qin, Cheng; Yu, Changshui; Shen, Yaou; Fang, Xiaodong; Chen, Lang; Min, Jiumeng; Cheng, Jiaowen; Zhao, Shancen; Xu, Meng; Luo, Yong; Yang, Yulan; Wu, Zhiming; Mao, Likai; Wu, Haiyang; Ling-Hu, Changying; Zhou, Huangkai; Lin, Haijian; González-Morales, Sandra; Trejo-Saavedra, Diana L.; Tian, Hao; Tang, Xin; Zhao, Maojun; Huang, Zhiyong; Zhou, Anwei; Yao, Xiaoming; Cui, Junjie; Li, Wenqi; Chen, Zhe; Feng, Yongqiang; Niu, Yongchao; Bi, Shimin; Yang, Xiuwei; Li, Weipeng; Cai, Huimin; Luo, Xirong; Montes-Hernández, Salvador; Leyva-González, Marco A.; Xiong, Zhiqiang; He, Xiujing; Bai, Lijun; Tan, Shu; Tang, Xiangqun; Liu, Dan; Liu, Jinwen; Zhang, Shangxing; Chen, Maoshan; Zhang, Lu; Zhang, Li; Zhang, Yinchao; Liao, Weiqin; Zhang, Yan; Wang, Min; Lv, Xiaodan; Wen, Bo; Liu, Hongjun; Luan, Hemi; Zhang, Yonggang; Yang, Shuang; Wang, Xiaodian; Xu, Jiaohui; Li, Xueqin; Li, Shuaicheng; Wang, Junyi; Palloix, Alain; Bosland, Paul W.; Li, Yingrui; Krogh, Anders; Rivera-Bustamante, Rafael F.; Herrera-Estrella, Luis; Yin, Ye; Yu, Jiping; Hu, Kailin; Zhang, Zhiming

2014-01-01

As an economic crop, pepper satisfies people’s spicy taste and has medicinal uses worldwide. To gain a better understanding of Capsicum evolution, domestication, and specialization, we present here the genome sequence of the cultivated pepper Zunla-1 (C. annuum L.) and its wild progenitor Chiltepin (C. annuum var. glabriusculum). We estimate that the pepper genome expanded ∼0.3 Mya (with respect to the genome of other Solanaceae) by a rapid amplification of retrotransposons elements, resulting in a genome comprised of ∼81% repetitive sequences. Approximately 79% of 3.48-Gb scaffolds containing 34,476 protein-coding genes were anchored to chromosomes by a high-density genetic map. Comparison of cultivated and wild pepper genomes with 20 resequencing accessions revealed molecular footprints of artificial selection, providing us with a list of candidate domestication genes. We also found that dosage compensation effect of tandem duplication genes probably contributed to the pungent diversification in pepper. The Capsicum reference genome provides crucial information for the study of not only the evolution of the pepper genome but also, the Solanaceae family, and it will facilitate the establishment of more effective pepper breeding programs. PMID:24591624
Multiscale Modeling of Polycrystalline NiTi Shape Memory Alloy under Various Plastic Deformation Conditions by Coupling Microstructure Evolution and Macroscopic Mechanical Response

PubMed Central

Jiang, Shuyong; Zhou, Tao; Tu, Jian; Shi, Laixin; Chen, Qiang; Yang, Mingbo

2017-01-01

Numerical modeling of microstructure evolution in various regions during uniaxial compression and canning compression of NiTi shape memory alloy (SMA) are studied through combined macroscopic and microscopic finite element simulation in order to investigate plastic deformation of NiTi SMA at 400 °C. In this approach, the macroscale material behavior is modeled with a relatively coarse finite element mesh, and then the corresponding deformation history in some selected regions in this mesh is extracted by the sub-model technique of finite element code ABAQUS and subsequently used as boundary conditions for the microscale simulation by means of crystal plasticity finite element method (CPFEM). Simulation results show that NiTi SMA exhibits an inhomogeneous plastic deformation at the microscale. Moreover, regions that suffered canning compression sustain more homogeneous plastic deformation by comparison with the corresponding regions subjected to uniaxial compression. The mitigation of inhomogeneous plastic deformation contributes to reducing the statistically stored dislocation (SSD) density in polycrystalline aggregation and also to reducing the difference of stress level in various regions of deformed NiTi SMA sample, and therefore sustaining large plastic deformation in the canning compression process. PMID:29027925
Multiscale Modeling of Polycrystalline NiTi Shape Memory Alloy under Various Plastic Deformation Conditions by Coupling Microstructure Evolution and Macroscopic Mechanical Response.

PubMed

Hu, Li; Jiang, Shuyong; Zhou, Tao; Tu, Jian; Shi, Laixin; Chen, Qiang; Yang, Mingbo

2017-10-13

Numerical modeling of microstructure evolution in various regions during uniaxial compression and canning compression of NiTi shape memory alloy (SMA) are studied through combined macroscopic and microscopic finite element simulation in order to investigate plastic deformation of NiTi SMA at 400 °C. In this approach, the macroscale material behavior is modeled with a relatively coarse finite element mesh, and then the corresponding deformation history in some selected regions in this mesh is extracted by the sub-model technique of finite element code ABAQUS and subsequently used as boundary conditions for the microscale simulation by means of crystal plasticity finite element method (CPFEM). Simulation results show that NiTi SMA exhibits an inhomogeneous plastic deformation at the microscale. Moreover, regions that suffered canning compression sustain more homogeneous plastic deformation by comparison with the corresponding regions subjected to uniaxial compression. The mitigation of inhomogeneous plastic deformation contributes to reducing the statistically stored dislocation (SSD) density in polycrystalline aggregation and also to reducing the difference of stress level in various regions of deformed NiTi SMA sample, and therefore sustaining large plastic deformation in the canning compression process.
Addition of a Hydrological Cycle to the EPIC Jupiter Model

NASA Astrophysics Data System (ADS)

Dowling, T. E.; Palotai, C. J.

2002-09-01

We present a progress report on the development of the EPIC atmospheric model to include clouds, moist convection, and precipitation. Two major goals are: i) to study the influence that convective water clouds have on Jupiter's jets and vortices, such as those to the northwest of the Great Red Spot, and ii) to predict ammonia-cloud evolution for direct comparison to visual images (instead of relying on surrogates for clouds like potential vorticity). Data structures in the model are now set up to handle the vapor, liquid, and solid phases of the most common chemical species in planetary atmospheres. We have adapted the Prather conservation of second-order moments advection scheme to the model, which yields high accuracy for dealing with cloud edges. In collaboration with computer scientists H. Dietz and T. Mattox at the U. Kentucky, we have built a dedicated 40-node parallel computer that achieves 34 Gflops (double precision) at 74 cents per Mflop, and have updated the EPIC-model code to use cache-aware memory layouts and other modern optimizations. The latest test-case results of cloud evolution in the model will be presented. This research is funded by NASA's Planetary Atmospheres and EPSCoR programs.
The evolution of small insertions and deletions in the coding genes of Drosophila melanogaster.

PubMed

Chong, Zechen; Zhai, Weiwei; Li, Chunyan; Gao, Min; Gong, Qiang; Ruan, Jue; Li, Juan; Jiang, Lan; Lv, Xuemei; Hungate, Eric; Wu, Chung-I

2013-12-01

Studies of protein evolution have focused on amino acid substitutions with much less systematic analysis on insertion and deletions (indels) in protein coding genes. We hence surveyed 7,500 genes between Drosophila melanogaster and D. simulans, using D. yakuba as an outgroup for this purpose. The evolutionary rate of coding indels is indeed low, at only 3% of that of nonsynonymous substitutions. As coding indels follow a geometric distribution in size and tend to fall in low-complexity regions of proteins, it is unclear whether selection or mutation underlies this low rate. To resolve the issue, we collected genomic sequences from an isogenic African line of D. melanogaster (ZS30) at a high coverage of 70× and analyzed indel polymorphism between ZS30 and the reference genome. In comparing polymorphism and divergence, we found that the divergence to polymorphism ratio (i.e., fixation index) for smaller indels (size ≤ 10 bp) is very similar to that for synonymous changes, suggesting that most of the within-species polymorphism and between-species divergence for indels are selectively neutral. Interestingly, deletions of larger sizes (size ≥ 11 bp and ≤ 30 bp) have a much higher fixation index than synonymous mutations and 44.4% of fixed middle-sized deletions are estimated to be adaptive. To our surprise, this pattern is not found for insertions. Protein indel evolution appear to be in a dynamic flux of neutrally driven expansion (insertions) together with adaptive-driven contraction (deletions), and these observations provide important insights for understanding the fitness of new mutations as well as the evolutionary driving forces for genomic evolution in Drosophila species.
Ef: Software for Nonrelativistic Beam Simulation by Particle-in-Cell Algorithm

NASA Astrophysics Data System (ADS)

Boytsov, A. Yu.; Bulychev, A. A.

2018-04-01

Understanding of particle dynamics is crucial in construction of electron guns, ion sources and other types of nonrelativistic beam devices. Apart from external guiding and focusing systems, a prominent role in evolution of such low-energy beams is played by particle-particle interaction. Numerical simulations taking into account these effects are typically accomplished by a well-known particle-in-cell method. In practice, for convenient work a simulation program should not only implement this method, but also support parallelization, provide integration with CAD systems and allow access to details of the simulation algorithm. To address the formulated requirements, development of a new open source code - Ef - has been started. It's current features and main functionality are presented. Comparison with several analytical models demonstrates good agreement between the numerical results and the theory. Further development plans are discussed.
Study on Fatigue Performance of Composite Bolted Joints with Bolt-Hole Delamination

NASA Astrophysics Data System (ADS)

Liu, M. J.; Yu, S.; Zhao, Q. Y.

2018-03-01

Fatigue performance of composite structure with imperfections is a challenging subject at present. Based on cohesive zone method and multi-continuum theory, delamination evolution response and fatigue life prediction of a 3D composite single-lap joint with a bolt-hole have been investigated through computer codes Abaqus and Fe-safe. Results from the comparison of a perfect composite bolted joint with another defect one indicates that a relatively small delamination damage around the bolt hole brings about significant degradation of local material performance. More notably, fatigue life of stress concentration region of composite bolted joints is highly sensitive to external loads, as an increase of 67% cyclic load amplitude leads to an decrease of 99.5% local fatigue life in this study. However, the numerical strategy for solving composite fatigue problems is meaningful to engineering works.
Gravity and count probabilities in an expanding universe

NASA Technical Reports Server (NTRS)

Bouchet, Francois R.; Hernquist, Lars

1992-01-01

The time evolution of nonlinear clustering on large scales in cold dark matter, hot dark matter, and white noise models of the universe is investigated using N-body simulations performed with a tree code. Count probabilities in cubic cells are determined as functions of the cell size and the clustering state (redshift), and comparisons are made with various theoretical models. We isolate the features that appear to be the result of gravitational instability, those that depend on the initial conditions, and those that are likely a consequence of numerical limitations. More specifically, we study the development of skewness, kurtosis, and the fifth moment in relation to variance, the dependence of the void probability on time as well as on sparseness of sampling, and the overall shape of the count probability distribution. Implications of our results for theoretical and observational studies are discussed.

Experiments and simulations of Richtmyer-Meshkov Instability with measured,volumetric initial conditions

NASA Astrophysics Data System (ADS)

Sewell, Everest; Ferguson, Kevin; Jacobs, Jeffrey; Greenough, Jeff; Krivets, Vitaliy

2016-11-01

We describe experiments of single-shock Richtmyer-Meskhov Instability (RMI) performed on the shock tube apparatus at the University of Arizona in which the initial conditions are volumetrically imaged prior to shock wave arrival. Initial perturbations play a major role in the evolution of RMI, and previous experimental efforts only capture a single plane of the initial condition. The method presented uses a rastered laser sheet to capture additional images throughout the depth of the initial condition immediately before the shock arrival time. These images are then used to reconstruct a volumetric approximation of the experimental perturbation. Analysis of the initial perturbations is performed, and then used as initial conditions in simulations using the hydrodynamics code ARES, developed at Lawrence Livermore National Laboratory (LLNL). Experiments are presented and comparisons are made with simulation results.
Human-specific protein isoforms produced by novel splice sites in the human genome after the human-chimpanzee divergence

PubMed Central

2012-01-01

Background Evolution of splice sites is a well-known phenomenon that results in transcript diversity during human evolution. Many novel splice sites are derived from repetitive elements and may not contribute to protein products. Here, we analyzed annotated human protein-coding exons and identified human-specific splice sites that arose after the human-chimpanzee divergence. Results We analyzed multiple alignments of the annotated human protein-coding exons and their respective orthologous mammalian genome sequences to identify 85 novel splice sites (50 splice acceptors and 35 donors) in the human genome. The novel protein-coding exons, which are expressed either constitutively or alternatively, produce novel protein isoforms by insertion, deletion, or frameshift. We found three cases in which the human-specific isoform conferred novel molecular function in the human cells: the human-specific IMUP protein isoform induces apoptosis of the trophoblast and is implicated in pre-eclampsia; the intronization of a part of SMOX gene exon produces inactive spermine oxidase; the human-specific NUB1 isoform shows reduced interaction with ubiquitin-like proteins, possibly affecting ubiquitin pathways. Conclusions Although the generation of novel protein isoforms does not equate to adaptive evolution, we propose that these cases are useful candidates for a molecular functional study to identify proteomic changes that might bring about novel phenotypes during human evolution. PMID:23148531
Center for Extended Magnetohydrodynamics Modeling - Final Technical Report

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

Parker, Scott

This project funding supported approximately 74 percent of a Ph.D. graduate student, not including costs of travel and supplies. We had a highly successful research project including the development of a second-order implicit electromagnetic kinetic ion hybrid model [Cheng 2013, Sturdevant 2016], direct comparisons with the extended MHD NIMROD code and kinetic simulation [Schnack 2013], modeling of slab tearing modes using the fully kinetic ion hybrid model and finally, modeling global tearing modes in cylindrical geometry using gyrokinetic simulation [Chen 2015, Chen 2016]. We developed an electromagnetic second-order implicit kinetic ion fluid electron hybrid model [Cheng 2013]. As a firstmore » step, we assumed isothermal electrons, but have included drift-kinetic electrons in similar models [Chen 2011]. We used this simulation to study the nonlinear evolution of the tearing mode in slab geometry, including nonlinear evolution and saturation [Cheng 2013]. Later, we compared this model directly to extended MHD calculations using the NIMROD code [Schnack 2013]. In this study, we investigated the ion-temperature-gradient instability with an extended MHD code for the first time and got reasonable agreement with the kinetic calculation in terms of linear frequency, growth rate and mode structure. We then extended this model to include orbit averaging and sub-cycling of the ions and compared directly to gyrokinetic theory [Sturdevant 2016]. This work was highlighted in an Invited Talk at the International Conference on the Numerical Simulation of Plasmas in 2015. The orbit averaging sub-cycling multi-scale algorithm is amenable to hybrid architectures with GPUS or math co-processors. Additionally, our participation in the Center for Extend Magnetohydrodynamics motivated our research on developing the capability for gyrokinetic simulation to model a global tearing mode. We did this in cylindrical geometry where the results could be benchmarked with existing eigenmode calculations. First, we developed a gyrokinetic code capable of simulating long wavelengths using a fluid electron model [Chen 2015]. We benchmarked this code with an eigenmode calculation. Besides having to rewrite the field solver due to the breakdown in the gyrokinetic ordering for long wavelengths, very high radial resolution was required. We developed a technique where we used the solution from the eigenmode solver to specify radial boundary conditions allowing for a very high radial resolution of the inner solution. Using this technique enabled us to use our direct algorithm with gyrokinetic ions and drift kinetic electrons [Chen 2016]. This work was highlighted in an Invited Talk at the American Physical Society - Division of Plasma Physics in 2015.« less
Sexual selection drives evolution and rapid turnover of male gene expression.

PubMed

Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Dean, Rebecca; Montgomery, Stephen H; Pointer, Marie A; Mank, Judith E

2015-04-07

The profound and pervasive differences in gene expression observed between males and females, and the unique evolutionary properties of these genes in many species, have led to the widespread assumption that they are the product of sexual selection and sexual conflict. However, we still lack a clear understanding of the connection between sexual selection and transcriptional dimorphism, often termed sex-biased gene expression. Moreover, the relative contribution of sexual selection vs. drift in shaping broad patterns of expression, divergence, and polymorphism remains unknown. To assess the role of sexual selection in shaping these patterns, we assembled transcriptomes from an avian clade representing the full range of sexual dimorphism and sexual selection. We use these species to test the links between sexual selection and sex-biased gene expression evolution in a comparative framework. Through ancestral reconstruction of sex bias, we demonstrate a rapid turnover of sex bias across this clade driven by sexual selection and show it to be primarily the result of expression changes in males. We use phylogenetically controlled comparative methods to demonstrate that phenotypic measures of sexual selection predict the proportion of male-biased but not female-biased gene expression. Although male-biased genes show elevated rates of coding sequence evolution, consistent with previous reports in a range of taxa, there is no association between sexual selection and rates of coding sequence evolution, suggesting that expression changes may be more important than coding sequence in sexual selection. Taken together, our results highlight the power of sexual selection to act on gene expression differences and shape genome evolution.
AX-GADGET: a new code for cosmological simulations of Fuzzy Dark Matter and Axion models

NASA Astrophysics Data System (ADS)

Nori, Matteo; Baldi, Marco

2018-05-01

We present a new module of the parallel N-Body code P-GADGET3 for cosmological simulations of light bosonic non-thermal dark matter, often referred as Fuzzy Dark Matter (FDM). The dynamics of the FDM features a highly non-linear Quantum Potential (QP) that suppresses the growth of structures at small scales. Most of the previous attempts of FDM simulations either evolved suppressed initial conditions, completely neglecting the dynamical effects of QP throughout cosmic evolution, or resorted to numerically challenging full-wave solvers. The code provides an interesting alternative, following the FDM evolution without impairing the overall performance. This is done by computing the QP acceleration through the Smoothed Particle Hydrodynamics (SPH) routines, with improved schemes to ensure precise and stable derivatives. As an extension of the P-GADGET3 code, it inherits all the additional physics modules implemented up to date, opening a wide range of possibilities to constrain FDM models and explore its degeneracies with other physical phenomena. Simulations are compared with analytical predictions and results of other codes, validating the QP as a crucial player in structure formation at small scales.
A Python Calculator for Supernova Remnant Evolution

NASA Astrophysics Data System (ADS)

Leahy, D. A.; Williams, J. E.

2017-05-01

A freely available Python code for modeling supernova remnant (SNR) evolution has been created. This software is intended for two purposes: to understand SNR evolution and to use in modeling observations of SNR for obtaining good estimates of SNR properties. It includes all phases for the standard path of evolution for spherically symmetric SNRs. In addition, alternate evolutionary models are available, including evolution in a cloudy ISM, the fractional energy-loss model, and evolution in a hot low-density ISM. The graphical interface takes in various parameters and produces outputs such as shock radius and velocity versus time, as well as SNR surface brightness profile and spectrum. Some interesting properties of SNR evolution are demonstrated using the program.
Evidence of birth-and-death evolution of 5S rRNA gene in Channa species (Teleostei, Perciformes).

PubMed

Barman, Anindya Sundar; Singh, Mamta; Singh, Rajeev Kumar; Lal, Kuldeep Kumar

2016-12-01

In higher eukaryotes, minor rDNA family codes for 5S rRNA that is arranged in tandem arrays and comprises of a highly conserved 120 bp long coding sequence with a variable non-transcribed spacer (NTS). Initially the 5S rDNA repeats are considered to be evolved by the process of concerted evolution. But some recent reports, including teleost fishes suggested that evolution of 5S rDNA repeat does not fit into the concerted evolution model and evolution of 5S rDNA family may be explained by a birth-and-death evolution model. In order to study the mode of evolution of 5S rDNA repeats in Perciformes fish species, nucleotide sequence and molecular organization of five species of genus Channa were analyzed in the present study. Molecular analyses revealed several variants of 5S rDNA repeats (four types of NTS) and networks created by a neighbor net algorithm for each type of sequences (I, II, III and IV) did not show a clear clustering in species specific manner. The stable secondary structure is predicted and upstream and downstream conserved regulatory elements were characterized. Sequence analyses also shown the presence of two putative pseudogenes in Channa marulius. Present study supported that 5S rDNA repeats in genus Channa were evolved under the process of birth-and-death.
OBJECT KINETIC MONTE CARLO SIMULATIONS OF MICROSTRUCTURE EVOLUTION

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

Nandipati, Giridhar; Setyawan, Wahyu; Heinisch, Howard L.

2013-09-30

The objective is to report the development of the flexible object kinetic Monte Carlo (OKMC) simulation code KSOME (kinetic simulation of microstructure evolution) which can be used to simulate microstructure evolution of complex systems under irradiation. In this report we briefly describe the capabilities of KSOME and present preliminary results for short term annealing of single cascades in tungsten at various primary-knock-on atom (PKA) energies and temperatures.
Simulation of Alfvén eigenmode bursts using a hybrid code for nonlinear magnetohydrodynamics and energetic particles

NASA Astrophysics Data System (ADS)

Todo, Y.; Berk, H. L.; Breizman, B. N.

2012-03-01

A hybrid simulation code for nonlinear magnetohydrodynamics (MHD) and energetic-particle dynamics has been extended to simulate recurrent bursts of Alfvén eigenmodes by implementing the energetic-particle source, collisions and losses. The Alfvén eigenmode bursts with synchronization of multiple modes and beam ion losses at each burst are successfully simulated with nonlinear MHD effects for the physics condition similar to a reduced simulation for a TFTR experiment (Wong et al 1991 Phys. Rev. Lett. 66 1874, Todo et al 2003 Phys. Plasmas 10 2888). It is demonstrated with a comparison between nonlinear MHD and linear MHD simulation results that the nonlinear MHD effects significantly reduce both the saturation amplitude of the Alfvén eigenmodes and the beam ion losses. Two types of time evolution are found depending on the MHD dissipation coefficients, namely viscosity, resistivity and diffusivity. The Alfvén eigenmode bursts take place for higher dissipation coefficients with roughly 10% drop in stored beam energy and the maximum amplitude of the dominant magnetic fluctuation harmonic δBm/n/B ~ 5 × 10-3 at the mode peak location inside the plasma. Quadratic dependence of beam ion loss rate on magnetic fluctuation amplitude is found for the bursting evolution in the nonlinear MHD simulation. For lower dissipation coefficients, the amplitude of the Alfvén eigenmodes is at steady levels δBm/n/B ~ 2 × 10-3 and the beam ion losses take place continuously. The beam ion pressure profiles are similar among the different dissipation coefficients, and the stored beam energy is higher for higher dissipation coefficients.
Colour cyclic code for Brillouin distributed sensors

NASA Astrophysics Data System (ADS)

Le Floch, Sébastien; Sauser, Florian; Llera, Miguel; Rochat, Etienne

2015-09-01

For the first time, a colour cyclic coding (CCC) is theoretically and experimentally demonstrated for Brillouin optical time-domain analysis (BOTDA) distributed sensors. Compared to traditional intensity-modulated cyclic codes, the code presents an additional gain of √2 while keeping the same number of sequences as for a colour coding. A comparison with a standard BOTDA sensor is realized and validates the theoretical coding gain.
Positive Selection during the Evolution of the Blood Coagulation Factors in the Context of Their Disease-Causing Mutations

PubMed Central

Rallapalli, Pavithra M.; Orengo, Christine A.; Studer, Romain A.; Perkins, Stephen J.

2014-01-01

Blood coagulation occurs through a cascade of enzymes and cofactors that produces a fibrin clot, while otherwise maintaining hemostasis. The 11 human coagulation factors (FG, FII–FXIII) have been identified across all vertebrates, suggesting that they emerged with the first vertebrates around 500 Ma. Human FVIII, FIX, and FXI are associated with thousands of disease-causing mutations. Here, we evaluated the strength of selective pressures on the 14 genes coding for the 11 factors during vertebrate evolution, and compared these with human mutations in FVIII, FIX, and FXI. Positive selection was identified for fibrinogen (FG), FIII, FVIII, FIX, and FX in the mammalian Primates and Laurasiatheria and the Sauropsida (reptiles and birds). This showed that the coagulation system in vertebrates was under strong selective pressures, perhaps to adapt against blood-invading pathogens. The comparison of these results with disease-causing mutations reported in FVIII, FIX, and FXI showed that the number of disease-causing mutations, and the probability of positive selection were inversely related to each other. It was concluded that when a site was under positive selection, it was less likely to be associated with disease-causing mutations. In contrast, sites under negative selection were more likely to be associated with disease-causing mutations and be destabilizing. A residue-by-residue comparison of the FVIII, FIX, and FXI sequence alignments confirmed this. This improved understanding of evolutionary changes in FVIII, FIX, and FXI provided greater insight into disease-causing mutations, and better assessments of the codon sites that may be mutated in applications of gene therapy. PMID:25158795
Insight into the evolution and origin of leprosy bacilli from the genome sequence of Mycobacterium lepromatosis

PubMed Central

Singh, Pushpendra; Benjak, Andrej; Schuenemann, Verena J.; Herbig, Alexander; Avanzi, Charlotte; Busso, Philippe; Nieselt, Kay; Krause, Johannes; Vera-Cabrera, Lucio; Cole, Stewart T.

2015-01-01

Mycobacterium lepromatosis is an uncultured human pathogen associated with diffuse lepromatous leprosy and a reactional state known as Lucio's phenomenon. By using deep sequencing with and without DNA enrichment, we obtained the near-complete genome sequence of M. lepromatosis present in a skin biopsy from a Mexican patient, and compared it with that of Mycobacterium leprae, which has undergone extensive reductive evolution. The genomes display extensive synteny and are similar in size (∼3.27 Mb). Protein-coding genes share 93% nucleotide sequence identity, whereas pseudogenes are only 82% identical. The events that led to pseudogenization of 50% of the genome likely occurred before divergence from their most recent common ancestor (MRCA), and both M. lepromatosis and M. leprae have since accumulated new pseudogenes or acquired specific deletions. Functional comparisons suggest that M. lepromatosis has lost several enzymes required for amino acid synthesis whereas M. leprae has a defective heme pathway. M. lepromatosis has retained all functions required to infect the Schwann cells of the peripheral nervous system and therefore may also be neuropathogenic. A phylogeographic survey of 227 leprosy biopsies by differential PCR revealed that 221 contained M. leprae whereas only six, all from Mexico, harbored M. lepromatosis. Phylogenetic comparisons indicate that M. lepromatosis is closer than M. leprae to the MRCA, and a Bayesian dating analysis suggests that they diverged from their MRCA approximately 13.9 Mya. Thus, despite their ancient separation, the two leprosy bacilli are remarkably conserved and still cause similar pathologic conditions. PMID:25831531
Two dimension MDW OCDMA code cross-correlation for reduction of phase induced intensity noise

NASA Astrophysics Data System (ADS)

Ahmed, Israa Sh.; Aljunid, Syed A.; Nordin, Junita M.; Dulaimi, Layth A. Khalil Al; Matem, Rima

2017-11-01

In this paper, we first review 2-D MDW code cross correlation equations and table to be improved significantly by using code correlation properties. These codes can be used in the synchronous optical CDMA systems for multi access interference cancellation and maximum suppress the phase induced intensity noise. Low Psr is due to the reduction of interference noise that is induced by the 2-D MDW code PIIN suppression. High data rate causes increases in BER, requires high effective power and severely deteriorates the system performance. The 2-D W/T MDW code has an excellent system performance where the value of PIIN is suppressed as low as possible at the optimum Psr with high data bit rate. The 2-D MDW code shows better tolerance to PIIN in comparison to others with enhanced system performance. We prove by numerical analysis that the PIIN maximally suppressed by MDW code through the minimizing property of cross correlation in comparison to 2-D PDC and 2-D MQC OCDMA code.scheme systems.
Comparison of ORSAT and SCARAB Reentry Analysis Tools for a Generic Satellite Test Case

NASA Technical Reports Server (NTRS)

Kelley, Robert L.; Hill, Nicole M.; Rochelle, W. C.; Johnson, Nicholas L.; Lips, T.

2010-01-01

Reentry analysis is essential to understanding the consequences of the full life cycle of a spacecraft. Since reentry is a key factor in spacecraft development, NASA and ESA have separately developed tools to assess the survivability of objects during reentry. Criteria such as debris casualty area and impact energy are particularly important to understanding the risks posed to people on Earth. Therefore, NASA and ESA have undertaken a series of comparison studies of their respective reentry codes for verification and improvements in accuracy. The NASA Object Reentry Survival Analysis Tool (ORSAT) and the ESA Spacecraft Atmospheric Reentry and Aerothermal Breakup (SCARAB) reentry analysis tools serve as standard codes for reentry survivability assessment of satellites. These programs predict whether an object will demise during reentry and calculate the debris casualty area of objects determined to survive, establishing the reentry risk posed to the Earth's population by surviving debris. A series of test cases have been studied for comparison and the most recent uses "Testsat," a conceptual satellite composed of generic parts, defined to use numerous simple shapes and various materials for a better comparison of the predictions of these two codes. This study is an improvement on the others in this series because of increased consistency in modeling techniques and variables. The overall comparison demonstrated that the two codes arrive at similar results. Either most objects modeled resulted in close agreement between the two codes, or if the difference was significant, the variance could be explained as a case of semantics in the model definitions. This paper presents the main results of ORSAT and SCARAB for the Testsat case and discusses the sources of any discovered differences. Discussion of the results of previous comparisons is made for a summary of differences between the codes and lessons learned from this series of tests.
Toward a theory of multilevel evolution: long-term information integration shapes the mutational landscape and enhances evolvability.

PubMed

Hogeweg, Paulien

2012-01-01

Most of evolutionary theory has abstracted away from how information is coded in the genome and how this information is transformed into traits on which selection takes place. While in the earliest stages of biological evolution, in the RNA world, the mapping from the genotype into function was largely predefined by the physical-chemical properties of the evolving entities (RNA replicators, e.g. from sequence to folded structure and catalytic sites), in present-day organisms, the mapping itself is the result of evolution. I will review results of several in silico evolutionary studies which examine the consequences of evolving the genetic coding, and the ways this information is transformed, while adapting to prevailing environments. Such multilevel evolution leads to long-term information integration. Through genome, network, and dynamical structuring, the occurrence and/or effect of random mutations becomes nonrandom, and facilitates rapid adaptation. This is what does happen in the in silico experiments. Is it also what did happen in biological evolution? I will discuss some data that suggest that it did. In any case, these results provide us with novel search images to tackle the wealth of biological data.
Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model

PubMed Central

Woltering, Joost M.; Duboule, Denis

2015-01-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. PMID:26238020
Effects of the plasma profiles on photon and pair production in ultrahigh intensity laser solid interaction

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

Tian, Y. X.; Jin, X. L., E-mail: jinxiaolin@uestc.edu.cn; Yan, W. Z.

The model of photon and pair production in strong field quantum electrodynamics is implemented into our 1D3V particle-in-cell code with Monte Carlo algorithm. Using this code, the evolution of the particles in ultrahigh intensity laser (∼10{sup 23} W/cm{sup 2}) interaction with aluminum foil target is observed. Four different initial plasma profiles are considered in the simulations. The effects of initial plasma profiles on photon and pair production, energy spectra, and energy evolution are analyzed. The results imply that one can set an optimal initial plasma profile to obtain the desired photon distributions.
Three stages in the evolution of the genetic code

NASA Technical Reports Server (NTRS)

Baumann, U.; Oro, J.

1993-01-01

A diversification of the genetic code based on the number of codons available for the proteinous amino acids is established. Three groups of amino acids during evolution of the code are distinguished. On the basis of their chemical complexity those amino acids emerging later in a translation process are derived. Codon number and chemical complexity indicate that His, Phe, Tyr, Cys and either Lys or Asn were introduced in the second stage, whereas the number of codons alone gives evidence that Trp and Met were introduced in the third stage. The amino acids of stage 1 use purine-rich codons, while all the amino acids introduced in the second stage, in contrast, use pyrimidines in the third position of their codons. A low abundance of pyrimidines during early translation is derived. This assumption is supported by experiments on non-enzymatic replication and interactions of hairpin loops with a complementary strand. A back extrapolation concludes a high purine content of the first nucleic acids, which gradually decreased during their evolution. Amino acids independently available from prebiotic synthesis were thus correlated to purine-rich codons. Implications on the prebiotic replication are discussed also in the light of recent codon usage data.
Validating the BISON fuel performance code to integral LWR experiments

DOE PAGES

Williamson, R. L.; Gamble, K. A.; Perez, D. M.; ...

2016-03-24

BISON is a modern finite element-based nuclear fuel performance code that has been under development at the Idaho National Laboratory (INL) since 2009. The code is applicable to both steady and transient fuel behavior and has been used to analyze a variety of fuel forms in 1D spherical, 2D axisymmetric, or 3D geometries. Code validation is underway and is the subject of this study. A brief overview of BISON’s computational framework, governing equations, and general material and behavioral models is provided. BISON code and solution verification procedures are described, followed by a summary of the experimental data used to datemore » for validation of Light Water Reactor (LWR) fuel. Validation comparisons focus on fuel centerline temperature, fission gas release, and rod diameter both before and following fuel-clad mechanical contact. Comparisons for 35 LWR rods are consolidated to provide an overall view of how the code is predicting physical behavior, with a few select validation cases discussed in greater detail. Our results demonstrate that 1) fuel centerline temperature comparisons through all phases of fuel life are very reasonable with deviations between predictions and experimental data within ±10% for early life through high burnup fuel and only slightly out of these bounds for power ramp experiments, 2) accuracy in predicting fission gas release appears to be consistent with state-of-the-art modeling and with the involved uncertainties and 3) comparison of rod diameter results indicates a tendency to overpredict clad diameter reduction early in life, when clad creepdown dominates, and more significantly overpredict the diameter increase late in life, when fuel expansion controls the mechanical response. In the initial rod diameter comparisons they were unsatisfactory and have lead to consideration of additional separate effects experiments to better understand and predict clad and fuel mechanical behavior. Results from this study are being used to define priorities for ongoing code development and validation activities.« less
Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

PubMed

Wolf, Yuri I; Makarova, Kira S; Yutin, Natalya; Koonin, Eugene V

2012-12-14

Collections of Clusters of Orthologous Genes (COGs) provide indispensable tools for comparative genomic analysis, evolutionary reconstruction and functional annotation of new genomes. Initially, COGs were made for all complete genomes of cellular life forms that were available at the time. However, with the accumulation of thousands of complete genomes, construction of a comprehensive COG set has become extremely computationally demanding and prone to error propagation, necessitating the switch to taxon-specific COG collections. Previously, we reported the collection of COGs for 41 genomes of Archaea (arCOGs). Here we present a major update of the arCOGs and describe evolutionary reconstructions to reveal general trends in the evolution of Archaea. The updated version of the arCOG database incorporates 91% of the pangenome of 120 archaea (251,032 protein-coding genes altogether) into 10,335 arCOGs. Using this new set of arCOGs, we performed maximum likelihood reconstruction of the genome content of archaeal ancestral forms and gene gain and loss events in archaeal evolution. This reconstruction shows that the last Common Ancestor of the extant Archaea was an organism of greater complexity than most of the extant archaea, probably with over 2,500 protein-coding genes. The subsequent evolution of almost all archaeal lineages was apparently dominated by gene loss resulting in genome streamlining. Overall, in the evolution of Archaea as well as a representative set of bacteria that was similarly analyzed for comparison, gene losses are estimated to outnumber gene gains at least 4 to 1. Analysis of specific patterns of gene gain in Archaea shows that, although some groups, in particular Halobacteria, acquire substantially more genes than others, on the whole, gene exchange between major groups of Archaea appears to be largely random, with no major 'highways' of horizontal gene transfer. The updated collection of arCOGs is expected to become a key resource for comparative genomics, evolutionary reconstruction and functional annotation of new archaeal genomes. Given that, in spite of the major increase in the number of genomes, the conserved core of archaeal genes appears to be stabilizing, the major evolutionary trends revealed here have a chance to stand the test of time. This article was reviewed by (for complete reviews see the Reviewers' Reports section): Dr. PLG, Prof. PF, Dr. PL (nominated by Prof. JPG).

MAFAGS-OS: New opacity sampling model atmospheres for A, F and G stars. I. The model and the solar flux

NASA Astrophysics Data System (ADS)

Grupp, F.

2004-06-01

We present a new opacity sampling model atmosphere code, named MAFAGS-OS. This code, designed for stars reaching from A0 down to G9 on a solar and metal poor main sequence and up to an evolutionary stage represented by the turnoff is introduced in its basic input physics and modelling techniques. Fe I bound-free cross-sections of \\citet{BAUTISTA97} are used and convection is treated according to \\citet{canuto91}. An αcm-parameter for the efficiency of convection of 0.82 is used as determined by \\citet{BERNKOPF98} from stellar evolution requirements. Within the process of opacity sampling, special attention is drawn to the matter of line selection. We show that a selection criterion, in which lines are chosen by their opacity weighted relative to the continuous background opacity, is useful and valid. The solar model calculated using this new code is shown to fit the measured solar flux distribution. It is also tested against the measured solar colours and leads to U-B=0.21 and B-V=0.64, in good agreement with observation. Comparison with measured centre-to-limb continuum data show only small improvement with respect to opacity-sampling type model atmospheres. This is the first of a series of 2 papers. Paper II will deal with the matter of temperature determination using Balmer lines and the infrared-flux method; furthermore it will present three ``standard'' stars analysed using this new model.
Gas stripping and mixing in galaxy clusters: a numerical comparison study

NASA Astrophysics Data System (ADS)

Heß, Steffen; Springel, Volker

2012-11-01

The ambient hot intrahalo gas in clusters of galaxies is constantly fed and stirred by infalling galaxies, a process that can be studied in detail with cosmological hydrodynamical simulations. However, different numerical methods yield discrepant predictions for crucial hydrodynamical processes, leading for example to different entropy profiles in clusters of galaxies. In particular, the widely used Lagrangian smoothed particle hydrodynamics (SPH) scheme is suspected to strongly damp fluid instabilities and turbulence, which are both crucial to establish the thermodynamic structure of clusters. In this study, we test to which extent our recently developed Voronoi particle hydrodynamics (VPH) scheme yields different results for the stripping of gas out of infalling galaxies and for the bulk gas properties of cluster. We consider both the evolution of isolated galaxy models that are exposed to a stream of intracluster medium or are dropped into cluster models, as well as non-radiative cosmological simulations of cluster formation. We also compare our particle-based method with results obtained with a fundamentally different discretization approach as implemented in the moving-mesh code AREPO. We find that VPH leads to noticeably faster stripping of gas out of galaxies than SPH, in better agreement with the mesh-code than with SPH. We show that despite the fact that VPH in its present form is not as accurate as the moving mesh code in our investigated cases, its improved accuracy of gradient estimates makes VPH an attractive alternative to SPH.
SHARP: A Spatially Higher-order, Relativistic Particle-in-cell Code

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

Shalaby, Mohamad; Broderick, Avery E.; Chang, Philip

Numerical heating in particle-in-cell (PIC) codes currently precludes the accurate simulation of cold, relativistic plasma over long periods, severely limiting their applications in astrophysical environments. We present a spatially higher-order accurate relativistic PIC algorithm in one spatial dimension, which conserves charge and momentum exactly. We utilize the smoothness implied by the usage of higher-order interpolation functions to achieve a spatially higher-order accurate algorithm (up to the fifth order). We validate our algorithm against several test problems—thermal stability of stationary plasma, stability of linear plasma waves, and two-stream instability in the relativistic and non-relativistic regimes. Comparing our simulations to exact solutionsmore » of the dispersion relations, we demonstrate that SHARP can quantitatively reproduce important kinetic features of the linear regime. Our simulations have a superior ability to control energy non-conservation and avoid numerical heating in comparison to common second-order schemes. We provide a natural definition for convergence of a general PIC algorithm: the complement of physical modes captured by the simulation, i.e., those that lie above the Poisson noise, must grow commensurately with the resolution. This implies that it is necessary to simultaneously increase the number of particles per cell and decrease the cell size. We demonstrate that traditional ways for testing for convergence fail, leading to plateauing of the energy error. This new PIC code enables us to faithfully study the long-term evolution of plasma problems that require absolute control of the energy and momentum conservation.« less
Antimicrobial peptide evolution in the Asiatic honey bee Apis cerana.

PubMed

Xu, Peng; Shi, Min; Chen, Xue-Xin

2009-01-01

The Asiatic honeybee, Apis cerana Fabricius, is an important honeybee species in Asian countries. It is still found in the wild, but is also one of the few bee species that can be domesticated. It has acquired some genetic advantages and significantly different biological characteristics compared with other Apis species. However, it has been less studied, and over the past two decades, has become a threatened species in China. We designed primers for the sequences of the four antimicrobial peptide cDNA gene families (abaecin, defensin, apidaecin, and hymenoptaecin) of the Western honeybee, Apis mellifera L. and identified all the antimicrobial peptide cDNA genes in the Asiatic honeybee for the first time. All the sequences were amplified by reverse transcriptase-polymerase chain reaction (RT-PCR). In all, 29 different defensin cDNA genes coding 7 different defensin peptides, 11 different abaecin cDNA genes coding 2 different abaecin peptides, 13 different apidaecin cDNA genes coding 4 apidaecin peptides and 34 different hymenoptaecin cDNA genes coding 13 different hymenoptaecin peptides were cloned and identified from the Asiatic honeybee adult workers. Detailed comparison of these four antimicrobial peptide gene families with those of the Western honeybee revealed that there are many similarities in the quantity and amino acid components of peptides in the abaecin, defensin and apidaecin families, while many more hymenoptaecin peptides are found in the Asiatic honeybee than those in the Western honeybee (13 versus 1). The results indicated that the Asiatic honeybee adult generated more variable antimicrobial peptides, especially hymenoptaecin peptides than the Western honeybee when stimulated by pathogens or injury. This suggests that, compared to the Western honeybee that has a longer history of domestication, selection on the Asiatic honeybee has favored the generation of more variable antimicrobial peptides as protection against pathogens.
StarHorse: a Bayesian tool for determining stellar masses, ages, distances, and extinctions for field stars

NASA Astrophysics Data System (ADS)

Queiroz, A. B. A.; Anders, F.; Santiago, B. X.; Chiappini, C.; Steinmetz, M.; Dal Ponte, M.; Stassun, K. G.; da Costa, L. N.; Maia, M. A. G.; Crestani, J.; Beers, T. C.; Fernández-Trincado, J. G.; García-Hernández, D. A.; Roman-Lopes, A.; Zamora, O.

2018-05-01

Understanding the formation and evolution of our Galaxy requires accurate distances, ages, and chemistry for large populations of field stars. Here, we present several updates to our spectrophotometric distance code, which can now also be used to estimate ages, masses, and extinctions for individual stars. Given a set of measured spectrophotometric parameters, we calculate the posterior probability distribution over a given grid of stellar evolutionary models, using flexible Galactic stellar-population priors. The code (called StarHorse) can accommodate different observational data sets, prior options, partially missing data, and the inclusion of parallax information into the estimated probabilities. We validate the code using a variety of simulated stars as well as real stars with parameters determined from asteroseismology, eclipsing binaries, and isochrone fits to star clusters. Our main goal in this validation process is to test the applicability of the code to field stars with known Gaia-like parallaxes. The typical internal precisions (obtained from realistic simulations of an APOGEE+Gaia-like sample) are {˜eq } 8 {per cent} in distance, {˜eq } 20 {per cent} in age, {˜eq } 6 {per cent} in mass, and ≃ 0.04 mag in AV. The median external precision (derived from comparisons with earlier work for real stars) varies with the sample used, but lies in the range of {˜eq } [0,2] {per cent} for distances, {˜eq } [12,31] {per cent} for ages, {˜eq } [4,12] {per cent} for masses, and ≃ 0.07 mag for AV. We provide StarHorse distances and extinctions for the APOGEE DR14, RAVE DR5, GES DR3, and GALAH DR1 catalogues.
Comparison of space radiation calculations for deterministic and Monte Carlo transport codes

NASA Astrophysics Data System (ADS)

Lin, Zi-Wei; Adams, James; Barghouty, Abdulnasser; Randeniya, Sharmalee; Tripathi, Ram; Watts, John; Yepes, Pablo

For space radiation protection of astronauts or electronic equipments, it is necessary to develop and use accurate radiation transport codes. Radiation transport codes include deterministic codes, such as HZETRN from NASA and UPROP from the Naval Research Laboratory, and Monte Carlo codes such as FLUKA, the Geant4 toolkit and HETC-HEDS. The deterministic codes and Monte Carlo codes complement each other in that deterministic codes are very fast while Monte Carlo codes are more elaborate. Therefore it is important to investigate how well the results of deterministic codes compare with those of Monte Carlo transport codes and where they differ. In this study we evaluate these different codes in their space radiation applications by comparing their output results in the same given space radiation environments, shielding geometry and material. Typical space radiation environments such as the 1977 solar minimum galactic cosmic ray environment are used as the well-defined input, and simple geometries made of aluminum, water and/or polyethylene are used to represent the shielding material. We then compare various outputs of these codes, such as the dose-depth curves and the flux spectra of different fragments and other secondary particles. These comparisons enable us to learn more about the main differences between these space radiation transport codes. At the same time, they help us to learn the qualitative and quantitative features that these transport codes have in common.
How the Geothermal Community Upped the Game for Computer Codes

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

None

The Geothermal Technologies Office Code Comparison Study brought 11 research institutions together to collaborate on coupled thermal, hydrologic, geomechanical, and geochemical numerical simulators. These codes have the potential to help facilitate widespread geothermal energy development.
Numerical algorithm comparison for the accurate and efficient computation of high-incidence vortical flow

NASA Technical Reports Server (NTRS)

Chaderjian, Neal M.

1991-01-01

Computations from two Navier-Stokes codes, NSS and F3D, are presented for a tangent-ogive-cylinder body at high angle of attack. Features of this steady flow include a pair of primary vortices on the leeward side of the body as well as secondary vortices. The topological and physical plausibility of this vortical structure is discussed. The accuracy of these codes are assessed by comparison of the numerical solutions with experimental data. The effects of turbulence model, numerical dissipation, and grid refinement are presented. The overall efficiency of these codes are also assessed by examining their convergence rates, computational time per time step, and maximum allowable time step for time-accurate computations. Overall, the numerical results from both codes compared equally well with experimental data, however, the NSS code was found to be significantly more efficient than the F3D code.
Toward a CFD nose-to-tail capability - Hypersonic unsteady Navier-Stokes code validation

NASA Technical Reports Server (NTRS)

Edwards, Thomas A.; Flores, Jolen

1989-01-01

Computational fluid dynamics (CFD) research for hypersonic flows presents new problems in code validation because of the added complexity of the physical models. This paper surveys code validation procedures applicable to hypersonic flow models that include real gas effects. The current status of hypersonic CFD flow analysis is assessed with the Compressible Navier-Stokes (CNS) code as a case study. The methods of code validation discussed to beyond comparison with experimental data to include comparisons with other codes and formulations, component analyses, and estimation of numerical errors. Current results indicate that predicting hypersonic flows of perfect gases and equilibrium air are well in hand. Pressure, shock location, and integrated quantities are relatively easy to predict accurately, while surface quantities such as heat transfer are more sensitive to the solution procedure. Modeling transition to turbulence needs refinement, though preliminary results are promising.
WEC3: Wave Energy Converter Code Comparison Project: Preprint

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

Combourieu, Adrien; Lawson, Michael; Babarit, Aurelien

This paper describes the recently launched Wave Energy Converter Code Comparison (WEC3) project and present preliminary results from this effort. The objectives of WEC3 are to verify and validate numerical modelling tools that have been developed specifically to simulate wave energy conversion devices and to inform the upcoming IEA OES Annex VI Ocean Energy Modelling Verification and Validation project. WEC3 is divided into two phases. Phase 1 consists of a code-to-code verification and Phase II entails code-to-experiment validation. WEC3 focuses on mid-fidelity codes that simulate WECs using time-domain multibody dynamics methods to model device motions and hydrodynamic coefficients to modelmore » hydrodynamic forces. Consequently, high-fidelity numerical modelling tools, such as Navier-Stokes computational fluid dynamics simulation, and simple frequency domain modelling tools were not included in the WEC3 project.« less
Convolutional coding combined with continuous phase modulation

NASA Technical Reports Server (NTRS)

Pizzi, S. V.; Wilson, S. G.

1985-01-01

Background theory and specific coding designs for combined coding/modulation schemes utilizing convolutional codes and continuous-phase modulation (CPM) are presented. In this paper the case of r = 1/2 coding onto a 4-ary CPM is emphasized, with short-constraint length codes presented for continuous-phase FSK, double-raised-cosine, and triple-raised-cosine modulation. Coding buys several decibels of coding gain over the Gaussian channel, with an attendant increase of bandwidth. Performance comparisons in the power-bandwidth tradeoff with other approaches are made.
Emergence and Evolution

PubMed Central

Bullwinkle, Tammy J.

2013-01-01

The aminoacyl-tRNA synthetases (aaRSs) are essential components of the protein synthesis machinery responsible for defining the genetic code by pairing the correct amino acids to their cognate tRNAs. The aaRSs are an ancient enzyme family believed to have origins that may predate the last common ancestor and as such they provide insights into the evolution and development of the extant genetic code. Although the aaRSs have long been viewed as a highly conserved group of enzymes, findings within the last couple of decades have started to demonstrate how diverse and versatile these enzymes really are. Beyond their central role in translation, aaRSs and their numerous homologs have evolved a wide array of alternative functions both inside and outside translation. Current understanding of the emergence of the aaRSs, and their subsequent evolution into a functionally diverse enzyme family, are discussed in this chapter. PMID:23478877
Multi-dimensional free-electron laser simulation codes : a comparison study.

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

Biedron, S. G.; Chae, Y. C.; Dejus, R. J.

A self-amplified spontaneous emission (SASE) free-electron laser (FEL) is under construction at the Advanced Photon Source (APS). Five FEL simulation codes were used in the design phase: GENESIS, GINGER, MEDUSA, RON, and TDA3D. Initial comparisons between each of these independent formulations show good agreement for the parameters of the APS SASE FEL.
Multi-Dimensional Free-Electron Laser Simulation Codes: A Comparison Study

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

Nuhn, Heinz-Dieter

A self-amplified spontaneous emission (SASE) free-electron laser (FEL) is under construction at the Advanced Photon Source (APS). Five FEL simulation codes were used in the design phase: GENESIS, GINGER, MEDUSA, RON, and TDA3D. Initial comparisons between each of these independent formulations show good agreement for the parameters of the APS SASE FEL.
The APS SASE FEL : modeling and code comparison.

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

Biedron, S. G.

A self-amplified spontaneous emission (SASE) free-electron laser (FEL) is under construction at the Advanced Photon Source (APS). Five FEL simulation codes were used in the design phase: GENESIS, GINGER, MEDUSA, RON, and TDA3D. Initial comparisons between each of these independent formulations show good agreement for the parameters of the APS SASE FEL.
Newspaper Ethics and Managing Editors: The Evolution of APME's Code.

ERIC Educational Resources Information Center

De Mott, John

A review of the 42-year development of the professional code of ethics of the Associated Press Managing Editors (APME) demonstrates an effort to elevate newspaper ethical standards around the country. Following the example of the American Society of Newspaper Editors in establishing its "Canons of Journalism" in 1923, the APME formed a…
Comparison of reversible methods for data compression

NASA Astrophysics Data System (ADS)

Heer, Volker K.; Reinfelder, Hans-Erich

1990-07-01

Widely differing methods for data compression described in the ACR-NEMA draft are used in medical imaging. In our contribution we will review various methods briefly and discuss the relevant advantages and disadvantages. In detail we evaluate 1st order DPCM pyramid transformation and S transformation. We compare as coding algorithms both fixed and adaptive Huffman coding and Lempel-Ziv coding. Our comparison is performed on typical medical images from CT MR DSA and DLR (Digital Luminescence Radiography). Apart from the achieved compression factors we take into account CPU time required and main memory requirement both for compression and for decompression. For a realistic comparison we have implemented the mentioned algorithms in the C program language on a MicroVAX II and a SPARC station 1. 2.
Comparison of Evolutionary (Genetic) Algorithm and Adjoint Methods for Multi-Objective Viscous Airfoil Optimizations

NASA Technical Reports Server (NTRS)

Pulliam, T. H.; Nemec, M.; Holst, T.; Zingg, D. W.; Kwak, Dochan (Technical Monitor)

2002-01-01

A comparison between an Evolutionary Algorithm (EA) and an Adjoint-Gradient (AG) Method applied to a two-dimensional Navier-Stokes code for airfoil design is presented. Both approaches use a common function evaluation code, the steady-state explicit part of the code,ARC2D. The parameterization of the design space is a common B-spline approach for an airfoil surface, which together with a common griding approach, restricts the AG and EA to the same design space. Results are presented for a class of viscous transonic airfoils in which the optimization tradeoff between drag minimization as one objective and lift maximization as another, produces the multi-objective design space. Comparisons are made for efficiency, accuracy and design consistency.
Origin and evolution of the long non-coding genes in the X-inactivation center.

PubMed

Romito, Antonio; Rougeulle, Claire

2011-11-01

Random X chromosome inactivation (XCI), the eutherian mechanism of X-linked gene dosage compensation, is controlled by a cis-acting locus termed the X-inactivation center (Xic). One of the striking features that characterize the Xic landscape is the abundance of loci transcribing non-coding RNAs (ncRNAs), including Xist, the master regulator of the inactivation process. Recent comparative genomic analyses have depicted the evolutionary scenario behind the origin of the X-inactivation center, revealing that this locus evolved from a region harboring protein-coding genes. During mammalian radiation, this ancestral protein-coding region was disrupted in the marsupial group, whilst it provided in eutherian lineage the starting material for the non-translated RNAs of the X-inactivation center. The emergence of non-coding genes occurred by a dual mechanism involving loss of protein-coding function of the pre-existing genes and integration of different classes of mobile elements, some of which modeled the structure and sequence of the non-coding genes in a species-specific manner. The rising genes started to produce transcripts that acquired function in regulating the epigenetic status of the X chromosome, as shown for Xist, its antisense Tsix, Jpx, and recently suggested for Ftx. Thus, the appearance of the Xic, which occurred after the divergence between eutherians and marsupials, was the basis for the evolution of random X inactivation as a strategy to achieve dosage compensation. Copyright © 2011. Published by Elsevier Masson SAS.
Recent evidence for evolution of the genetic code

NASA Technical Reports Server (NTRS)

Osawa, S.; Jukes, T. H.; Watanabe, K.; Muto, A.

1992-01-01

The genetic code, formerly thought to be frozen, is now known to be in a state of evolution. This was first shown in 1979 by Barrell et al. (G. Barrell, A. T. Bankier, and J. Drouin, Nature [London] 282:189-194, 1979), who found that the universal codons AUA (isoleucine) and UGA (stop) coded for methionine and tryptophan, respectively, in human mitochondria. Subsequent studies have shown that UGA codes for tryptophan in Mycoplasma spp. and in all nonplant mitochondria that have been examined. Universal stop codons UAA and UAG code for glutamine in ciliated protozoa (except Euplotes octacarinatus) and in a green alga, Acetabularia. E. octacarinatus uses UAA for stop and UGA for cysteine. Candida species, which are yeasts, use CUG (leucine) for serine. Other departures from the universal code, all in nonplant mitochondria, are CUN (leucine) for threonine (in yeasts), AAA (lysine) for asparagine (in platyhelminths and echinoderms), UAA (stop) for tyrosine (in planaria), and AGR (arginine) for serine (in several animal orders) and for stop (in vertebrates). We propose that the changes are typically preceded by loss of a codon from all coding sequences in an organism or organelle, often as a result of directional mutation pressure, accompanied by loss of the tRNA that translates the codon. The codon reappears later by conversion of another codon and emergence of a tRNA that translates the reappeared codon with a different assignment. Changes in release factors also contribute to these revised assignments. We also discuss the use of UGA (stop) as a selenocysteine codon and the early history of the code.

Radiant Energy Measurements from a Scaled Jet Engine Axisymmetric Exhaust Nozzle for a Baseline Code Validation Case

NASA Technical Reports Server (NTRS)

Baumeister, Joseph F.

1994-01-01

A non-flowing, electrically heated test rig was developed to verify computer codes that calculate radiant energy propagation from nozzle geometries that represent aircraft propulsion nozzle systems. Since there are a variety of analysis tools used to evaluate thermal radiation propagation from partially enclosed nozzle surfaces, an experimental benchmark test case was developed for code comparison. This paper briefly describes the nozzle test rig and the developed analytical nozzle geometry used to compare the experimental and predicted thermal radiation results. A major objective of this effort was to make available the experimental results and the analytical model in a format to facilitate conversion to existing computer code formats. For code validation purposes this nozzle geometry represents one validation case for one set of analysis conditions. Since each computer code has advantages and disadvantages based on scope, requirements, and desired accuracy, the usefulness of this single nozzle baseline validation case can be limited for some code comparisons.
Impact of dynamic rate coding aspects of mobile phone networks on forensic voice comparison.

PubMed

Alzqhoul, Esam A S; Nair, Balamurali B T; Guillemin, Bernard J

2015-09-01

Previous studies have shown that landline and mobile phone networks are different in their ways of handling the speech signal, and therefore in their impact on it. But the same is also true of the different networks within the mobile phone arena. There are two major mobile phone technologies currently in use today, namely the global system for mobile communications (GSM) and code division multiple access (CDMA) and these are fundamentally different in their design. For example, the quality of the coded speech in the GSM network is a function of channel quality, whereas in the CDMA network it is determined by channel capacity (i.e., the number of users sharing a cell site). This paper examines the impact on the speech signal of a key feature of these networks, namely dynamic rate coding, and its subsequent impact on the task of likelihood-ratio-based forensic voice comparison (FVC). Surprisingly, both FVC accuracy and precision are found to be better for both GSM- and CDMA-coded speech than for uncoded. Intuitively one expects FVC accuracy to increase with increasing coded speech quality. This trend is shown to occur for the CDMA network, but, surprisingly, not for the GSM network. Further, in respect to comparisons between these two networks, FVC accuracy for CDMA-coded speech is shown to be slightly better than for GSM-coded speech, particularly when the coded-speech quality is high, but in terms of FVC precision the two networks are shown to be very similar. Copyright © 2015 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.
Verification of Three Dimensional Triangular Prismatic Discrete Ordinates Transport Code ENSEMBLE-TRIZ by Comparison with Monte Carlo Code GMVP

NASA Astrophysics Data System (ADS)

Homma, Yuto; Moriwaki, Hiroyuki; Ohki, Shigeo; Ikeda, Kazumi

2014-06-01

This paper deals with verification of three dimensional triangular prismatic discrete ordinates transport calculation code ENSEMBLE-TRIZ by comparison with multi-group Monte Carlo calculation code GMVP in a large fast breeder reactor. The reactor is a 750 MWe electric power sodium cooled reactor. Nuclear characteristics are calculated at beginning of cycle of an initial core and at beginning and end of cycle of equilibrium core. According to the calculations, the differences between the two methodologies are smaller than 0.0002 Δk in the multi-plication factor, relatively about 1% in the control rod reactivity, and 1% in the sodium void reactivity.
Improving the coding and classification of ambulance data through the application of International Classification of Disease 10th revision.

PubMed

Cantwell, Kate; Morgans, Amee; Smith, Karen; Livingston, Michael; Dietze, Paul

2014-02-01

This paper aims to examine whether an adaptation of the International Classification of Disease (ICD) coding system can be applied retrospectively to final paramedic assessment data in an ambulance dataset with a view to developing more fine-grained, clinically relevant case definitions than are available through point-of-call data. Over 1.2 million case records were extracted from the Ambulance Victoria data warehouse. Data fields included dispatch code, cause (CN) and final primary assessment (FPA). Each FPA was converted to an ICD-10-AM code using word matching or best fit. ICD-10-AM codes were then converted into Major Diagnostic Categories (MDC). CN was aligned with the ICD-10-AM codes for external cause of morbidity and mortality. The most accurate results were obtained when ICD-10-AM codes were assigned using information from both FPA and CN. Comparison of cases coded as unconscious at point-of-call with the associated paramedic assessment highlighted the extra clinical detail obtained when paramedic assessment data are used. Ambulance paramedic assessment data can be aligned with ICD-10-AM and MDC with relative ease, allowing retrospective coding of large datasets. Coding of ambulance data using ICD-10-AM allows for comparison of not only ambulance service users but also with other population groups. WHAT IS KNOWN ABOUT THE TOPIC? There is no reliable and standard coding and categorising system for paramedic assessment data contained in ambulance service databases. WHAT DOES THIS PAPER ADD? This study demonstrates that ambulance paramedic assessment data can be aligned with ICD-10-AM and MDC with relative ease, allowing retrospective coding of large datasets. Representation of ambulance case types using ICD-10-AM-coded information obtained after paramedic assessment is more fine grained and clinically relevant than point-of-call data, which uses caller information before ambulance attendance. WHAT ARE THE IMPLICATIONS FOR PRACTITIONERS? This paper describes a model of coding using an internationally recognised standard coding and categorising system to support analysis of paramedic assessment. Ambulance data coded using ICD-10-AM allows for reliable reporting and comparison within the prehospital setting and across the healthcare industry.
Jet Noise Modeling for Suppressed and Unsuppressed Aircraft in Simulated Flight

NASA Technical Reports Server (NTRS)

Stone, James R.; Krejsa, Eugene A.; Clark, Bruce J; Berton, Jeffrey J.

2009-01-01

This document describes the development of further extensions and improvements to the jet noise model developed by Modern Technologies Corporation (MTC) for the National Aeronautics and Space Administration (NASA). The noise component extraction and correlation approach, first used successfully by MTC in developing a noise prediction model for two-dimensional mixer ejector (2DME) nozzles under the High Speed Research (HSR) Program, has been applied to dual-stream nozzles, then extended and improved in earlier tasks under this contract. Under Task 6, the coannular jet noise model was formulated and calibrated with limited scale model data, mainly at high bypass ratio, including a limited-range prediction of the effects of mixing-enhancement nozzle-exit chevrons on jet noise. Under Task 9 this model was extended to a wider range of conditions, particularly those appropriate for a Supersonic Business Jet, with an improvement in simulated flight effects modeling and generalization of the suppressor model. In the present task further comparisons are made over a still wider range of conditions from more test facilities. The model is also further generalized to cover single-stream nozzles of otherwise similar configuration. So the evolution of this prediction/analysis/correlation approach has been in a sense backward, from the complex to the simple; but from this approach a very robust capability is emerging. Also from these studies, some observations emerge relative to theoretical considerations. The purpose of this task is to develop an analytical, semi-empirical jet noise prediction method applicable to takeoff, sideline and approach noise of subsonic and supersonic cruise aircraft over a wide size range. The product of this task is an even more consistent and robust model for the Footprint/Radius (FOOTPR) code than even the Task 9 model. The model is validated for a wider range of cases and statistically quantified for the various reference facilities. The possible role of facility effects will thus be documented. Although the comparisons that can be accomplished within the limited resources of this task are not comprehensive, they provide a broad enough sampling to enable NASA to make an informed decision on how much further effort should be expended on such comparisons. The improved finalized model is incorporated into the FOOTPR code. MTC has also supported the adaptation of this code for incorporation in NASA s Aircraft Noise Prediction Program (ANOPP).
Numerical relativity for D dimensional axially symmetric space-times: Formalism and code tests

NASA Astrophysics Data System (ADS)

Zilhão, Miguel; Witek, Helvi; Sperhake, Ulrich; Cardoso, Vitor; Gualtieri, Leonardo; Herdeiro, Carlos; Nerozzi, Andrea

2010-04-01

The numerical evolution of Einstein’s field equations in a generic background has the potential to answer a variety of important questions in physics: from applications to the gauge-gravity duality, to modeling black hole production in TeV gravity scenarios, to analysis of the stability of exact solutions, and to tests of cosmic censorship. In order to investigate these questions, we extend numerical relativity to more general space-times than those investigated hitherto, by developing a framework to study the numerical evolution of D dimensional vacuum space-times with an SO(D-2) isometry group for D≥5, or SO(D-3) for D≥6. Performing a dimensional reduction on a (D-4) sphere, the D dimensional vacuum Einstein equations are rewritten as a 3+1 dimensional system with source terms, and presented in the Baumgarte, Shapiro, Shibata, and Nakamura formulation. This allows the use of existing 3+1 dimensional numerical codes with small adaptations. Brill-Lindquist initial data are constructed in D dimensions and a procedure to match them to our 3+1 dimensional evolution equations is given. We have implemented our framework by adapting the Lean code and perform a variety of simulations of nonspinning black hole space-times. Specifically, we present a modified moving puncture gauge, which facilitates long-term stable simulations in D=5. We further demonstrate the internal consistency of the code by studying convergence and comparing numerical versus analytic results in the case of geodesic slicing for D=5, 6.
Observing Stellar Clusters in the Computer

NASA Astrophysics Data System (ADS)

Borch, A.; Spurzem, R.; Hurley, J.

2006-08-01

We present a new approach to combine direct N-body simulations to stellar population synthesis modeling in order to model the dynamical evolution and color evolution of globular clusters at the same time. This allows us to model the spectrum, colors and luminosities of each star in the simulated cluster. For this purpose the NBODY6++ code (Spurzem 1999) is used, which is a parallel version of the NBODY code. J. Hurley implemented simple recipes to follow the changes of stellar masses, radii, and luminosities due to stellar evolution into the NBODY6++ code (Hurley et al. 2001), in the sense that each simulation particle represents one star. These prescriptions cover all evolutionary phases and solar to globular cluster metallicities. We used the stellar parameters obtained by this stellar evolution routine and coupled them to the stellar library BaSeL 2.0 (Lejeune et al. 1997). As a first application we investigated the integrated broad band colors of simulated clusters. We modeled tidally disrupted globular clusters and compared the results with isolated globular clusters. Due to energy equipartition we expected a relative blueing of tidally disrupted clusters, because of the higher escape probability of red, low-mass stars. This behaviour we actually observe for concentrated globular clusters. The mass-to-light ratio of isolated clusters follows exactly a color-M/L correlation, similar as described in Bell and de Jong (2001) in the case of spiral galaxies. At variance to this correlation, in tidally disrupted clusters the M/L ratio becomes significantly lower at the time of cluster dissolution. Hence, for isolated clusters the behavior of the stellar population is not influenced by dynamical evolution, whereas the stellar population of tidally disrupted clusters is strongly influenced by dynamical effects.
Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

PubMed

García, Miguel A; Costea, Mihai; Kuzmina, Maria; Stefanović, Saša

2014-04-01

The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.
Coalescing neutron stars - gravitational waves from polytropic models.

NASA Astrophysics Data System (ADS)

Ruffert, M.; Rampp, M.; Janka, H.-T.

1997-05-01

The dynamics, time evolution of the mass distribution, and gravitational wave signature of coalescing neutron stars described by polytropes are compared with three simulations published previously: (a) "Run 2" of Zhuge et al. (1994PhRvD..50.6247Z), (b) "Model III" of Shibata et al. (1992, Prog, Theor. Phys. 88, 1079), and (c) "Model A64" of Ruffert et al. (1996A&A...311..532R). We aim at studying the differences due to the use of different numerical methods, different implementations of the gravitational wave backreaction, and different equations of state. We integrate the three-dimensional Newtonian equations of hydrodynamics by the Riemann-solver based "Piecewise Parabolic Method" on an equidistant Cartesian grid. Comparison (a) confronts the results of our grid-based PPM scheme with those from an SPH code. We find that due to the lower numerical viscosity of the PPM code, the post-merging oscillations and pulsations can be followed for a longer time and lead to larger secondary and tertiary maxima of the gravitational wave luminosity and to a stronger peak of the gravitational wave spectrum at a frequency of about f=~1.8KHz when compared to the results of Zhuge et al. (1994PhRvD..50.6247Z). In case (b) two grid based codes with the same backreaction formalism but differing hydrodynamic integrators and slightly different initial conditions are compared. Instead of rotationally deformed initial neutron stars we use spherically shaped stars. Satisfactory agreement of the amplitude of the gravitational wave luminosity is established, although due to the different initial conditions a small time delay develops in the onset of the dynamical instability setting in when the two stars come very close. In (c) we find that using a polytropic equation of state instead of the high-density equation of state of Lattimer & Swesty (1991, Nucl. Phys. A535, 331) employed by Ruffert et al. (1996A&A...311..532R) does not change the overall dynamical evolution of the merger and yields agreement of the gravitational wave signature to within 20% accuracy. Whereas the polytropic law describes the dynamical behaviour of the bulk of the matter at and above nuclear density sufficiently well, we, however, find clear differences of the structure and evolution of the outer layers of the neutron stars where the stiffness of the equation of state is largely overestimated. This has important implications for questions like mass loss and disk formation during the merging of binary neutron stars.
Slow but not low: genomic comparisons reveal slower evolutionary rate and higher dN/dS in conifers compared to angiosperms

PubMed Central

2012-01-01

Background Comparative genomics can inform us about the processes of mutation and selection across diverse taxa. Among seed plants, gymnosperms have been lacking in genomic comparisons. Recent EST and full-length cDNA collections for two conifers, Sitka spruce (Picea sitchensis) and loblolly pine (Pinus taeda), together with full genome sequences for two angiosperms, Arabidopsis thaliana and poplar (Populus trichocarpa), offer an opportunity to infer the evolutionary processes underlying thousands of orthologous protein-coding genes in gymnosperms compared with an angiosperm orthologue set. Results Based upon pairwise comparisons of 3,723 spruce and pine orthologues, we found an average synonymous genetic distance (dS) of 0.191, and an average dN/dS ratio of 0.314. Using a fossil-established divergence time of 140 million years between spruce and pine, we extrapolated a nucleotide substitution rate of 0.68 × 10-9 synonymous substitutions per site per year. When compared to angiosperms, this indicates a dramatically slower rate of nucleotide substitution rates in conifers: on average 15-fold. Coincidentally, we found a three-fold higher dN/dS for the spruce-pine lineage compared to the poplar-Arabidopsis lineage. This joint occurrence of a slower evolutionary rate in conifers with higher dN/dS, and possibly positive selection, showcases the uniqueness of conifer genome evolution. Conclusions Our results are in line with documented reduced nucleotide diversity, conservative genome evolution and low rates of diversification in conifers on the one hand and numerous examples of local adaptation in conifers on the other hand. We propose that reduced levels of nucleotide mutation in large and long-lived conifer trees, coupled with large effective population size, were the main factors leading to slow substitution rates but retention of beneficial mutations. PMID:22264329
A verification of the gyrokinetic microstability codes GEM, GYRO, and GS2

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

Bravenec, R. V.; Chen, Y.; Wan, W.

2013-10-15

A previous publication [R. V. Bravenec et al., Phys. Plasmas 18, 122505 (2011)] presented favorable comparisons of linear frequencies and nonlinear fluxes from the Eulerian gyrokinetic codes gyro[J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] and gs2[W. Dorland et al., Phys. Rev. Lett. 85, 5579 (2000)]. The motivation was to verify the codes, i.e., demonstrate that they correctly solve the gyrokinetic-Maxwell equations. The premise was that it is highly unlikely for both codes to yield the same incorrect results. In this work, we add the Lagrangian particle-in-cell code gem[Y. Chen and S. Parker, J. Comput. Phys.more » 220, 839 (2007)] to the comparisons, not simply to add another code, but also to demonstrate that the codes' algorithms do not matter. We find good agreement of gem with gyro and gs2 for the plasma conditions considered earlier, thus establishing confidence that the codes are verified and that ongoing validation efforts for these plasma parameters are warranted.« less
Comparative analysis of complete chloroplast genome sequence and inversion variation in Lasthenia burkei (Madieae, Asteraceae).

PubMed

Walker, Joseph F; Zanis, Michael J; Emery, Nancy C

2014-04-01

Complete chloroplast genome studies can help resolve relationships among large, complex plant lineages such as Asteraceae. We present the first whole plastome from the Madieae tribe and compare its sequence variation to other chloroplast genomes in Asteraceae. We used high throughput sequencing to obtain the Lasthenia burkei chloroplast genome. We compared sequence structure and rates of molecular evolution in the small single copy (SSC), large single copy (LSC), and inverted repeat (IR) regions to those for eight Asteraceae accessions and one Solanaceae accession. The chloroplast sequence of L. burkei is 150 746 bp and contains 81 unique protein coding genes and 4 coding ribosomal RNA sequences. We identified three major inversions in the L. burkei chloroplast, all of which have been found in other Asteraceae lineages, and a previously unreported inversion in Lactuca sativa. Regions flanking inversions contained tRNA sequences, but did not have particularly high G + C content. Substitution rates varied among the SSC, LSC, and IR regions, and rates of evolution within each region varied among species. Some observed differences in rates of molecular evolution may be explained by the relative proportion of coding to noncoding sequence within regions. Rates of molecular evolution vary substantially within and among chloroplast genomes, and major inversion events may be promoted by the presence of tRNAs. Collectively, these results provide insight into different mechanisms that may promote intramolecular recombination and the inversion of large genomic regions in the plastome.
Mechanisms of haplotype divergence at the RGA08 nucleotide-binding leucine-rich repeat gene locus in wild banana (Musa balbisiana).

PubMed

Baurens, Franc-Christophe; Bocs, Stéphanie; Rouard, Mathieu; Matsumoto, Takashi; Miller, Robert N G; Rodier-Goud, Marguerite; MBéguié-A-MBéguié, Didier; Yahiaoui, Nabila

2010-07-16

Comparative sequence analysis of complex loci such as resistance gene analog clusters allows estimating the degree of sequence conservation and mechanisms of divergence at the intraspecies level. In banana (Musa sp.), two diploid wild species Musa acuminata (A genome) and Musa balbisiana (B genome) contribute to the polyploid genome of many cultivars. The M. balbisiana species is associated with vigour and tolerance to pests and disease and little is known on the genome structure and haplotype diversity within this species. Here, we compare two genomic sequences of 253 and 223 kb corresponding to two haplotypes of the RGA08 resistance gene analog locus in M. balbisiana "Pisang Klutuk Wulung" (PKW). Sequence comparison revealed two regions of contrasting features. The first is a highly colinear gene-rich region where the two haplotypes diverge only by single nucleotide polymorphisms and two repetitive element insertions. The second corresponds to a large cluster of RGA08 genes, with 13 and 18 predicted RGA genes and pseudogenes spread over 131 and 152 kb respectively on each haplotype. The RGA08 cluster is enriched in repetitive element insertions, in duplicated non-coding intergenic sequences including low complexity regions and shows structural variations between haplotypes. Although some allelic relationships are retained, a large diversity of RGA08 genes occurs in this single M. balbisiana genotype, with several RGA08 paralogs specific to each haplotype. The RGA08 gene family has evolved by mechanisms of unequal recombination, intragenic sequence exchange and diversifying selection. An unequal recombination event taking place between duplicated non-coding intergenic sequences resulted in a different RGA08 gene content between haplotypes pointing out the role of such duplicated regions in the evolution of RGA clusters. Based on the synonymous substitution rate in coding sequences, we estimated a 1 million year divergence time for these M. balbisiana haplotypes. A large RGA08 gene cluster identified in wild banana corresponds to a highly variable genomic region between haplotypes surrounded by conserved flanking regions. High level of sequence identity (70 to 99%) of the genic and intergenic regions suggests a recent and rapid evolution of this cluster in M. balbisiana.
Divergent evolutionary rates in vertebrate and mammalian specific conserved non-coding elements (CNEs) in echolocating mammals.

PubMed

Davies, Kalina T J; Tsagkogeorga, Georgia; Rossiter, Stephen J

2014-12-19

The majority of DNA contained within vertebrate genomes is non-coding, with a certain proportion of this thought to play regulatory roles during development. Conserved Non-coding Elements (CNEs) are an abundant group of putative regulatory sequences that are highly conserved across divergent groups and thus assumed to be under strong selective constraint. Many CNEs may contain regulatory factor binding sites, and their frequent spatial association with key developmental genes - such as those regulating sensory system development - suggests crucial roles in regulating gene expression and cellular patterning. Yet surprisingly little is known about the molecular evolution of CNEs across diverse mammalian taxa or their role in specific phenotypic adaptations. We examined 3,110 vertebrate-specific and ~82,000 mammalian-specific CNEs across 19 and 9 mammalian orders respectively, and tested for changes in the rate of evolution of CNEs located in the proximity of genes underlying the development or functioning of auditory systems. As we focused on CNEs putatively associated with genes underlying the development/functioning of auditory systems, we incorporated echolocating taxa in our dataset because of their highly specialised and derived auditory systems. Phylogenetic reconstructions of concatenated CNEs broadly recovered accepted mammal relationships despite high levels of sequence conservation. We found that CNE substitution rates were highest in rodents and lowest in primates, consistent with previous findings. Comparisons of CNE substitution rates from several genomic regions containing genes linked to auditory system development and hearing revealed differences between echolocating and non-echolocating taxa. Wider taxonomic sampling of four CNEs associated with the homeobox genes Hmx2 and Hmx3 - which are required for inner ear development - revealed family-wise variation across diverse bat species. Specifically within one family of echolocating bats that utilise frequency-modulated echolocation calls varying widely in frequency and intensity high levels of sequence divergence were found. Levels of selective constraint acting on CNEs differed both across genomic locations and taxa, with observed variation in substitution rates of CNEs among bat species. More work is needed to determine whether this variation can be linked to echolocation, and wider taxonomic sampling is necessary to fully document levels of conservation in CNEs across diverse taxa.
A universal genomic coordinate translator for comparative genomics

PubMed Central

2014-01-01

Background Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Results Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Conclusions Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken. PMID:24976580
A universal genomic coordinate translator for comparative genomics.

PubMed

Zamani, Neda; Sundström, Görel; Meadows, Jennifer R S; Höppner, Marc P; Dainat, Jacques; Lantz, Henrik; Haas, Brian J; Grabherr, Manfred G

2014-06-30

Genomic duplications constitute major events in the evolution of species, allowing paralogous copies of genes to take on fine-tuned biological roles. Unambiguously identifying the orthology relationship between copies across multiple genomes can be resolved by synteny, i.e. the conserved order of genomic sequences. However, a comprehensive analysis of duplication events and their contributions to evolution would require all-to-all genome alignments, which increases at N2 with the number of available genomes, N. Here, we introduce Kraken, software that omits the all-to-all requirement by recursively traversing a graph of pairwise alignments and dynamically re-computing orthology. Kraken scales linearly with the number of targeted genomes, N, which allows for including large numbers of genomes in analyses. We first evaluated the method on the set of 12 Drosophila genomes, finding that orthologous correspondence computed indirectly through a graph of multiple synteny maps comes at minimal cost in terms of sensitivity, but reduces overall computational runtime by an order of magnitude. We then used the method on three well-annotated mammalian genomes, human, mouse, and rat, and show that up to 93% of protein coding transcripts have unambiguous pairwise orthologous relationships across the genomes. On a nucleotide level, 70 to 83% of exons match exactly at both splice junctions, and up to 97% on at least one junction. We last applied Kraken to an RNA-sequencing dataset from multiple vertebrates and diverse tissues, where we confirmed that brain-specific gene family members, i.e. one-to-many or many-to-many homologs, are more highly correlated across species than single-copy (i.e. one-to-one homologous) genes. Not limited to protein coding genes, Kraken also identifies thousands of newly identified transcribed loci, likely non-coding RNAs that are consistently transcribed in human, chimpanzee and gorilla, and maintain significant correlation of expression levels across species. Kraken is a computational genome coordinate translator that facilitates cross-species comparisons, distinguishes orthologs from paralogs, and does not require costly all-to-all whole genome mappings. Kraken is freely available under LPGL from http://github.com/nedaz/kraken.
The analysis of convolutional codes via the extended Smith algorithm

NASA Technical Reports Server (NTRS)

Mceliece, R. J.; Onyszchuk, I.

1993-01-01

Convolutional codes have been the central part of most error-control systems in deep-space communication for many years. Almost all such applications, however, have used the restricted class of (n,1), also known as 'rate 1/n,' convolutional codes. The more general class of (n,k) convolutional codes contains many potentially useful codes, but their algebraic theory is difficult and has proved to be a stumbling block in the evolution of convolutional coding systems. In this article, the situation is improved by describing a set of practical algorithms for computing certain basic things about a convolutional code (among them the degree, the Forney indices, a minimal generator matrix, and a parity-check matrix), which are usually needed before a system using the code can be built. The approach is based on the classic Forney theory for convolutional codes, together with the extended Smith algorithm for polynomial matrices, which is introduced in this article.
Comparative modelling of lower hybrid current drive with two launcher designs in the Tore Supra tokamak

NASA Astrophysics Data System (ADS)

Nilsson, E.; Decker, J.; Peysson, Y.; Artaud, J.-F.; Ekedahl, A.; Hillairet, J.; Aniel, T.; Basiuk, V.; Goniche, M.; Imbeaux, F.; Mazon, D.; Sharma, P.

2013-08-01

Fully non-inductive operation with lower hybrid current drive (LHCD) in the Tore Supra tokamak is achieved using either a fully active multijunction (FAM) launcher or a more recent ITER-relevant passive active multijunction (PAM) launcher, or both launchers simultaneously. While both antennas show comparable experimental efficiencies, the analysis of stability properties in long discharges suggest different current profiles. We present comparative modelling of LHCD with the two different launchers to characterize the effect of the respective antenna spectra on the driven current profile. The interpretative modelling of LHCD is carried out using a chain of codes calculating, respectively, the global discharge evolution (tokamak simulator METIS), the spectrum at the antenna mouth (LH coupling code ALOHA), the LH wave propagation (ray-tracing code C3PO), and the distribution function (3D Fokker-Planck code LUKE). Essential aspects of the fast electron dynamics in time, space and energy are obtained from hard x-ray measurements of fast electron bremsstrahlung emission using a dedicated tomographic system. LHCD simulations are validated by systematic comparisons between these experimental measurements and the reconstructed signal calculated by the code R5X2 from the LUKE electron distribution. An excellent agreement is obtained in the presence of strong Landau damping (found under low density and high-power conditions in Tore Supra) for which the ray-tracing model is valid for modelling the LH wave propagation. Two aspects of the antenna spectra are found to have a significant effect on LHCD. First, the driven current is found to be proportional to the directivity, which depends upon the respective weight of the main positive and main negative lobes and is particularly sensitive to the density in front of the antenna. Second, the position of the main negative lobe in the spectrum is different for the two launchers. As this lobe drives a counter-current, the resulting driven current profile is also different for the FAM and PAM launchers.
Next-generation sequencing of the Trichinella murrelli mitochondrial genome allows comprehensive comparison of its divergence from the principal agent of human trichinellosis, Trichinella spiralis.

PubMed

Webb, Kristen M; Rosenthal, Benjamin M

2011-01-01

The mitochondrial genome's non-recombinant mode of inheritance and relatively rapid rate of evolution has promoted its use as a marker for studying the biogeographic history and evolutionary interrelationships among many metazoan species. A modest portion of the mitochondrial genome has been defined for 12 species and genotypes of parasites in the genus Trichinella, but its adequacy in representing the mitochondrial genome as a whole remains unclear, as the complete coding sequence has been characterized only for Trichinella spiralis. Here, we sought to comprehensively describe the extent and nature of divergence between the mitochondrial genomes of T. spiralis (which poses the most appreciable zoonotic risk owing to its capacity to establish persistent infections in domestic pigs) and Trichinella murrelli (which is the most prevalent species in North American wildlife hosts, but which poses relatively little risk to the safety of pork). Next generation sequencing methodologies and scaffold and de novo assembly strategies were employed. The entire protein-coding region was sequenced (13,917 bp), along with a portion of the highly repetitive non-coding region (1524 bp) of the mitochondrial genome of T. murrelli with a combined average read depth of 250 reads. The accuracy of base calling, estimated from coding region sequence was found to exceed 99.3%. Genome content and gene order was not found to be significantly different from that of T. spiralis. An overall inter-species sequence divergence of 9.5% was estimated. Significant variation was identified when the amount of variation between species at each gene is compared to the average amount of variation between species across the coding region. Next generation sequencing is a highly effective means to obtain previously unknown mitochondrial genome sequence. Particular to parasites, the extremely deep coverage achieved through this method allows for the detection of sequence heterogeneity between the multiple individuals that necessarily comprise such templates. Copyright © 2010 Elsevier B.V. All rights reserved.
Origin and evolution of spliceosomal introns

PubMed Central

2012-01-01

Evolution of exon-intron structure of eukaryotic genes has been a matter of long-standing, intensive debate. The introns-early concept, later rebranded ‘introns first’ held that protein-coding genes were interrupted by numerous introns even at the earliest stages of life's evolution and that introns played a major role in the origin of proteins by facilitating recombination of sequences coding for small protein/peptide modules. The introns-late concept held that introns emerged only in eukaryotes and new introns have been accumulating continuously throughout eukaryotic evolution. Analysis of orthologous genes from completely sequenced eukaryotic genomes revealed numerous shared intron positions in orthologous genes from animals and plants and even between animals, plants and protists, suggesting that many ancestral introns have persisted since the last eukaryotic common ancestor (LECA). Reconstructions of intron gain and loss using the growing collection of genomes of diverse eukaryotes and increasingly advanced probabilistic models convincingly show that the LECA and the ancestors of each eukaryotic supergroup had intron-rich genes, with intron densities comparable to those in the most intron-rich modern genomes such as those of vertebrates. The subsequent evolution in most lineages of eukaryotes involved primarily loss of introns, with only a few episodes of substantial intron gain that might have accompanied major evolutionary innovations such as the origin of metazoa. The original invasion of self-splicing Group II introns, presumably originating from the mitochondrial endosymbiont, into the genome of the emerging eukaryote might have been a key factor of eukaryogenesis that in particular triggered the origin of endomembranes and the nucleus. Conversely, splicing errors gave rise to alternative splicing, a major contribution to the biological complexity of multicellular eukaryotes. There is no indication that any prokaryote has ever possessed a spliceosome or introns in protein-coding genes, other than relatively rare mobile self-splicing introns. Thus, the introns-first scenario is not supported by any evidence but exon-intron structure of protein-coding genes appears to have evolved concomitantly with the eukaryotic cell, and introns were a major factor of evolution throughout the history of eukaryotes. This article was reviewed by I. King Jordan, Manuel Irimia (nominated by Anthony Poole), Tobias Mourier (nominated by Anthony Poole), and Fyodor Kondrashov. For the complete reports, see the Reviewers’ Reports section. PMID:22507701

Acceptance of Evolution Increases with Student Academic Level: A Comparison Between a Secular and a Religious College

PubMed Central

Paz-y-Miño C., Guillermo

2012-01-01

Acceptance of evolution among the general public, high schools, teachers, and scientists has been documented in the USA; little is known about college students’ views on evolution; this population is relevant since it transits from a high-school/parent-protective environment to an independent role in societal decisions. Here we compare perspectives about evolution, creationism, and intelligent design (ID) between a secular (S) and a religious (R) college in the Northeastern USA. Interinstitutional comparisons showed that 64% (mean S + R) biology majors vs. 42/62% (S/R) nonmajors supported the exclusive teaching of evolution in science classes; 24/29% (S/R) biology majors vs. 26/38% (S/R) nonmajors perceived ID as both alternative to evolution and/or scientific theory about the origin of life; 76% (mean S + R) biology majors and nonmajors accepted evolutionary explanations about the origin of life; 86% (mean S + R) biology majors vs. 79% (mean S + R) nonmajors preferred science courses where human evolution is discussed; 76% (mean S+R) biology majors vs. 79% (mean S + R) nonmajors welcomed questions about evolution in exams and/or thought that such questions should always be in exams; and 66% (mean S + R) biology majors vs. 46% (mean S + R) nonmajors admitted they accept evolution openly and/or privately. Intrainstitutional comparisons showed that overall acceptance of evolution among biologists (S or R) increased gradually from the freshman to the senior year, due to exposure to upper-division courses with evolutionary content. College curricular/pedagogical reform should fortify evolution literacy at all education levels, particularly among nonbiologists. PMID:22957109
Insights into the evolution of Darwin’s finches from comparative analysis of the Geospiza magnirostris genome sequence

PubMed Central

2013-01-01

Background A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin’s (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2–3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris. Results 13,291 protein-coding genes were predicted from a 991.0 Mb G. magnirostris genome assembly. We then defined gene orthology relationships and constructed whole genome alignments between the G. magnirostris and other vertebrate genomes. We estimate that 15% of genomic sequence is functionally constrained between G. magnirostris and zebra finch. Genic evolutionary rate comparisons indicate that similar selective pressures acted along the G. magnirostris and zebra finch lineages suggesting that historical effective population size values have been similar in both lineages. 21 otherwise highly conserved genes were identified that each show evidence for positive selection on amino acid changes in the Darwin's finch lineage. Two of these genes (Igf2r and Pou1f1) have been implicated in beak morphology changes in Darwin’s finches. Five of 47 genes showing evidence of positive selection in early passerine evolution have cilia related functions, and may be examples of adaptively evolving reproductive proteins. Conclusions These results provide insights into past evolutionary processes that have shaped G. magnirostris genes and its genome, and provide the necessary foundation upon which to build population genomics resources that will shed light on more contemporaneous adaptive and non-adaptive processes that have contributed to the evolution of the Darwin’s finches. PMID:23402223
Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots

PubMed Central

Stukenbrock, Eva H.; Dutheil, Julien Y.

2018-01-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae. We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. PMID:29263029
Fine-Scale Recombination Maps of Fungal Plant Pathogens Reveal Dynamic Recombination Landscapes and Intragenic Hotspots.

PubMed

Stukenbrock, Eva H; Dutheil, Julien Y

2018-03-01

Meiotic recombination is an important driver of evolution. Variability in the intensity of recombination across chromosomes can affect sequence composition, nucleotide variation, and rates of adaptation. In many organisms, recombination events are concentrated within short segments termed recombination hotspots. The variation in recombination rate and positions of recombination hotspot can be studied using population genomics data and statistical methods. In this study, we conducted population genomics analyses to address the evolution of recombination in two closely related fungal plant pathogens: the prominent wheat pathogen Zymoseptoria tritici and a sister species infecting wild grasses Z. ardabiliae We specifically addressed whether recombination landscapes, including hotspot positions, are conserved in the two recently diverged species and if recombination contributes to rapid evolution of pathogenicity traits. We conducted a detailed simulation analysis to assess the performance of methods of recombination rate estimation based on patterns of linkage disequilibrium, in particular in the context of high nucleotide diversity. Our analyses reveal overall high recombination rates, a lack of suppressed recombination in centromeres, and significantly lower recombination rates on chromosomes that are known to be accessory. The comparison of the recombination landscapes of the two species reveals a strong correlation of recombination rate at the megabase scale, but little correlation at smaller scales. The recombination landscapes in both pathogen species are dominated by frequent recombination hotspots across the genome including coding regions, suggesting a strong impact of recombination on gene evolution. A significant but small fraction of these hotspots colocalize between the two species, suggesting that hotspot dynamics contribute to the overall pattern of fast evolving recombination in these species. Copyright © 2018 Stukenbrock and Dutheil.
Rapid evolution of cis-regulatory sequences via local point mutations

NASA Technical Reports Server (NTRS)

Stone, J. R.; Wray, G. A.

2001-01-01

Although the evolution of protein-coding sequences within genomes is well understood, the same cannot be said of the cis-regulatory regions that control transcription. Yet, changes in gene expression are likely to constitute an important component of phenotypic evolution. We simulated the evolution of new transcription factor binding sites via local point mutations. The results indicate that new binding sites appear and become fixed within populations on microevolutionary timescales under an assumption of neutral evolution. Even combinations of two new binding sites evolve very quickly. We predict that local point mutations continually generate considerable genetic variation that is capable of altering gene expression.
Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1989-01-01

The performance of bandwidth efficient trellis codes on channels with phase jitter, or those disturbed by jamming and impulse noise is analyzed. An heuristic algorithm for construction of bandwidth efficient trellis codes with any constraint length up to about 30, any signal constellation, and any code rate was developed. Construction of good distance profile trellis codes for sequential decoding and comparison of random coding bounds of trellis coded modulation schemes are also discussed.
Evolution in the block: common elements of 5S rDNA organization and evolutionary patterns in distant fish genera.

PubMed

Campo, Daniel; García-Vázquez, Eva

2012-01-01

The 5S rDNA is organized in the genome as tandemly repeated copies of a structural unit composed of a coding sequence plus a nontranscribed spacer (NTS). The coding region is highly conserved in the evolution, whereas the NTS vary in both length and sequence. It has been proposed that 5S rRNA genes are members of a gene family that have arisen through concerted evolution. In this study, we describe the molecular organization and evolution of the 5S rDNA in the genera Lepidorhombus and Scophthalmus (Scophthalmidae) and compared it with already known 5S rDNA of the very different genera Merluccius (Merluccidae) and Salmo (Salmoninae), to identify common structural elements or patterns for understanding 5S rDNA evolution in fish. High intra- and interspecific diversity within the 5S rDNA family in all the genera can be explained by a combination of duplications, deletions, and transposition events. Sequence blocks with high similarity in all the 5S rDNA members across species were identified for the four studied genera, with evidences of intense gene conversion within noncoding regions. We propose a model to explain the evolution of the 5S rDNA, in which the evolutionary units are blocks of nucleotides rather than the entire sequences or single nucleotides. This model implies a "two-speed" evolution: slow within blocks (homogenized by recombination) and fast within the gene family (diversified by duplications and deletions).
Testing a one-dimensional prescription of dynamical shear mixing with a two-dimensional hydrodynamic simulation

NASA Astrophysics Data System (ADS)

Edelmann, P. V. F.; Röpke, F. K.; Hirschi, R.; Georgy, C.; Jones, S.

2017-07-01

Context. The treatment of mixing processes is still one of the major uncertainties in 1D stellar evolution models. This is mostly due to the need to parametrize and approximate aspects of hydrodynamics in hydrostatic codes. In particular, the effect of hydrodynamic instabilities in rotating stars, for example, dynamical shear instability, evades consistent description. Aims: We intend to study the accuracy of the diffusion approximation to dynamical shear in hydrostatic stellar evolution models by comparing 1D models to a first-principle hydrodynamics simulation starting from the same initial conditions. Methods: We chose an initial model calculated with the stellar evolution code GENEC that is just at the onset of a dynamical shear instability but does not show any other instabilities (e.g., convection). This was mapped to the hydrodynamics code SLH to perform a 2D simulation in the equatorial plane. We compare the resulting profiles in the two codes and compute an effective diffusion coefficient for the hydro simulation. Results: Shear instabilities develop in the 2D simulation in the regions predicted by linear theory to become unstable in the 1D stellar evolution model. Angular velocity and chemical composition is redistributed in the unstable region, thereby creating new unstable regions. After a period of time, the system settles in a symmetric, steady state, which is Richardson stable everywhere in the 2D simulation, whereas the instability remains for longer in the 1D model due to the limitations of the current implementation in the 1D code. A spatially resolved diffusion coefficient is extracted by comparing the initial and final profiles of mean atomic mass. Conclusions: The presented simulation gives a first insight on hydrodynamics of shear instabilities in a real stellar environment and even allows us to directly extract an effective diffusion coefficient. We see evidence for a critical Richardson number of 0.25 as regions above this threshold remain stable for the course of the simulation. The movie of the simulation is available at http://www.aanda.org
International comparison of sudden unexpected death in infancy rates using a newly proposed set of cause-of-death codes.

PubMed

Taylor, Barry J; Garstang, Joanna; Engelberts, Adele; Obonai, Toshimasa; Cote, Aurore; Freemantle, Jane; Vennemann, Mechtild; Healey, Matt; Sidebotham, Peter; Mitchell, Edwin A; Moon, Rachel Y

2015-11-01

Comparing rates of sudden unexpected death in infancy (SUDI) in different countries and over time is difficult, as these deaths are certified differently in different countries, and, even within the same jurisdiction, changes in this death certification process have occurred over time. To identify if International Classification of Diseases-10 (ICD-10) codes are being applied differently in different countries, and to develop a more robust tool for international comparison of these types of deaths. Usage of six ICD-10 codes, which code for the majority of SUDI, was compared for the years 2002-2010 in eight high-income countries. There was a great variability in how each country codes SUDI. For example, the proportion of SUDI coded as sudden infant death syndrome (R95) ranged from 32.6% in Japan to 72.5% in Germany. The proportion of deaths coded as accidental suffocation and strangulation in bed (W75) ranged from 1.1% in Germany to 31.7% in New Zealand. Japan was the only country to consistently use the R96 code, with 44.8% of SUDI attributed to that code. The lowest, overall, SUDI rate was seen in the Netherlands (0.19/1000 live births (LB)), and the highest in New Zealand (1.00/1000 LB). SUDI accounted for one-third to half of postneonatal mortality in 2002-2010 for all of the countries except for the Netherlands. The proposed set of ICD-10 codes encompasses the codes used in different countries for most SUDI cases. Use of these codes will allow for better international comparisons and tracking of trends over time. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.
The InterFrost benchmark of Thermo-Hydraulic codes for cold regions hydrology - first inter-comparison results

NASA Astrophysics Data System (ADS)

Grenier, Christophe; Roux, Nicolas; Anbergen, Hauke; Collier, Nathaniel; Costard, Francois; Ferrry, Michel; Frampton, Andrew; Frederick, Jennifer; Holmen, Johan; Jost, Anne; Kokh, Samuel; Kurylyk, Barret; McKenzie, Jeffrey; Molson, John; Orgogozo, Laurent; Rivière, Agnès; Rühaak, Wolfram; Selroos, Jan-Olof; Therrien, René; Vidstrand, Patrik

2015-04-01

The impacts of climate change in boreal regions has received considerable attention recently due to the warming trends that have been experienced in recent decades and are expected to intensify in the future. Large portions of these regions, corresponding to permafrost areas, are covered by water bodies (lakes, rivers) that interact with the surrounding permafrost. For example, the thermal state of the surrounding soil influences the energy and water budget of the surface water bodies. Also, these water bodies generate taliks (unfrozen zones below) that disturb the thermal regimes of permafrost and may play a key role in the context of climate change. Recent field studies and modeling exercises indicate that a fully coupled 2D or 3D Thermo-Hydraulic (TH) approach is required to understand and model the past and future evolution of landscapes, rivers, lakes and associated groundwater systems in a changing climate. However, there is presently a paucity of 3D numerical studies of permafrost thaw and associated hydrological changes, and the lack of study can be partly attributed to the difficulty in verifying multi-dimensional results produced by numerical models. Numerical approaches can only be validated against analytical solutions for a purely thermic 1D equation with phase change (e.g. Neumann, Lunardini). When it comes to the coupled TH system (coupling two highly non-linear equations), the only possible approach is to compare the results from different codes to provided test cases and/or to have controlled experiments for validation. Such inter-code comparisons can propel discussions to try to improve code performances. A benchmark exercise was initialized in 2014 with a kick-off meeting in Paris in November. Participants from USA, Canada, Germany, Sweden and France convened, representing altogether 13 simulation codes. The benchmark exercises consist of several test cases inspired by existing literature (e.g. McKenzie et al., 2007) as well as new ones. They range from simpler, purely thermal cases (benchmark T1) to more complex, coupled 2D TH cases (benchmarks TH1, TH2, and TH3). Some experimental cases conducted in cold room complement the validation approach. A web site hosted by LSCE (Laboratoire des Sciences du Climat et de l'Environnement) is an interaction platform for the participants and hosts the test cases database at the following address: https://wiki.lsce.ipsl.fr/interfrost. The results of the first stage of the benchmark exercise will be presented. We will mainly focus on the inter-comparison of participant results for the coupled cases (TH1, TH2 & TH3). Further perspectives of the exercise will also be presented. Extensions to more complex physical conditions (e.g. unsaturated conditions and geometrical deformations) are contemplated. In addition, 1D vertical cases of interest to the Climate Modeling community will be proposed. Keywords: Permafrost; Numerical modeling; River-soil interaction; Arctic systems; soil freeze-thaw
GPS receiver CODE bias estimation: A comparison of two methods

NASA Astrophysics Data System (ADS)

McCaffrey, Anthony M.; Jayachandran, P. T.; Themens, D. R.; Langley, R. B.

2017-04-01

The Global Positioning System (GPS) is a valuable tool in the measurement and monitoring of ionospheric total electron content (TEC). To obtain accurate GPS-derived TEC, satellite and receiver hardware biases, known as differential code biases (DCBs), must be estimated and removed. The Center for Orbit Determination in Europe (CODE) provides monthly averages of receiver DCBs for a significant number of stations in the International Global Navigation Satellite Systems Service (IGS) network. A comparison of the monthly receiver DCBs provided by CODE with DCBs estimated using the minimization of standard deviations (MSD) method on both daily and monthly time intervals, is presented. Calibrated TEC obtained using CODE-derived DCBs, is accurate to within 0.74 TEC units (TECU) in differenced slant TEC (sTEC), while calibrated sTEC using MSD-derived DCBs results in an accuracy of 1.48 TECU.
Jet and electromagnetic tomography (JET) of extreme phases of matter in heavy-ion collisions

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

Heinz, Ulrich

2015-08-31

The Ohio State University (OSU) group contributed to the deliverables of the JET Collaboration three major products: 1. The code package iEBE-VISHNU for modeling the dynamical evolution of the soft medium created in relativistic heavy-ion collisions, from its creation all the way to final freeze-out using a hybrid approach that interfaces a free-streaming partonic pre-equilbrium stage with a (2+1)-dimensional viscous relativistic fluid dynamical stage for the quark-gluon plasma (QGP) phase and the microscopic hadron cascade UrQMD for the hadronic rescattering and freeze-out stage. Except for UrQMD, all dynamical evolution components and interfaces were developed at OSU and tested and implementedmore » in collaboration with the Duke University group. 2. An electromagnetic radiation module for the calculation of thermal photon emission from the QGP and hadron resonance gas stages of a heavy-ion collision, with emission rates that have been corrected for viscous effects in the expanding medium consistent with the bulk evolution. The electromagnetic radiation module was developed under OSU leadership in collaboration with the McGill group and has been integrated in the iEBE-VISHNU code package. 3. An interface between the Monte Carlo jet shower evolution and hadronization codes developed by the Wayne State University (WSU), McGill and Texas A&M groups and the iEBE-VISHNU bulk evolution code, for performing jet quenching and jet shape modification studies in a realistically modeled evolving medium that was tuned to measured soft hadron data. Building on work performed at OSU for the theoretical framework used to describe the interaction of jets with the medium, initial work on the jet shower Monte Carlo was started at OSU and moved to WSU when OSU Visiting Assistant Professor Abhijit Majumder accepted a tenure track faculty position at WSU in September 2011. The jet-hydro interface was developed at OSU and WSU and tested and implemented in collaboration with the McGill, Texas A&M, and LBNL groups.« less
Genome sequence, comparative analysis and haplotype structure of the domestic dog.

PubMed

Lindblad-Toh, Kerstin; Wade, Claire M; Mikkelsen, Tarjei S; Karlsson, Elinor K; Jaffe, David B; Kamal, Michael; Clamp, Michele; Chang, Jean L; Kulbokas, Edward J; Zody, Michael C; Mauceli, Evan; Xie, Xiaohui; Breen, Matthew; Wayne, Robert K; Ostrander, Elaine A; Ponting, Chris P; Galibert, Francis; Smith, Douglas R; DeJong, Pieter J; Kirkness, Ewen; Alvarez, Pablo; Biagi, Tara; Brockman, William; Butler, Jonathan; Chin, Chee-Wye; Cook, April; Cuff, James; Daly, Mark J; DeCaprio, David; Gnerre, Sante; Grabherr, Manfred; Kellis, Manolis; Kleber, Michael; Bardeleben, Carolyne; Goodstadt, Leo; Heger, Andreas; Hitte, Christophe; Kim, Lisa; Koepfli, Klaus-Peter; Parker, Heidi G; Pollinger, John P; Searle, Stephen M J; Sutter, Nathan B; Thomas, Rachael; Webber, Caleb; Baldwin, Jennifer; Abebe, Adal; Abouelleil, Amr; Aftuck, Lynne; Ait-Zahra, Mostafa; Aldredge, Tyler; Allen, Nicole; An, Peter; Anderson, Scott; Antoine, Claudel; Arachchi, Harindra; Aslam, Ali; Ayotte, Laura; Bachantsang, Pasang; Barry, Andrew; Bayul, Tashi; Benamara, Mostafa; Berlin, Aaron; Bessette, Daniel; Blitshteyn, Berta; Bloom, Toby; Blye, Jason; Boguslavskiy, Leonid; Bonnet, Claude; Boukhgalter, Boris; Brown, Adam; Cahill, Patrick; Calixte, Nadia; Camarata, Jody; Cheshatsang, Yama; Chu, Jeffrey; Citroen, Mieke; Collymore, Alville; Cooke, Patrick; Dawoe, Tenzin; Daza, Riza; Decktor, Karin; DeGray, Stuart; Dhargay, Norbu; Dooley, Kimberly; Dooley, Kathleen; Dorje, Passang; Dorjee, Kunsang; Dorris, Lester; Duffey, Noah; Dupes, Alan; Egbiremolen, Osebhajajeme; Elong, Richard; Falk, Jill; Farina, Abderrahim; Faro, Susan; Ferguson, Diallo; Ferreira, Patricia; Fisher, Sheila; FitzGerald, Mike; Foley, Karen; Foley, Chelsea; Franke, Alicia; Friedrich, Dennis; Gage, Diane; Garber, Manuel; Gearin, Gary; Giannoukos, Georgia; Goode, Tina; Goyette, Audra; Graham, Joseph; Grandbois, Edward; Gyaltsen, Kunsang; Hafez, Nabil; Hagopian, Daniel; Hagos, Birhane; Hall, Jennifer; Healy, Claire; Hegarty, Ryan; Honan, Tracey; Horn, Andrea; Houde, Nathan; Hughes, Leanne; Hunnicutt, Leigh; Husby, M; Jester, Benjamin; Jones, Charlien; Kamat, Asha; Kanga, Ben; Kells, Cristyn; Khazanovich, Dmitry; Kieu, Alix Chinh; Kisner, Peter; Kumar, Mayank; Lance, Krista; Landers, Thomas; Lara, Marcia; Lee, William; Leger, Jean-Pierre; Lennon, Niall; Leuper, Lisa; LeVine, Sarah; Liu, Jinlei; Liu, Xiaohong; Lokyitsang, Yeshi; Lokyitsang, Tashi; Lui, Annie; Macdonald, Jan; Major, John; Marabella, Richard; Maru, Kebede; Matthews, Charles; McDonough, Susan; Mehta, Teena; Meldrim, James; Melnikov, Alexandre; Meneus, Louis; Mihalev, Atanas; Mihova, Tanya; Miller, Karen; Mittelman, Rachel; Mlenga, Valentine; Mulrain, Leonidas; Munson, Glen; Navidi, Adam; Naylor, Jerome; Nguyen, Tuyen; Nguyen, Nga; Nguyen, Cindy; Nguyen, Thu; Nicol, Robert; Norbu, Nyima; Norbu, Choe; Novod, Nathaniel; Nyima, Tenchoe; Olandt, Peter; O'Neill, Barry; O'Neill, Keith; Osman, Sahal; Oyono, Lucien; Patti, Christopher; Perrin, Danielle; Phunkhang, Pema; Pierre, Fritz; Priest, Margaret; Rachupka, Anthony; Raghuraman, Sujaa; Rameau, Rayale; Ray, Verneda; Raymond, Christina; Rege, Filip; Rise, Cecil; Rogers, Julie; Rogov, Peter; Sahalie, Julie; Settipalli, Sampath; Sharpe, Theodore; Shea, Terrance; Sheehan, Mechele; Sherpa, Ngawang; Shi, Jianying; Shih, Diana; Sloan, Jessie; Smith, Cherylyn; Sparrow, Todd; Stalker, John; Stange-Thomann, Nicole; Stavropoulos, Sharon; Stone, Catherine; Stone, Sabrina; Sykes, Sean; Tchuinga, Pierre; Tenzing, Pema; Tesfaye, Senait; Thoulutsang, Dawa; Thoulutsang, Yama; Topham, Kerri; Topping, Ira; Tsamla, Tsamla; Vassiliev, Helen; Venkataraman, Vijay; Vo, Andy; Wangchuk, Tsering; Wangdi, Tsering; Weiand, Michael; Wilkinson, Jane; Wilson, Adam; Yadav, Shailendra; Yang, Shuli; Yang, Xiaoping; Young, Geneva; Yu, Qing; Zainoun, Joanne; Zembek, Lisa; Zimmer, Andrew; Lander, Eric S

2005-12-08

Here we report a high-quality draft genome sequence of the domestic dog (Canis familiaris), together with a dense map of single nucleotide polymorphisms (SNPs) across breeds. The dog is of particular interest because it provides important evolutionary information and because existing breeds show great phenotypic diversity for morphological, physiological and behavioural traits. We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes. Notably, the majority of the most highly conserved non-coding sequences in mammalian genomes are clustered near a small subset of genes with important roles in development. Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds. The current SNP map now makes it possible for genome-wide association studies to identify genes responsible for diseases and traits, with important consequences for human and companion animal health.
Neutrino probe comparisons of supernovae as a function of redshift

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

Fryer, Christopher Lee

2009-01-01

We compare aspects of supernova explosions produced in the current epoch against those produced in the first round of star formation. Although the total final mass of stars can change dramatically between these two epochs due to different mass-loss rates from winds, their cores remam very similar. The core structure is more sensitive to the stellar evolution code than it is to the amount of metals. As such, current stellar models produce supernovae from first stars that look very similar to that of stars produced in the current epoch. The neutrino signal, a powerful probe of the inner core, ismore » identical to the few percent level for both star formation epochs. A change in the neutrino signal in the supernova population between these two star formation epochs will only arise if the initial mass function is altered.« less
Model-Invariant Hybrid Computations of Separated Flows for RCA Standard Test Cases

NASA Technical Reports Server (NTRS)

Woodruff, Stephen

2016-01-01

NASA's Revolutionary Computational Aerosciences (RCA) subproject has identified several smooth-body separated flows as standard test cases to emphasize the challenge these flows present for computational methods and their importance to the aerospace community. Results of computations of two of these test cases, the NASA hump and the FAITH experiment, are presented. The computations were performed with the model-invariant hybrid LES-RANS formulation, implemented in the NASA code VULCAN-CFD. The model- invariant formulation employs gradual LES-RANS transitions and compensation for model variation to provide more accurate and efficient hybrid computations. Comparisons revealed that the LES-RANS transitions employed in these computations were sufficiently gradual that the compensating terms were unnecessary. Agreement with experiment was achieved only after reducing the turbulent viscosity to mitigate the effect of numerical dissipation. The stream-wise evolution of peak Reynolds shear stress was employed as a measure of turbulence dynamics in separated flows useful for evaluating computations.
Complete mitochondrial genome sequence of Indian medium carp, Labeo gonius (Hamilton, 1822) and its comparison with other related carp species.

PubMed

Behera, Bijay Kumar; Kumari, Kavita; Baisvar, Vishwamitra Singh; Rout, Ajaya Kumar; Pakrashi, Sudip; Paria, Prasenjet; Jena, J K

2017-01-01

In the present study, the complete mitochondrial genome sequence of Labeo gonius is reported using PGM sequencer (Ion Torrent). The complete mitogenome of L. gonius is obtained by the de novo sequences assembly of genomic reads using the Torrent Mapping Alignment Program (TMAP) which is 16 614 bp in length. The mitogenome of L. gonius comprised of 13 protein-coding genes, 22 tRNAs, 2 rRNA genes, and D-loop as control region along with gene order and organization, being similar to most of other fish mitogenomes of NCBI databases. The mitogenome in the present study has 99% similarity to the complete mitogenome sequence of Labeo fimbriatus, as reported earlier. The phylogenetic analysis of Cypriniformes depicted that their mitogenomes are closely related to each other. The complete mitogenome sequence of L. gonius would be helpful in understanding the population genetics, phylogenetics, and evolution of Indian Carps.
Astrophysical Connections to Collapsing Radiative Shock Experiments

NASA Astrophysics Data System (ADS)

Reighard, A. B.; Hansen, J. F.; Bouquet, S.; Koenig, M.

2005-10-01

Radiative shocks occur in many high-energy density explosions, but prove difficult to create in laboratory experiments or to fully model with astrophysical codes. Low astrophysical densities combined with powerful explosions provide ideal conditions for producing radiative shocks. Here we describe an experiment significant to astrophysical shocks, which produces a driven, planar radiative shock in low density Xe gas. Including radiation effects precludes scaling experiments directly to astrophysical conditions via Euler equations, as can be done in purely hydrodynamic experiments. We use optical depth considerations to make comparisons between the driven shock in xenon and specific astrophysical phenomena. This planar shock may be subject to thin shell instabilities similar to those affecting the evolution of astrophysical shocks. This research was sponsored by the National Nuclear Security Administration under the Stewardship Science Academic Alliances program through DOE Research Grants DE-FG52-03NA00064, DE-FG53-2005-NA26014, and other grants and contracts.
Study of fission fragment de-excitation by gamma-ray spectrometry with the EXILL experiment

NASA Astrophysics Data System (ADS)

Materna, Thomas; a, Michal Rapał; Letourneau, Alain; Marchix, Anthony; Litaize, Olivier; Sérot, Olivier; Urban, Waldemar; Blanc, Aurélien; Jentschel, Michael; Köster, Ulli; Mutti, Paolo; Soldner, Torsten; Simpson, Gary; Ur, Călin A.; France, Gilles de

2017-09-01

A large array of Ge detectors installed at ILL, around a 235U target irradiated with cold neutrons, (EXILL) allowed measurement of prompt gamma-ray cascades occurring in fission fragments with an unambiguous determination of fragments. Here we present preliminary results of a systematic comparison between experimental γ-ray intensities and those obtained from the Monte-Carlo simulation code FIFRELIN, which is dedicated to the de-excitation of fission fragments. Major γ-ray intensities in the 142Ba and 92Kr fission products, extracted from EXILL data, were compared to FIFRELIN, as well as to reported values (when available) obtained with EUROGAM2 in the spontaneous fission of 248Cm. The evolution of γ-ray intensities in 92Kr versus the complementary partner in fission (i.e. versus the total number of evaporated neutrons by the fission pair) was then extracted and compared to FIFRELIN.
Comparing the coding of complications in Queensland and Victorian admitted patient data.

PubMed

Michel, Jude L; Cheng, Diana; Jackson, Terri J

2011-08-01

To examine differences between Queensland and Victorian coding of hospital-acquired conditions and suggest ways to improve the usefulness of these data in the monitoring of patient safety events. Secondary analysis of admitted patient episode data collected in Queensland and Victoria. Comparison of depth of coding, and patterns in the coding of ten commonly coded complications of five elective procedures. Comparison of the mean complication codes assigned per episode revealed Victoria assigns more valid codes than Queensland for all procedures, with the difference between the states being significantly different in all cases. The proportion of the codes flagged as complications was consistently lower for Queensland when comparing 10 common complications for each of the five selected elective procedures. The estimated complication rates for the five procedures showed Victoria to have an apparently higher complication rate than Queensland for 35 of the 50 complications examined. Our findings demonstrate that the coding of complications is more comprehensive in Victoria than in Queensland. It is known that inconsistencies exist between states in routine hospital data quality. Comparative use of patient safety indicators should be viewed with caution until standards are improved across Australia. More exploration of data quality issues is needed to identify areas for improvement.
Enforcing dust mass conservation in 3D simulations of tightly coupled grains with the PHANTOM SPH code

NASA Astrophysics Data System (ADS)

Ballabio, G.; Dipierro, G.; Veronesi, B.; Lodato, G.; Hutchison, M.; Laibe, G.; Price, D. J.

2018-06-01

We describe a new implementation of the one-fluid method in the SPH code PHANTOM to simulate the dynamics of dust grains in gas protoplanetary discs. We revise and extend previously developed algorithms by computing the evolution of a new fluid quantity that produces a more accurate and numerically controlled evolution of the dust dynamics. Moreover, by limiting the stopping time of uncoupled grains that violate the assumptions of the terminal velocity approximation, we avoid fatal numerical errors in mass conservation. We test and validate our new algorithm by running 3D SPH simulations of a large range of disc models with tightly and marginally coupled grains.

New Directions in Giant Planet Formation

NASA Astrophysics Data System (ADS)

Youdin, Andrew

The proposed research will explore the limits of the core accretion mechanism for forming giant planets, both in terms of timescale and orbital distance. This theoretical research will be useful in interpreting the results of ongoing exoplanet searches. The effects of radiogenic heating and aerodynamic accretion of pebbles and boulders will be included in time-dependent models of atmospheric structure and growth. To investigate these issues, we will develop and publicly share a protoplanet atmospheric evolution code as an extension of the MESA stellar evolution code. By focusing on relevant processes in the early stages of giant planet formation, we can refine model predictions for exoplanet searches at a wide range of stellar ages and distances from the host star.
A Vorticity-preserving Hydrodynamical Scheme for Modeling Accretion Disk Flows

NASA Astrophysics Data System (ADS)

Seligman, Darryl; Laughlin, Gregory

2017-10-01

Vortices, turbulence, and unsteady nonlaminar flows are likely both prominent and dynamically important features of astrophysical disks. Such strongly nonlinear phenomena are often difficult, however, to simulate accurately, and are generally amenable to analytic treatment only in idealized form. In this paper, we explore the evolution of compressible two-dimensional flows using an implicit dual-time hydrodynamical scheme that strictly conserves vorticity (if applied to simulate inviscid flows for which Kelvin’s Circulation Theorem is applicable). The algorithm is based on the work of Lerat et al., who proposed it in the context of terrestrial applications such as the blade-vortex interactions generated by helicopter rotors. We present several tests of Lerat et al.'s vorticity-preserving approach, which we have implemented to second-order accuracy, providing side-by-side comparisons with other algorithms that are frequently used in protostellar disk simulations. The comparison codes include one based on explicit, second-order van Leer advection, one based on spectral methods, and another that implements a higher-order Godunov solver. Our results suggest that the Lerat et al. algorithm will be useful for simulations of astrophysical environments in which vortices play a dynamical role, and where strong shocks are not expected.
Spectropolarimetric Inversions of the Ca II 8542 Å Line in an M-class Solar Flare

NASA Astrophysics Data System (ADS)

Kuridze, D.; Henriques, V. M. J.; Mathioudakis, M.; Rouppe van der Voort, L.; de la Cruz Rodríguez, J.; Carlsson, M.

2018-06-01

We study the M1.9-class solar flare SOL2015-09-27T10:40 UT using high-resolution full Stokes imaging spectropolarimetry of the Ca II 8542 Å line obtained with the CRISP imaging spectropolarimeter at the Swedish 1-m Solar Telescope. Spectropolarimetric inversions using the non-LTE code NICOLE are used to construct semiempirical models of the flaring atmosphere to investigate the structure and evolution of the flare temperature and magnetic field. A comparison of the temperature stratification in flaring and nonflaring areas reveals strong heating of the flare ribbon during the flare peak. The polarization signals of the ribbon in the chromosphere during the flare maximum become stronger when compared to its surroundings and to pre- and post-flare profiles. Furthermore, a comparison of the response functions to perturbations in the line-of-sight magnetic field and temperature in flaring and nonflaring atmospheres shows that during the flare, the Ca II 8542 Å line is more sensitive to the lower atmosphere where the magnetic field is expected to be stronger. The chromospheric magnetic field was also determined with the weak-field approximation, which led to results similar to those obtained with the NICOLE inversions.
Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.

PubMed

Robinson, Oscar; Dylus, David; Dessimoz, Christophe

2016-08-01

Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io, a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license. © The Author 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
DOE Office of Scientific and Technical Information (OSTI.GOV)

Popovich, P.; Carter, T. A.; Friedman, B.

Numerical simulation of plasma turbulence in the Large Plasma Device (LAPD) [W. Gekelman, H. Pfister, Z. Lucky et al., Rev. Sci. Instrum. 62, 2875 (1991)] is presented. The model, implemented in the BOUndary Turbulence code [M. Umansky, X. Xu, B. Dudson et al., Contrib. Plasma Phys. 180, 887 (2009)], includes three-dimensional (3D) collisional fluid equations for plasma density, electron parallel momentum, and current continuity, and also includes the effects of ion-neutral collisions. In nonlinear simulations using measured LAPD density profiles but assuming constant temperature profile for simplicity, self-consistent evolution of instabilities and nonlinearly generated zonal flows results in a saturatedmore » turbulent state. Comparisons of these simulations with measurements in LAPD plasmas reveal good qualitative and reasonable quantitative agreement, in particular in frequency spectrum, spatial correlation, and amplitude probability distribution function of density fluctuations. For comparison with LAPD measurements, the plasma density profile in simulations is maintained either by direct azimuthal averaging on each time step, or by adding particle source/sink function. The inferred source/sink values are consistent with the estimated ionization source and parallel losses in LAPD. These simulations lay the groundwork for more a comprehensive effort to test fluid turbulence simulation against LAPD data.« less
AN EXACT SOLUTION FOR THE ASSESSMENT OF NONEQUILIBRIUM SORPTION OF RADIONUCLIDES IN THE VADOSE ZONE

EPA Science Inventory

In a report on model evaluation, the authors ran the HYDRUS Code, among other transport codes, to evaluate the impacts of nonequilibrium sorption sites on the time-evolution of 99Tc and 90Sr through the vadose zone. Since our evaluation was based on a rather low, annual recharge...
Genetics of Cerebellar and Neocortical Expansion in Anthropoid Primates: A Comparative Approach

PubMed Central

Harrison, Peter W.; Montgomery, Stephen H.

2017-01-01

What adaptive changes in brain structure and function underpin the evolution of increased cognitive performance in humans and our close relatives? Identifying the genetic basis of brain evolution has become a major tool in answering this question. Numerous cases of positive selection, altered gene expression or gene duplication have been identified that may contribute to the evolution of the neocortex, which is widely assumed to play a predominant role in cognitive evolution. However, the components of the neocortex co-evolve with other functionally interdependent regions of the brain, most notably in the cerebellum. The cerebellum is linked to a range of cognitive tasks and expanded rapidly during hominoid evolution. Here we present data that suggest that, across anthropoid primates, protein-coding genes with known roles in cerebellum development were just as likely to be targeted by selection as genes linked to cortical development. Indeed, based on currently available gene ontology data, protein-coding genes with known roles in cerebellum development are more likely to have evolved adaptively during hominoid evolution. This is consistent with phenotypic data suggesting an accelerated rate of cerebellar expansion in apes that is beyond that predicted from scaling with the neocortex in other primates. Finally, we present evidence that the strength of selection on specific genes is associated with variation in the volume of either the neocortex or the cerebellum, but not both. This result provides preliminary evidence that co-variation between these brain components during anthropoid evolution may be at least partly regulated by selection on independent loci, a conclusion that is consistent with recent intraspecific genetic analyses and a mosaic model of brain evolution that predicts adaptive evolution of brain structure. PMID:28683440
A Cross-Cultural Comparison of Korean and American Science Teachers' Views of Evolution and the Nature of Science

NASA Astrophysics Data System (ADS)

Kim, Sun Young; Nehm, Ross H.

2011-01-01

Despite a few international comparisons of the evolutionary beliefs of the general public, comparatively less research has focused on science teachers. Cross-cultural studies offer profitable opportunities for exploring the interactions among knowledge and belief variables in regard to evolution in different socio-cultural contexts. We investigated the evolutionary worldviews of pre-service science teachers from Asia (specifically South Korea), a region often excluded from international comparisons. We compared Korean and American science teachers': (1) understandings of evolution and the nature of science, and (2) acceptance of evolution in order to elucidate how knowledge and belief relationships are manifested in different cultural contexts. We found that Korean science teachers exhibited 'moderate' evolutionary acceptance levels comparable to or lower than American science teacher samples. Gender was significantly related to Korean teachers' evolution content knowledge and acceptance of evolution, with female Christian biology teachers displaying the lowest values on all measures. Korean science teachers' understandings of nature of science were significantly related to their acceptance and understanding of evolution; this relationship appears to transcend cultural boundaries. Our new data on Korean teachers, combined with studies from more than 20 other nations, expose the global nature of science teacher ambivalence or antipathy toward evolutionary knowledge.
Impact of Neutrino Opacities on Core-collapse Supernova Simulations

NASA Astrophysics Data System (ADS)

Kotake, Kei; Takiwaki, Tomoya; Fischer, Tobias; Nakamura, Ko; Martínez-Pinedo, Gabriel

2018-02-01

The accurate description of neutrino opacities is central to both the core-collapse supernova (CCSN) phenomenon and the validity of the explosion mechanism itself. In this work, we study in a systematic fashion the role of a variety of well-selected neutrino opacities in CCSN simulations where the multi-energy, three-flavor neutrino transport is solved using the isotropic diffusion source approximation (IDSA) scheme. To verify our code, we first present results from one-dimensional (1D) simulations following the core collapse, bounce, and ∼250 ms postbounce of a 15 {M}ȯ star using a standard set of neutrino opacities by Bruenn. A detailed comparison with published results supports the reliability of our three-flavor IDSA scheme using the standard opacity set. We then investigate in 1D simulations how individual opacity updates lead to differences with the baseline run with the standard opacity set. Through detailed comparisons with previous work, we check the validity of our implementation of each update in a step-by-step manner. Individual neutrino opacities with the largest impact on the overall evolution in 1D simulations are selected for systematic comparisons in our two-dimensional (2D) simulations. Special attention is given to the criterion of explodability in the 2D models. We discuss the implications of these results as well as its limitations and the requirements for future, more elaborate CCSN modeling.
Light transport feature for SCINFUL.

PubMed

Etaati, G R; Ghal-Eh, N

2008-03-01

An extended version of the scintillator response function prediction code SCINFUL has been developed by incorporating PHOTRACK, a Monte Carlo light transport code. Comparisons of calculated and experimental results for organic scintillators exposed to neutrons show that the extended code improves the predictive capability of SCINFUL.
Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model.

PubMed

Woltering, Joost M; Duboule, Denis

2015-11-01

The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
Importance of the nature of comparison conditions for testing theory-based interventions: comment on Michie and Prestwich (2010).

PubMed

Williams, David M

2010-09-01

Comments on the original article 'Are interventions theory-based? Development of a theory coding scheme' by Susan Michie and Andrew Prestwich (see record 2010-00152-001). In their admirable effort to develop a coding scheme for the theoretical contribution of intervention research, Michie and Prestwich rightly point out the importance of the presence of a comparison condition when examining the effect of an intervention on targeted theoretical variables and behavioral outcomes (Table 2, item 15). However, they fail to discuss the critical importance of the nature of the comparison condition. Weaker comparison conditions will yield stronger intervention effects; stronger comparison conditions will yield a stronger science of behavior change. (c) 2010 APA, all rights reserved).
Application of thin-layer Navier-Stokes equations near maximum lift

NASA Technical Reports Server (NTRS)

Anderson, W. K.; Thomas, J. L.; Rumsey, C. L.

1984-01-01

The flowfield about a NACA 0012 airfoil at a Mach number of 0.3 and Reynolds number of 1 million is computed through an angle of attack range, up to 18 deg, corresponding to conditions up to and beyond the maximum lift coefficient. Results obtained using the compressible thin-layer Navier-Stokes equations are presented as well as results from the compressible Euler equations with and without a viscous coupling procedure. The applicability of each code is assessed and many thin-layer Navier-Stokes benchmark solutions are obtained which can be used for comparison with other codes intended for use at high angles of attack. Reasonable agreement of the Navier-Stokes code with experiment and the viscous-inviscid interaction code is obtained at moderate angles of attack. An unsteady solution is obtained with the thin-layer Navier-Stokes code at the highest angle of attack considered. The maximum lift coefficient is overpredicted, however, in comparison to experimental data, which is attributed to the presence of a laminar separation bubble near the leading edge not modeled in the computations. Two comparisons with experimental data are also presented at a higher Mach number.
A Comparison of Three Navier-Stokes Solvers for Exhaust Nozzle Flowfields

NASA Technical Reports Server (NTRS)

Georgiadis, Nicholas J.; Yoder, Dennis A.; Debonis, James R.

1999-01-01

A comparison of the NPARC, PAB, and WIND (previously known as NASTD) Navier-Stokes solvers is made for two flow cases with turbulent mixing as the dominant flow characteristic, a two-dimensional ejector nozzle and a Mach 1.5 elliptic jet. The objective of the work is to determine if comparable predictions of nozzle flows can be obtained from different Navier-Stokes codes employed in a multiple site research program. A single computational grid was constructed for each of the two flows and used for all of the Navier-Stokes solvers. In addition, similar k-e based turbulence models were employed in each code, and boundary conditions were specified as similarly as possible across the codes. Comparisons of mass flow rates, velocity profiles, and turbulence model quantities are made between the computations and experimental data. The computational cost of obtaining converged solutions with each of the codes is also documented. Results indicate that all of the codes provided similar predictions for the two nozzle flows. Agreement of the Navier-Stokes calculations with experimental data was good for the ejector nozzle. However, for the Mach 1.5 elliptic jet, the calculations were unable to accurately capture the development of the three dimensional elliptic mixing layer.
Omissions in the synthetic theory of evolution.

PubMed

Frías L, Daniel

2010-01-01

The Synthetic Theory of Evolution is the most unifying theory of life science. This theory has dominated scientific thought in explaining the mechanisms involved in speciation. However, there are some omissions that have delayed the understanding of some aspects of the mechanisms of organic evolution, principally: 1) the bridge between somatic and germinal cells, especially in some phylum of invertebrates and vertebrates; 2) horizontal genetic transferences and the importance of viruses in host adaptation and evolution; 3) the role of non-coding DNA and non-transcriptional genes; 4) homeotic evolution and the limitations of gradual evolution; and 5) excessive emphasis on extrinsic barriers to animal speciation. This paper reviews each of these topics in an effort to contribute to a better comprehension of organic evolution. Molecular findings suggest the need for a new evolutionary synthesis.
Modeling impurity production and transport during ELM transients in a DIII-D lower single null configuration.

NASA Astrophysics Data System (ADS)

Hogan, J.; Fenstermacher, M.; Groth, M.; West, P.; Coster, D.; Thomas, P.

2003-10-01

Better understanding of carbon production and eventual pathways is an important need for ITER. ELM events can provide a significant carbon source, and small scale experiments predict significant dependence of C production rates on incident deuterium flux and surface temperature, quantities which change significantly during an ELM event. Thus, development of better quantitative models has been hampered by lack of sufficient time resolution during ELMs. Recent progress on DIII-D has significantly improved the spectroscopic resolution [1, 2]. Measured CIII evolution during low- and high-density DIII-D LSN ELMy H-modes (type I and type I-III, respectively) has been compared with modeling using the solps5.0/Eirene99 coupled edge code, and the CASTEM- 2000 3-D, time dependent thermal analysis code. The latter provides time-resolved absolute surface temperature distributions for the cases described in [2]. Comparison with observations using the Roth et al annealing model for chemical sputtering finds qualitative agreement. However, the transition in ELM type/frequency as density increases is the most important factor, and this is an input to the calculation given the present state of first principles ELM models. [1] M Fenstermacher et al EPS2003 [2] M Groth et al J Nucl Mater 2003
Evolution of cholinesterases in the animal kingdom.

PubMed

Pezzementi, Leo; Chatonnet, Arnaud

2010-09-06

Cholinesterases emerged from a family of enzymes and proteins with adhesion properties. This family is absent in plants and expanded in multicellular animals. True cholinesterases appeared in triploblastic animals together with the cholinergic system. Lineage specific duplications resulted in two acetylcholinesterases in most hexapods and in up to four genes in nematodes. In vertebrates the duplication leading to acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) is now considered to be an ancient event which occurred before the split of osteichthyes. The product of one or the other of the paralogues is responsible for the physiological hydrolysis of acetylcholine, depending on the species lineage and tissue considered. The BChE gene seems to have been lost in some fish lineages. The complete genome of amphioxus (Branchiostoma floridae: cephalochordate) contains a large number of duplicated genes or pseudogenes of cholinesterases. Sequence comparison and tree constructions raise the question of considering the atypical ChE studied in this organism as a representative of ancient BChE. Thus nematodes, arthropods, annelids, molluscs, and vertebrates typically possess two paralogous genes coding for cholinesterases. The origin of the duplication(s) is discussed. The mode of attachment through alternative C-terminal coding exons seems to have evolved independently from the catalytic part of the gene. Copyright (c) 2010 Elsevier Ireland Ltd. All rights reserved.
Quantitative analysis of vacuum-ultraviolet radiation from nanosecond laser-zinc interaction

NASA Astrophysics Data System (ADS)

Parchamy, Homaira; Szilagyi, John; Masnavi, Majid; Richardson, Martin

2018-07-01

The paper reports measurements of the vacuum-ultraviolet spectral irradiances of a flat zinc target over a wavelength region of 124-164 nm generated by 10 and 60 ns duration low-intensities, 5 ×109 - 3 ×1010 W cm-2, 1.06 μm wavelength laser pulses. Maximum radiation conversion efficiencies of 2.5%/2πsr and 0.8%/2πsr were measured for 60 and 10 ns laser pulses at the intensities of 5 ×109 and 1.4 ×1010 W cm-2, respectively. Atomic structure calculations using a relativistic configuration-interaction, flexible atomic code and a developed non-local thermodynamic equilibrium population kinetics model in comparison to the experimental spectra detected by the Seya-Namioka type monochromator reveal the strong broadband experimental emission originates mainly from 3d94p-3d94s, 3d94d-3d94p and 3d84p-3d84s, 3d84d-3d84p unresolved-transition arrays of double and triple ionized zinc, respectively. Two-dimensional radiation-hydrodynamics code is used to investigate time-space plasma evolution and spectral radiation of a 10 ns full-width-at-half-maximum Gaussian laser pulse-zinc interaction.
Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS < 1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.
Three stages during the evolution of the genetic code. [Abstract only

NASA Technical Reports Server (NTRS)

Baumann, U.; Oro, J.

1994-01-01

A diversification of the genetic code based on the number of codons available for the proteinous amino acids is established. Three groups of amino acids during evolution of the code are distinguished. On the basis of their chemical complexity and a small codon number those amino acids emerging later in a translation process are derived. Both criteria indicate that His, Phe, Tyr, Cys and either Lys or Asn were introduced in the second stage, whereas the number of codons alone gives evidence that Trp and Met were introduced in the third stage. The amino acids of stage one use purines rich codons, thus purines have been retained in their third codon position. All the amino acids introduced in the second stage, in contrast, use pyrimidines in this codon position. A low abundance of pyrimidines during early translation is derived. This assumption is supported by experiments on non enzymatic replication and interactions of DNA hairpin loops with a complementary strand. A back extrapolation concludes a high purine content of the first nucleic acids which gradually decreased during their evolution. Amino acids independently available form prebiotic synthesis were thus correlated to purine rich codons. Conclusions on prebiotic replication are discussed also in the light of recent codon usage data.

Higher-Order Advection-Based Remap of Magnetic Fields in an Arbitrary Lagrangian-Eulerian Code

NASA Astrophysics Data System (ADS)

Cornille, Brian; White, Dan

2017-10-01

We will present methods formulated for the Eulerian advection stage of an arbitrary Lagrangian-Eulerian code for the new addition of magnetohydrodynamic (MHD) effects. The various physical fields are advanced in time using a Lagrangian formulation of the system. When this Lagrangian motion produces substantial distortion of the mesh, it can be difficult or impossible to progress the simulation forward. This is overcome by relaxation of the mesh while the physical fields are frozen. The code has already successfully been extended to include evolution of magnetic field diffusion during the Lagrangian motion stage. This magnetic field is discretized using an H(div) compatible finite element basis. The advantage of this basis is that the divergence-free constraint of magnetic fields is maintained exactly during the Lagrangian motion evolution. Our goal is to preserve this property during Eulerian advection as well. We will demonstrate this property and the importance of MHD effects in several numerical experiments. In pulsed-power experiments magnetic fields may be imposed or spontaneously generated. When these magnetic fields are present, the evolution of the experiment may differ from a comparable configuration without magnetic fields. Prepared by LLNL under Contract DE-AC52-07NA27344. Supported by DOE CSGF under Grant Number DE-FG02-97ER25308.
The new semi-analytic code GalICS 2.0 - reproducing the galaxy stellar mass function and the Tully-Fisher relation simultaneously

NASA Astrophysics Data System (ADS)

Cattaneo, A.; Blaizot, J.; Devriendt, J. E. G.; Mamon, G. A.; Tollet, E.; Dekel, A.; Guiderdoni, B.; Kucukbas, M.; Thob, A. C. R.

2017-10-01

GalICS 2.0 is a new semi-analytic code to model the formation and evolution of galaxies in a cosmological context. N-body simulations based on a Planck cosmology are used to construct halo merger trees, track subhaloes, compute spins and measure concentrations. The accretion of gas on to galaxies and the morphological evolution of galaxies are modelled with prescriptions derived from hydrodynamic simulations. Star formation and stellar feedback are described with phenomenological models (as in other semi-analytic codes). GalICS 2.0 computes rotation speeds from the gravitational potential of the dark matter, the disc and the central bulge. As the rotation speed depends not only on the virial velocity but also on the ratio of baryons to dark matter within a galaxy, our calculation predicts a different Tully-Fisher relation from models in which vrot ∝ vvir. This is why, GalICS 2.0 is able to reproduce the galaxy stellar mass function and the Tully-Fisher relation simultaneously. Our results are also in agreement with halo masses from weak lensing and satellite kinematics, gas fractions, the relation between star formation rate (SFR) and stellar mass, the evolution of the cosmic SFR density, bulge-to-disc ratios, disc sizes and the Faber-Jackson relation.
EG and G and NASA face seal codes comparison

NASA Technical Reports Server (NTRS)

Basu, Prit

1994-01-01

This viewgraph presentation presents the following results for the example comparison: EG&G code with face deformations suppressed and SPIRALG agree well with each other as well as with the experimental data; 0 rpm stiffness data calculated by EG&G code are about 70-100 percent lower than that by SPIRALG; there is no appreciable difference between 0 rpm and 16,000 rpm stiffness and damping coefficients calculated by SPIRALG; and the film damping above 500 psig calculated by SPIRALG is much higher than the O-Ring secondary seal damping (e.g. 50 lbf.s/in).
Experimental research and comparison of LDPC and RS channel coding in ultraviolet communication systems.

PubMed

Wu, Menglong; Han, Dahai; Zhang, Xiang; Zhang, Feng; Zhang, Min; Yue, Guangxin

2014-03-10

We have implemented a modified Low-Density Parity-Check (LDPC) codec algorithm in ultraviolet (UV) communication system. Simulations are conducted with measured parameters to evaluate the LDPC-based UV system performance. Moreover, LDPC (960, 480) and RS (18, 10) are implemented and experimented via a non-line-of-sight (NLOS) UV test bed. The experimental results are in agreement with the simulation and suggest that based on the given power and 10(-3)bit error rate (BER), in comparison with an uncoded system, average communication distance increases 32% with RS code, while 78% with LDPC code.
Mitigation of lava flow invasion hazard through optimized barrier configuration aided by numerical simulation: The case of the 2001 Etna eruption

NASA Astrophysics Data System (ADS)

Scifoni, S.; Coltelli, M.; Marsella, M.; Proietti, C.; Napoleoni, Q.; Vicari, A.; Del Negro, C.

2010-04-01

Lava flow spreading along the flanks of Etna volcano often produces damages to the land and proprieties. The impact of these eruptions could be mitigated by building artificial barriers for controlling and slowing down the lava, as recently experienced in 1983, 1991-1993, 2001 and 2002. This study investigates how numerical simulations can be adopted for evaluating the effectiveness of barrier construction and for optimizing their geometry, considering as test case the lava flows emplaced on Etna's south flank during 2001. The flow temporal evolutions were reconstructed deriving the effusion rate trends, together with the pre-eruption topography were adopted as input data of the MAGFLOW simulation code. Three simulations were then conducted to simulate lava flow with and without barriers. The first aimed at verifying the reconstruction of the effusion rate trends, while the others at assessing the performance of the barrier system realized during the eruption in comparison with an alternative solution here proposed. A quantitative analysis carried out on the first simulation confirms the suitability of the selected test case. The comparison of the three simulated thickness distributions showed both the effectiveness of the barriers in slowing down the lava flow and the sensitivity of the MAGFLOW code to the topographical variations represented by the barriers. Finally, for reducing both the time necessary to erect the barrier and the barrier environmental impact, the gabion's barrier construction was analyzed. The implemented and tested procedure enforces the capability of using numerical simulations for designing optimized lava flow barriers aimed at making swifter mitigatory actions upon lava flows and improving the effectiveness of civil protection interventions during emergencies.
Comparison of Space Radiation Calculations from Deterministic and Monte Carlo Transport Codes

NASA Technical Reports Server (NTRS)

Adams, J. H.; Lin, Z. W.; Nasser, A. F.; Randeniya, S.; Tripathi, r. K.; Watts, J. W.; Yepes, P.

2010-01-01

The presentation outline includes motivation, radiation transport codes being considered, space radiation cases being considered, results for slab geometry, results from spherical geometry, and summary. ///////// main physics in radiation transport codes hzetrn uprop fluka geant4, slab geometry, spe, gcr,
TOPLHA and ALOHA: comparison between Lower Hybrid wave coupling codes

NASA Astrophysics Data System (ADS)

Meneghini, Orso; Hillairet, J.; Goniche, M.; Bilato, R.; Voyer, D.; Parker, R.

2008-11-01

TOPLHA and ALOHA are wave coupling simulation tools for LH antennas. Both codes are able to account for realistic 3D antenna geometries and use a 1D plasma model. In the framework of a collaboration between MIT and CEA laboratories, the two codes have been extensively compared. In TOPLHA the EM problem is self consistently formulated by means of a set of multiple coupled integral equations having as domain the triangles of the meshed antenna surface. TOPLHA currently uses the FELHS code for modeling the plasma response. ALOHA instead uses a mode matching approach and its own plasma model. Comparisons have been done for several plasma scenarios on different antenna designs: an array of independent waveguides, a multi-junction antenna and a passive/active multi-junction antenna. When simulating the same geometry and plasma conditions the two codes compare remarkably well both for the reflection coefficients and for the launched spectra. The different approach of the two codes to solve the same problem strengthens the confidence in the final results.
VizieR Online Data Catalog: Evolution of rotating very massive LC stars (Kohler, 2015)

NASA Astrophysics Data System (ADS)

Kohler, K.; Langer, N.; de Koter, A.; de Mink, S. E.; Crowther, P. A.; Evans, C. J.; Grafener, G.; Sana, H.; Sanyal, D.; Schneider, F. R. N.; Vink, J. S.

2014-11-01

A dense model grid with chemical composition appropriate for the Large Magellanic Cloud is presented. A one-dimensional hydrodynamic stellar evolution code was used to compute our models on the main sequence, taking into account rotation, transport of angular momentum by magnetic fields and stellar wind mass loss. We present stellar evolution models with initial masses of 70-500M⊙ and with initial surface rotational velocities of 0-550km/s. (2 data files).
Ancient DNA sequence revealed by error-correcting codes.

PubMed

Brandão, Marcelo M; Spoladore, Larissa; Faria, Luzinete C B; Rocha, Andréa S L; Silva-Filho, Marcio C; Palazzo, Reginaldo

2015-07-10

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code.
Ancient DNA sequence revealed by error-correcting codes

PubMed Central

Brandão, Marcelo M.; Spoladore, Larissa; Faria, Luzinete C. B.; Rocha, Andréa S. L.; Silva-Filho, Marcio C.; Palazzo, Reginaldo

2015-01-01

A previously described DNA sequence generator algorithm (DNA-SGA) using error-correcting codes has been employed as a computational tool to address the evolutionary pathway of the genetic code. The code-generated sequence alignment demonstrated that a residue mutation revealed by the code can be found in the same position in sequences of distantly related taxa. Furthermore, the code-generated sequences do not promote amino acid changes in the deviant genomes through codon reassignment. A Bayesian evolutionary analysis of both code-generated and homologous sequences of the Arabidopsis thaliana malate dehydrogenase gene indicates an approximately 1 MYA divergence time from the MDH code-generated sequence node to its paralogous sequences. The DNA-SGA helps to determine the plesiomorphic state of DNA sequences because a single nucleotide alteration often occurs in distantly related taxa and can be found in the alternative codon patterns of noncanonical genetic codes. As a consequence, the algorithm may reveal an earlier stage of the evolution of the standard code. PMID:26159228
Comparison of codes assessing galactic cosmic radiation exposure of aircraft crew.

PubMed

Bottollier-Depois, J F; Beck, P; Bennett, B; Bennett, L; Bütikofer, R; Clairand, I; Desorgher, L; Dyer, C; Felsberger, E; Flückiger, E; Hands, A; Kindl, P; Latocha, M; Lewis, B; Leuthold, G; Maczka, T; Mares, V; McCall, M J; O'Brien, K; Rollet, S; Rühm, W; Wissmann, F

2009-10-01

The assessment of the exposure to cosmic radiation onboard aircraft is one of the preoccupations of bodies responsible for radiation protection. Cosmic particle flux is significantly higher onboard aircraft than at ground level and its intensity depends on the solar activity. The dose is usually estimated using codes validated by the experimental data. In this paper, a comparison of various codes is presented, some of them are used routinely, to assess the dose received by the aircraft crew caused by the galactic cosmic radiation. Results are provided for periods close to solar maximum and minimum and for selected flights covering major commercial routes in the world. The overall agreement between the codes, particularly for those routinely used for aircraft crew dosimetry, was better than +/-20 % from the median in all but two cases. The agreement within the codes is considered to be fully satisfactory for radiation protection purposes.
Secure ADS-B authentication system and method

NASA Technical Reports Server (NTRS)

Viggiano, Marc J (Inventor); Valovage, Edward M (Inventor); Samuelson, Kenneth B (Inventor); Hall, Dana L (Inventor)

2010-01-01

A secure system for authenticating the identity of ADS-B systems, including: an authenticator, including a unique id generator and a transmitter transmitting the unique id to one or more ADS-B transmitters; one or more ADS-B transmitters, including a receiver receiving the unique id, one or more secure processing stages merging the unique id with the ADS-B transmitter's identification, data and secret key and generating a secure code identification and a transmitter transmitting a response containing the secure code and ADSB transmitter's data to the authenticator; the authenticator including means for independently determining each ADS-B transmitter's secret key, a receiver receiving each ADS-B transmitter's response, one or more secure processing stages merging the unique id, ADS-B transmitter's identification and data and generating a secure code, and comparison processing comparing the authenticator-generated secure code and the ADS-B transmitter-generated secure code and providing an authentication signal based on the comparison result.
User's manual for Axisymmetric Diffuser Duct (ADD) code. Volume 1: General ADD code description

NASA Technical Reports Server (NTRS)

Anderson, O. L.; Hankins, G. B., Jr.; Edwards, D. E.

1982-01-01

This User's Manual contains a complete description of the computer codes known as the AXISYMMETRIC DIFFUSER DUCT code or ADD code. It includes a list of references which describe the formulation of the ADD code and comparisons of calculation with experimental flows. The input/output and general use of the code is described in the first volume. The second volume contains a detailed description of the code including the global structure of the code, list of FORTRAN variables, and descriptions of the subroutines. The third volume contains a detailed description of the CODUCT code which generates coordinate systems for arbitrary axisymmetric ducts.
Modelling of the physico-chemical behaviour of clay minerals with a thermo-kinetic model taking into account particles morphology in compacted material.

NASA Astrophysics Data System (ADS)

Sali, D.; Fritz, B.; Clément, C.; Michau, N.

2003-04-01

Modelling of fluid-mineral interactions is largely used in Earth Sciences studies to better understand the involved physicochemical processes and their long-term effect on the materials behaviour. Numerical models simplify the processes but try to preserve their main characteristics. Therefore the modelling results strongly depend on the data quality describing initial physicochemical conditions for rock materials, fluids and gases, and on the realistic way of processes representations. The current geo-chemical models do not well take into account rock porosity and permeability and the particle morphology of clay minerals. In compacted materials like those considered as barriers in waste repositories, low permeability rocks like mudstones or compacted powders will be used : they contain mainly fine particles and the geochemical models used for predicting their interactions with fluids tend to misjudge their surface areas, which are fundamental parameters in kinetic modelling. The purpose of this study was to improve how to take into account the particles morphology in the thermo-kinetic code KINDIS and the reactive transport code KIRMAT. A new function was integrated in these codes, considering the reaction surface area as a volume depending parameter and the calculated evolution of the mass balance in the system was coupled with the evolution of reactive surface areas. We made application exercises for numerical validation of these new versions of the codes and the results were compared with those of the pre-existing thermo-kinetic code KINDIS. Several points are highlighted. Taking into account reactive surface area evolution during simulation modifies the predicted mass transfers related to fluid-minerals interactions. Different secondary mineral phases are also observed during modelling. The evolution of the reactive surface parameter helps to solve the competition effects between different phases present in the system which are all able to fix the chemical elements mobilised by the water-minerals interaction processes. To validate our model we simulated the compacted bentonite (MX80) studied for engineered barriers for radioactive waste confinement and mainly composed of Na-Ca-montmorillonite. The study of particles morphology and reactive surfaces evolutions reveals that aqueous ions have a complex behaviour, especially when competitions between various mineral phases occur. In that case, our model predicts a preferential precipitation of finest particles, favouring smectites instead of zeolites. This work is a part of a PhD Thesis supported by Andra, the French Radioactive Waste Management Agency.
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus

PubMed Central

Scannell, Devin R.; Zill, Oliver A.; Rokas, Antonis; Payen, Celia; Dunham, Maitreya J.; Eisen, Michael B.; Rine, Jasper; Johnston, Mark; Hittinger, Chris Todd

2011-01-01

High-quality, well-annotated genome sequences and standardized laboratory strains fuel experimental and evolutionary research. We present improved genome sequences of three species of Saccharomyces sensu stricto yeasts: S. bayanus var. uvarum (CBS 7001), S. kudriavzevii (IFO 1802T and ZP 591), and S. mikatae (IFO 1815T), and describe their comparison to the genomes of S. cerevisiae and S. paradoxus. The new sequences, derived by assembling millions of short DNA sequence reads together with previously published Sanger shotgun reads, have vastly greater long-range continuity and far fewer gaps than the previously available genome sequences. New gene predictions defined a set of 5261 protein-coding orthologs across the five most commonly studied Saccharomyces yeasts, enabling a re-examination of the tempo and mode of yeast gene evolution and improved inferences of species-specific gains and losses. To facilitate experimental investigations, we generated genetically marked, stable haploid strains for all three of these Saccharomyces species. These nearly complete genome sequences and the collection of genetically marked strains provide a valuable toolset for comparative studies of gene function, metabolism, and evolution, and render Saccharomyces sensu stricto the most experimentally tractable model genus. These resources are freely available and accessible through www.SaccharomycesSensuStricto.org. PMID:22384314
A Tradeoff Drives the Evolution of Reduced Metal Resistance in Natural Populations of Yeast

PubMed Central

Chang, Shang-Lin; Leu, Jun-Yi

2011-01-01

Various types of genetic modification and selective forces have been implicated in the process of adaptation to novel or adverse environments. However, the underlying molecular mechanisms are not well understood in most natural populations. Here we report that a set of yeast strains collected from Evolution Canyon (EC), Israel, exhibit an extremely high tolerance to the heavy metal cadmium. We found that cadmium resistance is primarily caused by an enhanced function of a metal efflux pump, PCA1. Molecular analyses demonstrate that this enhancement can be largely attributed to mutations in the promoter sequence, while mutations in the coding region have a minor effect. Reconstruction experiments show that three single nucleotide substitutions in the PCA1 promoter quantitatively increase its activity and thus enhance the cells' cadmium resistance. Comparison among different yeast species shows that the critical nucleotides found in EC strains are conserved and functionally important for cadmium resistance in other species, suggesting that they represent an ancestral type. However, these nucleotides had diverged in most Saccharomyces cerevisiae populations, which gave cells growth advantages under conditions where cadmium is low or absent. Our results provide a rare example of a selective sweep in yeast populations driven by a tradeoff in metal resistance. PMID:21483812
Comparison of intraspecific, interspecific and intergeneric chloroplast diversity in Cycads

PubMed Central

Jiang, Guo-Feng; Hinsinger, Damien Daniel; Strijk, Joeri Sergej

2016-01-01

Cycads are among the most threatened plant species. Increasing the availability of genomic information by adding whole chloroplast data is a fundamental step in supporting phylogenetic studies and conservation efforts. Here, we assemble a dataset encompassing three taxonomic levels in cycads, including ten genera, three species in the genus Cycas and two individuals of C. debaoensis. Repeated sequences, SSRs and variations of the chloroplast were analyzed at the intraspecific, interspecific and intergeneric scale, and using our sequence data, we reconstruct a phylogenomic tree for cycads. The chloroplast was 162,094 bp in length, with 133 genes annotated, including 87 protein-coding, 37 tRNA and 8 rRNA genes. We found 7 repeated sequences and 39 SSRs. Seven loci showed promising levels of variations for application in DNA-barcoding. The chloroplast phylogeny confirmed the division of Cycadales in two suborders, each of them being monophyletic, revealing a contradiction with the current family circumscription and its evolution. Finally, 10 intraspecific SNPs were found. Our results showed that despite the extremely restricted distribution range of C. debaoensis, using complete chloroplast data is useful not only in intraspecific studies, but also to improve our understanding of cycad evolution and in defining conservation strategies for this emblematic group. PMID:27558458
Comparative and functional characterization of intragenic tandem repeats in 10 Aspergillus genomes.

PubMed

Gibbons, John G; Rokas, Antonis

2009-03-01

Intragenic tandem repeats (ITRs) are consecutive repeats of three or more nucleotides found in coding regions. ITRs are the underlying cause of several human genetic diseases and have been associated with phenotypic variation, including pathogenesis, in several clades of the tree of life. We have examined the evolution and functional role of ITRs in 10 genomes spanning the fungal genus Aspergillus, a clade of relevance to medicine, agriculture, and industry. We identified several hundred ITRs in each of the species examined. ITR content varied extensively between species, with an average 79% of ITRs unique to a given species. For the fraction of conserved ITR regions, sequence comparisons within species and between close relatives revealed that they were highly variable. ITR-containing proteins were evolutionarily less conserved, compositionally distinct, and overrepresented for domains associated with cell-surface localization and function relative to the rest of the proteome. Furthermore, ITRs were preferentially found in proteins involved in transcription, cellular communication, and cell-type differentiation but were underrepresented in proteins involved in metabolism and energy. Importantly, although ITRs were evolutionarily labile, their functional associations appeared. To be remarkably conserved across eukaryotes. Fungal ITRs likely participate in a variety of developmental processes and cell-surface-associated functions, suggesting that their contribution to fungal lifestyle and evolution may be more general than previously assumed.
The Bauschinger Effect in Autofrettaged Tubes- A Comparison of Models Including the ASME Code

DTIC Science & Technology

1998-06-01

possible error in Division 3 of Section Vm of the ASME Boiler and Pressure Vessel Code . They show that the empirical method used in the code to...Discussion presented by DP Kendall We appreciate the acknowledgement in the Kendall discussion that Division 3 of Section VIII of the ASME Boiler and Pressure Vessel Code may
The accuracy of seminumerical reionization models in comparison with radiative transfer simulations

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-06-01

We have developed a modular seminumerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I), and single-ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different seminumerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the seminumerical approaches produce similar H II and He II morphologies and power spectra of the H I 21 cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double-ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our seminumerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20 per cent ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggest that constraining ionizing emissivity-sensitive parameters from seminumerical galaxy formation-reionization models are subject to photon nonconservation.

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

PubMed Central

Salzberg, Steven L; Sommer, Daniel D; Schatz, Michael C; Phillippy, Adam M; Rabinowicz, Pablo D; Tsuge, Seiji; Furutani, Ayako; Ochiai, Hirokazu; Delcher, Arthur L; Kelley, David; Madupu, Ramana; Puiu, Daniela; Radune, Diana; Shumway, Martin; Trapnell, Cole; Aparna, Gudlur; Jha, Gopaljee; Pandey, Alok; Patil, Prabhu B; Ishihara, Hiromichi; Meyer, Damien F; Szurek, Boris; Verdier, Valerie; Koebnik, Ralf; Dow, J Maxwell; Ryan, Robert P; Hirata, Hisae; Tsuyumu, Shinji; Won Lee, Sang; Ronald, Pamela C; Sonti, Ramesh V; Van Sluys, Marie-Anne; Leach, Jan E; White, Frank F; Bogdanove, Adam J

2008-01-01

Background Xanthomonas oryzae pv. oryzae causes bacterial blight of rice (Oryza sativa L.), a major disease that constrains production of this staple crop in many parts of the world. We report here on the complete genome sequence of strain PXO99A and its comparison to two previously sequenced strains, KACC10331 and MAFF311018, which are highly similar to one another. Results The PXO99A genome is a single circular chromosome of 5,240,075 bp, considerably longer than the genomes of the other strains (4,941,439 bp and 4,940,217 bp, respectively), and it contains 5083 protein-coding genes, including 87 not found in KACC10331 or MAFF311018. PXO99A contains a greater number of virulence-associated transcription activator-like effector genes and has at least ten major chromosomal rearrangements relative to KACC10331 and MAFF311018. PXO99A contains numerous copies of diverse insertion sequence elements, members of which are associated with 7 out of 10 of the major rearrangements. A rapidly-evolving CRISPR (clustered regularly interspersed short palindromic repeats) region contains evidence of dozens of phage infections unique to the PXO99A lineage. PXO99A also contains a unique, near-perfect tandem repeat of 212 kilobases close to the replication terminus. Conclusion Our results provide striking evidence of genome plasticity and rapid evolution within Xanthomonas oryzae pv. oryzae. The comparisons point to sources of genomic variation and candidates for strain-specific adaptations of this pathogen that help to explain the extraordinary diversity of Xanthomonas oryzae pv. oryzae genotypes and races that have been isolated from around the world. PMID:18452608
Rapid Evolution of Virulence and Drug Resistance in the Emerging Zoonotic Pathogen Streptococcus suis

PubMed Central

Holden, Matthew T. G.; Hauser, Heidi; Sanders, Mandy; Ngo, Thi Hoa; Cherevach, Inna; Cronin, Ann; Goodhead, Ian; Mungall, Karen; Quail, Michael A.; Price, Claire; Rabbinowitsch, Ester; Sharp, Sarah; Croucher, Nicholas J.; Chieu, Tran Bich; Thi Hoang Mai, Nguyen; Diep, To Song; Chinh, Nguyen Tran; Kehoe, Michael; Leigh, James A.; Ward, Philip N.; Dowson, Christopher G.; Whatmore, Adrian M.; Chanter, Neil; Iversen, Pernille; Gottschalk, Marcelo; Slater, Josh D.; Smith, Hilde E.; Spratt, Brian G.; Xu, Jianguo; Ye, Changyun; Bentley, Stephen; Barrell, Barclay G.; Schultsz, Constance; Maskell, Duncan J.; Parkhill, Julian

2009-01-01

Background Streptococcus suis is a zoonotic pathogen that infects pigs and can occasionally cause serious infections in humans. S. suis infections occur sporadically in human Europe and North America, but a recent major outbreak has been described in China with high levels of mortality. The mechanisms of S. suis pathogenesis in humans and pigs are poorly understood. Methodology/Principal Findings The sequencing of whole genomes of S. suis isolates provides opportunities to investigate the genetic basis of infection. Here we describe whole genome sequences of three S. suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam. Comparative genomic analysis was used to investigate the variability of these strains. S. suis is phylogenetically distinct from other Streptococcus species for which genome sequences are currently available. Accordingly, ∼40% of the ∼2 Mb genome is unique in comparison to other Streptococcus species. Finer genomic comparisons within the species showed a high level of sequence conservation; virtually all of the genome is common to the S. suis strains. The only exceptions are three ∼90 kb regions, present in the two isolates from humans, composed of integrative conjugative elements and transposons. Carried in these regions are coding sequences associated with drug resistance. In addition, small-scale sequence variation has generated pseudogenes in putative virulence and colonization factors. Conclusions/Significance The genomic inventories of genetically related S. suis strains, isolated from distinct hosts and diseases, exhibit high levels of conservation. However, the genomes provide evidence that horizontal gene transfer has contributed to the evolution of drug resistance. PMID:19603075
No variation and low synonymous substitution rates in coral mtDNA despite high nuclear variation

PubMed Central

Hellberg, Michael E

2006-01-01

Background The mitochondrial DNA (mtDNA) of most animals evolves more rapidly than nuclear DNA, and often shows higher levels of intraspecific polymorphism and population subdivision. The mtDNA of anthozoans (corals, sea fans, and their kin), by contrast, appears to evolve slowly. Slow mtDNA evolution has been reported for several anthozoans, however this slow pace has been difficult to put in phylogenetic context without parallel surveys of nuclear variation or calibrated rates of synonymous substitution that could permit quantitative rate comparisons across taxa. Here, I survey variation in the coding region of a mitochondrial gene from a coral species (Balanophyllia elegans) known to possess high levels of nuclear gene variation, and estimate synonymous rates of mtDNA substitution by comparison to another coral (Tubastrea coccinea). Results The mtDNA surveyed (630 bp of cytochrome oxidase subunit I) was invariant among individuals sampled from 18 populations spanning 3000 km of the range of B. elegans, despite high levels of variation and population subdivision for allozymes over these same populations. The synonymous substitution rate between B. elegans and T. coccinea (0.05%/site/106 years) is similar to that in most plants, but 50–100 times lower than rates typical for most animals. In addition, while substitutions to mtDNA in most animals exhibit a strong bias toward transitions, mtDNA from these corals does not. Conclusion Slow rates of mitochondrial nucleotide substitution result in low levels of intraspecific mtDNA variation in corals, even when nuclear loci vary. Slow mtDNA evolution appears to be the basal condition among eukaryotes. mtDNA substitution rates switch from slow to fast abruptly and unidirectionally. This switch may stem from the loss of just one or a few mitochondrion-specific DNA repair or replication genes. PMID:16542456
The accuracy of semi-numerical reionization models in comparison with radiative transfer simulations

NASA Astrophysics Data System (ADS)

Hutter, Anne

2018-03-01

We have developed a modular semi-numerical code that computes the time and spatially dependent ionization of neutral hydrogen (H I), neutral (He I) and singly ionized helium (He II) in the intergalactic medium (IGM). The model accounts for recombinations and provides different descriptions for the photoionization rate that are used to calculate the residual H I fraction in ionized regions. We compare different semi-numerical reionization schemes to a radiative transfer (RT) simulation. We use the RT simulation as a benchmark, and find that the semi-numerical approaches produce similar H II and He II morphologies and power spectra of the H I 21cm signal throughout reionization. As we do not track partial ionization of He II, the extent of the double ionized helium (He III) regions is consistently smaller. In contrast to previous comparison projects, the ionizing emissivity in our semi-numerical scheme is not adjusted to reproduce the redshift evolution of the RT simulation, but directly derived from the RT simulation spectra. Among schemes that identify the ionized regions by the ratio of the number of ionization and absorption events on different spatial smoothing scales, we find those that mark the entire sphere as ionized when the ionization criterion is fulfilled to result in significantly accelerated reionization compared to the RT simulation. Conversely, those that flag only the central cell as ionized yield very similar but slightly delayed redshift evolution of reionization, with up to 20% ionizing photons lost. Despite the overall agreement with the RT simulation, our results suggests that constraining ionizing emissivity sensitive parameters from semi-numerical galaxy formation-reionization models are subject to photon nonconservation.
Comparing TCV experimental VDE responses with DINA code simulations

NASA Astrophysics Data System (ADS)

Favez, J.-Y.; Khayrutdinov, R. R.; Lister, J. B.; Lukash, V. E.

2002-02-01

The DINA free-boundary equilibrium simulation code has been implemented for TCV, including the full TCV feedback and diagnostic systems. First results showed good agreement with control coil perturbations and correctly reproduced certain non-linear features in the experimental measurements. The latest DINA code simulations, presented in this paper, exploit discharges with different cross-sectional shapes and different vertical instability growth rates which were subjected to controlled vertical displacement events (VDEs), extending previous work with the DINA code on the DIII-D tokamak. The height of the TCV vessel allows observation of the non-linear evolution of the VDE growth rate as regions of different vertical field decay index are crossed. The vertical movement of the plasma is found to be well modelled. For most experiments, DINA reproduces the S-shape of the vertical displacement in TCV with excellent precision. This behaviour cannot be modelled using linear time-independent models because of the predominant exponential shape due to the unstable pole of any linear time-independent model. The other most common equilibrium parameters like the plasma current Ip, the elongation κ, the triangularity δ, the safety factor q, the ratio between the averaged plasma kinetic pressure and the pressure of the poloidal magnetic field at the edge of the plasma βp, and the internal self inductance li also show acceptable agreement. The evolution of the growth rate γ is estimated and compared with the evolution of the closed-loop growth rate calculated with the RZIP linear model, confirming the origin of the observed behaviour.
Revealing the long-term landscape evolution of the South Atlantic passive continental margin, Brazil and Namibia, by thermokinematic numerical modeling using the software code Pecube.

NASA Astrophysics Data System (ADS)

Stippich, Christian; Glasmacher, Ulrich Anton; Hackspacher, Peter

2015-04-01

The aim of the research is to quantify the long-term landscape evolution of the South Atlantic passive continental margin (SAPCM) in SE-Brazil and NW-Namibia. Excellent onshore outcrop conditions and complete rift to post-rift archives between Sao Paulo and Porto Alegre and in the transition from Namibia to Angola (onshore Walvis ridge) allow a high precision quantification of exhumation, and uplift rates, influencing physical parameters, long-term acting forces, and process-response systems. Research will integrate the published and partly published thermochronological data from Brazil and Namibia, and test lately published new concepts on causes of long-term landscape evolution at rifted margins. The climate-continental margin-mantle coupled process-response system is caused by the interaction between endogenous and exogenous forces, which are related to the mantle-process driven rift - drift - passive continental margin evolution of the South Atlantic, and the climate change since the Early/Late Cretaceous climate maximum. Special emphasis will be given to the influence of long-living transform faults such as the Florianopolis Fracture Zone (FFZ) on the long-term topography evolution of the SAPCM's. A long-term landscape evolution model with process rates will be achieved by thermo-kinematic 3-D modeling (software code PECUBE1,2 and FastScape3). Testing model solutions obtained for a multidimensional parameter space against the real thermochronological and geomorphological data set, the most likely combinations of parameter rates, and values can be constrained. The data and models will allow separating the exogenous and endogenous forces and their process rates. References 1. Braun, J., 2003. Pecube: A new finite element code to solve the 3D heat transport equation including the effects of a time-varying, finite amplitude surface topography. Computers and Geosciences, v.29, pp.787-794. 2. Braun, J., van der Beek, P., Valla, P., Robert, X., Herman, F., Goltzbacj, C., Pedersen, V., Perry, C., Simon-Labric, T., Prigent, C. 2012. Quantifying rates of landscape evolution and tectonic processes by thermochronology and numerical modeling of crustal heat transport using PECUBE. Tectonophysics, v.524-525, pp.1-28. 3. Braun, J. and Willett, S.D., 2013. A very efficient, O(n), implicit and parallel method to solve the basic stream power law equation governing fluvial incision and landscape evolution. Geomorphology, v.180-181, 170-179.
A Cross-Cultural Comparison of Korean and American Science Teachers' Views of Evolution and the Nature of Science

ERIC Educational Resources Information Center

Kim, Sun Young; Nehm, Ross H.

2011-01-01

Despite a few international comparisons of the evolutionary beliefs of the general public, comparatively less research has focused on science teachers. Cross-cultural studies offer profitable opportunities for exploring the interactions among knowledge and belief variables in regard to evolution in different socio-cultural contexts. We…
Studies of Planet Formation using a Hybrid N-body + Planetesimal Code

NASA Technical Reports Server (NTRS)

Kenyon, Scott J.; Bromley, Benjamin C.; Salamon, Michael (Technical Monitor)

2005-01-01

The goal of our proposal was to use a hybrid multi-annulus planetesimal/n-body code to examine the planetesimal theory, one of the two main theories of planet formation. We developed this code to follow the evolution of numerous 1 m to 1 km planetesimals as they collide, merge, and grow into full-fledged planets. Our goal was to apply the code to several well-posed, topical problems in planet formation and to derive observational consequences of the models. We planned to construct detailed models to address two fundamental issues: 1) icy planets - models for icy planet formation will demonstrate how the physical properties of debris disks, including the Kuiper Belt in our solar system, depend on initial conditions and input physics; and 2) terrestrial planets - calculations following the evolution of 1-10 km planetesimals into Earth-mass planets and rings of dust will provide a better understanding of how terrestrial planets form and interact with their environment. During the past year, we made progress on each issue. Papers published in 2004 are summarized. Summaries of work to be completed during the first half of 2005 and work planned for the second half of 2005 are included.
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.

PubMed

Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D

2012-01-01

Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
Space Radiation Transport Codes: A Comparative Study for Galactic Cosmic Rays Environment

NASA Astrophysics Data System (ADS)

Tripathi, Ram; Wilson, John W.; Townsend, Lawrence W.; Gabriel, Tony; Pinsky, Lawrence S.; Slaba, Tony

For long duration and/or deep space human missions, protection from severe space radiation exposure is a challenging design constraint and may be a potential limiting factor. The space radiation environment consists of galactic cosmic rays (GCR), solar particle events (SPE), trapped radiation, and includes ions of all the known elements over a very broad energy range. These ions penetrate spacecraft materials producing nuclear fragments and secondary particles that damage biological tissues, microelectronic devices, and materials. In deep space missions, where the Earth's magnetic field does not provide protection from space radiation, the GCR environment is significantly enhanced due to the absence of geomagnetic cut-off and is a major component of radiation exposure. Accurate risk assessments critically depend on the accuracy of the input information as well as radiation transport codes used, and so systematic verification of codes is necessary. In this study, comparisons are made between the deterministic code HZETRN2006 and the Monte Carlo codes HETC-HEDS and FLUKA for an aluminum shield followed by a water target exposed to the 1977 solar minimum GCR spectrum. Interaction and transport of high charge ions present in GCR radiation environment provide a more stringent constraint in the comparison of the codes. Dose, dose equivalent and flux spectra are compared; details of the comparisons will be discussed, and conclusions will be drawn for future directions.
Advanced simulation of mixed-material erosion/evolution and application to low and high-Z containing plasma facing components

NASA Astrophysics Data System (ADS)

Brooks, J. N.; Hassanein, A.; Sizyuk, T.

2013-07-01

Plasma interactions with mixed-material surfaces are being analyzed using advanced modeling of time-dependent surface evolution/erosion. Simulations use the REDEP/WBC erosion/redeposition code package coupled to the HEIGHTS package ITMC-DYN mixed-material formation/response code, with plasma parameter input from codes and data. We report here on analysis for a DIII-D Mo/C containing tokamak divertor. A DIII-D/DiMES probe experiment simulation predicts that sputtered molybdenum from a 1 cm diameter central spot quickly saturates (˜4 s) in the 5 cm diameter surrounding carbon probe surface, with subsequent re-sputtering and transport to off-probe divertor regions, and with high (˜50%) redeposition on the Mo spot. Predicted Mo content in the carbon agrees well with post-exposure probe data. We discuss implications and mixed-material analysis issues for Be/W mixing at the ITER outer divertor, and Li, C, Mo mixing at an NSTX divertor.
Evolution and Diversity of the Human Hepatitis D Virus Genome

PubMed Central

Huang, Chi-Ruei; Lo, Szecheng J.

2010-01-01

Human hepatitis delta virus (HDV) is the smallest RNA virus in genome. HDV genome is divided into a viroid-like sequence and a protein-coding sequence which could have originated from different resources and the HDV genome was eventually constituted through RNA recombination. The genome subsequently diversified through accumulation of mutations selected by interactions between the mutated RNA and proteins with host factors to successfully form the infectious virions. Therefore, we propose that the conservation of HDV nucleotide sequence is highly related with its functionality. Genome analysis of known HDV isolates shows that the C-terminal coding sequences of large delta antigen (LDAg) are the highest diversity than other regions of protein-coding sequences but they still retain biological functionality to interact with the heavy chain of clathrin can be selected and maintained. Since viruses interact with many host factors, including escaping the host immune response, how to design a program to predict RNA genome evolution is a great challenging work. PMID:20204073
Non-coding RNAs' partitioning in the evolution of photosynthetic organisms via energy transduction and redox signaling.

PubMed

Kotakis, Christos

2015-01-01

Ars longa, vita brevis -Hippocrates Chloroplasts and mitochondria are genetically semi-autonomous organelles inside the plant cell. These constructions formed after endosymbiosis and keep evolving throughout the history of life. Experimental evidence is provided for active non-coding RNAs (ncRNAs) in these prokaryote-like structures, and a possible functional imprinting on cellular electrophysiology by those RNA entities is described. Furthermore, updated knowledge on RNA metabolism of organellar genomes uncovers novel inter-communication bridges with the nucleus. This class of RNA molecules is considered as a unique ontogeny which transforms their biological role as a genetic rheostat into a synchronous biochemical one that can affect the energetic charge and redox homeostasis inside cells. A hypothesis is proposed where such modulation by non-coding RNAs is integrated with genetic signals regulating gene transfer. The implications of this working hypothesis are discussed, with particular reference to ncRNAs involvement in the organellar and nuclear genomes evolution since their integrity is functionally coupled with redox signals in photosynthetic organisms.
Compression performance comparison in low delay real-time video for mobile applications

NASA Astrophysics Data System (ADS)

Bivolarski, Lazar

2012-10-01

This article compares the performance of several current video coding standards in the conditions of low-delay real-time in a resource constrained environment. The comparison is performed using the same content and the metrics and mix of objective and perceptual quality metrics. The metrics results in different coding schemes are analyzed from a point of view of user perception and quality of service. Multiple standards are compared MPEG-2, MPEG4 and MPEG-AVC and well and H.263. The metrics used in the comparison include SSIM, VQM and DVQ. Subjective evaluation and quality of service are discussed from a point of view of perceptual metrics and their incorporation in the coding scheme development process. The performance and the correlation of results are presented as a predictor of the performance of video compression schemes.
Comparisons of survival predictions using survival risk ratios based on International Classification of Diseases, Ninth Revision and Abbreviated Injury Scale trauma diagnosis codes.

PubMed

Clarke, John R; Ragone, Andrew V; Greenwald, Lloyd

2005-09-01

We conducted a comparison of methods for predicting survival using survival risk ratios (SRRs), including new comparisons based on International Classification of Diseases, Ninth Revision (ICD-9) versus Abbreviated Injury Scale (AIS) six-digit codes. From the Pennsylvania trauma center's registry, all direct trauma admissions were collected through June 22, 1999. Patients with no comorbid medical diagnoses and both ICD-9 and AIS injury codes were used for comparisons based on a single set of data. SRRs for ICD-9 and then for AIS diagnostic codes were each calculated two ways: from the survival rate of patients with each diagnosis and when each diagnosis was an isolated diagnosis. Probabilities of survival for the cohort were calculated using each set of SRRs by the multiplicative ICISS method and, where appropriate, the minimum SRR method. These prediction sets were then internally validated against actual survival by the Hosmer-Lemeshow goodness-of-fit statistic. The 41,364 patients had 1,224 different ICD-9 injury diagnoses in 32,261 combinations and 1,263 corresponding AIS injury diagnoses in 31,755 combinations, ranging from 1 to 27 injuries per patient. All conventional ICD-9-based combinations of SRRs and methods had better Hosmer-Lemeshow goodness-of-fit statistic fits than their AIS-based counterparts. The minimum SRR method produced better calibration than the multiplicative methods, presumably because it did not magnify inaccuracies in the SRRs that might occur with multiplication. Predictions of survival based on anatomic injury alone can be performed using ICD-9 codes, with no advantage from extra coding of AIS diagnoses. Predictions based on the single worst SRR were closer to actual outcomes than those based on multiplying SRRs.
Concatenated coding for low date rate space communications.

NASA Technical Reports Server (NTRS)

Chen, C. H.

1972-01-01

In deep space communications with distant planets, the data rate as well as the operating SNR may be very low. To maintain the error rate also at a very low level, it is necessary to use a sophisticated coding system (longer code) without excessive decoding complexity. The concatenated coding has been shown to meet such requirements in that the error rate decreases exponentially with the overall length of the code while the decoder complexity increases only algebraically. Three methods of concatenating an inner code with an outer code are considered. Performance comparison of the three concatenated codes is made.
Early Evolution of Conserved Regulatory Sequences Associated with Development in Vertebrates

PubMed Central

McEwen, Gayle K.; Goode, Debbie K.; Parker, Hugo J.; Woolfe, Adam; Callaway, Heather; Elgar, Greg

2009-01-01

Comparisons between diverse vertebrate genomes have uncovered thousands of highly conserved non-coding sequences, an increasing number of which have been shown to function as enhancers during early development. Despite their extreme conservation over 500 million years from humans to cartilaginous fish, these elements appear to be largely absent in invertebrates, and, to date, there has been little understanding of their mode of action or the evolutionary processes that have modelled them. We have now exploited emerging genomic sequence data for the sea lamprey, Petromyzon marinus, to explore the depth of conservation of this type of element in the earliest diverging extant vertebrate lineage, the jawless fish (agnathans). We searched for conserved non-coding elements (CNEs) at 13 human gene loci and identified lamprey elements associated with all but two of these gene regions. Although markedly shorter and less well conserved than within jawed vertebrates, identified lamprey CNEs are able to drive specific patterns of expression in zebrafish embryos, which are almost identical to those driven by the equivalent human elements. These CNEs are therefore a unique and defining characteristic of all vertebrates. Furthermore, alignment of lamprey and other vertebrate CNEs should permit the identification of persistent sequence signatures that are responsible for common patterns of expression and contribute to the elucidation of the regulatory language in CNEs. Identifying the core regulatory code for development, common to all vertebrates, provides a foundation upon which regulatory networks can be constructed and might also illuminate how large conserved regulatory sequence blocks evolve and become fixed in genomic DNA. PMID:20011110
3D-MHD Simulations of the Madison Dynamo Experiment

NASA Astrophysics Data System (ADS)

Bayliss, R. A.; Forest, C. B.; Wright, J. C.; O'Connell, R.

2003-10-01

Growth, saturation and turbulent evolution of the Madison dynamo experiment is investigated numerically using a 3-D pseudo-spectral simulation of the MHD equations; results of the simulations are used to predict behavior of the experiment. The code solves the self-consistent full evolution of the magnetic and velocity fields. The code uses a spectral representation via spherical harmonic basis functions of the vector fields in longitude and latitude, and fourth order finite differences in the radial direction. The magnetic field evolution has been benchmarked against the laminar kinematic dynamo predicted by M.L. Dudley and R.W. James [Proc. R. Soc. Lond. A 425. 407-429 (1989)]. Initial results indicate that saturation of the magnetic field occurs so that the resulting perturbed backreaction of the induced magnetic field changes the velocity field such that it would no longer be linearly unstable, suggesting non-linear terms are necessary for explaining the resulting state. Saturation and self-excitation depend in detail upon the magnetic Prandtl number.
Application of MCT Failure Criterion using EFM

DTIC Science & Technology

2010-03-26

because HELIUS:MCT™ does not facilitate this. Attempts have been made to use ABAQUS native thermal expansion model combined in addition to Helius-MCT... ABAQUS using a user defined element subroutine EFM. Comparisons have been made between the analysis results using EFM-MCT code and HELIUS:MCT™ code...using the Element-Failure Method (EFM) in ABAQUS . The EFM-MCT has been implemented in ABAQUS using a user defined element subroutine EFM. Comparisons
The "periodic table" of the genetic code: A new way to look at the code and the decoding process.

PubMed

Komar, Anton A

2016-01-01

Henri Grosjean and Eric Westhof recently presented an information-rich, alternative view of the genetic code, which takes into account current knowledge of the decoding process, including the complex nature of interactions between mRNA, tRNA and rRNA that take place during protein synthesis on the ribosome, and it also better reflects the evolution of the code. The new asymmetrical circular genetic code has a number of advantages over the traditional codon table and the previous circular diagrams (with a symmetrical/clockwise arrangement of the U, C, A, G bases). Most importantly, all sequence co-variances can be visualized and explained based on the internal logic of the thermodynamics of codon-anticodon interactions.

Comment on ‘egs_brachy: a versatile and fast Monte Carlo code for brachytherapy’

NASA Astrophysics Data System (ADS)

Yegin, Gultekin

2018-02-01

In a recent paper (Chamberland et al 2016 Phys. Med. Biol. 61 8214) develop a new Monte Carlo code called egs_brachy for brachytherapy treatments. It is based on EGSnrc, and written in the C++ programming language. In order to benchmark the egs_brachy code, the authors use it in various test case scenarios in which complex geometry conditions exist. Another EGSnrc based brachytherapy dose calculation engine, BrachyDose, is used for dose comparisons. The authors fail to prove that egs_brachy can produce reasonable dose values for brachytherapy sources in a given medium. The dose comparisons in the paper are erroneous and misleading. egs_brachy should not be used in any further research studies unless and until all the potential bugs are fixed in the code.
Design evolution of large wind turbine generators

NASA Technical Reports Server (NTRS)

Spera, D. A.

1979-01-01

During the past five years, the goals of economy and reliability have led to a significant evolution in the basic design--both external and internal--of large wind turbine systems. To show the scope and nature of recent changes in wind turbine designs, development of three types are described: (1) system configuration developments; (2) computer code developments; and (3) blade technology developments.
Selection platforms for directed evolution in synthetic biology

PubMed Central

Tizei, Pedro A.G.; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B.

2016-01-01

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules–gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function–be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. PMID:27528765
Selection platforms for directed evolution in synthetic biology.

PubMed

Tizei, Pedro A G; Csibra, Eszter; Torres, Leticia; Pinheiro, Vitor B

2016-08-15

Life on Earth is incredibly diverse. Yet, underneath that diversity, there are a number of constants and highly conserved processes: all life is based on DNA and RNA; the genetic code is universal; biology is limited to a small subset of potential chemistries. A vast amount of knowledge has been accrued through describing and characterizing enzymes, biological processes and organisms. Nevertheless, much remains to be understood about the natural world. One of the goals in Synthetic Biology is to recapitulate biological complexity from simple systems made from biological molecules-gaining a deeper understanding of life in the process. Directed evolution is a powerful tool in Synthetic Biology, able to bypass gaps in knowledge and capable of engineering even the most highly conserved biological processes. It encompasses a range of methodologies to create variation in a population and to select individual variants with the desired function-be it a ligand, enzyme, pathway or even whole organisms. Here, we present some of the basic frameworks that underpin all evolution platforms and review some of the recent contributions from directed evolution to synthetic biology, in particular methods that have been used to engineer the Central Dogma and the genetic code. © 2016 The Author(s).
An improved algorithm for evaluating trellis phase codes

NASA Technical Reports Server (NTRS)

Mulligan, M. G.; Wilson, S. G.

1982-01-01

A method is described for evaluating the minimum distance parameters of trellis phase codes, including CPFSK, partial response FM, and more importantly, coded CPM (continuous phase modulation) schemes. The algorithm provides dramatically faster execution times and lesser memory requirements than previous algorithms. Results of sample calculations and timing comparisons are included.
An improved algorithm for evaluating trellis phase codes

NASA Technical Reports Server (NTRS)

Mulligan, M. G.; Wilson, S. G.

1984-01-01

A method is described for evaluating the minimum distance parameters of trellis phase codes, including CPFSK, partial response FM, and more importantly, coded CPM (continuous phase modulation) schemes. The algorithm provides dramatically faster execution times and lesser memory requirements than previous algorithms. Results of sample calculations and timing comparisons are included.
Overlooking the obvious: a meta-analytic comparison of digit symbol coding tasks and other cognitive measures in schizophrenia.

PubMed

Dickinson, Dwight; Ramsey, Mary E; Gold, James M

2007-05-01

In focusing on potentially localizable cognitive impairments, the schizophrenia meta-analytic literature has overlooked the largest single impairment: on digit symbol coding tasks. To compare the magnitude of the schizophrenia impairment on coding tasks with impairments on other traditional neuropsychological instruments. MEDLINE and PsycINFO electronic databases and reference lists from identified articles. English-language studies from 1990 to present, comparing performance of patients with schizophrenia and healthy controls on coding tasks and cognitive measures representing at least 2 other cognitive domains. Of 182 studies identified, 40 met all criteria for inclusion in the meta-analysis. Means, standard deviations, and sample sizes were extracted for digit symbol coding and 36 other cognitive variables. In addition, we recorded potential clinical moderator variables, including chronicity/severity, medication status, age, and education, and potential study design moderators, including coding task variant, matching, and study publication date. Main analyses synthesized data from 37 studies comprising 1961 patients with schizophrenia and 1444 comparison subjects. Combination of mean effect sizes across studies by means of a random effects model yielded a weighted mean effect for digit symbol coding of g = -1.57 (95% confidence interval, -1.66 to -1.48). This effect compared with a grand mean effect of g = -0.98 and was significantly larger than effects for widely used measures of episodic memory, executive functioning, and working memory. Moderator variable analyses indicated that clinical and study design differences between studies had little effect on the coding task effect. Comparison with previous meta-analyses suggested that current results were representative of the broader literature. Subsidiary analysis of data from relatives of patients with schizophrenia also suggested prominent coding task impairments in this group. The 5-minute digit symbol coding task, reliable and easy to administer, taps an information processing inefficiency that is a central feature of the cognitive deficit in schizophrenia and deserves systematic investigation.
Probing the Boundaries of Orthology: The Unanticipated Rapid Evolution of Drosophila centrosomin

PubMed Central

Eisman, Robert C.; Kaufman, Thomas C.

2013-01-01

The rapid evolution of essential developmental genes and their protein products is both intriguing and problematic. The rapid evolution of gene products with simple protein folds and a lack of well-characterized functional domains typically result in a low discovery rate of orthologous genes. Additionally, in the absence of orthologs it is difficult to study the processes and mechanisms underlying rapid evolution. In this study, we have investigated the rapid evolution of centrosomin (cnn), an essential gene encoding centrosomal protein isoforms required during syncytial development in Drosophila melanogaster. Until recently the rapid divergence of cnn made identification of orthologs difficult and questionable because Cnn violates many of the assumptions underlying models for protein evolution. To overcome these limitations, we have identified a group of insect orthologs and present conserved features likely to be required for the functions attributed to cnn in D. melanogaster. We also show that the rapid divergence of Cnn isoforms is apparently due to frequent coding sequence indels and an accelerated rate of intronic additions and eliminations. These changes appear to be buffered by multi-exon and multi-reading frame maximum potential ORFs, simple protein folds, and the splicing machinery. These buffering features also occur in other genes in Drosophila and may help prevent potentially deleterious mutations due to indels in genes with large coding exons and exon-dense regions separated by small introns. This work promises to be useful for future investigations of cnn and potentially other rapidly evolving genes and proteins. PMID:23749319
A family of chaotic pure analog coding schemes based on baker's map function

NASA Astrophysics Data System (ADS)

Liu, Yang; Li, Jing; Lu, Xuanxuan; Yuen, Chau; Wu, Jun

2015-12-01

This paper considers a family of pure analog coding schemes constructed from dynamic systems which are governed by chaotic functions—baker's map function and its variants. Various decoding methods, including maximum likelihood (ML), minimum mean square error (MMSE), and mixed ML-MMSE decoding algorithms, have been developed for these novel encoding schemes. The proposed mirrored baker's and single-input baker's analog codes perform a balanced protection against the fold error (large distortion) and weak distortion and outperform the classical chaotic analog coding and analog joint source-channel coding schemes in literature. Compared to the conventional digital communication system, where quantization and digital error correction codes are used, the proposed analog coding system has graceful performance evolution, low decoding latency, and no quantization noise. Numerical results show that under the same bandwidth expansion, the proposed analog system outperforms the digital ones over a wide signal-to-noise (SNR) range.
Systematic Comparison of Photoionized Plasma Codes with Application to Spectroscopic Studies of AGN in X-Rays

NASA Technical Reports Server (NTRS)

Mehdipour, M.; Kaastra, J. S.; Kallman, T.

2016-01-01

Atomic data and plasma models play a crucial role in the diagnosis and interpretation of astrophysical spectra, thus influencing our understanding of the Universe. In this investigation we present a systematic comparison of the leading photoionization codes to determine how much their intrinsic differences impact X-ray spectroscopic studies of hot plasmas in photoionization equilibrium. We carry out our computations using the Cloudy, SPEX, and XSTAR photoionization codes, and compare their derived thermal and ionization states for various ionizing spectral energy distributions. We examine the resulting absorption-line spectra from these codes for the case of ionized outflows in active galactic nuclei. By comparing the ionic abundances as a function of ionization parameter, we find that on average there is about 30 deviation between the codes in where ionic abundances peak. For H-like to B-like sequence ions alone, this deviation in is smaller at about 10 on average. The comparison of the absorption-line spectra in the X-ray band shows that there is on average about 30 deviation between the codes in the optical depth of the lines produced at log 1 to 2, reducing to about 20 deviation at log 3. We also simulate spectra of the ionized outflows with the current and upcoming high-resolution X-ray spectrometers, on board XMM-Newton, Chandra, Hitomi, and Athena. From these simulations we obtain the deviation on the best-fit model parameters, arising from the use of different photoionization codes, which is about 10 to40. We compare the modeling uncertainties with the observational uncertainties from the simulations. The results highlight the importance of continuous development and enhancement of photoionization codes for the upcoming era of X-ray astronomy with Athena.
Linear and nonlinear verification of gyrokinetic microstability codes

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

Bravenec, R. V.; Candy, J.; Barnes, M.

2011-12-15

Verification of nonlinear microstability codes is a necessary step before comparisons or predictions of turbulent transport in toroidal devices can be justified. By verification we mean demonstrating that a code correctly solves the mathematical model upon which it is based. Some degree of verification can be accomplished indirectly from analytical instability threshold conditions, nonlinear saturation estimates, etc., for relatively simple plasmas. However, verification for experimentally relevant plasma conditions and physics is beyond the realm of analytical treatment and must rely on code-to-code comparisons, i.e., benchmarking. The premise is that the codes are verified for a given problem or set ofmore » parameters if they all agree within a specified tolerance. True verification requires comparisons for a number of plasma conditions, e.g., different devices, discharges, times, and radii. Running the codes and keeping track of linear and nonlinear inputs and results for all conditions could be prohibitive unless there was some degree of automation. We have written software to do just this and have formulated a metric for assessing agreement of nonlinear simulations. We present comparisons, both linear and nonlinear, between the gyrokinetic codes GYRO[J. Candy and R. E. Waltz, J. Comput. Phys. 186, 545 (2003)] and GS2[W. Dorland, F. Jenko, M. Kotschenreuther, and B. N. Rogers, Phys. Rev. Lett. 85, 5579 (2000)]. We do so at the mid-radius for the same discharge as in earlier work [C. Holland, A. E. White, G. R. McKee, M. W. Shafer, J. Candy, R. E. Waltz, L. Schmitz, and G. R. Tynan, Phys. Plasmas 16, 052301 (2009)]. The comparisons include electromagnetic fluctuations, passing and trapped electrons, plasma shaping, one kinetic impurity, and finite Debye-length effects. Results neglecting and including electron collisions (Lorentz model) are presented. We find that the linear frequencies with or without collisions agree well between codes, as do the time averages of the nonlinear fluxes without collisions. With collisions, the differences between the time-averaged fluxes are larger than the uncertainties defined as the oscillations of the fluxes, with the GS2 fluxes consistently larger (or more positive) than those from GYRO. However, the electrostatic fluxes are much smaller than those without collisions (the electromagnetic energy flux is negligible in both cases). In fact, except for the electron energy fluxes, the absolute magnitudes of the differences in fluxes with collisions are the same or smaller than those without. None of the fluxes exhibit large absolute differences between codes. Beyond these results, the specific linear and nonlinear benchmarks proposed here, as well as the underlying methodology, provide the basis for a wide variety of future verification efforts.« less
A multiphysics and multiscale software environment for modeling astrophysical systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; Harfst, Stefan; Groen, Derek; Fujii, Michiko; Nualláin, Breanndán Ó.; Glebbeek, Evert; Heggie, Douglas; Lombardi, James; Hut, Piet; Angelou, Vangelis; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Gaburov, Evghenii; Izzard, Rob; Jurić, Mario; Justham, Stephen; Sottoriva, Andrea; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

2009-05-01

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a "Noah's Ark" milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.
Review of the 9th NLTE code comparison workshop

DOE PAGES

Piron, Robin; Gilleron, Franck; Aglitskiy, Yefim; ...

2017-02-24

Here, we review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.
Transport methods and interactions for space radiations

NASA Technical Reports Server (NTRS)

Wilson, John W.; Townsend, Lawrence W.; Schimmerling, Walter S.; Khandelwal, Govind S.; Khan, Ferdous S.; Nealy, John E.; Cucinotta, Francis A.; Simonsen, Lisa C.; Shinn, Judy L.; Norbury, John W.

1991-01-01

A review of the program in space radiation protection at the Langley Research Center is given. The relevant Boltzmann equations are given with a discussion of approximation procedures for space applications. The interaction coefficients are related to solution of the many-body Schroedinger equation with nuclear and electromagnetic forces. Various solution techniques are discussed to obtain relevant interaction cross sections with extensive comparison with experiments. Solution techniques for the Boltzmann equations are discussed in detail. Transport computer code validation is discussed through analytical benchmarking, comparison with other codes, comparison with laboratory experiments and measurements in space. Applications to lunar and Mars missions are discussed.
Review of the 9th NLTE code comparison workshop

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

Piron, Robin; Gilleron, Franck; Aglitskiy, Yefim

Here, we review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.
Review of the 9th NLTE code comparison workshop

NASA Astrophysics Data System (ADS)

Piron, R.; Gilleron, F.; Aglitskiy, Y.; Chung, H.-K.; Fontes, C. J.; Hansen, S. B.; Marchuk, O.; Scott, H. A.; Stambulchik, E.; Ralchenko, Yu.

2017-06-01

We review the 9th NLTE code comparison workshop, which was held in the Jussieu campus, Paris, from November 30th to December 4th, 2015. This time, the workshop was mainly focused on a systematic investigation of iron NLTE steady-state kinetics and emissivity, over a broad range of temperature and density. Through these comparisons, topics such as modeling of the dielectronic processes, density effects or the effect of an external radiation field were addressed. The K-shell spectroscopy of iron plasmas was also addressed, notably through the interpretation of tokamak and laser experimental spectra.
Update to the NASA Lewis Ice Accretion Code LEWICE

NASA Technical Reports Server (NTRS)

Wright, William B.

1994-01-01

This report is intended as an update to NASA CR-185129 'User's Manual for the NASA Lewis Ice Accretion Prediction Code (LEWICE).' It describes modifications and improvements made to this code as well as changes to the input and output files, interactive input, and graphics output. The comparison of this code to experimental data is shown to have improved as a result of these modifications.
High School Biology Teachers' Views on Teaching Evolution: Implications for Science Teacher Educators

NASA Astrophysics Data System (ADS)

Hermann, Ronald S.

2013-06-01

In the US, there may be few scientific concepts that students maintain preconceived ideas about as strongly and passionately as they do with regard to evolution. At the confluence of a multitude of social, religious, political, and scientific factors lies the biology teacher. This phenomenological study provides insight into the salient aspects of teaching evolution as viewed by public high school biology teachers. Transcribed interviews were coded, and data were sorted resulting in key themes regarding teachers' views of evolution education. These themes are presented against the backdrop of extant literature on the teaching and learning of evolution. Suggestions for science teacher educators are presented such that we can modify teacher preparation programs to better prepare science teachers to meet the challenges of teaching evolution.
Evaluation of COBRA III-C and SABRE-I (wire wrap version) computational results by comparison with steady-state data from a 19-pin internally guard heated sodium cooled bundle with a six-channel central blockage (THORS bundle 3C). [LMFBR

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

Dearing, J F; Rose, S D; Nelson, W R

The predicted computational results of two well-known sub-channel analysis codes, COBRA-III-C and SABRE-I (wire wrap version), have been evaluated by comparison with steady state temperature data from the THORS Facility at ORNL. Both codes give good predictions of transverse and axial temperatures when compared with wire wrap thermocouple data. The crossflow velocity profiles predicted by these codes are similar which is encouraging since the wire wrap models are based on different assumptions.
Analysis of thermo-chemical nonequilibrium models for carbon dioxide flows

NASA Technical Reports Server (NTRS)

Rock, Stacey G.; Candler, Graham V.; Hornung, Hans G.

1992-01-01

The aerothermodynamics of thermochemical nonequilibrium carbon dioxide flows is studied. The chemical kinetics models of McKenzie and Park are implemented in separate three-dimensional computational fluid dynamics codes. The codes incorporate a five-species gas model characterized by a translational-rotational and a vibrational temperature. Solutions are obtained for flow over finite length elliptical and circular cylinders. The computed flowfields are then employed to calculate Mach-Zehnder interferograms for comparison with experimental data. The accuracy of the chemical kinetics models is determined through this comparison. Also, the methodology of the three-dimensional thermochemical nonequilibrium code is verified by the reproduction of the experiments.

The Impact of Total Liberalization of Domestic Air Transport on the Social Welfare and on the Dynamic of Competition: Comparison Between the United States and the European Union

NASA Technical Reports Server (NTRS)

Zbidi, Karim

2003-01-01

Since the lst of April 1997 date of the implementation of the third package of the liberalization, air transport, within the european Union has become totally liberalized. In the United States the deregulation of domestic air traffic was earlier and faster since it took place in October 1978 after the adoption of the only act of deregulation. This paper, in its first part, deals with the liberalization of the industry of air traffic in the european union. After a comparison with US system based on market demand, fare policy and network restrictions, we present our descriptive results coming from treatments on the OAG data. These results present several aspects such as the evolution of the competitive structure of the intra-european routes, the level of airport dominance and the growth of hub structure. The second part of the paper presents models of entry in the airline industry. As profitability" of route flown explains correctly decisions taken by airlines to serve or not a route, the paper focuses on the specification and the estimation of the determinants of city, pair profitability in the european union. Treatments done on the OAG data show a rapid development of leasing space agreement (partial and total) and code sharing practices between 1995 and 2000 in Europe that's why we differentiate first between the two type of competitive strategy of entry(direct entry and leasing space agreement) and second between the competitive strategy of entry and the alliance strategy of code sharing. So the estimation of model will be able to answer the question if the european air transport market is contestable and in case not to see if the decision of entry is more directed by the level of airport dominance (as in the domestic United States market)or essentially by the competitive structure of the routes. We try to explain the nature of entry(directleasing or code sharing) by the different levels of these two determinants.
Comparison of the LLNL ALE3D and AKTS Thermal Safety Computer Codes for Calculating Times to Explosion in ODTX and STEX Thermal Cookoff Experiments

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

Wemhoff, A P; Burnham, A K

2006-04-05

Cross-comparison of the results of two computer codes for the same problem provides a mutual validation of their computational methods. This cross-validation exercise was performed for LLNL's ALE3D code and AKTS's Thermal Safety code, using the thermal ignition of HMX in two standard LLNL cookoff experiments: the One-Dimensional Time to Explosion (ODTX) test and the Scaled Thermal Explosion (STEX) test. The chemical kinetics model used in both codes was the extended Prout-Tompkins model, a relatively new addition to ALE3D. This model was applied using ALE3D's new pseudospecies feature. In addition, an advanced isoconversional kinetic approach was used in the AKTSmore » code. The mathematical constants in the Prout-Tompkins code were calibrated using DSC data from hermetically sealed vessels and the LLNL optimization code Kinetics05. The isoconversional kinetic parameters were optimized using the AKTS Thermokinetics code. We found that the Prout-Tompkins model calculations agree fairly well between the two codes, and the isoconversional kinetic model gives very similar results as the Prout-Tompkins model. We also found that an autocatalytic approach in the beta-delta phase transition model does affect the times to explosion for some conditions, especially STEX-like simulations at ramp rates above 100 C/hr, and further exploration of that effect is warranted.« less
Analytical ice shape predictions for flight in natural icing conditions

NASA Technical Reports Server (NTRS)

Berkowitz, Brian M.; Riley, James T.

1988-01-01

LEWICE is an analytical ice prediction code that has been evaluated against icing tunnel data, but on a more limited basis against flight data. Ice shapes predicted by LEWICE is compared with experimental ice shapes accreted on the NASA Lewis Icing Research Aircraft. The flight data selected for comparison includes liquid water content recorded using a hot wire device and droplet distribution data from a laser spectrometer; the ice shape is recorded using stereo photography. The main findings are as follows: (1) An equivalent sand grain roughness correlation different from that used for LEWICE tunnel comparisons must be employed to obtain satisfactory results for flight; (2) Using this correlation and making no other changes in the code, the comparisons to ice shapes accreted in flight are in general as good as the comparisons to ice shapes accreted in the tunnel (as in the case of tunnel ice shapes, agreement is least reliable for large glaze ice shapes at high angles of attack); (3) In some cases comparisons can be somewhat improved by utilizing the code so as to take account of the variation of parameters such as liquid water content, which may vary significantly in flight.
Genome Sequencing of the Phytoseiid Predatory Mite Metaseiulus occidentalis Reveals Completely Atomized Hox Genes and Superdynamic Intron Evolution

PubMed Central

Hoy, Marjorie A.; Waterhouse, Robert M.; Wu, Ke; Estep, Alden S.; Ioannidis, Panagiotis; Palmer, William J.; Pomerantz, Aaron F.; Simão, Felipe A.; Thomas, Jainy; Jiggins, Francis M.; Murphy, Terence D.; Pritham, Ellen J.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Gibbs, Richard A.; Richards, Stephen

2016-01-01

Metaseiulus occidentalis is an eyeless phytoseiid predatory mite employed for the biological control of agricultural pests including spider mites. Despite appearances, these predator and prey mites are separated by some 400 Myr of evolution and radically different lifestyles. We present a 152-Mb draft assembly of the M. occidentalis genome: Larger than that of its favored prey, Tetranychus urticae, but considerably smaller than those of many other chelicerates, enabling an extremely contiguous and complete assembly to be built—the best arachnid to date. Aided by transcriptome data, genome annotation cataloged 18,338 protein-coding genes and identified large numbers of Helitron transposable elements. Comparisons with other arthropods revealed a particularly dynamic and turbulent genomic evolutionary history. Its genes exhibit elevated molecular evolution, with strikingly high numbers of intron gains and losses, in stark contrast to the deer tick Ixodes scapularis. Uniquely among examined arthropods, this predatory mite’s Hox genes are completely atomized, dispersed across the genome, and it encodes five copies of the normally single-copy RNA processing Dicer-2 gene. Examining gene families linked to characteristic biological traits of this tiny predator provides initial insights into processes of sex determination, development, immune defense, and how it detects, disables, and digests its prey. As the first reference genome for the Phytoseiidae, and for any species with the rare sex determination system of parahaploidy, the genome of the western orchard predatory mite improves genomic sampling of chelicerates and provides invaluable new resources for functional genomic analyses of this family of agriculturally important mites. PMID:26951779
Analysis of electrophoresis performance

NASA Technical Reports Server (NTRS)

Roberts, Glyn O.

1988-01-01

A flexible efficient computer code is being developed to simulate electrophoretic separation phenomena, in either a cylindrical or a rectangular geometry. The code will computer the evolution in time of the concentrations of an arbitrary number of chemical species, and of the temperature, pH distribution, conductivity, electric field, and fluid motion. Use of nonuniform meshes and fast accurate implicit time-stepping will yield accurate answers at economical cost.
Refactoring the Genetic Code for Increased Evolvability

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

Pines, Gur; Winkler, James D.; Pines, Assaf

ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of singlemore » nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology. IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.« less
Refactoring the Genetic Code for Increased Evolvability

DOE PAGES

Pines, Gur; Winkler, James D.; Pines, Assaf; ...

2017-11-14

ABSTRACT The standard genetic code is robust to mutations during transcription and translation. Point mutations are likely to be synonymous or to preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best-performing mutant requires replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter a single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of singlemore » nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyperevolvable organism that could serve as an ideal platform for directed evolution experiments. We then conclude by evaluating the challenges of constructing such recoded organisms and their potential applications within the field of synthetic biology. IMPORTANCE The conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene via common error-prone methods. Here, we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transitions to a larger pool of amino acids and with a greater extent of chemical differences, based on a single nucleotide replacement within the codon, thus increasing evolvability both at the single-gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement, along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation, and fitness maximization.« less
Expansion by whole genome duplication and evolution of the sox gene family in teleost fish

PubMed Central

Naville, Magali; Volff, Jean-Nicolas

2017-01-01

It is now recognized that several rounds of whole genome duplication (WGD) have occurred during the evolution of vertebrates, but the link between WGDs and phenotypic diversification remains unsolved. We have investigated in this study the impact of the teleost-specific WGD on the evolution of the sox gene family in teleostean fishes. The sox gene family, which encodes for transcription factors, has essential role in morphology, physiology and behavior of vertebrates and teleosts, the current largest group of vertebrates. We have first redrawn the evolution of all sox genes identified in eleven teleost genomes using a comparative genomic approach including phylogenetic and synteny analyses. We noticed, compared to tetrapods, an important expansion of the sox family: 58% (11/19) of sox genes are duplicated in teleost genomes. Furthermore, all duplicated sox genes, except sox17 paralogs, are derived from the teleost-specific WGD. Then, focusing on five sox genes, analyzing the evolution of coding and non-coding sequences, as well as the expression patterns in fish embryos and adult tissues, we demonstrated that these paralogs followed lineage-specific evolutionary trajectories in teleost genomes. This work, based on whole genome data from multiple teleostean species, supports the contribution of WGDs to the expansion of gene families, as well as to the emergence of genomic differences between lineages that might promote genetic and phenotypic diversity in teleosts. PMID:28738066
In the Beginning was a Mutualism - On the Origin of Translation

NASA Astrophysics Data System (ADS)

Vitas, Marko; Dobovišek, Andrej

2018-04-01

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.
Validation of the SINDA/FLUINT code using several analytical solutions

NASA Technical Reports Server (NTRS)

Keller, John R.

1995-01-01

The Systems Improved Numerical Differencing Analyzer and Fluid Integrator (SINDA/FLUINT) code has often been used to determine the transient and steady-state response of various thermal and fluid flow networks. While this code is an often used design and analysis tool, the validation of this program has been limited to a few simple studies. For the current study, the SINDA/FLUINT code was compared to four different analytical solutions. The thermal analyzer portion of the code (conduction and radiative heat transfer, SINDA portion) was first compared to two separate solutions. The first comparison examined a semi-infinite slab with a periodic surface temperature boundary condition. Next, a small, uniform temperature object (lumped capacitance) was allowed to radiate to a fixed temperature sink. The fluid portion of the code (FLUINT) was also compared to two different analytical solutions. The first study examined a tank filling process by an ideal gas in which there is both control volume work and heat transfer. The final comparison considered the flow in a pipe joining two infinite reservoirs of pressure. The results of all these studies showed that for the situations examined here, the SINDA/FLUINT code was able to match the results of the analytical solutions.
10Gbps 2D MGC OCDMA Code over FSO Communication System

NASA Astrophysics Data System (ADS)

Professor Urmila Bhanja, Associate, Dr.; Khuntia, Arpita; Alamasety Swati, (Student

2017-08-01

Currently, wide bandwidth signal dissemination along with low latency is a leading requisite in various applications. Free space optical wireless communication has introduced as a realistic technology for bridging the gap in present high data transmission fiber connectivity and as a provisional backbone for rapidly deployable wireless communication infrastructure. The manuscript highlights on the implementation of 10Gbps SAC-OCDMA FSO communications using modified two dimensional Golomb code (2D MGC) that possesses better auto correlation, minimum cross correlation and high cardinality. A comparison based on pseudo orthogonal (PSO) matrix code and modified two dimensional Golomb code (2D MGC) is developed in the proposed SAC OCDMA-FSO communication module taking different parameters into account. The simulative outcome signifies that the communication radius is bounded by the multiple access interference (MAI). In this work, a comparison is made in terms of bit error rate (BER), and quality factor (Q) based on modified two dimensional Golomb code (2D MGC) and PSO matrix code. It is observed that the 2D MGC yields better results compared to the PSO matrix code. The simulation results are validated using optisystem version 14.
Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.
Comparison of LEWICE 1.6 and LEWICE/NS with IRT experimental data from modern air foil tests

DOT National Transportation Integrated Search

1998-01-01

A research project is underway at NASA Lewis to produce a computer code which can accurately predict ice growth under any meteorological conditions for any aircraft surface. The most recent release of this code is LEWICE 1.6. This code is modular in ...
A Comparison of Fatigue Design Methods

DTIC Science & Technology

2001-04-05

Boiler and Pressure Vessel Code does not...Engineers, "ASME Boiler and Pressure Vessel Code ," ASME, 3 Park Ave., New York, NY 10016-5990. [4] Langer, B. F., "Design of Pressure Vessels Involving... and Pressure Vessel Code [3] presents these methods and has expanded the procedures to other pressure vessels besides nuclear pressure vessels. B.
The Effects of Stellar Dynamics on the Evolution of Young, Dense Stellar Systems

NASA Astrophysics Data System (ADS)

Belkus, H.; van Bever, J.; Vanbeveren, D.

In this paper, we report on first results of a project in Brussels in which we study the effects of stellar dynamics on the evolution of young dense stellar systems using 3 decades of expertise in massive-star evolution and our population (number and spectral) synthesis code. We highlight an unconventionally formed object scenario (UFO-scenario) for Wolf Rayet binaries and study the effects of a luminous blue variable-type instability wind mass-loss formalism on the formation of intermediate-mass black holes.
Proceedings of the MEVTV Workshop on The Evolution of Magma Bodies on Mars

NASA Technical Reports Server (NTRS)

Mouginis-Mark, P. (Editor); Holloway, J. (Editor)

1990-01-01

The workshop focused on many of the diverse approaches related to the evolution of magma bodies on Mars that have been pursued during the course of the Mars Evolution of Volcanism, Tectonism, and Volatiles (MEVTV) Program. Approximately 35 scientists from the Mars volcanology, petrology, geochemistry, and modeling communities attended. Segments of the meeting concentrated of laboratory analyses and investigations of SNC meteorites, the interpretation of Viking Orbiter and Lander datasets, and the interpretation of computer codes that model volcanic and tectonic processes on Mars. Abstracts of these reports are presented.
Shape Optimization of Rubber Bushing Using Differential Evolution Algorithm

PubMed Central

2014-01-01

The objective of this study is to design rubber bushing at desired level of stiffness characteristics in order to achieve the ride quality of the vehicle. A differential evolution algorithm based approach is developed to optimize the rubber bushing through integrating a finite element code running in batch mode to compute the objective function values for each generation. Two case studies were given to illustrate the application of proposed approach. Optimum shape parameters of 2D bushing model were determined by shape optimization using differential evolution algorithm. PMID:25276848
Time-dependent simulations of disk-embedded planetary atmospheres

NASA Astrophysics Data System (ADS)

Stökl, A.; Dorfi, E. A.

2014-03-01

At the early stages of evolution of planetary systems, young Earth-like planets still embedded in the protoplanetary disk accumulate disk gas gravitationally into planetary atmospheres. The established way to study such atmospheres are hydrostatic models, even though in many cases the assumption of stationarity is unlikely to be fulfilled. Furthermore, such models rely on the specification of a planetary luminosity, attributed to a continuous, highly uncertain accretion of planetesimals onto the surface of the solid core. We present for the first time time-dependent, dynamic simulations of the accretion of nebula gas into an atmosphere around a proto-planet and the evolution of such embedded atmospheres while integrating the thermal energy budget of the solid core. The spherical symmetric models computed with the TAPIR-Code (short for The adaptive, implicit RHD-Code) range from the surface of the rocky core up to the Hill radius where the surrounding protoplanetary disk provides the boundary conditions. The TAPIR-Code includes the hydrodynamics equations, gray radiative transport and convective energy transport. The results indicate that diskembedded planetary atmospheres evolve along comparatively simple outlines and in particular settle, dependent on the mass of the solid core, at characteristic surface temperatures and planetary luminosities, quite independent on numerical parameters and initial conditions. For sufficiently massive cores, this evolution ultimately also leads to runaway accretion and the formation of a gas planet.
Molecular Evolution of Aminoacyl tRNA Synthetase Proteins in the Early History of Life

NASA Astrophysics Data System (ADS)

Fournier, Gregory P.; Andam, Cheryl P.; Alm, Eric J.; Gogarten, J. Peter

2011-12-01

Aminoacyl-tRNA synthetases (aaRS) consist of several families of functionally conserved proteins essential for translation and protein synthesis. Like nearly all components of the translation machinery, most aaRS families are universally distributed across cellular life, being inherited from the time of the Last Universal Common Ancestor (LUCA). However, unlike the rest of the translation machinery, aaRS have undergone numerous ancient horizontal gene transfers, with several independent events detected between domains, and some possibly involving lineages diverging before the time of LUCA. These transfers reveal the complexity of molecular evolution at this early time, and the chimeric nature of genomes within cells that gave rise to the major domains. Additionally, given the role of these protein families in defining the amino acids used for protein synthesis, sequence reconstruction of their pre-LUCA ancestors can reveal the evolutionary processes at work in the origin of the genetic code. In particular, sequence reconstructions of the paralog ancestors of isoleucyl- and valyl- RS provide strong empirical evidence that at least for this divergence, the genetic code did not co-evolve with the aaRSs; rather, both amino acids were already part of the genetic code before their cognate aaRSs diverged from their common ancestor. The implications of this observation for the early evolution of RNA-directed protein biosynthesis are discussed.
Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds.

PubMed

Dean, Rebecca; Harrison, Peter W; Wright, Alison E; Zimmer, Fabian; Mank, Judith E

2015-10-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

The effects of sex-biased gene expression and X-linkage on rates of sequence evolution in Drosophila.

PubMed

Campos, José Luis; Johnston, Keira; Charlesworth, Brian

2017-12-08

A faster rate of adaptive evolution of X-linked genes compared with autosomal genes (the faster-X effect) can be caused by the fixation of recessive or partially recessive advantageous mutations. This effect should be largest for advantageous mutations that affect only male fitness, and least for mutations that affect only female fitness. We tested these predictions in Drosophila melanogaster by using coding and functionally significant non-coding sequences of genes with different levels of sex-biased expression. Consistent with theory, nonsynonymous substitutions in most male-biased and unbiased genes show faster adaptive evolution on the X. However, genes with very low recombination rates do not show such an effect, possibly as a consequence of Hill-Robertson interference. Contrary to expectation, there was a substantial faster-X effect for female-biased genes. After correcting for recombination rate differences, however, female-biased genes did not show a faster X-effect. Similar analyses of non-coding UTRs and long introns showed a faster-X effect for all groups of genes, other than introns of female-biased genes. Given the strong evidence that deleterious mutations are mostly recessive or partially recessive, we would expect a slower rate of evolution of X-linked genes for slightly deleterious mutations that become fixed by genetic drift. Surprisingly, we found little evidence for this after correcting for recombination rate, implying that weakly deleterious mutations are mostly close to being semidominant. This is consistent with evidence from polymorphism data, which we use to test how models of selection that assume semidominance with no sex-specific fitness effects may bias estimates of purifying selection. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Monitoring Cosmic Radiation Risk: Comparisons between Observations and Predictive Codes for Naval Aviation

DTIC Science & Technology

2009-01-01

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and...radiation transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the...same dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6
Monitoring Cosmic Radiation Risk: Comparisons Between Observations and Predictive Codes for Naval Aviation

DTIC Science & Technology

2009-07-05

proton PARMA PHITS -based Analytical Radiation Model in the Atmosphere PCAIRE Predictive Code for Aircrew Radiation Exposure PHITS Particle and Heavy...transport code utilized is called PARMA ( PHITS based Analytical Radiation Model in the Atmosphere) [36]. The particle fluxes calculated from the input...dose equivalent coefficient regulations from the ICRP-60 regulations. As a result, the transport codes utilized by EXPACS ( PHITS ) and CARI-6 (PARMA
Comparison of deterministic and stochastic approaches for isotopic concentration and decay heat uncertainty quantification on elementary fission pulse

NASA Astrophysics Data System (ADS)

Lahaye, S.; Huynh, T. D.; Tsilanizara, A.

2016-03-01

Uncertainty quantification of interest outputs in nuclear fuel cycle is an important issue for nuclear safety, from nuclear facilities to long term deposits. Most of those outputs are functions of the isotopic vector density which is estimated by fuel cycle codes, such as DARWIN/PEPIN2, MENDEL, ORIGEN or FISPACT. CEA code systems DARWIN/PEPIN2 and MENDEL propagate by two different methods the uncertainty from nuclear data inputs to isotopic concentrations and decay heat. This paper shows comparisons between those two codes on a Uranium-235 thermal fission pulse. Effects of nuclear data evaluation's choice (ENDF/B-VII.1, JEFF-3.1.1 and JENDL-2011) is inspected in this paper. All results show good agreement between both codes and methods, ensuring the reliability of both approaches for a given evaluation.
New class of photonic quantum error correction codes

NASA Astrophysics Data System (ADS)

Silveri, Matti; Michael, Marios; Brierley, R. T.; Salmilehto, Juha; Albert, Victor V.; Jiang, Liang; Girvin, S. M.

We present a new class of quantum error correction codes for applications in quantum memories, communication and scalable computation. These codes are constructed from a finite superposition of Fock states and can exactly correct errors that are polynomial up to a specified degree in creation and destruction operators. Equivalently, they can perform approximate quantum error correction to any given order in time step for the continuous-time dissipative evolution under these errors. The codes are related to two-mode photonic codes but offer the advantage of requiring only a single photon mode to correct loss (amplitude damping), as well as the ability to correct other errors, e.g. dephasing. Our codes are also similar in spirit to photonic ''cat codes'' but have several advantages including smaller mean occupation number and exact rather than approximate orthogonality of the code words. We analyze how the rate of uncorrectable errors scales with the code complexity and discuss the unitary control for the recovery process. These codes are realizable with current superconducting qubit technology and can increase the fidelity of photonic quantum communication and memories.
A comparison of cosmological hydrodynamic codes

NASA Technical Reports Server (NTRS)

Kang, Hyesung; Ostriker, Jeremiah P.; Cen, Renyue; Ryu, Dongsu; Hernquist, Lars; Evrard, August E.; Bryan, Greg L.; Norman, Michael L.

1994-01-01

We present a detailed comparison of the simulation results of various hydrodynamic codes. Starting with identical initial conditions based on the cold dark matter scenario for the growth of structure, with parameters h = 0.5 Omega = Omega(sub b) = 1, and sigma(sub 8) = 1, we integrate from redshift z = 20 to z = O to determine the physical state within a representative volume of size L(exp 3) where L = 64 h(exp -1) Mpc. Five indenpendent codes are compared: three of them Eulerian mesh-based and two variants of the smooth particle hydrodynamics 'SPH' Lagrangian approach. The Eulerian codes were run at N(exp 3) = (32(exp 3), 64(exp 3), 128(exp 3), and 256(exp 3)) cells, the SPH codes at N(exp 3) = 32(exp 3) and 64(exp 3) particles. Results were then rebinned to a 16(exp 3) grid with the exception that the rebinned data should converge, by all techniques, to a common and correct result as N approaches infinity. We find that global averages of various physical quantities do, as expected, tend to converge in the rebinned model, but that uncertainites in even primitive quantities such as (T), (rho(exp 2))(exp 1/2) persists at the 3%-17% level achieve comparable and satisfactory accuracy for comparable computer time in their treatment of the high-density, high-temeprature regions as measured in the rebinned data; the variance among the five codes (at highest resolution) for the mean temperature (as weighted by rho(exp 2) is only 4.5%. Examined at high resolution we suspect that the density resolution is better in the SPH codes and the thermal accuracy in low-density regions better in the Eulerian codes. In the low-density, low-temperature regions the SPH codes have poor accuracy due to statiscal effects, and the Jameson code gives the temperatures which are too high, due to overuse of artificial viscosity in these high Mach number regions. Overall the comparison allows us to better estimate errors; it points to ways of improving this current generation ofhydrodynamic codes and of suiting their use to problems which exploit their best individual features.
The (De-)evolution of Evolution Games: A Content Analysis of the Representation of Evolution Through Natural Selection in Digital Games

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

NASA Technical Reports Server (NTRS)

Ohtsuki, Keiji

2005-01-01

The goal of this research was to understand dynamical processes related to the evolution of size distribution of particles in planetary rings and application of theoretical results to explain features in the present rings of giant planets. We studied velocity evolution and accretion rates of ring particles in the Roche zone. We developed a new numerical code for the evolution of ring particle size distribution, which takes into account the above results for particle velocity evolution and accretion rates. We also studied radial diffusion rate of ring particles due to inelastic collisions and gravitational encounters. Many of these results can be also applied to dynamical evolution of a planetesimal disk. Finally, we studied rotation rates of moonlets and particles in planetary rings, which would influence the accretional evolution of these bodies. We describe our key accomplishments during the past three years in more detail in the following.
Unraveling patterns of site-to-site synonymous rates variation and associated gene properties of protein domains and families.

PubMed

Dimitrieva, Slavica; Anisimova, Maria

2014-01-01

In protein-coding genes, synonymous mutations are often thought not to affect fitness and therefore are not subject to natural selection. Yet increasingly, cases of non-neutral evolution at certain synonymous sites were reported over the last decade. To evaluate the extent and the nature of site-specific selection on synonymous codons, we computed the site-to-site synonymous rate variation (SRV) and identified gene properties that make SRV more likely in a large database of protein-coding gene families and protein domains. To our knowledge, this is the first study that explores the determinants and patterns of the SRV in real data. We show that the SRV is widespread in the evolution of protein-coding sequences, putting in doubt the validity of the synonymous rate as a standard neutral proxy. While protein domains rarely undergo adaptive evolution, the SRV appears to play important role in optimizing the domain function at the level of DNA. In contrast, protein families are more likely to evolve by positive selection, but are less likely to exhibit SRV. Stronger SRV was detected in genes with stronger codon bias and tRNA reusage, those coding for proteins with larger number of interactions or forming larger number of structures, located in intracellular components and those involved in typically conserved complex processes and functions. Genes with extreme SRV show higher expression levels in nearly all tissues. This indicates that codon bias in a gene, which often correlates with gene expression, may often be a site-specific phenomenon regulating the speed of translation along the sequence, consistent with the co-translational folding hypothesis. Strikingly, genes with SRV were strongly overrepresented for metabolic pathways and those associated with several genetic diseases, particularly cancers and diabetes.
Functional interrogation of non-coding DNA through CRISPR genome editing

PubMed Central

Canver, Matthew C.; Bauer, Daniel E.; Orkin, Stuart H.

2017-01-01

Methodologies to interrogate non-coding regions have lagged behind coding regions despite comprising the vast majority of the genome. However, the rapid evolution of clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing has provided a multitude of novel techniques for laboratory investigation including significant contributions to the toolbox for studying non-coding DNA. CRISPR-mediated loss-of-function strategies rely on direct disruption of the underlying sequence or repression of transcription without modifying the targeted DNA sequence. CRISPR-mediated gain-of-function approaches similarly benefit from methods to alter the targeted sequence through integration of customized sequence into the genome as well as methods to activate transcription. Here we review CRISPR-based loss- and gain-of-function techniques for the interrogation of non-coding DNA. PMID:28288828
JEWEL 2.0.0: directions for use

NASA Astrophysics Data System (ADS)

Zapp, Korinna

2014-02-01

In this publication the first official release of the Jewel 2.0.0 code [The first version Jewel 1 (Zapp et al. in Eur Phys J C 60:617, 2009) could only treat elastic scattering explicitly and the code was never published, The code can be downloaded from the official Jewel homepage http://jewel.hepforge.org] is presented. Jewel is a Monte Carlo event generator simulating QCD jet evolution in heavy-ion collisions. It treats the interplay of QCD radiation and re-scattering in a medium with fully microscopic dynamics in a consistent perturbative framework with minimal assumptions. After a qualitative introduction into the physics of Jewel detailed information about the practical aspects of using the code is given. The code is available from the official Jewel homepage http://jewel.hepforge.org.
Revisiting Fenton Hill Phase I reservoir creation and stimulation mechanisms through the GTO code comparison effort

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

Fu, Pengcheng; Mcclure, Mark; Shiozawa, Sogo

A series of experiments performed at the Fenton Hill hot dry rock site after stage 2 drilling of Phase I reservoir provided intriguing field observations on the reservoir’s responses to injection and venting under various conditions. Two teams participating in the US DOE Geothermal Technologies Office (GTO)’s Code Comparison Study (CCS) used different numerical codes to model these five experiments with the objective of inferring the hydraulic stimulation mechanism involved. The codes used by the two teams are based on different numerical principles, and the assumptions made were also different, due to intrinsic limitations in the codes and the modelers’more » personal interpretations of the field observations. Both sets of models were able to produce the most important field observations and both found that it was the combination of the vertical gradient of the fracture opening pressure, injection volume, and the use/absence of proppant that yielded the different outcomes of the five experiments.« less
Time evolution of an SLR reference frame

NASA Astrophysics Data System (ADS)

Angermann, D.; Gerstl, M.; Kelm, R.; Müller, H.; Seemüller, W.; Vei, M.

2002-07-01

On the basis of LAGEOS-1 and LAGEOS-2 data we computed a 10-years (1990-2000) solution for SLR station positions and velocities. The paper describes the data processing with the DGFI software package DOGS. We present results for station coordinates and their time variation for 41 stations of the global SLR network, and discuss the stability and time evolution of the SLR reference frame established in the same way. We applied different methods to assess the quality and consistency of the SLR results. The results presented in this paper include: (1) a time series of weekly estimated station coordinates; (2) a comparison of a 10-year LAGEOS-1 and LAGEOS-2 solution; (3) a comparison of 2.5-year solutions with the combined 10-year solution to assess the internal stability and the time evolution of the SLR reference frame; (4) a comparison of the SLR reference frame with ITRF97; and (5) a comparison of SLR station velocities with those of ITRF97 and NNR NUVEL-1A.
Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila.

PubMed

Castellano, David; Coronado-Zamora, Marta; Campos, Jose L; Barbadilla, Antonio; Eyre-Walker, Adam

2016-02-01

Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
The Arrow of Time in the Collapse of Collisionless Self-gravitating Systems: Non-validity of the Vlasov-Poisson Equation during Violent Relaxation

NASA Astrophysics Data System (ADS)

Beraldo e Silva, Leandro; de Siqueira Pedra, Walter; Sodré, Laerte; Perico, Eder L. D.; Lima, Marcos

2017-09-01

The collapse of a collisionless self-gravitating system, with the fast achievement of a quasi-stationary state, is driven by violent relaxation, with a typical particle interacting with the time-changing collective potential. It is traditionally assumed that this evolution is governed by the Vlasov-Poisson equation, in which case entropy must be conserved. We run N-body simulations of isolated self-gravitating systems, using three simulation codes, NBODY-6 (direct summation without softening), NBODY-2 (direct summation with softening), and GADGET-2 (tree code with softening), for different numbers of particles and initial conditions. At each snapshot, we estimate the Shannon entropy of the distribution function with three different techniques: Kernel, Nearest Neighbor, and EnBiD. For all simulation codes and estimators, the entropy evolution converges to the same limit as N increases. During violent relaxation, the entropy has a fast increase followed by damping oscillations, indicating that violent relaxation must be described by a kinetic equation other than the Vlasov-Poisson equation, even for N as large as that of astronomical structures. This indicates that violent relaxation cannot be described by a time-reversible equation, shedding some light on the so-called “fundamental paradox of stellar dynamics.” The long-term evolution is well-described by the orbit-averaged Fokker-Planck model, with Coulomb logarithm values in the expected range 10{--}12. By means of NBODY-2, we also study the dependence of the two-body relaxation timescale on the softening length. The approach presented in the current work can potentially provide a general method for testing any kinetic equation intended to describe the macroscopic evolution of N-body systems.
A 1-D evolutionary model for icy satellites, applied to Enceladus

NASA Astrophysics Data System (ADS)

Prialnik, Dina; Malamud, Uri

2015-11-01

A 1-D long-term evolution code for icy satellites is presented, which couples multiple processes: water migration, geochemical reactions, water and silicate phase transitions, crystallization, compaction by self-gravity, and ablation. The code takes into account various energy sources: tidal heating, radiogenic heating, geochemical energy released by serpentinization or absorbed by mineral dehydration, gravitational energy, and insolation. It includes heat transport by conduction, convection, and advection.The code is applied to Enceladus, by guessing the initial conditions that would render a structure compatible with present-day observations, and adopting a homogeneous initial structure. Assuming that the satellite has been losing water continually along its evolution, it follows that it was formed as a more massive, more ice-rich and more porous object, and gradually transformed into its present day state, due to sustained tidal heating. Several initial compositions and evolution scenarios are considered, and the evolution is simulated for the age of the Solar System. The results corresponding to the present configuration are confronted with the available observational constraints. The present configuration is shown to be differentiated into a pure icy mantle, several tens of km thick, overlying a rocky core, composed of dehydrated rock in the central part and hydrated rock in the outer part. Such a differentiated structure is obtained not only for Enceladus, but for other medium size ice-rich bodies as well.Predictions for Enceladus are a higher rock/ice mass ratio than previously assumed, and a thinner ice mantle, compatible with recent estimates based on gravity field measurements. Although, obviously, the 1-D model cannot be used to explain local phenomena, it sheds light on the internal structure invoked in explanations of localized features and activities.
Role of Utility and Inference in the Evolution of Functional Information

PubMed Central

Sharov, Alexei A.

2009-01-01

Functional information means an encoded network of functions in living organisms from molecular signaling pathways to an organism’s behavior. It is represented by two components: code and an interpretation system, which together form a self-sustaining semantic closure. Semantic closure allows some freedom between components because small variations of the code are still interpretable. The interpretation system consists of inference rules that control the correspondence between the code and the function (phenotype) and determines the shape of the fitness landscape. The utility factor operates at multiple time scales: short-term selection drives evolution towards higher survival and reproduction rate within a given fitness landscape, and long-term selection favors those fitness landscapes that support adaptability and lead to evolutionary expansion of certain lineages. Inference rules make short-term selection possible by shaping the fitness landscape and defining possible directions of evolution, but they are under control of the long-term selection of lineages. Communication normally occurs within a set of agents with compatible interpretation systems, which I call communication system. Functional information cannot be directly transferred between communication systems with incompatible inference rules. Each biological species is a genetic communication system that carries unique functional information together with inference rules that determine evolutionary directions and constraints. This view of the relation between utility and inference can resolve the conflict between realism/positivism and pragmatism. Realism overemphasizes the role of inference in evolution of human knowledge because it assumes that logic is embedded in reality. Pragmatism substitutes usefulness for truth and therefore ignores the advantage of inference. The proposed concept of evolutionary pragmatism rejects the idea that logic is embedded in reality; instead, inference rules are constructed within each communication system to represent reality and they evolve towards higher adaptability on a long time scale. PMID:20160960
Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds

PubMed Central

Dean, Rebecca; Harrison, Peter W.; Wright, Alison E.; Zimmer, Fabian; Mank, Judith E.

2015-01-01

The elevated rate of evolution for genes on sex chromosomes compared with autosomes (Fast-X or Fast-Z evolution) can result either from positive selection in the heterogametic sex or from nonadaptive consequences of reduced relative effective population size. Recent work in birds suggests that Fast-Z of coding sequence is primarily due to relaxed purifying selection resulting from reduced relative effective population size. However, gene sequence and gene expression are often subject to distinct evolutionary pressures; therefore, we tested for Fast-Z in gene expression using next-generation RNA-sequencing data from multiple avian species. Similar to studies of Fast-Z in coding sequence, we recover clear signatures of Fast-Z in gene expression; however, in contrast to coding sequence, our data indicate that Fast-Z in expression is due to positive selection acting primarily in females. In the soma, where gene expression is highly correlated between the sexes, we detected Fast-Z in both sexes, although at a higher rate in females, suggesting that many positively selected expression changes in females are also expressed in males. In the gonad, where intersexual correlations in expression are much lower, we detected Fast-Z for female gene expression, but crucially, not males. This suggests that a large amount of expression variation is sex-specific in its effects within the gonad. Taken together, our results indicate that Fast-Z evolution of gene expression is the product of positive selection acting on recessive beneficial alleles in the heterogametic sex. More broadly, our analysis suggests that the adaptive potential of Z chromosome gene expression may be much greater than that of gene sequence, results which have important implications for the role of sex chromosomes in speciation and sexual selection. PMID:26067773
Anticipatory Mechanisms in Evolutionary Living Systems

NASA Astrophysics Data System (ADS)

Dubois, Daniel M.; Holmberg, Stig C.

2010-11-01

This paper deals firstly with a revisiting of Darwin's theory of Natural Selection. Darwin in his book never uses the word "evolution", but shows a clear position about mutability of species. Darwin's Natural Selection was mainly inspired by the anticipatory Artificial Selection by humans in domestication, and the Malthus struggle for existence. Darwin showed that the struggle for existence leads to the preservation of the most divergent offspring of any one species. He cited several times the canon of "Natura non facit saltum". He spoke about the origin of life from some one primordial form, into which life was first breathed. Finally, Darwin made anticipation about the future researches in psychology. This paper cites the work of Ernst Mayr who was the first, after 90 years of an intense scientific debate, to present a new and stable Darwinian paradigm as the "Evolutionary Synthesis" in 1942. To explain what is life, the Living Systems Theory (LST) by J. G. Miller is presented. It is showed that the Autopoietic Systems Theory of Varela et al is also a fundamental component of living systems. In agreement with Darwin, the natural selection is a necessary condition for transformation of biological systems, but is not a sufficient condition. Thus, in this paper we conjecture that an anticipatory evolutionary mechanism exists with the genetic code that is a self-replicating and self-modifying anticipatory program. As demonstrated by Nobel laureate McClintock, evolution in genomes is programmed. The word "program" comes from "pro-gram" meaning to write before, by anticipation, and means a plan for the programming of a mechanism, or a sequence of coded instructions that can be inserted into a mechanism, or a sequence of coded instructions, as genes of behavioural responses, that is part of an organism. For example, cell death may be programmed by what is called the apoptosis. This definitively is a great breakthrough in our understanding of biological evolution. Hence, it is possible to formulate a new principle of evolution, i.e. the principle of Double Anticipatory Loop (DAL) of evolution: Biological evolution is driven by interaction between a mindless environment that is passively selecting the fittest inhabitants and purposeful anticipatory living systems, which are actively selecting and creating their own environment. Evolution on the genome level is trigged by environmental stress but guided by an inherent program.
Improvements to the construction of binary black hole initial data

NASA Astrophysics Data System (ADS)

Ossokine, Serguei; Foucart, Francois; Pfeiffer, Harald P.; Boyle, Michael; Szilágyi, Béla

2015-12-01

Construction of binary black hole initial data is a prerequisite for numerical evolutions of binary black holes. This paper reports improvements to the binary black hole initial data solver in the spectral Einstein code, to allow robust construction of initial data for mass-ratio above 10:1, and for dimensionless black hole spins above 0.9, while improving efficiency for lower mass-ratios and spins. We implement a more flexible domain decomposition, adaptive mesh refinement and an updated method for choosing free parameters. We also introduce a new method to control and eliminate residual linear momentum in initial data for precessing systems, and demonstrate that it eliminates gravitational mode mixing during the evolution. Finally, the new code is applied to construct initial data for hyperbolic scattering and for binaries with very small separation.

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