Directional photofluidization lithography: micro/nanostructural evolution by photofluidic motions of azobenzene materials.

PubMed

Lee, Seungwoo; Kang, Hong Suk; Park, Jung-Ki

2012-04-24

This review demonstrates directional photofluidization lithography (DPL), which makes it possible to fabricate a generic and sophisticated micro/nanoarchitecture that would be difficult or impossible to attain with other methods. In particular, DPL differs from many of the existing micro/nanofabrication methods in that the post-treatment (i.e., photofluidization), after the preliminary fabrication process of the original micro/nanostructures, plays a pivotal role in the various micro/nanostructural evolutions including the deterministic reshaping of architectures, the reduction of structural roughness, and the dramatic enhancement of pattern resolution. Also, DPL techniques are directly compatible with a parallel and scalable micro/nanofabrication. Thus, DPL with such extraordinary advantages in micro/nanofabrication could provide compelling opportunities for basic micro/nanoscale science as well as for general technology applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rapid directed evolution of stabilized proteins with cellular high-throughput encapsulation solubilization and screening (CHESS).

PubMed

Yong, K J; Scott, D J

2015-03-01

Directed evolution is a powerful method for engineering proteins towards user-defined goals and has been used to generate novel proteins for industrial processes, biological research and drug discovery. Typical directed evolution techniques include cellular display, phage display, ribosome display and water-in-oil compartmentalization, all of which physically link individual members of diverse gene libraries to their translated proteins. This allows the screening or selection for a desired protein function and subsequent isolation of the encoding gene from diverse populations. For biotechnological and industrial applications there is a need to engineer proteins that are functional under conditions that are not compatible with these techniques, such as high temperatures and harsh detergents. Cellular High-throughput Encapsulation Solubilization and Screening (CHESS), is a directed evolution method originally developed to engineer detergent-stable G proteins-coupled receptors (GPCRs) for structural biology. With CHESS, library-transformed bacterial cells are encapsulated in detergent-resistant polymers to form capsules, which serve to contain mutant genes and their encoded proteins upon detergent mediated solubilization of cell membranes. Populations of capsules can be screened like single cells to enable rapid isolation of genes encoding detergent-stable protein mutants. To demonstrate the general applicability of CHESS to other proteins, we have characterized the stability and permeability of CHESS microcapsules and employed CHESS to generate thermostable, sodium dodecyl sulfate (SDS) resistant green fluorescent protein (GFP) mutants, the first soluble proteins to be engineered using CHESS. © 2014 Wiley Periodicals, Inc.

Determining Selection across Heterogeneous Landscapes: A Perturbation-Based Method and Its Application to Modeling Evolution in Space.

PubMed

Wickman, Jonas; Diehl, Sebastian; Blasius, Bernd; Klausmeier, Christopher A; Ryabov, Alexey B; Brännström, Åke

2017-04-01

Spatial structure can decisively influence the way evolutionary processes unfold. To date, several methods have been used to study evolution in spatial systems, including population genetics, quantitative genetics, moment-closure approximations, and individual-based models. Here we extend the study of spatial evolutionary dynamics to eco-evolutionary models based on reaction-diffusion equations and adaptive dynamics. Specifically, we derive expressions for the strength of directional and stabilizing/disruptive selection that apply both in continuous space and to metacommunities with symmetrical dispersal between patches. For directional selection on a quantitative trait, this yields a way to integrate local directional selection across space and determine whether the trait value will increase or decrease. The robustness of this prediction is validated against quantitative genetics. For stabilizing/disruptive selection, we show that spatial heterogeneity always contributes to disruptive selection and hence always promotes evolutionary branching. The expression for directional selection is numerically very efficient and hence lends itself to simulation studies of evolutionary community assembly. We illustrate the application and utility of the expressions for this purpose with two examples of the evolution of resource utilization. Finally, we outline the domain of applicability of reaction-diffusion equations as a modeling framework and discuss their limitations.

Dynamics of the human brain network revealed by time-frequency effective connectivity in fNIRS

PubMed Central

Vergotte, Grégoire; Torre, Kjerstin; Chirumamilla, Venkata Chaitanya; Anwar, Abdul Rauf; Groppa, Sergiu; Perrey, Stéphane; Muthuraman, Muthuraman

2017-01-01

Functional near infrared spectroscopy (fNIRS) is a promising neuroimaging method for investigating networks of cortical regions over time. We propose a directed effective connectivity method (TPDC) allowing the capture of both time and frequency evolution of the brain’s networks using fNIRS data acquired from healthy subjects performing a continuous finger-tapping task. Using this method we show the directed connectivity patterns among cortical motor regions involved in the task and their significant variations in the strength of information flow exchanges. Intra and inter-hemispheric connections during the motor task with their temporal evolution are also provided. Characterisation of the fluctuations in brain connectivity opens up a new way to assess the organisation of the brain to adapt to changing task constraints, or under pathological conditions. PMID:29188123

A model of directional selection applied to the evolution of drug resistance in HIV-1.

PubMed

Seoighe, Cathal; Ketwaroo, Farahnaz; Pillay, Visva; Scheffler, Konrad; Wood, Natasha; Duffet, Rodger; Zvelebil, Marketa; Martinson, Neil; McIntyre, James; Morris, Lynn; Hide, Winston

2007-04-01

Understanding how pathogens acquire resistance to drugs is important for the design of treatment strategies, particularly for rapidly evolving viruses such as HIV-1. Drug treatment can exert strong selective pressures and sites within targeted genes that confer resistance frequently evolve far more rapidly than the neutral rate. Rapid evolution at sites that confer resistance to drugs can be used to help elucidate the mechanisms of evolution of drug resistance and to discover or corroborate novel resistance mutations. We have implemented standard maximum likelihood methods that are used to detect diversifying selection and adapted them for use with serially sampled reverse transcriptase (RT) coding sequences isolated from a group of 300 HIV-1 subtype C-infected women before and after single-dose nevirapine (sdNVP) to prevent mother-to-child transmission. We have also extended the standard models of codon evolution for application to the detection of directional selection. Through simulation, we show that the directional selection model can provide a substantial improvement in sensitivity over models of diversifying selection. Five of the sites within the RT gene that are known to harbor mutations that confer resistance to nevirapine (NVP) strongly supported the directional selection model. There was no evidence that other mutations that are known to confer NVP resistance were selected in this cohort. The directional selection model, applied to serially sampled sequences, also had more power than the diversifying selection model to detect selection resulting from factors other than drug resistance. Because inference of selection from serial samples is unlikely to be adversely affected by recombination, the methods we describe may have general applicability to the analysis of positive selection affecting recombining coding sequences when serially sampled data are available.

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

USDA-ARS?s Scientific Manuscript database

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

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-01-01

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

Quantum trajectories for time-dependent adiabatic master equations

NASA Astrophysics Data System (ADS)

Yip, Ka Wa; Albash, Tameem; Lidar, Daniel A.

2018-02-01

We describe a quantum trajectories technique for the unraveling of the quantum adiabatic master equation in Lindblad form. By evolving a complex state vector of dimension N instead of a complex density matrix of dimension N2, simulations of larger system sizes become feasible. The cost of running many trajectories, which is required to recover the master equation evolution, can be minimized by running the trajectories in parallel, making this method suitable for high performance computing clusters. In general, the trajectories method can provide up to a factor N advantage over directly solving the master equation. In special cases where only the expectation values of certain observables are desired, an advantage of up to a factor N2 is possible. We test the method by demonstrating agreement with direct solution of the quantum adiabatic master equation for 8-qubit quantum annealing examples. We also apply the quantum trajectories method to a 16-qubit example originally introduced to demonstrate the role of tunneling in quantum annealing, which is significantly more time consuming to solve directly using the master equation. The quantum trajectories method provides insight into individual quantum jump trajectories and their statistics, thus shedding light on open system quantum adiabatic evolution beyond the master equation.

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

NASA Astrophysics Data System (ADS)

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

2016-09-01

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

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning.

PubMed

Davatzikos, Christos

2016-10-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. Copyright © 2016. Published by Elsevier B.V.

Computational neuroanatomy using brain deformations: From brain parcellation to multivariate pattern analysis and machine learning

PubMed Central

Davatzikos, Christos

2017-01-01

The past 20 years have seen a mushrooming growth of the field of computational neuroanatomy. Much of this work has been enabled by the development and refinement of powerful, high-dimensional image warping methods, which have enabled detailed brain parcellation, voxel-based morphometric analyses, and multivariate pattern analyses using machine learning approaches. The evolution of these 3 types of analyses over the years has overcome many challenges. We present the evolution of our work in these 3 directions, which largely follows the evolution of this field. We discuss the progression from single-atlas, single-registration brain parcellation work to current ensemble-based parcellation; from relatively basic mass-univariate t-tests to optimized regional pattern analyses combining deformations and residuals; and from basic application of support vector machines to generative-discriminative formulations of multivariate pattern analyses, and to methods dealing with heterogeneity of neuroanatomical patterns. We conclude with discussion of some of the future directions and challenges. PMID:27514582

Fast and robust brain tumor segmentation using level set method with multiple image information.

PubMed

Lok, Ka Hei; Shi, Lin; Zhu, Xianlun; Wang, Defeng

2017-01-01

Brain tumor segmentation is a challenging task for its variation in intensity. The phenomenon is caused by the inhomogeneous content of tumor tissue and the choice of imaging modality. In 2010 Zhang developed the Selective Binary Gaussian Filtering Regularizing Level Set (SBGFRLS) model that combined the merits of edge-based and region-based segmentation. To improve the SBGFRLS method by modifying the singed pressure force (SPF) term with multiple image information and demonstrate effectiveness of proposed method on clinical images. In original SBGFRLS model, the contour evolution direction mainly depends on the SPF. By introducing a directional term in SPF, the metric could control the evolution direction. The SPF is altered by statistic values enclosed by the contour. This concept can be extended to jointly incorporate multiple image information. The new SPF term is expected to bring a solution for blur edge problem in brain tumor segmentation. The proposed method is validated with clinical images including pre- and post-contrast magnetic resonance images. The accuracy and robustness is compared with sensitivity, specificity, DICE similarity coefficient and Jaccard similarity index. Experimental results show improvement, in particular the increase of sensitivity at the same specificity, in segmenting all types of tumors except for the diffused tumor. The novel brain tumor segmentation method is clinical-oriented with fast, robust and accurate implementation and a minimal user interaction. The method effectively segmented homogeneously enhanced, non-enhanced, heterogeneously-enhanced, and ring-enhanced tumor under MR imaging. Though the method is limited by identifying edema and diffuse tumor, several possible solutions are suggested to turn the curve evolution into a fully functional clinical diagnosis tool.

Directional Darwinian Selection in proteins.

PubMed

McClellan, David A

2013-01-01

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

Distinguishing between direct and indirect directional couplings in large oscillator networks: Partial or non-partial phase analyses?

NASA Astrophysics Data System (ADS)

Rings, Thorsten; Lehnertz, Klaus

2016-09-01

We investigate the relative merit of phase-based methods for inferring directional couplings in complex networks of weakly interacting dynamical systems from multivariate time-series data. We compare the evolution map approach and its partialized extension to each other with respect to their ability to correctly infer the network topology in the presence of indirect directional couplings for various simulated experimental situations using coupled model systems. In addition, we investigate whether the partialized approach allows for additional or complementary indications of directional interactions in evolving epileptic brain networks using intracranial electroencephalographic recordings from an epilepsy patient. For such networks, both direct and indirect directional couplings can be expected, given the brain's connection structure and effects that may arise from limitations inherent to the recording technique. Our findings indicate that particularly in larger networks (number of nodes ≫10 ), the partialized approach does not provide information about directional couplings extending the information gained with the evolution map approach.

Programming cells by multiplex genome engineering and accelerated evolution.

PubMed

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

2009-08-13

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

Assessing directed evolution methods for the generation of biosynthetic enzymes with potential in drug biosynthesis

PubMed Central

Nannemann, David P; Birmingham, William R; Scism, Robert A; Bachmann, Brian O

2011-01-01

To address the synthesis of increasingly structurally diverse small-molecule drugs, methods for the generation of efficient and selective biological catalysts are becoming increasingly important. ‘Directed evolution’ is an umbrella term referring to a variety of methods for improving or altering the function of enzymes using a nature-inspired twofold strategy of mutagenesis followed by selection. This article provides an objective assessment of the effectiveness of directed evolution campaigns in generating enzymes with improved catalytic parameters for new substrates from the last decade, excluding studies that aimed to select for only improved physical properties and those that lack kinetic characterization. An analysis of the trends of methodologies and their success rates from 81 qualifying examples in the literature reveals the average fold improvement for kcat (or Vmax), Km and kcat/Km to be 366-, 12- and 2548-fold, respectively, whereas the median fold improvements are 5.4, 3 and 15.6. Further analysis by enzyme class, library-generation methodology and screening methodology explores relationships between successful campaigns and the methodologies employed. PMID:21644826

Polishing the craft of genetic diversity creation in directed evolution.

PubMed

Tee, Kang Lan; Wong, Tuck Seng

2013-12-01

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

A Nonstationary Markov Model Detects Directional Evolution in Hymenopteran Morphology.

PubMed

Klopfstein, Seraina; Vilhelmsen, Lars; Ronquist, Fredrik

2015-11-01

Directional evolution has played an important role in shaping the morphological, ecological, and molecular diversity of life. However, standard substitution models assume stationarity of the evolutionary process over the time scale examined, thus impeding the study of directionality. Here we explore a simple, nonstationary model of evolution for discrete data, which assumes that the state frequencies at the root differ from the equilibrium frequencies of the homogeneous evolutionary process along the rest of the tree (i.e., the process is nonstationary, nonreversible, but homogeneous). Within this framework, we develop a Bayesian approach for testing directional versus stationary evolution using a reversible-jump algorithm. Simulations show that when only data from extant taxa are available, the success in inferring directionality is strongly dependent on the evolutionary rate, the shape of the tree, the relative branch lengths, and the number of taxa. Given suitable evolutionary rates (0.1-0.5 expected substitutions between root and tips), accounting for directionality improves tree inference and often allows correct rooting of the tree without the use of an outgroup. As an empirical test, we apply our method to study directional evolution in hymenopteran morphology. We focus on three character systems: wing veins, muscles, and sclerites. We find strong support for a trend toward loss of wing veins and muscles, while stationarity cannot be ruled out for sclerites. Adding fossil and time information in a total-evidence dating approach, we show that accounting for directionality results in more precise estimates not only of the ancestral state at the root of the tree, but also of the divergence times. Our model relaxes the assumption of stationarity and reversibility by adding a minimum of additional parameters, and is thus well suited to studying the nature of the evolutionary process in data sets of limited size, such as morphology and ecology. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists.

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

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

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

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

Collisional Evolution of the Enceladus Neutral Cloud

NASA Technical Reports Server (NTRS)

Cassidy, T. A.; Johnson, R. E.; Hendrix, A. R.

2011-01-01

Water vapor ejected from Saturn's small moon Enceladus easily escapes its meager gravity to form a Saturn-encircling cloud with a low collision rate. Observations show that the cloud is quite broad in the radial direction, and we show here that collisions, though quite rare, may be largely responsible for this radial spreading. We modeled this cloud using the Direct Simulation Monte Carlo method, as fluid methods would be inappropriate for such a tenuous gas.

The Minimum-Mass Surface Density of the Solar Nebula using the Disk Evolution Equation

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2005-01-01

The Hayashi minimum-mass power law representation of the pre-solar nebula (Hayashi 1981, Prog. Theo. Phys.70,35) is revisited using analytic solutions of the disk evolution equation. A new cumulative-planetary-mass-model (an integrated form of the surface density) is shown to predict a smoother surface density compared with methods based on direct estimates of surface density from planetary data. First, a best-fit transcendental function is applied directly to the cumulative planetary mass data with the surface density obtained by direct differentiation. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the planetary data. The latter model indicates a decay rate of r -1/2 in the inner disk followed by a rapid decay which results in a sharper outer boundary than predicted by the minimum mass model. The model is shown to be a good approximation to the finite-size early Solar Nebula and by extension to extra solar protoplanetary disks.

Perioperative goal-directed haemodynamic therapy based on flow parameters: a concept in evolution.

PubMed

Meng, L; Heerdt, P M

2016-12-01

Haemodynamic management incorporating direct or surrogate stroke volume monitoring has experienced a rapid evolution, because of emergence of the "goal-directed therapy" concept and technological developments aimed at providing a parameter leading to the goal. Nonetheless, consensus on both definitions of the ideal "goal" and strategies for achieving it remain elusive. For this review, we first consider basic physiological and patient monitoring factors relevant to the concept of "fluid responsiveness", and then focus upon randomized controlled trials and meta-analyses involving goal-directed haemodynamic therapy based on various flow parameters. Finally, we discuss the current status of noninvasive methods for monitoring fluid responsiveness. © The Author 2016. Published by Oxford University Press on behalf of the British Journal of Anaesthesia. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.

PubMed

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

2017-03-17

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

Direct Numerical Simulation of Fingering Instabilities in Coating Flows

NASA Astrophysics Data System (ADS)

Eres, Murat H.; Schwartz, Leonard W.

1998-11-01

We consider stability and finger formation in free surface flows. Gravity driven downhill drainage and temperature gradient driven climbing flows are two examples of such problems. The former situation occurs when a mound of viscous liquid on a vertical wall is allowed to flow. Constant surface shear stress due to temperature gradients (Marangoni stress) can initiate the latter problem. The evolution equations are derived using the lubrication approximation. We also include the effects of finite-contact angles in the evolution equations using a disjoining pressure model. Evolution equations for both problems are solved using an efficient alternating-direction-implicit method. For both problems a one-dimensional base state is established, that is steady in a moving reference frame. This base state is unstable to transverse perturbations. The transverse wavenumbers for the most rapidly growing modes are found through direct numerical solution of the nonlinear evolution equations, and are compared with published experimental results. For a range of finite equilibrium contact angles, the fingers can grow without limit leading to semi-finite steady fingers in a moving coordinate system. A computer generated movie of the nonlinear simulation results, for several sets of input parameters, will be shown.

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).

Continuous in vitro evolution of a ribozyme ligase: a model experiment for the evolution of a biomolecule.

PubMed

Ledbetter, Michael P; Hwang, Tony W; Stovall, Gwendolyn M; Ellington, Andrew D

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. In vitro directed evolution (IVDE) frequently serves as a model system for the study of Darwinian evolution but produces noticeable phenotypic shifts in a matter of hours. An IVDE demonstration lab would serve to both directly demonstrate how Darwinian selection can act on a pool of variants and introduce students to an essential method of modern molecular biology. To produce an IVDE demonstration lab, continuous IVDE of a T500 ribozyme ligase population has been paired with a fluorescent strand displacement reporter system to visualize the selection of improved catalytic function. A ribozyme population is taken through rounds of isothermal amplification dependent on the self-ligation of a T7 promoter. As the population is selectively enriched with better ligase activity, the strand displacement system allows for the monitoring of the population's ligation rate. The strand displacement reporter system permits the detection of ligated ribozyme. Once ligated with the T7 promoter, the 5' end of the ribozyme displaces paired fluorophore-quencher oligonucleotides, in turn, generating visible signal upon UV light excitation. As the ligation rate of the population increases, due to the selection for faster ligating species, the fluorescent signal develops more rapidly. The pairing of the continuous isothermal system with the fluorescent reporting scheme allows any user, provided with minimal materials, to model the continuous directed evolution of a biomolecule. Copyright © 2013 Wiley-Liss, Inc.

Controlling the enantioselectivity of enzymes by directed evolution: Practical and theoretical ramifications

PubMed Central

Reetz, Manfred T.

2004-01-01

A fundamentally new approach to asymmetric catalysis in organic chemistry is described based on the in vitro evolution of enantioselective enzymes. It comprises the appropriate combination of gene mutagenesis and expression coupled with an efficient high-throughput screening system for evaluating enantioselectivity (enantiomeric excess assay). Several such cycles lead to a “Darwinistic” process, which is independent of any knowledge concerning the structure or the mechanism of the enzyme being evolved. The challenge is to choose the optimal mutagenesis methods to navigate efficiently in protein sequence space. As a first example, the combination of error-prone mutagenesis, saturation mutagenesis, and DNA-shuffling led to a dramatic enhancement of enantioselectivity of a lipase acting as a catalyst in the kinetic resolution of a chiral ester. Mutations at positions remote from the catalytically active center were identified, a surprising finding, which was explained on the basis of a novel relay mechanism. The scope and limitations of the method are discussed, including the prospect of directed evolution of stereoselective hybrid catalysts composed of robust protein hosts in which transition metal centers have been implanted. PMID:15079053

Low rank alternating direction method of multipliers reconstruction for MR fingerprinting.

PubMed

Assländer, Jakob; Cloos, Martijn A; Knoll, Florian; Sodickson, Daniel K; Hennig, Jürgen; Lattanzi, Riccardo

2018-01-01

The proposed reconstruction framework addresses the reconstruction accuracy, noise propagation and computation time for magnetic resonance fingerprinting. Based on a singular value decomposition of the signal evolution, magnetic resonance fingerprinting is formulated as a low rank (LR) inverse problem in which one image is reconstructed for each singular value under consideration. This LR approximation of the signal evolution reduces the computational burden by reducing the number of Fourier transformations. Also, the LR approximation improves the conditioning of the problem, which is further improved by extending the LR inverse problem to an augmented Lagrangian that is solved by the alternating direction method of multipliers. The root mean square error and the noise propagation are analyzed in simulations. For verification, in vivo examples are provided. The proposed LR alternating direction method of multipliers approach shows a reduced root mean square error compared to the original fingerprinting reconstruction, to a LR approximation alone and to an alternating direction method of multipliers approach without a LR approximation. Incorporating sensitivity encoding allows for further artifact reduction. The proposed reconstruction provides robust convergence, reduced computational burden and improved image quality compared to other magnetic resonance fingerprinting reconstruction approaches evaluated in this study. Magn Reson Med 79:83-96, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

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

NASA Astrophysics Data System (ADS)

Moradi, Behzad; Mirzaei, Abdolreza

2016-11-01

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

The Evolution of Methods of Air Traffic Control.

DTIC Science & Technology

1984-01-01

Constraints: The fundemental presupposition of this method is that it is only the aircraft which can make the choice of the most cost-efficient profile...the direct operating costs but the return on investment in the ground equipment. Similarly in operational terms, improving the day-to-day quality of

Analytical method development for directed enzyme evolution research: a high throughput high-performance liquid chromatography method for analysis of ribose and ribitol and a capillary electrophoresis method for the separation of ribose enantiomers.

PubMed

Sun, Baoguo; Miller, Gregory; Lee, Wan Yee; Ho, Kelvin; Crowe, Michael A; Partridge, Leslie

2013-01-04

Analytical methods were developed for a directed enzyme evolution research programme, which pursued high performance enzymes to produce high quality L-ribose using large scale biocatalytic reaction. A high throughput HPLC method with evaporative light-scattering detection was developed to test ribose and ribitol in the enzymatic reaction, a β-cyclobond 2000 analytical column separated ribose and ribitol in 2.3 min, a C(18) guard column was used as an on-line filter to clean up the enzyme sample matrix and a short gradient was applied to wash the column, the enzymatic reaction solution can be directly injected after quenching. Total run time of each sample was approx. 4 min which provided capability of screening 4×96-well plates/day/instrument. Meanwhile, a capillary electrophoresis method was developed for the separation of ribose enantiomers, while 7-aminonaphthalene-1,3-disulfonic acid was used as derivatisation reagent and 25 mM tetraborate with 5 mM β-cyclodextrin was used as electrolyte. 0.35%of D-ribose in L-ribose can be detected which can be translated into 99.3% ee of L-ribose. Derivatisation reagent and sample matrix did not interfere with the measurement. Copyright © 2012 Elsevier B.V. All rights reserved.

Modeling HIV-1 Drug Resistance as Episodic Directional Selection

PubMed Central

Murrell, Ben; de Oliveira, Tulio; Seebregts, Chris; Kosakovsky Pond, Sergei L.; Scheffler, Konrad

2012-01-01

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance. PMID:22589711

Modeling HIV-1 drug resistance as episodic directional selection.

PubMed

Murrell, Ben; de Oliveira, Tulio; Seebregts, Chris; Kosakovsky Pond, Sergei L; Scheffler, Konrad

2012-01-01

The evolution of substitutions conferring drug resistance to HIV-1 is both episodic, occurring when patients are on antiretroviral therapy, and strongly directional, with site-specific resistant residues increasing in frequency over time. While methods exist to detect episodic diversifying selection and continuous directional selection, no evolutionary model combining these two properties has been proposed. We present two models of episodic directional selection (MEDS and EDEPS) which allow the a priori specification of lineages expected to have undergone directional selection. The models infer the sites and target residues that were likely subject to directional selection, using either codon or protein sequences. Compared to its null model of episodic diversifying selection, MEDS provides a superior fit to most sites known to be involved in drug resistance, and neither one test for episodic diversifying selection nor another for constant directional selection are able to detect as many true positives as MEDS and EDEPS while maintaining acceptable levels of false positives. This suggests that episodic directional selection is a better description of the process driving the evolution of drug resistance.

Compartmentalized partnered replication for the directed evolution of genetic parts and circuits.

PubMed

Abil, Zhanar; Ellefson, Jared W; Gollihar, Jimmy D; Watkins, Ella; Ellington, Andrew D

2017-12-01

Compartmentalized partnered replication (CPR) is an emulsion-based directed evolution method based on a robust and modular phenotype-genotype linkage. In contrast to other in vivo directed evolution approaches, CPR largely mitigates host fitness effects due to a relatively short expression time of the gene of interest. CPR is based on gene circuits in which the selection of a 'partner' function from a library leads to the production of a thermostable polymerase. After library preparation, bacteria produce partner proteins that can potentially lead to enhancement of transcription, translation, gene regulation, and other aspects of cellular metabolism that reinforce thermostable polymerase production. Individual cells are then trapped in water-in-oil emulsion droplets in the presence of primers and dNTPs, followed by the recovery of the partner genes via emulsion PCR. In this step, droplets with cells expressing partner proteins that promote polymerase production will produce higher copy numbers of the improved partner gene. The resulting partner genes can subsequently be recloned for the next round of selection. Here, we present a step-by-step guideline for the procedure by providing examples of (i) selection of T7 RNA polymerases that recognize orthogonal promoters and (ii) selection of tRNA for enhanced amber codon suppression. A single round of CPR should take ∼3-5 d, whereas a whole directed evolution can be performed in 3-10 rounds, depending on selection efficiency.

Towards the construction of high-quality mutagenesis libraries.

PubMed

Li, Heng; Li, Jing; Jin, Ruinan; Chen, Wei; Liang, Chaoning; Wu, Jieyuan; Jin, Jian-Ming; Tang, Shuang-Yan

2018-07-01

To improve the quality of mutagenesis libraries in directed evolution strategy. In the process of library transformation, transformants which have been shown to take up more than one plasmid might constitute more than 20% of the constructed library, thereby extensively impairing the quality of the library. We propose a practical transformation method to prevent the occurrence of multiple-plasmid transformants while maintaining high transformation efficiency. A visual library model containing plasmids expressing different fluorescent proteins was used. Multiple-plasmid transformants can be reduced through optimizing plasmid DNA amount used for transformation based on the positive correlation between the occurrence frequency of multiple-plasmid transformants and the logarithmic ratio of plasmid molecules to competent cells. This method provides a simple solution for a seemingly common but often neglected problem, and should be valuable for improving the quality of mutagenesis libraries to enhance the efficiency of directed evolution strategies.

Biocatalysts for the pharmaceutical industry created by structure-guided directed evolution of stereoselective enzymes.

PubMed

Li, Guangyue; Wang, Jian-Bo; Reetz, Manfred T

2018-04-01

Enzymes have been used for a long time as catalysts in the asymmetric synthesis of chiral intermediates needed in the production of therapeutic drugs. However, this alternative to man-made catalysts has suffered traditionally from distinct limitations, namely the often observed wrong or insufficient enantio- and/or regioselectivity, low activity, narrow substrate range, and insufficient thermostability. With the advent of directed evolution, these problems can be generally solved. The challenge is to develop and apply the most efficient mutagenesis methods which lead to highest-quality mutant libraries requiring minimal screening. Structure-guided saturation mutagenesis and its iterative form have emerged as the method of choice for evolving stereo- and regioselective mutant enzymes needed in the asymmetric synthesis of chiral intermediates. The number of (industrial) applications in the preparation of chiral pharmaceuticals is rapidly increasing. This review features and analyzes typical case studies. Copyright © 2017 Elsevier Ltd. All rights reserved.

Electromagnetic induction heating for single crystal graphene growth: morphology control by rapid heating and quenching

NASA Astrophysics Data System (ADS)

Wu, Chaoxing; Li, Fushan; Chen, Wei; Veeramalai, Chandrasekar Perumal; Ooi, Poh Choon; Guo, Tailiang

2015-03-01

The direct observation of single crystal graphene growth and its shape evolution is of fundamental importance to the understanding of graphene growth physicochemical mechanisms and the achievement of wafer-scale single crystalline graphene. Here we demonstrate the controlled formation of single crystal graphene with varying shapes, and directly observe the shape evolution of single crystal graphene by developing a localized-heating and rapid-quenching chemical vapor deposition (CVD) system based on electromagnetic induction heating. Importantly, rational control of circular, hexagonal, and dendritic single crystalline graphene domains can be readily obtained for the first time by changing the growth condition. Systematic studies suggest that the graphene nucleation only occurs during the initial stage, while the domain density is independent of the growth temperatures due to the surface-limiting effect. In addition, the direct observation of graphene domain shape evolution is employed for the identification of competing growth mechanisms including diffusion-limited, attachment-limited, and detachment-limited processes. Our study not only provides a novel method for morphology-controlled graphene synthesis, but also offers fundamental insights into the kinetics of single crystal graphene growth.

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

PubMed

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

2013-01-27

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

Protein consensus-based surface engineering (ProCoS): a computer-assisted method for directed protein evolution.

PubMed

Shivange, Amol V; Hoeffken, Hans Wolfgang; Haefner, Stefan; Schwaneberg, Ulrich

2016-12-01

Protein consensus-based surface engineering (ProCoS) is a simple and efficient method for directed protein evolution combining computational analysis and molecular biology tools to engineer protein surfaces. ProCoS is based on the hypothesis that conserved residues originated from a common ancestor and that these residues are crucial for the function of a protein, whereas highly variable regions (situated on the surface of a protein) can be targeted for surface engineering to maximize performance. ProCoS comprises four main steps: ( i ) identification of conserved and highly variable regions; ( ii ) protein sequence design by substituting residues in the highly variable regions, and gene synthesis; ( iii ) in vitro DNA recombination of synthetic genes; and ( iv ) screening for active variants. ProCoS is a simple method for surface mutagenesis in which multiple sequence alignment is used for selection of surface residues based on a structural model. To demonstrate the technique's utility for directed evolution, the surface of a phytase enzyme from Yersinia mollaretii (Ymphytase) was subjected to ProCoS. Screening just 1050 clones from ProCoS engineering-guided mutant libraries yielded an enzyme with 34 amino acid substitutions. The surface-engineered Ymphytase exhibited 3.8-fold higher pH stability (at pH 2.8 for 3 h) and retained 40% of the enzyme's specific activity (400 U/mg) compared with the wild-type Ymphytase. The pH stability might be attributed to a significantly increased (20 percentage points; from 9% to 29%) number of negatively charged amino acids on the surface of the engineered phytase.

[A group of new experiments on molecular evolution].

PubMed

Zhu, Xin-Yu; Xie, Xiao-Ling; Chen, Pei-Lin

2004-07-01

This paper presents a group of new experiments on molecular evolution. It allows students to get acquaint with the basic process of the reconstruction of phylogenetic tree using DNA or protein sequences, and to acquire the correct viewpoint how to affect the result of reconstruction when different tree-building methods, materials and parameters were used. This group of experiments are also characteristic of the opening and exploring, which accords with the direction and demand of experimental teaching reform.

Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance.

PubMed

Nyerges, Ákos; Csörgő, Bálint; Draskovits, Gábor; Kintses, Bálint; Szili, Petra; Ferenc, Györgyi; Révész, Tamás; Ari, Eszter; Nagy, István; Bálint, Balázs; Vásárhelyi, Bálint Márk; Bihari, Péter; Számel, Mónika; Balogh, Dávid; Papp, Henrietta; Kalapis, Dorottya; Papp, Balázs; Pál, Csaba

2018-06-19

Antibiotic development is frequently plagued by the rapid emergence of drug resistance. However, assessing the risk of resistance development in the preclinical stage is difficult. Standard laboratory evolution approaches explore only a small fraction of the sequence space and fail to identify exceedingly rare resistance mutations and combinations thereof. Therefore, new rapid and exhaustive methods are needed to accurately assess the potential of resistance evolution and uncover the underlying mutational mechanisms. Here, we introduce directed evolution with random genomic mutations (DIvERGE), a method that allows an up to million-fold increase in mutation rate along the full lengths of multiple predefined loci in a range of bacterial species. In a single day, DIvERGE generated specific mutation combinations, yielding clinically significant resistance against trimethoprim and ciprofloxacin. Many of these mutations have remained previously undetected or provide resistance in a species-specific manner. These results indicate pathogen-specific resistance mechanisms and the necessity of future narrow-spectrum antibacterial treatments. In contrast to prior claims, we detected the rapid emergence of resistance against gepotidacin, a novel antibiotic currently in clinical trials. Based on these properties, DIvERGE could be applicable to identify less resistance-prone antibiotics at an early stage of drug development. Finally, we discuss potential future applications of DIvERGE in synthetic and evolutionary biology. Copyright © 2018 the Author(s). Published by PNAS.

Detection of biological threats. A challenge for directed molecular evolution.

PubMed

Petrenko, Valery A; Sorokulova, Iryna B

2004-08-01

The probe technique originated from early attempts of Anton van Leeuwenhoek to contrast microorganisms under the microscope using plant juices, successful staining of tubercle bacilli with synthetic dyes by Paul Ehrlich and discovery of a stain for differentiation of gram-positive and gram-negative bacteria by Hans Christian Gram. The technique relies on the principle that pathogens have unique structural features, which can be recognized by specifically labeled organic molecules. A hundred years of extensive screening efforts led to discovery of a limited assortment of organic probes that are used for identification and differentiation of bacteria. A new challenge--continuous monitoring of biological threats--requires long lasting molecular probes capable of tight specific binding of pathogens in unfavorable conditions. To respond to the challenge, probe technology is being revolutionized by utilizing methods of combinatorial chemistry, phage display and directed molecular evolution. This review describes how molecular evolution methods are applied for development of peptide, antibody and phage probes, and summarizes the author's own data on development of landscape phage probes against Salmonella typhimurium. The performance of the probes in detection of Salmonella is illustrated by a precipitation test, enzyme-linked immunosorbent assay (ELISA), fluorescence-activated cell sorting (FACS) and fluorescent, optical and electron microscopy.

Environmental Epigenetics and a Unified Theory of the Molecular Aspects of Evolution: A Neo-Lamarckian Concept that Facilitates Neo-Darwinian Evolution.

PubMed

Skinner, Michael K

2015-04-26

Environment has a critical role in the natural selection process for Darwinian evolution. The primary molecular component currently considered for neo-Darwinian evolution involves genetic alterations and random mutations that generate the phenotypic variation required for natural selection to act. The vast majority of environmental factors cannot directly alter DNA sequence. Epigenetic mechanisms directly regulate genetic processes and can be dramatically altered by environmental factors. Therefore, environmental epigenetics provides a molecular mechanism to directly alter phenotypic variation generationally. Lamarck proposed in 1802 the concept that environment can directly alter phenotype in a heritable manner. Environmental epigenetics and epigenetic transgenerational inheritance provide molecular mechanisms for this process. Therefore, environment can on a molecular level influence the phenotypic variation directly. The ability of environmental epigenetics to alter phenotypic and genotypic variation directly can significantly impact natural selection. Neo-Lamarckian concept can facilitate neo-Darwinian evolution. A unified theory of evolution is presented to describe the integration of environmental epigenetic and genetic aspects of evolution. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

A behavioral perspective on fishing-induced evolution.

PubMed

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

2008-08-01

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

Charge order-superfluidity transition in a two-dimensional system of hard-core bosons and emerging domain structures

NASA Astrophysics Data System (ADS)

Moskvin, A. S.; Panov, Yu. D.; Rybakov, F. N.; Borisov, A. B.

2017-11-01

We have used high-performance parallel computations by NVIDIA graphics cards applying the method of nonlinear conjugate gradients and Monte Carlo method to observe directly the developing ground state configuration of a two-dimensional hard-core boson system with decrease in temperature, and its evolution with deviation from a half-filling. This has allowed us to explore unconventional features of a charge order—superfluidity phase transition, specifically, formation of an irregular domain structure, emergence of a filamentary superfluid structure that condenses within of the charge-ordered phase domain antiphase boundaries, and formation and evolution of various topological structures.

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

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

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

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

Estimating the change in asymptotic direction due to secular changes in the geomagnetic field

NASA Technical Reports Server (NTRS)

Flueckiger, E. O.; Smart, D. F.; Shea, M. A.; Gentile, L. C.; Bathurat, A. A.

1985-01-01

The concept of geomagnetic optics, as described by the asymptotic directions of approach, is extremely useful in the analysis of cosmic radiation data. However, when changes in cutoff occur as a result of evolution in the geomagnetic field, there are corresponding changes in the asymptotic cones of acceptance. A method is introduced of estimating the change in the asymptotic direction of approach for vertically incident cosmic ray particles from a reference set of directions at a specific epoch by considering the change in the geomagnetic cutoff.

Research on Capturing of Customer Requirements Based on Innovation Theory

NASA Astrophysics Data System (ADS)

junwu, Ding; dongtao, Yang; zhenqiang, Bao

To exactly and effectively capture customer requirements information, a new customer requirements capturing modeling method was proposed. Based on the analysis of function requirement models of previous products and the application of technology system evolution laws of the Theory of Innovative Problem Solving (TRIZ), the customer requirements could be evolved from existing product designs, through modifying the functional requirement unit and confirming the direction of evolution design. Finally, a case study was provided to illustrate the feasibility of the proposed approach.

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

NASA Astrophysics Data System (ADS)

Guha, Anirban; Rahmani, Mona; Lawrence, Gregory

2012-11-01

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

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

PubMed

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

2014-01-01

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

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

PubMed

Hyyti, Janne; Escoto, Esmerando; Steinmeyer, Günter

2017-10-01

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

The Changing Role of the Clinical Microbiology Laboratory in Defining Resistance in Gram-negatives.

PubMed

Endimiani, Andrea; Jacobs, Michael R

2016-06-01

The evolution of resistance in Gram-negatives has challenged the clinical microbiology laboratory to implement new methods for their detection. Multidrug-resistant strains present major challenges to conventional and new detection methods. More rapid pathogen identification and antimicrobial susceptibility testing have been developed for use directly on specimens, including fluorescence in situ hybridization tests, automated polymerase chain reaction systems, microarrays, mass spectroscopy, next-generation sequencing, and microfluidics. Review of these methods shows the advances that have been made in rapid detection of resistance in cultures, but limited progress in direct detection from specimens. Copyright © 2016 Elsevier Inc. All rights reserved.

Remote monitoring of environmental particulate pollution - A problem in inversion of first-kind integral equations

NASA Technical Reports Server (NTRS)

Fymat, A. L.

1975-01-01

The determination of the microstructure, chemical nature, and dynamical evolution of scattering particulates in the atmosphere is considered. A description is given of indirect sampling techniques which can circumvent most of the difficulties associated with direct sampling techniques, taking into account methods based on scattering, extinction, and diffraction of an incident light beam. Approaches for reconstructing the particulate size distribution from the direct and the scattered radiation are discussed. A new method is proposed for determining the chemical composition of the particulates and attention is given to the relevance of methods of solution involving first kind Fredholm integral equations.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

Directed evolution methods for improving polypeptide folding and solubility and superfolder fluorescent proteins generated thereby

DOEpatents

Waldo, Geoffrey S.

2007-09-18

The current invention provides methods of improving folding of polypeptides using a poorly folding domain as a component of a fusion protein comprising the poorly folding domain and a polypeptide of interest to be improved. The invention also provides novel green fluorescent proteins (GFPs) and red fluorescent proteins that have enhanced folding properties.

The Effect of Strain Rate on the Evolution of Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Michael M.; Merriam, Marshal (Technical Monitor)

1996-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of irrotational plane strain applied at three different strain rates have been generated. The strain geometry is such that the flow is compressed in the streamwise direction and expanded in the cross-stream direction with the spanwise direction being unstrained. This geometry is the temporally evolving analogue of a spatially evolving wake in an adverse pressure gradient. A pseudospectral numerical method with up to 16 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, Re, of about 2,000. Although the evolutions of many statistics are nearly collapsed when plotted against total strain, there are some differences owing to the different strain rate histories. The impact of strain-rate on the wake spreading rate, the peak velocity deficit, the Reynolds stress profiles, and the flow structure is examined.

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

PubMed

Spötl, Christoph

2005-09-01

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

The modern temperature-accelerated dynamics approach

DOE PAGES

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

2016-06-01

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

On the kinematics of scalar iso-surfaces in turbulent flow

NASA Astrophysics Data System (ADS)

Blakeley, Brandon C.; Riley, James J.; Storti, Duane W.; Wang, Weirong

2017-11-01

The behavior of scalar iso-surfaces in turbulent flows is of fundamental interest and importance in a number of problems, e.g., the stoichiometric surface in non-premixed reactions, and the turbulent/non-turbulent interface in localized turbulent shear flows. Of particular interest here is the behavior of the average surface area per unit volume, Σ. We report on the use of direct numerical simulations and sophisticated surface tracking techniques to directly compute Σ and model its evolution. We consider two different scalar configurations in decaying, isotropic turbulence: first, the iso-surface is initially homogenous and isotropic in space, second, the iso-surface is initially planar. A novel method of computing integral properties from regularly-sampled values of a scalar function is leveraged to provide accurate estimates of Σ. Guided by simulation results, modeling is introduced from two perspectives. The first approach models the various terms in the evolution equation for Σ, while the second uses Rice's theorem to model Σ directly. In particular, the two principal effects on the evolution of Σ, i.e., the growth of the surface area due to local surface stretching, and the ultimate decay due to molecular destruction, are addressed.

Simulation of gene evolution under directional mutational pressure

NASA Astrophysics Data System (ADS)

Dudkiewicz, Małgorzata; Mackiewicz, Paweł; Kowalczuk, Maria; Mackiewicz, Dorota; Nowicka, Aleksandra; Polak, Natalia; Smolarczyk, Kamila; Banaszak, Joanna; R. Dudek, Mirosław; Cebrat, Stanisław

2004-05-01

The two main mechanisms generating the genetic diversity, mutation and recombination, have random character but they are biased which has an effect on the generation of asymmetry in the bacterial chromosome structure and in the protein coding sequences. Thus, like in a case of two chiral molecules-the two possible orientations of a gene in relation to the topology of a chromosome are not equivalent. Assuming that the sequence of a gene may oscillate only between certain limits of its structural composition means that the gene could be forced out of these limits by the directional mutation pressure, in the course of evolution. The probability of the event depends on the time the gene stays under the same mutation pressure. Inversion of the gene changes the directional mutational pressure to the reciprocal one and hence it changes the distance of the gene to its lower and upper bound of the structural tolerance. Using Monte Carlo methods we were able to simulate the evolution of genes under experimentally found mutational pressure, assuming simple mechanisms of selection. We found that the mutation and recombination should work in accordance to lower their negative effects on the function of the products of coding sequences.

Strain transfer through film-substrate interface and surface curvature evolution during a tensile test

NASA Astrophysics Data System (ADS)

He, Wei; Han, Meidong; Goudeau, Philippe; Bourhis, Eric Le; Renault, Pierre-Olivier; Wang, Shibin; Li, Lin-an

2018-03-01

Uniaxial tensile tests on polyimide-supported thin metal films are performed to respectively study the macroscopic strain transfer through an interface and the surface curvature evolution. With a dual digital image correlation (DIC) system, the strains of the film and the substrate can be simultaneously measured in situ during the tensile test. For the true strains below 2% (far beyond the films' elastic limit), a complete longitudinal strain transfer is present irrespective of the film thickness, residual stresses and microstructure. By means of an optical surface profiler, the three-dimensional (3D) topography of film surface can be obtained during straining. As expected, the profile of the specimen center remains almost flat in the tensile direction. Nevertheless, a relatively significant curvature evolution (of the same order with the initial curvature induced by residual stresses) is observed along the transverse direction as a result of a Poisson's ratio mismatch between the film and the substrate. Furthermore, finite element method (FEM) has been performed to simulate the curvature evolution considering the geometric nonlinearity and the perfect strain transfer at the interface, which agrees well with the experimental results.

Phase-field modeling of the beta to omega phase transformation in Zr–Nb alloys

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

Yeddu, Hemantha Kumar; Lookman, Turab

A three-dimensional elastoplastic phase-field model is developed, using the Finite Element Method (FEM), for modeling the athermal beta to omega phase transformation in Zr–Nb alloys by including plastic deformation and strain hardening of the material. The microstructure evolution during athermal transformation as well as under different stress states, e.g. uni-axial tensile and compressive, bi-axial tensile and compressive, shear and tri-axial loadings, is studied. The effects of plasticity, stress states and the stress loading direction on the microstructure evolution as well as on the mechanical properties are studied. The input data corresponding to a Zr – 8 at.% Nb alloy aremore » acquired from experimental studies as well as by using the CALPHAD method. Our simulations show that the four different omega variants grow as ellipsoidal shaped particles. Our results show that due to stress relaxation, the athermal phase transformation occurs slightly more readily in the presence of plasticity compared to that in its absence. The evolution of omega phase is different under different stress states, which leads to the differences in the mechanical properties of the material. The variant selection mechanism, i.e. formation of different variants under different stress loading directions, is also nicely captured by our model.« less

Two Stochastic Phases of Tick-wise Price Fluctuation and the Price Prediction Generator

NASA Astrophysics Data System (ADS)

Tanaka-Yamawaki, Mieko; Tokuoka, Seiji

2007-07-01

We report in this paper the existence of two different stochastic phases in the tick-wise price fluctuations. Based on this observation, we improve our old method of developing the evolutional strategy to predict the direction of the tick-wise price movements. We obtain a stable predictive power even in the region where the old method had a difficulty.

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression, direct costs, mating constraints, and polyandry as a threshold trait.

PubMed

Duthie, A Bradley; Bocedi, Greta; Reid, Jane M

2016-09-01

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual-based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Thermography detection on the fatigue damage

NASA Astrophysics Data System (ADS)

Yang, Bing

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

Expanding the metabolic engineering toolbox with directed evolution.

PubMed

Abatemarco, Joseph; Hill, Andrew; Alper, Hal S

2013-12-01

Cellular systems can be engineered into factories that produce high-value chemicals from renewable feedstock. Such an approach requires an expanded toolbox for metabolic engineering. Recently, protein engineering and directed evolution strategies have started to play a growing and critical role within metabolic engineering. This review focuses on the various ways in which directed evolution can be applied in conjunction with metabolic engineering to improve product yields. Specifically, we discuss the application of directed evolution on both catalytic and non-catalytic traits of enzymes, on regulatory elements, and on whole genomes in a metabolic engineering context. We demonstrate how the goals of metabolic pathway engineering can be achieved in part through evolving cellular parts as opposed to traditional approaches that rely on gene overexpression and deletion. Finally, we discuss the current limitations in screening technology that hinder the full implementation of a metabolic pathway-directed evolution approach. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crack classification and evolution in anisotropic shale during cyclic loading tests by acoustic emission

NASA Astrophysics Data System (ADS)

Wang, Miaomiao; Tan, Chengxuan; Meng, Jing; Yang, Baicun; Li, Yuan

2017-08-01

Characterization and evolution of the cracking mode in shale formation is significant, as fracture networks are an important element in shale gas exploitation. In this study we determine the crack modes and evolution in anisotropic shale under cyclic loading using the acoustic emission (AE) parameter-analysis method based on the average frequency and RA (rise-time/amplitude) value. Shale specimens with bedding-plane orientations parallel and perpendicular to the axial loading direction were subjected to loading cycles with increasing peak values until failure occurred. When the loading was parallel to the bedding plane, most of the cracks at failure were shear cracks, while tensile cracks were dominant in the specimens that were loaded normal to the bedding direction. The evolution of the crack mode in the shale specimens observed in the loading-unloading sequence except for the first cycle can be divided into three stages: (I) no or several cracks (AE events) form as a result of the Kaiser effect, (II) tensile and shear cracks increase steadily at nearly equal proportions, (III) tensile cracks and shear cracks increase abruptly, with more cracks forming in one mode than in the other. As the dominant crack motion is influenced by the bedding, the failure mechanism is discussed based on the evolution of the different crack modes. Our conclusions can increase our understanding of the formation mechanism of fracture networks in the field.

Characteristics of temporal evolution of particle density and electron temperature in helicon discharge

NASA Astrophysics Data System (ADS)

Yang, Xiong; Cheng, Mousen; Guo, Dawei; Wang, Moge; Li, Xiaokang

2017-10-01

On the basis of considering electrochemical reactions and collision relations in detail, a direct numerical simulation model of a helicon plasma discharge with three-dimensional two-fluid equations was employed to study the characteristics of the temporal evolution of particle density and electron temperature. With the assumption of weak ionization, the Maxwell equations coupled with the plasma parameters were directly solved in the whole computational domain. All of the partial differential equations were solved by the finite element solver in COMSOL MultiphysicsTM with a fully coupled method. In this work, the numerical cases were calculated with an Ar working medium and a Shoji-type antenna. The numerical results indicate that there exist two distinct modes of temporal evolution of the electron and ground atom density, which can be explained by the ion pumping effect. The evolution of the electron temperature is controlled by two schemes: electromagnetic wave heating and particle collision cooling. The high RF power results in a high peak electron temperature while the high gas pressure leads to a low steady temperature. In addition, an OES experiment using nine Ar I lines was conducted using a modified CR model to verify the validity of the results by simulation, showing that the trends of temporal evolution of electron density and temperature are well consistent with the numerically simulated ones.

Efficient preparation of shuffled DNA libraries through recombination (Gateway) cloning.

PubMed

Lehtonen, Soili I; Taskinen, Barbara; Ojala, Elina; Kukkurainen, Sampo; Rahikainen, Rolle; Riihimäki, Tiina A; Laitinen, Olli H; Kulomaa, Markku S; Hytönen, Vesa P

2015-01-01

Efficient and robust subcloning is essential for the construction of high-diversity DNA libraries in the field of directed evolution. We have developed a more efficient method for the subcloning of DNA-shuffled libraries by employing recombination cloning (Gateway). The Gateway cloning procedure was performed directly after the gene reassembly reaction, without additional purification and amplification steps, thus simplifying the conventional DNA shuffling protocols. Recombination-based cloning, directly from the heterologous reassembly reaction, conserved the high quality of the library and reduced the time required for the library construction. The described method is generally compatible for the construction of DNA-shuffled gene libraries. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

A modified estimation distribution algorithm based on extreme elitism.

PubMed

Gao, Shujun; de Silva, Clarence W

2016-12-01

An existing estimation distribution algorithm (EDA) with univariate marginal Gaussian model was improved by designing and incorporating an extreme elitism selection method. This selection method highlighted the effect of a few top best solutions in the evolution and advanced EDA to form a primary evolution direction and obtain a fast convergence rate. Simultaneously, this selection can also keep the population diversity to make EDA avoid premature convergence. Then the modified EDA was tested by means of benchmark low-dimensional and high-dimensional optimization problems to illustrate the gains in using this extreme elitism selection. Besides, no-free-lunch theorem was implemented in the analysis of the effect of this new selection on EDAs. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Automated system for periodontal disease diagnosis

NASA Astrophysics Data System (ADS)

Albalat, Salvador E.; Alcaniz-Raya, Mariano L.; Juan, M. Carmen; Grau Colomer, Vincente; Monserrat, Carlos

1997-04-01

Evolution of periodontal disease is one of the most important data for the clinicians in order to achieve correct planning and treatment. Clinical measure of the periodontal sulcus depth is the most important datum to know the exact state of periodontal disease. These measures must be done periodically study bone resorption evolution around teeth. Time factor of resorption indicates aggressiveness of periodontitis. Manual probes are commonly used with direct reading. Mechanical probes give automatic signal but this method uses complicated and heavy probes that are only limited for University researchers. Probe position must be the same to have right diagnosis. Digital image analysis of periodontal probing provides practical, accurate and easy tool. Gum and plaque index could also be digitally measured with this method.

Beam width evolution of astigmatic hollow Gaussian beams in highly nonlocal nonlinear media

NASA Astrophysics Data System (ADS)

Yang, Zhen-Feng; Jiang, Xue-Song; Yang, Zhen-Jun; Li, Jian-Xing; Zhang, Shu-Min

We investigate the beam width evolution of astigmatic hollow Gaussian beams propagating in highly nonlocal nonlinear media. The input-power-induced different evolutions of the beam width are illustrated: (i) the beam widths in two transverse directions are compressed or broadened at the same time; (ii) the beam width in one transverse direction keeps invariant, and the other is compressed or broadened; (iii) furthermore, the beam width in one transverse direction is compressed, whereas it in the other transverse direction is broadened.

Method and apparatus for controlling gas evolution from chemical reactions

DOEpatents

Skorpik, James R.; Dodson, Michael G.

1999-01-01

The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846.

Towards a rational theory for CFD global stability

NASA Technical Reports Server (NTRS)

Baker, A. J.; Iannelli, G. S.

1989-01-01

The fundamental notion of the consistent stability of semidiscrete analogues of evolution PDEs is explored. Lyapunov's direct method is used to develop CFD semidiscrete algorithms which yield the TVD constraint as a special case. A general formula for supplying dissipation parameters for arbitrary multidimensional conservation law systems is proposed. The reliability of the method is demonstrated by the results of two numerical tests for representative Euler shocked flows.

Numerical Study on the Tensile Behavior of 3D Four Directional Cylindrical Braided Composite Shafts

NASA Astrophysics Data System (ADS)

Zhao, Guoqi; Wang, Jiayi; Hao, Wenfeng; Liu, Yinghua; Luo, Ying

2017-10-01

The tensile behavior of 3D four directional cylindrical braided composite shafts was analyzed with the numerical method. The unit cell models for the 3D four directional cylindrical braided composite shafts with various braiding angles were constructed with ABAQUS. Hashin's failure criterion was used to analyze the tensile strength and the damage evolution of the unit cells. The influence of the braiding angle on the tensile behavior of the 3D four directional cylindrical braided composite shafts was analyzed. The numerical results showed that the tensile strength along the braiding direction increased as the braiding angle decreased. These results should play an integral role in the design of braiding composites shafts.

Directed evolution of enzymes using microfluidic chips

NASA Astrophysics Data System (ADS)

Pilát, Zdeněk.; Ježek, Jan; Šmatlo, Filip; Kaůka, Jan; Zemánek, Pavel

2016-12-01

Enzymes are highly versatile and ubiquitous biological catalysts. They can greatly accelerate large variety of reactions, while ensuring appropriate catalytic activity and high selectivity. These properties make enzymes attractive biocatalysts for a wide range of industrial and biomedical applications. Over the last two decades, directed evolution of enzymes has transformed the field of protein engineering. We have devised microfluidic systems for directed evolution of haloalkane dehalogenases in emulsion droplets. In such a device, individual bacterial cells producing mutated variants of the same enzyme are encapsulated in microdroplets and supplied with a substrate. The conversion of a substrate by the enzyme produced by a single bacterium changes the pH in the droplet which is signalized by pH dependent fluorescence probe. The droplets with the highest enzymatic activity can be separated directly on the chip by dielectrophoresis and the resultant cell lineage can be used for enzyme production or for further rounds of directed evolution. This platform is applicable for fast screening of large libraries in directed evolution experiments requiring mutagenesis at multiple sites of a protein structure.

When does female multiple mating evolve to adjust inbreeding? Effects of inbreeding depression, direct costs, mating constraints, and polyandry as a threshold trait

PubMed Central

Duthie, A. Bradley; Bocedi, Greta; Reid, Jane M.

2016-01-01

Polyandry is often hypothesized to evolve to allow females to adjust the degree to which they inbreed. Multiple factors might affect such evolution, including inbreeding depression, direct costs, constraints on male availability, and the nature of polyandry as a threshold trait. Complex models are required to evaluate when evolution of polyandry to adjust inbreeding is predicted to arise. We used a genetically explicit individual‐based model to track the joint evolution of inbreeding strategy and polyandry defined as a polygenic threshold trait. Evolution of polyandry to avoid inbreeding only occurred given strong inbreeding depression, low direct costs, and severe restrictions on initial versus additional male availability. Evolution of polyandry to prefer inbreeding only occurred given zero inbreeding depression and direct costs, and given similarly severe restrictions on male availability. However, due to its threshold nature, phenotypic polyandry was frequently expressed even when strongly selected against and hence maladaptive. Further, the degree to which females adjusted inbreeding through polyandry was typically very small, and often reflected constraints on male availability rather than adaptive reproductive strategy. Evolution of polyandry solely to adjust inbreeding might consequently be highly restricted in nature, and such evolution cannot necessarily be directly inferred from observed magnitudes of inbreeding adjustment. PMID:27464756

Quantum gates by periodic driving.

PubMed

Shi, Z C; Wang, W; Yi, X X

2016-02-25

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions-it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation.

Dynamical Evolution of Meteoroid Streams, Developments Over the Last 30 Years

NASA Technical Reports Server (NTRS)

Williams, I. P.

2011-01-01

As soon as reliable methods for observationally determining the heliocentric orbits of meteoroids and hence the mean orbit of a meteoroid stream in the 1950s and 60s, astronomers strived to investigate the evolution of the orbit under the effects of gravitational perturbations from the planets. At first, the limitations in the capabilities of computers, both in terms of speed and memory, placed severe restrictions on what was possible to do. As a consequence, secular perturbation methods, where the perturbations are averaged over one orbit became the norm. The most popular of these is the Halphen- Goryachev method which was used extensively until the early 1980s. The main disadvantage of these methods lies in the fact that close encounter can be missed, however they remain useful for performing very long-term integrations. Direct integration methods determine the effects of the perturbing forces at many points on an orbit. This give a better picture of the orbital evolution of an individual meteoroid, but many meteoroids have to be integrated in order to obtain a realistic picture of the evolution of a meteoroid stream. The notion of generating a family of hypothetical meteoroids to represent a stream and directly integrate the motion of each was probably first used by Williams Murray & Hughes (1979), to investigate the Quadrantids. Because of computing limitations, only 10 test meteoroids were used. Only two years later, Hughes et. al. (1981) had increased the number of particles 20-fold to 200 while after a further year, Fox Williams and Hughes used 500 000 test meteoroids to model the Geminid stream. With such a number of meteoroids it was possible for the first time to produce a realistic cross-section of the stream on the ecliptic. From that point on there has been a continued increase in the number of meteoroids, the length of time over which integration is carried out and the frequency with which results can be plotted so that it is now possible to produce moving images of the stream. As a consequence, over recent years, emphasis has moved to considering stream formation and the role fragmentation plays in this.

Why human milk is more nutritious than cow milk

NASA Astrophysics Data System (ADS)

Voorhoeve, Niels; Allan, Douglas C.; Moret, M. A.; Zebende, G. F.; Phillips, J. C.

2018-05-01

The evolution of milk, the key infant nutrient, is analyzed using a novel thermodynamic molecular method. The method is general, and it has many advantages compared to conventional molecular dynamics simulations. It is much simpler, and it connects amino acid sequences directly to function, often without knowing detailed "folded" globular structures. It emphasizes synchronized critical fluctuations due to long-range correlations in globular curvatures. The titled question has not been answered, or even discussed successfully, by other molecular methods.

Evolution of cardiorespiratory interactions with age

PubMed Central

Iatsenko, D.; Bernjak, A.; Stankovski, T.; Shiogai, Y.; Owen-Lynch, P. J.; Clarkson, P. B. M.; McClintock, P. V. E.; Stefanovska, A.

2013-01-01

We describe an analysis of cardiac and respiratory time series recorded from 189 subjects of both genders aged 16–90. By application of the synchrosqueezed wavelet transform, we extract the respiratory and cardiac frequencies and phases with better time resolution than is possible with the marked events procedure. By treating the heart and respiration as coupled oscillators, we then apply a method based on Bayesian inference to find the underlying coupling parameters and their time dependence, deriving from them measures such as synchronization, coupling directionality and the relative contributions of different mechanisms. We report a detailed analysis of the reconstructed cardiorespiratory coupling function, its time evolution and age dependence. We show that the direct and indirect respiratory modulations of the heart rate both decrease with age, and that the cardiorespiratory coupling becomes less stable and more time-variable. PMID:23858485

Evolution of cardiorespiratory interactions with age.

PubMed

Iatsenko, D; Bernjak, A; Stankovski, T; Shiogai, Y; Owen-Lynch, P J; Clarkson, P B M; McClintock, P V E; Stefanovska, A

2013-08-28

We describe an analysis of cardiac and respiratory time series recorded from 189 subjects of both genders aged 16-90. By application of the synchrosqueezed wavelet transform, we extract the respiratory and cardiac frequencies and phases with better time resolution than is possible with the marked events procedure. By treating the heart and respiration as coupled oscillators, we then apply a method based on Bayesian inference to find the underlying coupling parameters and their time dependence, deriving from them measures such as synchronization, coupling directionality and the relative contributions of different mechanisms. We report a detailed analysis of the reconstructed cardiorespiratory coupling function, its time evolution and age dependence. We show that the direct and indirect respiratory modulations of the heart rate both decrease with age, and that the cardiorespiratory coupling becomes less stable and more time-variable.

Heading in the right direction: thermodynamics-based network analysis and pathway engineering.

PubMed

Ataman, Meric; Hatzimanikatis, Vassily

2015-12-01

Thermodynamics-based network analysis through the introduction of thermodynamic constraints in metabolic models allows a deeper analysis of metabolism and guides pathway engineering. The number and the areas of applications of thermodynamics-based network analysis methods have been increasing in the last ten years. We review recent applications of these methods and we identify the areas that such analysis can contribute significantly, and the needs for future developments. We find that organisms with multiple compartments and extremophiles present challenges for modeling and thermodynamics-based flux analysis. The evolution of current and new methods must also address the issues of the multiple alternatives in flux directionalities and the uncertainties and partial information from analytical methods. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Probing galaxy growth through metallicity scaling relations over the past 12 Gyr of cosmic history

NASA Astrophysics Data System (ADS)

Sanders, Ryan; MOSDEF team

2018-01-01

A primary goal of galaxy evolution studies is to understand the processes governing the growth of the baryonic content of galaxies over cosmic history. Observations of galaxy metallicity scaling relations and their evolution with redshift, in combination with chemical evolution models, provide unique insight into the interplay between star formation, gas accretion, and feedback/outflows. I present measurements of the stellar mass-gas phase metallicity relation and its evolution over the past 12 Gyr from z~0 to z~3.5, utilizing data from the Mosfire Deep Evolution Field survey that uniquely provides rest-frame optical spectra of >1000 uniformly-selected galaxies at z=1.3-3.8. We find evolution towards lower metallicity at fixed stellar mass with increasing redshift that is consistent with current cosmological simulations including chemical evolution, with a large evolution of ~0.3 dex from z~0 to z~2.5 and minor evolution of <0.1 dex from z~2.5 to z~3.5. We unambiguously confirm the existence of star-formation rate dependence of the mass-metallicity relation at high redshift for the first time. A clear view of cosmic chemical evolution requires accounting for systematic biases in galaxy metallicity measurements at both low and high redshifts. We use a set of empirically-based models to correct for diffuse ionized gas contamination that biases metallicity estimates from z~0 global galaxy spectra. Evolving properties of ionized gas such as electron density, ionization parameter, hardness of the ionizing spectrum, and chemical abundance patterns may render locally-calibrated metallicity estimators unreliable at high redshifts. Using strong-line ratios alone, it is extremely difficult to break degenerate solutions between pure metallicity evolution and additional evolution of the ionization parameter and/or shape of the ionizing spectrum. Temperature-sensitive auroral-line measurements provide a way to directly and independently measure metallicities, breaking these degeneracies. We present measurements of auroral [OIII]4363 and direct-method metallicities at z>2, and discuss the potential of current and next-generation observational facilities to obtain statistical auroral-line samples at high redshifts.

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

NASA Technical Reports Server (NTRS)

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

1991-01-01

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

In vivo evolution of antimicrobial resistance in a series of Staphylococcus aureus patient isolates: the entire picture or a cautionary tale?

PubMed Central

van Hal, Sebastiaan J.; Steen, Jason A.; Espedido, Björn A.; Grimmond, Sean M.; Cooper, Matthew A.; Holden, Matthew T. G.; Bentley, Stephen D.; Gosbell, Iain B.; Jensen, Slade O.

2014-01-01

Objectives To obtain an expanded understanding of antibiotic resistance evolution in vivo, particularly in the context of vancomycin exposure. Methods The whole genomes of six consecutive methicillin-resistant Staphylococcus aureus blood culture isolates (ST239-MRSA-III) from a single patient exposed to various antimicrobials (over a 77 day period) were sequenced and analysed. Results Variant analysis revealed the existence of non-susceptible sub-populations derived from a common susceptible ancestor, with the predominant circulating clone(s) selected for by type and duration of antimicrobial exposure. Conclusions This study highlights the dynamic nature of bacterial evolution and that non-susceptible sub-populations can emerge from clouds of variation upon antimicrobial exposure. Diagnostically, this has direct implications for sample selection when using whole-genome sequencing as a tool to guide clinical therapy. In the context of bacteraemia, deep sequencing of bacterial DNA directly from patient blood samples would avoid culture ‘bias’ and identify mutations associated with circulating non-susceptible sub-populations, some of which may confer cross-resistance to alternate therapies. PMID:24047554

Boundary-Layer Receptivity and Integrated Transition Prediction

NASA Technical Reports Server (NTRS)

Chang, Chau-Lyan; Choudhari, Meelan

2005-01-01

The adjoint parabold stability equations (PSE) formulation is used to calculate the boundary layer receptivity to localized surface roughness and suction for compressible boundary layers. Receptivity efficiency functions predicted by the adjoint PSE approach agree well with results based on other nonparallel methods including linearized Navier-Stokes equations for both Tollmien-Schlichting waves and crossflow instability in swept wing boundary layers. The receptivity efficiency function can be regarded as the Green's function to the disturbance amplitude evolution in a nonparallel (growing) boundary layer. Given the Fourier transformed geometry factor distribution along the chordwise direction, the linear disturbance amplitude evolution for a finite size, distributed nonuniformity can be computed by evaluating the integral effects of both disturbance generation and linear amplification. The synergistic approach via the linear adjoint PSE for receptivity and nonlinear PSE for disturbance evolution downstream of the leading edge forms the basis for an integrated transition prediction tool. Eventually, such physics-based, high fidelity prediction methods could simulate the transition process from the disturbance generation through the nonlinear breakdown in a holistic manner.

Azimuthal correlations between directed and elliptic flow in heavy ion collisions

NASA Astrophysics Data System (ADS)

Wu, Feng-Juan; Shan, Lian-Qiang; Zhang, Jing-Bo; Tang, Gui-Xin; Huo, Lei

2008-12-01

A method for investigating the azimuthal correlations between directed and elliptic flow in heavy ion collisions is described. The transverse anisotropy of particle emission at AGS energies is investigated within the RQMD model. It is found that the azimuthal correlations between directed and elliptic flow are sensitive to the incident energy and impact parameter. The fluctuations in the initial stage and dynamical evolution of heavy ion collisions are not negligible. Supported by Natural Science Foundation of Heilongjiang Province (A0208) and Science Foundation of Harbin Institute of Technology (HIT.2002.47, HIT.2003.33)

Fluid dynamic modeling of nano-thermite reactions

NASA Astrophysics Data System (ADS)

Martirosyan, Karen S.; Zyskin, Maxim; Jenkins, Charles M.; Yuki Horie, Yasuyuki

2014-03-01

This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stage of reaction and allows the investigation of "slower" reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.

Fluid dynamic modeling of nano-thermite reactions

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

Martirosyan, Karen S., E-mail: karen.martirosyan@utb.edu; Zyskin, Maxim; Jenkins, Charles M.

2014-03-14

This paper presents a direct numerical method based on gas dynamic equations to predict pressure evolution during the discharge of nanoenergetic materials. The direct numerical method provides for modeling reflections of the shock waves from the reactor walls that generates pressure-time fluctuations. The results of gas pressure prediction are consistent with the experimental evidence and estimates based on the self-similar solution. Artificial viscosity provides sufficient smoothing of shock wave discontinuity for the numerical procedure. The direct numerical method is more computationally demanding and flexible than self-similar solution, in particular it allows study of a shock wave in its early stagemore » of reaction and allows the investigation of “slower” reactions, which may produce weaker shock waves. Moreover, numerical results indicate that peak pressure is not very sensitive to initial density and reaction time, providing that all the material reacts well before the shock wave arrives at the end of the reactor.« less

A Non-Intrusive GMA Welding Process Quality Monitoring System Using Acoustic Sensing.

PubMed

Cayo, Eber Huanca; Alfaro, Sadek Crisostomo Absi

2009-01-01

Most of the inspection methods used for detection and localization of welding disturbances are based on the evaluation of some direct measurements of welding parameters. This direct measurement requires an insertion of sensors during the welding process which could somehow alter the behavior of the metallic transference. An inspection method that evaluates the GMA welding process evolution using a non-intrusive process sensing would allow not only the identification of disturbances during welding runs and thus reduce inspection time, but would also reduce the interference on the process caused by the direct sensing. In this paper a nonintrusive method for weld disturbance detection and localization for weld quality evaluation is demonstrated. The system is based on the acoustic sensing of the welding electrical arc. During repetitive tests in welds without disturbances, the stability acoustic parameters were calculated and used as comparison references for the detection and location of disturbances during the weld runs.

A Non-Intrusive GMA Welding Process Quality Monitoring System Using Acoustic Sensing

PubMed Central

Cayo, Eber Huanca; Alfaro, Sadek Crisostomo Absi

2009-01-01

Most of the inspection methods used for detection and localization of welding disturbances are based on the evaluation of some direct measurements of welding parameters. This direct measurement requires an insertion of sensors during the welding process which could somehow alter the behavior of the metallic transference. An inspection method that evaluates the GMA welding process evolution using a non-intrusive process sensing would allow not only the identification of disturbances during welding runs and thus reduce inspection time, but would also reduce the interference on the process caused by the direct sensing. In this paper a nonintrusive method for weld disturbance detection and localization for weld quality evaluation is demonstrated. The system is based on the acoustic sensing of the welding electrical arc. During repetitive tests in welds without disturbances, the stability acoustic parameters were calculated and used as comparison references for the detection and location of disturbances during the weld runs. PMID:22399990

Direct detection of male quality can facilitate the evolution of female choosiness and indicators of good genes: Evolution across a continuum of indicator mechanisms.

PubMed

Dhole, Sumit; Stern, Caitlin A; Servedio, Maria R

2018-04-01

The evolution of mating displays as indicators of male quality has been the subject of extensive theoretical and empirical research for over four decades. Research has also addressed the evolution of female mate choice favoring such indicators. Yet, much debate still exists about whether displays can evolve through the indirect benefits of female mate choice. Here, we use a population genetic model to investigate how the extent to which females can directly detect male quality influences the evolution of female choosiness and male displays. We use a continuum framework that incorporates indicator mechanisms that are traditionally modeled separately. Counter to intuition, we find that intermediate levels of direct detection of male quality can facilitate, rather than impede, the evolution of female choosiness and male displays in broad regions of this continuum. We examine how this evolution is driven by selective forces on genetic quality and on the display, and find that direct detection of male quality results in stronger indirect selection favoring female choosiness. Our results imply that displays maybe more likely to evolve when female choosiness has already evolved to discriminate perceptible forms of male quality. They also highlight the importance of considering general female choosiness, as well as preference, in studies of "good genes." © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Method and apparatus for controlling gas evolution from chemical reactions

DOEpatents

Skorpik, J.R.; Dodson, M.G.

1999-05-25

The present invention is directed toward monitoring a thermally driven gas evolving chemical reaction with an acoustic apparatus. Signals from the acoustic apparatus are used to control a heater to prevent a run-away condition. A digestion module in combination with a robotic arm further automate physical handling of sample material reaction vessels. The invention is especially useful for carrying out sample procedures defined in EPA Methods SW-846. 8 figs.

A self-consistent field method for galactic dynamics

NASA Technical Reports Server (NTRS)

Hernquist, Lars; Ostriker, Jeremiah P.

1992-01-01

The present study describes an algorithm for evolving collisionless stellar systems in order to investigate the evolution of systems with density profiles like the R exp 1/4 law, using only a few terms in the expansions. A good fit is obtained for a truncated isothermal distribution, which renders the method appropriate for galaxies with flat rotation curves. Calculations employing N of about 10 exp 6-7 are straightforward on existing supercomputers, making possible simulations having significantly smoother fields than with direct methods such as tree-codes. Orbits are found in a given static or time-dependent gravitational field; the potential, phi(r, t) is revised from the resultant density, rho(r, t). Possible scientific uses of this technique are discussed, including tidal perturbations of dwarf galaxies, the adiabatic growth of central masses in spheroidal galaxies, instabilities in realistic galaxy models, and secular processes in galactic evolution.

Microbial detection method based on sensing molecular hydrogen

NASA Technical Reports Server (NTRS)

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

1974-01-01

A simple method for detecting bacteria, based on the time of hydrogen evolution, was developed and tested against various members of the Enterobacteriaceae group. The test system consisted of (1) two electrodes, platinum and a reference electrode, (2) a buffer amplifier, and (3) a strip-chart recorder. Hydrogen evolution was measured by an increase in voltage in the negative (cathodic) direction. A linear relationship was established between inoculum size and the time hydrogen was detected (lag period). Lag times ranged from 1 h for 1 million cells/ml to 7 h for 1 cell/ml. For each 10-fold decrease in inoculum, length of the lag period increased 60 to 70 min. Based on the linear relationship between inoculum and lag period, these results indicate the potential application of the hydrogen-sensing method for rapidly detecting coliforms and other gas-producing microorganisms in a variety of clinical, food, and other samples.

Directional Communication in Evolved Multiagent Teams

DTIC Science & Technology

2013-06-10

decentralized localization proposed by Franchi et al. [9]. Overall, the significant advantage of directional communication over non- directional...reception benefits the evolution of communicating autonomous agents because it simplifies the language required to express positional information, which...systems. This paper hypothesizes that such directional reception benefits the evolution of communicating autonomous agents because it simplifies the

Direct dating of human fossils.

PubMed

Grün, Rainer

2006-01-01

The methods that can be used for the direct dating of human remains comprise of radiocarbon, U-series, electron spin resonance (ESR), and amino acid racemization (AAR). This review gives an introduction to these methods in the context of dating human bones and teeth. Recent advances in ultrafiltration techniques have expanded the dating range of radiocarbon. It now seems feasible to reliably date bones up to 55,000 years. New developments in laser ablation mass spectrometry permit the in situ analysis of U-series isotopes, thus providing a rapid and virtually non-destructive dating method back to about 300,000 years. This is of particular importance when used in conjunction with non-destructive ESR analysis. New approaches in AAR analysis may lead to a renaissance of this method. The potential and present limitations of these direct dating techniques are discussed for sites relevant to the reconstruction of modern human evolution, including Florisbad, Border Cave, Tabun, Skhul, Qafzeh, Vindija, Banyoles, and Lake Mungo. (c) 2006 Wiley-Liss, Inc.

Quantum information and the problem of mechanisms of biological evolution.

PubMed

Melkikh, Alexey V

2014-01-01

One of the most important conditions for replication in early evolution is the de facto elimination of the conformational degrees of freedom of the replicators, the mechanisms of which remain unclear. In addition, realistic evolutionary timescales can be established based only on partially directed evolution, further complicating this issue. A division of the various evolutionary theories into two classes has been proposed based on the presence or absence of a priori information about the evolving system. A priori information plays a key role in solving problems in evolution. Here, a model of partially directed evolution, based on the learning automata theory, which includes a priori information about the fitness space, is proposed. A potential repository of such prior information is the states of biologically important molecules. Thus, the need for extended evolutionary synthesis is discussed. Experiments to test the hypothesis of partially directed evolution are proposed. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

The evolution of trade-offs under directional and correlational selection.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2012-08-01

Using quantitative genetic theory, we develop predictions for the evolution of trade-offs in response to directional and correlational selection. We predict that directional selection favoring an increase in one trait in a trade-off will result in change in the intercept but not the slope of the trade-off function, with the mean value of the selected trait increasing and that of the correlated trait decreasing. Natural selection will generally favor an increase in some combination of trait values, which can be represented as directional selection on an index value. Such selection induces both directional and correlational selection on the component traits. Theory predicts that selection on an index value will also change the intercept but not the slope of the trade-off function but because of correlational selection, the direction of change in component traits may be in the same or opposite directions. We test these predictions using artificial selection on the well-established trade-off between fecundity and flight capability in the cricket, Gryllus firmus and compare the empirical results with a priori predictions made using genetic parameters from a separate half-sibling experiment. Our results support the predictions and illustrate the complexity of trade-off evolution when component traits are subject to both directional and correlational selection. © 2012 The Author(s). Evolution© 2012 The Society for the Study of Evolution.

Analytical approaches for MCPD esters and glycidyl esters in food and biological samples: a review and future perspectives.

PubMed

Crews, C; Chiodini, A; Granvogl, M; Hamlet, C; Hrnčiřík, K; Kuhlmann, J; Lampen, A; Scholz, G; Weisshaar, R; Wenzl, T; Jasti, P R; Seefelder, W

2013-01-01

Esters of 2 - and 3-monochloropropane-1,2-diol (MCPD) and glycidol esters are important contaminants of processed edible oils used as foods or food ingredients. This review describes the occurrence and analysis of MCPD esters and glycidol esters in vegetable oils and some other foods. The focus is on the analytical methods based on both direct and indirect methods. Methods of analysis applied to oils and lipid extracts of foods have been based on transesterification to free MCPD and determination by gas chromatography-mass spectrometry (indirect methods) and by high-performance liquid chromatography-mass spectrometry (direct methods). The evolution and performance of the different methods is described and their advantages and disadvantages are discussed. The application of direct and indirect methods to the analysis of foods and to research studies is described. The metabolism and fate of MCPD esters and glycidol esters in biological systems and the methods used to study these in body tissues studies are described. A clear understanding of the chemistry of the methods is important when choosing those suitable for the desired application, and will contribute to the mitigation of these contaminants.

Optimization of controllability and robustness of complex networks by edge directionality

NASA Astrophysics Data System (ADS)

Liang, Man; Jin, Suoqin; Wang, Dingjie; Zou, Xiufen

2016-09-01

Recently, controllability of complex networks has attracted enormous attention in various fields of science and engineering. How to optimize structural controllability has also become a significant issue. Previous studies have shown that an appropriate directional assignment can improve structural controllability; however, the evolution of the structural controllability of complex networks under attacks and cascading has always been ignored. To address this problem, this study proposes a new edge orientation method (NEOM) based on residual degree that changes the link direction while conserving topology and directionality. By comparing the results with those of previous methods in two random graph models and several realistic networks, our proposed approach is demonstrated to be an effective and competitive method for improving the structural controllability of complex networks. Moreover, numerical simulations show that our method is near-optimal in optimizing structural controllability. Strikingly, compared to the original network, our method maintains the structural controllability of the network under attacks and cascading, indicating that the NEOM can also enhance the robustness of controllability of networks. These results alter the view of the nature of controllability in complex networks, change the understanding of structural controllability and affect the design of network models to control such networks.

Directed evolution and synthetic biology applications to microbial systems.

PubMed

Bassalo, Marcelo C; Liu, Rongming; Gill, Ryan T

2016-06-01

Biotechnology applications require engineering complex multi-genic traits. The lack of knowledge on the genetic basis of complex phenotypes restricts our ability to rationally engineer them. However, complex phenotypes can be engineered at the systems level, utilizing directed evolution strategies that drive whole biological systems toward desired phenotypes without requiring prior knowledge of the genetic basis of the targeted trait. Recent developments in the synthetic biology field accelerates the directed evolution cycle, facilitating engineering of increasingly complex traits in biological systems. In this review, we summarize some of the most recent advances in directed evolution and synthetic biology that allows engineering of complex traits in microbial systems. Then, we discuss applications that can be achieved through engineering at the systems level. Copyright © 2016 Elsevier Ltd. All rights reserved.

Engineering Biosynthesis of Non-ribosomal Peptides and Polyketides by Directed Evolution.

PubMed

Rui, Zhe; Zhang, Wenjun

2016-01-01

Non-ribosomal peptides (NRPs) and polyketides (PKs) play key roles in pharmaceutical industry due to their promising biological activities. The structural complexity of NRPs and PKs, however, creates significant synthetic challenges for producing these natural products and their analogues by purely chemical means. Alternatively, difficult syntheses can be achieved by using biosynthetic enzymes with improved efficiency and altered selectivity that are acquired from directed evolution. Key to the successful directed evolution is the methodology of screening/selection. This review summarizes the screening/selection strategies that have been employed to improve or modify the functions of non-ribosomal peptide synthetases (NRPSs) and polyketide synthases (PKSs), in the hope of triggering the wide adoption of the directed evolution approaches in the engineered biosynthesis of NRPs and PKs for drug discovery.

Using THz Spectroscopy, Evolutionary Network Analysis Methods, and MD Simulation to Map the Evolution of Allosteric Communication Pathways in c-Type Lysozymes.

PubMed

Woods, Kristina N; Pfeffer, Juergen

2016-01-01

It is now widely accepted that protein function is intimately tied with the navigation of energy landscapes. In this framework, a protein sequence is not described by a distinct structure but rather by an ensemble of conformations. And it is through this ensemble that evolution is able to modify a protein's function by altering its landscape. Hence, the evolution of protein functions involves selective pressures that adjust the sampling of the conformational states. In this work, we focus on elucidating the evolutionary pathway that shaped the function of individual proteins that make-up the mammalian c-type lysozyme subfamily. Using both experimental and computational methods, we map out specific intermolecular interactions that direct the sampling of conformational states and accordingly, also underlie shifts in the landscape that are directly connected with the formation of novel protein functions. By contrasting three representative proteins in the family we identify molecular mechanisms that are associated with the selectivity of enhanced antimicrobial properties and consequently, divergent protein function. Namely, we link the extent of localized fluctuations involving the loop separating helices A and B with shifts in the equilibrium of the ensemble of conformational states that mediate interdomain coupling and concurrently moderate substrate binding affinity. This work reveals unique insights into the molecular level mechanisms that promote the progression of interactions that connect the immune response to infection with the nutritional properties of lactation, while also providing a deeper understanding about how evolving energy landscapes may define present-day protein function. © The Author 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Acoustic emission evolution during sliding friction of Hadfield steel single crystal

NASA Astrophysics Data System (ADS)

Lychagin, D. V.; Novitskaya, O. S.; Kolubaev, A. V.; Sizova, O. V.

2017-12-01

Friction is a complex dynamic process. Direct observation of processes occurring in the friction zone is impossible due to a small size of a real contact area and, as a consequence, requires various additional methods applicable to monitor a tribological contact state. One of such methods consists in the analysis of acoustic emission data of a tribological contact. The use of acoustic emission entails the problem of interpreting physical sources of signals. In this paper, we analyze the evolution of acoustic emission signal frames in friction of Hadfield steel single crystals. The chosen crystallographic orientation of single crystals enables to identify four stages related to friction development as well as acoustic emission signals inherent in these stages. Acoustic emission signal parameters are studied in more detail by the short-time Fourier transform used to determine the time variation of the median frequency and its power spectrum. The results obtained will facilitate the development of a more precise method to monitor the tribological contact based on the acoustic emission method.

Dynamic evolution of light-induced orientation of dye-doped liquid crystals in liquid phase studied by time-resolved optically heterodyned optical Kerr effect technique.

PubMed

Yang, Pei; Liu, Liying; Xu, Lei

2008-02-28

Transient evolution of light-induced molecular reorientation both in 1-amino-anthraquinone (1AAQ) dye and azobenzene doped isotropic liquid crystals (LCs) were studied by time-resolved optically heterodyned optical Kerr effect method. The results give clear direct experimental proof that under short pulse (30 ps) excitation, LC molecules orientate toward the excitation light polarization direction in the 1AAQ/LC system. However, LC molecular orientation becomes orthogonal to the light polarization in azobenzene/LC system. Time-resolved excited-state absorption of 1AAQ and wavelength dependent excited-state absorption of azobenzene were also observed and their contributions to the early dynamics of the third order optical responses of the two systems were confirmed. A simplified two-level mean-field theory was derived to reveal the intensity dependence of orientation enhancement factor in azobenzene/LC system considering the photoisomerization process.

Methodology Development in Directed Evolution: Exploring Options when Applying Triple-Code Saturation Mutagenesis.

PubMed

Qu, Ge; Lonsdale, Richard; Yao, Peiyuan; Li, Guangyue; Liu, Beibei; Reetz, Manfred T; Sun, Zhoutong

2018-02-02

Directed evolution of stereo- or regioselective enzymes as catalysts in asymmetric transformations is of particular interest in organic synthesis. Upon evolving these biocatalysts, screening is the bottleneck. To beat the numbers problem most effectively, methods and strategies for building "small but smart" mutant libraries have been developed. Herein, we compared two different strategies regarding the application of triple-code saturation mutagenesis (TCSM) at multiresidue sites of the Thermoanaerobacter brockii alcohol dehydrogenase by using distinct reduced amino-acid alphabets. By using the synthetically difficult-to-reduce prochiral ketone tetrahydrofuran-3-one as a substrate, highly R- and S-selective variants were obtained (92-99 % ee) with minimal screening. The origin of stereoselectivity was provided by molecular dynamics analyses, which is discussed in terms of the Bürgi-Dunitz trajectory. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Pulse electrodeposition of CoFe thin films covered with layered double hydroxides as a fast route to prepare enhanced catalysts for oxygen evolution reaction

NASA Astrophysics Data System (ADS)

Sakita, Alan M. P.; Noce, Rodrigo Della; Vallés, Elisa; Benedetti, Assis V.

2018-03-01

A novel, ultra-fast, and one-step method for obtaining an effective catalyst for oxygen evolution reaction is proposed. The procedure consists in direct electrodeposition, in a free-nitrate bath, of CoFe alloy films covered with layered double hydroxides (LDH), by potentiostatic mode, in continuous or pulsed regime. The catalyst is directly formed on glassy carbon substrates. The best-prepared catalyst material reveals a mixed morphology with granular and dendritic CoFe alloy covered with a sponge of CoFe-LDH containing a Cl interlayer. An overpotential of η10 mA = 286 mV, with a Tafel slope of 48 mV dec-1, is obtained for the OER which displays the enhanced properties of the catalyst. These improved results demonstrate the competitiveness and efficacy of our proposal for the production of OER catalysts.

An Equation-Free Reduced-Order Modeling Approach to Tropical Pacific Simulation

NASA Astrophysics Data System (ADS)

Wang, Ruiwen; Zhu, Jiang; Luo, Zhendong; Navon, I. M.

2009-03-01

The “equation-free” (EF) method is often used in complex, multi-scale problems. In such cases it is necessary to know the closed form of the required evolution equations about oscopic variables within some applied fields. Conceptually such equations exist, however, they are not available in closed form. The EF method can bypass this difficulty. This method can obtain oscopic information by implementing models at a microscopic level. Given an initial oscopic variable, through lifting we can obtain the associated microscopic variable, which may be evolved using Direct Numerical Simulations (DNS) and by restriction, we can obtain the necessary oscopic information and the projective integration to obtain the desired quantities. In this paper we apply the EF POD-assisted method to the reduced modeling of a large-scale upper ocean circulation in the tropical Pacific domain. The computation cost is reduced dramatically. Compared with the POD method, the method provided more accurate results and it did not require the availability of any explicit equations or the right-hand side (RHS) of the evolution equation.

Nonadiabatic Ab Initio Molecular Dynamics with the Floating Occupation Molecular Orbital-Complete Active Space Configuration Interaction Method [Non-Adiabatic Ab Initio Molecular Dynamics with Floating Occupation Molecular Orbitals CASCI Method

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

Hollas, Daniel; Sistik, Lukas; Hohenstein, Edward G.

Here, we show that the floating occupation molecular orbital complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the widely used complete active space self-consistent field (CASSCF) method in direct nonadiabatic dynamics simulations. We have simulated photodynamics of three archetypal molecules in photodynamics: ethylene, methaniminium cation, and malonaldehyde. We compared the time evolution of electronic populations and reaction mechanisms as revealed by the FOMO-CASCI and CASSCF approaches. Generally, the two approaches provide similar results. Some dynamical differences are observed, but these can be traced back to energetically minor differences in the potential energy surfaces. We suggest thatmore » the FOMO-CASCI method represents, due to its efficiency and stability, a promising approach for direct ab initio dynamics in the excited state.« less

Bio-Inspired Engineering of Protein-Based Heat Sensors

DTIC Science & Technology

2004-01-01

of Thermosensitive Proteins. 23 3.1 Introduction 23 3.2 Low Stringency PCR Identification of TRPV1 Homologues from Pit Viper Trigeminal Ganglion...Methods and Results. 24 3.3 Directed Evolution of TRPV1 Protein. 25 3.4 Methods and Results 25 3.5 References 27 Pappas, TC F49620-01-1-0552 3 1. Unique...cation channel TRPV1 . Thermal nociceptive neurons are fairly plentiful, and thus benefited studies linking TRPVI to thermal responses. The snake pit

A mass-conserving mixed Fourier-Galerkin B-Spline-collocation method for Direct Numerical Simulation of the variable-density Navier-Stokes equations

NASA Astrophysics Data System (ADS)

Reuter, Bryan; Oliver, Todd; Lee, M. K.; Moser, Robert

2017-11-01

We present an algorithm for a Direct Numerical Simulation of the variable-density Navier-Stokes equations based on the velocity-vorticity approach introduced by Kim, Moin, and Moser (1987). In the current work, a Helmholtz decomposition of the momentum is performed. Evolution equations for the curl and the Laplacian of the divergence-free portion are formulated by manipulation of the momentum equations and the curl-free portion is reconstructed by enforcing continuity. The solution is expanded in Fourier bases in the homogeneous directions and B-Spline bases in the inhomogeneous directions. Discrete equations are obtained through a mixed Fourier-Galerkin and collocation weighted residual method. The scheme is designed such that the numerical solution conserves mass locally and globally by ensuring the discrete divergence projection is exact through the use of higher order splines in the inhomogeneous directions. The formulation is tested on multiple variable-density flow problems.

A Multistep Algorithm for the Radiation Hydrodynamical Transport of Cosmological Ionization Fronts and Ionized Flows

NASA Astrophysics Data System (ADS)

Whalen, Daniel; Norman, Michael L.

2006-02-01

Radiation hydrodynamical transport of ionization fronts (I-fronts) in the next generation of cosmological reionization simulations holds the promise of predicting UV escape fractions from first principles as well as investigating the role of photoionization in feedback processes and structure formation. We present a multistep integration scheme for radiative transfer and hydrodynamics for accurate propagation of I-fronts and ionized flows from a point source in cosmological simulations. The algorithm is a photon-conserving method that correctly tracks the position of I-fronts at much lower resolutions than nonconservative techniques. The method applies direct hierarchical updates to the ionic species, bypassing the need for the costly matrix solutions required by implicit methods while retaining sufficient accuracy to capture the true evolution of the fronts. We review the physics of ionization fronts in power-law density gradients, whose analytical solutions provide excellent validation tests for radiation coupling schemes. The advantages and potential drawbacks of direct and implicit schemes are also considered, with particular focus on problem time-stepping, which if not properly implemented can lead to morphologically plausible I-front behavior that nonetheless departs from theory. We also examine the effect of radiation pressure from very luminous central sources on the evolution of I-fronts and flows.

The macroevolution of size and complexity in insect male genitalia

PubMed Central

Rudoy, Andrey

2016-01-01

The evolution of insect male genitalia has received much attention, but there is still a lack of data on the macroevolutionary origin of its extraordinary variation. We used a calibrated molecular phylogeny of 71 of the 150 known species of the beetle genus Limnebius to study the evolution of the size and complexity of the male genitalia in its two subgenera, Bilimneus, with small species with simple genitalia, and Limnebius s.str., with a much larger variation in size and complexity. We reconstructed ancestral values of complexity (perimeter and fractal dimension of the aedeagus) and genital and body size with Bayesian methods. Complexity evolved more in agreement with a Brownian model, although with evidence of weak directional selection to a decrease or increase in complexity in the two subgenera respectively, as measured with an excess of branches with negative or positive change. On the contrary, aedeagus size, the variable with the highest rates of evolution, had a lower phylogenetic signal, without significant differences between the two subgenera in the average change of the individual branches of the tree. Aedeagus size also had a lower correlation with time and no evidence of directional selection. Rather than to directional selection, it thus seems that the higher diversity of the male genitalia in Limnebius s.str. is mostly due to the larger variance of the phenotypic change in the individual branches of the tree for all measured variables. PMID:27114865

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

PubMed

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

2013-01-01

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

Co-evolutionary Analysis of Domains in Interacting Proteins Reveals Insights into Domain–Domain Interactions Mediating Protein–Protein Interactions

PubMed Central

Jothi, Raja; Cherukuri, Praveen F.; Tasneem, Asba; Przytycka, Teresa M.

2006-01-01

Recent advances in functional genomics have helped generate large-scale high-throughput protein interaction data. Such networks, though extremely valuable towards molecular level understanding of cells, do not provide any direct information about the regions (domains) in the proteins that mediate the interaction. Here, we performed co-evolutionary analysis of domains in interacting proteins in order to understand the degree of co-evolution of interacting and non-interacting domains. Using a combination of sequence and structural analysis, we analyzed protein–protein interactions in F1-ATPase, Sec23p/Sec24p, DNA-directed RNA polymerase and nuclear pore complexes, and found that interacting domain pair(s) for a given interaction exhibits higher level of co-evolution than the noninteracting domain pairs. Motivated by this finding, we developed a computational method to test the generality of the observed trend, and to predict large-scale domain–domain interactions. Given a protein–protein interaction, the proposed method predicts the domain pair(s) that is most likely to mediate the protein interaction. We applied this method on the yeast interactome to predict domain–domain interactions, and used known domain–domain interactions found in PDB crystal structures to validate our predictions. Our results show that the prediction accuracy of the proposed method is statistically significant. Comparison of our prediction results with those from two other methods reveals that only a fraction of predictions are shared by all the three methods, indicating that the proposed method can detect known interactions missed by other methods. We believe that the proposed method can be used with other methods to help identify previously unrecognized domain–domain interactions on a genome scale, and could potentially help reduce the search space for identifying interaction sites. PMID:16949097

Spatiotemporal evolution of the chlorophyll a trend in the North Atlantic Ocean.

PubMed

Zhang, Min; Zhang, Yuanling; Shu, Qi; Zhao, Chang; Wang, Gang; Wu, Zhaohua; Qiao, Fangli

2018-01-15

Analyses of the chlorophyll a concentration (chla) from satellite ocean color products have suggested the decadal-scale variability of chla linked to the climate change. The decadal-scale variability in chla is both spatially and temporally non-uniform. We need to understand the spatiotemporal evolution of chla in decadal or multi-decadal timescales to better evaluate its linkage to climate variability. Here, the spatiotemporal evolution of the chla trend in the North Atlantic Ocean for the period 1997-2016 is analyzed using the multidimensional ensemble empirical mode decomposition method. We find that this variable trend signal of chla shows a dipole pattern between the subpolar gyre and along the Gulf Stream path, and propagation along the opposite direction of the North Atlantic Current. This propagation signal has an overlapping variability of approximately twenty years. Our findings suggest that the spatiotemporal evolution of chla during the two most recent decades is part of the multidecadal variations and possibly regulated by the changes of Atlantic Meridional Overturning Circulation, whereas the mechanisms of such evolution patterns still need to be explored. Copyright © 2017 Elsevier B.V. All rights reserved.

Testing of some assumptions about biodegradability in soil as measured by carbon dioxide evolution

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

El-Din Sharabi, N.; Bartha, R.

1993-04-01

The Toxic Substance Control Act calls for a premanufacturing review of novel chemical substances including their biodegradability. Carbon dioxide evolution, using non-labeled carbon or [sup 14]C, is a common method of testing. This study examines assumptions of carbon dioxide evolution testing. Test substances used included: glucose, adipic acid, benzoic acid, and n-hexadecane. Chemical composition other than carbon content appears to influence minimally the percentages conversion to CO[sub 2]. However, that although CO[sub 2] evolution seemed proportional to the carbon content and concentration of the test substance, at least one-half of the evolved net CO[sub 2] did not come directly frommore » the test substance. Conversion to CO[sub 2] in the soil appeared to depend on carbon content only. In experiments of 1 month or longer, the net CO[sub 2] evolution in response to substrate may be above 100% of the added substrate carbon. Whether this applies to all substrate additions remains to be studied. The authors conclude that net CO[sub 2] and [sup 14]CO[sub 2] evolution measurements are useful as a first-tier tests for assessing biodegradability in soil. 11 refs., 6 figs.« less

Quantum entanglement in strong-field ionization

NASA Astrophysics Data System (ADS)

Majorosi, Szilárd; Benedict, Mihály G.; Czirják, Attila

2017-10-01

We investigate the time evolution of quantum entanglement between an electron, liberated by a strong few-cycle laser pulse, and its parent ion core. Since the standard procedure is numerically prohibitive in this case, we propose a method to quantify the quantum correlation in such a system: we use the reduced density matrices of the directional subspaces along the polarization of the laser pulse and along the transverse directions as building blocks for an approximate entanglement entropy. We present our results, based on accurate numerical simulations, in terms of several of these entropies, for selected values of the peak electric-field strength and the carrier-envelope phase difference of the laser pulse. The time evolution of the mutual entropy of the electron and the ion-core motion along the direction of the laser polarization is similar to our earlier results based on a simple one-dimensional model. However, taking into account also the dynamics perpendicular to the laser polarization reveals a surprisingly different entanglement dynamics above the laser intensity range corresponding to pure tunneling: the quantum entanglement decreases with time in the over-the-barrier ionization regime.

Common Envelope Evolution: Implications for Post-AGB Stars and Planetary Nebulae

NASA Astrophysics Data System (ADS)

Nordhaus, J.

2017-10-01

Common envelopes (CE) are of broad interest as they represent one method by which binaries with initially long-period orbits of a few years can be converted into short-period orbits of a few hours. Despite their importance, the brief lifetimes of CE phases make them difficult to directly observe. Nevertheless, CE interactions are potentially common, can produce a diverse array of nebular shapes, and can accommodate current post-AGB and planetary nebula outflow constraints. Here, I discuss ongoing theoretical and computational work on CEs and speculate on what lies ahead for determining accurate outcomes of this elusive phase of evolution.

Determining the Stellar Initial Mass by Means of the 17O/18O Ratio on the AGB

NASA Astrophysics Data System (ADS)

De Nutte, Rutger; Decin, Leen; Olofsson, Hans; de Koter, Alex; Karakas, Amanda; Lombaert, Robin; Milam, Stefanie; Ramstedt, Sofia; Stancliffe, Richard; Homan, Ward; Van de Sande, Marie

2016-07-01

This poster presentsnewly obtainedcircumstellar 12C17O and 12C18O line observations, from which theline intensity are then related directly tothe 17O/18O surface abundance ratiofor a sample of nine AGB stars covering the three spectral types ().These ratios are evaluated in relation to a fundamental stellar evolution parameters: the stellar initial mass. The17O/18O ratio is shown to function as an effective method of determining the initial stellar mass. Through comparison with predictions bystellar evolution models, accurate initial mass estimates are calculated for all nine sources.

Using Noise and Fluctuations for In Situ Measurements of Nitrogen Diffusion Depth.

PubMed

Samoila, Cornel; Ursutiu, Doru; Schleer, Walter-Harald; Jinga, Vlad; Nascov, Victor

2016-10-05

In manufacturing processes involving diffusion (of C, N, S, etc.), the evolution of the layer depth is of the utmost importance: the success of the entire process depends on this parameter. Currently, nitriding is typically either calibrated using a "post process" method or controlled via indirect measurements (H2, O2, H2O + CO2). In the absence of "in situ" monitoring, any variation in the process parameters (gas concentration, temperature, steel composition, distance between sensors and furnace chamber) can cause expensive process inefficiency or failure. Indirect measurements can prevent process failure, but uncertainties and complications may arise in the relationship between the measured parameters and the actual diffusion process. In this paper, a method based on noise and fluctuation measurements is proposed that offers direct control of the layer depth evolution because the parameters of interest are measured in direct contact with the nitrided steel (represented by the active electrode). The paper addresses two related sets of experiments. The first set of experiments consisted of laboratory tests on nitrided samples using Barkhausen noise and yieded a linear relationship between the frequency exponent in the Hooge equation and the nitriding time. For the second set, a specific sensor based on conductivity noise (at the nitriding temperature) was built for shop-floor experiments. Although two different types of noise were measured in these two sets of experiments, the use of the frequency exponent to monitor the process evolution remained valid.

Using Noise and Fluctuations for In Situ Measurements of Nitrogen Diffusion Depth

PubMed Central

Samoila, Cornel; Ursutiu, Doru; Schleer, Walter-Harald; Jinga, Vlad; Nascov, Victor

2016-01-01

In manufacturing processes involving diffusion (of C, N, S, etc.), the evolution of the layer depth is of the utmost importance: the success of the entire process depends on this parameter. Currently, nitriding is typically either calibrated using a “post process” method or controlled via indirect measurements (H2, O2, H2O + CO2). In the absence of “in situ” monitoring, any variation in the process parameters (gas concentration, temperature, steel composition, distance between sensors and furnace chamber) can cause expensive process inefficiency or failure. Indirect measurements can prevent process failure, but uncertainties and complications may arise in the relationship between the measured parameters and the actual diffusion process. In this paper, a method based on noise and fluctuation measurements is proposed that offers direct control of the layer depth evolution because the parameters of interest are measured in direct contact with the nitrided steel (represented by the active electrode). The paper addresses two related sets of experiments. The first set of experiments consisted of laboratory tests on nitrided samples using Barkhausen noise and yielded a linear relationship between the frequency exponent in the Hooge equation and the nitriding time. For the second set, a specific sensor based on conductivity noise (at the nitriding temperature) was built for shop-floor experiments. Although two different types of noise were measured in these two sets of experiments, the use of the frequency exponent to monitor the process evolution remained valid. PMID:28773941

A level set approach for shock-induced α-γ phase transition of RDX

NASA Astrophysics Data System (ADS)

Josyula, Kartik; Rahul; De, Suvranu

2018-02-01

We present a thermodynamically consistent level sets approach based on regularization energy functional which can be directly incorporated into a Galerkin finite element framework to model interface motion. The regularization energy leads to a diffusive form of flux that is embedded within the level sets evolution equation which maintains the signed distance property of the level set function. The scheme is shown to compare well with the velocity extension method in capturing the interface position. The proposed level sets approach is employed to study the α-γphase transformation in RDX single crystal shocked along the (100) plane. Example problems in one and three dimensions are presented. We observe smooth evolution of the phase interface along the shock direction in both models. There is no diffusion of the interface during the zero level set evolution in the three dimensional model. The level sets approach is shown to capture the characteristics of the shock-induced α-γ phase transformation such as stress relaxation behind the phase interface and the finite time required for the phase transformation to complete. The regularization energy based level sets approach is efficient, robust, and easy to implement.

Regolith evolution in the laboratory - Scaling dissimilar comminution experiments

NASA Technical Reports Server (NTRS)

Cintala, Mark J.; Horz, Friedrich

1990-01-01

Repeated impacts into fragmental targets simulating unconsolidated debris on planetary surfaces have provided empirical insight into the evolution of planetary regoliths. The techniques of dimensional analysis have been employed to quantify and examine the relationships between the more important variables in the evolution of these experimental regoliths. Application of this method to the results of 10 experimental series shows that the quantity of comminuted target mass is directly proportional to (1) the number of impacts, (2) the diameter of the projectile, (3) the mean size of the crystals, (4) the mean grain size of the evolving regolith, (5) the total target mass, (6) the impactor density, and (7) the ratio of the impact velocity to the velocity of sound in the target rock. The comminuted mass is inversely proportional to the density of the target rock and the sorting of the regolith.

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

DOE PAGES

Merritt, Elizabeth Catherine; Doss, Forrest William

2016-07-06

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. Lastly, the evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

Efficient solution of the Wigner-Liouville equation using a spectral decomposition of the force field

NASA Astrophysics Data System (ADS)

Van de Put, Maarten L.; Sorée, Bart; Magnus, Wim

2017-12-01

The Wigner-Liouville equation is reformulated using a spectral decomposition of the classical force field instead of the potential energy. The latter is shown to simplify the Wigner-Liouville kernel both conceptually and numerically as the spectral force Wigner-Liouville equation avoids the numerical evaluation of the highly oscillatory Wigner kernel which is nonlocal in both position and momentum. The quantum mechanical evolution is instead governed by a term local in space and non-local in momentum, where the non-locality in momentum has only a limited range. An interpretation of the time evolution in terms of two processes is presented; a classical evolution under the influence of the averaged driving field, and a probability-preserving quantum-mechanical generation and annihilation term. Using the inherent stability and reduced complexity, a direct deterministic numerical implementation using Chebyshev and Fourier pseudo-spectral methods is detailed. For the purpose of illustration, we present results for the time-evolution of a one-dimensional resonant tunneling diode driven out of equilibrium.

Wavelet analysis methods for radiography of multidimensional growth of planar mixing layers

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

Merritt, E. C., E-mail: emerritt@lanl.gov; Doss, F. W.

2016-07-15

The counter-propagating shear campaign is examining instability growth and its transition to turbulence in the high-energy-density physics regime using a laser-driven counter-propagating flow platform. In these experiments, we observe consistent complex break-up of and structure growth in a tracer layer placed at the shear flow interface during the instability growth phase. We present a wavelet-transform based analysis technique capable of characterizing the scale- and directionality-resolved average intensity perturbations in static radiographs of the experiment. This technique uses the complete spatial information available in each radiograph to describe the structure evolution. We designed this analysis technique to generate a two-dimensional powermore » spectrum for each radiograph from which we can recover information about structure widths, amplitudes, and orientations. The evolution of the distribution of power in the spectra for an experimental series is a potential metric for quantifying the structure size evolution as well as a system’s evolution towards isotropy.« less

Non-adaptive plasticity potentiates rapid adaptive evolution of gene expression in nature.

PubMed

Ghalambor, Cameron K; Hoke, Kim L; Ruell, Emily W; Fischer, Eva K; Reznick, David N; Hughes, Kimberly A

2015-09-17

Phenotypic plasticity is the capacity for an individual genotype to produce different phenotypes in response to environmental variation. Most traits are plastic, but the degree to which plasticity is adaptive or non-adaptive depends on whether environmentally induced phenotypes are closer or further away from the local optimum. Existing theories make conflicting predictions about whether plasticity constrains or facilitates adaptive evolution. Debate persists because few empirical studies have tested the relationship between initial plasticity and subsequent adaptive evolution in natural populations. Here we show that the direction of plasticity in gene expression is generally opposite to the direction of adaptive evolution. We experimentally transplanted Trinidadian guppies (Poecilia reticulata) adapted to living with cichlid predators to cichlid-free streams, and tested for evolutionary divergence in brain gene expression patterns after three to four generations. We find 135 transcripts that evolved parallel changes in expression within the replicated introduction populations. These changes are in the same direction exhibited in a native cichlid-free population, suggesting rapid adaptive evolution. We find 89% of these transcripts exhibited non-adaptive plastic changes in expression when the source population was reared in the absence of predators, as they are in the opposite direction to the evolved changes. By contrast, the remaining transcripts exhibiting adaptive plasticity show reduced population divergence. Furthermore, the most plastic transcripts in the source population evolved reduced plasticity in the introduction populations, suggesting strong selection against non-adaptive plasticity. These results support models predicting that adaptive plasticity constrains evolution, whereas non-adaptive plasticity potentiates evolution by increasing the strength of directional selection. The role of non-adaptive plasticity in evolution has received relatively little attention; however, our results suggest that it may be an important mechanism that predicts evolutionary responses to new environments.

Galactic nuclei evolution with spinning black holes: method and implementation

NASA Astrophysics Data System (ADS)

Fiacconi, Davide; Sijacki, Debora; Pringle, J. E.

2018-04-01

Supermassive black holes at the centre of galactic nuclei mostly grow in mass through gas accretion over cosmic time. This process also modifies the angular momentum (or spin) of black holes, both in magnitude and in orientation. Despite being often neglected in galaxy formation simulations, spin plays a crucial role in modulating accretion power, driving jet feedback, and determining recoil velocity of coalescing black hole binaries. We present a new accretion model for the moving-mesh code AREPO that incorporates (i) mass accretion through a thin α-disc, and (ii) spin evolution through the Bardeen-Petterson effect. We use a diverse suite of idealised simulations to explore the physical connection between spin evolution and larger scale environment. We find that black holes with mass ≲ 107 M⊙ experience quick alignment with the accretion disc. This favours prolonged phases of spin-up, and the spin direction evolves according to the gas inflow on timescales as short as ≲ 100 Myr, which might explain the observed jet direction distribution in Seyfert galaxies. Heavier black holes (≳ 108 M⊙) are instead more sensitive to the local gas kinematic. Here we find a wider distribution in spin magnitudes: spin-ups are favoured if gas inflow maintains a preferential direction, and spin-downs occur for nearly isotropic infall, while the spin direction does not change much over short timescales ˜100 Myr. We therefore conclude that supermassive black holes with masses ≳ 5 × 108 M⊙ may be the ideal testbed to determine the main mode of black hole fuelling over cosmic time.

Improving Glyphosate Oxidation Activity of Glycine Oxidase from Bacillus cereus by Directed Evolution

PubMed Central

Zhan, Tao; Zhang, Kai; Chen, Yangyan; Lin, Yongjun; Wu, Gaobing; Zhang, Lili; Yao, Pei; Shao, Zongze; Liu, Ziduo

2013-01-01

Glyphosate, a broad spectrum herbicide widely used in agriculture all over the world, inhibits 5-enolpyruvylshikimate-3-phosphate synthase in the shikimate pathway, and glycine oxidase (GO) has been reported to be able to catalyze the oxidative deamination of various amines and cleave the C-N bond in glyphosate. Here, in an effort to improve the catalytic activity of the glycine oxidase that was cloned from a glyphosate-degrading marine strain of Bacillus cereus (BceGO), we used a bacteriophage T7 lysis-based method for high-throughput screening of oxidase activity and engineered the gene encoding BceGO by directed evolution. Six mutants exhibiting enhanced activity toward glyphosate were screened from two rounds of error-prone PCR combined with site directed mutagenesis, and the beneficial mutations of the six evolved variants were recombined by DNA shuffling. Four recombinants were generated and, when compared with the wild-type BceGO, the most active mutant B3S1 showed the highest activity, exhibiting a 160-fold increase in substrate affinity, a 326-fold enhancement in catalytic efficiency against glyphosate, with little difference between their pH and temperature stabilities. The role of these mutations was explored through structure modeling and molecular docking, revealing that the Arg51 mutation is near the active site and could be an important residue contributing to the stabilization of glyphosate binding, while the role of the remaining mutations is unclear. These results provide insight into the application of directed evolution in optimizing glycine oxidase function and have laid a foundation for the development of glyphosate-tolerant crops. PMID:24223901

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

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

Tan, L.; Kim, B. K.; Was, G. S.

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Evolution dependence of vanadium nitride nanoprecipitates on directionality of ion irradiation

DOE PAGES

Tan, L.; Kim, B. K.; Was, G. S.

2017-09-06

The influence of the directionality of Fe 2+ ion irradiation on the evolution of vanadium nitride platelet–shaped nanoprecipitates at 500 °C was investigated in this paper in a ferritic alloy using transmission electron microscopy. When the ion-irradiation direction was approximately aligned with the initial particle length, particles grew longer and sectioned into shorter lengths at higher doses, resulting in increased particle densities. As ion-irradiation direction deviated from particle-length direction, some particles sectioned lengthwise and then dissolved, resulting in decreased particle densities. Surviving particles were transformed into parallelograms with a different orientation relationship with the matrix. Finally, nanoprecipitate evolution dependence onmore » beam-nanoprecipitate orientation is a process that may be different from reactor irradiation.« less

Etch Profile Simulation Using Level Set Methods

NASA Technical Reports Server (NTRS)

Hwang, Helen H.; Meyyappan, Meyya; Arnold, James O. (Technical Monitor)

1997-01-01

Etching and deposition of materials are critical steps in semiconductor processing for device manufacturing. Both etching and deposition may have isotropic and anisotropic components, due to directional sputtering and redeposition of materials, for example. Previous attempts at modeling profile evolution have used so-called "string theory" to simulate the moving solid-gas interface between the semiconductor and the plasma. One complication of this method is that extensive de-looping schemes are required at the profile corners. We will present a 2D profile evolution simulation using level set theory to model the surface. (1) By embedding the location of the interface in a field variable, the need for de-looping schemes is eliminated and profile corners are more accurately modeled. This level set profile evolution model will calculate both isotropic and anisotropic etch and deposition rates of a substrate in low pressure (10s mTorr) plasmas, considering the incident ion energy angular distribution functions and neutral fluxes. We will present etching profiles of Si substrates in Ar/Cl2 discharges for various incident ion energies and trench geometries.

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

Taheri, M; Teslich, N; Lu, J P

An in situ method for studying the role of laser energy on the microstructural evolution of polycrystalline Si is presented. By monitoring both laser energy and microstructural evolution simultaneously in the dynamic transmission electron microscope, information on grain size and defect concentration can be correlated directly with processing conditions. This proof of principle study provides fundamental scientific information on the crystallization process that has technological importance for the development of thin film transistors. In conclusion, we successfully developed a method for studying UV laser processing of Si films in situ on nanosecond time scales, with ultimate implications for TFT applicationmore » improvements. In addition to grain size distribution as a function of laser energy density, we found that grain size scaled with laser energy in general. We showed that nanosecond time resolution allowed us to see the nucleation and growth front during processing, which will help further the understanding of microstructural evolution of poly-Si films for electronic applications. Future studies, coupled with high resolution TEM, will be performed to study grain boundary migration, intergranular defects, and grain size distribution with respect to laser energy and adsorption depth.« less

A Study to Determine the Evolution of Advances in Medical Technology Expected in the Next 25 Years and Possible Impacts on Coast Guard Operations and Support Programs.

DTIC Science & Technology

1980-05-01

abnormalities in pressure tracings of the systemic, the central venous or pulmonary arterial circulation. At some sites (especially the Latter-Day Saints...accurate measurement of central venous pressure has been by direct venous cannulation. However, a group of Swiss doctors has extended the principle of... venous stop flow pressure to develop a noninvasive method of measuring central venous pressure. The method consists of venous auscultation at the thoracic

Extraterrestrial civilizations: Problems of their evolution

NASA Technical Reports Server (NTRS)

Leskov, L. V.

1987-01-01

The problem of finding extraterrestrial civilizations and establishing contact with them is directly related to the problem of their evolution. Possible patterns in this evolution and the stages in the evolution of extraterrestrial civilizations are examined.

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

PubMed

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

2014-01-01

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

Inferring the Limit Behavior of Some Elementary Cellular Automata

NASA Astrophysics Data System (ADS)

Ruivo, Eurico L. P.; de Oliveira, Pedro P. B.

Cellular automata locally define dynamical systems, discrete in space, time and in the state variables, capable of displaying arbitrarily complex global emergent behavior. One core question in the study of cellular automata refers to their limit behavior, that is, to the global dynamical features in an infinite time evolution. Previous works have shown that for finite time evolutions, the dynamics of one-dimensional cellular automata can be described by regular languages and, therefore, by finite automata. Such studies have shown the existence of growth patterns in the evolution of such finite automata for some elementary cellular automata rules and also inferred the limit behavior of such rules based upon the growth patterns; however, the results on the limit behavior were obtained manually, by direct inspection of the structures that arise during the time evolution. Here we present the formalization of an automatic method to compute such structures. Based on this, the rules of the elementary cellular automata space were classified according to the existence of a growth pattern in their finite automata. Also, we present a method to infer the limit graph of some elementary cellular automata rules, derived from the analysis of the regular expressions that describe their behavior in finite time. Finally, we analyze some attractors of two rules for which we could not compute the whole limit set.

Nucleotide exchange and excision technology DNA shuffling and directed evolution.

PubMed

Speck, Janina; Stebel, Sabine C; Arndt, Katja M; Müller, Kristian M

2011-01-01

Remarkable success in optimizing complex properties within DNA and proteins has been achieved by directed evolution. In contrast to various random mutagenesis methods and high-throughput selection methods, the number of available DNA shuffling procedures is limited, and protocols are often difficult to adjust. The strength of the nucleotide exchange and excision technology (NExT) DNA shuffling described here is the robust, efficient, and easily controllable DNA fragmentation step based on random incorporation of the so-called 'exchange nucleotides' by PCR. The exchange nucleotides are removed enzymatically, followed by chemical cleavage of the DNA backbone. The oligonucleotide pool is reassembled into full-length genes by internal primer extension, and the recombined gene library is amplified by standard PCR. The technique has been demonstrated by shuffling a defined gene library of chloramphenicol acetyltransferase variants using uridine as fragmentation defining exchange nucleotide. Substituting 33% of the dTTP with dUTP in the incorporation PCR resulted in shuffled clones with an average parental fragment size of 86 bases and revealed a mutation rate of only 0.1%. Additionally, a computer program (NExTProg) has been developed that predicts the fragment size distribution depending on the relative amount of the exchange nucleotide.

The Experiment and Numerical Simulation of Composite Countersunk-head Fasteners Pull-through Mechanical Behavior

NASA Astrophysics Data System (ADS)

Mu, Junwu; Guan, Zhidong; Bian, Tianya; Li, Zengshan; Wang, Kailun; Liu, Sui

2014-10-01

Fasteners made of the anisotropic carbon/carbon (C/C) composite material have been developed for joining C/C composite material components in the high-temperature environment. The fastener specimens are fabricated from the C/C composites which are made from laminated carbon cloths with Z-direction carbon fibers being punctured as perform. Densification process cycles such as the thermal gradient chemical vapor infiltration (CVI) technology were repeated to obtain high density C/C composites fastener. The fasteners were machined parallel to the carbon cloths (X-Y direction). A method was proposed to test pull-through mechanical behavior of the countersunk-head C/C composite material fasteners. The damage morphologies of the fasteners were observed through the charge coupled device (CCD) and the scanning electron microscope (SEM). The internal micro-structure were observed through the high-resolution Mirco-CT systems. Finally, an excellent simulation of the C/C composite countersunk-head fasteners were performed with the finite element method (FEM), in which the damage evolution model of the fastener was established based on continuum damage mechanics. The simulation is correspond well with the test result . The damage evolution process and the relation between the countersunk depth and the ultimate load was investigated.

Directed Evolution as a Powerful Synthetic Biology Tool

PubMed Central

Cobb, Ryan E.; Sun, Ning; Zhao, Huimin

2012-01-01

At the heart of synthetic biology lies the goal of rationally engineering a complete biological system to achieve a specific objective, such as bioremediation and synthesis of a valuable drug, chemical, or biofuel molecule. However, the inherent complexity of natural biological systems has heretofore precluded generalized application of this approach. Directed evolution, a process which mimics Darwinian selection on a laboratory scale, has allowed significant strides to be made in the field of synthetic biology by allowing rapid identification of desired properties from large libraries of variants. Improvement in biocatalyst activity and stability, engineering of biosynthetic pathways, tuning of functional regulatory systems and logic circuits, and development of desired complex phenotypes in industrial host organisms have all been achieved by way of directed evolution. Here, we review recent contributions of directed evolution to synthetic biology at the protein, pathway, network, and whole cell levels. PMID:22465795

Major Hurdles for the Evolution of Sociality.

PubMed

Korb, Judith; Heinze, Jürgen

2016-01-01

Why do most animals live solitarily, while complex social life is restricted to a few cooperatively breeding vertebrates and social insects? Here, we synthesize concepts and theories in social evolution and discuss its underlying ecological causes. Social evolution can be partitioned into (a) formation of stable social groups, (b) evolution of helping, and (c) transition to a new evolutionary level. Stable social groups rarely evolve due to competition over food and/or reproduction. Food competition is overcome in social insects with central-place foraging or bonanza-type food resources, whereas competition over reproduction commonly occurs because staying individuals are rarely sterile. Hence, the evolution of helping is shaped by direct and indirect fitness options and helping is only altruism if it reduces the helper's direct fitness. The helper's capability to gain direct fitness also creates within-colony conflict. This prevents transition to a new evolutionary level.

Eye evolution and its functional basis.

PubMed

Nilsson, Dan-E

2013-03-01

Eye evolution is driven by the evolution of visually guided behavior. Accumulation of gradually more demanding behaviors have continuously increased the performance requirements on the photoreceptor organs. Starting with nondirectional photoreception, I argue for an evolutionary sequence continuing with directional photoreception, low-resolution vision, and finally, high-resolution vision. Calculations of the physical requirements for these four sensory tasks show that they correlate with major innovations in eye evolution and thus work as a relevant classification for a functional analysis of eye evolution. Together with existing molecular and morphological data, the functional analysis suggests that urbilateria had a simple set of rhabdomeric and ciliary receptors used for directional photoreception, and that organ duplications, positional shifts and functional shifts account for the diverse patterns of eyes and photoreceptors seen in extant animals. The analysis also suggests that directional photoreception evolved independently at least twice before the last common ancestor of bilateria and proceeded several times independently to true vision in different bilaterian and cnidarian groups. This scenario is compatible with Pax-gene expression in eye development in the different animal groups. The whole process from the first opsin to high-resolution vision took about 170 million years and was largely completed by the onset of the Cambrian, about 530 million years ago. Evolution from shadow detectors to multiple directional photoreceptors has further led to secondary cases of eye evolution in bivalves, fan worms, and chitons.

Secondary phloem diversity and evolution in Bignonieae (Bignoniaceae)

PubMed Central

Pace, Marcelo R.; Alcantara, Suzana; Lohmann, Lúcia G.; Angyalossy, Veronica

2015-01-01

Background and Aims Phloem evolution has been explored in the literature across very broad scales, either for vascular plants as a whole or for major plant groups, such as the monocotyledons or the former dicotyledons. However, it has never been examined in a way that would elucidate evolutionary shifts leading to the diversification of phloem in single lineages. Therefore, the present study explores in detail the patterns of phloem evolution in the tribe Bignonieae (Bignoniaceae). This group represents a particularly good model for phloem studies since it is known to have a very conspicuous and diverse phloem. Methods A total of 19 phloem characters were coded in 56 species from all 21 genera currently recognized in the tribe Bignonieae, accounting for phloem wedge growth and for all the anatomical cell diversity encountered in the phloem. Phloem evolution was explored by reconstructing ancestral character states using maximum-likelihood assumptions with a time-calibrated molecular phylogeny for the group. Directionality and the effect of phylogenetic transformations in the current variation of quantitative traits and evolutionary correlations of selected discrete phloem traits were also tested under a maximum-likelihood approach. Key Results Individual phloem features are quite diverse in the tribe, but generally conserved within smaller clades. Contrasting phloem patterns were found when comparing major groups, with certain lineages having the phloem marked by a background of phloem fibres where all other cells are embedded, tangentially arranged sieve tubes and sieve-tubecentric parenchyma. In contrast, other lineages exhibited a scarcely fibrous phloem, regularly stratified phloem, sieve tube elements in radial or diffuse arrangement, and diffuse parenchyma. We found signals of directional evolution in fibre abundance and number of sieve areas, which increased in the ‘Fridericia and allies extended clade’ and decreased in the ‘Multiples of four extended clade’, resulting in no signal of directionality when the whole Bignonieae was considered. In contrast, no indication of directional evolution was found for the axial parenchyma, either in single clades within Bignonieae or in the entire tribe. Positive correlation was found between sieve element length and both sieve plate type and the presence of a storied structure. Correlated evolution was also found between fibre abundance and several traits, such as sieve tube arrangement, sieve plate type, parenchyma arrangement, ray lignification and number of companion cells. Conclusions The secondary phloem of Bignonieae is extremely diverse, with sister lineages exhibiting distinct phloem anatomies derived from contrasting patterns of evolution in fibre abundance. Fibre abundance in the tribe has diversified in correlation with sieve tube arrangement, sieve tube morphology, number of companion cells and parenchyma type. The results challenge long-standing hypotheses regarding general trends in cell abundance and morphological cell evolution within the phloem, and demonstrate the need to expand studies in phloem anatomy both at a narrow taxonomic scale and at a broad one, such as to families and orders. PMID:26311709

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

PubMed Central

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

2013-01-01

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

Limitations of inclusive fitness.

PubMed

Allen, Benjamin; Nowak, Martin A; Wilson, Edward O

2013-12-10

Until recently, inclusive fitness has been widely accepted as a general method to explain the evolution of social behavior. Affirming and expanding earlier criticism, we demonstrate that inclusive fitness is instead a limited concept, which exists only for a small subset of evolutionary processes. Inclusive fitness assumes that personal fitness is the sum of additive components caused by individual actions. This assumption does not hold for the majority of evolutionary processes or scenarios. To sidestep this limitation, inclusive fitness theorists have proposed a method using linear regression. On the basis of this method, it is claimed that inclusive fitness theory (i) predicts the direction of allele frequency changes, (ii) reveals the reasons for these changes, (iii) is as general as natural selection, and (iv) provides a universal design principle for evolution. In this paper we evaluate these claims, and show that all of them are unfounded. If the objective is to analyze whether mutations that modify social behavior are favored or opposed by natural selection, then no aspect of inclusive fitness theory is needed.

Locating and targeting moving tumors with radiation beams

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

Dieterich, Sonja; Cleary, Kevin; D'Souza, Warren

2008-12-15

The current climate of rapid technological evolution is reflected in newer and better methods to modulate and direct radiation beams for cancer therapy. This Vision 20/20 paper focuses on part of this evolution, locating and targeting moving tumors. The two processes are somewhat independent and in principle different implementations of the locating and targeting processes can be interchanged. Advanced localization and targeting methods have an impact on treatment planning and also present new challenges for quality assurance (QA), that of verifying real-time delivery. Some methods to locate and target moving tumors with radiation beams are currently FDA approved for clinicalmore » use--and this availability and implementation will increase with time. Extensions of current capabilities will be the integration of higher order dimensionality, such as rotation and deformation in addition to translation, into the estimate of the patient pose and real-time reoptimization and adaption of delivery to the dynamically changing anatomy of cancer patients.« less

Contextualising primate origins--an ecomorphological framework.

PubMed

Soligo, Christophe; Smaers, Jeroen B

2016-04-01

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

Boltzmann, Darwin and Directionality theory

NASA Astrophysics Data System (ADS)

Demetrius, Lloyd A.

2013-09-01

Boltzmann’s statistical thermodynamics is a mathematical theory which relates the macroscopic properties of aggregates of interacting molecules with the laws of their interaction. The theory is based on the concept thermodynamic entropy, a statistical measure of the extent to which energy is spread throughout macroscopic matter. Macroscopic evolution of material aggregates is quantitatively explained in terms of the principle: Thermodynamic entropy increases as the composition of the aggregate changes under molecular collision. Darwin’s theory of evolution is a qualitative theory of the origin of species and the adaptation of populations to their environment. A central concept in the theory is fitness, a qualitative measure of the capacity of an organism to contribute to the ancestry of future generations. Macroscopic evolution of populations of living organisms can be qualitatively explained in terms of a neo-Darwinian principle: Fitness increases as the composition of the population changes under variation and natural selection. Directionality theory is a quantitative model of the Darwinian argument of evolution by variation and selection. This mathematical theory is based on the concept evolutionary entropy, a statistical measure which describes the rate at which an organism appropriates energy from the environment and reinvests this energy into survivorship and reproduction. According to directionality theory, microevolutionary dynamics, that is evolution by mutation and natural selection, can be quantitatively explained in terms of a directionality principle: Evolutionary entropy increases when the resources are diverse and of constant abundance; but decreases when the resource is singular and of variable abundance. This report reviews the analytical and empirical support for directionality theory, and invokes the microevolutionary dynamics of variation and selection to delineate the principles which govern macroevolutionary dynamics of speciation and extinction. We also elucidate the relation between thermodynamic entropy, which pertains to the extent of energy spreading and sharing within inanimate matter, and evolutionary entropy, which refers to the rate of energy appropriation from the environment and allocation within living systems. We show that the entropic principle of thermodynamics is the limit as R→0, M→∞, (where R denote the resource production rate, and M denote population size) of the entropic principle of evolution. We exploit this relation between the thermodynamic and evolutionary tenets to propose a physico-chemical model of the transition from inanimate matter which is under thermodynamic selection, to living systems which are subject to evolutionary selection. Life history variation and the evolution of senescence The evolutionary dynamics of speciation and extinction Evolutionary trends in body size. The origin of sporadic forms of cancer and neurological diseases, and the evolution of cooperation are important recent applications of directionality theory. These applications, which draw from the medical sciences and sociobiology, appeal to methods which lie outside the formalism described in this report. A companion review, Demetrius and Gundlach (submitted for publication), gives an account of these applications.An important aspect of this report pertains to the connection between statistical mechanics and evolutionary theory and its implications towards understanding the processes which underlie the emergence of living systems from inanimate matter-a problem which has recently attracted considerable attention, Morowitz (1992), Eigen (1992), Dyson (2000), Pross (2012).The connection between the two disciplines can be addressed by appealing to certain extremal principles which are considered the mainstay of the respective theories.The extremal principle in statistical mechanics can be stated as follows:

The evolution of phenotypic integration: How directional selection reshapes covariation in mice.

PubMed

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-10-01

Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. © 2017 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Chaos, oscillation and the evolution of indirect reciprocity in n-person games.

PubMed

Suzuki, Shinsuke; Akiyama, Eizo

2008-06-21

Evolution of cooperation among genetically unrelated individuals has been of considerable concern in various fields such as biology, economics, and psychology. The evolution of cooperation is often explained by reciprocity. Under reciprocity, cooperation can prevail in a society because a donor of cooperation receives reciprocation from the recipient of the cooperation, called direct reciprocity, or from someone else in the community, called indirect reciprocity. Nowak and Sigmund [1993. Chaos and the evolution of cooperation. Proc. Natl. Acad. Sci. USA 90, 5091-5094] have demonstrated that directly reciprocal cooperation in two-person prisoner's dilemma games with mutation of strategies can be maintained dynamically as periodic or chaotic oscillation. Furthermore, Eriksson and Lindgren [2005. Cooperation driven by mutations in multi-person Prisoner's Dilemma. J. Theor. Biol. 232, 399-409] have reported that directly reciprocal cooperation in n-person prisoner's dilemma games (n>2) can be maintained as periodic oscillation. Is dynamic cooperation observed only in direct reciprocity? Results of this study show that indirectly reciprocal cooperation in n-person prisoner's dilemma games can be maintained dynamically as periodic or chaotic oscillation. This is, to our knowledge, the first demonstration of chaos in indirect reciprocity. Furthermore, the results show that oscillatory dynamics are observed in common in the evolution of reciprocal cooperation whether for direct or indirect.

Quantum gates by periodic driving

PubMed Central

Shi, Z. C.; Wang, W.; Yi, X. X.

2016-01-01

Topological quantum computation has been extensively studied in the past decades due to its robustness against decoherence. One way to realize the topological quantum computation is by adiabatic evolutions—it requires relatively long time to complete a gate, so the speed of quantum computation slows down. In this work, we present a method to realize single qubit quantum gates by periodic driving. Compared to adiabatic evolution, the single qubit gates can be realized at a fixed time much shorter than that by adiabatic evolution. The driving fields can be sinusoidal or square-well field. With the sinusoidal driving field, we derive an expression for the total operation time in the high-frequency limit, and an exact analytical expression for the evolution operator without any approximations is given for the square well driving. This study suggests that the period driving could provide us with a new direction in regulations of the operation time in topological quantum computation. PMID:26911900

Graph Structured Program Evolution: Evolution of Loop Structures

NASA Astrophysics Data System (ADS)

Shirakawa, Shinichi; Nagao, Tomoharu

Recently, numerous automatic programming techniques have been developed and applied in various fields. A typical example is genetic programming (GP), and various extensions and representations of GP have been proposed thus far. Complex programs and hand-written programs, however, may contain several loops and handle multiple data types. In this chapter, we propose a new method called Graph Structured Program Evolution (GRAPE). The representation of GRAPE is a graph structure; therefore, it can represent branches and loops using this structure. Each programis constructed as an arbitrary directed graph of nodes and a data set. The GRAPE program handles multiple data types using the data set for each type, and the genotype of GRAPE takes the form of a linear string of integers. We apply GRAPE to three test problems, factorial, exponentiation, and list sorting, and demonstrate that the optimum solution in each problem is obtained by the GRAPE system.

Nested Tracking Graphs

DOE PAGES

Lukasczyk, Jonas; Weber, Gunther; Maciejewski, Ross; ...

2017-06-01

Tracking graphs are a well established tool in topological analysis to visualize the evolution of components and their properties over time, i.e., when components appear, disappear, merge, and split. However, tracking graphs are limited to a single level threshold and the graphs may vary substantially even under small changes to the threshold. To examine the evolution of features for varying levels, users have to compare multiple tracking graphs without a direct visual link between them. We propose a novel, interactive, nested graph visualization based on the fact that the tracked superlevel set components for different levels are related to eachmore » other through their nesting hierarchy. This approach allows us to set multiple tracking graphs in context to each other and enables users to effectively follow the evolution of components for different levels simultaneously. We show the effectiveness of our approach on datasets from finite pointset methods, computational fluid dynamics, and cosmology simulations.« less

Directed evolution of bacteriorhodopsin for applications in bioelectronics

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Ranaghan, Matthew J.; Birge, Robert R.

2013-01-01

In nature, biological systems gradually evolve through complex, algorithmic processes involving mutation and differential selection. Evolution has optimized biological macromolecules for a variety of functions to provide a comparative advantage. However, nature does not optimize molecules for use in human-made devices, as it would gain no survival advantage in such cooperation. Recent advancements in genetic engineering, most notably directed evolution, have allowed for the stepwise manipulation of the properties of living organisms, promoting the expansion of protein-based devices in nanotechnology. In this review, we highlight the use of directed evolution to optimize photoactive proteins, with an emphasis on bacteriorhodopsin (BR), for device applications. BR, a highly stable light-activated proton pump, has shown great promise in three-dimensional optical memories, real-time holographic processors and artificial retinas. PMID:23676894

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

The fitness of an existing phenotype and of a potential mutant should generally depend on the frequencies of other existing phenotypes. Adaptive evolution driven by such frequency-dependent fitness functions can be analyzed effectively using adaptive dynamics theory, assuming rare mutation and asexual reproduction. When possible mutations are restricted to certain directions due to developmental, physiological, or physical constraints, the resulting adaptive evolution may be restricted to subspaces (constraint surfaces) with fewer dimensionalities than the original trait spaces. To analyze such dynamics along constraint surfaces efficiently, we develop a Lagrange multiplier method in the framework of adaptive dynamics theory. On constraint surfaces of arbitrary dimensionalities described with equality constraints, our method efficiently finds local evolutionarily stable strategies, convergence stable points, and evolutionary branching points. We also derive the conditions for the existence of evolutionary branching points on constraint surfaces when the shapes of the surfaces can be chosen freely. Copyright © 2016 Elsevier Ltd. All rights reserved.

Stretch or contraction induced inversion of rectification in diblock molecular junctions

NASA Astrophysics Data System (ADS)

Zhang, Guang-Ping; Hu, Gui-Chao; Song, Yang; Xie, Zhen; Wang, Chuan-Kui

2013-09-01

Based on ab initio theory and nonequilibrium Green's function method, the effect of stretch or contraction on the rectification in diblock co-oligomer molecular diodes is investigated theoretically. Interestingly, an inversion of rectifying direction induced by stretching or contracting the molecular junctions, which is closely related to the number of the pyrimidinyl-phenyl units, is proposed. The analysis of the molecular projected self-consistent Hamiltonian and the evolution of the frontier molecular orbitals as well as transmission coefficients under external biases gives an inside view of the observed results. It reveals that the asymmetric molecular level shift and asymmetric evolution of orbital wave functions under biases are competitive mechanisms for rectification. The stretching or contracting induced inversion of the rectification is due to the conversion of the dominant mechanism. This work suggests a feasible technique to manipulate the rectification performance in molecular diodes by use of the mechanically controllable method.

Unusual Domain Structure and Filamentary Superfluidity for 2D Hard-Core Bosons in Insulating Charge-Ordered Phase

NASA Astrophysics Data System (ADS)

Panov, Yu. D.; Moskvin, A. S.; Rybakov, F. N.; Borisov, A. B.

2016-12-01

We made use of a special algorithm for compute unified device architecture for NVIDIA graphics cards, a nonlinear conjugate-gradient method to minimize energy functional, and Monte-Carlo technique to directly observe the forming of the ground state configuration for the 2D hard-core bosons by lowering the temperature and its evolution with deviation away from half-filling. The novel technique allowed us to examine earlier implications and uncover novel features of the phase transitions, in particular, look upon the nucleation of the odd domain structure, emergence of filamentary superfluidity nucleated at the antiphase domain walls of the charge-ordered phase, and nucleation and evolution of different topological structures.

Plant domestication slows pest evolution.

PubMed

Turcotte, Martin M; Lochab, Amaneet K; Turley, Nash E; Johnson, Marc T J

2015-09-01

Agricultural practices such as breeding resistant varieties and pesticide use can cause rapid evolution of pest species, but it remains unknown how plant domestication itself impacts pest contemporary evolution. Using experimental evolution on a comparative phylogenetic scale, we compared the evolutionary dynamics of a globally important economic pest - the green peach aphid (Myzus persicae) - growing on 34 plant taxa, represented by 17 crop species and their wild relatives. Domestication slowed aphid evolution by 13.5%, maintained 10.4% greater aphid genotypic diversity and 5.6% higher genotypic richness. The direction of evolution (i.e. which genotypes increased in frequency) differed among independent domestication events but was correlated with specific plant traits. Individual-based simulation models suggested that domestication affects aphid evolution directly by reducing the strength of selection and indirectly by increasing aphid density and thus weakening genetic drift. Our results suggest that phenotypic changes during domestication can alter pest evolutionary dynamics. © 2015 John Wiley & Sons Ltd/CNRS.

Simple versus complex models of trait evolution and stasis as a response to environmental change

NASA Astrophysics Data System (ADS)

Hunt, Gene; Hopkins, Melanie J.; Lidgard, Scott

2015-04-01

Previous analyses of evolutionary patterns, or modes, in fossil lineages have focused overwhelmingly on three simple models: stasis, random walks, and directional evolution. Here we use likelihood methods to fit an expanded set of evolutionary models to a large compilation of ancestor-descendant series of populations from the fossil record. In addition to the standard three models, we assess more complex models with punctuations and shifts from one evolutionary mode to another. As in previous studies, we find that stasis is common in the fossil record, as is a strict version of stasis that entails no real evolutionary changes. Incidence of directional evolution is relatively low (13%), but higher than in previous studies because our analytical approach can more sensitively detect noisy trends. Complex evolutionary models are often favored, overwhelmingly so for sequences comprising many samples. This finding is consistent with evolutionary dynamics that are, in reality, more complex than any of the models we consider. Furthermore, the timing of shifts in evolutionary dynamics varies among traits measured from the same series. Finally, we use our empirical collection of evolutionary sequences and a long and highly resolved proxy for global climate to inform simulations in which traits adaptively track temperature changes over time. When realistically calibrated, we find that this simple model can reproduce important aspects of our paleontological results. We conclude that observed paleontological patterns, including the prevalence of stasis, need not be inconsistent with adaptive evolution, even in the face of unstable physical environments.

Evolution of network architecture in a granular material under compression

NASA Astrophysics Data System (ADS)

Bassett, Danielle

As a granular material is compressed, the particles and forces within the system arrange to form complex and heterogeneous collective structures. However, capturing and characterizing the dynamic nature of the intrinsic inhomogeneity and mesoscale architecture of granular systems can be challenging. Here, we utilize multilayer networks as a framework for directly quantifying the evolution of mesoscale architecture in a compressed granular system. We examine a quasi-two-dimensional aggregate of photoelastic disks, subject to biaxial compressions through a series of small, quasistatic steps. Treating particles as network nodes and inter-particle forces as network edges, we construct a multilayer network for the system by linking together the series of static force networks that exist at each strain step. We then extract the inherent mesoscale structure from the system by using a generalization of community detection methods to multilayer networks, and we define quantitative measures to characterize the reconfiguration and evolution of this structure throughout the compression process. To test the sensitivity of the network model to particle properties, we examine whether the method can distinguish a subsystem of low-friction particles within a bath of higher-friction particles. We find that this can be done by considering the network of tangential forces, and that the community structure is better able to separate the subsystem than consideration of the local inter-particle forces alone. The results discussed throughout this study suggest that these novel network science techniques may provide a direct way to compare and classify data from systems under different external conditions or with different physical makeup. National Science Foundation (BCS-1441502, PHY-1554488, and BCS-1631550).

Direct electrochemical reduction of metal-oxides

DOEpatents

Redey, Laszlo I.; Gourishankar, Karthick

2003-01-01

A method of controlling the direct electrolytic reduction of a metal oxide or mixtures of metal oxides to the corresponding metal or metals. A non-consumable anode and a cathode and a salt electrolyte with a first reference electrode near the non-consumable anode and a second reference electrode near the cathode are used. Oxygen gas is produced and removed from the cell. The anode potential is compared to the first reference electrode to prevent anode dissolution and gas evolution other than oxygen, and the cathode potential is compared to the second reference electrode to prevent production of reductant metal from ions in the electrolyte.

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Large Scale Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1997-01-01

Jet noise is a major concern in the design of commercial aircraft. Studies by various researchers suggest that aerodynamic noise is a major contributor to jet noise. Some of these studies indicate that most of the aerodynamic jet noise due to turbulent mixing occurs when there is a rapid variation in turbulent structure, i.e. rapidly growing or decaying vortices. The objective of this research was to simulate a compressible round jet to study the non-linear evolution of vortices and the resulting acoustic radiations. In particular, to understand the effect of turbulence structure on the noise. An ideal technique to study this problem is Direct Numerical Simulations(DNS), because it provides precise control on the initial and boundary conditions that lead to the turbulent structures studied. It also provides complete 3-dimensional time dependent data. Since the dynamics of a temporally evolving jet are not greatly different from those, of a spatially evolving jet, a temporal jet problem was solved, using periodicity ill the direction of the jet axis. This enables the application of Fourier spectral methods in the streamwise direction. Physically this means that turbulent structures in the jet are repeated in successive downstream cells instead of being gradually modified downstream into a jet plume. The DNS jet simulation helps us understand the various turbulent scales and mechanisms of turbulence generation in the evolution of a compressible round jet. These accurate flow solutions will be used in future research to estimate near-field acoustic radiation by computing the total outward flux across a surface and determine how it is related to the evolution of the turbulent solutions. Furthermore, these simulations allow us to investigate the sensitivity of acoustic radiations to inlet/boundary conditions, with possible application to active noise suppression. In addition, the data generated can be used to compute various turbulence quantities such as mean velocities, turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved Direct Numerical Simulation (DNS) of a turbulent jet flow is produced.

A method to deconvolve stellar rotational velocities II. The probability distribution function via Tikhonov regularization

NASA Astrophysics Data System (ADS)

Christen, Alejandra; Escarate, Pedro; Curé, Michel; Rial, Diego F.; Cassetti, Julia

2016-10-01

Aims: Knowing the distribution of stellar rotational velocities is essential for understanding stellar evolution. Because we measure the projected rotational speed v sin I, we need to solve an ill-posed problem given by a Fredholm integral of the first kind to recover the "true" rotational velocity distribution. Methods: After discretization of the Fredholm integral we apply the Tikhonov regularization method to obtain directly the probability distribution function for stellar rotational velocities. We propose a simple and straightforward procedure to determine the Tikhonov parameter. We applied Monte Carlo simulations to prove that the Tikhonov method is a consistent estimator and asymptotically unbiased. Results: This method is applied to a sample of cluster stars. We obtain confidence intervals using a bootstrap method. Our results are in close agreement with those obtained using the Lucy method for recovering the probability density distribution of rotational velocities. Furthermore, Lucy estimation lies inside our confidence interval. Conclusions: Tikhonov regularization is a highly robust method that deconvolves the rotational velocity probability density function from a sample of v sin I data directly without the need for any convergence criteria.

A general theory of evolution based on energy efficiency: its implications for diseases.

PubMed

Yun, Anthony J; Lee, Patrick Y; Doux, John D; Conley, Buford R

2006-01-01

We propose a general theory of evolution based on energy efficiency. Life represents an emergent property of energy. The earth receives energy from cosmic sources such as the sun. Biologic life can be characterized by the conversion of available energy into complex systems. Direct energy converters such as photosynthetic microorganisms and plants transform light energy into high-energy phosphate bonds that fuel biochemical work. Indirect converters such as herbivores and carnivores predominantly feed off the food chain supplied by these direct converters. Improving energy efficiency confers competitive advantage in the contest among organisms for energy. We introduce a term, return on energy (ROE), as a measure of energy efficiency. We define ROE as a ratio of the amount of energy acquired by a system to the amount of energy consumed to generate that gain. Life-death cycling represents a tactic to sample the environment for innovations that allow increases in ROE to develop over generations rather than an individual lifespan. However, the variation-selection strategem of Darwinian evolution may define a particular tactic rather than an overarching biological paradigm. A theory of evolution based on competition for energy and driven by improvements in ROE both encompasses prior notions of evolution and portends post-Darwinian mechanisms. Such processes may involve the exchange of non-genetic traits that improve ROE, as exemplified by cognitive adaptations or memes. Under these circumstances, indefinite persistence may become favored over life-death cycling, as increases in ROE may then occur more efficiently within a single lifespan rather than over multiple generations. The key to this transition may involve novel methods to address the promotion of health and cognitive plasticity. We describe the implications of this theory for human diseases.

Pursuing Darwin’s curious parallel: Prospects for a science of cultural evolution

PubMed Central

2017-01-01

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities. PMID:28739929

Pursuing Darwin's curious parallel: Prospects for a science of cultural evolution.

PubMed

Mesoudi, Alex

2017-07-24

In the past few decades, scholars from several disciplines have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and other forms of socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. Appropriate differences between genetic and cultural change are taken seriously, such as the possibility in the latter of nonrandomly guided variation or transformation, blending inheritance, and one-to-many transmission. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and the use of phylogenetic methods to reconstruct cultural macroevolution. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography on cultural evolution, the empirical validity of assumed social learning biases, the relative role of transformative and selective processes, and the use of quantitative phylogenetic and multilevel selection models to understand past and present dynamics of society-level change. I conclude by highlighting the interdisciplinary challenges of studying cultural evolution, including its relation to the traditional social sciences and humanities.

The Mass-Metallicity Relation with the Direct Method on Stacked Spectra of SDSS Galaxies

NASA Astrophysics Data System (ADS)

Andrews, Brett H.; Martini, Paul

2013-03-01

The relation between galaxy stellar mass and gas-phase metallicity is a sensitive diagnostic of the main processes that drive galaxy evolution, namely cosmological gas inflow, metal production in stars, and gas outflow via galactic winds. We employed the direct method to measure the metallicities of ~200,000 star-forming galaxies from the Sloan Digital Sky Survey that were stacked in bins of (1) stellar mass and (2) both stellar mass and star formation rate (SFR) to significantly enhance the signal-to-noise ratio of the weak [O III] λ4363 and [O II] λλ7320, 7330 auroral lines required to apply the direct method. These metallicity measurements span three decades in stellar mass from log(M sstarf/M ⊙) = 7.4-10.5, which allows the direct method mass-metallicity relation to simultaneously capture the high-mass turnover and extend a full decade lower in mass than previous studies that employed more uncertain strong line methods. The direct method mass-metallicity relation rises steeply at low mass (O/H vprop M sstarf 1/2) until it turns over at log(M sstarf/M ⊙) = 8.9 and asymptotes to 12 + log(O/H) = 8.8 at high mass. The direct method mass-metallicity relation has a steeper slope, a lower turnover mass, and a factor of two to three greater dependence on SFR than strong line mass-metallicity relations. Furthermore, the SFR-dependence appears monotonic with stellar mass, unlike strong line mass-metallicity relations. We also measure the N/O abundance ratio, an important tracer of star formation history, and find the clear signature of primary and secondary nitrogen enrichment. N/O correlates tightly with oxygen abundance, and even more so with stellar mass.

Unified anomaly suppression and boundary extraction in laser radar range imagery based on a joint curve-evolution and expectation-maximization algorithm.

PubMed

Feng, Haihua; Karl, William Clem; Castañon, David A

2008-05-01

In this paper, we develop a new unified approach for laser radar range anomaly suppression, range profiling, and segmentation. This approach combines an object-based hybrid scene model for representing the range distribution of the field and a statistical mixture model for the range data measurement noise. The image segmentation problem is formulated as a minimization problem which jointly estimates the target boundary together with the target region range variation and background range variation directly from the noisy and anomaly-filled range data. This formulation allows direct incorporation of prior information concerning the target boundary, target ranges, and background ranges into an optimal reconstruction process. Curve evolution techniques and a generalized expectation-maximization algorithm are jointly employed as an efficient solver for minimizing the objective energy, resulting in a coupled pair of object and intensity optimization tasks. The method directly and optimally extracts the target boundary, avoiding a suboptimal two-step process involving image smoothing followed by boundary extraction. Experiments are presented demonstrating that the proposed approach is robust to anomalous pixels (missing data) and capable of producing accurate estimation of the target boundary and range values from noisy data.

Plasma-Assisted Growth of Silicon Nanowires by Sn Catalyst: Step-by-Step Observation

NASA Astrophysics Data System (ADS)

Tang, Jian; Maurice, Jean-Luc; Chen, Wanghua; Misra, Soumyadeep; Foldyna, Martin; Johnson, Erik V.; Roca i Cabarrocas, Pere

2016-10-01

A comprehensive study of the silicon nanowire growth process has been carried out. Silicon nanowires were grown by plasma-assisted-vapor-solid method using tin as a catalyst. We have focused on the evolution of the silicon nanowire density, morphology, and crystallinity. For the first time, the initial growth stage, which determines the nanowire (NW) density and growth direction, has been observed step by step. We provide direct evidence of the merging of Sn catalyst droplets and the formation of Si nanowires during the first 10 s of growth. We found that the density of Sn droplets decreases from 9000 Sn droplets/μm2 to 2000 droplets/μm2 after just 10 s of growth. Moreover, the long and straight nanowire density decreases from 170/μm2 after 2 min of growth to less than 10/μm2 after 90 min. This strong reduction in nanowire density is accompanied by an evolution of their morphology from cylindrical to conical, then to bend conical, and finally, to a bend inverted conical shape. Moreover, the changes in the crystalline structure of nanowires are from (i) monocrystalline to (ii) monocrystalline core/defective crystalline shell and then to (iii) monocrystalline core/defective crystalline shell/amorphous shell. The evolutions of NW properties have been explained in detail.

Modeling the evolution of lithium-ion particle contact distributions using a fabric tensor approach

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

Stershic, A. J.; Simunovic, S.; Nanda, J.

2015-08-25

Electrode microstructure and processing can strongly influence lithium-ion battery performance such as capacity retention, power, and rate. Battery electrodes are multi-phase composite structures wherein conductive diluents and binder bond active material to a current collector. The structure and response of this composite network during repeated electrochemical cycling directly affects battery performance characteristics. We propose the fabric tensor formalism for describing the structure and evolution of the electrode microstructure. Fabric tensors are directional measures of particulate assemblies based on inter-particle connectivity, relating to the structural and transport properties of the electrode. Fabric tensor analysis is applied to experimental data-sets for positivemore » electrode made of lithium nickel manganese cobalt oxide, captured by X-ray tomography for several compositions and consolidation pressures. We show that fabric tensors capture the evolution of inter-particle contact distribution and are therefore good measures for the internal state of and electronic transport within the electrode. The fabric tensor analysis is also applied to Discrete Element Method (DEM) simulations of electrode microstructures using spherical particles with size distributions from the tomography. Furthermore, these results do not follow the experimental trends, which indicates that the particle size distribution alone is not a sufficient measure for the electrode microstructures in DEM simulations.« less

Pricing of American style options with an adjoint process correction method

NASA Astrophysics Data System (ADS)

Jaekel, Uwe

2005-07-01

Pricing of American options is a more complicated problem than pricing of European options. In this work a formula is derived that allows the computation of the early exercise premium, i.e. the price difference between these two option types in terms of an adjoint process evolving in the reversed time direction of the original process determining the evolution of the European price. We show how this equation can be utilised to improve option price estimates from numerical schemes like finite difference or Monte Carlo methods.

Numerical computation of linear instability of detonations

NASA Astrophysics Data System (ADS)

Kabanov, Dmitry; Kasimov, Aslan

2017-11-01

We propose a method to study linear stability of detonations by direct numerical computation. The linearized governing equations together with the shock-evolution equation are solved in the shock-attached frame using a high-resolution numerical algorithm. The computed results are processed by the Dynamic Mode Decomposition technique to generate dispersion relations. The method is applied to the reactive Euler equations with simple-depletion chemistry as well as more complex multistep chemistry. The results are compared with those known from normal-mode analysis. We acknowledge financial support from King Abdullah University of Science and Technology.

Continuous "in vitro" Evolution of a Ribozyme Ligase: A Model Experiment for the Evolution of a Biomolecule

ERIC Educational Resources Information Center

Ledbetter, Michael P.; Hwang, Tony W.; Stovall, Gwendolyn M.; Ellington, Andrew D.

2013-01-01

Evolution is a defining criterion of life and is central to understanding biological systems. However, the timescale of evolutionary shifts in phenotype limits most classroom evolution experiments to simple probability simulations. "In vitro" directed evolution (IVDE) frequently serves as a model system for the study of Darwinian…

Nonmathematical concepts of selection, evolutionary energy, and levels of evolution.

PubMed

Darlington, P J

1972-05-01

The place of mathematics in hypotheticodeductive processes and in biological research is discussed. (Natural) Selection is defined and described as differential elimination of performed sets at any level. Sets and acting sets are groups of units (themselves sets of smaller units) at any level that may or do interact. A pseudomathematical equation describes directional change (evolution) in sets at any level. Selection is the ram of evolution; it cannot generate, but can only direct, evolutionary energy. The energy of evolution is derived from molecular or chemical levels, is transmitted upwards through the increasingly complex sets of sets that form living systems, and is turned in directions determined by the sum of selective processes, at different levels, which may either supplement or oppose each other. All evolutionary processes conform to the pseudomathematical equation referred to above, use energy as described above, and have a P/OE (ratio of programming to open-endedness) that cannot be measured, but can be related to other P/OE values. Phylogeny and ontogeny are compared as processes af directional change with set selection. Stages in the evolution of multi-cellular individuals are suggested, and are essentially the same as stages in the evolution of some multi-individual insect societies. Thinking is considered as a part of ontogeny involving an irreversible, nonrepetitive process of set selection in the brain.

Computing Finite-Time Lyapunov Exponents with Optimally Time Dependent Reduction

NASA Astrophysics Data System (ADS)

Babaee, Hessam; Farazmand, Mohammad; Sapsis, Themis; Haller, George

2016-11-01

We present a method to compute Finite-Time Lyapunov Exponents (FTLE) of a dynamical system using Optimally Time-Dependent (OTD) reduction recently introduced by H. Babaee and T. P. Sapsis. The OTD modes are a set of finite-dimensional, time-dependent, orthonormal basis {ui (x , t) } |i=1N that capture the directions associated with transient instabilities. The evolution equation of the OTD modes is derived from a minimization principle that optimally approximates the most unstable directions over finite times. To compute the FTLE, we evolve a single OTD mode along with the nonlinear dynamics. We approximate the FTLE from the reduced system obtained from projecting the instantaneous linearized dynamics onto the OTD mode. This results in a significant reduction in the computational cost compared to conventional methods for computing FTLE. We demonstrate the efficiency of our method for double Gyre and ABC flows. ARO project 66710-EG-YIP.

BIOINSPIRED DESIGN AND DIRECTED EVOLUTION OF IRON CONTAINING ENZYMES FOR GREENSYNTHETIC PROCESSES AND BIOREMEDIATION

EPA Science Inventory

SU833912
Title: Bioinspired Design and Directed Evolution of Iron Containing Enzymes for Green Synthetic Processes and BioremediationEdward I. Solomon, Shaun D. Wong, Lei Liu, Caleb B. Bell, IIICynthia Nolt-Helms
Project Period: August 15, 2008 - August 14,...

Molecular evolution and the latitudinal biodiversity gradient.

PubMed

Dowle, E J; Morgan-Richards, M; Trewick, S A

2013-06-01

Species density is higher in the tropics (low latitude) than in temperate regions (high latitude) resulting in a latitudinal biodiversity gradient (LBG). The LBG must be generated by differential rates of speciation and/or extinction and/or immigration among regions, but the role of each of these processes is still unclear. Recent studies examining differences in rates of molecular evolution have inferred a direct link between rate of molecular evolution and rate of speciation, and postulated these as important drivers of the LBG. Here we review the molecular genetic evidence and examine the factors that might be responsible for differences in rates of molecular evolution. Critical to this is the directionality of the relationship between speciation rates and rates of molecular evolution.

Evolving a Behavioral Repertoire for a Walking Robot.

PubMed

Cully, A; Mouret, J-B

2016-01-01

Numerous algorithms have been proposed to allow legged robots to learn to walk. However, most of these algorithms are devised to learn walking in a straight line, which is not sufficient to accomplish any real-world mission. Here we introduce the Transferability-based Behavioral Repertoire Evolution algorithm (TBR-Evolution), a novel evolutionary algorithm that simultaneously discovers several hundreds of simple walking controllers, one for each possible direction. By taking advantage of solutions that are usually discarded by evolutionary processes, TBR-Evolution is substantially faster than independently evolving each controller. Our technique relies on two methods: (1) novelty search with local competition, which searches for both high-performing and diverse solutions, and (2) the transferability approach, which combines simulations and real tests to evolve controllers for a physical robot. We evaluate this new technique on a hexapod robot. Results show that with only a few dozen short experiments performed on the robot, the algorithm learns a repertoire of controllers that allows the robot to reach every point in its reachable space. Overall, TBR-Evolution introduced a new kind of learning algorithm that simultaneously optimizes all the achievable behaviors of a robot.

In-vitro engineering of novel bioactivity in the natural enzymes

NASA Astrophysics Data System (ADS)

Tiwari, Vishvanath

2016-10-01

Enzymes catalyze various biochemical functions with high efficiency and specificity. In-vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing and structure-based designing using chemical modifications. Similarly, combined computational and in-vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme. DNA shuffling, error prone PCR and staggered extension process are used to artificially redesign active site of enzyme, which can alter its efficiency and specificity. Modifications of the enzyme can lead to the discovery of new path of molecular evolution, designing of efficient enzymes, locating active sites and crucial residues, shift in substrate and cofactor specificity. The methods and thermodynamics of in-vitro designing of the enzyme are also discussed. Similarly, engineered thermophilic and psychrophilic enzymes attain substrate specificity and activity of mesophilic enzymes that may also be beneficial for industry and therapeutics.

Continuous Adaptive Population Reduction (CAPR) for Differential Evolution Optimization.

PubMed

Wong, Ieong; Liu, Wenjia; Ho, Chih-Ming; Ding, Xianting

2017-06-01

Differential evolution (DE) has been applied extensively in drug combination optimization studies in the past decade. It allows for identification of desired drug combinations with minimal experimental effort. This article proposes an adaptive population-sizing method for the DE algorithm. Our new method presents improvements in terms of efficiency and convergence over the original DE algorithm and constant stepwise population reduction-based DE algorithm, which would lead to a reduced number of cells and animals required to identify an optimal drug combination. The method continuously adjusts the reduction of the population size in accordance with the stage of the optimization process. Our adaptive scheme limits the population reduction to occur only at the exploitation stage. We believe that continuously adjusting for a more effective population size during the evolutionary process is the major reason for the significant improvement in the convergence speed of the DE algorithm. The performance of the method is evaluated through a set of unimodal and multimodal benchmark functions. In combining with self-adaptive schemes for mutation and crossover constants, this adaptive population reduction method can help shed light on the future direction of a completely parameter tune-free self-adaptive DE algorithm.

Evolution of double white dwarf binaries undergoing direct-impact accretion: Implications for gravitational wave astronomy

NASA Astrophysics Data System (ADS)

Kremer, Kyle; Breivik, Katelyn; Larson, Shane L.; Kalogera, Vassiliki

2017-01-01

For close double white dwarf binaries, the mass-transfer phenomenon known as direct-impact accretion (when the mass transfer stream impacts the accretor directly rather than forming a disc) may play a pivotal role in the long-term evolution of the systems. In this analysis, we explore the long-term evolution of white dwarf binaries accreting through direct-impact and explore implications of such systems to gravitational wave astronomy. We cover a broad range of parameter space which includes initial component masses and the strength of tidal coupling, and show that these systems, which lie firmly within the LISA frequency range, show strong negative chirps which can last as long as several million years. Detections of double white dwarf systems in the direct-impact phase by detectors such as LISA would provide astronomers with unique ways of probing the physics governing close compact object binaries.

A Phase-Space Approach to Collisionless Stellar Systems Using a Particle Method

NASA Astrophysics Data System (ADS)

Hozumi, Shunsuke

1997-10-01

A particle method for reproducing the phase space of collisionless stellar systems is described. The key idea originates in Liouville's theorem, which states that the distribution function (DF) at time t can be derived from tracing necessary orbits back to t = 0. To make this procedure feasible, a self-consistent field (SCF) method for solving Poisson's equation is adopted to compute the orbits of arbitrary stars. As an example, for the violent relaxation of a uniform density sphere, the phase-space evolution generated by the current method is compared to that obtained with a phase-space method for integrating the collisionless Boltzmann equation, on the assumption of spherical symmetry. Excellent agreement is found between the two methods if an optimal basis set for the SCF technique is chosen. Since this reproduction method requires only the functional form of initial DFs and does not require any assumptions to be made about the symmetry of the system, success in reproducing the phase-space evolution implies that there would be no need of directly solving the collisionless Boltzmann equation in order to access phase space even for systems without any special symmetries. The effects of basis sets used in SCF simulations on the reproduced phase space are also discussed.

Nonlinear derating of high-intensity focused ultrasound beams using Gaussian modal sums.

PubMed

Dibaji, Seyed Ahmad Reza; Banerjee, Rupak K; Soneson, Joshua E; Myers, Matthew R

2013-11-01

A method is introduced for using measurements made in water of the nonlinear acoustic pressure field produced by a high-intensity focused ultrasound transducer to compute the acoustic pressure and temperature rise in a tissue medium. The acoustic pressure harmonics generated by nonlinear propagation are represented as a sum of modes having a Gaussian functional dependence in the radial direction. While the method is derived in the context of Gaussian beams, final results are applicable to general transducer profiles. The focal acoustic pressure is obtained by solving an evolution equation in the axial variable. The nonlinear term in the evolution equation for tissue is modeled using modal amplitudes measured in water and suitably reduced using a combination of "source derating" (experiments in water performed at a lower source acoustic pressure than in tissue) and "endpoint derating" (amplitudes reduced at the target location). Numerical experiments showed that, with proper combinations of source derating and endpoint derating, direct simulations of acoustic pressure and temperature in tissue could be reproduced by derating within 5% error. Advantages of the derating approach presented include applicability over a wide range of gains, ease of computation (a single numerical quadrature is required), and readily obtained temperature estimates from the water measurements.

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p + p collisions at s = 510 GeV

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

Adare, A.; Aidala, C.; Ajitanand, N. N.

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at √s=510 GeV. Correlations of charged hadrons of 0.7T<10 GeV/c with π 0 mesons of 4T<15 GeV/c or isolated direct photons of 7T direct photon or π 0. Nonperturbative evolution effects are extracted from Gaussian fits to the away-side inclusive-charged-hadron yields for different trigger-particle transverse momenta (pmore » $$trig\\atop{T}$$). The Gaussian widths and root mean square of p out are reported as a function of the interaction hard scale p$$trig\\atop{T}$$ to investigate possible transverse-momentum-dependent evolution differences between the π 0-h ± and direct photon-h ± correlations and factorization breaking effects. The widths are found to decrease with p$$trig\\atop{T}$$, which indicates that the Collins-Soper-Sterman soft factor is not driving the evolution with the hard scale in nearly back-to-back dihadron and direct photon-hadron production in p+p collisions. This behavior is in contrast to Drell-Yan and semi-inclusive deep-inelastic scattering measurements.« less

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p + p collisions at s = 510 GeV

DOE PAGES

Adare, A.; Aidala, C.; Ajitanand, N. N.; ...

2017-04-04

Dihadron and isolated direct photon-hadron angular correlations are measured in p+p collisions at √s=510 GeV. Correlations of charged hadrons of 0.7T<10 GeV/c with π 0 mesons of 4T<15 GeV/c or isolated direct photons of 7T direct photon or π 0. Nonperturbative evolution effects are extracted from Gaussian fits to the away-side inclusive-charged-hadron yields for different trigger-particle transverse momenta (pmore » $$trig\\atop{T}$$). The Gaussian widths and root mean square of p out are reported as a function of the interaction hard scale p$$trig\\atop{T}$$ to investigate possible transverse-momentum-dependent evolution differences between the π 0-h ± and direct photon-h ± correlations and factorization breaking effects. The widths are found to decrease with p$$trig\\atop{T}$$, which indicates that the Collins-Soper-Sterman soft factor is not driving the evolution with the hard scale in nearly back-to-back dihadron and direct photon-hadron production in p+p collisions. This behavior is in contrast to Drell-Yan and semi-inclusive deep-inelastic scattering measurements.« less

On the modified grain-size-distribution method to evaluate the dynamic recrystallisation fraction in AISI 304 stainless steel

NASA Astrophysics Data System (ADS)

Hong, D. H.; Park, J. K.

2018-04-01

The purpose of the present work was to verify the grain size distribution (GSD) method, which was recently proposed by one of the present authors as a method for evaluating the fraction of dynamic recrystallisation (DRX) in a microalloyed medium carbon steel. To verify the GSD-method, we have selected a 304 stainless steel as a model system and have measured the evolution of the overall grain size distribution (including both the recrystallised and unrecrystallised grains) during hot compression at 1,000 °C in a Gleeble machine; the DRX fraction estimated using the GSD method is compared with the experimentally measured value via EBSD. The results show that the previous GSD method tends to overestimate the DRX fraction due to the utilisation of a plain lognormal distribution function (LDF). To overcome this shortcoming, we propose a modified GSD-method wherein an area-weighted LDF, in place of a plain LDF, is employed to model the evolution of GSD during hot deformation. Direct measurement of the DRX fraction using EBSD confirms that the modified GSD-method provides a reliable method for evaluating the DRX fraction from the experimentally measured GSDs. Reasonable agreement between the DRX fraction and softening fraction suggests that the Kocks-Mecking method utilising the Voce equation can be satisfactorily used to model the work hardening and dynamic recovery behaviour of steels during hot deformation.

Rapid 3D NMR using the filter diagonalization method: application to oligosaccharides derivatized with 13C-labeled acetyl groups

NASA Astrophysics Data System (ADS)

Armstrong, Geoffrey S.; Cano, Kristin E.; Mandelshtam, Vladimir A.; Shaka, A. J.; Bendiak, Brad

2004-09-01

Rapid 3D NMR spectroscopy of oligosaccharides having isotopically labeled acetyl "isotags" was made possible with high resolution in the indirect dimensions using the filter diagonalization method (FDM). A pulse sequence was designed for the optimal correlation of acetyl methyl protons, methyl carbons, and carbonyl carbons. The multi-dimensional nature of the FDM, coupled with the advantages of constant-time evolution periods, resulted in marked improvements over Fourier transform (FT) and mirror-image linear prediction (MI-LP) processing methods. The three methods were directly compared using identical data sets. A highly resolved 3D spectrum was achieved with the FDM using a very short experimental time (28 min).

Rapid 3D NMR using the filter diagonalization method: application to oligosaccharides derivatized with 13C-labeled acetyl groups.

PubMed

Armstrong, Geoffrey S; Cano, Kristin E; Mandelshtam, Vladimir A; Shaka, A J; Bendiak, Brad

2004-09-01

Rapid 3D NMR spectroscopy of oligosaccharides having isotopically labeled acetyl "isotags" was made possible with high resolution in the indirect dimensions using the filter diagonalization method (FDM). A pulse sequence was designed for the optimal correlation of acetyl methyl protons, methyl carbons, and carbonyl carbons. The multi-dimensional nature of the FDM, coupled with the advantages of constant-time evolution periods, resulted in marked improvements over Fourier transform (FT) and mirror-image linear prediction (MI-LP) processing methods. The three methods were directly compared using identical data sets. A highly resolved 3D spectrum was achieved with the FDM using a very short experimental time (28 min).

The ReaxFF reactive force-field: Development, applications, and future directions

DOE PAGES

Senftle, Thomas; Hong, Sungwook; Islam, Md Mahbubul; ...

2016-03-04

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFFmore » method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. As a result, this article provides an overview of the development, application, and future directions of the ReaxFF method.« less

Optimizing the deposition of hydrogen evolution sites on suspended semiconductor particles using on-line photocatalytic reforming of aqueous methanol solutions.

PubMed

Busser, G Wilma; Mei, Bastian; Muhler, Martin

2012-11-01

The deposition of hydrogen evolution sites on photocatalysts is a crucial step in the multistep process of synthesizing a catalyst that is active for overall photocatalytic water splitting. An alternative approach to conventional photodeposition was developed, applying the photocatalytic reforming of aqueous methanol solutions to deposit metal particles on semiconductor materials such as Ga₂O₃ and (Ga₀.₆ Zn₀.₄)(N₀.₆O₀.₄). The method allows optimizing the loading of the co-catalysts based on the stepwise addition of their precursors and the continuous online monitoring of the evolved hydrogen. Moreover, a synergetic effect between different co-catalysts can be directly established. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Degeneration and domestication of a selfish gene in yeast: molecular evolution versus site-directed mutagenesis.

PubMed

Koufopanou, Vassiliki; Burt, Austin

2005-07-01

VDE is a homing endonuclease gene in yeasts with an unusual evolutionary history including horizontal transmission, degeneration, and domestication into the mating-type switching locus HO. We investigate here the effects of these features on its molecular evolution. In addition, we correlate rates of evolution with results from site-directed mutagenesis studies. Functional elements have lower rates of evolution than degenerate ones and higher conservation at functionally important sites. However, functionally important and unimportant sites are equally likely to have been involved in the evolution of new function during the domestication of VDE into HO. The domestication event also indicates that VDE has been lost in some species and that VDE has been present in yeasts for more than 50 Myr.

Convergence of Domain Architecture, Structure, and Ligand Affinity in Animal and Plant RNA-Binding Proteins.

PubMed

Dias, Raquel; Manny, Austin; Kolaczkowski, Oralia; Kolaczkowski, Bryan

2017-06-01

Reconstruction of ancestral protein sequences using phylogenetic methods is a powerful technique for directly examining the evolution of molecular function. Although ancestral sequence reconstruction (ASR) is itself very efficient, downstream functional, and structural studies necessary to characterize when and how changes in molecular function occurred are often costly and time-consuming, currently limiting ASR studies to examining a relatively small number of discrete functional shifts. As a result, we have very little direct information about how molecular function evolves across large protein families. Here we develop an approach combining ASR with structure and function prediction to efficiently examine the evolution of ligand affinity across a large family of double-stranded RNA binding proteins (DRBs) spanning animals and plants. We find that the characteristic domain architecture of DRBs-consisting of 2-3 tandem double-stranded RNA binding motifs (dsrms)-arose independently in early animal and plant lineages. The affinity with which individual dsrms bind double-stranded RNA appears to have increased and decreased often across both animal and plant phylogenies, primarily through convergent structural mechanisms involving RNA-contact residues within the β1-β2 loop and a small region of α2. These studies provide some of the first direct information about how protein function evolves across large gene families and suggest that changes in molecular function may occur often and unassociated with major phylogenetic events, such as gene or domain duplications. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Effect of Swirl on Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1998-01-01

Direct Numerical Simulation (DNS) is used to study the mechanism of generation and evolution of turbulence structures in a temporally evolving supersonic swirling round jet and also to examine the resulting acoustic radiations. Fourier spectral expansions are used in the streamwise and azimuthal directions and a 1-D b-spline Galerkin representation is used in the radial direction. Spectral-like accuracy is achieved using this numerical scheme. Direct numerical simulations, using the b-spline spectral method, are carried out starting from mean flow initial conditions which are perturbed by the most unstable linear stability eigenfunctions. It is observed that the initial helical instability waves evolve into helical vortices which eventually breakdown into smaller scales of turbulence. 'Rib' structures similar to those seen in incompressible mixing layer flow of Rogers and Moserl are observed. The jet core breakdown stage exhibits increased acoustic radiations.

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal

PubMed Central

Ackerly, David

2009-01-01

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to ≈300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification. PMID:19843698

Conservatism and diversification of plant functional traits: Evolutionary rates versus phylogenetic signal.

PubMed

Ackerly, David

2009-11-17

The concepts of niche conservatism and adaptive radiation have played central roles in the study of evolution and ecological diversification. With respect to phenotypic evolution, the two processes may be seen as opposite ends of a spectrum; however, there is no straightforward method for the comparative analysis of trait evolution that will identify these contrasting scenarios. Analysis of the rate of phenotypic evolution plays an important role in this context and merits increased attention. In this article, independent contrasts are used to estimate rates of evolution for continuous traits under a Brownian motion model of evolution. A unit for the rate of phenotypic diversification is introduced: the felsen, in honor of J. Felsenstein, is defined as an increase of one unit per million years in the variance among sister taxa of ln-transformed trait values. The use of a standardized unit of measurement facilitates comparisons among clades and traits. Rates of diversification of three functional traits (plant height, leaf size, and seed size) were estimated for four to six woody plant clades (Acer, Aesculus, Ceanothus, Arbutoideae, Hawaiian lobeliads, and the silversword alliance) for which calibrated phylogenies were available. For height and leaf size, rates were two to approximately 300 times greater in the Hawaiian silversword alliance than in the other clades considered. These results highlight the value of direct estimates of rates of trait evolution for comparative analysis of adaptive radiation, niche conservatism, and trait diversification.

Collection Directions: The Evolution of Library Collections and Collecting

ERIC Educational Resources Information Center

Dempsey, Lorcan; Malpas, Constance; Lavoie, Brian

2014-01-01

This article takes a broad view of the evolution of collecting behaviors in a network environment and suggests some future directions based on various simple models. The authors look at the changing dynamics of print collections, at the greater engagement with research and learning behaviors, and at trends in scholarly communication. The goal is…

Directional selection in temporally replicated studies is remarkably consistent.

PubMed

Morrissey, Michael B; Hadfield, Jarrod D

2012-02-01

Temporal variation in selection is a fundamental determinant of evolutionary outcomes. A recent paper presented a synthetic analysis of temporal variation in selection in natural populations. The authors concluded that there is substantial variation in the strength and direction of selection over time, but acknowledged that sampling error would result in estimates of selection that were more variable than the true values. We reanalyze their dataset using techniques that account for the necessary effect of sampling error to inflate apparent levels of variation and show that directional selection is remarkably constant over time, both in magnitude and direction. Thus we cannot claim that the available data support the existence of substantial temporal heterogeneity in selection. Nonetheless, we conject that temporal variation in selection could be important, but that there are good reasons why it may not appear in the available data. These new analyses highlight the importance of applying techniques that estimate parameters of the distribution of selection, rather than parameters of the distribution of estimated selection (which will reflect both sampling error and "real" variation in selection); indeed, despite availability of methods for the former, focus on the latter has been common in synthetic reviews of the aspects of selection in nature, and can lead to serious misinterpretations. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

The evolution of phenotypic integration: How directional selection reshapes covariation in mice

PubMed Central

Penna, Anna; Melo, Diogo; Bernardi, Sandra; Oyarzabal, Maria Inés; Marroig, Gabriel

2017-01-01

Abstract Variation is the basis for evolution, and understanding how variation can evolve is a central question in biology. In complex phenotypes, covariation plays an even more important role, as genetic associations between traits can bias and alter evolutionary change. Covariation can be shaped by complex interactions between loci, and this genetic architecture can also change during evolution. In this article, we analyzed mouse lines experimentally selected for changes in size to address the question of how multivariate covariation changes under directional selection, as well as to identify the consequences of these changes to evolution. Selected lines showed a clear restructuring of covariation in their cranium and, instead of depleting their size variation, these lines increased their magnitude of integration and the proportion of variation associated with the direction of selection. This result is compatible with recent theoretical works on the evolution of covariation that take the complexities of genetic architecture into account. This result also contradicts the traditional view of the effects of selection on available covariation and suggests a much more complex view of how populations respond to selection. PMID:28685813

Company Profile: Selventa, Inc.

PubMed

Fryburg, David A; Latino, Louis J; Tagliamonte, John; Kenney, Renee D; Song, Diane H; Levine, Arnold J; de Graaf, David

2012-08-01

Selventa, Inc. (MA, USA) is a biomarker discovery company that enables personalized healthcare. Originally founded as Genstruct, Inc., Selventa has undergone significant evolution from a technology-based service provider to an active partner in the development of diagnostic tests, functioning as a molecular dashboard of disease activity using a unique platform. As part of that evolution, approximately 2 years ago the company was rebranded as Selventa to reflect its new identity and mission. The contributions to biomedical research by Selventa are based on in silico, reverse-engineering methods to determine biological causality. That is, given a set of in vitro or in vivo biological observations, which biological mechanisms can explain the measured results? Facilitated by a large and carefully curated knowledge base, these in silico methods generated new insights into the mechanisms driving a disease. As Selventa's methods would enable biomarker discovery and be directly applicable to generating novel diagnostics, the scientists at Selventa have focused on the development of predictive biomarkers of response in autoimmune and oncologic diseases. Selventa is presently building a portfolio of independent, as well as partnered, biomarker projects with the intention to create diagnostic tests that predict response to therapy.

UAV survey of a Thyrrenian micro-tidal beach for shoreline evolution update

NASA Astrophysics Data System (ADS)

Benassai, Guido; Pugliano, Giovanni; Di Paola, Gianluigi; Mucerino, Luigi

2015-04-01

Coastal geomorphology requires increasingly accurate topographic information of the beach systems to perform reliable simulation of coastal erosion, flooding phenomena, and coastal vulnerability assessment. Among the range of terrestrial and aerial methods available to produce such a dataset, this study tests the utility of low-altitude aerial imageries collected by Unmanned Aerial Vehicle (UAV). The image-based approach was selected whilst searching for a rapid, inexpensive, and highly automated method, able to produce 3D information from unstructured aerial images. In particular, it was used to generate a high-resolution Digital Surface Model (DSM) of the micro-tidal beach of Serapo - Gaeta (LT) in order to obtain recent update of erosional/accretional trends already established through historical shoreline evolution. A UAV exacopter (fig. 1a) was used, weighing about 2500g, carrying on board a GPS and multi-directional accelerometer to ensure a recovery of the beach features (fig. 1b) through a sweep with constant speed, direction and altitude. The on-board camera was a Canon 16M pixels, with fixed and constant focal takeoff in order to perform the 3D cloud points. Six adjacent strips were performed for the survey realization with pictures taken every second in sequence, in order to allow a minimum 80% overlap. A direct on site survey was also carried out with a DGPS for the placement of GPS markers and the geo-referencing of the final product (fig. 1c). Each flight with constant speed, direction and altitude recorded from 500 to 800 shots. The height of flight was dictated by the scale of the final report, an altitude of 100m was used for the beach survey. The topographic survey on the ground for the placement of the control points was performed with the Trimble R6 DGPS in RTK mode. The long-term shoreline evolution was obtained by a sixty-year historical shoreline time-series, through the analysis of a number of aerial photographs dating from 1954 to 2013. The shoreline change analysis was performed using the ArcGis 9.3 extension Digital Shoreline Analysis System (DSAS), v. 3.2 (Thieler et al., 2005). Transects orthogonal to the shoreline were generated at 100m intervals along the 1,4 km stretch of beach studied. The DSAS allowed the calculation of the rates of erosion/accretion between points, on the basis of the distance between them and the elapsed time, assuming changes to be linear processes. The rate of change of shoreline positions was evaluated at 14 points. The availability of shoreline data of the years 1954, 2000, 2006, 2008 and 2013 allowed to obtain the shoreline evolution trend in the last 60 years. Moreover, the UAV survey allowed to update the shoreline evolution and to obtain the volume of sediment lost by erosion, in order to suggest the locations and the amount of possible replenishments.

The direct cooling tail method for X-ray burst analysis to constrain neutron star masses and radii

NASA Astrophysics Data System (ADS)

Suleimanov, Valery F.; Poutanen, Juri; Nättilä, Joonas; Kajava, Jari J. E.; Revnivtsev, Mikhail G.; Werner, Klaus

2017-04-01

Determining neutron star (NS) radii and masses can help to understand the properties of matter at supra-nuclear densities. Thermal emission during thermonuclear X-ray bursts from NSs in low-mass X-ray binaries provides a unique opportunity to study NS parameters, because of the high fluxes, large luminosity variations and the related changes in the spectral properties. The standard cooling tail method uses hot NS atmosphere models to convert the observed spectral evolution during cooling stages of X-ray bursts to the Eddington flux FEdd and the stellar angular size Ω. These are then translated to the constraints on the NS mass M and radius R. Here we present the improved, direct cooling tail method that generalizes the standard approach. First, we adjust the cooling tail method to account for the bolometric correction to the flux. Then, we fit the observed dependence of the blackbody normalization on flux with a theoretical model directly on the M-R plane by interpolating theoretical dependences to a given gravity, hence ensuring only weakly informative priors for M and R instead of FEdd and Ω. The direct cooling method is demonstrated using a photospheric radius expansion burst from SAX J1810.8-2609, which has happened when the system was in the hard state. Comparing to the standard cooling tail method, the confidence regions are shifted by 1σ towards larger radii, giving R = 11.5-13.0 km at M = 1.3-1.8 M⊙ for this NS.

The Surface Density Distribution in the Solar Nebula

NASA Technical Reports Server (NTRS)

Davis, Sanford S.

2004-01-01

The commonly used minimum mass power law representation of the pre-solar nebula is reanalyzed using a new cumulative-mass-model. This model predicts a smoother surface density approximation compared with methods based on direct computation of surface density. The density is quantified using two independent analytical formulations. First, a best-fit transcendental function is applied directly to the basic planetary data. Next a solution to the time-dependent disk evolution equation is parametrically adapted to the solar nebula data. The latter model is shown to be a good approximation to the finite-size early Solar Nebula, and by extension to other extra solar protoplanetary disks.

Once upon Multivariate Analyses: When They Tell Several Stories about Biological Evolution.

PubMed

Renaud, Sabrina; Dufour, Anne-Béatrice; Hardouin, Emilie A; Ledevin, Ronan; Auffray, Jean-Christophe

2015-01-01

Geometric morphometrics aims to characterize of the geometry of complex traits. It is therefore by essence multivariate. The most popular methods to investigate patterns of differentiation in this context are (1) the Principal Component Analysis (PCA), which is an eigenvalue decomposition of the total variance-covariance matrix among all specimens; (2) the Canonical Variate Analysis (CVA, a.k.a. linear discriminant analysis (LDA) for more than two groups), which aims at separating the groups by maximizing the between-group to within-group variance ratio; (3) the between-group PCA (bgPCA) which investigates patterns of between-group variation, without standardizing by the within-group variance. Standardizing within-group variance, as performed in the CVA, distorts the relationships among groups, an effect that is particularly strong if the variance is similarly oriented in a comparable way in all groups. Such shared direction of main morphological variance may occur and have a biological meaning, for instance corresponding to the most frequent standing genetic variation in a population. Here we undertake a case study of the evolution of house mouse molar shape across various islands, based on the real dataset and simulations. We investigated how patterns of main variance influence the depiction of among-group differentiation according to the interpretation of the PCA, bgPCA and CVA. Without arguing about a method performing 'better' than another, it rather emerges that working on the total or between-group variance (PCA and bgPCA) will tend to put the focus on the role of direction of main variance as line of least resistance to evolution. Standardizing by the within-group variance (CVA), by dampening the expression of this line of least resistance, has the potential to reveal other relevant patterns of differentiation that may otherwise be blurred.

Evolution of availability of curcumin inside poly-lactic-co-glycolic acid nanoparticles: impact on antioxidant and antinitrosant properties

PubMed Central

Betbeder, Didier; Lipka, Emmanuelle; Howsam, Mike; Carpentier, Rodolphe

2015-01-01

Purpose Curcumin exhibits antioxidant properties potentially beneficial for human health; however, its use in clinical applications is limited by its poor solubility and relative instability. Nanoparticles exhibit interesting features for the efficient distribution and delivery of curcumin into cells, and could also increase curcumin stability in biological systems. There is a paucity of information regarding the evolution of the antioxidant properties of nanoparticle-encapsulated curcumin. Method We described a simple method of curcumin encapsulation in poly-lactic-co-glycolic acid (PLGA) nanoparticles without the use of detergent. We assessed, in epithelial cells and in an acellular model, the evolution of direct antioxidant and antinitrosant properties of free versus PLGA-encapsulated curcumin after storage under different conditions (light vs darkness, 4°C vs 25°C vs 37°C). Results In epithelial cells, endocytosis and efflux pump inhibitors showed that the increased antioxidant activity of PLGA-encapsulated curcumin relied on bypassing the efflux pump system. Acellular assays showed that the antioxidant effect of curcumin was greater when loaded in PLGA nanoparticles. Furthermore, we observed that light decreased, though heat restored, antioxidant activity of PLGA-encapsulated curcumin, probably by modulating the accessibility of curcumin to reactive oxygen species, an observation supported by results from quenching experiments. Moreover, we demonstrated a direct antinitrosant activity of curcumin, enhanced by PLGA encapsulation, which was increased by light exposure. Conclusion These results suggest that the antioxidant and antinitrosant activities of encapsulated curcumin are light sensitive and that nanoparticle modifications over time and with temperature may facilitate curcumin contact with reactive oxygen species. These results highlight the importance of understanding effects of nanoparticle maturation on an encapsulated drug’s activity. PMID:26345627

On the application of ENO scheme with subcell resolution to conservation laws with stiff source terms

NASA Technical Reports Server (NTRS)

Chang, Shih-Hung

1991-01-01

Two approaches are used to extend the essentially non-oscillatory (ENO) schemes to treat conservation laws with stiff source terms. One approach is the application of the Strang time-splitting method. Here the basic ENO scheme and the Harten modification using subcell resolution (SR), ENO/SR scheme, are extended this way. The other approach is a direct method and a modification of the ENO/SR. Here the technique of ENO reconstruction with subcell resolution is used to locate the discontinuity within a cell and the time evolution is then accomplished by solving the differential equation along characteristics locally and advancing in the characteristic direction. This scheme is denoted ENO/SRCD (subcell resolution - characteristic direction). All the schemes are tested on the equation of LeVeque and Yee (NASA-TM-100075, 1988) modeling reacting flow problems. Numerical results show that these schemes handle this intriguing model problem very well, especially with ENO/SRCD which produces perfect resolution at the discontinuity.

Statistical evidence for common ancestry: Application to primates.

PubMed

Baum, David A; Ané, Cécile; Larget, Bret; Solís-Lemus, Claudia; Ho, Lam Si Tung; Boone, Peggy; Drummond, Chloe P; Bontrager, Martin; Hunter, Steven J; Saucier, William

2016-06-01

Since Darwin, biologists have come to recognize that the theory of descent from common ancestry (CA) is very well supported by diverse lines of evidence. However, while the qualitative evidence is overwhelming, we also need formal methods for quantifying the evidential support for CA over the alternative hypothesis of separate ancestry (SA). In this article, we explore a diversity of statistical methods using data from the primates. We focus on two alternatives to CA, species SA (the separate origin of each named species) and family SA (the separate origin of each family). We implemented statistical tests based on morphological, molecular, and biogeographic data and developed two new methods: one that tests for phylogenetic autocorrelation while correcting for variation due to confounding ecological traits and a method for examining whether fossil taxa have fewer derived differences than living taxa. We overwhelmingly rejected both species and family SA with infinitesimal P values. We compare these results with those from two companion papers, which also found tremendously strong support for the CA of all primates, and discuss future directions and general philosophical issues that pertain to statistical testing of historical hypotheses such as CA. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Differential DNA Methylation Analysis without a Reference Genome.

PubMed

Klughammer, Johanna; Datlinger, Paul; Printz, Dieter; Sheffield, Nathan C; Farlik, Matthias; Hadler, Johanna; Fritsch, Gerhard; Bock, Christoph

2015-12-22

Genome-wide DNA methylation mapping uncovers epigenetic changes associated with animal development, environmental adaptation, and species evolution. To address the lack of high-throughput methods for DNA methylation analysis in non-model organisms, we developed an integrated approach for studying DNA methylation differences independent of a reference genome. Experimentally, our method relies on an optimized 96-well protocol for reduced representation bisulfite sequencing (RRBS), which we have validated in nine species (human, mouse, rat, cow, dog, chicken, carp, sea bass, and zebrafish). Bioinformatically, we developed the RefFreeDMA software to deduce ad hoc genomes directly from RRBS reads and to pinpoint differentially methylated regions between samples or groups of individuals (http://RefFreeDMA.computational-epigenetics.org). The identified regions are interpreted using motif enrichment analysis and/or cross-mapping to annotated genomes. We validated our method by reference-free analysis of cell-type-specific DNA methylation in the blood of human, cow, and carp. In summary, we present a cost-effective method for epigenome analysis in ecology and evolution, which enables epigenome-wide association studies in natural populations and species without a reference genome. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

A Generalized DBMS to Support Diversified Data.

DTIC Science & Technology

1987-07-21

interest on bonds ). Hence. they require a definition of subtraction which yields 30 days as the answer to the above computation. Only a user-defined...STON85]. Alternately. one can follow the standard scheduler model [BERNS1] in which a module is callable by code in the access methods when a...direction for evolution . These could include when to cease investigating alternate plans. and the ability to specify one’s own optimizer parameters

Large Scale Turbulent Structures in Supersonic Jets

NASA Technical Reports Server (NTRS)

Rao, Ram Mohan; Lundgren, Thomas S.

1997-01-01

Jet noise is a major concern in the design of commercial aircraft. Studies by various researchers suggest that aerodynamic noise is a major contributor to jet noise. Some of these studies indicate that most of the aerodynamic jet noise due to turbulent mixing occurs when there is a rapid variation in turbulent structure, i.e. rapidly growing or decaying vortices. The objective of this research was to simulate a compressible round jet to study the non-linear evolution of vortices and the resulting acoustic radiations. In particular, to understand the effect of turbulence structure on the noise. An ideal technique to study this problem is Direct Numerical Simulations (DNS), because it provides precise control on the initial and boundary conditions that lead to the turbulent structures studied. It also provides complete 3-dimensional time dependent data. Since the dynamics of a temporally evolving jet are not greatly different from those of a spatially evolving jet, a temporal jet problem was solved, using periodicity in the direction of the jet axis. This enables the application of Fourier spectral methods in the streamwise direction. Physically this means that turbulent structures in the jet are repeated in successive downstream cells instead of being gradually modified downstream into a jet plume. The DNS jet simulation helps us understand the various turbulent scales and mechanisms of turbulence generation in the evolution of a compressible round jet. These accurate flow solutions will be used in future research to estimate near-field acoustic radiation by computing the total outward flux across a surface and determine how it is related to the evolution of the turbulent solutions. Furthermore, these simulations allow us to investigate the sensitivity of acoustic radiations to inlet/boundary conditions, with possible appli(,a- tion to active noise suppression. In addition, the data generated can be used to compute, various turbulence quantities such as mean velocities, turbulent stresses, etc. which will aid in turbulence modeling. This report will be presented in two chapters. The first chapter describes some work on the linear stability of a supersonic round jet and the implications of this for the jet noise problem. The second chapter is an extensive discussion of numerical work using the spectral method which we use to solve the compressible Navier-Stokes equations to study turbulent jet flows. The method uses Fourier expansions in the azimuthal and streamwise direction and a 1-D B-spline basis representation in the radial direction. The B-spline basis is locally supported and this ensures block diagonal matrix equations which can be solved in O(N) steps. This is a modification of a boundary layer code developed by Robert Moser. A very accurate highly resolved DNS of a turbulent jet flow is produced.

Temporal and spatial evolution characteristics of water environment quality in Heze

NASA Astrophysics Data System (ADS)

Gao, Qian; Zhao, Qiang; Li, Xiumei

2018-06-01

The evolution of water environment is relatively complicated. The study of its characteristics is helpful to grasp the general direction of spatial and temporal evolution of water environment in Heze city, and to carry out water resources development and water environment protection more rationally. The comprehensive pollution index method for calculation, and the observed data are handled by Excel. In order to facilitate the analysis of the basin, Arcgis is utilized to map the watershed map. In addition, for the spatial evolution, surfer12 is used to analyze the spatial evolution characteristics the spatial evolution, and to draw the pictures of spatial evolution of chemical oxygen demand and water quality evolution. The study shows that: (1) In Heze, the quality of water environment has been improved year by year from 2006 to 2013. In 2014, the water environment has deteriorated. The content of volatile phenol has increased greatly, and the evolution trend of COD is close to the trend of the comprehensive pollution index. (2) In terms of Spatial state of water environment, the water quality of Zhuzhao New River and Wanfu River is poor, and Dongyu River water quality is better. Zhuzhao New River and Wanfu River water qualityis often worse than grade V or V, and Dongyu River water quality is mostly maintained in the grade Ⅳ. Through the analysis on the spatial revolution characteristics of water quality and chemical oxygen demand(COD),as a result, water quality is poor in the northern region,and the water quality in the southern region is better in Heze. Although the water quality has changed in recent years, the overall pattern is relatively stable.

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

NASA Technical Reports Server (NTRS)

Koshti, Ajay M. (Inventor)

2017-01-01

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

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

NASA Technical Reports Server (NTRS)

Koshti, Ajay M. (Inventor)

2015-01-01

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

Deviation from the line of least resistance does not exclude genetic constraints: a comment on Berner et al. (2010).

PubMed

Hansen, Thomas F; Voje, Kjetil L

2011-06-01

Berner et al. (2010) found that freshwater adaptation of three-spined sticklebacks had not followed the direction of maximal evolvability. Based on this, they suggested that ancestral variance structure has not appreciably biased adaptive diversification. We reanalyze their data to show that evolution has happened in directions of much larger than average evolvability, and we conclude that their data are consistent with an influence of ancestral variational constraints. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Direct numerical simulations of a reacting turbulent mixing layer by a pseudospectral-spectral element method

NASA Technical Reports Server (NTRS)

Mcmurtry, Patrick A.; Givi, Peyman

1992-01-01

An account is given of the implementation of the spectral-element technique for simulating a chemically reacting, spatially developing turbulent mixing layer. Attention is given to experimental and numerical studies that have investigated the development, evolution, and mixing characteristics of shear flows. A mathematical formulation is presented of the physical configuration of the spatially developing reacting mixing layer, in conjunction with a detailed representation of the spectral-element method's application to the numerical simulation of mixing layers. Results from 2D and 3D calculations of chemically reacting mixing layers are given.

Teaching Evolution & the Nature of Science.

ERIC Educational Resources Information Center

Farber, Paul

2003-01-01

The theory of evolution provides direction in many fields, such as ecology, genetics, and embryology. Examines issues concerning the teaching of the subject in the United States. Presents a case study approach to teach about the nature of science using the theory of evolution. (SOE)

Time evolution of photon-pulse propagation in scattering and absorbing media: The dynamic radiative transfer system

NASA Astrophysics Data System (ADS)

Georgakopoulos, A.; Politopoulos, K.; Georgiou, E.

2018-03-01

A new dynamic-system approach to the problem of radiative transfer inside scattering and absorbing media is presented, directly based on first-hand physical principles. This method, the Dynamic Radiative Transfer System (DRTS), employs a dynamical system formality using a global sparse matrix, which characterizes the physical, optical and geometrical properties of the material-volume of interest. The new system state is generated by the above time-independent matrix, using simple matrix-vector multiplication for each subsequent time step. DRTS is capable of calculating accurately the time evolution of photon propagation in media of complex structure and shape. The flexibility of DRTS allows the integration of time-dependent sources, boundary conditions, different media and several optical phenomena like reflection and refraction in a unified and consistent way. Various examples of DRTS simulation results are presented for ultra-fast light pulse 3-D propagation, demonstrating greatly reduced computational cost and resource requirements compared to other methods.

Preparing tomorrow's behavioral medicine scientists and practitioners: a survey of future directions for education and training.

PubMed

Goldstein, Carly M; Minges, Karl E; Schoffman, Danielle E; Cases, Mallory G

2017-02-01

Behavioral medicine training is due for an overhaul given the rapid evolution of the field, including a tight funding climate, changing job prospects, and new research and industry collaborations. The purpose of the present study was to collect responses from trainee and practicing members of a multidisciplinary professional society about their perceptions of behavioral medicine training and their suggestions for changes to training for future behavioral medicine scientists and practitioners. A total of 162 faculty and 110 students (total n = 272) completed a web-based survey on strengths of their current training programs and ideas for changes. Using a mixed-methods approach, the survey findings are used to highlight seven key areas for improved preparation of the next generation of behavioral medicine scientists and practitioners, which are grant writing, interdisciplinary teamwork, advanced statistics and methods, evolving research program, publishable products from coursework, evolution and use of theory, and non-traditional career paths.

Evolution of genetic architecture under directional selection.

PubMed

Hansen, Thomas F; Alvarez-Castro, José M; Carter, Ashley J R; Hermisson, Joachim; Wagner, Günter P

2006-08-01

We investigate the multilinear epistatic model under mutation-limited directional selection. We confirm previous results that only directional epistasis, in which genes on average reinforce or diminish each other's effects, contribute to the initial evolution of mutational effects. Thus, either canalization or decanalization can occur under directional selection, depending on whether positive or negative epistasis is prevalent. We then focus on the evolution of the epistatic coefficients themselves. In the absence of higher-order epistasis, positive pairwise epistasis will tend to weaken relative to additive effects, while negative pairwise epistasis will tend to become strengthened. Positive third-order epistasis will counteract these effects, while negative third-order epistasis will reinforce them. More generally, gene interactions of all orders have an inherent tendency for negative changes under directional selection, which can only be modified by higher-order directional epistasis. We identify three types of nonadditive quasi-equilibrium architectures that, although not strictly stable, can be maintained for an extended time: (1) nondirectional epistatic architectures; (2) canalized architectures with strong epistasis; and (3) near-additive architectures in which additive effects keep increasing relative to epistasis.

Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model.

PubMed

Xiao, Qingtai; Xu, Jianxin; Wang, Hua

2016-08-16

A new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform, and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target.

Three dimensional modelling of grain boundary interaction and evolution during directional solidification of multi-crystalline silicon

NASA Astrophysics Data System (ADS)

Jain, T.; Lin, H. K.; Lan, C. W.

2018-03-01

The development of grain structures during directional solidification of multi-crystalline silicon (mc-Si) plays a crucial role in the materials quality for silicon solar cells. Three dimensional (3D) modelling of the grain boundary (GB) interaction and evolution based on phase fields by considering anisotropic GB energy and mobility for mc-Si is carried out for the first time to elucidate the process. The energy and mobility of GBs are allowed to depend on misorientation and the GB plane. To examine the correctness of our method, the known the coincident site lattice (CSL) combinations such as (∑ a + ∑ b → ∑ a × b) or (∑ a + ∑ b → ∑ a / b) are verified. We frther discuss how to use the GB normal to characterize a ∑ 3 twin GB into a tilt or a twist one, and show the interaction between tilt and twist ∑ 3 twin GBs. Two experimental scenarios are considered for comparison and the results are in good agreement with the experiments as well as the theoretical predictions.

Quantifying the evolution of flow boiling bubbles by statistical testing and image analysis: toward a general model

PubMed Central

Xiao, Qingtai; Xu, Jianxin; Wang, Hua

2016-01-01

A new index, the estimate of the error variance, which can be used to quantify the evolution of the flow patterns when multiphase components or tracers are difficultly distinguishable, was proposed. The homogeneity degree of the luminance space distribution behind the viewing windows in the direct contact boiling heat transfer process was explored. With image analysis and a linear statistical model, the F-test of the statistical analysis was used to test whether the light was uniform, and a non-linear method was used to determine the direction and position of a fixed source light. The experimental results showed that the inflection point of the new index was approximately equal to the mixing time. The new index has been popularized and applied to a multiphase macro mixing process by top blowing in a stirred tank. Moreover, a general quantifying model was introduced for demonstrating the relationship between the flow patterns of the bubble swarms and heat transfer. The results can be applied to investigate other mixing processes that are very difficult to recognize the target. PMID:27527065

Multi-spacecraft Observations of the Coronal and Interplanetary Evolution of a Solar Eruption Associated with Two Active Regions

NASA Astrophysics Data System (ADS)

Hu, H.; Liu, Y. D.; Wang, R.; Zhao, X.; Zhu, B.; Yang, Z.

2017-12-01

We investigate the coronal and interplanetary evolution of a coronal mass ejection (CME) launched on 2010 September 4 from a source region linking two active regions (ARs), 11101 and 11103, using extreme ultraviolet imaging, magnetogram, white-light, and in situ observations from SDO, STEREO, SOHO, VEX, and Wind. A potential-field source-surface model is employed to examine the configuration of the coronal magnetic field surrounding the source region. The graduated cylindrical shell model and a triangulation method are applied to determine the kinematics of the CME in the corona and interplanetary space. From the remote sensing and in situ observations, we obtain some key results: (1) the CME was deflected in both the eastward and southward directions in the low corona by the magnetic pressure from the two ARs, and possibly interacted with another ejection, which caused that the CME arrived at VEX that was longitudinally distant from the source region; (2) although VEX was closer to the Sun, the observed and derived CME arrival times at VEX are not earlier than those at Wind, which suggests the importance of determining both the frontal shape and propagation direction of the CME in interplanetary space; and (3) the ICME was compressed in the radial direction while the longitudinal transverse size was extended.

Multi-Model approach to reconstruct the Mediterranean Freshwater Evolution

NASA Astrophysics Data System (ADS)

Simon, Dirk; Marzocchi, Alice; Flecker, Rachel; Lunt, Dan; Hilgen, Frits; Meijer, Paul

2016-04-01

Today the Mediterranean Sea is isolated from the global ocean by the Strait of Gibraltar. This restricted nature causes the Mediterranean basin to react more sensitively to climatic and tectonic related phenomena than the global ocean. Not just eustatic sea-level and regional river run-off, but also gateway tectonics and connectivity between sub-basins are leaving an enhanced fingerprint in its geological record. To understand its evolution, it is crucial to understand how these different effects are coupled. The Miocene-Pliocene sedimentary record of the Mediterranean shows alternations in composition and colour and has been astronomically tuned. Around the Miocene-Pliocene Boundary the most extreme changes occur in the Mediterranean Sea. About 6% of the salt in the global ocean deposited in the Mediterranean Region, forming an approximately 2 km thick salt layer, which is still present today. This extreme event is named the Messinian Salinity Crisis (MSC, 5.97-5.33 Ma). The gateway and climate evolution is not well constrained for this time, which makes it difficult to distinguish which of the above mentioned drivers might have triggered the MSC. We, therefore, decided to tackle this problem via a multi-model approach: (1) We calculate the Mediterranean freshwater evolution via 30 atmosphere-ocean-vegetation simulations (using HadCM3L), to which we fitted to a function, using a regression model. This allows us to directly relate the orbital curves to evaporation, precipitation and run off. The resulting freshwater evolution can be directly correlated to other sedimentary and proxy records in the late Miocene. (2) By feeding the new freshwater evolution curve into a box/budget model we can predict the salinity and strontium evolution of the Mediterranean for a certain Atlantic-Mediterranean gateway. (3) By comparing these results to the known salinity thresholds of gypsum and halite saturation of sea water, but also to the late Miocene Mediterranean strontium record, we can infer how the connectivity between global ocean and the Mediterranean must have changed through time in order to cause the MSC. (4) Such a connectivity evolution will give us the basis to understand the interplay between eustatic sea-level and regional tectonic changes in the Gibraltar region. Here we present the detailed method, the results and the applications of this multi-model approach.

Directed evolution of polymerase function by compartmentalized self-replication.

PubMed

Ghadessy, F J; Ong, J L; Holliger, P

2001-04-10

We describe compartmentalized self-replication (CSR), a strategy for the directed evolution of enzymes, especially polymerases. CSR is based on a simple feedback loop consisting of a polymerase that replicates only its own encoding gene. Compartmentalization serves to isolate individual self-replication reactions from each other. In such a system, adaptive gains directly (and proportionally) translate into genetic amplification of the encoding gene. CSR has applications in the evolution of polymerases with novel and useful properties. By using three cycles of CSR, we obtained variants of Taq DNA polymerase with 11-fold higher thermostability than the wild-type enzyme or with a >130-fold increased resistance to the potent inhibitor heparin. Insertion of an extra stage into the CSR cycle before the polymerase reaction allows its application to enzymes other than polymerases. We show that nucleoside diphosphate kinase and Taq polymerase can form such a cooperative CSR cycle based on reciprocal catalysis, whereby nucleoside diphosphate kinase produces the substrates required for the replication of its own gene. We also find that in CSR the polymerase genes themselves evolve toward more efficient replication. Thus, polymerase genes and their encoded polypeptides cooperate to maximize postselection copy number. CSR should prove useful for the directed evolution of enzymes, particularly DNA or RNA polymerases, as well as for the design and study of in vitro self-replicating systems mimicking prebiotic evolution and viral replication.

A high-order time-parallel scheme for solving wave propagation problems via the direct construction of an approximate time-evolution operator

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

Haut, T. S.; Babb, T.; Martinsson, P. G.

2015-06-16

Our manuscript demonstrates a technique for efficiently solving the classical wave equation, the shallow water equations, and, more generally, equations of the form ∂u/∂t=Lu∂u/∂t=Lu, where LL is a skew-Hermitian differential operator. The idea is to explicitly construct an approximation to the time-evolution operator exp(τL)exp(τL) for a relatively large time-step ττ. Recently developed techniques for approximating oscillatory scalar functions by rational functions, and accelerated algorithms for computing functions of discretized differential operators are exploited. Principal advantages of the proposed method include: stability even for large time-steps, the possibility to parallelize in time over many characteristic wavelengths and large speed-ups over existingmore » methods in situations where simulation over long times are required. Numerical examples involving the 2D rotating shallow water equations and the 2D wave equation in an inhomogenous medium are presented, and the method is compared to the 4th order Runge–Kutta (RK4) method and to the use of Chebyshev polynomials. The new method achieved high accuracy over long-time intervals, and with speeds that are orders of magnitude faster than both RK4 and the use of Chebyshev polynomials.« less

Inter-laboratory verification of European pharmacopoeia monograph on derivative spectrophotometry method and its application for chitosan hydrochloride.

PubMed

Marković, Bojan; Ignjatović, Janko; Vujadinović, Mirjana; Savić, Vedrana; Vladimirov, Sote; Karljiković-Rajić, Katarina

2015-01-01

Inter-laboratory verification of European pharmacopoeia (EP) monograph on derivative spectrophotometry (DS) method and its application for chitosan hydrochloride was carried out on two generation of instruments (earlier GBC Cintra 20 and current technology TS Evolution 300). Instruments operate with different versions of Savitzky-Golay algorithm and modes of generating digital derivative spectra. For resolution power parameter, defined as the amplitude ratio A/B in DS method EP monograph, comparable results were obtained only with algorithm's parameters smoothing points (SP) 7 and the 2nd degree polynomial and those provided corresponding data with other two modes on TS Evolution 300 Medium digital indirect and Medium digital direct. Using quoted algorithm's parameters, the differences in percentages between the amplitude ratio A/B averages, were within accepted criteria (±3%) for assay of drug product for method transfer. The deviation of 1.76% for the degree of deacetylation assessment of chitosan hydrochloride, determined on two instruments, (amplitude (1)D202; the 2nd degree polynomial and SP 9 in Savitzky-Golay algorithm), was acceptable, since it was within allowed criteria (±2%) for assay deviation of drug substance, for method transfer in pharmaceutical analyses. Copyright © 2015 Elsevier B.V. All rights reserved.

Evolutionary divergence of mitochondrial genomes in two Tetranychus species distributed across different climates.

PubMed

Sun, J-T; Jin, P-Y; Hoffmann, A A; Duan, X-Z; Dai, J; Hu, G; Xue, X-F; Hong, X-Y

2018-05-24

There is increasing evidence that mitochondrial genomes (mitogenomes) can be under selection, whereas the selective regimes shaping mitogenome evolution remain largely unclear. To test for mitochondrial genome evolution in relation to the climate adaptation, we explored mtDNA variation in two spider mite (Tetranychus) species, which distribute across different climates. We sequenced 26 complete mitogenomes of T. truncatus which occurs in both warm and cold regions, and 9 complete mitogenomes of T. pueraricola which is only restricted in warm regions. Patterns of evolution in the two species mitogenomes were compared through a series of d N /d S methods and physicochemical profiles of amino acid replacements. We found that (1) the mitogenomes of both species were under widespread purifying selection. (2) Elevated directional adaptive selection was observed in the T. truncatus mitogenome, perhaps linked to the cold climates adaptation of T. truncatus. (3) The strength of selection varied across genes, and diversifying positive selection detected on ND4 and ATP6 pointed to their crucial roles during adaptation to different climatic conditions. This study gained insight into the mitogenome evolution in relation to the climate adaptation. This article is protected by copyright. All rights reserved. © 2018 The Royal Entomological Society.

A general strategy for the evolution of bond-forming enzymes using yeast display

PubMed Central

Chen, Irwin; Dorr, Brent M.; Liu, David R.

2011-01-01

The ability to routinely generate efficient protein catalysts of bond-forming reactions chosen by researchers, rather than nature, is a long-standing goal of the molecular life sciences. Here, we describe a directed evolution strategy for enzymes that catalyze, in principle, any bond-forming reaction. The system integrates yeast display, enzyme-mediated bioconjugation, and fluorescence-activated cell sorting to isolate cells expressing proteins that catalyze the coupling of two substrates chosen by the researcher. We validated the system using model screens for Staphylococcus aureus sortase A–catalyzed transpeptidation activity, resulting in enrichment factors of 6,000-fold after a single round of screening. We applied the system to evolve sortase A for improved catalytic activity. After eight rounds of screening, we isolated variants of sortase A with up to a 140-fold increase in LPETG-coupling activity compared with the starting wild-type enzyme. An evolved sortase variant enabled much more efficient labeling of LPETG-tagged human CD154 expressed on the surface of HeLa cells compared with wild-type sortase. Because the method developed here does not rely on any particular screenable or selectable property of the substrates or product, it represents a powerful alternative to existing enzyme evolution methods. PMID:21697512

Craniofacial form and function in Metriorhynchidae (Crocodylomorpha: Thalattosuchia): modelling phenotypic evolution with maximum-likelihood methods.

PubMed

Young, Mark T; Bell, Mark A; Brusatte, Stephen L

2011-12-23

Metriorhynchid crocodylomorphs were the only group of archosaurs to fully adapt to a pelagic lifestyle. During the Jurassic and Early Cretaceous, this group diversified into a variety of ecological and morphological types, from large super-predators with a broad short snout and serrated teeth to specialized piscivores/teuthophages with an elongate tubular snout and uncarinated teeth. Here, we use an integrated repertoire of geometric morphometric (form), biomechanical finite-element analysis (FEA; function) and phylogenetic data to examine the nature of craniofacial evolution in this clade. FEA stress values significantly correlate with morphometric values representing skull length and breadth, indicating that form and function are associated. Maximum-likelihood methods, which assess which of several models of evolution best explain the distribution of form and function data on a phylogenetic tree, show that the two major metriorhynchid subclades underwent different evolutionary modes. In geosaurines, both form and function are best explained as evolving under 'random' Brownian motion, whereas in metriorhynchines, the form metrics are best explained as evolving under stasis and the function metric as undergoing a directional change (towards most efficient low-stress piscivory). This suggests that the two subclades were under different selection pressures, and that metriorhynchines with similar skull shape were driven to become functionally divergent.

Conflicts of interest and the evolution of decision sharing

PubMed Central

Conradt, Larissa; Roper, Timothy J.

2008-01-01

Social animals regularly face consensus decisions whereby they choose, collectively, between mutually exclusive actions. Such decisions often involve conflicts of interest between group members with respect to preferred action. Conflicts could, in principle, be resolved, either by sharing decisions between members (‘shared decisions’) or by one ‘dominant’ member making decisions on behalf of the whole group (‘unshared decisions’). Both, shared and unshared decisions, have been observed. However, it is unclear as to what favours the evolution of either decision type. Here, after a brief literature review, we present a novel method, involving a combination of self-organizing system and game theory modelling, of investigating the evolution of shared and unshared decisions. We apply the method to decisions on movement direction. We find that both, shared and unshared, decisions can evolve without individuals having a global overview of the group's behaviour or any knowledge about other members' preferences or intentions. Selection favours unshared over shared decisions when conflicts are high relative to grouping benefits, and vice versa. These results differ from those of group decision models relating to activity timings. We attribute this to fundamental differences between collective decisions about modalities that are disjunct (here, space) or continuous (here, time) with respect to costs/benefits. PMID:19073479

Models of Protocellular Structure, Function and Evolution

NASA Technical Reports Server (NTRS)

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

2001-01-01

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

The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex.

PubMed

Merker, Matthias; Kohl, Thomas A; Niemann, Stefan; Supply, Philip

2017-01-01

Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.

Antagonistic responses to natural and sexual selection and the sex-specific evolution of cuticular hydrocarbons in Drosophila simulans.

PubMed

Sharma, Manmohan D; Hunt, John; Hosken, David J

2012-03-01

Natural and sexual selection are classically thought to oppose one another, and although there is evidence for this, direct experimental demonstrations of this antagonism are largely lacking. Here, we assessed the effects of sexual and natural selection on the evolution of cuticular hydrocarbons (CHCs), a character subject to both modes of selection, in Drosophila simulans. Natural selection and sexual selection were manipulated in a fully factorial design, and after 27 generations of experimental evolution, the responses of male and female CHCs were assessed. The effects of natural and sexual selection differed greatly across the sexes. The responses of female CHCs were generally small, but CHCs evolved predominantly in the direction of natural selection. For males, profiles evolved via sexual and natural selection, as well as through the interaction between the two, with some male CHC components only evolving in the direction of natural selection when sexual selection was relaxed. These results indicate sex-specific responses to selection, and that sexual and natural selection act antagonistically for at least some combinations of CHCs. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Biophysical models of protein evolution: Understanding the patterns of evolutionary sequence divergence

PubMed Central

Echave, Julian; Wilke, Claus O.

2018-01-01

For decades, rates of protein evolution have been interpreted in terms of the vague concept of “functional importance”. Slowly evolving proteins or sites within proteins were assumed to be more functionally important and thus subject to stronger selection pressure. More recently, biophysical models of protein evolution, which combine evolutionary theory with protein biophysics, have completely revolutionized our view of the forces that shape sequence divergence. Slowly evolving proteins have been found to evolve slowly because of selection against toxic misfolding and misinteractions, linking their rate of evolution primarily to their abundance. Similarly, most slowly evolving sites in proteins are not directly involved in function, but mutating them has large impacts on protein structure and stability. Here, we review the studies of the emergent field of biophysical protein evolution that have shaped our current understanding of sequence divergence patterns. We also propose future research directions to develop this nascent field. PMID:28301766

Orbit-based analysis of nonlinear energetic ion dynamics in tokamaks. II. Mechanisms for rapid chirping and convective amplification

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

Bierwage, Andreas; Shinohara, Kouji

2016-04-15

The nonlinear interactions between shear Alfvén modes and tangentially injected beam ions in the 150–400 keV range are studied numerically in realistic geometry for a JT-60U tokamak scenario. In Paper I, which was reported in the companion paper, the recently developed orbit-based resonance analysis method was used to track the resonant frequency of fast ions during their nonlinear evolution subject to large magnetic and electric drifts. Here, that method is applied to map the wave-particle power transfer from the canonical guiding center phase space into the frequency-radius plane, where it can be directly compared with the evolution of the fluctuation spectramore » of fast-ion-driven modes. Using this technique, we study the nonlinear dynamics of strongly driven shear Alfvén modes with low toroidal mode numbers n = 1 and n = 3. In the n = 3 case, both chirping and convective amplification can be attributed to the mode following the resonant frequency of the radially displaced particles, i.e., the usual one-dimensional phase locking process. In the n = 1 case, a new chirping mechanism is found, which involves multiple dimensions, namely, wave-particle trapping in the radial direction and phase mixing across velocity coordinates.« less

GAMA/H-ATLAS: a meta-analysis of SFR indicators - comprehensive measures of the SFR-M* relation and cosmic star formation history at z < 0.4

NASA Astrophysics Data System (ADS)

Davies, L. J. M.; Driver, S. P.; Robotham, A. S. G.; Grootes, M. W.; Popescu, C. C.; Tuffs, R. J.; Hopkins, A.; Alpaslan, M.; Andrews, S. K.; Bland-Hawthorn, J.; Bremer, M. N.; Brough, S.; Brown, M. J. I.; Cluver, M. E.; Croom, S.; da Cunha, E.; Dunne, L.; Lara-López, M. A.; Liske, J.; Loveday, J.; Moffett, A. J.; Owers, M.; Phillipps, S.; Sansom, A. E.; Taylor, E. N.; Michalowski, M. J.; Ibar, E.; Smith, M.; Bourne, N.

2016-09-01

We present a meta-analysis of star formation rate (SFR) indicators in the Galaxy And Mass Assembly (GAMA) survey, producing 12 different SFR metrics and determining the SFR-M* relation for each. We compare and contrast published methods to extract the SFR from each indicator, using a well-defined local sample of morphologically selected spiral galaxies, which excludes sources which potentially have large recent changes to their SFR. The different methods are found to yield SFR-M* relations with inconsistent slopes and normalizations, suggesting differences between calibration methods. The recovered SFR-M* relations also have a large range in scatter which, as SFRs of the targets may be considered constant over the different time-scales, suggests differences in the accuracy by which methods correct for attenuation in individual targets. We then recalibrate all SFR indicators to provide new, robust and consistent luminosity-to-SFR calibrations, finding that the most consistent slopes and normalizations of the SFR-M* relations are obtained when recalibrated using the radiation transfer method of Popescu et al. These new calibrations can be used to directly compare SFRs across different observations, epochs and galaxy populations. We then apply our calibrations to the GAMA II equatorial data set and explore the evolution of star formation in the local Universe. We determine the evolution of the normalization to the SFR-M* relation from 0 < z < 0.35 - finding consistent trends with previous estimates at 0.3 < z < 1.2. We then provide the definitive z < 0.35 cosmic star formation history, SFR-M* relation and its evolution over the last 3 billion years.

Evolution Acceptance and Epistemological Beliefs of College Biology Students

ERIC Educational Resources Information Center

Borgerding, Lisa A.; Deniz, Hasan; Anderson, Elizabeth Shevock

2017-01-01

Evolutionary theory is central to biology, and scientifically accurate evolution instruction is promoted within national and state standards documents. Previous literature has identified students' epistemological beliefs as potential predictors of evolution acceptance. The present work seeks to explore more directly how student views of evolution…

Method of generating ploynucleotides encoding enhanced folding variants

DOEpatents

Bradbury, Andrew M.; Kiss, Csaba; Waldo, Geoffrey S.

2017-05-02

The invention provides directed evolution methods for improving the folding, solubility and stability (including thermostability) characteristics of polypeptides. In one aspect, the invention provides a method for generating folding and stability-enhanced variants of proteins, including but not limited to fluorescent proteins, chromophoric proteins and enzymes. In another aspect, the invention provides methods for generating thermostable variants of a target protein or polypeptide via an internal destabilization baiting strategy. Internally destabilization a protein of interest is achieved by inserting a heterologous, folding-destabilizing sequence (folding interference domain) within DNA encoding the protein of interest, evolving the protein sequences adjacent to the heterologous insertion to overcome the destabilization (using any number of mutagenesis methods), thereby creating a library of variants. The variants in the library are expressed, and those with enhanced folding characteristics selected.

NEXT GENERATION OF TELESCOPES OR DYNAMICS REQUIRED TO DETERMINE IF EXO-MOONS HAVE PROGRADE OR RETROGRADE ORBITS

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

Lewis, Karen M.; Fujii, Yuka

2014-08-20

We survey the methods proposed in the literature for detecting moons of extrasolar planets in terms of their ability to distinguish between prograde and retrograde moon orbits, an important tracer of the moon formation channel. We find that most moon detection methods, in particular, sensitive methods for detecting moons of transiting planets, cannot observationally distinguishing prograde and retrograde moon orbits. The prograde and retrograde cases can only be distinguished where the dynamical evolution of the orbit due to, e.g., three body effects is detectable, where one of the two cases is dynamically unstable, or where new observational facilities, which canmore » implement a technique capable of differentiating the two cases, come online. In particular, directly imaged planets are promising targets because repeated spectral and photometric measurements, which are required to determine moon orbit direction, could also be conducted with the primary interest of characterizing the planet itself.« less

Evolution of complex fruiting-body morphologies in homobasidiomycetes.

PubMed Central

Hibbett, David S; Binder, Manfred

2002-01-01

The fruiting bodies of homobasidiomycetes include some of the most complex forms that have evolved in the fungi, such as gilled mushrooms, bracket fungi and puffballs ('pileate-erect') forms. Homobasidiomycetes also include relatively simple crust-like 'resupinate' forms, however, which account for ca. 13-15% of the described species in the group. Resupinate homobasidiomycetes have been interpreted either as a paraphyletic grade of plesiomorphic forms or a polyphyletic assemblage of reduced forms. The former view suggests that morphological evolution in homobasidiomycetes has been marked by independent elaboration in many clades, whereas the latter view suggests that parallel simplification has been a common mode of evolution. To infer patterns of morphological evolution in homobasidiomycetes, we constructed phylogenetic trees from a dataset of 481 species and performed ancestral state reconstruction (ASR) using parsimony and maximum likelihood (ML) methods. ASR with both parsimony and ML implies that the ancestor of the homobasidiomycetes was resupinate, and that there have been multiple gains and losses of complex forms in the homobasidiomycetes. We also used ML to address whether there is an asymmetry in the rate of transformations between simple and complex forms. Models of morphological evolution inferred with ML indicate that the rate of transformations from simple to complex forms is about three to six times greater than the rate of transformations in the reverse direction. A null model of morphological evolution, in which there is no asymmetry in transformation rates, was rejected. These results suggest that there is a 'driven' trend towards the evolution of complex forms in homobasidiomycetes. PMID:12396494

Nonperturbative-transverse-momentum effects and evolution in dihadron and direct photon-hadron angular correlations in p +p collisions at √{s } =510 GeV

NASA Astrophysics Data System (ADS)

Adare, A.; Aidala, C.; Ajitanand, N. N.; Akiba, Y.; Akimoto, R.; Alexander, J.; Alfred, M.; Andrieux, V.; Aoki, K.; Apadula, N.; Aramaki, Y.; Asano, H.; Atomssa, E. T.; Awes, T. C.; Ayuso, C.; Azmoun, B.; Babintsev, V.; Bai, M.; Bai, X.; Bandara, N. S.; Bannier, B.; Barish, K. N.; Bathe, S.; Baublis, V.; Baumann, C.; Baumgart, S.; Bazilevsky, A.; Beaumier, M.; Beckman, S.; Belmont, R.; Berdnikov, A.; Berdnikov, Y.; Black, D.; Blau, D. S.; Boer, M.; Bok, J. S.; Boyle, K.; Brooks, M. L.; Bryslawskyj, J.; Buesching, H.; Bumazhnov, V.; Butler, C.; Butsyk, S.; Campbell, S.; Canoa Roman, V.; Cervantes, R.; Chen, C.-H.; Chi, C. Y.; Chiu, M.; Choi, I. J.; Choi, J. B.; Choi, S.; Christiansen, P.; Chujo, T.; Cianciolo, V.; Citron, Z.; Cole, B. A.; Connors, M.; Cronin, N.; Crossette, N.; Csanád, M.; Csörgő, T.; Danley, T. W.; Datta, A.; Daugherity, M. S.; David, G.; Deblasio, K.; Dehmelt, K.; Denisov, A.; Deshpande, A.; Desmond, E. J.; Ding, L.; Dion, A.; Dixit, D.; Do, J. H.; D'Orazio, L.; Drapier, O.; Drees, A.; Drees, K. A.; Dumancic, M.; Durham, J. M.; Durum, A.; Elder, T.; Engelmore, T.; Enokizono, A.; En'yo, H.; Esumi, S.; Eyser, K. O.; Fadem, B.; Fan, W.; Feege, N.; Fields, D. E.; Finger, M.; Finger, M.; Fleuret, F.; Fokin, S. L.; Frantz, J. E.; Franz, A.; Frawley, A. D.; Fukao, Y.; Fukuda, Y.; Fusayasu, T.; Gainey, K.; Gal, C.; Gallus, P.; Garg, P.; Garishvili, A.; Garishvili, I.; Ge, H.; Giordano, F.; Glenn, A.; Gong, X.; Gonin, M.; Goto, Y.; Granier de Cassagnac, R.; Grau, N.; Greene, S. V.; Grosse Perdekamp, M.; Gu, Y.; Gunji, T.; Guragain, H.; Hachiya, T.; Haggerty, J. S.; Hahn, K. I.; Hamagaki, H.; Hamilton, H. F.; Han, S. Y.; Hanks, J.; Hasegawa, S.; Haseler, T. O. S.; Hashimoto, K.; Hayano, R.; He, X.; Hemmick, T. K.; Hester, T.; Hill, J. C.; Hill, K.; Hollis, R. S.; Homma, K.; Hong, B.; Hoshino, T.; Hotvedt, N.; Huang, J.; Huang, S.; Ichihara, T.; Ikeda, Y.; Imai, K.; Imazu, Y.; Imrek, J.; Inaba, M.; Iordanova, A.; Isenhower, D.; Isinhue, A.; Ito, Y.; Ivanishchev, D.; Jacak, B. V.; Jeon, S. J.; Jezghani, M.; Ji, Z.; Jia, J.; Jiang, X.; Johnson, B. M.; Joo, E.; Joo, K. S.; Jorjadze, V.; Jouan, D.; Jumper, D. S.; Kamin, J.; Kanda, S.; Kang, B. H.; Kang, J. H.; Kang, J. S.; Kapukchyan, D.; Kapustinsky, J.; Karthas, S.; Kawall, D.; Kazantsev, A. V.; Key, J. A.; Khachatryan, V.; Khandai, P. K.; Khanzadeev, A.; Kihara, K.; Kijima, K. M.; Kim, C.; Kim, D. H.; Kim, D. J.; Kim, E.-J.; Kim, H.-J.; Kim, M. H.; Kim, M.; Kim, Y.-J.; Kim, Y. K.; Kincses, D.; Kistenev, E.; Klatsky, J.; Kleinjan, D.; Kline, P.; Koblesky, T.; Kofarago, M.; Komkov, B.; Koster, J.; Kotchetkov, D.; Kotov, D.; Krizek, F.; Kudo, S.; Kurita, K.; Kurosawa, M.; Kwon, Y.; Lacey, R.; Lai, Y. S.; Lajoie, J. G.; Lallow, E. O.; Lebedev, A.; Lee, D. M.; Lee, G. H.; Lee, J.; Lee, K. B.; Lee, K. S.; Lee, S.; Lee, S. H.; Leitch, M. J.; Leitgab, M.; Leung, Y. H.; Lewis, B.; Lewis, N. A.; Li, X.; Li, X.; Lim, S. H.; Liu, L. D.; Liu, M. X.; Loggins, V.-R.; Loggins, V.-R.; Lovasz, K.; Lynch, D.; Maguire, C. F.; Majoros, T.; Makdisi, Y. I.; Makek, M.; Malaev, M.; Manion, A.; Manko, V. I.; Mannel, E.; Masuda, H.; McCumber, M.; McGaughey, P. L.; McGlinchey, D.; McKinney, C.; Meles, A.; Mendoza, M.; Meredith, B.; Miake, Y.; Mibe, T.; Mignerey, A. C.; Mihalik, D. E.; Miller, A. J.; Milov, A.; Mishra, D. K.; Mitchell, J. T.; Mitsuka, G.; Miyasaka, S.; Mizuno, S.; Mohanty, A. K.; Mohapatra, S.; Montuenga, P.; Moon, T.; Morrison, D. P.; Morrow, S. I. M.; Moskowitz, M.; Moukhanova, T. V.; Murakami, T.; Murata, J.; Mwai, A.; Nagae, T.; Nagai, K.; Nagamiya, S.; Nagashima, K.; Nagashima, T.; Nagle, J. L.; Nagy, M. I.; Nakagawa, I.; Nakagomi, H.; Nakamiya, Y.; Nakamura, K. R.; Nakamura, T.; Nakano, K.; Nattrass, C.; Netrakanti, P. K.; Nihashi, M.; Niida, T.; Nouicer, R.; Novák, T.; Novitzky, N.; Novotny, R.; Nyanin, A. S.; O'Brien, E.; Ogilvie, C. A.; Oide, H.; Okada, K.; Orjuela Koop, J. D.; Osborn, J. D.; Oskarsson, A.; Ottino, G. J.; Ozawa, K.; Pak, R.; Pantuev, V.; Papavassiliou, V.; Park, I. H.; Park, J. S.; Park, S.; Park, S. K.; Pate, S. F.; Patel, L.; Patel, M.; Peng, J.-C.; Peng, W.; Perepelitsa, D. V.; Perera, G. D. N.; Peressounko, D. Yu.; Perezlara, C. E.; Perry, J.; Petti, R.; Phipps, M.; Pinkenburg, C.; Pinson, R.; Pisani, R. P.; Pun, A.; Purschke, M. L.; Qu, H.; Rak, J.; Ravinovich, I.; Read, K. F.; Reynolds, D.; Riabov, V.; Riabov, Y.; Richardson, E.; Richford, D.; Rinn, T.; Riveli, N.; Roach, D.; Rolnick, S. D.; Rosati, M.; Rowan, Z.; Rubin, J. G.; Runchey, J.; Ryu, M. S.; Safonov, A. S.; Sahlmueller, B.; Saito, N.; Sakaguchi, T.; Sako, H.; Samsonov, V.; Sarsour, M.; Sato, K.; Sato, S.; Sawada, S.; Schaefer, B.; Schmoll, B. K.; Schmoll, B. K.; Sedgwick, K.; Seele, J.; Seidl, R.; Sekiguchi, Y.; Sen, A.; Seto, R.; Sett, P.; Sexton, A.; Sharma, D.; Shaver, A.; Shein, I.; Shibata, T.-A.; Shigaki, K.; Shimomura, M.; Shioya, T.; Shoji, K.; Shukla, P.; Sickles, A.; Silva, C. L.; Silvermyr, D.; Singh, B. K.; Singh, C. P.; Singh, V.; Skolnik, M.; Slunečka, M.; Smith, K. L.; Snowball, M.; Solano, S.; Soltz, R. A.; Sondheim, W. E.; Sorensen, S. P.; Sourikova, I. V.; Stankus, P. W.; Steinberg, P.; Stenlund, E.; Stepanov, M.; Ster, A.; Stoll, S. P.; Stone, M. R.; Sugitate, T.; Sukhanov, A.; Sumita, T.; Sun, J.; Syed, S.; Sziklai, J.; Takahara, A.; Takeda, A.; Taketani, A.; Tanaka, Y.; Tanida, K.; Tannenbaum, M. J.; Tarafdar, S.; Taranenko, A.; Tarnai, G.; Tennant, E.; Tieulent, R.; Timilsina, A.; Todoroki, T.; Tomášek, M.; Torii, H.; Towell, C. L.; Towell, M.; Towell, R.; Towell, R. S.; Tserruya, I.; Ueda, Y.; Ujvari, B.; van Hecke, H. W.; Vargyas, M.; Vazquez-Carson, S.; Vazquez-Zambrano, E.; Veicht, A.; Velkovska, J.; Vértesi, R.; Virius, M.; Vrba, V.; Vukman, N.; Vznuzdaev, E.; Wang, X. R.; Wang, Z.; Watanabe, D.; Watanabe, K.; Watanabe, Y.; Watanabe, Y. S.; Wei, F.; Whitaker, S.; Wolin, S.; Wong, C. P.; Woody, C. L.; Wysocki, M.; Xia, B.; Xu, C.; Xu, Q.; Xue, L.; Yalcin, S.; Yamaguchi, Y. L.; Yamamoto, H.; Yanovich, A.; Yin, P.; Yokkaichi, S.; Yoo, J. H.; Yoon, I.; You, Z.; Younus, I.; Yu, H.; Yushmanov, I. E.; Zajc, W. A.; Zelenski, A.; Zharko, S.; Zhou, S.; Zou, L.; Phenix Collaboration

2017-04-01

Dihadron and isolated direct photon-hadron angular correlations are measured in p +p collisions at √{s }=510 GeV . Correlations of charged hadrons of 0.7

Macroscopic dielectric function within time-dependent density functional theory—Real time evolution versus the Casida approach

NASA Astrophysics Data System (ADS)

Sander, Tobias; Kresse, Georg

2017-02-01

Linear optical properties can be calculated by solving the time-dependent density functional theory equations. Linearization of the equation of motion around the ground state orbitals results in the so-called Casida equation, which is formally very similar to the Bethe-Salpeter equation. Alternatively one can determine the spectral functions by applying an infinitely short electric field in time and then following the evolution of the electron orbitals and the evolution of the dipole moments. The long wavelength response function is then given by the Fourier transformation of the evolution of the dipole moments in time. In this work, we compare the results and performance of these two approaches for the projector augmented wave method. To allow for large time steps and still rely on a simple difference scheme to solve the differential equation, we correct for the errors in the frequency domain, using a simple analytic equation. In general, we find that both approaches yield virtually indistinguishable results. For standard density functionals, the time evolution approach is, with respect to the computational performance, clearly superior compared to the solution of the Casida equation. However, for functionals including nonlocal exchange, the direct solution of the Casida equation is usually much more efficient, even though it scales less beneficial with the system size. We relate this to the large computational prefactors in evaluating the nonlocal exchange, which renders the time evolution algorithm fairly inefficient.

Simulated aging of lubricant oils by chemometric treatment of infrared spectra: potential antioxidant properties of sulfur structures.

PubMed

Amat, Sandrine; Braham, Zeineb; Le Dréau, Yveline; Kister, Jacky; Dupuy, Nathalie

2013-03-30

Lubricant oils are complex mixtures of base oils and additives. The evolution of their performance over time strongly depends on its resistance to thermal oxidation. Sulfur compounds revealed interesting antioxidant properties. This study presents a method to evaluate the lubricant oil oxidation. Two samples, a synthetic and a paraffinic base oils, were tested pure and supplemented with seven different sulfur compounds. An aging cell adapted to a Fourier Transform InfraRed (FT-IR) spectrometer allows the continuous and direct analysis of the oxidative aging of base oils. Two approaches were applied to study the oxidation/anti-oxidation phenomena. The first one leads to define a new oxidative spectroscopic index based on a reduced spectral range where the modifications have been noticed (from 3050 to 2750 cm(-1)). The second method is based on chemometric treatments of whole spectra (from 4000 to 400 cm(-1)) to extract underlying information. A SIMPLe-to-use Interactive Self Modeling Analysis (SIMPLISMA) method has been used to identify more precisely the chemical species produced or degraded during the thermal treatment and to follow their evolution. Pure spectra of different species present in oil were obtained without prior information of their existence. The interest of this tool is to supply relative quantitative information reflecting evolution of the relative abundance of the different products over thermal aging. Results obtained by these two ways have been compared to estimate their concordance. Copyright © 2013 Elsevier B.V. All rights reserved.

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.

[Improvement of thermostability of beta-1,3-1,4-glucanase from Bacillus amyloliquefaciens BS5582 through in vitro evolution].

PubMed

Qin, Jiufu; Gao, Weiwei; Li, Qi; Li, Yongxian; Zheng, Feiyun; Liu, Chunfeng; Gu, Guoxian

2010-09-01

In vitro evolution methods are often used to modify protein with improved characteristics. We developed a directed evolution protocol to enhance the thermostability of the beta-1,3-1,4-glucanase. The thermostability of the enzyme was significantly improved after two rounds of directed evolution. Three variants with higher thermostability were obtained. The mutant enzymes were further analyzed by their melting temperature, halftime and kinetic parameters. Comparing to intact enzyme, the T50 of mutant enzymes 2-JF-01, 2-JF-02 and 2-JF-03 were increased by 2.2 degrees C, 5.5 degrees C and 3.5 degrees C, respectively, the halftime (t1/2, 60 degrees C) of mutant enzymes 2-JF-01, 2-JF-02 and 2-JF-03 were shortened by 4,13 and 17 min, respectively, the V(max) of mutant enzymes were decreased by 8.3%, 2.6% and 10.6%, respectively, while K(m) of mutant enzymes were nearly unchanged. Sequence analysis revealed seven single amino acid mutant happened among three mutant enzymes, such as 2-JF-01 (N36S, G213R), 2-JF-02 (C86R, S115I, N150G) and 2-JF-03 (E156V, K105R). Homology-modeling showed that five of seven substituted amino acids were located on the surface of or in hole of protein. 42.8% of substituted amino acids were arginine, which indicated that arginine may play a role in the improvement of the thermostability of the beta-1,3-1,4-glucanase.This study provide some intresting results of the structural basis of the thermostability of beta-1,3-1,4-glucanase,and provide some new point of view in modifying enzyme for future industrial use.

Defining a relationship between incident wave parameters and morphologic evolution of shoals on ebb tidal deltas using long term X-band radar observation from RIOS

NASA Astrophysics Data System (ADS)

Humberston, J. L.; McNinch, J.; Lippmann, T. C.

2016-12-01

The morphology of tidal inlet ebb-shoals varies dynamically over time, particularly in response to large wave events. Understanding which wave qualities most influence shoals' evolution would support advancements in sediment bypassing models as well as targeted maintenance dredging for hydrographic purposes. Unfortunately, shallow and rapidly changing bathymetry, turbid waters and ambiguous wave speeds resulting from multiple shoaling and de-shoaling areas limits many traditional surveying techniques from obtaining the spatial and temporal resolution necessary to effectively characterize shoal development. The Radar Inlet Observing System (RIOS) is a uniquely designed mobile X-band radar system that can be deployed to inlet environments and, using roof-mounted solar panels and an automatically triggered highly efficient diesel generator, run automated hourly collections and wirelessly stream data for up to several months at a time in nearly all weather and water conditions. During 2015 and early 2016, RIOS was deployed to St. Augustine Inlet, FL., New River Inlet, N.C., and Oregon Inlet, N.C. for periods of one to six months to allow for measureable shoal evolution. During deployments, ten minute collections (at 1 Hz) were conducted every hour and the data gridded to a 5m alongshore/cross-shore grid. Raw intensity returns were time-averaged and analyzed to define three metrics of shoal evolution: movement direction, movement velocity and inferred bathymetry. For each location and time period, wave frequencies, wave directions and significant wave heights were collected from the nearest wave-buoy. Time lapse videos of shoal positions were inspected and used in concert with cross-correlations values from each pair of shoal and wave parameters to determine the incident wave qualities most strongly relating to shoal evolution. Preliminary results suggest wave height, more than frequency, controls shoal movement. Wave direction and size collaboratively appear to direct the shoal's alongshore movement direction as well as general trends of morphologic evolution.

Identification of the critical residues responsible for differential reactivation of the triosephosphate isomerases of two trypanosomes

PubMed Central

Rodríguez-Bolaños, Monica; Cabrera, Nallely

2016-01-01

The reactivation of triosephosphate isomerase (TIM) from unfolded monomers induced by guanidine hydrochloride involves different amino acids of its sequence in different stages of protein refolding. We describe a systematic mutagenesis method to find critical residues for certain physico-chemical properties of a protein. The two similar TIMs of Trypanosoma brucei and Trypanosoma cruzi have different reactivation velocities and efficiencies. We used a small number of chimeric enzymes, additive mutants and planned site-directed mutants to produce an enzyme from T. brucei with 13 mutations in its sequence, which reactivates fast and efficiently like wild-type (WT) TIM from T. cruzi, and another enzyme from T. cruzi, with 13 slightly altered mutations, which reactivated slowly and inefficiently like the WT TIM of T. brucei. Our method is a shorter alternative to random mutagenesis, saturation mutagenesis or directed evolution to find multiple amino acids critical for certain properties of proteins. PMID:27733588

On the application of subcell resolution to conservation laws with stiff source terms

NASA Technical Reports Server (NTRS)

Chang, Shih-Hung

1989-01-01

LeVeque and Yee recently investigated a one-dimensional scalar conservation law with stiff source terms modeling the reacting flow problems and discovered that for the very stiff case most of the current finite difference methods developed for non-reacting flows would produce wrong solutions when there is a propagating discontinuity. A numerical scheme, essentially nonoscillatory/subcell resolution - characteristic direction (ENO/SRCD), is proposed for solving conservation laws with stiff source terms. This scheme is a modification of Harten's ENO scheme with subcell resolution, ENO/SR. The locations of the discontinuities and the characteristic directions are essential in the design. Strang's time-splitting method is used and time evolutions are done by advancing along the characteristics. Numerical experiment using this scheme shows excellent results on the model problem of LeVeque and Yee. Comparisons of the results of ENO, ENO/SR, and ENO/SRCD are also presented.

Phase and amplitude analysis in time-frequency space--application to voluntary finger movement.

PubMed

Ginter, J; Blinowska, K J; Kamiński, M; Durka, P J

2001-09-30

Two methods operating in time-frequency space were applied to analysis of EEG activity accompanying voluntary finger movements. The first one, based on matching pursuit approach provided high-resolution distributions of power in time-frequency space. The phenomena of event related desynchronization (ERD) and synchronization (ERS) were investigated without the need of band-pass filtering. Time evolution of mu- and beta-components was observed in a detailed way. The second method was based on a multichannel autoregressive model (MVAR) adapted for investigation of short-time changes in EEG signal. The direction and spectral content of the EEG activity propagation was estimated by means of short-time directed transfer function (SDTF). The evidence of 'cross-talk' between different areas of motor and sensory cortex was found. The earlier known phenomena, connected with voluntary movements, were confirmed and a new evidence concerning focal ERD/surround ERS and beta activity post-movement synchronization was found.

Drift-wave turbulence and zonal flow generation.

PubMed

Balescu, R

2003-10-01

Drift-wave turbulence in a plasma is analyzed on the basis of the wave Liouville equation, describing the evolution of the distribution function of wave packets (quasiparticles) characterized by position x and wave vector k. A closed kinetic equation is derived for the ensemble-averaged part of this function by the methods of nonequilibrium statistical mechanics. It has the form of a non-Markovian advection-diffusion equation describing coupled diffusion processes in x and k spaces. General forms of the diffusion coefficients are obtained in terms of Lagrangian velocity correlations. The latter are calculated in the decorrelation trajectory approximation, a method recently developed for an accurate measure of the important trapping phenomena of particles in the rugged electrostatic potential. The analysis of individual decorrelation trajectories provides an illustration of the fragmentation of drift-wave structures in the radial direction and the generation of long-wavelength structures in the poloidal direction that are identified as zonal flows.

Complex-envelope alternating-direction-implicit FDTD method for simulating active photonic devices with semiconductor/solid-state media.

PubMed

Singh, Gurpreet; Ravi, Koustuban; Wang, Qian; Ho, Seng-Tiong

2012-06-15

A complex-envelope (CE) alternating-direction-implicit (ADI) finite-difference time-domain (FDTD) approach to treat light-matter interaction self-consistently with electromagnetic field evolution for efficient simulations of active photonic devices is presented for the first time (to our best knowledge). The active medium (AM) is modeled using an efficient multilevel system of carrier rate equations to yield the correct carrier distributions, suitable for modeling semiconductor/solid-state media accurately. To include the AM in the CE-ADI-FDTD method, a first-order differential system involving CE fields in the AM is first set up. The system matrix that includes AM parameters is then split into two time-dependent submatrices that are then used in an efficient ADI splitting formula. The proposed CE-ADI-FDTD approach with AM takes 22% of the time as the approach of the corresponding explicit FDTD, as validated by semiconductor microdisk laser simulations.

Lazy Updating of hubs can enable more realistic models by speeding up stochastic simulations

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

Ehlert, Kurt; Loewe, Laurence, E-mail: loewe@wisc.edu; Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin 53715

2014-11-28

To respect the nature of discrete parts in a system, stochastic simulation algorithms (SSAs) must update for each action (i) all part counts and (ii) each action's probability of occurring next and its timing. This makes it expensive to simulate biological networks with well-connected “hubs” such as ATP that affect many actions. Temperature and volume also affect many actions and may be changed significantly in small steps by the network itself during fever and cell growth, respectively. Such trends matter for evolutionary questions, as cell volume determines doubling times and fever may affect survival, both key traits for biological evolution.more » Yet simulations often ignore such trends and assume constant environments to avoid many costly probability updates. Such computational convenience precludes analyses of important aspects of evolution. Here we present “Lazy Updating,” an add-on for SSAs designed to reduce the cost of simulating hubs. When a hub changes, Lazy Updating postpones all probability updates for reactions depending on this hub, until a threshold is crossed. Speedup is substantial if most computing time is spent on such updates. We implemented Lazy Updating for the Sorting Direct Method and it is easily integrated into other SSAs such as Gillespie's Direct Method or the Next Reaction Method. Testing on several toy models and a cellular metabolism model showed >10× faster simulations for its use-cases—with a small loss of accuracy. Thus we see Lazy Updating as a valuable tool for some special but important simulation problems that are difficult to address efficiently otherwise.« less

Automating Microbial Directed Evolution For Bioengineering Applications

NASA Astrophysics Data System (ADS)

Lee, A.; Demachkie, I. S.; Sardesh, N.; Arismendi, D.; Ouandji, C.; Wang, J.; Blaich, J.; Gentry, D.

2016-12-01

From a micro-biology perspective, directed evolution is a technique that uses controlled environmental pressures to select for a desired phenotype. Directed evolution has the distinct advantage over rational design of not needing extensive knowledge of the genome or pathways associated with a microorganism to induce phenotypes. However, there are currently limitations to the applicability of this technique including being time-consuming, error-prone, and dependent on existing assays that may lack selectivity for the given phenotype. The AADEC (Autonomous Adaptive Directed Evolution Chamber) system is a proof-of-concept instrument to automate and improve the technique such that directed evolution can be used more effectively as a general bioengineering tool. A series of tests using the automated system and comparable by-hand survival assay measurements have been carried out using UV-C radiation and Escherichia coli cultures in order to demonstrate the advantages of the AADEC versus traditional implementations of directed evolution such as random mutagenesis. AADEC uses UV-C exposure as both a source of environmental stress and mutagenesis, so in order to evaluate the UV-C tolerance obtained from the cultures, a manual UV-C exposure survival assay was developed alongside the device to compare the survival fractions at a fixed dosage. This survival assay involves exposing E.coli to UV-C radiation using a custom-designed exposure hood to control the flux and dose. Surviving cells are counted then transferred to the next iteration and so on for several iterations to calculate the survival fractions for each exposure iteration. This survival assay primarily serves as a baseline for the AADEC device, allowing quantification of the differences between the AADEC system over the manual approach. The primary data of comparison is survival fractions; this is obtained by optical density and plate counts in the manual assay and by optical density growth curve fits pre- and post-exposure in the automated case. This data can then be compiled to calculate trends over the iterations to characterize increasing UV-C resistance of the E.coli strains. The observed trends are statistically indistinguishable through several iterations from both sources.

Possible impact of global warming on the evolution of hemagglutinins from influenza a viruses.

PubMed

Yan, Shaomin; Wu, Guang

2011-02-01

To determine if global warming has an impact on the evolution of hemagglutinins from influenza A viruses, because both global warming and influenza pandemics/epidemics threaten the world. 4 706 hemagglutinins from influenza A viruses sampled from 1956 to 2009 were converted to a time-series to show their evolutionary process and compared with the global, northern hemisphere and southern hemisphere temperatures, to determine if their trends run in similar or opposite directions. Point-to-point comparisons between temperature and quantified hemagglutinins were performed for all species and for the major prevailing species. The comparisons show that the trends for both hemagglutinin evolution and temperature change run in a similar direction. Global warming has a consistent and progressive impact on the hemagglutinin evolution of influenza A viruses.

Bacteria-directed construction of hollow TiO2 micro/nanostructures with enhanced photocatalytic hydrogen evolution activity.

PubMed

Zhou, Han; Fan, Tongxiang; Ding, Jian; Zhang, Di; Guo, Qixin

2012-03-12

A general method has been developed for the synthesis of various hollow TiO2 micro/nanostructures with bacteria as templates to further study the structural effect on photocatalytic hydrogen evolution properties. TiO2 hollow spheres and hollow tubes, served as prototypes, are obtained via a surface sol-gel process using cocci and bacillus as biotemplates, respectively. The formation mechanisms are based on absorption of metal-alkoxide molecules from solution onto functional cell wall surfaces and subsequent hydrolysis to give nanometer-thick oxide layers. The UV-Vis absorption spectrum shows that the porous TiO2 hollow spheres have enhanced light harvesting property compared with the corresponding solid counterpart. This could be attributed to their unique hollow porous micro/nanostructures with microsized hollow cavities and nanovoids which could bring about multiple scattering and rayleigh scattering of light, respectively. The hollow TiO2 structures exhibit superior photocatalytic hydrogen evolution activities under UV and visible light irradiation in the presence of sacrificial reagents. The hydrogen evolution rate of hollow structures is about 3.6 times higher than the solid counterpart and 1.5 times higher than P25-TiO2. This work demonstrates the structural effect on enhancing the photocatalytic hydrogen evolution performance which would pave a new pathway to tailor and improve catalytic properties over a broad range.

Evolution of precopulatory and post-copulatory strategies of inbreeding avoidance and associated polyandry.

PubMed

Duthie, A B; Bocedi, G; Germain, R R; Reid, J M

2018-01-01

Inbreeding depression is widely hypothesized to drive adaptive evolution of precopulatory and post-copulatory mechanisms of inbreeding avoidance, which in turn are hypothesized to affect evolution of polyandry (i.e. female multiple mating). However, surprisingly little theory or modelling critically examines selection for precopulatory or post-copulatory inbreeding avoidance, or both strategies, given evolutionary constraints and direct costs, or examines how evolution of inbreeding avoidance strategies might feed back to affect evolution of polyandry. Selection for post-copulatory inbreeding avoidance, but not for precopulatory inbreeding avoidance, requires polyandry, whereas interactions between precopulatory and post-copulatory inbreeding avoidance might cause functional redundancy (i.e. 'degeneracy') potentially generating complex evolutionary dynamics among inbreeding strategies and polyandry. We used individual-based modelling to quantify evolution of interacting precopulatory and post-copulatory inbreeding avoidance and associated polyandry given strong inbreeding depression and different evolutionary constraints and direct costs. We found that evolution of post-copulatory inbreeding avoidance increased selection for initially rare polyandry and that evolution of a costly inbreeding avoidance strategy became negligible over time given a lower-cost alternative strategy. Further, fixed precopulatory inbreeding avoidance often completely precluded evolution of polyandry and hence post-copulatory inbreeding avoidance, but fixed post-copulatory inbreeding avoidance did not preclude evolution of precopulatory inbreeding avoidance. Evolution of inbreeding avoidance phenotypes and associated polyandry is therefore affected by evolutionary feedbacks and degeneracy. All else being equal, evolution of precopulatory inbreeding avoidance and resulting low polyandry is more likely when post-copulatory inbreeding avoidance is precluded or costly, and evolution of post-copulatory inbreeding avoidance greatly facilitates evolution of costly polyandry. © The Authors. Journal of Evolutionary Biology published by John Wiley & Sons Ltd on behalf of European Society for Evolutionary Biology.

TRIADS: A phase-resolving model for nonlinear shoaling of directional wave spectra

NASA Astrophysics Data System (ADS)

Sheremet, Alex; Davis, Justin R.; Tian, Miao; Hanson, Jeffrey L.; Hathaway, Kent K.

2016-03-01

We investigate the performance of TRIADS, a numerical implementation of a phase-resolving, nonlinear, spectral model describing directional wave evolution in intermediate and shallow water. TRIADS simulations of shoaling waves generated by Hurricane Bill, 2009 are compared to directional spectral estimates based on observations collected at the Field Research Facility of the US Army Corps Of Engineers, at Duck, NC. Both the ability of the model to capture the processes essential to the nonlinear wave evolution, and the efficiency of the numerical implementations are analyzed and discussed.

Microstructural Evolution in Intensively Melt Sheared Direct Chill Cast Al-Alloys

NASA Astrophysics Data System (ADS)

Jones, S.; Rao, A. K. Prasada; Patel, J. B.; Scamans, G. M.; Fan, Z.

The work presented here introduces the novel melt conditioned direct chill casting (MC-DC) technology, where intensive melt shearing is applied to the conventional direct-chill casting process. MC-DC casting can successfully produce high quality Al-alloy billets. The results obtained from 80 mm diameter billets cast at speed of 200 mm/min show that MC-DC casting of Al-alloys, substantially refines the microstructure and reduces macro-segregation. In this paper, we present the preliminary results and discuss microstructural evolution during MC-DC casting of Al-alloys.

Comparison of ionospheric plasma drifts obtained by different techniques

NASA Astrophysics Data System (ADS)

Kouba, Daniel; Arikan, Feza; Arikan, Orhan; Toker, Cenk; Mosna, Zbysek; Gok, Gokhan; Rejfek, Lubos; Ari, Gizem

2016-07-01

Ionospheric observatory in Pruhonice (Czech Republic, 50N, 14.9E) provides regular ionospheric sounding using Digisonde DPS-4D. The paper is focused on F-region vertical drift data. Vertical component of the drift velocity vector can be estimated by several methods. Digisonde DPS-4D allows sounding in drift mode with direct output represented by drift velocity vector. The Digisonde located in Pruhonice provides direct drift measurement routinely once per 15 minutes. However, also other different techniques can be found in the literature, for example the indirect estimation based on the temporal evolution of measured ionospheric characteristics is often used for calculation of the vertical drift component. The vertical velocity is thus estimated according to the change of characteristics scaled from the classical quarter-hour ionograms. In present paper direct drift measurement is compared with technique based on measuring of the virtual height at fixed frequency from the F-layer trace on ionogram, technique based on variation of h`F and hmF. This comparison shows possibility of using different methods for calculating vertical drift velocity and their relationship to the direct measurement used by Digisonde. This study is supported by the Joint TUBITAK 114E092 and AS CR 14/001 projects.

Effects of air flow directions on composting process temperature profile

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

Kulcu, Recep; Yaldiz, Osman

2008-07-01

In this study, chicken manure mixed with carnation wastes was composted by using three different air flow directions: R1-sucking (downward), R2-blowing (upward) and R3-mixed. The aim was to find out the most appropriate air flow direction type for composting to provide more homogenous temperature distribution in the reactors. The efficiency of each aeration method was evaluated by monitoring the evolution of parameters such as temperature, moisture content, CO{sub 2} and O{sub 2} ratio in the material and dry material losses. Aeration of the reactors was managed by radial fans. The results showed that R3 resulted in a more homogenous temperaturemore » distribution and high dry material loss throughout the composting process. The most heterogeneous temperature distribution and the lowest dry material loss were obtained in R2.« less

A tomographic test of cosmological principle using the JLA compilation of type Ia supernovae

NASA Astrophysics Data System (ADS)

Chang, Zhe; Lin, Hai-Nan; Sang, Yu; Wang, Sai

2018-05-01

We test the cosmological principle by fitting a dipolar modulation of distance modulus and searching for an evolution of this modulation with respect to cosmological redshift. Based on a redshift tomographic method, we divide the Joint Light-curve Analysis compilation of supernovae of type Ia into different redshift bins, and employ a Markov-Chain Monte-Carlo method to infer the anisotropic amplitude and direction in each redshift bin. However, we do not find any significant deviations from the cosmological principle, and the anisotropic amplitude is stringently constrained to be less than a few thousandths at 95% confidence level.

Collapse of ultrashort spatiotemporal pulses described by the cubic generalized Kadomtsev-Petviashvili equation

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

Leblond, Herve; Kremer, David; Mihalache, Dumitru

2010-03-15

By using a reductive perturbation method, we derive from Maxwell-Bloch equations a cubic generalized Kadomtsev-Petviashvili equation for ultrashort spatiotemporal optical pulse propagation in cubic (Kerr-like) media without the use of the slowly varying envelope approximation. We calculate the collapse threshold for the propagation of few-cycle spatiotemporal pulses described by the generic cubic generalized Kadomtsev-Petviashvili equation by a direct numerical method and compare it to analytic results based on a rigorous virial theorem. Besides, typical evolution of the spectrum (integrated over the transverse spatial coordinate) is given and a strongly asymmetric spectral broadening of ultrashort spatiotemporal pulses during collapse is evidenced.

Multiplexed genome engineering and genotyping methods applications for synthetic biology and metabolic engineering.

PubMed

Wang, Harris H; Church, George M

2011-01-01

Engineering at the scale of whole genomes requires fundamentally new molecular biology tools. Recent advances in recombineering using synthetic oligonucleotides enable the rapid generation of mutants at high efficiency and specificity and can be implemented at the genome scale. With these techniques, libraries of mutants can be generated, from which individuals with functionally useful phenotypes can be isolated. Furthermore, populations of cells can be evolved in situ by directed evolution using complex pools of oligonucleotides. Here, we discuss ways to utilize these multiplexed genome engineering methods, with special emphasis on experimental design and implementation. Copyright © 2011 Elsevier Inc. All rights reserved.

Kinetic Rate Kernels via Hierarchical Liouville-Space Projection Operator Approach.

PubMed

Zhang, Hou-Dao; Yan, YiJing

2016-05-19

Kinetic rate kernels in general multisite systems are formulated on the basis of a nonperturbative quantum dissipation theory, the hierarchical equations of motion (HEOM) formalism, together with the Nakajima-Zwanzig projection operator technique. The present approach exploits the HEOM-space linear algebra. The quantum non-Markovian site-to-site transfer rate can be faithfully evaluated via projected HEOM dynamics. The developed method is exact, as evident by the comparison to the direct HEOM evaluation results on the population evolution.

Computation of direct and inverse mutations with the SEGM web server (Stochastic Evolution of Genetic Motifs): an application to splice sites of human genome introns.

PubMed

Benard, Emmanuel; Michel, Christian J

2009-08-01

We present here the SEGM web server (Stochastic Evolution of Genetic Motifs) in order to study the evolution of genetic motifs both in the direct evolutionary sense (past-present) and in the inverse evolutionary sense (present-past). The genetic motifs studied can be nucleotides, dinucleotides and trinucleotides. As an example of an application of SEGM and to understand its functionalities, we give an analysis of inverse mutations of splice sites of human genome introns. SEGM is freely accessible at http://lsiit-bioinfo.u-strasbg.fr:8080/webMathematica/SEGM/SEGM.html directly or by the web site http://dpt-info.u-strasbg.fr/~michel/. To our knowledge, this SEGM web server is to date the only computational biology software in this evolutionary approach.

Deducing multiple interfacial dynamics during polymeric foaming.

PubMed

Chandan, Mohammed Rehaan; Naskar, Nilanjon; Das, Anuja; Mukherjee, Rabibrata; Harikrishnan, Gopalakrishna Pillai

2018-06-15

Several interfacial phenomena are active during polymeric foaming, the dynamics of which significantly influence terminal stability, cell structure and in turn the thermo-mechanical properties of temporally evolved foam. Understanding these dynamics is important in achieving desired foam properties. Here, we introduce a method to simultaneously portray the time evolution of bubble growth, lamella thinning and Plateau border drainage, occurring during reactive polymeric foaming. In this method, we initially conduct bulk and surface shear rheology under polymerizing and non-foaming conditions. In a subsequent step, foaming experiments were conducted in a rheometer. The microscopic structural dimensions pertaining to the terminal values of the dynamics of each interfacial phenomena are then measured using a combination of scanning electron microscopy, optical microscopy and imaging ellipsometry, after the foaming is over. The measured surface and bulk rheological parameters are incorporated in time evolution equations that are derived from mass and momentum transport occurring when a model viscoelastic fluid is foamed by gas dispersion. Analytical and numerical solutions to these equations portray the dynamics. We demonstrate this method for a series of reactive polyurethane foams generated from different chemical sources. The effectiveness of our method is in simultaneously obtaining these dynamics that are difficult to directly monitor due to short active durations over multiple length scales.

On the asymptotic evolution of finite energy Airy wave functions.

PubMed

Chamorro-Posada, P; Sánchez-Curto, J; Aceves, A B; McDonald, G S

2015-06-15

In general, there is an inverse relation between the degree of localization of a wave function of a certain class and its transform representation dictated by the scaling property of the Fourier transform. We report that in the case of finite energy Airy wave packets a simultaneous increase in their localization in the direct and transform domains can be obtained as the apodization parameter is varied. One consequence of this is that the far-field diffraction rate of a finite energy Airy beam decreases as the beam localization at the launch plane increases. We analyze the asymptotic properties of finite energy Airy wave functions using the stationary phase method. We obtain one dominant contribution to the long-term evolution that admits a Gaussian-like approximation, which displays the expected reduction of its broadening rate as the input localization is increased.

Directional cultural change by modification and replacement of memes.

PubMed

Cardoso, Gonçalo C; Atwell, Jonathan W

2011-01-01

Evolutionary approaches to culture remain contentious. A source of contention is that cultural mutation may be substantial and, if it drives cultural change, then current evolutionary models are not adequate. But we lack studies quantifying the contribution of mutations to directional cultural change. We estimated the contribution of one type of cultural mutations--modification of memes--to directional cultural change using an amenable study system: learned birdsongs in a species that recently entered an urban habitat. Many songbirds have higher minimum song frequency in cities, to alleviate masking by low-frequency noise. We estimated that the input of meme modifications in an urban songbird population explains about half the extent of the population divergence in song frequency. This contribution of cultural mutations is large, but insufficient to explain the entire population divergence. The remaining divergence is due to selection of memes or creation of new memes. We conclude that the input of cultural mutations can be quantitatively important, unlike in genetic evolution, and that it operates together with other mechanisms of cultural evolution. For this and other traits, in which the input of cultural mutations might be important, quantitative studies of cultural mutation are necessary to calibrate realistic models of cultural evolution. © 2010 The Author(s). Evolution© 2010 The Society for the Study of Evolution.

Exponential blocking-temperature distribution in ferritin extracted from magnetization measurements

NASA Astrophysics Data System (ADS)

Lee, T. H.; Choi, K.-Y.; Kim, G.-H.; Suh, B. J.; Jang, Z. H.

2014-11-01

We developed a direct method to extract the zero-field zero-temperature anisotropy energy barrier distribution of magnetic particles in the form of a blocking-temperature distribution. The key idea is to modify measurement procedures slightly to make nonequilibrium magnetization calculations (including the time evolution of magnetization) easier. We applied this method to the biomagnetic molecule ferritin and successfully reproduced field-cool magnetization by using the extracted distribution. We find that the resulting distribution is more like an exponential type and that the distribution cannot be correlated simply to the widely known log-normal particle-size distribution. The method also allows us to determine the values of the zero-temperature coercivity and Bloch coefficient, which are in good agreement with those determined from other techniques.

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

Du, Jincheng; Rimsza, Jessica

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Application of theoretical methods to increase succinate production in engineered strains.

PubMed

Valderrama-Gomez, M A; Kreitmayer, D; Wolf, S; Marin-Sanguino, A; Kremling, A

2017-04-01

Computational methods have enabled the discovery of non-intuitive strategies to enhance the production of a variety of target molecules. In the case of succinate production, reviews covering the topic have not yet analyzed the impact and future potential that such methods may have. In this work, we review the application of computational methods to the production of succinic acid. We found that while a total of 26 theoretical studies were published between 2002 and 2016, only 10 studies reported the successful experimental implementation of any kind of theoretical knowledge. None of the experimental studies reported an exact application of the computational predictions. However, the combination of computational analysis with complementary strategies, such as directed evolution and comparative genome analysis, serves as a proof of concept and demonstrates that successful metabolic engineering can be guided by rational computational methods.

Spacelike matching to null infinity

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

Zenginoglu, Anil; Tiglio, Manuel

2009-07-15

We present two methods to include the asymptotic domain of a background spacetime in null directions for numerical solutions of evolution equations so that both the radiation extraction problem and the outer boundary problem are solved. The first method is based on the geometric conformal approach, the second is a coordinate based approach. We apply these methods to the case of a massless scalar wave equation on a Kerr spacetime. Our methods are designed to allow existing codes to reach the radiative zone by including future null infinity in the computational domain with relatively minor modifications. We demonstrate the flexibilitymore » of the methods by considering both Boyer-Lindquist and ingoing Kerr coordinates near the black hole. We also confirm numerically predictions concerning tail decay rates for scalar fields at null infinity in Kerr spacetime due to Hod for the first time.« less

Variation of River Islands around a Large City along the Yangtze River from Satellite Remote Sensing Images

PubMed Central

Shi, Haiyun; Gao, Chao; Dong, Changming; Xia, Changshui; Xu, Guanglai

2017-01-01

River islands are sandbars formed by scouring and silting. Their evolution is affected by several factors, among which are runoff and sediment discharge. The spatial-temporal evolution of seven river islands in the Nanjing Section of the Yangtze River of China was examined using TM (Thematic Mapper) and ETM (Enhanced Thematic Mapper)+ images from 1985 to 2015 at five year intervals. The following approaches were applied in this study: the threshold value method, binarization model, image registration, image cropping, convolution and cluster analysis. Annual runoff and sediment discharge data as measured at the Datong hydrological station upstream of Nanjing section were also used to determine the roles and impacts of various factors. The results indicated that: (1) TM/ETM+ images met the criteria of information extraction of river islands; (2) generally, the total area of these islands in this section and their changing rate decreased over time; (3) sediment and river discharge were the most significant factors in island evolution. They directly affect river islands through silting or erosion. Additionally, anthropocentric influences could play increasingly important roles. PMID:28953218

Underlying Principles of Natural Selection in Network Evolution: Systems Biology Approach

PubMed Central

Chen, Bor-Sen; Wu, Wei-Sheng

2007-01-01

Systems biology is a rapidly expanding field that integrates diverse areas of science such as physics, engineering, computer science, mathematics, and biology toward the goal of elucidating the underlying principles of hierarchical metabolic and regulatory systems in the cell, and ultimately leading to predictive understanding of cellular response to perturbations. Because post-genomics research is taking place throughout the tree of life, comparative approaches offer a way for combining data from many organisms to shed light on the evolution and function of biological networks from the gene to the organismal level. Therefore, systems biology can build on decades of theoretical work in evolutionary biology, and at the same time evolutionary biology can use the systems biology approach to go in new uncharted directions. In this study, we present a review of how the post-genomics era is adopting comparative approaches and dynamic system methods to understand the underlying design principles of network evolution and to shape the nascent field of evolutionary systems biology. Finally, the application of evolutionary systems biology to robust biological network designs is also discussed from the synthetic biology perspective. PMID:19468310

Comparison of forcing functions in magnetohydrodynamics

NASA Astrophysics Data System (ADS)

McKay, Mairi E.; Linkmann, Moritz; Clark, Daniel; Chalupa, Adam A.; Berera, Arjun

2017-11-01

Results are presented of direct numerical simulations of incompressible, homogeneous magnetohydrodynamic turbulence without a mean magnetic field, subject to different mechanical forcing functions commonly used in the literature. Specifically, the forces are negative damping (which uses the large-scale velocity field as a forcing function), a nonhelical random force, and a nonhelical static sinusoidal force (analogous to helical ABC forcing). The time evolution of the three ideal invariants (energy, magnetic helicity, and cross helicity), the time-averaged energy spectra, the energy ratios, and the dissipation ratios are examined. All three forcing functions produce qualitatively similar steady states with regard to the time evolution of the energy and magnetic helicity. However, differences in the cross-helicity evolution are observed, particularly in the case of the static sinusoidal method of energy injection. Indeed, an ensemble of sinusoidally forced simulations with identical parameters shows significant variations in the cross helicity over long time periods, casting some doubt on the validity of the principle of ergodicity in systems in which the injection of helicity cannot be controlled. Cross helicity can unexpectedly enter the system through the forcing function and must be carefully monitored.

Glycomics: revealing the dynamic ecology and evolution of sugar molecules.

PubMed

Springer, Stevan A; Gagneux, Pascal

2016-03-01

Sugars are the most functionally and structurally diverse molecules in the biological world. Glycan structures range from tiny single monosaccharide units to giant chains thousands of units long. Some glycans are branched, their monosaccharides linked together in many different combinations and orientations. Some exist as solitary molecules; others are conjugated to proteins and lipids and alter their collective functional properties. In addition to structural and storage roles, glycan molecules participate in and actively regulate physiological and developmental processes. Glycans also mediate cellular interactions within and between individuals. Their roles in ecology and evolution are pivotal, but not well studied because glycan biochemistry requires different methods than standard molecular biology practice. The properties of glycans are in some ways convenient, and in others challenging. Glycans vary on organismal timescales, and in direct response to physiological and ecological conditions. Their mature structures are physical records of both genetic and environmental influences during maturation. We describe the scope of natural glycan variation and discuss how studying glycans will allow researchers to further integrate the fields of ecology and evolution. Copyright © 2015 Elsevier B.V. All rights reserved.

Transition regime from step-flow to step-bunching in the growth of epitaxial SrRuO3 on (001) SrTiO3

NASA Astrophysics Data System (ADS)

Gura, Anna; Bertino, Giulia; Bein, Benjamin; Dawber, Matthew

2018-04-01

We present a study of the surface morphology of SrRuO3 thin films grown on TiO2 terminated (001) SrTiO3 substrates using an off-axis RF magnetron sputtering deposition technique. We investigated the step bunching formation and the evolution of the films by varying deposition parameters. The thin films were characterized using atomic force microscopy methods, allowing us to study the various growth regimes of SrRuO3 as a function of the growth parameters. We observe a strong influence of both the miscut angle and growth temperature on the evolution of the SrRuO3 surface morphology. In addition, a thickness dependence is present. Remarkably, the formation of a smooth, regular, and uniform "fish-skin" structure at the step-bunch transition is observed. The fish-skin morphology results from the merging of 2D flat islands predicted by previous models. The direct observation of surface evolution allows us to better understand the different growth regimes of SrRuO3 thin films.

Gene regulation in amphioxus: An insight from transgenic studies in amphioxus and vertebrates.

PubMed

Kozmikova, Iryna; Kozmik, Zbynek

2015-12-01

Cephalochordates, commonly known as amphioxus or lancelets, are the most basal subphylum of chordates. Cephalochordates are thus key to understanding the origin of vertebrates and molecular mechanisms underlying vertebrate evolution. The evolution of developmental control mechanisms during invertebrate-to-vertebrate transition involved not only gene duplication events, but also specific changes in spatial and temporal expression of many genes. To get insight into the spatiotemporal regulation of gene expression during invertebrate-to-vertebrate transition, functional studies of amphioxus gene regulatory elements are highly warranted. Here, we review transgenic studies performed in amphioxus and vertebrates using promoters and enhancers derived from the genome of Branchiostoma floridae. We describe the current methods of transgenesis in amphioxus, provide evidence of Tol2 transposon-generated transgenic embryos of Branchiostoma lanceolatum and discuss possible future directions. We envision that comparative transgenic analysis of gene regulatory sequences in the context of amphioxus and vertebrate embryos will likely provide an important mechanistic insight into the evolution of vertebrate body plan. Copyright © 2015 Elsevier B.V. All rights reserved.

In Situ Investigation of the Evolution of Lattice Strain and Stresses in Austenite and Martensite During Quenching and Tempering of Steel

NASA Astrophysics Data System (ADS)

Villa, M.; Niessen, F.; Somers, M. A. J.

2018-01-01

Energy dispersive synchrotron X-ray diffraction was applied to investigate in situ the evolution of lattice strains and stresses in austenite and martensite during quenching and tempering of a soft martensitic stainless steel. In one experiment, lattice strains in austenite and martensite were measured in situ in the direction perpendicular to the sample surface during an austenitization, quenching, and tempering cycle. In a second experiment, the sin2 ψ method was applied in situ during the austenite-to-martensite transformation to distinguish between macro- and phase-specific micro-stresses and to follow the evolution of these stresses during transformation. Martensite formation evokes compressive stress in austenite that is balanced by tensile stress in martensite. Tempering to 748 K (475 °C) leads to partial relaxation of these stresses. Additionally, data reveal that (elastic) lattice strain in austenite is not hydrostatic but hkl dependent, which is ascribed to plastic deformation of this phase during martensite formation and is considered responsible for anomalous behavior of the 200 γ reflection.

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

PubMed Central

Quick, Josh; Grubaugh, Nathan D; Pullan, Steven T; Claro, Ingra M; Smith, Andrew D; Gangavarapu, Karthik; Oliveira, Glenn; Robles-Sikisaka, Refugio; Rogers, Thomas F; Beutler, Nathan A; Burton, Dennis R; Lewis-Ximenez, Lia Laura; de Jesus, Jaqueline Goes; Giovanetti, Marta; Hill, Sarah; Black, Allison; Bedford, Trevor; Carroll, Miles W; Nunes, Marcio; Alcantara, Luiz Carlos; Sabino, Ester C; Baylis, Sally A; Faria, Nuno; Loose, Matthew; Simpson, Jared T; Pybus, Oliver G; Andersen, Kristian G; Loman, Nicholas J

2018-01-01

Genome sequencing has become a powerful tool for studying emerging infectious diseases; however, genome sequencing directly from clinical samples without isolation remains challenging for viruses such as Zika, where metagenomic sequencing methods may generate insufficient numbers of viral reads. Here we present a protocol for generating coding-sequence complete genomes comprising an online primer design tool, a novel multiplex PCR enrichment protocol, optimised library preparation methods for the portable MinION sequencer (Oxford Nanopore Technologies) and the Illumina range of instruments, and a bioinformatics pipeline for generating consensus sequences. The MinION protocol does not require an internet connection for analysis, making it suitable for field applications with limited connectivity. Our method relies on multiplex PCR for targeted enrichment of viral genomes from samples containing as few as 50 genome copies per reaction. Viral consensus sequences can be achieved starting with clinical samples in 1-2 days following a simple laboratory workflow. This method has been successfully used by several groups studying Zika virus evolution and is facilitating an understanding of the spread of the virus in the Americas. PMID:28538739

Highly efficient direct Z-scheme WO3/CdS-diethylenetriamine photocatalyst and its enhanced photocatalytic H2 evolution under visible light irradiation

NASA Astrophysics Data System (ADS)

Hu, Taiping; Li, Pengfei; Zhang, Jinfeng; Liang, Changhao; Dai, Kai

2018-06-01

Cadmium sulfide (CdS) has demonstrated great promise in artificial photocataytic hydrogen (H2) production. However, the serious photocorrosion hinders its effective interaction and real-life application. In this work, a typical direct Z-scheme WO3/CdS-diethylenetriamine (CdS-DETA) composite has been designed via facile in-situ solvothermal method, which exhibits excellent H2 production properties in visible light region. In this system, the inorganic-organic CdS-DETA nanobelts (NBs) possess enough active sites and large surface area for the encouraging nanojunction structure information. Furthermore, we also systematically calculated energy band structure and investigated charge transfer of the WO3/CdS-DETA by PL and photocurrent test, the results demonstrated that the suitable band gap matching between CdS-DETA and WO3 and high redox potential improve the separation of photogenerated holes and electrons, restraining intrinsic photocorrosion of CdS as well as improving the photocatalytic activity. 5%WO3/CdS-DETA presented the most outstanding H2 evolution rate (15522 μmol g-1 h-1), which is twice higher than that of pure CdS-DETA. WO3/CdS-DETA composites also presented high stability after three recycle H2 production experiment. Finally, direct Z-scheme photocatalytic mechanism is calculated.

High-Throughput Screening Assay for Laccase Engineering toward Lignosulfonate Valorization

PubMed Central

Rodríguez-Escribano, David; de Salas, Felipe; Camarero, Susana

2017-01-01

Lignin valorization is a pending issue for the integrated conversion of lignocellulose in consumer goods. Lignosulfonates (LS) are the main technical lignins commercialized today. However, their molecular weight should be enlarged to meet application requirements as additives or dispersing agents. Oxidation of lignosulfonates with fungal oxidoreductases, such as laccases, can increase the molecular weight of lignosulfonates by the cross-linking of lignin phenols. To advance in this direction, we describe here the development of a high-throughput screening (HTS) assay for the directed evolution of laccases, with lignosulfonate as substrate and the Folin–Ciocalteau reagent (FCR), to detect the decrease in phenolic content produced upon polymerization of lignosulfonate by the enzyme. Once the reaction conditions were adjusted to the 96-well-plate format, the enzyme for validating the assay was selected from a battery of high-redox-potential laccase variants functionally expressed in S. cerevisiae (the preferred host for the directed evolution of fungal oxidoreductases). The colorimetric response (absorbance at 760 nm) correlated with laccase activity secreted by the yeast. The HTS assay was reproducible (coefficient of variation (CV) = 15%) and sensitive enough to detect subtle differences in activity among yeast clones expressing a laccase mutant library obtained by error-prone PCR (epPCR). The method is therefore feasible for screening thousands of clones during the precise engineering of laccases toward valorization of lignosulfonates. PMID:28820431

Multi-spacecraft Observations of the Coronal and Interplanetary Evolution of a Solar Eruption Associated with Two Active Regions

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

Hu, Huidong; Liu, Ying D.; Wang, Rui

We investigate the coronal and interplanetary evolution of a coronal mass ejection (CME) launched on 2010 September 4 from a source region linking two active regions (ARs), 11101 and 11103, using extreme ultraviolet imaging, magnetogram, white-light, and in situ observations from SDO , STEREO , SOHO , VEX , and Wind . A potential-field source-surface model is employed to examine the configuration of the coronal magnetic field surrounding the source region. The graduated cylindrical shell model and a triangulation method are applied to determine the kinematics of the CME in the corona and interplanetary space. From the remote sensing andmore » in situ observations, we obtain some key results: (1) the CME was deflected in both the eastward and southward directions in the low corona by the magnetic pressure from the two ARs, and possibly interacted with another ejection, which caused that the CME arrived at VEX that was longitudinally distant from the source region; (2) although VEX was closer to the Sun, the observed and derived CME arrival times at VEX are not earlier than those at Wind , which suggests the importance of determining both the frontal shape and propagation direction of the CME in interplanetary space; and (3) the ICME was compressed in the radial direction while the longitudinal transverse size was extended.« less

High-Throughput Screening Assay for Laccase Engineering toward Lignosulfonate Valorization

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

Rodriguez-Escribano, David; de Salas, Felipe; Pardo, Isabel

Lignin valorization is a pending issue for the integrated conversion of lignocellulose in consumer goods. Lignosulfonates (LS) are the main technical lignins commercialized today. However, their molecular weight should be enlarged to meet application requirements as additives or dispersing agents. Oxidation of lignosulfonates with fungal oxidoreductases, such as laccases, can increase the molecular weight of lignosulfonates by the cross-linking of lignin phenols. To advance in this direction, we describe here the development of a high-throughput screening (HTS) assay for the directed evolution of laccases, with lignosulfonate as substrate and the Folin-Ciocalteau reagent (FCR), to detect the decrease in phenolic contentmore » produced upon polymerization of lignosulfonate by the enzyme. Once the reaction conditions were adjusted to the 96-well-plate format, the enzyme for validating the assay was selected from a battery of high-redox-potential laccase variants functionally expressed in S. cerevisiae (the preferred host for the directed evolution of fungal oxidoreductases). The colorimetric response (absorbance at 760 nm) correlated with laccase activity secreted by the yeast. The HTS assay was reproducible (coefficient of variation (CV) = 15%) and sensitive enough to detect subtle differences in activity among yeast clones expressing a laccase mutant library obtained by error-prone PCR (epPCR). As a result, the method is therefore feasible for screening thousands of clones during the precise engineering of laccases toward valorization of lignosulfonates.« less

High-Throughput Screening Assay for Laccase Engineering toward Lignosulfonate Valorization

DOE PAGES

Rodriguez-Escribano, David; de Salas, Felipe; Pardo, Isabel; ...

2017-08-18

Lignin valorization is a pending issue for the integrated conversion of lignocellulose in consumer goods. Lignosulfonates (LS) are the main technical lignins commercialized today. However, their molecular weight should be enlarged to meet application requirements as additives or dispersing agents. Oxidation of lignosulfonates with fungal oxidoreductases, such as laccases, can increase the molecular weight of lignosulfonates by the cross-linking of lignin phenols. To advance in this direction, we describe here the development of a high-throughput screening (HTS) assay for the directed evolution of laccases, with lignosulfonate as substrate and the Folin-Ciocalteau reagent (FCR), to detect the decrease in phenolic contentmore » produced upon polymerization of lignosulfonate by the enzyme. Once the reaction conditions were adjusted to the 96-well-plate format, the enzyme for validating the assay was selected from a battery of high-redox-potential laccase variants functionally expressed in S. cerevisiae (the preferred host for the directed evolution of fungal oxidoreductases). The colorimetric response (absorbance at 760 nm) correlated with laccase activity secreted by the yeast. The HTS assay was reproducible (coefficient of variation (CV) = 15%) and sensitive enough to detect subtle differences in activity among yeast clones expressing a laccase mutant library obtained by error-prone PCR (epPCR). As a result, the method is therefore feasible for screening thousands of clones during the precise engineering of laccases toward valorization of lignosulfonates.« less

Statistically validated mobile communication networks: the evolution of motifs in European and Chinese data

NASA Astrophysics Data System (ADS)

Li, Ming-Xia; Palchykov, Vasyl; Jiang, Zhi-Qiang; Kaski, Kimmo; Kertész, János; Miccichè, Salvatore; Tumminello, Michele; Zhou, Wei-Xing; Mantegna, Rosario N.

2014-08-01

Big data open up unprecedented opportunities for investigating complex systems, including society. In particular, communication data serve as major sources for computational social sciences, but they have to be cleaned and filtered as they may contain spurious information due to recording errors as well as interactions, like commercial and marketing activities, not directly related to the social network. The network constructed from communication data can only be considered as a proxy for the network of social relationships. Here we apply a systematic method, based on multiple-hypothesis testing, to statistically validate the links and then construct the corresponding Bonferroni network, generalized to the directed case. We study two large datasets of mobile phone records, one from Europe and the other from China. For both datasets we compare the raw data networks with the corresponding Bonferroni networks and point out significant differences in the structures and in the basic network measures. We show evidence that the Bonferroni network provides a better proxy for the network of social interactions than the original one. Using the filtered networks, we investigated the statistics and temporal evolution of small directed 3-motifs and concluded that closed communication triads have a formation time scale, which is quite fast and typically intraday. We also find that open communication triads preferentially evolve into other open triads with a higher fraction of reciprocated calls. These stylized facts were observed for both datasets.

DEVELOPMENTAL PALEOBIOLOGY OF THE VERTEBRATE SKELETON.

PubMed

Rücklin, Martin; Donoghue, Philip C J; Cunningham, John A; Marone, Federica; Stampanoni, Marco

2014-07-01

Studies of the development of organisms can reveal crucial information on homology of structures. Developmental data are not peculiar to living organisms, and they are routinely preserved in the mineralized tissues that comprise the vertebrate skeleton, allowing us to obtain direct insight into the developmental evolution of this most formative of vertebrate innovations. The pattern of developmental processes is recorded in fossils as successive stages inferred from the gross morphology of multiple specimens and, more reliably and routinely, through the ontogenetic stages of development seen in the skeletal histology of individuals. Traditional techniques are destructive and restricted to a 2-D plane with the third dimension inferred. Effective non-invasive methods of visualizing paleohistology to reconstruct developmental stages of the skeleton are necessary. In a brief survey of paleohistological techniques we discuss the pros and cons of these methods. The use of tomographic methods to reconstruct development of organs is exemplified by the study of the placoderm dentition. Testing evidence for the presence of teeth in placoderms, the first jawed vertebrates, we compare the methods that have been used. These include inferring the development from morphology, and using serial sectioning, microCT or synchrotron X-ray tomographic microscopy (SRXTM) to reconstruct growth stages and directions of growth. The ensuing developmental interpretations are biased by the methods and degree of inference. The most direct and reliable method is using SRXTM data to trace sclerochronology. The resulting developmental data can be used to resolve homology and test hypotheses on the origin of evolutionary novelties.

Validation of an LES Model for Soot Evolution against DNS Data in Turbulent Jet Flames

NASA Astrophysics Data System (ADS)

Mueller, Michael

2012-11-01

An integrated modeling approach for soot evolution in turbulent reacting flows is validated against three-dimensional Direct Numerical Simulation (DNS) data in a set of n-heptane nonpremixed temporal jet flames. As in the DNS study, the evolution of the soot population is described statistically with the Hybrid Method of Moments (HMOM). The oxidation of the fuel and formation of soot precursors are described with the Radiation Flamelet/Progress Variable (RFPV) model that includes an additional transport equation for Polycyclic Aromatic Hydrocarbons (PAH) to account for the slow chemistry governing these species. In addition, the small-scale interactions between soot, chemistry, and turbulence are described with a presumed subfilter PDF approach that accounts for the very large spatial intermittency characterizing soot in turbulent reacting flows. The DNS dataset includes flames at three different Damköhler numbers to study the influence of global mixing rates on the evolution of PAH and soot. In this work, the ability of the model to capture these trends quantitatively as Damköhler number varies is investigated. In order to reliably assess the LES approach, the LES is initialized from the filtered DNS data after an initial transitional period in an effort to minimize the hydrodynamic differences between the DNS and the LES.

Irrational exuberance for resolved species trees.

PubMed

Hahn, Matthew W; Nakhleh, Luay

2016-01-01

Phylogenomics has largely succeeded in its aim of accurately inferring species trees, even when there are high levels of discordance among individual gene trees. These resolved species trees can be used to ask many questions about trait evolution, including the direction of change and number of times traits have evolved. However, the mapping of traits onto trees generally uses only a single representation of the species tree, ignoring variation in the gene trees used to construct it. Recognizing that genes underlie traits, these results imply that many traits follow topologies that are discordant with the species topology. As a consequence, standard methods for character mapping will incorrectly infer the number of times a trait has evolved. This phenomenon, dubbed "hemiplasy," poses many problems in analyses of character evolution. Here we outline these problems, explaining where and when they are likely to occur. We offer several ways in which the possible presence of hemiplasy can be diagnosed, and discuss multiple approaches to dealing with the problems presented by underlying gene tree discordance when carrying out character mapping. Finally, we discuss the implications of hemiplasy for general phylogenetic inference, including the possible drawbacks of the widespread push for "resolved" species trees. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

The effect of cultural interaction on cumulative cultural evolution.

PubMed

Nakahashi, Wataru

2014-07-07

Cultural transmission and cultural evolution are important for animals, especially for humans. I developed a new analytical model of cultural evolution, in which each newborn learns cultural traits from multiple individuals (exemplars) in parental generation, individually explores around learned cultural traits, judges the utility of known cultural traits, and adopts a mature cultural trait. Cultural evolutionary speed increases when individuals explore a wider range of cultural traits, accurately judge the skill level of cultural traits (strong direct bias), do not strongly conform to the population mean, increase the exploration range according to the variety of socially learned cultural traits (condition dependent exploration), and make smaller errors in social learning. Number of exemplars, population size, similarity of cultural traits between exemplars, and one-to-many transmission have little effect on cultural evolutionary speed. I also investigated how cultural interaction between two populations with different mean skill levels affects their cultural evolution. A population sometimes increases in skill level more if it encounters a less skilled population than if it does not encounter anyone. A less skilled population sometimes exceeds a more skilled population in skill level by cultural interaction between both populations. The appropriateness of this analytical method is confirmed by individual-based simulations. Copyright © 2014 Elsevier Ltd. All rights reserved.

A new theory of phylogeny inference through construction of multidimensional vector space.

PubMed

Kitazoe, Y; Kurihara, Y; Narita, Y; Okuhara, Y; Tominaga, A; Suzuki, T

2001-05-01

Here, a new theory of molecular phylogeny is developed in a multidimensional vector space (MVS). The molecular evolution is represented as a successive splitting of branch vectors in the MVS. The end points of these vectors are the extant species and indicate the specific directions reflected by their individual histories of evolution in the past. This representation makes it possible to infer the phylogeny (evolutionary histories) from the spatial positions of the end points. Search vectors are introduced to draw out the groups of species distributed around them. These groups are classified according to the nearby order of branches with them. A law of physics is applied to determine the species positions in the MVS. The species are regarded as the particles moving in time according to the equation of motion, finally falling into the lowest-energy state in spite of their randomly distributed initial condition. This falling into the ground state results in the construction of an MVS in which the relative distances between two particles are equal to the substitution distances. The species positions are obtained prior to the phylogeny inference. Therefore, as the number of species increases, the species vectors can be more specific in an MVS of a larger size, such that the vector analysis gives a more stable and reliable topology. The efficacy of the present method was examined by using computer simulations of molecular evolution in which all the branch- and end-point sequences of the trees are known in advance. In the phylogeny inference from the end points with 100 multiple data sets, the present method consistently reconstructed the correct topologies, in contrast to standard methods. In applications to 185 vertebrates in the alpha-hemoglobin, the vector analysis drew out the two lineage groups of birds and mammals. A core member of the mammalian radiation appeared at the base of the mammalian lineage. Squamates were isolated from the bird lineage to compose the outgroup, while the other living reptilians were directly coupled with birds without forming any sister groups. This result is in contrast to the morphological phylogeny and is also different from those of recent molecular analyses.

Predicting Position on Teaching Creationism (Instead of Evolution) in Public Schools

ERIC Educational Resources Information Center

Lac, Andrew; Hemovich, Vanessa; Himelfarb, Igor

2010-01-01

The federal government has repeatedly denied the introduction of creationism into public schools as it is a direct violation of the separation of church and state. Little is known about those who would opt to eliminate evolution in scientific curriculum altogether. The authors examined this more extreme anti-evolution perspective in a nationally…

A discrete mathematical model of the dynamic evolution of a transportation network

NASA Astrophysics Data System (ADS)

Malinetskii, G. G.; Stepantsov, M. E.

2009-09-01

A dynamic model of the evolution of a transportation network is proposed. The main feature of this model is that the evolution of the transportation network is not a process of centralized transportation optimization. Rather, its dynamic behavior is a result of the system self-organization that occurs in the course of the satisfaction of needs in goods transportation and the evolution of the infrastructure of the network nodes. Nonetheless, the possibility of soft control of the network evolution direction is taken into account.

Unsteady fluid dynamics around a hovering wing

NASA Astrophysics Data System (ADS)

Krishna, Swathi; Green, Melissa; Mulleners, Karen

2017-11-01

The unsteady flow around a hovering flat plate wing has been investigated experimentally using particle image velocimetry and direct force measurements. The measurements are conducted on a wing that rotates symmetrically about the stroke reversal at a reduced frequency of k = 0.32 and Reynolds number of Re = 220 . The Lagrangian finite-time Lyapunov exponent method is used to analyse the unsteady flow fields by identifying dynamically relevant flow features such as the primary leading edge vortex (LEV), secondary vortices, and topological saddles, and their evolution within a flapping cycle. The flow evolution is divided into four stages that are characterised by the LEV (a)emergence, (b)growth, (c)lift-off, and (d)breakdown and decay. Tracking saddle points is shown to be helpful in defining the LEV lift-off which occurs at the maximum stroke velocity. The flow fields are correlated with the aerodynamic forces revealing that the maximum lift and drag are observed just before LEV lift-off. The end of wing rotation in the beginning of the stroke stimulates a change in the direction of the LEV growth and the start of rotation at the end of the stroke triggers the breakdown of the LEV.

An integrative method for testing form–function linkages and reconstructed evolutionary pathways of masticatory specialization

PubMed Central

Tseng, Z. Jack; Flynn, John J.

2015-01-01

Morphology serves as a ubiquitous proxy in macroevolutionary studies to identify potential adaptive processes and patterns. Inferences of functional significance of phenotypes or their evolution are overwhelmingly based on data from living taxa. Yet, correspondence between form and function has been tested in only a few model species, and those linkages are highly complex. The lack of explicit methodologies to integrate form and function analyses within a deep-time and phylogenetic context weakens inferences of adaptive morphological evolution, by invoking but not testing form–function linkages. Here, we provide a novel approach to test mechanical properties at reconstructed ancestral nodes/taxa and the strength and direction of evolutionary pathways in feeding biomechanics, in a case study of carnivorous mammals. Using biomechanical profile comparisons that provide functional signals for the separation of feeding morphologies, we demonstrate, using experimental optimization criteria on estimation of strength and direction of functional changes on a phylogeny, that convergence in mechanical properties and degree of evolutionary optimization can be decoupled. This integrative approach is broadly applicable to other clades, by using quantitative data and model-based tests to evaluate interpretations of function from morphology and functional explanations for observed macroevolutionary pathways. PMID:25994295

Individual-based models for adaptive diversification in high-dimensional phenotype spaces.

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

Most theories of evolutionary diversification are based on equilibrium assumptions: they are either based on optimality arguments involving static fitness landscapes, or they assume that populations first evolve to an equilibrium state before diversification occurs, as exemplified by the concept of evolutionary branching points in adaptive dynamics theory. Recent results indicate that adaptive dynamics may often not converge to equilibrium points and instead generate complicated trajectories if evolution takes place in high-dimensional phenotype spaces. Even though some analytical results on diversification in complex phenotype spaces are available, to study this problem in general we need to reconstruct individual-based models from the adaptive dynamics generating the non-equilibrium dynamics. Here we first provide a method to construct individual-based models such that they faithfully reproduce the given adaptive dynamics attractor without diversification. We then show that a propensity to diversify can be introduced by adding Gaussian competition terms that generate frequency dependence while still preserving the same adaptive dynamics. For sufficiently strong competition, the disruptive selection generated by frequency-dependence overcomes the directional evolution along the selection gradient and leads to diversification in phenotypic directions that are orthogonal to the selection gradient. Copyright © 2015 Elsevier Ltd. All rights reserved.

rGO-ZnO nanocomposites for high electrocatalytic effect on water oxidation obtained by microwave-hydrothermal method

NASA Astrophysics Data System (ADS)

Romeiro, Fernanda C.; Rodrigues, Mônica A.; Silva, Luiz A. J.; Catto, Ariadne C.; da Silva, Luis F.; Longo, Elson; Nossol, Edson; Lima, Renata C.

2017-11-01

Reduced graphene oxide-zinc oxide (rGO-ZnO) nanocomposites were successfully synthesized using a facile microwave-hydrothermal method under mild conditions, and their electrocatalytic properties towards O2 evolution were investigated. The microwave radiation played an important role in obtainment of well dispersed ZnO nanoparticles directly on reduced graphene oxide sheets without any additional reducing reagents or passivation agent. X-ray diffraction (XRD), Raman and infrared spectroscopies indicated the reduction of GO as well as the successful synthesis of rGO-ZnO nanocomposites. The chemical states of the samples were shown by XPS analyses. Due to the synergic effect, the resulting nanocomposites exhibited high electronic interaction between ZnO and rGO sheets, which improved the electrocatalytic oxidation of water with low onset potential of 0.48 V (vs. Ag/AgCl) in neutral pH and long-term stability, with high current density during electrolysis. The overpotential for water oxidation decreased in alkaline pH, suggesting useful insight on the catalytic mechanism for O2 evolution.

Scientific discovery as a combinatorial optimisation problem: How best to navigate the landscape of possible experiments?

PubMed Central

Kell, Douglas B

2012-01-01

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a ‘landscape’ representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems ‘hard’, but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the ‘best’ experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes. PMID:22252984

Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments?

PubMed

Kell, Douglas B

2012-03-01

A considerable number of areas of bioscience, including gene and drug discovery, metabolic engineering for the biotechnological improvement of organisms, and the processes of natural and directed evolution, are best viewed in terms of a 'landscape' representing a large search space of possible solutions or experiments populated by a considerably smaller number of actual solutions that then emerge. This is what makes these problems 'hard', but as such these are to be seen as combinatorial optimisation problems that are best attacked by heuristic methods known from that field. Such landscapes, which may also represent or include multiple objectives, are effectively modelled in silico, with modern active learning algorithms such as those based on Darwinian evolution providing guidance, using existing knowledge, as to what is the 'best' experiment to do next. An awareness, and the application, of these methods can thereby enhance the scientific discovery process considerably. This analysis fits comfortably with an emerging epistemology that sees scientific reasoning, the search for solutions, and scientific discovery as Bayesian processes. Copyright © 2012 WILEY Periodicals, Inc.

Increasing the power of accelerated molecular dynamics methods and plans to exploit the coming exascale

NASA Astrophysics Data System (ADS)

Voter, Arthur

Many important materials processes take place on time scales that far exceed the roughly one microsecond accessible to molecular dynamics simulation. Typically, this long-time evolution is characterized by a succession of thermally activated infrequent events involving defects in the material. In the accelerated molecular dynamics (AMD) methodology, known characteristics of infrequent-event systems are exploited to make reactive events take place more frequently, in a dynamically correct way. For certain processes, this approach has been remarkably successful, offering a view of complex dynamical evolution on time scales of microseconds, milliseconds, and sometimes beyond. We have recently made advances in all three of the basic AMD methods (hyperdynamics, parallel replica dynamics, and temperature accelerated dynamics (TAD)), exploiting both algorithmic advances and novel parallelization approaches. I will describe these advances, present some examples of our latest results, and discuss what should be possible when exascale computing arrives in roughly five years. Funded by the U.S. Department of Energy, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, and by the Los Alamos Laboratory Directed Research and Development program.

Assessing Multivariate Constraints to Evolution across Ten Long-Term Avian Studies

PubMed Central

Teplitsky, Celine; Tarka, Maja; Møller, Anders P.; Nakagawa, Shinichi; Balbontín, Javier; Burke, Terry A.; Doutrelant, Claire; Gregoire, Arnaud; Hansson, Bengt; Hasselquist, Dennis; Gustafsson, Lars; de Lope, Florentino; Marzal, Alfonso; Mills, James A.; Wheelwright, Nathaniel T.; Yarrall, John W.; Charmantier, Anne

2014-01-01

Background In a rapidly changing world, it is of fundamental importance to understand processes constraining or facilitating adaptation through microevolution. As different traits of an organism covary, genetic correlations are expected to affect evolutionary trajectories. However, only limited empirical data are available. Methodology/Principal Findings We investigate the extent to which multivariate constraints affect the rate of adaptation, focusing on four morphological traits often shown to harbour large amounts of genetic variance and considered to be subject to limited evolutionary constraints. Our data set includes unique long-term data for seven bird species and a total of 10 populations. We estimate population-specific matrices of genetic correlations and multivariate selection coefficients to predict evolutionary responses to selection. Using Bayesian methods that facilitate the propagation of errors in estimates, we compare (1) the rate of adaptation based on predicted response to selection when including genetic correlations with predictions from models where these genetic correlations were set to zero and (2) the multivariate evolvability in the direction of current selection to the average evolvability in random directions of the phenotypic space. We show that genetic correlations on average decrease the predicted rate of adaptation by 28%. Multivariate evolvability in the direction of current selection was systematically lower than average evolvability in random directions of space. These significant reductions in the rate of adaptation and reduced evolvability were due to a general nonalignment of selection and genetic variance, notably orthogonality of directional selection with the size axis along which most (60%) of the genetic variance is found. Conclusions These results suggest that genetic correlations can impose significant constraints on the evolution of avian morphology in wild populations. This could have important impacts on evolutionary dynamics and hence population persistence in the face of rapid environmental change. PMID:24608111

Evolution of egoism on semi-directed and undirected Barabási-Albert networks

NASA Astrophysics Data System (ADS)

Lima, F. W. S.

2015-05-01

Through Monte Carlo simulations, we study the evolution of the four strategies: Ethnocentric, altruistic, egoistic and cosmopolitan in one community of individuals. Interactions and reproduction among computational agents are simulated on undirected and semi-directed Barabási-Albert (BA) networks. We study the Hammond-Axelrod (HA) model on undirected and semi-directed BA networks for the asexual reproduction case. With a small modification in the traditional HA model, our simulations showed that egoism wins, differently from other results found in the literature where ethnocentric strategy is common. Here, mechanisms such as reciprocity are absent.

Reconstructing the Cenozoic evolution of the mantle: Implications for mantle plume dynamics under the Pacific and Indian plates

NASA Astrophysics Data System (ADS)

Glišović, Petar; Forte, Alessandro M.

2014-03-01

The lack of knowledge of the initial thermal state of the mantle in the geological past is an outstanding problem in mantle convection. The resolution of this problem also requires the modelling of 3-D mantle evolution that yields maximum consistency with a wide suite of geophysical constraints. Quantifying the robustness of the reconstructed thermal evolution is another major concern. To solve and estimate the robustness of the time-reversed (inverse) problem of mantle convection, we analyse two different numerical techniques: the quasi-reversible (QRV) and the backward advection (BAD) methods. Our investigation extends over the 65 Myr interval encompassing the Cenozoic era using a pseudo-spectral solution for compressible-flow thermal convection in 3-D spherical geometry. We find that the two dominant issues for solving the inverse problem of mantle convection are the choice of horizontally-averaged temperature (i.e., geotherm) and mechanical surface boundary conditions. We find, in particular, that the inclusion of thermal boundary layers that yield Earth-like heat flux at the top and bottom of the mantle has a critical impact on the reconstruction of mantle evolution. We have developed a new regularisation scheme for the QRV method using a time-dependent regularisation function. This revised implementation of the QRV method delivers time-dependent reconstructions of mantle heterogeneity that reveal: (1) the stability of Pacific and African ‘large low shear velocity provinces’ (LLSVP) over the last 65 Myr; (2) strong upward deflections of the CMB topography at 65 Ma beneath: the North Atlantic, the south-central Pacific, the East Pacific Rise (EPR) and the eastern Antarctica; (3) an anchored deep-mantle plume ascending directly under the EPR (Easter and Pitcairn hotspots) throughout the Cenozoic era; and (4) the appearance of the transient Reunion plume head beneath the western edge of the Deccan Plateau at 65 Ma. Our reconstructions of Cenozoic mantle evolution thus suggest that mantle plumes play a key role in driving surface tectonic processes and large-scale volcanism.

The 2-10 keV unabsorbed luminosity function of AGN from the LSS, CDFS, and COSMOS surveys

NASA Astrophysics Data System (ADS)

Ranalli, P.; Koulouridis, E.; Georgantopoulos, I.; Fotopoulou, S.; Hsu, L.-T.; Salvato, M.; Comastri, A.; Pierre, M.; Cappelluti, N.; Carrera, F. J.; Chiappetti, L.; Clerc, N.; Gilli, R.; Iwasawa, K.; Pacaud, F.; Paltani, S.; Plionis, E.; Vignali, C.

2016-05-01

The XMM-Large scale structure (XMM-LSS), XMM-Cosmological evolution survey (XMM-COSMOS), and XMM-Chandra deep field south (XMM-CDFS) surveys are complementary in terms of sky coverage and depth. Together, they form a clean sample with the least possible variance in instrument effective areas and point spread function. Therefore this is one of the best samples available to determine the 2-10 keV luminosity function of active galactic nuclei (AGN) and their evolution. The samples and the relevant corrections for incompleteness are described. A total of 2887 AGN is used to build the LF in the luminosity interval 1042-1046 erg s-1 and in the redshift interval 0.001-4. A new method to correct for absorption by considering the probability distribution for the column density conditioned on the hardness ratio is presented. The binned luminosity function and its evolution is determined with a variant of the Page-Carrera method, which is improved to include corrections for absorption and to account for the full probability distribution of photometric redshifts. Parametric models, namely a double power law with luminosity and density evolution (LADE) or luminosity-dependent density evolution (LDDE), are explored using Bayesian inference. We introduce the Watanabe-Akaike information criterion (WAIC) to compare the models and estimate their predictive power. Our data are best described by the LADE model, as hinted by the WAIC indicator. We also explore the recently proposed 15-parameter extended LDDE model and find that this extension is not supported by our data. The strength of our method is that it provides unabsorbed, non-parametric estimates, credible intervals for luminosity function parameters, and a model choice based on predictive power for future data. Based on observations obtained with XMM-Newton, an ESA science mission with instruments and contributions directly funded by ESA member states and NASA.Tables with the samples of the posterior probability distributions are only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/590/A80

Expanding the Nucleotide and Sugar 1-Phosphate Promiscuity of Nucleotidyltransferase RmlA via Directed Evolution

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

Moretti, Rocco; Chang, Aram; Peltier-Pain, Pauline

2012-03-15

Directed evolution is a valuable technique to improve enzyme activity in the absence of a priori structural knowledge, which can be typically enhanced via structure-guided strategies. In this study, a combination of both whole-gene error-prone polymerase chain reaction and site-saturation mutagenesis enabled the rapid identification of mutations that improved RmlA activity toward non-native substrates. These mutations have been shown to improve activities over 10-fold for several targeted substrates, including non-native pyrimidine- and purine-based NTPs as well as non-native d- and l-sugars (both a- and b-isomers). This study highlights the first broadly applicable high throughput sugar-1-phosphate nucleotidyltransferase screen and the firstmore » proof of concept for the directed evolution of this enzyme class toward the identification of uniquely permissive RmlA variants.« less

A Novel Application of Synthetic Biology and Directed Evolution to Engineer Phage-based Antibiotics

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

Wu, Meiye

The emergence of multiple drug resistant bacteria poses threats to human health, agriculture and food safety. Annually over 100,000 deaths and up to $20 billion loss to the U.S. economy are attributed to multiple drug resistant bacteria. With only four new chemical antibiotics in the drug development pipeline, we are in dire need of new solutions to address the emerging threat of multiple drug resistance. We propose a paradigm-changing approach to address the multi-drug resistant bacteria problem by utilizing Synthetic Biology (SynBio) methodologies to create and evolve “designer” bacteriophages or phages – viruses that specifically infect bacteria – to infectmore » and kill newly emerging pathogenic bacterial strains WITHOUT the need for chemical antibiotics. A major advantage of using phage to combat pathogenic bacteria is that phages can co-evolve with their bacterial host, and Sandia can be the first in the world to establish an industrial scale Synthetic Biology pipeline for phage directed evolution for safe, targeted, customizable solution to bacterial drug resistance. Since there is no existing phage directed evolution effort within or outside of Sandia, this proposal is suitable as a high-risk LDRD effort to create the first pipeline for such an endeavor. The high potential reward nature of this proposal will be the immediate impact in decontamination and restoration of surfaces and infrastructure, with longer term impact in human or animal therapeutics. The synthetic biology and screening approaches will lead to fundamental knowledge of phage/bacteria co-evolution, making Sandia a world leader in directed evolution of bacteriophages.« less

Darwin's legacy II: why biology is not physics, or why it has taken a century to see the dependence of genes on the environment.

PubMed

Singh, Rama S

2015-01-01

Genes and environment make the organism. Darwin stood firm in his denial of any direct role of environment in the modification of heredity. His theory of evolution heralded two debates: one about the importance and adequacy of natural selection as the main mechanism of evolution, and the other about the role of genes versus environment in the modification of phenotype and evolution. Here, I provide an overview of the second debate and show that the reasons for the gene versus environment battle were twofold: first, there was confusion about the role of environment in modifying the inheritance of a trait versus the evolution of that trait, and second, there was misunderstanding about the meaning of environment and its interaction with genes in the production of phenotypes. It took nearly a century to see that environment does not directly affect the inheritance of a phenotype (i.e., its heredity), but it is nevertheless the primary mover of phenotypic evolution. Effects of genes and environment are not separate but interdependent. One cannot separate the effect of genes from that of environment, or nature from nurture. To answer the question posed in the title, it is partly because the 20th century has been a century of unending progress in genetics. But also because unlike physics, biology is not colorblind; progress in biology has often been delayed beyond the Kuhnian paradigm change due to built-in interest in negating the influence of environment. Those who are against evolution, of course, cannot be expected to understand the role of environment in evolution. Those for it, many biologists included, believing in the supremacy of genes empowers them by giving adaptation a solely gene-directed (self-driven) "teleological" interpretation.

The anisotropy of 3D shock evolution and its connection to the longitudinal distribution of SEP properties

NASA Astrophysics Data System (ADS)

Feng, L.; Inhester, B.; Wei, Y.; Guo, J.; Plowman, J.; West, M. J.

2016-12-01

We Follow the 3D evolution of a coronal shock from its birth in the AIA field of view (FOV) to its propagation in interplanetary space till Mars. The shock structure is identified using the center-median filtering method which is applied to EUV observations including SDO/AIA and Proba2/SWAP. Then 3D shock morphology is reconstructed with the mask-fitting method (Feng et al. 2012,2013) from the triple-view observations at Earth, STEREO A and B in the FOV from EUV through coronagraph to heliospheric images. The mask-fitting method allows us to obtain a better shape of the 3D shock and calculate the anisotropy of shock evolution. The shock signals were later recorded in in-situ data by Messenger (0.39 AU), Venus Express (0.72 AU), WIND/ACE (1AU), STEREO B (1.03AU), Mars Science Laboratory (1.20AU), and Mars Express(1.52AU). These spacecraft were located at different distances and different longitudes relative to the Sun. Therefore, the corresponding in-situ data can provide further constraint on the shock dynamics along different directions on one hand, on the other hand reveal longitudinal distributions of SEPs in a wide angle of about 120 degrees. We also run ENLIL simulations based on the derived 3D shock morphology and dynamics. The magnetic field connectivity to aforementioned spacecraft and the obtained shock characteristics (e.g., shock geometry, speed, Alfven Mach number, etc.) at cobpoint can help with the understanding of the SEP properties (e.g., energy spectra) measured at different longitudes.

Modeling of microstructure evolution in direct metal laser sintering: A phase field approach

NASA Astrophysics Data System (ADS)

Nandy, Jyotirmoy; Sarangi, Hrushikesh; Sahoo, Seshadev

2017-02-01

Direct Metal Laser Sintering (DMLS) is a new technology in the field of additive manufacturing, which builds metal parts in a layer by layer fashion directly from the powder bed. The process occurs within a very short time period with rapid solidification rate. Slight variations in the process parameters may cause enormous change in the final build parts. The physical and mechanical properties of the final build parts are dependent on the solidification rate which directly affects the microstructure of the material. Thus, the evolving of microstructure plays a vital role in the process parameters optimization. Nowadays, the increase in computational power allows for direct simulations of microstructures during materials processing for specific manufacturing conditions. In this study, modeling of microstructure evolution of Al-Si-10Mg powder in DMLS process was carried out by using a phase field approach. A MATLAB code was developed to solve the set of phase field equations, where simulation parameters include temperature gradient, laser scan speed and laser power. The effects of temperature gradient on microstructure evolution were studied and found that with increase in temperature gradient, the dendritic tip grows at a faster rate.

The evolution of costly mate choice against segregation distorters.

PubMed

Manser, Andri; Lindholm, Anna K; Weissing, Franz J

2017-12-01

The evolution of female preference for male genetic quality remains a controversial topic in sexual selection research. One well-known problem, known as the lek paradox, lies in understanding how variation in genetic quality is maintained in spite of natural selection and sexual selection against low-quality alleles. Here, we theoretically investigate a scenario where females pay a direct fitness cost to avoid males carrying an autosomal segregation distorter. We show that preference evolution is greatly facilitated under such circumstances. Because the distorter is transmitted in a non-Mendelian fashion, it can be maintained in the population despite directional sexual selection. The preference helps females avoid fitness costs associated with the distorter. Interestingly, we find that preference evolution is limited if the choice allele induces a very strong preference or if distortion is very strong. Moreover, the preference can only persist in the presence of a signal that reliably indicates a male's distorter genotype. Hence, even in a system where the lek paradox does not play a major role, costly preferences can only spread under specific circumstances. We discuss the importance of distorter systems for the evolution of costly female choice and potential implications for the use of artificial distorters in pest control. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

The evolution of fairness through spite

PubMed Central

Forber, Patrick; Smead, Rory

2014-01-01

The presence of apparently irrational fair play in the ultimatum game remains a focal point for studies in the evolution of social behaviour. We investigate the role of negative assortment in the evolution of fair play in the ultimatum game. Spite—social behaviour that inflicts harm with no direct benefit to the actor—can evolve when it is disproportionally directed at individuals playing different strategies. The introduction of negative assortment alters the dynamics in a way that increases the chance fairness evolves, but at a cost: spite also evolves. Fairness is usually linked to cooperation and prosocial behaviour, but this study shows that it may have evolutionary links to harmful antisocial behaviour. PMID:24523265

Analysis of Fundus Fluorescein Angiogram Based on the Hessian Matrix of Directional Curvelet Sub-bands and Distance Regularized Level Set Evolution.

PubMed

Soltanipour, Asieh; Sadri, Saeed; Rabbani, Hossein; Akhlaghi, Mohammad Reza

2015-01-01

This paper presents a new procedure for automatic extraction of the blood vessels and optic disk (OD) in fundus fluorescein angiogram (FFA). In order to extract blood vessel centerlines, the algorithm of vessel extraction starts with the analysis of directional images resulting from sub-bands of fast discrete curvelet transform (FDCT) in the similar directions and different scales. For this purpose, each directional image is processed by using information of the first order derivative and eigenvalues obtained from the Hessian matrix. The final vessel segmentation is obtained using a simple region growing algorithm iteratively, which merges centerline images with the contents of images resulting from modified top-hat transform followed by bit plane slicing. After extracting blood vessels from FFA image, candidates regions for OD are enhanced by removing blood vessels from the FFA image, using multi-structure elements morphology, and modification of FDCT coefficients. Then, canny edge detector and Hough transform are applied to the reconstructed image to extract the boundary of candidate regions. At the next step, the information of the main arc of the retinal vessels surrounding the OD region is used to extract the actual location of the OD. Finally, the OD boundary is detected by applying distance regularized level set evolution. The proposed method was tested on the FFA images from angiography unit of Isfahan Feiz Hospital, containing 70 FFA images from different diabetic retinopathy stages. The experimental results show the accuracy more than 93% for vessel segmentation and more than 87% for OD boundary extraction.

Directly Observing Micelle Fusion and Growth in Solution by Liquid-Cell Transmission Electron Microscopy

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

Parent, Lucas R.; Bakalis, Evangelos; Ramírez-Hernández, Abelardo

Amphiphilic small molecules and polymers form commonplace nanoscale macromolecular compartments and bilayers, and as such are truly essential components in all cells and in many cellular processes. The nature of these architectures, including their formation, phase changes, and stimuli-response behaviors, is necessary for the most basic functions of life, and over the past half-century, these natural micellar structures have inspired a vast diversity of industrial products, from biomedicines to detergents, lubricants, and coatings. The importance of these materials and their ubiquity have made them the subject of intense investigation regarding their nanoscale dynamics with increasing interest in obtaining sufficient temporalmore » and spatial resolution to directly observe nanoscale processes. However, the vast majority of experimental methods involve either bulk-averaging techniques including light, neutron, and X-ray scattering, or are static in nature including even the most advanced cryogenic transmission electron microscopy techniques. Here, we employ in situ liquid-cell transmission electron microscopy (LCTEM) to directly observe the evolution of individual amphiphilic block copolymer micellar nanoparticles in solution, in real time with nanometer spatial resolution. These observations, made on a proof-of-concept bioconjugate polymer amphiphile, revealed growth and evolution occurring by unimer addition processes and by particle-particle collision-and-fusion events. The experimental approach, combining direct LCTEM observation, quantitative analysis of LCTEM data, and correlated in silico simulations, provides a unique view of solvated soft matter nanoassemblies as they morph and evolve in time and space, enabling us to capture these phenomena in solution.« less

Analysis of Fundus Fluorescein Angiogram Based on the Hessian Matrix of Directional Curvelet Sub-bands and Distance Regularized Level Set Evolution

PubMed Central

Soltanipour, Asieh; Sadri, Saeed; Rabbani, Hossein; Akhlaghi, Mohammad Reza

2015-01-01

This paper presents a new procedure for automatic extraction of the blood vessels and optic disk (OD) in fundus fluorescein angiogram (FFA). In order to extract blood vessel centerlines, the algorithm of vessel extraction starts with the analysis of directional images resulting from sub-bands of fast discrete curvelet transform (FDCT) in the similar directions and different scales. For this purpose, each directional image is processed by using information of the first order derivative and eigenvalues obtained from the Hessian matrix. The final vessel segmentation is obtained using a simple region growing algorithm iteratively, which merges centerline images with the contents of images resulting from modified top-hat transform followed by bit plane slicing. After extracting blood vessels from FFA image, candidates regions for OD are enhanced by removing blood vessels from the FFA image, using multi-structure elements morphology, and modification of FDCT coefficients. Then, canny edge detector and Hough transform are applied to the reconstructed image to extract the boundary of candidate regions. At the next step, the information of the main arc of the retinal vessels surrounding the OD region is used to extract the actual location of the OD. Finally, the OD boundary is detected by applying distance regularized level set evolution. The proposed method was tested on the FFA images from angiography unit of Isfahan Feiz Hospital, containing 70 FFA images from different diabetic retinopathy stages. The experimental results show the accuracy more than 93% for vessel segmentation and more than 87% for OD boundary extraction. PMID:26284170

Effects of Space Environment on Flow and Concentration During Directional Solidification

NASA Technical Reports Server (NTRS)

Benjapiyaporn, C.; Timchenko, V.; Leonardi, E.; deVahlDavis, G.; deGroh, H. C., III

2000-01-01

A study of directional solidification of a weak binary alloy (specifically, Bi - 1 at% Sn) based on the fixed grid single domain approach is being undertaken. The enthalpy method is used to solve for the temperature field over the computational domain including both the solid and liquid phases; latent heat evolution is treated with the aid of an effective specific heat coefficient. A source term accounting for the release of solute into the liquid during solidification has been incorporated into the solute transport equation. The vorticity-stream function formulation is used to describe thermosolutal convection in the liquid region. In this paper we numerically investigate the effects of g-jitter on directional solidification. A background gravity of 1 micro-g has been assumed, and new results for the effects of periodic disturbances over a range of amplitudes and frequencies on solute field and segregation have been presented.

Structural phylogeny by profile extraction and multiple superimposition using electrostatic congruence as a discriminator

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

Chakraborty, Sandeep; Rao, Basuthkar J.; Baker, Nathan A.

2013-04-01

Phylogenetic analysis of proteins using multiple sequence alignment (MSA) assumes an underlying evolutionary relationship in these proteins which occasionally remains undetected due to considerable sequence divergence. Structural alignment programs have been developed to unravel such fuzzy relationships. However, none of these structure based methods have used electrostatic properties to discriminate between spatially equivalent residues. We present a methodology for MSA of a set of related proteins with known structures using electrostatic properties as an additional discriminator (STEEP). STEEP first extracts a profile, then generates a multiple structural superimposition providing a consolidated spatial framework for comparing residues and finally emits themore » MSA. Residues that are aligned differently by including or excluding electrostatic properties can be targeted by directed evolution experiments to transform the enzymatic properties of one protein into another. We have compared STEEP results to those obtained from a MSA program (ClustalW) and a structural alignment method (MUSTANG) for chymotrypsin serine proteases. Subsequently, we used PhyML to generate phylogenetic trees for the serine and metallo-β-lactamase superfamilies from the STEEP generated MSA, and corroborated the accepted relationships in these superfamilies. We have observed that STEEP acts as a functional classifier when electrostatic congruence is used as a discriminator, and thus identifies potential targets for directed evolution experiments. In summary, STEEP is unique among phylogenetic methods for its ability to use electrostatic congruence to specify mutations that might be the source of the functional divergence in a protein family. Based on our results, we also hypothesize that the active site and its close vicinity contains enough information to infer the correct phylogeny for related proteins.« less

Application of the Fokker-Planck molecular mixing model to turbulent scalar mixing using moment methods

NASA Astrophysics Data System (ADS)

Madadi-Kandjani, E.; Fox, R. O.; Passalacqua, A.

2017-06-01

An extended quadrature method of moments using the β kernel density function (β -EQMOM) is used to approximate solutions to the evolution equation for univariate and bivariate composition probability distribution functions (PDFs) of a passive scalar for binary and ternary mixing. The key element of interest is the molecular mixing term, which is described using the Fokker-Planck (FP) molecular mixing model. The direct numerical simulations (DNSs) of Eswaran and Pope ["Direct numerical simulations of the turbulent mixing of a passive scalar," Phys. Fluids 31, 506 (1988)] and the amplitude mapping closure (AMC) of Pope ["Mapping closures for turbulent mixing and reaction," Theor. Comput. Fluid Dyn. 2, 255 (1991)] are taken as reference solutions to establish the accuracy of the FP model in the case of binary mixing. The DNSs of Juneja and Pope ["A DNS study of turbulent mixing of two passive scalars," Phys. Fluids 8, 2161 (1996)] are used to validate the results obtained for ternary mixing. Simulations are performed with both the conditional scalar dissipation rate (CSDR) proposed by Fox [Computational Methods for Turbulent Reacting Flows (Cambridge University Press, 2003)] and the CSDR from AMC, with the scalar dissipation rate provided as input and obtained from the DNS. Using scalar moments up to fourth order, the ability of the FP model to capture the evolution of the shape of the PDF, important in turbulent mixing problems, is demonstrated. Compared to the widely used assumed β -PDF model [S. S. Girimaji, "Assumed β-pdf model for turbulent mixing: Validation and extension to multiple scalar mixing," Combust. Sci. Technol. 78, 177 (1991)], the β -EQMOM solution to the FP model more accurately describes the initial mixing process with a relatively small increase in computational cost.

A review of the irradiation evolution of dispersed oxide nanoparticles in the b.c.c. Fe-Cr system: Current understanding and future directions

NASA Astrophysics Data System (ADS)

Wharry, Janelle P.; Swenson, Matthew J.; Yano, Kayla H.

2017-04-01

Thus far, a number of studies have investigated the irradiation evolution of oxide nanoparticles in b.c.c. Fe-Cr based oxide dispersion strengthened (ODS) alloys. But given the inconsistent experimental conditions, results have been widely variable and inconclusive. Crystal structure and chemistry changes differ from experiment to experiment, and the total nanoparticle volume fraction has been observed to both increase and decrease. Furthermore, there has not yet been a comprehensive review of the archival literature. In this paper, we summarize the existing studies on nanoparticle irradiation evolution. We note significant observations with respect to oxide nanoparticle crystallinity, composition, size, and number density. We discuss four possible contributing mechanisms for nanoparticle evolution: ballistic dissolution, Ostwald ripening, irradiation-enhanced diffusion, and homogeneous nucleation. Finally, we propose future directions to achieve a more comprehensive understanding of irradiation effects on oxide nanoparticles in ODS alloys.

In the Shadow of Intelligent Design: The Teaching of Evolution

ERIC Educational Resources Information Center

Cleaves, Anna; Toplis, Rob

2007-01-01

The theory of evolution by natural selection is contrasted in the media, and in some schools, with creationist ideas, in which the diversity of life on Earth is said to be the result of direct species-by-species creation, not of evolution. More recently, the Intelligent Design movement has claimed that "certain features of the universe and of…

Flow Modulation and Force Control of Flapping Wings

DTIC Science & Technology

2014-10-29

evolution of which reflect the wing morphology and kinematics. While the near-wake vortex system directly reflects the action of the wing on the...at 8 different stroke positions, which demonstrate the evolution of the vortex wake structure. The contour plot of Z vorticity at X-Y plane (Z...20 Figure 14. Smoke patterns showing the evolution of the flow structure in an

Directed evolution of cell size in Escherichia coli.

PubMed

Yoshida, Mari; Tsuru, Saburo; Hirata, Naoko; Seno, Shigeto; Matsuda, Hideo; Ying, Bei-Wen; Yomo, Tetsuya

2014-12-17

In bacteria, cell size affects chromosome replication, the assembly of division machinery, cell wall synthesis, membrane synthesis and ultimately growth rate. In addition, cell size can also be a target for Darwinian evolution for protection from predators. This strong coupling of cell size and growth, however, could lead to the introduction of growth defects after size evolution. An important question remains: can bacterial cell size change and/or evolve without imposing a growth burden? The directed evolution of particular cell sizes, without a growth burden, was tested with a laboratory Escherichia coli strain. Cells of defined size ranges were collected by a cell sorter and were subsequently cultured. This selection-propagation cycle was repeated, and significant changes in cell size were detected within 400 generations. In addition, the width of the size distribution was altered. The changes in cell size were unaccompanied by a growth burden. Whole genome sequencing revealed that only a few mutations in genes related to membrane synthesis conferred the size evolution. In conclusion, bacterial cell size could evolve, through a few mutations, without growth reduction. The size evolution without growth reduction suggests a rapid evolutionary change to diverse cell sizes in bacterial survival strategies.

Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication.

PubMed

Brödel, Andreas K; Jaramillo, Alfonso; Isalan, Mark

2017-09-01

Directed evolution is a powerful tool to improve the characteristics of biomolecules. Here we present a protocol for the intracellular evolution of proteins with distinct differences and advantages in comparison with established techniques. These include the ability to select for a particular function from a library of protein variants inside cells, minimizing undesired coevolution and propagation of nonfunctional library members, as well as allowing positive and negative selection logics using basally active promoters. A typical evolution experiment comprises the following stages: (i) preparation of a combinatorial M13 phagemid (PM) library expressing variants of the gene of interest (GOI) and preparation of the Escherichia coli host cells; (ii) multiple rounds of an intracellular selection process toward a desired activity; and (iii) the characterization of the evolved target proteins. The system has been developed for the selection of new orthogonal transcription factors (TFs) but is capable of evolving any gene-or gene circuit function-that can be linked to conditional M13 phage replication. Here we demonstrate our approach using as an example the directed evolution of the bacteriophage λ cI TF against two synthetic bidirectional promoters. The evolved TF variants enable simultaneous activation and repression against their engineered promoters and do not cross-react with the wild-type promoter, thus ensuring orthogonality. This protocol requires no special equipment, allowing synthetic biologists and general users to evolve improved biomolecules within ∼7 weeks.

Directed evolution of GH43 ß-xylosidase XylBH43 thermal stability and L186 saturation

USDA-ARS?s Scientific Manuscript database

Directed evolution of ß-xylosidase XylBH43 using DNA family shuffling identified three mutations R45K, M69P, and L186Y that affect thermal stability parameter Kt0.5 by -1.8±0.1 º C, 1.7±0.3 º C, and 3.2±0.4 º C, respectively. In addition, a cluster of four mutations near hairpin loop-D83 improved K...

Primary combination of phase-field and discrete dislocation dynamics methods for investigating athermal plastic deformation in various realistic Ni-base single crystal superalloy microstructures

NASA Astrophysics Data System (ADS)

Gao, Siwen; Rajendran, Mohan Kumar; Fivel, Marc; Ma, Anxin; Shchyglo, Oleg; Hartmaier, Alexander; Steinbach, Ingo

2015-10-01

Three-dimensional discrete dislocation dynamics (DDD) simulations in combination with the phase-field method are performed to investigate the influence of different realistic Ni-base single crystal superalloy microstructures with the same volume fraction of {γ\\prime} precipitates on plastic deformation at room temperature. The phase-field method is used to generate realistic microstructures as the boundary conditions for DDD simulations in which a constant high uniaxial tensile load is applied along different crystallographic directions. In addition, the lattice mismatch between the γ and {γ\\prime} phases is taken into account as a source of internal stresses. Due to the high antiphase boundary energy and the rare formation of superdislocations, precipitate cutting is not observed in the present simulations. Therefore, the plastic deformation is mainly caused by dislocation motion in γ matrix channels. From a comparison of the macroscopic mechanical response and the dislocation evolution for different microstructures in each loading direction, we found that, for a given {γ\\prime} phase volume fraction, the optimal microstructure should possess narrow and homogeneous γ matrix channels.

Directed evolution of an endoinulinase from Talaromyces purpureogenus toward efficient production of inulooligosaccharides.

PubMed

Afriat-Jurnou, Livnat; Cohen, Rami; Paluy, Irina; Ben-Adiva, Ran; Yadid, Itamar

2018-02-01

Inulinases are fructofuranosyl hydrolases that target the β-2,1 linkage of inulin and hydrolyze it into fructose, glucose and inulooligosaccharides (IOS), the latter are of growing interest as dietary fibers. Inulinases from various microorganisms have been purified, characterized and produced for industrial applications. However, there remains a need for inulinases with increased catalytic activity and better production yields to improve the hydrolysis process and fulfill the growing industrial demands for specific fibers. In this study, we used directed enzyme evolution to increase the yield and activity of an endoinulinase enzyme originated from the filamentous fungus Talaromyces purpureogenus (Penicillium purpureogenum ATCC4713). Our directed evolution approach yielded variants showing up to fivefold improvements in soluble enzyme production compared to the starting point which enabled high-yield production of highly purified recombinant enzyme. The distribution of the enzymatic reaction products demonstrated that after 24 h of incubation, the main product (57%) had a degree of polymerization of 3 (DP3). To the best of our knowledge, this is the first application of directed enzyme evolution to improve inulooligosaccharide production. The approach enabled the screening of large genetic libraries within short time frames and facilitated screening for improved enzymatic activities and properties, such as substrate specificity, product range, thermostability and pH optimum. © 2018 American Institute of Chemical Engineers Biotechnol. Prog., 2018. © 2018 American Institute of Chemical Engineers.

DNS of Flows over Periodic Hills using a Discontinuous-Galerkin Spectral-Element Method

NASA Technical Reports Server (NTRS)

Diosady, Laslo T.; Murman, Scott M.

2014-01-01

Direct numerical simulation (DNS) of turbulent compressible flows is performed using a higher-order space-time discontinuous-Galerkin finite-element method. The numerical scheme is validated by performing DNS of the evolution of the Taylor-Green vortex and turbulent flow in a channel. The higher-order method is shown to provide increased accuracy relative to low-order methods at a given number of degrees of freedom. The turbulent flow over a periodic array of hills in a channel is simulated at Reynolds number 10,595 using an 8th-order scheme in space and a 4th-order scheme in time. These results are validated against previous large eddy simulation (LES) results. A preliminary analysis provides insight into how these detailed simulations can be used to improve Reynoldsaveraged Navier-Stokes (RANS) modeling

Evidence of Twisted Flux-Tube Emergence in Active Regions

NASA Astrophysics Data System (ADS)

Poisson, M.; Mandrini, C. H.; Démoulin, P.; López Fuentes, M.

2015-03-01

Elongated magnetic polarities are observed during the emergence phase of bipolar active regions (ARs). These extended features, called magnetic tongues, are interpreted as a consequence of the azimuthal component of the magnetic flux in the toroidal flux-tubes that form ARs. We develop a new systematic and user-independent method to identify AR tongues. Our method is based on determining and analyzing the evolution of the AR main polarity inversion line (PIL). The effect of the tongues is quantified by measuring the acute angle [ τ] between the orientation of the PIL and the direction orthogonal to the AR main bipolar axis. We apply a simple model to simulate the emergence of a bipolar AR. This model lets us interpret the effect of magnetic tongues on parameters that characterize ARs ( e.g. the PIL inclination and the tilt angles, and their evolution). In this idealized kinematic emergence model, τ is a monotonically increasing function of the twist and has the same sign as the magnetic helicity. We systematically apply our procedure to a set of bipolar ARs (41 ARs) that were observed emerging in line-of-sight magnetograms over eight years. For most of the cases studied, the tongues only have a small influence on the AR tilt angle since tongues have a much lower magnetic flux than the more concentrated main polarities. From the observed evolution of τ, corrected for the temporal evolution of the tilt angle and its final value when the AR is fully emerged, we estimate the average number of turns in the subphotospherically emerging flux-rope. These values for the 41 observed ARs are below unity, except for one. This indicates that subphotospheric flux-ropes typically have a low amount of twist, i.e. highly twisted flux-tubes are rare. Our results demonstrate that the evolution of the PIL is a robust indicator of the presence of tongues and constrains the amount of twist in emerging flux-tubes.

Brachistochrone of entanglement for spin chains

NASA Astrophysics Data System (ADS)

Carlini, Alberto; Koike, Tatsuhiko

2017-03-01

We analytically investigate the role of entanglement in time-optimal state evolution as an application of the quantum brachistochrone, a general method for obtaining the optimal time-dependent Hamiltonian for reaching a target quantum state. As a model, we treat two qubits indirectly coupled through an intermediate qubit that is directly controllable, which represents a typical situation in quantum information processing. We find the time-optimal unitary evolution law and quantify residual entanglement by the two-tangle between the indirectly coupled qubits, for all possible sets of initial pure quantum states of a tripartite system. The integrals of the motion of the brachistochrone are determined by fixing the minimal time at which the residual entanglement is maximized. Entanglement plays a role for W and Greenberger-Horne-Zeilinger (GHz) initial quantum states, and for the bi-separable initial state in which the indirectly coupled qubits have a nonzero value of the 2-tangle.

Social dilemma alleviated by sharing the gains with immediate neighbors

NASA Astrophysics Data System (ADS)

Wu, Zhi-Xi; Yang, Han-Xin

2014-01-01

We study the evolution of cooperation in the evolutionary spatial prisoner's dilemma game (PDG) and snowdrift game (SG), within which a fraction α of the payoffs of each player gained from direct game interactions is shared equally by the immediate neighbors. The magnitude of the parameter α therefore characterizes the degree of the relatedness among the neighboring players. By means of extensive Monte Carlo simulations as well as an extended mean-field approximation method, we trace the frequency of cooperation in the stationary state. We find that plugging into relatedness can significantly promote the evolution of cooperation in the context of both studied games. Unexpectedly, cooperation can be more readily established in the spatial PDG than that in the spatial SG, given that the degree of relatedness and the cost-to-benefit ratio of mutual cooperation are properly formulated. The relevance of our model with the stakeholder theory is also briefly discussed.

Predicting Hot Deformation of AA5182 Sheet

NASA Astrophysics Data System (ADS)

Lee, John T.; Carpenter, Alexander J.; Jodlowski, Jakub P.; Taleff, Eric M.

Aluminum 5000-series alloy sheet materials exhibit substantial ductilities at hot and warm temperatures, even when grain size is not particularly fine. The relatively high strain-rate sensitivity exhibited by these non-superplastic materials, when deforming under solute-drag creep, is a primary contributor to large tensile ductilities. This active deformation mechanism influences both plastic flow and microstructure evolution across conditions of interest for hot- and warm-forming. Data are presented from uniaxial tensile and biaxial bulge tests of AA5182 sheet material at elevated temperatures. These data are used to construct a material constitutive model for plastic flow, which is applied in finite-element-method (FEM) simulations of plastic deformation under multiaxial stress states. Simulation results are directly compared against experimental data to explore the usefulness of this constitutive model. The effects of temperature and stress state on plastic response and microstructure evolution are discussed.

Management of Dynamic Biomedical Terminologies: Current Status and Future Challenges

PubMed Central

Dos Reis, J. C.; Pruski, C.

2015-01-01

Summary Objectives Controlled terminologies and their dependent artefacts provide a consensual understanding of a domain while reducing ambiguities and enabling reasoning. However, the evolution of a domain’s knowledge directly impacts these terminologies and generates inconsistencies in the underlying biomedical information systems. In this article, we review existing work addressing the dynamic aspect of terminologies as well as their effects on mappings and semantic annotations. Methods We investigate approaches related to the identification, characterization and propagation of changes in terminologies, mappings and semantic annotations including techniques to update their content. Results and conclusion Based on the explored issues and existing methods, we outline open research challenges requiring investigation in the near future. PMID:26293859

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

PubMed

Cortez, Michael H; Patel, Swati

2017-07-01

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

Selection methods regulate evolution of cooperation in digital evolution

PubMed Central

Lichocki, Paweł; Floreano, Dario; Keller, Laurent

2014-01-01

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

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

EON: software for long time simulations of atomic scale systems

NASA Astrophysics Data System (ADS)

Chill, Samuel T.; Welborn, Matthew; Terrell, Rye; Zhang, Liang; Berthet, Jean-Claude; Pedersen, Andreas; Jónsson, Hannes; Henkelman, Graeme

2014-07-01

The EON software is designed for simulations of the state-to-state evolution of atomic scale systems over timescales greatly exceeding that of direct classical dynamics. States are defined as collections of atomic configurations from which a minimization of the potential energy gives the same inherent structure. The time evolution is assumed to be governed by rare events, where transitions between states are uncorrelated and infrequent compared with the timescale of atomic vibrations. Several methods for calculating the state-to-state evolution have been implemented in EON, including parallel replica dynamics, hyperdynamics and adaptive kinetic Monte Carlo. Global optimization methods, including simulated annealing, basin hopping and minima hopping are also implemented. The software has a client/server architecture where the computationally intensive evaluations of the interatomic interactions are calculated on the client-side and the state-to-state evolution is managed by the server. The client supports optimization for different computer architectures to maximize computational efficiency. The server is written in Python so that developers have access to the high-level functionality without delving into the computationally intensive components. Communication between the server and clients is abstracted so that calculations can be deployed on a single machine, clusters using a queuing system, large parallel computers using a message passing interface, or within a distributed computing environment. A generic interface to the evaluation of the interatomic interactions is defined so that empirical potentials, such as in LAMMPS, and density functional theory as implemented in VASP and GPAW can be used interchangeably. Examples are given to demonstrate the range of systems that can be modeled, including surface diffusion and island ripening of adsorbed atoms on metal surfaces, molecular diffusion on the surface of ice and global structural optimization of nanoparticles.

The Evolution of Networked Computing in the Teaching of Japanese as a Foreign Language.

ERIC Educational Resources Information Center

Harrison, Richard

1998-01-01

Reviews the evolution of Internet-based projects in Japanese computer-assisted language learning and suggests future directions in which the field may develop, based on emerging network technology and learning theory. (Author/VWL)

Optimizing combined GPR, OSL and LiDAR (GOaL) to extract paleoenvironmental records and decipher shoreline evolution

NASA Astrophysics Data System (ADS)

Dougherty, A. J.; Choi, J. H.; Turney, C. S.; Dosseto, A.

2017-12-01

Records of past sea levels, storms, sediment supply and their impacts on the coastline are crucial for projecting likely shoreline changes resulting from anthropogenic warming. High-resolution geophysics, geochronology, and remote sensing techniques offer an optimal way to extract these records and decipher shoreline evolution. These methods include Light Detection and Ranging (LiDAR for imaging barrier morphologies in three dimensions), Ground Penetrating Radar (GPR for detecting paleo-dune, beach and nearshore stratigraphy) and Optically Stimulated Luminescence (OSL for dating deposition of sand grains along paleoshorelines). Each of these teqniques have been applied to coastal research over the decades since they were first introduced. Recently there has been a rapid increase their use since LiDAR became more available, GPR more user-friendly, and OSL more accessible. These methods have the potential to produce both detailed and voluminous datasets that can overwhelm or obscure significant features, such that discrepancies in analysis and/or presentation may lead to erroneous interpretations. In contrast, when utilized correctly on prograded barriers these methods (independently or in various combinations) have produced storm records, constructed sea-level curves, quantified sediment budgets, and deciphered coastal evolution. Therefore, combining the application of GPR, OSL, and LiDAR (GOaL) on one prograded barrier has the potential to generate detailed records of storms, sea level, and sediment supply for that coastline. Obtaining this GOaL hat-trick can provide valuable insights into how these three factors influenced past and future barrier evolution. Here we argue that systematically achieving GOaL hat-tricks on some of the 300+ prograded barriers worldwide would allow us to disentangle local patterns of sediment supply from regional effects of storms or global changes in sea level, allowing direct comparison to climate proxy records. To fully realize this aim requires standardization of methods to optimize results. The impetus for this initiative is to establish a framework for consistent data analysis that maximizes the potential of GOaL to contribute to climate change research and assist coastal communities in mitigating future impacts of global warming.

Non-Abelian gauge preheating

NASA Astrophysics Data System (ADS)

Adshead, Peter; Giblin, John T.; Weiner, Zachary J.

2017-12-01

We study preheating in models where a scalar inflaton is directly coupled to a non-Abelian S U (2 ) gauge field. In particular, we examine m2ϕ2 inflation with a conformal, dilatonlike coupling to the non-Abelian sector. We describe a numerical scheme that combines lattice gauge theory with standard finite difference methods applied to the scalar field. We show that a significant tachyonic instability allows for efficient preheating, which is parametrically suppressed by increasing the non-Abelian self-coupling. Additionally, we comment on the technical implementation of the evolution scheme and setting initial conditions.

Real space mapping of Li-ion transport in amorphous Si anodes with nanometer resolution.

PubMed

Balke, Nina; Jesse, Stephen; Kim, Yoongu; Adamczyk, Leslie; Tselev, Alexander; Ivanov, Ilia N; Dudney, Nancy J; Kalinin, Sergei V

2010-09-08

The electrical bias driven Li-ion motion in silicon anode materials in thin film battery heterostructures is investigated using electrochemical strain microscopy (ESM), which is a newly developed scanning probe microscopy based characterization method. ESM utilizes the intrinsic link between bias-controlled Li-ion concentration and molar volume of electrode materials, providing the capability for studies on the sub-20 nm scale, and allows the relationship between Li-ion flow and microstructure to be established. The evolution of Li-ion transport during the battery charging is directly observed.

Continuous directed evolution of aminoacyl-tRNA synthetases

PubMed Central

Bryson, David I.; Fan, Chenguang; Guo, Li-Tao; Miller, Corwin; Söll, Dieter; Liu, David R.

2017-01-01

Directed evolution of orthogonal aminoacyl-tRNA synthetases (AARSs) enables site-specific installation of non-canonical amino acids (ncAAs) into proteins. Traditional evolution techniques typically produce AARSs with greatly reduced activity and selectivity compared to their wild-type counterparts. We designed phage-assisted continuous evolution (PACE) selections to rapidly produce highly active and selective orthogonal AARSs through hundreds of generations of evolution. PACE of a chimeric Methanosarcina spp. pyrrolysyl-tRNA synthetase (PylRS) improved its enzymatic efficiency (kcat/KMtRNA) 45-fold compared to the parent enzyme. Transplantation of the evolved mutations into other PylRS-derived synthetases improved yields of proteins containing non-canonical residues up to 9.7-fold. Simultaneous positive and negative selection PACE over 48 h greatly improved the selectivity of a promiscuous Methanocaldococcus jannaschii tyrosyl-tRNA synthetase variant for site-specific incorporation of p-iodo-L-phenylalanine. These findings offer new AARSs that increase the utility of orthogonal translation systems and establish the capability of PACE to efficiently evolve orthogonal AARSs with high activity and amino acid specificity. PMID:29035361

Mapping the Geometric Evolution of Protein Folding Motor.

PubMed

Jerath, Gaurav; Hazam, Prakash Kishore; Shekhar, Shashi; Ramakrishnan, Vibin

2016-01-01

Polypeptide chain has an invariant main-chain and a variant side-chain sequence. How the side-chain sequence determines fold in terms of its chemical constitution has been scrutinized extensively and verified periodically. However, a focussed investigation on the directive effect of side-chain geometry may provide important insights supplementing existing algorithms in mapping the geometrical evolution of protein chains and its structural preferences. Geometrically, folding of protein structure may be envisaged as the evolution of its geometric variables: ϕ, and ψ dihedral angles of polypeptide main-chain directed by χ1, and χ2 of side chain. In this work, protein molecule is metaphorically modelled as a machine with 4 rotors ϕ, ψ, χ1 and χ2, with its evolution to the functional fold is directed by combinations of its rotor directions. We observe that differential rotor motions lead to different secondary structure formations and the combinatorial pattern is unique and consistent for particular secondary structure type. Further, we found that combination of rotor geometries of each amino acid is unique which partly explains how different amino acid sequence combinations have unique structural evolution and functional adaptation. Quantification of these amino acid rotor preferences, resulted in the generation of 3 substitution matrices, which later on plugged in the BLAST tool, for evaluating their efficiency in aligning sequences. We have employed BLOSUM62 and PAM30 as standard for primary evaluation. Generation of substitution matrices is a logical extension of the conceptual framework we attempted to build during the development of this work. Optimization of matrices following the conventional routines and possible application with biologically relevant data sets are beyond the scope of this manuscript, though it is a part of the larger project design.

A nudging-based data assimilation method: the Back and Forth Nudging (BFN) algorithm

NASA Astrophysics Data System (ADS)

Auroux, D.; Blum, J.

2008-03-01

This paper deals with a new data assimilation algorithm, called Back and Forth Nudging. The standard nudging technique consists in adding to the equations of the model a relaxation term that is supposed to force the observations to the model. The BFN algorithm consists in repeatedly performing forward and backward integrations of the model with relaxation (or nudging) terms, using opposite signs in the direct and inverse integrations, so as to make the backward evolution numerically stable. This algorithm has first been tested on the standard Lorenz model with discrete observations (perfect or noisy) and compared with the variational assimilation method. The same type of study has then been performed on the viscous Burgers equation, comparing again with the variational method and focusing on the time evolution of the reconstruction error, i.e. the difference between the reference trajectory and the identified one over a time period composed of an assimilation period followed by a prediction period. The possible use of the BFN algorithm as an initialization for the variational method has also been investigated. Finally the algorithm has been tested on a layered quasi-geostrophic model with sea-surface height observations. The behaviours of the two algorithms have been compared in the presence of perfect or noisy observations, and also for imperfect models. This has allowed us to reach a conclusion concerning the relative performances of the two algorithms.

The orbital evolution of NEA 30825 1900 TG1

NASA Astrophysics Data System (ADS)

Timoshkova, E. I.

2008-02-01

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

The 25 kW power module evolution study. Part 3: Conceptual designs for power module evolution. Volume 1: Power module evolution

NASA Technical Reports Server (NTRS)

1979-01-01

Candidate power module confugurations which will directly support an evolutionary scenario allowing growth from 25 kW to 100 kW are described. The growth rationale is structured to support a nominal scenario for sortie mission support to the POrbiter and to free-flying payloads during the 1983 to 1990 era.

Experimental investigations of an AC pulse heating method for vehicular high power lithium-ion batteries at subzero temperatures

NASA Astrophysics Data System (ADS)

Zhu, Jiangong; Sun, Zechang; Wei, Xuezhe; Dai, Haifeng; Gu, Weijun

2017-11-01

Effect of the AC (alternating current) pulse heating method on battery SoH (state of health) for large laminated power lithium-ion batteries at low temperature is investigated experimentally. Firstly, excitation current frequencies, amplitudes, and voltage limitations on cell temperature evolution are studied. High current amplitudes facilitate the heat accumulation and temperature rise. Low frequency region serves as a good innovation to heat the battery because of the large impedance. Wide voltage limitations also enjoy better temperature evolution owing to the less current modulation, but the temperature difference originated from various voltage limitations attenuates due to the decrement of impedance resulting from the temperature rise. Experiments with the thermocouple-embedded cell manifest good temperature homogeneity between the battery surface and interior during the AC heating process. Secondly, the cell capacity, Direct Current resistance and Electrochemical Impedance Spectroscopy are all calibrated to assess the battery SoH after the hundreds of AC pulse heating cycles. Also, all cells are disassembled to investigate the battery internal morphology with the employment of Scanning Electron Microscope and Energy-Dispersive x-ray Spectroscopy techniques. The results indicate that the AC heating method does not aggravate the cell degradation even in the low frequency range (0.5 Hz) under the normal voltage protection limitation.

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

PubMed

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

2016-02-01

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

Observations of Fabric Development in Polycrystalline Ice at Basal Pressures: Methods and Initial Results

NASA Astrophysics Data System (ADS)

Breton, D. J.; Baker, I.; Cole, D. M.

2012-12-01

Understanding and predicting the flow of polycrystalline ice is crucial to ice sheet modeling and paleoclimate reconstruction from ice cores. Ice flow rates depend strongly on the fabric (i.e. the distribution of grain sizes and crystallographic orientations) which evolves over time and enhances the flow rate in the direction of applied stress. The mechanisms for fabric evolution in ice have been extensively studied at atmospheric pressures, but little work has been done to observe these processes at the high pressures experienced deep within ice sheets where long-term changes in ice rheology are expected to have significance. We conducted compressive creep tests on a 917 kg m-3 polycrystalline ice specimen at 20 MPa hydrostatic pressure, thus simulating ~2,000 m depth. Initial specimen grain orientations were random, typical grain diameters were 1.2 mm, and the applied creep stress was 0.3 MPa. Subsequent microstructural analyses on the deformed specimen and a similarly prepared, undeformed specimen allowed characterization of crystal fabric evolution under pressure. Our microstructural analysis technique simultaneously collected grain shape and size data from Scanning Electron Microscope (SEM) micrographs and obtained crystallographic orientation data via Electron BackScatter Diffraction (EBSD). Combining these measurements allows rapid analysis of the ice fabric over large numbers of grains, yielding statistically useful numbers of grain size and full c- and a-axis grain orientation data. The combined creep and microstructural data demonstrate pressure-dependent effects on the mechanical and microstructural evolution of polycrystalline ice. We discuss possible mechanisms for the observed phenomena, and future directions for hydrostatic creep testing.

Measurement and potential barrier evolution analysis of cold field emission in fracture fabricated Si nanogap

NASA Astrophysics Data System (ADS)

Banerjee, Amit; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

2017-06-01

Cold field emission characteristics of a fracture fabricated Si nanogap (˜100 nm) were investigated with an ascending electric field (voltage) sweep. The nanogap was formed by controlled fracture of a free-standing silicon micro-beam along <111> direction by a microelectromechanical device, which results in flat, smooth, and conformal electrode pairs. This facilitates simultaneous large area emission, which gives rise to a significant current at low bias voltage, which usually remains indiscernible in nanogaps of this size. The measured emission current-voltage (I-V) characteristics clearly depict two distinct regimes: a linear (I ∝ V) regime at low bias voltage and a nonlinear [ln(I/V 2) ∝ V -1] regime at high bias voltage, separated by a transition point. We propose that the linear regime is owed to direct tunneling of electrons, whereas the nonlinear regime is due to Fowler-Nordheim type emission. This proposition essentially implies that the tunneling potential barrier gradually evolved from a rectangular shape to a triangular shape with increasing field (V). This type of evolution is usually observed in molecular size gaps. We have attempted to correlate the I-V curves acquired through the experiments with the electric field induced barrier shape evolution by numerical calculations involving standard quantum mechanics. The observed linear regime at low bias voltage (<5 V) in a relatively large size gap (˜100 nm) is attributed to the fabrication method adopted in this study. The reported study and the fabricated device are significant for developing a futuristic thermotunneling refrigerator that will find a wide range of application in nanoelectronic devices.

Darwin Assembly: fast, efficient, multi-site bespoke mutagenesis

PubMed Central

Cozens, Christopher

2018-01-01

Abstract Engineering proteins for designer functions and biotechnological applications almost invariably requires (or at least benefits from) multiple mutations to non-contiguous residues. Several methods for multiple site-directed mutagenesis exist, but there remains a need for fast and simple methods to efficiently introduce such mutations – particularly for generating large, high quality libraries for directed evolution. Here, we present Darwin Assembly, which can deliver high quality libraries of >108 transformants, targeting multiple (>10) distal sites with minimal wild-type contamination (<0.25% of total population) and which takes a single working day from purified plasmid to library transformation. We demonstrate its efficacy with whole gene codon reassignment of chloramphenicol acetyl transferase, mutating 19 codons in a single reaction in KOD DNA polymerase and generating high quality, multiple-site libraries in T7 RNA polymerase and Tgo DNA polymerase. Darwin Assembly uses commercially available enzymes, can be readily automated, and offers a cost-effective route to highly complex and customizable library generation. PMID:29409059

NMR imaging of density distributions in tablets.

PubMed

Djemai, A; Sinka, I C

2006-08-17

This paper describes the use of (1)H nuclear magnetic resonance (NMR) for 3D mapping of the relative density distribution in pharmaceutical tablets manufactured under controlled conditions. The tablets are impregnated with a compatible liquid. The technique involves imaging of the presence of liquid which occupies the open pore space. The method does not require special calibration as the signal is directly proportional to the porosity for the imaging conditions used. The NMR imaging method is validated using uniform density flat faced tablets and also by direct comparison with X-ray computed tomography. The results illustrate (1) the effect of die wall friction on density distribution by compressing round, curved faced tablets using clean and pre-lubricated tooling, (2) the evolution of density distribution during compaction for both clean and pre-lubricated die wall conditions, by imaging tablets compressed to different compaction forces, and (3) the effect of tablet image on density distribution by compressing two complex shape tablets in identical dies to the same average density using punches with different geometries.

Benefits of rotational ground motions for planetary seismology

NASA Astrophysics Data System (ADS)

Donner, S.; Joshi, R.; Hadziioannou, C.; Nunn, C.; van Driel, M.; Schmelzbach, C.; Wassermann, J. M.; Igel, H.

2017-12-01

Exploring the internal structure of planetary objects is fundamental to understand the evolution of our solar system. In contrast to Earth, planetary seismology is hampered by the limited number of stations available, often just a single one. Classic seismology is based on the measurement of three components of translational ground motion. Its methods are mainly developed for a larger number of available stations. Therefore, the application of classical seismological methods to other planets is very limited. Here, we show that the additional measurement of three components of rotational ground motion could substantially improve the situation. From sparse or single station networks measuring translational and rotational ground motions it is possible to obtain additional information on structure and source. This includes direct information on local subsurface seismic velocities, separation of seismic phases, propagation direction of seismic energy, crustal scattering properties, as well as moment tensor source parameters for regional sources. The potential of this methodology will be highlighted through synthetic forward and inverse modeling experiments.

Direct method of design and stress analysis of rotating disks with temperature gradient

NASA Technical Reports Server (NTRS)

Manson, S S

1950-01-01

A method is presented for the determination of the contour of disks, typified by those of aircraft gas turbines, to incorporate arbitrary elastic-stress distributions resulting from either centrifugal or combined centrifugal and thermal effects. The specified stress may be radial, tangential, or any combination of the two. Use is made of the finite-difference approach in solving the stress equations, the amount of computation necessary in the evolution of a design being greatly reduced by the judicious selection of point stations by the aid of a design chart. Use of the charts and of a preselected schedule of point stations is also applied to the direct problem of finding the elastic and plastic stress distribution in disks of a given design, thereby effecting a great reduction in the amount of calculation. Illustrative examples are presented to show computational procedures in the determination of a new design and in analyzing an existing design for elastic stress and for stresses resulting from plastic flow.

Radiative transport produced by oblique illumination of turbid media with collimated beams

NASA Astrophysics Data System (ADS)

Gardner, Adam R.; Kim, Arnold D.; Venugopalan, Vasan

2013-06-01

We examine the general problem of light transport initiated by oblique illumination of a turbid medium with a collimated beam. This situation has direct relevance to the analysis of cloudy atmospheres, terrestrial surfaces, soft condensed matter, and biological tissues. We introduce a solution approach to the equation of radiative transfer that governs this problem, and develop a comprehensive spherical harmonics expansion method utilizing Fourier decomposition (SHEFN). The SHEFN approach enables the solution of problems lacking azimuthal symmetry and provides both the spatial and directional dependence of the radiance. We also introduce the method of sequential-order smoothing that enables the calculation of accurate solutions from the results of two sequential low-order approximations. We apply the SHEFN approach to determine the spatial and angular dependence of both internal and boundary radiances from strongly and weakly scattering turbid media. These solutions are validated using more costly Monte Carlo simulations and reveal important insights regarding the evolution of the radiant field generated by oblique collimated beams spanning ballistic and diffusely scattering regimes.

Analytic study of solutions for a (3 + 1) -dimensional generalized KP equation

NASA Astrophysics Data System (ADS)

Gao, Hui; Cheng, Wenguang; Xu, Tianzhou; Wang, Gangwei

2018-03-01

The (3 + 1) -dimensional generalized KP (gKP) equation is an important nonlinear partial differential equation in theoretical and mathematical physics which can be used to describe nonlinear wave motion. Through the Hirota bilinear method, one-solition, two-solition and N-solition solutions are derived via symbolic computation. Two classes of lump solutions, rationally localized in all directions in space, to the dimensionally reduced cases in (2 + 1)-dimensions, are constructed by using a direct method based on the Hirota bilinear form of the equation. It implies that we can derive the lump solutions of the reduced gKP equation from positive quadratic function solutions to the aforementioned bilinear equation. Meanwhile, we get interaction solutions between a lump and a kink of the gKP equation. The lump appears from a kink and is swallowed by it with the change of time. This work offers a possibility which can enrich the variety of the dynamical features of solutions for higher-dimensional nonlinear evolution equations.

Emerging directions in the study of the ecology and evolution of plant-animal mutualistic networks: a review.

PubMed

Gu, Hao; Goodale, Eben; Chen, Jin

2015-03-18

The study of mutualistic plant and animal networks is an emerging field of ecological research. We reviewed progress in this field over the past 30 years. While earlier studies mostly focused on network structure, stability, and biodiversity maintenance, recent studies have investigated the conservation implications of mutualistic networks, specifically the influence of invasive species and how networks respond to habitat loss. Current research has also focused on evolutionary questions including phylogenetic signal in networks, impact of networks on the coevolution of interacting partners, and network influences on the evolution of interacting species. We outline some directions for future research, particularly the evolution of specialization in mutualistic networks, and provide concrete recommendations for environmental managers.

Incorporation of Plasticity and Damage Into an Orthotropic Three-Dimensional Model with Tabulated Input Suitable for Use in Composite Impact Problems

NASA Technical Reports Server (NTRS)

Goldberg, Robert K.; Carney, Kelly S.; DuBois, Paul; Hoffarth, Canio; Rajan, Subramaniam; Blackenhorn, Gunther

2015-01-01

The need for accurate material models to simulate the deformation, damage and failure of polymer matrix composites under impact conditions is becoming critical as these materials are gaining increased usage in the aerospace and automotive industries. While there are several composite material models currently available within commercial transient dynamic finite element codes, several features have been identified as being lacking in the currently available material models that could substantially enhance the predictive capability of the impact simulations. A specific desired feature pertains to the incorporation of both plasticity and damage within the material model. Another desired feature relates to using experimentally based tabulated stress-strain input to define the evolution of plasticity and damage as opposed to specifying discrete input properties (such as modulus and strength) and employing analytical functions to track the response of the material. To begin to address these needs, a combined plasticity and damage model suitable for use with both solid and shell elements is being developed for implementation within the commercial code LS-DYNA. The plasticity model is based on extending the Tsai-Wu composite failure model into a strain-hardening based orthotropic plasticity model with a non-associative flow rule. The evolution of the yield surface is determined based on tabulated stress-strain curves in the various normal and shear directions and is tracked using the effective plastic strain. The effective plastic strain is computed by using the non-associative flow rule in combination with appropriate numerical methods. To compute the evolution of damage, a strain equivalent semi-coupled formulation is used, in which a load in one direction results in a stiffness reduction in multiple coordinate directions. A specific laminated composite is examined to demonstrate the process of characterizing and analyzing the response of a composite using the developed model.

On the wall-normal velocity of the compressible boundary-layer equations

NASA Technical Reports Server (NTRS)

Pruett, C. David

1991-01-01

Numerical methods for the compressible boundary-layer equations are facilitated by transformation from the physical (x,y) plane to a computational (xi,eta) plane in which the evolution of the flow is 'slow' in the time-like xi direction. The commonly used Levy-Lees transformation results in a computationally well-behaved problem for a wide class of non-similar boundary-layer flows, but it complicates interpretation of the solution in physical space. Specifically, the transformation is inherently nonlinear, and the physical wall-normal velocity is transformed out of the problem and is not readily recovered. In light of recent research which shows mean-flow non-parallelism to significantly influence the stability of high-speed compressible flows, the contribution of the wall-normal velocity in the analysis of stability should not be routinely neglected. Conventional methods extract the wall-normal velocity in physical space from the continuity equation, using finite-difference techniques and interpolation procedures. The present spectrally-accurate method extracts the wall-normal velocity directly from the transformation itself, without interpolation, leaving the continuity equation free as a check on the quality of the solution. The present method for recovering wall-normal velocity, when used in conjunction with a highly-accurate spectral collocation method for solving the compressible boundary-layer equations, results in a discrete solution which is extraordinarily smooth and accurate, and which satisfies the continuity equation nearly to machine precision. These qualities make the method well suited to the computation of the non-parallel mean flows needed by spatial direct numerical simulations (DNS) and parabolized stability equation (PSE) approaches to the analysis of stability.

Evolution in response to direct and indirect ecological effects in pitcher plant inquiline communities.

PubMed

terHorst, Casey P

2010-12-01

Ecologists have long recognized the importance of indirect ecological effects on species abundances, coexistence, and diversity. However, the evolutionary consequences of indirect interactions are rarely considered. Here I conduct selection experiments and examine the evolutionary response of Colpoda sp., a ciliated protozoan, to other members of the inquiline community of purple pitcher plants (Sarracenia purpurea). I measured the evolution of six traits in response to (1) predation by mosquito larvae, (2) competition from other ciliated protozoans, and (3) simultaneous predation and competition. The latter treatment incorporated both direct effects and indirect effects due to interactions between predators and competitors. Population growth rate and cell size evolved in response to direct effects of predators and competitors. However, trait values in the multispecies treatment were similar to those in the monoculture treatment, indicating that direct effects were offset by strong indirect effects on the evolution of traits. For most of the traits measured, indirect effects were opposed to, and often stronger than, direct effects. These indirect effects occurred as a result of behavioral changes of the predator in the presence of competitors and as a result of reduced densities of competitors in the presence of predators. Incorporating indirect effects provides a more realistic description of how species evolve in complex natural communities.

Selection on skewed characters and the paradox of stasis.

PubMed

Bonamour, Suzanne; Teplitsky, Céline; Charmantier, Anne; Crochet, Pierre-André; Chevin, Luis-Miguel

2017-11-01

Observed phenotypic responses to selection in the wild often differ from predictions based on measurements of selection and genetic variance. An overlooked hypothesis to explain this paradox of stasis is that a skewed phenotypic distribution affects natural selection and evolution. We show through mathematical modeling that, when a trait selected for an optimum phenotype has a skewed distribution, directional selection is detected even at evolutionary equilibrium, where it causes no change in the mean phenotype. When environmental effects are skewed, Lande and Arnold's (1983) directional gradient is in the direction opposite to the skew. In contrast, skewed breeding values can displace the mean phenotype from the optimum, causing directional selection in the direction of the skew. These effects can be partitioned out using alternative selection estimates based on average derivatives of individual relative fitness, or additive genetic covariances between relative fitness and trait (Robertson-Price identity). We assess the validity of these predictions using simulations of selection estimation under moderate sample sizes. Ecologically relevant traits may commonly have skewed distributions, as we here exemplify with avian laying date - repeatedly described as more evolutionarily stable than expected - so this skewness should be accounted for when investigating evolutionary dynamics in the wild. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Effect of Processing Pressure on Isolated Pore Formation during Controlled Directional Solidification in Small Channels

NASA Technical Reports Server (NTRS)

Cox, Matthew C.; Anilkumar, Amrutur V.; Grugel, RIchard N.; Lee, Chun P.

2008-01-01

Directional solidification experiments were performed, using succinonitrile saturated with nitrogen gas, to examine the effects of in-situ processing pressure changes on the formation growth, and evolution of an isolated, cylindrical gaseous pore. A novel solidification facility, capable of processing thin cylindrical samples (I.D. < 1.0 mm), under controlled pressure conditions, was used for the experiments. A new experimental method for growing the isolated pore from a seed bubble is introduced. The experimental results indicate that an in-situ processing pressure change will result in either a transient change in pore diameter or a complete termination of pore growth, indicating that pressure changes can be used as a control parameter to terminate bubble growth. A simple analytical model has been introduced to explain the experimental observations.

Reynolds Stress Balance in Plane Wakes Subjected to Irrotational Strains

NASA Technical Reports Server (NTRS)

Rogers, Miichael M.; Merriam, Marshal (Technical Monitor)

1997-01-01

Direct numerical simulations of time-evolving turbulent plane wakes developing in the presence of various irrotational plane strains have been generated. A pseudospectral numerical method with up to 25 million modes is used to solve the equations in a reference frame moving with the irrotational strain. The initial condition for each simulation is taken from a previous turbulent self-similar plane wake direct numerical simulation at a velocity deficit Reynolds number, R(sub e), of about 2,000. All the terms in the equations governing the evolution of the Reynolds stresses have been calculated. The relative importance of the various terms is examined for the different strain geometries and the behavior of the individual terms is used to better assess whether the strained wakes are evolving self-similarly.

Evaluation of thermal behavior during laser metal deposition using optical pyrometry and numerical simulation

NASA Astrophysics Data System (ADS)

Dubrov, Alexander V.; Zavalov, Yuri N.; Mirzade, Fikret K.; Dubrov, Vladimir D.

2017-06-01

3D mathematical model of non-stationary processes of heat and mass transfer was developed for additive manufacturing of materials by direct laser metal deposition. The model takes into account self-consistent dynamics of free surface, temperature fields, and melt flow speeds. Evolution of free surface is modelled using combined Volume of Fluid and Level-Set method. Article presents experimental results of the measurement of temperature distribution in the area of bead formation by direct laser metal deposition, using multi-channel pyrometer, that is based on two-color sensors line. A comparison of experimental data with the results of numerical modeling was carried out. Features of thermal dynamics on the surface of melt pool have been detected, which were caused by thermo-capillary convection.

Enzymes useful for chiral compound synthesis: structural biology, directed evolution, and protein engineering for industrial use.

PubMed

Kataoka, Michihiko; Miyakawa, Takuya; Shimizu, Sakayu; Tanokura, Masaru

2016-07-01

Biocatalysts (enzymes) have many advantages as catalysts for the production of useful compounds as compared to chemical catalysts. The stereoselectivity of the enzymes is one advantage, and thus the stereoselective production of chiral compounds using enzymes is a promising approach. Importantly, industrial application of the enzymes for chiral compound production requires the discovery of a novel useful enzyme or enzyme function; furthermore, improving the enzyme properties through protein engineering and directed evolution approaches is significant. In this review, the significance of several enzymes showing stereoselectivity (quinuclidinone reductase, aminoalcohol dehydrogenase, old yellow enzyme, and threonine aldolase) in chiral compound production is described, and the improvement of these enzymes using protein engineering and directed evolution approaches for further usability is discussed. Currently, enzymes are widely used as catalysts for the production of chiral compounds; however, for further use of enzymes in chiral compound production, improvement of enzymes should be more essential, as well as discovery of novel enzymes and enzyme functions.

Niche construction, sources of selection and trait coevolution.

PubMed

Laland, Kevin; Odling-Smee, John; Endler, John

2017-10-06

Organisms modify and choose components of their local environments. This 'niche construction' can alter ecological processes, modify natural selection and contribute to inheritance through ecological legacies. Here, we propose that niche construction initiates and modifies the selection directly affecting the constructor, and on other species, in an orderly, directed and sustained manner. By dependably generating specific environmental states, niche construction co-directs adaptive evolution by imposing a consistent statistical bias on selection. We illustrate how niche construction can generate this evolutionary bias by comparing it with artificial selection. We suggest that it occupies the middle ground between artificial and natural selection. We show how the perspective leads to testable predictions related to: (i) reduced variance in measures of responses to natural selection in the wild; (ii) multiple trait coevolution, including the evolution of sequences of traits and patterns of parallel evolution; and (iii) a positive association between niche construction and biodiversity. More generally, we submit that evolutionary biology would benefit from greater attention to the diverse properties of all sources of selection.

Effect of differential speed rolling on the texture evolution of Mg-4Zn-1Gd alloy

NASA Astrophysics Data System (ADS)

Shim, Myeong-Shik; Suh, Byeong-Chan; Kim, Jae H.; Kim, Nack J.

2015-05-01

The microstructural and texture evolution during differential speed rolling process of Mg 4Zn-1Gd (wt%) alloy have been investigated by means of electron backscatter diffraction observation and texture analysis. The angular distribution of basal poles are inclined about 10° from the normal direction towards the rolling direction and the maximum intensities of basal poles are decreased, compared to the conventional rolling process. Such an inclination of angular distribution of basal poles can be induced by the operation of shear stress along the rolling direction, as much as one quarter of tensile stress along the RD and one quarter of compressive stress along the ND. When the reduction ratios in differential speed rolling increase, there is no difference in texture evolution although there is a significant change in activated twinning systems. In addition, the engineering stresses after differential speed rolling are also similar to that after conventional rolling process, while ductility and stretch formability in the former are worse than those in the latter.

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

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

Li, Yulan; Hu, Shenyang; Sun, Xin

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

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

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

Li, Yulan; Hu, Shenyang; Sun, Xin

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

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

DOE PAGES

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

2017-04-14

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

Epoch-based likelihood models reveal no evidence for accelerated evolution of viviparity in squamate reptiles in response to cenozoic climate change.

PubMed

King, Benedict; Lee, Michael S Y

2015-09-01

A broad scale analysis of the evolution of viviparity across nearly 4,000 species of squamates revealed that origins increase in frequency toward the present, raising the question of whether rates of change have accelerated. We here use simulations to show that the increased frequency is within the range expected given that the number of squamate lineages also increases with time. Novel, epoch-based methods implemented in BEAST (which allow rates of discrete character evolution to vary across time-slices) also give congruent results, with recent epochs having very similar rates to older epochs. Thus, contrary to expectations, there was no accelerated burst of origins of viviparity in response to global cooling during the Cenozoic or glacial cycles during the Plio-Pleistocene. However, if one accepts the conventional view that viviparity is more likely to evolve than to be lost, and also the evidence here that viviparity has evolved with similar regularity throughout the last 200 Ma, then the absence of large, ancient clades of viviparous squamates (analogs to therian mammals) requires explanation. Viviparous squamate lineages might be more prone to extinction than are oviparous lineages, due to their prevalance at high elevations and latitudes and thus greater susceptibility to climate fluctuations. If so, the directional bias in character evolution would be offset by the bias in extinction rates. © 2015 Wiley Periodicals, Inc.

Evosystem Services: Rapid Evolution and the Provision of Ecosystem Services.

PubMed

Rudman, Seth M; Kreitzman, Maayan; Chan, Kai M A; Schluter, Dolph

2017-06-01

Evolution is recognized as the source of all organisms, and hence many ecosystem services. However, the role that contemporary evolution might play in maintaining and enhancing specific ecosystem services has largely been overlooked. Recent advances at the interface of ecology and evolution have demonstrated how contemporary evolution can shape ecological communities and ecosystem functions. We propose a definition and quantitative criteria to study how rapid evolution affects ecosystem services (here termed contemporary evosystem services) and present plausible scenarios where such services might exist. We advocate for the direct measurement of contemporary evosystem services to improve understanding of how changing environments will alter resource availability and human well-being, and highlight the potential utility of managing rapid evolution for future ecosystem services. Copyright © 2017 Elsevier Ltd. All rights reserved.

A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution.

PubMed

Blanquart, Samuel; Lartillot, Nicolas

2006-11-01

Variations of nucleotidic composition affect phylogenetic inference conducted under stationary models of evolution. In particular, they may cause unrelated taxa sharing similar base composition to be grouped together in the resulting phylogeny. To address this problem, we developed a nonstationary and nonhomogeneous model accounting for compositional biases. Unlike previous nonstationary models, which are branchwise, that is, assume that base composition only changes at the nodes of the tree, in our model, the process of compositional drift is totally uncoupled from the speciation events. In addition, the total number of events of compositional drift distributed across the tree is directly inferred from the data. We implemented the method in a Bayesian framework, relying on Markov Chain Monte Carlo algorithms, and applied it to several nucleotidic data sets. In most cases, the stationarity assumption was rejected in favor of our nonstationary model. In addition, we show that our method is able to resolve a well-known artifact. By Bayes factor evaluation, we compared our model with 2 previously developed nonstationary models. We show that the coupling between speciations and compositional shifts inherent to branchwise models may lead to an overparameterization, resulting in a lesser fit. In some cases, this leads to incorrect conclusions, concerning the nature of the compositional biases. In contrast, our compound model more flexibly adapts its effective number of parameters to the data sets under investigation. Altogether, our results show that accounting for nonstationary sequence evolution may require more elaborate and more flexible models than those currently used.

Effects of high pressure on microstructure evolution and crystallization mechanisms during solidification of nickel

NASA Astrophysics Data System (ADS)

Zhang, Hai-Tao; Mo, Yun-Fei; Liu, Rang-Su; Tian, Ze-An; Liu, Hai-Rong; Hou, Zhao-Yang; Zhou, Li-Li; Liang, Yong-Chao; Peng, Ping

2018-03-01

To deeply understand the effects of high pressure on microstructural evolutions and crystallization mechanisms of liquid metal Ni during solidification process, MD simulation studies have been performed under 7 pressures of 0 ˜ 30 GPa, at cooling rate of 1.0 × 1011 K s-1. Adopting several microstructural analyzing methods, especially the cluster-type index method (CTIM-2) to analyze the local microstructures in the system. It is found that the pressure has important influence on the formation and evolution of microstructures, especially of the main basic clusters in the system. All the simulation systems are directly solidified into crystal structures, and the 1421, 1422, 1441 and 1661 bond-types, as well the FCC (12 0 0 0 12 0), HCP (12 0 0 0 6 6) and BCC (14 6 0 8 0 0) clusters play a key role in the microstructure transitions from liquid to crystal structures. The crystallization temperature T c is enhanced almost linearly with the increase of pressure. Highly interesting, it is found for the first time that there is an important phase transformation point from FCC to BCC structures between 20 ˜ 22.5 GPa during the solidification processes from the same initial liquid system at the same cooling rate. And the effect of increasing pressure is similar to that of decreasing cooling rate for the phase transformation of microstructures during solidification process of liquid metal Ni system, though they have different concrete effecting mechanisms.

Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution.

PubMed

Zanno, Lindsay E; Makovicky, Peter J

2011-01-04

Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs--a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet.

Herbivorous ecomorphology and specialization patterns in theropod dinosaur evolution

PubMed Central

Zanno, Lindsay E.; Makovicky, Peter J.

2011-01-01

Interpreting key ecological parameters, such as diet, of extinct organisms without the benefit of direct observation or explicit fossil evidence poses a formidable challenge for paleobiological studies. To date, dietary categorizations of extinct taxa are largely generated by means of modern analogs; however, for many species the method is subject to considerable ambiguity. Here we present a refined approach for assessing trophic habits in fossil taxa and apply the method to coelurosaurian dinosaurs—a clade for which diet is particularly controversial. Our findings detect 21 morphological features that exhibit statistically significant correlations with extrinsic fossil evidence of coelurosaurian herbivory, such as stomach contents and a gastric mill. These traits represent quantitative, extrinsically founded proxies for identifying herbivorous ecomorphology in fossils and are robust despite uncertainty in phylogenetic relationships among major coelurosaurian subclades. The distribution of these features suggests that herbivory was widespread among coelurosaurians, with six major subclades displaying morphological evidence of the diet, and that contrary to previous thought, hypercarnivory was relatively rare and potentially secondarily derived. Given the potential for repeated, independent evolution of herbivory in Coelurosauria, we also test for repetitive patterns in the appearance of herbivorous traits within sublineages using rank concordance analysis. We find evidence for a common succession of increasing specialization to herbivory in the subclades Ornithomimosauria and Oviraptorosauria, perhaps underlain by intrinsic functional and/or developmental constraints, as well as evidence indicating that the early evolution of a beak in coelurosaurians correlates with an herbivorous diet. PMID:21173263

Real-space finite-difference approach for multi-body systems: path-integral renormalization group method and direct energy minimization method.

PubMed

Sasaki, Akira; Kojo, Masashi; Hirose, Kikuji; Goto, Hidekazu

2011-11-02

The path-integral renormalization group and direct energy minimization method of practical first-principles electronic structure calculations for multi-body systems within the framework of the real-space finite-difference scheme are introduced. These two methods can handle higher dimensional systems with consideration of the correlation effect. Furthermore, they can be easily extended to the multicomponent quantum systems which contain more than two kinds of quantum particles. The key to the present methods is employing linear combinations of nonorthogonal Slater determinants (SDs) as multi-body wavefunctions. As one of the noticeable results, the same accuracy as the variational Monte Carlo method is achieved with a few SDs. This enables us to study the entire ground state consisting of electrons and nuclei without the need to use the Born-Oppenheimer approximation. Recent activities on methodological developments aiming towards practical calculations such as the implementation of auxiliary field for Coulombic interaction, the treatment of the kinetic operator in imaginary-time evolutions, the time-saving double-grid technique for bare-Coulomb atomic potentials and the optimization scheme for minimizing the total-energy functional are also introduced. As test examples, the total energy of the hydrogen molecule, the atomic configuration of the methylene and the electronic structures of two-dimensional quantum dots are calculated, and the accuracy, availability and possibility of the present methods are demonstrated.

Ultrafast Synthesis and Related Phase Evolution of Mg2Si and Mg2Sn Compounds

NASA Astrophysics Data System (ADS)

Zhang, Qiang; Lu, Qiangbing; Yan, Yonggao; Su, Xianli; Tang, Xinfeng

2017-05-01

Both Mg2Si and Mg2Sn compounds were synthesized by an ultra-fast self-propagating high-temperature synthesis (SHS) method. The data regarding SHS were obtained via theoretical calculation combined with experiments, showing that the adiabatic temperature T ad and ignition temperature T ig of Mg2Si are a little higher than those of Mg2Sn. The mechanism of phase evolution and the concomitant microstructure evolution during the synthesis process of Mg2Si and Mg2Sn compounds were investigated by adopting SHS technique coupled with a sudden quenching treatment. Differential scanning calorimetry (DSC), field emission scanning electron microscopy (FESEM), and x-ray powder diffraction (XRD) results indicate that Mg2Si compound can be directly synthesized through the reaction of Mg and Si elements at around 850 K. Correspondingly, the formation of Mg2Sn needs to undergo melting of Sn and the subsequent feeble reaction between Mg and Sn elements before the large scale transformation at 730 K. As the groundwork, this research embodies great significance for future study on the ultrafast SHS process of the ternary Mg2Si1- x Sn x solid solutions.

Accounting for rate variation among lineages in comparative demographic analyses.

PubMed

Hope, Andrew G; Ho, Simon Y W; Malaney, Jason L; Cook, Joseph A; Talbot, Sandra L

2014-09-01

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies. © 2014 The Author(s). Evolution © 2014 The Society for the Study of Evolution.

Visualizing Complex Environments in the Geo- and BioSciences

NASA Astrophysics Data System (ADS)

Prabhu, A.; Fox, P. A.; Zhong, H.; Eleish, A.; Ma, X.; Zednik, S.; Morrison, S. M.; Moore, E. K.; Muscente, D.; Meyer, M.; Hazen, R. M.

2017-12-01

Earth's living and non-living components have co-evolved for 4 billion years through numerous positive and negative feedbacks. Earth and life scientists have amassed vast amounts of data in diverse fields related to planetary evolution through deep time-mineralogy and petrology, paleobiology and paleontology, paleotectonics and paleomagnetism, geochemistry and geochrononology, genomics and proteomics, and more. Integrating the data from these complimentary disciplines is very useful in gaining an understanding of the evolution of our planet's environment. The integrated data however, represent many extremely complex environments. In order to gain insights and make discoveries using this data, it is important for us to model and visualize these complex environments. As part of work in understanding the "Co-Evolution of Geo and Biospheres using Data Driven Methodologies," we have developed several visualizations to help represent the information stored in the datasets from complimentary disciplines. These visualizations include 2D and 3D force directed Networks, Chord Diagrams, 3D Klee Diagrams. Evolving Network Diagrams, Skyline Diagrams and Tree Diagrams. Combining these visualizations with the results of machine learning and data analysis methods leads to a powerful way to discover patterns and relationships about the Earth's past and today's changing environment.

FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants.

PubMed

Bednar, David; Beerens, Koen; Sebestova, Eva; Bendl, Jaroslav; Khare, Sagar; Chaloupkova, Radka; Prokop, Zbynek; Brezovsky, Jan; Baker, David; Damborsky, Jiri

2015-11-01

There is great interest in increasing proteins' stability to enhance their utility as biocatalysts, therapeutics, diagnostics and nanomaterials. Directed evolution is a powerful, but experimentally strenuous approach. Computational methods offer attractive alternatives. However, due to the limited reliability of predictions and potentially antagonistic effects of substitutions, only single-point mutations are usually predicted in silico, experimentally verified and then recombined in multiple-point mutants. Thus, substantial screening is still required. Here we present FireProt, a robust computational strategy for predicting highly stable multiple-point mutants that combines energy- and evolution-based approaches with smart filtering to identify additive stabilizing mutations. FireProt's reliability and applicability was demonstrated by validating its predictions against 656 mutations from the ProTherm database. We demonstrate that thermostability of the model enzymes haloalkane dehalogenase DhaA and γ-hexachlorocyclohexane dehydrochlorinase LinA can be substantially increased (ΔTm = 24°C and 21°C) by constructing and characterizing only a handful of multiple-point mutants. FireProt can be applied to any protein for which a tertiary structure and homologous sequences are available, and will facilitate the rapid development of robust proteins for biomedical and biotechnological applications.

Structure and tectonic evolution of the NE segment of the Polish-Ukrainian Carpathians during the Late Cenozoic: subsurface cross-sections and palinspastic models

NASA Astrophysics Data System (ADS)

Kuśmierek, Jan; Baran, Urszula

2016-08-01

The discrepant arrangement of the Carpathian nappes and syntectonic deposits of the Carpathian Foredeep reveals the oroclinal migration of the subduction direction of the platform margin during the Late Cenozoic. Formation of the nappes was induced by their detachment from disintegrated segments of the European Platform; the segments were shortened as a result of their vertical rotation in zones of compressional sutures. It finds expression in local occurrence of the backward vergence of folding against the generally forward vergence toward the Carpathian Foredeep. The precompressional configuration of sedimentation areas of particular nappes was reconstructed with application of the palinspastic method, on the basis of the hitherto undervalued model which emphasizes the influence of the subduction and differentiated morphology of the platform basement on the tectonic evolution of the fold and thrust belt. Superposition of the palaeogeographic representations and the present geometry of the orogen allows understanding of the impact of the magnitudes of tectonic displacements on the differentiation of the geological structure in the NE segment of the Carpathians. The differentiation has inspired different views of Polish and Ukrainian geologists on structural classification and evolution of the frontal thrusts.

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.

Evolution of the frequency chirp of Gaussian pulses and beams when passing through a pulse compressor.

PubMed

Li, Derong; Lv, Xiaohua; Bowlan, Pamela; Du, Rui; Zeng, Shaoqun; Luo, Qingming

2009-09-14

The evolution of the frequency chirp of a laser pulse inside a classical pulse compressor is very different for plane waves and Gaussian beams, although after propagating through the last (4th) dispersive element, the two models give the same results. In this paper, we have analyzed the evolution of the frequency chirp of Gaussian pulses and beams using a method which directly obtains the spectral phase acquired by the compressor. We found the spatiotemporal couplings in the phase to be the fundamental reason for the difference in the frequency chirp acquired by a Gaussian beam and a plane wave. When the Gaussian beam propagates, an additional frequency chirp will be introduced if any spatiotemporal couplings (i.e. angular dispersion, spatial chirp or pulse front tilt) are present. However, if there are no couplings present, the chirp of the Gaussian beam is the same as that of a plane wave. When the Gaussian beam is well collimated, the introduced frequency chirp predicted by the plane wave and Gaussian beam models are in closer agreement. This work improves our understanding of pulse compressors and should be helpful for optimizing dispersion compensation schemes in many applications of femtosecond laser pulses.

Two dimensional kinetic analysis of electrostatic harmonic plasma waves

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

Fonseca-Pongutá, E. C.; Ziebell, L. F.; Gaelzer, R.

2016-06-15

Electrostatic harmonic Langmuir waves are virtual modes excited in weakly turbulent plasmas, first observed in early laboratory beam-plasma experiments as well as in rocket-borne active experiments in space. However, their unequivocal presence was confirmed through computer simulated experiments and subsequently theoretically explained. The peculiarity of harmonic Langmuir waves is that while their existence requires nonlinear response, their excitation mechanism and subsequent early time evolution are governed by essentially linear process. One of the unresolved theoretical issues regards the role of nonlinear wave-particle interaction process over longer evolution time period. Another outstanding issue is that existing theories for these modes aremore » limited to one-dimensional space. The present paper carries out two dimensional theoretical analysis of fundamental and (first) harmonic Langmuir waves for the first time. The result shows that harmonic Langmuir wave is essentially governed by (quasi)linear process and that nonlinear wave-particle interaction plays no significant role in the time evolution of the wave spectrum. The numerical solutions of the two-dimensional wave spectra for fundamental and harmonic Langmuir waves are also found to be consistent with those obtained by direct particle-in-cell simulation method reported in the literature.« less

The Seasonal Evolution of Sea Ice Floe Size Distribution

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. “The Seasonal Evolution of Sea Ice Floe Size Distribution... seasonally in the southern Beaufort and Chukchi Seas region. OBJECTIVES The objective of this work was to determine the seasonal evolution of the...summer melt season using (4). The technique allows for the direct observation of lateral melt and the 3 calculation of changes in floe perimeter, and

Directionality theory and the evolution of body size.

PubMed

Demetrius, L

2000-12-07

Directionality theory, a dynamic theory of evolution that integrates population genetics with demography, is based on the concept of evolutionary entropy, a measure of the variability in the age of reproducing individuals in a population. The main tenets of the theory are three principles relating the response to the ecological constraints a population experiences, with trends in entropy as the population evolves under mutation and natural selection. (i) Stationary size or fluctuations around a stationary size (bounded growth): a unidirectional increase in entropy; (ii) prolonged episodes of exponential growth (unbounded growth), large population size: a unidirectional decrease in entropy; and (iii) prolonged episodes of exponential growth (unbounded growth), small population size: random, non-directional change in entropy. We invoke these principles, together with an allometric relationship between entropy, and the morphometric variable body size, to provide evolutionary explanations of three empirical patterns pertaining to trends in body size, namely (i) Cope's rule, the tendency towards size increase within phyletic lineages; (ii) the island rule, which pertains to changes in body size that occur as species migrate from mainland populations to colonize island habitats; and (iii) Bergmann's rule, the tendency towards size increase with increasing latitude. The observation that these ecotypic patterns can be explained in terms of the directionality principles for entropy underscores the significance of evolutionary entropy as a unifying concept in forging a link between micro-evolution, the dynamics of gene frequency change, and macro-evolution, dynamic changes in morphometric variables.

Publications of the exobiology program for 1989: A special bibliography

NASA Technical Reports Server (NTRS)

1991-01-01

A listing of 1989 publications resulting from research supported by the Exobiology Program is presented. Research supported by the Exobiology Program is explored in the following areas: (1) cosmic evolution of biogenic compounds; (2) prebiotic evolution; (3) early evolution of life; (4) and evolution of advanced life. Pre-mission and pre-project activities supporting these areas are supported in the areas of solar system exploration and search for extraterrestrial intelligence. The planetary protection subject area is included here because of its direct relevance to the Exobiology Program.

Influence of particle shape on the microstructure evolution and the mechanical properties of granular materials

NASA Astrophysics Data System (ADS)

Tian, Jianqiu; Liu, Enlong; Jiang, Lian; Jiang, Xiaoqiong; Sun, Yi; Xu, Ran

2018-06-01

In order to study the influence of particle shape on the microstructure evolution and the mechanical properties of granular materials, a two-dimensional DEM analysis of samples with three particle shapes, including circular particles, triangular particles, and elongated particles, is proposed here to simulate the direct shear tests of coarse-grained soils. For the numerical test results, analyses are conducted in terms of particle rotations, fabric evolution, and average path length evolution. A modified Rowe's stress-dilatancy equation is also proposed and successfully fitted onto simulation data.

DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites.

PubMed

Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia

2014-12-20

Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.

Evolution of genitalia: theories, evidence, and new directions.

PubMed

Eberhard, William G

2010-01-01

Many hypotheses have been proposed to explain why male intromittent genitalia consistently tend to diverge more rapidly than other body traits of the same individuals in a wide range of animal taxa. Currently the two most popular involve sexual selection: sexually antagonistic coevolution (SAC) and cryptic female choice (CFC). A review of the most extensive attempts to discriminate between these two hypotheses indicates that SAC is not likely to have played a major role in explaining this pattern of genital evolution. Promising lines for future, more direct tests of CFC include experimental modification of male genital form and female sensory abilities, analysis of possible male-female dialogues during copulation, and direct observations of genital behavior.

Temporal evolution of a Current Sheet with Initial Finite Perturbations by Three-dimensional MHD Simulations

NASA Astrophysics Data System (ADS)

Yokoyama, Takaaki

Temporal evolution of a current sheet with initial perturbations is studied by using the threedimensional resistive magnetohydrodynamic (MHD) simulations. The magnetic reconnection is considered to be the main engine of the energy rele ase in solar flares. The structure of the diffusion region is, however, not stil l understood under the circumstances with enormously large magnetic Reynolds num ber as the solar corona. In particular, the relationship between the flare's macroscopic physics and the microscopic ones are unclear. It is generally believed that the MHD turbulence s hould play a role in the intermediate scale. The initial current sheet is in an approximately hydromagnetic equilibrium with anti-parallel magnetic field in the y-direction. We imposed a finite-amplitude perturbations (=50ee what happens. Special attention is paid upon the evolution of a three-dimens ional structure in the direction along the initial electric current (z-direction ). Our preliminary results are as follows: (1) In the early phase of the evolut ion, high wavenumber modes in the z-direction are excited and grow. (2) Many "X "-type neutral points (lines) are generated along the magnetic neutral line (pla ne) in the current sheet. When they evolve into the non-linear phase, three-dime nsional structures in the z-direction also evolve. The spatial scale in the z-di rection seems to be almost comparable with that in the xy-plane. (3) The energy release rate is reduced in case of 3D simulations compared with 2D ones probably because of the reduction of the inflow cross sections by the formation of pattc hy structures in the current sheet.

Temporal slow-growth formulation for direct numerical simulation of compressible wall-bounded flows

NASA Astrophysics Data System (ADS)

Topalian, Victor; Oliver, Todd A.; Ulerich, Rhys; Moser, Robert D.

2017-08-01

A slow-growth formulation for DNS of wall-bounded turbulent flow is developed and demonstrated to enable extension of slow-growth modeling concepts to wall-bounded flows with complex physics. As in previous slow-growth approaches, the formulation assumes scale separation between the fast scales of turbulence and the slow evolution of statistics such as the mean flow. This separation enables the development of approaches where the fast scales of turbulence are directly simulated while the forcing provided by the slow evolution is modeled. The resulting model admits periodic boundary conditions in the streamwise direction, which avoids the need for extremely long domains and complex inflow conditions that typically accompany spatially developing simulations. Further, it enables the use of efficient Fourier numerics. Unlike previous approaches [Guarini, Moser, Shariff, and Wray, J. Fluid Mech. 414, 1 (2000), 10.1017/S0022112000008466; Maeder, Adams, and Kleiser, J. Fluid Mech. 429, 187 (2001), 10.1017/S0022112000002718; Spalart, J. Fluid Mech. 187, 61 (1988), 10.1017/S0022112088000345], the present approach is based on a temporally evolving boundary layer and is specifically tailored to give results for calibration and validation of Reynolds-averaged Navier-Stokes (RANS) turbulence models. The use of a temporal homogenization simplifies the modeling, enabling straightforward extension to flows with complicating features, including cold and blowing walls. To generate data useful for calibration and validation of RANS models, special care is taken to ensure that the mean slow-growth forcing is closed in terms of the mean and other quantities that appear in standard RANS models, ensuring that there is no confounding between typical RANS closures and additional closures required for the slow-growth problem. The performance of the method is demonstrated on two problems: an essentially incompressible, zero-pressure-gradient boundary layer and a transonic boundary layer over a cooled, transpiring wall. The results show that the approach produces flows that are qualitatively similar to other slow-growth methods as well as spatially developing simulations and that the method can be a useful tool in investigating wall-bounded flows with complex physics.

Screening glycosynthase libraries with a fluoride chemosensor assay independently of enzyme specificity: identification of a transitional hydrolase to synthase mutant.

PubMed

Andrés, Eduardo; Aragunde, Hugo; Planas, Antoni

2014-03-01

Glycosynthases have become efficient tools for the enzymatic synthesis of oligosaccharides, glycoconjugates and polysaccharides. Enzyme-directed evolution approaches are applied to improve the performance of current glycosynthases and engineer specificity for non-natural substrates. However, simple and general screening methods are required since most of the reported assays are specific for each particular enzyme. In the present paper, we report a general screening assay that is independent of enzyme specificity, and implemented in an HTS (high-throughput screening) format for the screening of cell extracts in directed evolution experiments. Fluoride ion is a general by-product released in all glycosynthase reactions with glycosyl fluoride donors. The new assay is based on the use of a specific chemical sensor (a silyl ether of a fluorogenic methylumbelliferone) to transduce fluoride concentration into a fluorescence signal. As a proof-of-concept, it has been applied to a nucleophile saturation mutant library of Bacillus licheniformis 1,3-1,4-β-glucanase. Beyond the expected mutations at the glutamic acid (catalytic) nucleophile, other variants have been shown to acquire glycosynthase activity. Surprisingly, an aspartic acid for glutamic acid replacement renders a highly active glycosynthase, but still retains low hydrolase activity. It appears as an intermediate state between glycosyl hydrolase and glycosynthase.

Models of Protocellular Structure, Function and Evolution

NASA Technical Reports Server (NTRS)

New, Michael H.; Pohorille, Andrew; Szostak, Jack W.; Keefe, Tony; Lanyi, Janos K.

2001-01-01

In the absence of any record of protocells, the most direct way to test our understanding of the origin of cellular life is to construct laboratory models that capture important features of protocellular systems. Such efforts are currently underway in a collaborative project between NASA-Ames, Harvard Medical School and University of California. They are accompanied by computational studies aimed at explaining self-organization of simple molecules into ordered structures. The centerpiece of this project is a method for the in vitro evolution of protein enzymes toward arbitrary catalytic targets. A similar approach has already been developed for nucleic acids in which a small number of functional molecules are selected from a large, random population of candidates. The selected molecules are next vastly multiplied using the polymerase chain reaction. A mutagenic approach, in which the sequences of selected molecules are randomly altered, can yield further improvements in performance or alterations of specificities. Unfortunately, the catalytic potential of nucleic acids is rather limited. Proteins are more catalytically capable but cannot be directly amplified. In the new technique, this problem is circumvented by covalently linking each protein of the initial, diverse, pool to the RNA sequence that codes for it. Then, selection is performed on the proteins, but the nucleic acids are replicated. Additional information is contained in the original extended abstract.

Selection is more intelligent than design: improving the affinity of a bivalent ligand through directed evolution.

PubMed

Ahmad, Kareem M; Xiao, Yi; Soh, H Tom

2012-12-01

Multivalent molecular interactions can be exploited to dramatically enhance the performance of an affinity reagent. The enhancement in affinity and specificity achieved with a multivalent construct depends critically on the effectiveness of the scaffold that joins the ligands, as this determines their positions and orientations with respect to the target molecule. Currently, no generalizable design rules exist for construction of an optimal multivalent ligand for targets with known structures, and the design challenge remains an insurmountable obstacle for the large number of proteins whose structures are not known. As an alternative to such design-based strategies, we report here a directed evolution-based method for generating optimal bivalent aptamers. To demonstrate this approach, we fused two thrombin aptamers with a randomized DNA sequence and used a microfluidic in vitro selection strategy to isolate scaffolds with exceptionally high affinities. Within five rounds of selection, we generated a bivalent aptamer that binds thrombin with an apparent dissociation constant (K(d)) <10 pM, representing a ∼200-fold improvement in binding affinity over the monomeric aptamers and a ∼15-fold improvement over the best designed bivalent construct. The process described here can be used to produce high-affinity multivalent aptamers and could potentially be adapted to other classes of biomolecules.

How Can Evolution Learn?

PubMed

Watson, Richard A; Szathmáry, Eörs

2016-02-01

The theory of evolution links random variation and selection to incremental adaptation. In a different intellectual domain, learning theory links incremental adaptation (e.g., from positive and/or negative reinforcement) to intelligent behaviour. Specifically, learning theory explains how incremental adaptation can acquire knowledge from past experience and use it to direct future behaviours toward favourable outcomes. Until recently such cognitive learning seemed irrelevant to the 'uninformed' process of evolution. In our opinion, however, new results formally linking evolutionary processes to the principles of learning might provide solutions to several evolutionary puzzles - the evolution of evolvability, the evolution of ecological organisation, and evolutionary transitions in individuality. If so, the ability for evolution to learn might explain how it produces such apparently intelligent designs. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modelling of anisotropic growth in biological tissues. A new approach and computational aspects.

PubMed

Menzel, A

2005-03-01

In this contribution, we develop a theoretical and computational framework for anisotropic growth phenomena. As a key idea of the proposed phenomenological approach, a fibre or rather structural tensor is introduced, which allows the description of transversely isotropic material behaviour. Based on this additional argument, anisotropic growth is modelled via appropriate evolution equations for the fibre while volumetric remodelling is realised by an evolution of the referential density. Both the strength of the fibre as well as the density follow Wolff-type laws. We however elaborate on two different approaches for the evolution of the fibre direction, namely an alignment with respect to strain or with respect to stress. One of the main benefits of the developed framework is therefore the opportunity to address the evolutions of the fibre strength and the fibre direction separately. It is then straightforward to set up appropriate integration algorithms such that the developed framework fits nicely into common, finite element schemes. Finally, several numerical examples underline the applicability of the proposed formulation.

Sex Ratio Bias Leads to the Evolution of Sex Role Reversal in Honey Locust Beetles.

PubMed

Fritzsche, Karoline; Booksmythe, Isobel; Arnqvist, Göran

2016-09-26

The reversal of conventional sex roles was enigmatic to Darwin, who suggested that it may evolve when sex ratios are female biased [1]. Here we present direct evidence confirming Darwin's hypothesis. We investigated mating system evolution in a sex-role-reversed beetle (Megabruchidius dorsalis) using experimental evolution under manipulated sex ratios and food regimes. In female-biased populations, where reproductive competition among females was intensified, females evolved to be more attractive and the sex roles became more reversed. Interestingly, female-specific mating behavior evolved more rapidly than male-specific mating behavior. We show that sexual selection due to reproductive competition can be strong in females and can target much the same traits as in males of species with conventional mating systems. Our study highlights two central points: the role of ecology in directing sexual selection and the role that females play in mating system evolution. Copyright © 2016 Elsevier Ltd. All rights reserved.

Observation of direct evolution from antiferromagnetism to superconductivity in C u1 -xL ixFeAs (0 ≤x ≤1.0 )

NASA Astrophysics Data System (ADS)

Li, Kunkun; Yuan, Duanduan; Guo, Jiangang; Chen, Xiaolong

2018-04-01

We report the structure, antiferromagnetism, and superconductivity in C u1 -xL ixFeAs (0 ≤x ≤1.0 ) samples. A direct evolution from antiferromagnetism to superconductivity is observed as increasing doping level of Li. A phase diagram is constructed to show this evolution, which features no coexistence region between superconductivity and antiferromagnetism. This behavior shows that antiferromagnetic CuFeAs can be regarded as a parent compound to the observed superconductivity by equivalent doping, which is different from the cases with other FeAs-based superconductors. Structural analyses and first-principles calculations indicate that the anion height of F e2A s2 tetrahedral layer plays a crucial role on the physical properties. Moreover, the simple Fermi surface nesting picture adopted to explain the evolution from spin-density wave to superconductor in other FeAs-based superconductors might be not applicable to C u1 -xL ixFeAs .

Integration of ambient seismic noise monitoring, displacement and meteorological measurements to infer the temperature-controlled long-term evolution of a complex prone-to-fall cliff

NASA Astrophysics Data System (ADS)

Colombero, C.; Baillet, L.; Comina, C.; Jongmans, D.; Larose, E.; Valentin, J.; Vinciguerra, S.

2018-06-01

Monitoring the temporal evolution of resonance frequencies and velocity changes detected from ambient seismic noise recordings can help in recognizing reversible and irreversible modifications within unstable rock volumes. With this aim, the long-term ambient seismic noise data set acquired at the potentially unstable cliff of Madonna delSasso (NW Italian Alps) was analysed in this study, using both spectral analysis and cross-correlation techniques. Noise results were integrated and compared with direct displacement measurements and meteorological data, to understand the long-term evolution of the cliff. No irreversible modifications in the stability of the site were detected over the monitored period. Conversely, daily and seasonal air temperature fluctuations were found to control resonance frequency values, amplitudes and directivities and to induce reversible velocity changes within the fractured rock mass. The immediate modification in the noise parameters due to temperature fluctuations was interpreted as the result of rock mass thermal expansion and contraction, inducing variations in the contact stiffness along the fractures isolating two unstable compartments. Differences with previous case studies were highlighted in the long-term evolution of noise spectral amplitudes and directivities, due to the complex 3-D fracture setting of the site and to the combined effects of the two unstable compartments.

Directed evolution of an angiopoietin-2 ligand trap by somatic hypermutation and cell surface display.

PubMed

Brindle, Nicholas P J; Sale, Julian E; Arakawa, Hiroshi; Buerstedde, Jean-Marie; Nuamchit, Teonchit; Sharma, Shikha; Steele, Kathryn H

2013-11-15

Tie2 is a receptor tyrosine kinase that is essential for the development and maintenance of blood vessels through binding the soluble ligands angiopoietin 1 (Ang1) and 2 (Ang2). Ang1 is constitutively produced by perivascular cells and is protective of the adult vasculature. Ang2 plays an important role in blood vessel formation and is normally expressed during development. However, its re-expression in disease states, including cancer and sepsis, results in destabilization of blood vessels contributing to the pathology of these conditions. Ang2 is thus an attractive therapeutic target. Here we report the directed evolution of a ligand trap for Ang2 by harnessing the B cell somatic hypermutation machinery and coupling this to selectable cell surface display of a Tie2 ectodomain. Directed evolution produced an unexpected combination of mutations resulting in loss of Ang1 binding but maintenance of Ang2 binding. A soluble form of the evolved ectodomain binds Ang2 but not Ang1. Furthermore, the soluble evolved ectodomain blocks Ang2 effects on endothelial cells without interfering with Ang1 activity. Our study has created a novel Ang2 ligand trap and provided proof of concept for combining surface display and exogenous gene diversification in B cells for evolution of a non-immunoglobulin target.

Directed evolution of new and improved enzyme functions using an evolutionary intermediate and multidirectional search.

PubMed

Porter, Joanne L; Boon, Priscilla L S; Murray, Tracy P; Huber, Thomas; Collyer, Charles A; Ollis, David L

2015-02-20

The ease with which enzymes can be adapted from their native roles and engineered to function specifically for industrial or commercial applications is crucial to enabling enzyme technology to advance beyond its current state. Directed evolution is a powerful tool for engineering enzymes with improved physical and catalytic properties and can be used to evolve enzymes where lack of structural information may thwart the use of rational design. In this study, we take the versatile and diverse α/β hydrolase fold framework, in the form of dienelactone hydrolase, and evolve it over three unique sequential evolutions with a total of 14 rounds of screening to generate a series of enzyme variants. The native enzyme has a low level of promiscuous activity toward p-nitrophenyl acetate but almost undetectable activity toward larger p-nitrophenyl esters. Using p-nitrophenyl acetate as an evolutionary intermediate, we have generated variants with altered specificity and catalytic activity up to 3 orders of magnitude higher than the native enzyme toward the larger nonphysiological p-nitrophenyl ester substrates. Several variants also possess increased stability resulting from the multidimensional approach to screening. Crystal structure analysis and substrate docking show how the enzyme active site changes over the course of the evolutions as either a direct or an indirect result of mutations.

Thermal plasticity of growth and development varies adaptively among alternative developmental pathways.

PubMed

Kivelä, Sami M; Svensson, Beatrice; Tiwe, Alma; Gotthard, Karl

2015-09-01

Polyphenism, the expression of discrete alternative phenotypes, is often a consequence of a developmental switch. Physiological changes induced by a developmental switch potentially affect reaction norms, but the evolution and existence of alternative reaction norms remains poorly understood. Here, we demonstrate that, in the butterfly Pieris napi (Lepidoptera: Pieridae), thermal reaction norms of several life history traits vary adaptively among switch-induced alternative developmental pathways of diapause and direct development. The switch was affected both by photoperiod and temperature, ambient temperature during late development having the potential to override earlier photoperiodic cues. Directly developing larvae had higher development and growth rates than diapausing ones across the studied thermal gradient. Reaction norm shapes also differed between the alternative developmental pathways, indicating pathway-specific selection on thermal sensitivity. Relative mass increments decreased linearly with increasing temperature and were higher under direct development than diapause. Contrary to predictions, population phenology did not explain trait variation or thermal sensitivity, but our experimental design probably lacks power for finding subtle phenology effects. We demonstrate adaptive differentiation in thermal reaction norms among alternative phenotypes, and suggest that the consequences of an environmentally dependent developmental switch primarily drive the evolution of alternative thermal reaction norms in P. napi. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

Evolution of divergent female mating preference in response to experimental sexual selection.

PubMed

Debelle, Allan; Ritchie, Michael G; Snook, Rhonda R

2014-09-01

Sexual selection is predicted to drive the coevolution of mating signals and preferences (mating traits) within populations, and could play a role in speciation if sexual isolation arises due to mating trait divergence between populations. However, few studies have demonstrated that differences in mating traits between populations result from sexual selection alone. Experimental evolution is a promising approach to directly examine the action of sexual selection on mating trait divergence among populations. We manipulated the opportunity for sexual selection (low vs. high) in populations of Drosophila pseudoobscura. Previous studies on these experimental populations have shown that sexual selection manipulation resulted in the divergence between sexual selection treatments of several courtship song parameters, including interpulse interval (IPI) which markedly influences male mating success. Here, we measure female preference for IPI using a playback design to test for preference divergence between the sexual selection treatments after 130 generations of experimental sexual selection. The results suggest that female preference has coevolved with male signal, in opposite directions between the sexual selection treatments, providing direct evidence of the ability of sexual selection to drive the divergent coevolution of mating traits between populations. We discuss the implications in the context sexual selection and speciation. © 2014 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

On the instability of wave-fields with JONSWAP spectra to inhomogeneous disturbances, and the consequent long-time evolution

NASA Astrophysics Data System (ADS)

Ribal, A.; Stiassnie, M.; Babanin, A.; Young, I.

2012-04-01

The instability of two-dimensional wave-fields and its subsequent evolution in time are studied by means of the Alber equation for narrow-banded random surface-waves in deep water subject to inhomogeneous disturbances. A linear partial differential equation (PDE) is obtained after applying an inhomogeneous disturbance to the Alber's equation and based on the solution of this PDE, the instability of the ocean wave surface is studied for a JONSWAP spectrum, which is a realistic ocean spectrum with variable directional spreading and steepness. The steepness of the JONSWAP spectrum depends on γ and α which are the peak-enhancement factor and energy scale of the spectrum respectively and it is found that instability depends on the directional spreading, α and γ. Specifically, if the instability stops due to the directional spreading, increase of the steepness by increasing α or γ can reactivate it. This result is in qualitative agreement with the recent large-scale experiment and new theoretical results. In the instability area of α-γ plane, a long-time evolution has been simulated by integrating Alber's equation numerically and recurrent evolution is obtained which is the stochastic counterpart of the Fermi-Pasta-Ulam recurrence obtained for the cubic Schrödinger equation.

Stability of a Cu0.7Co2.3O4 electrode during the oxygen evolution reaction for alkaline anion-exchange membrane water electrolysis

NASA Astrophysics Data System (ADS)

Kang, Kyoung Eun; Kim, Chi Ho; Lee, Myung Sup; Jung, Chang Wook; Kim, Yang Do; Lee, Jae Ho

2018-01-01

The electrode materials for oxygen evolution, especially non-platinum group metal oxides, have attracted increasing attention. Among the spinel-type transition metal oxides, Cu0.7Co2.3O4 powders were evaluated as a potential replacement for expensive dimensionally stabilized anode materials. Cu0.7Co2.3O4 powder for use as an electrode material for oxygen evolution in an alkaline anion-exchange membrane water electrolyzer was prepared using a thermal decomposition method. The Cu0.7Co2.3O4 powders heat-treated at 250 °C exhibited the same X-ray diffraction patterns without any secondary phases as the Co3O4 spinel structure did. The Cu0.7Co2.3O4 powders heat-treated at 250 °C for 30 minutes showed the smallest mean particle size of approximately 376 nm with the powders having a homogeneous shape and size distribution. The fine powders with a relatively homogeneous size distribution showed a higher current density during the oxygen evolution reaction. The lifetime of the Cu0.7Co2.3O4 electrode was relatively long at a low current density, but was quickly shortened due to physical detachment of the Cu0.7Co2.3O4 powders as the current density was increased. This study showed that the efficiency and the stability of Cu0.7Co2.3O4 powders during the oxygen evolution reaction were related directly to the active electrode area.

A method for the direct numerical simulation of hypersonic boundary-layer instability with finite-rate chemistry

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

Marxen, Olaf, E-mail: olaf.marxen@vki.ac.be; Aeronautics and Aerospace Department, von Karman Institute for Fluid Dynamics, Chaussée de Waterloo, 72, 1640 Rhode-St-Genèse; Magin, Thierry E.

2013-12-15

A new numerical method is presented here that allows to consider chemically reacting gases during the direct numerical simulation of a hypersonic fluid flow. The method comprises the direct coupling of a solver for the fluid mechanical model and a library providing the physio-chemical model. The numerical method for the fluid mechanical model integrates the compressible Navier–Stokes equations using an explicit time advancement scheme and high-order finite differences. This Navier–Stokes code can be applied to the investigation of laminar-turbulent transition and boundary-layer instability. The numerical method for the physio-chemical model provides thermodynamic and transport properties for different gases as wellmore » as chemical production rates, while here we exclusively consider a five species air mixture. The new method is verified for a number of test cases at Mach 10, including the one-dimensional high-temperature flow downstream of a normal shock, a hypersonic chemical reacting boundary layer in local thermodynamic equilibrium and a hypersonic reacting boundary layer with finite-rate chemistry. We are able to confirm that the diffusion flux plays an important role for a high-temperature boundary layer in local thermodynamic equilibrium. Moreover, we demonstrate that the flow for a case previously considered as a benchmark for the investigation of non-equilibrium chemistry can be regarded as frozen. Finally, the new method is applied to investigate the effect of finite-rate chemistry on boundary layer instability by considering the downstream evolution of a small-amplitude wave and comparing results with those obtained for a frozen gas as well as a gas in local thermodynamic equilibrium.« less

Half-century research developments in maritime accidents: Future directions.

PubMed

Luo, Meifeng; Shin, Sung-Ho

2016-04-19

Over the past 50 years, research in maritime accidents has undergone a series of fundamental changes. Understanding the evolution of these changes can help maritime communities to know what has been done in the past, how maritime safety can be improved in the future, and how to reduce or eliminate the risks to ships, the lives aboard them, the cargo they carry, and the marine environment. This study conducts a comprehensive literature review on research in maritime accidents, comprising 572 papers published in 125 journals over the 50 years from 1965 to 2014. The patterns of evolution of the researchers, the journals, the disciplines involved, the research methods, the major issues and causes, and the data sources are identified, and the changes explained. We find that the main focus of research in maritime accidents has shifted over the past 50 years from naval architecture to human error, and may continue to expand into socio-economic factors. In addition, future research in maritime accidents will be multi-disciplinary, use multiple data sources, and adopt advanced research methods, to account for complex interactions between the natural environment, the development of naval technology, human behavior, and shipping market conditions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Origins of Montessori Programming for Dementia

PubMed Central

Camp, Cameron J.

2011-01-01

The focus of this article is on the evolution of the use of Montessori educational methods as the basis for creating interventions for persons with dementia. The account of this evolution is autobiographical, as the development of Montessori Programming for Dementia (MPD) initially was through the efforts of myself and my research associates. My initial exposure to Maria Montessori’s work came as a result of my involvement with my own children’s education. This exposure influenced ongoing research on development of cognitive interventions for persons with dementia. A brief description of Montessori’s work with children and the educational methods she developed is followed by a description of how this approach can be translated into development of activities for persons with dementia. Assessment tools to document effects of MPD were created, focusing on observational tools to measure engagement and affect during individual and group activities programming for persons with dementia. Examples of the use of MPD by researchers, staff members, and family members are given, as well as examples of how persons with dementia can provide MPD to other persons with dementia or to children. Finally, examples of MPD’s dissemination internationally and future directions for research are presented. PMID:23515663

Origins of Montessori Programming for Dementia.

PubMed

Camp, Cameron J

2010-01-01

The focus of this article is on the evolution of the use of Montessori educational methods as the basis for creating interventions for persons with dementia. The account of this evolution is autobiographical, as the development of Montessori Programming for Dementia (MPD) initially was through the efforts of myself and my research associates. My initial exposure to Maria Montessori's work came as a result of my involvement with my own children's education. This exposure influenced ongoing research on development of cognitive interventions for persons with dementia. A brief description of Montessori's work with children and the educational methods she developed is followed by a description of how this approach can be translated into development of activities for persons with dementia. Assessment tools to document effects of MPD were created, focusing on observational tools to measure engagement and affect during individual and group activities programming for persons with dementia. Examples of the use of MPD by researchers, staff members, and family members are given, as well as examples of how persons with dementia can provide MPD to other persons with dementia or to children. Finally, examples of MPD's dissemination internationally and future directions for research are presented.

Enzymatic Functionalization of Carbon-Hydrogen Bonds1

PubMed Central

Lewis, Jared C.; Coelho, Pedro S.

2010-01-01

The development of new catalytic methods to functionalize carbon-hydrogen (C-H) bonds continues to progress at a rapid pace due to the significant economic and environmental benefits of these transformations over traditional synthetic methods. In nature, enzymes catalyze regio- and stereoselective C-H bond functionalization using transformations ranging from hydroxylation to hydroalkylation under ambient reaction conditions. The efficiency of these enzymes relative to analogous chemical processes has led to their increased use as biocatalysts in preparative and industrial applications. Furthermore, unlike small molecule catalysts, enzymes can be systematically optimized via directed evolution for a particular application and can be expressed in vivo to augment the biosynthetic capability of living organisms. While a variety of technical challenges must still be overcome for practical application of many enzymes for C-H bond functionalization, continued research on natural enzymes and on novel artificial metalloenzymes will lead to improved synthetic processes for efficient synthesis of complex molecules. In this critical review, we discuss the most prevalent mechanistic strategies used by enzymes to functionalize non-acidic C-H bonds, the application and evolution of these enzymes for chemical synthesis, and a number of potential biosynthetic capabilities uniquely enabled by these powerful catalysts. PMID:21079862

MOF-derived Cu-Pd/nanoporous carbon composite as an efficient catalyst for hydrogen evolution reaction: A comparison between hydrothermal and electrochemical synthesis

NASA Astrophysics Data System (ADS)

Mandegarzad, Sakineh; Raoof, Jahan Bakhsh; Hosseini, Sayed Reza; Ojani, Reza

2018-04-01

In this study, a novel catalyst based on Cu-Pd bimetallic nanoparticles supported on nanoporous carbon composite (NPCC) is successfully fabricated through three-step process and used as an electrocatalyst towards hydrogen evolution reaction (HER). At the first step, MOF-199 is synthesized via two distinct strategies; (1) hydrothermal (HT) and (2) electrochemical (EC). Next, the synthesized MOF-199 is used as a template in order to prepare Cu/NPCC by direct carbonization under N2 atmosphere followed by galvanic replacement reaction of Cu metals by PdII ions. All the prepared materials are characterized by X-ray diffraction (XRD), energy-dispersive X-ray spectroscopy (EDS), scanning electron microscopy (SEM), and nitrogen adsorption/desorption measurements. The effect of synthesis method of MOF-199 on the electrocatalytic activity of the final product towards HER is investigated. The electrochemical measurements indicate that Cu-Pd/NPCC derived from the MOF prepared by EC method (Cu-Pd/NPCC/EC) exhibits an enhanced catalytic activity towards HER in H2SO4 solution than the Cu-Pd/NPCC/HT. This improvement may be attributed to using of supporting electrolyte in the preparation of Cu-Pd/NPCC/EC.

A new kernel-based fuzzy level set method for automated segmentation of medical images in the presence of intensity inhomogeneity.

PubMed

Rastgarpour, Maryam; Shanbehzadeh, Jamshid

2014-01-01

Researchers recently apply an integrative approach to automate medical image segmentation for benefiting available methods and eliminating their disadvantages. Intensity inhomogeneity is a challenging and open problem in this area, which has received less attention by this approach. It has considerable effects on segmentation accuracy. This paper proposes a new kernel-based fuzzy level set algorithm by an integrative approach to deal with this problem. It can directly evolve from the initial level set obtained by Gaussian Kernel-Based Fuzzy C-Means (GKFCM). The controlling parameters of level set evolution are also estimated from the results of GKFCM. Moreover the proposed algorithm is enhanced with locally regularized evolution based on an image model that describes the composition of real-world images, in which intensity inhomogeneity is assumed as a component of an image. Such improvements make level set manipulation easier and lead to more robust segmentation in intensity inhomogeneity. The proposed algorithm has valuable benefits including automation, invariant of intensity inhomogeneity, and high accuracy. Performance evaluation of the proposed algorithm was carried on medical images from different modalities. The results confirm its effectiveness for medical image segmentation.

Experimental Evolution with Caenorhabditis Nematodes

PubMed Central

Teotónio, Henrique; Estes, Suzanne; Phillips, Patrick C.; Baer, Charles F.

2017-01-01

The hermaphroditic nematode Caenorhabditis elegans has been one of the primary model systems in biology since the 1970s, but only within the last two decades has this nematode also become a useful model for experimental evolution. Here, we outline the goals and major foci of experimental evolution with C. elegans and related species, such as C. briggsae and C. remanei, by discussing the principles of experimental design, and highlighting the strengths and limitations of Caenorhabditis as model systems. We then review three exemplars of Caenorhabditis experimental evolution studies, underlining representative evolution experiments that have addressed the: (1) maintenance of genetic variation; (2) role of natural selection during transitions from outcrossing to selfing, as well as the maintenance of mixed breeding modes during evolution; and (3) evolution of phenotypic plasticity and its role in adaptation to variable environments, including host–pathogen coevolution. We conclude by suggesting some future directions for which experimental evolution with Caenorhabditis would be particularly informative. PMID:28592504

An improved probabilistic approach for linking progenitor and descendant galaxy populations using comoving number density

NASA Astrophysics Data System (ADS)

Wellons, Sarah; Torrey, Paul

2017-06-01

Galaxy populations at different cosmic epochs are often linked by cumulative comoving number density in observational studies. Many theoretical works, however, have shown that the cumulative number densities of tracked galaxy populations not only evolve in bulk, but also spread out over time. We present a method for linking progenitor and descendant galaxy populations which takes both of these effects into account. We define probability distribution functions that capture the evolution and dispersion of galaxy populations in number density space, and use these functions to assign galaxies at redshift zf probabilities of being progenitors/descendants of a galaxy population at another redshift z0. These probabilities are used as weights for calculating distributions of physical progenitor/descendant properties such as stellar mass, star formation rate or velocity dispersion. We demonstrate that this probabilistic method provides more accurate predictions for the evolution of physical properties than the assumption of either a constant number density or an evolving number density in a bin of fixed width by comparing predictions against galaxy populations directly tracked through a cosmological simulation. We find that the constant number density method performs least well at recovering galaxy properties, the evolving method density slightly better and the probabilistic method best of all. The improvement is present for predictions of stellar mass as well as inferred quantities such as star formation rate and velocity dispersion. We demonstrate that this method can also be applied robustly and easily to observational data, and provide a code package for doing so.

Evolution of flare ribbons, electric currents, and quasi-separatrix layers during an X-class flare

NASA Astrophysics Data System (ADS)

Janvier, M.; Savcheva, A.; Pariat, E.; Tassev, S.; Millholland, S.; Bommier, V.; McCauley, P.; McKillop, S.; Dougan, F.

2016-07-01

Context. The standard model for eruptive flares has been extended to three dimensions (3D) in the past few years. This model predicts typical J-shaped photospheric footprints of the coronal current layer, forming at similar locations as the quasi-separatrix layers (QSLs). Such a morphology is also found for flare ribbons observed in the extreme ultraviolet (EUV) band, and in nonlinear force-free field (NLFFF) magnetic field extrapolations and models. Aims: We study the evolution of the photospheric traces of the current density and flare ribbons, both obtained with the Solar Dynamics Observatory instruments. We aim to compare their morphology and their time evolution, before and during the flare, with the topological features found in a NLFFF model. Methods: We investigated the photospheric current evolution during the 06 September 2011 X-class flare (SOL2011-09-06T22:20) occurring in NOAA AR 11283 from observational data of the magnetic field obtained with the Helioseismic and Magnetic Imager aboard the Solar Dynamics Observatory. We compared this evolution with that of the flare ribbons observed in the EUV filters of the Atmospheric Imager Assembly. We also compared the observed electric current density and the flare ribbon morphology with that of the QSLs computed from the flux rope insertion method-NLFFF model. Results: The NLFFF model shows the presence of a fan-spine configuration of overlying field lines, due to the presence of a parasitic polarity, embedding an elongated flux rope that appears in the observations as two parts of a filament. The QSL signatures of the fan configuration appear as a circular flare ribbon that encircles the J-shaped ribbons related to the filament ejection. The QSLs, evolved via a magnetofrictional method, also show similar morphology and evolution as both the current ribbons and the EUV flare ribbons obtained several times during the flare. Conclusions: For the first time, we propose a combined analysis of the photospheric traces of an eruptive flare, in a complex topology, with direct measurements of electric currents and QSLs from observational data and a magnetic field model. The results, obtained by two different and independent approaches 1) confirm previous results of current increase during the impulsive phase of the flare and 2) show how NLFFF models can capture the essential physical signatures of flares even in a complex magnetic field topology. A movie associated to Fig. 1 is available in electronic form at http://www.aanda.org

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

Sidler, Rolf, E-mail: rsidler@gmail.com; Carcione, José M.; Holliger, Klaus

We present a novel numerical approach for the comprehensive, flexible, and accurate simulation of poro-elastic wave propagation in 2D polar coordinates. An important application of this method and its extensions will be the modeling of complex seismic wave phenomena in fluid-filled boreholes, which represents a major, and as of yet largely unresolved, computational problem in exploration geophysics. In view of this, we consider a numerical mesh, which can be arbitrarily heterogeneous, consisting of two or more concentric rings representing the fluid in the center and the surrounding porous medium. The spatial discretization is based on a Chebyshev expansion in themore » radial direction and a Fourier expansion in the azimuthal direction and a Runge–Kutta integration scheme for the time evolution. A domain decomposition method is used to match the fluid–solid boundary conditions based on the method of characteristics. This multi-domain approach allows for significant reductions of the number of grid points in the azimuthal direction for the inner grid domain and thus for corresponding increases of the time step and enhancements of computational efficiency. The viability and accuracy of the proposed method has been rigorously tested and verified through comparisons with analytical solutions as well as with the results obtained with a corresponding, previously published, and independently benchmarked solution for 2D Cartesian coordinates. Finally, the proposed numerical solution also satisfies the reciprocity theorem, which indicates that the inherent singularity associated with the origin of the polar coordinate system is adequately handled.« less

Methods of geometrical integration in accelerator physics

NASA Astrophysics Data System (ADS)

Andrianov, S. N.

2016-12-01

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

Genetic algorithms as global random search methods

NASA Technical Reports Server (NTRS)

Peck, Charles C.; Dhawan, Atam P.

1995-01-01

Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that the schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solutions and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

Genetic algorithms as global random search methods

NASA Technical Reports Server (NTRS)

Peck, Charles C.; Dhawan, Atam P.

1995-01-01

Genetic algorithm behavior is described in terms of the construction and evolution of the sampling distributions over the space of candidate solutions. This novel perspective is motivated by analysis indicating that that schema theory is inadequate for completely and properly explaining genetic algorithm behavior. Based on the proposed theory, it is argued that the similarities of candidate solutions should be exploited directly, rather than encoding candidate solution and then exploiting their similarities. Proportional selection is characterized as a global search operator, and recombination is characterized as the search process that exploits similarities. Sequential algorithms and many deletion methods are also analyzed. It is shown that by properly constraining the search breadth of recombination operators, convergence of genetic algorithms to a global optimum can be ensured.

Inferring internal properties of Earth's core dynamics and their evolution from surface observations and a numerical geodynamo model

NASA Astrophysics Data System (ADS)

Aubert, J.; Fournier, A.

2011-10-01

Over the past decades, direct three-dimensional numerical modelling has been successfully used to reproduce the main features of the geodynamo. Here we report on efforts to solve the associated inverse problem, aiming at inferring the underlying properties of the system from the sole knowledge of surface observations and the first principle dynamical equations describing the convective dynamo. To this end we rely on twin experiments. A reference model time sequence is first produced and used to generate synthetic data, restricted here to the large-scale component of the magnetic field and its rate of change at the outer boundary. Starting from a different initial condition, a second sequence is next run and attempts are made to recover the internal magnetic, velocity and buoyancy anomaly fields from the sparse surficial data. In order to reduce the vast underdetermination of this problem, we use stochastic inversion, a linear estimation method determining the most likely internal state compatible with the observations and some prior knowledge, and we also implement a sequential evolution algorithm in order to invert time-dependent surface observations. The prior is the multivariate statistics of the numerical model, which are directly computed from a large number of snapshots stored during a preliminary direct run. The statistics display strong correlation between different harmonic degrees of the surface observations and internal fields, provided they share the same harmonic order, a natural consequence of the linear coupling of the governing dynamical equations and of the leading influence of the Coriolis force. Synthetic experiments performed with a weakly nonlinear model yield an excellent quantitative retrieval of the internal structure. In contrast, the use of a strongly nonlinear (and more realistic) model results in less accurate static estimations, which in turn fail to constrain the unobserved small scales in the time integration of the evolution scheme. Evaluating the quality of forecasts of the system evolution against the reference solution, we show that our scheme can improve predictions based on linear extrapolations on forecast horizons shorter than the system e-folding time. Still, in the perspective of forthcoming data assimilation activities, our study underlines the need of advanced estimation techniques able to cope with the moderate to strong nonlinearities present in the geodynamo.

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

PubMed

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

2005-01-01

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

Single nucleotide variations: Biological impact and theoretical interpretation

PubMed Central

Katsonis, Panagiotis; Koire, Amanda; Wilson, Stephen Joseph; Hsu, Teng-Kuei; Lua, Rhonald C; Wilkins, Angela Dawn; Lichtarge, Olivier

2014-01-01

Genome-wide association studies (GWAS) and whole-exome sequencing (WES) generate massive amounts of genomic variant information, and a major challenge is to identify which variations drive disease or contribute to phenotypic traits. Because the majority of known disease-causing mutations are exonic non-synonymous single nucleotide variations (nsSNVs), most studies focus on whether these nsSNVs affect protein function. Computational studies show that the impact of nsSNVs on protein function reflects sequence homology and structural information and predict the impact through statistical methods, machine learning techniques, or models of protein evolution. Here, we review impact prediction methods and discuss their underlying principles, their advantages and limitations, and how they compare to and complement one another. Finally, we present current applications and future directions for these methods in biological research and medical genetics. PMID:25234433

Atomistic Computer Simulations of Water Interactions and Dissolution of Inorganic Glasses

DOE PAGES

Du, Jincheng; Rimsza, Jessica

2017-09-01

Computational simulations at the atomistic level play an increasing important role in understanding the structures, behaviors, and the structure-property relationships of glass and amorphous materials. In this paper, we reviewed atomistic simulation methods ranging from first principles calculations and ab initio molecular dynamics (AIMD), to classical molecular dynamics (MD) and meso-scale kinetic Monte Carlo (KMC) simulations and their applications to glass-water interactions and glass dissolutions. Particularly, the use of these simulation methods in understanding the reaction mechanisms of water with oxide glasses, water-glass interfaces, hydrated porous silica gels formation, the structure and properties of multicomponent glasses, and microstructure evolution aremore » reviewed. Here, the advantages and disadvantageous of these methods are discussed and the current challenges and future direction of atomistic simulations in glass dissolution are presented.« less

Visualization of anisotropic-isotropic phase transformation dynamics in battery electrode particles

DOE PAGES

Wang, Jiajun; Karen Chen-Wiegart, Yu-chen; Eng, Christopher; ...

2016-08-12

Anisotropy, or alternatively, isotropy of phase transformations extensively exist in a number of solid-state materials, with performance depending on the three-dimensional transformation features. Fundamental insights into internal chemical phase evolution allow manipulating materials with desired functionalities, and can be developed via real-time multi-dimensional imaging methods. In this paper, we report a five-dimensional imaging method to track phase transformation as a function of charging time in individual lithium iron phosphate battery cathode particles during delithiation. The electrochemically driven phase transformation is initially anisotropic with a preferred boundary migration direction, but becomes isotropic as delithiation proceeds further. We also observe the expectedmore » two-phase coexistence throughout the entire charging process. Finally, we expect this five-dimensional imaging method to be broadly applicable to problems in energy, materials, environmental and life sciences.« less

Fast Simulations of Gas Sloshing and Cold Front Formation

NASA Technical Reports Server (NTRS)

Roediger, E.; ZuHone, J. A.

2011-01-01

We present a simplified and fast method for simulating minor mergers between galaxy clusters. Instead of following the evolution of the dark matter halos directly by the N-body method, we employ a rigid potential approximation for both clusters. The simulations are run in the rest frame of the more massive cluster and account for the resulting inertial accelerations in an optimised way. We test the reliability of this method for studies of minor merger induced gas sloshing by performing a one-to-one comparison between our simulations and hydro+N-body ones. We find that the rigid potential approximation reproduces the sloshing-related features well except for two artefacts: the temperature just outside the cold fronts is slightly over-predicted, and the outward motion of the cold fronts is delayed by typically 200 Myr. We discuss reasons for both artefacts.

Fast Simulations of Gas Sloshing and Cold Front Formation

NASA Technical Reports Server (NTRS)

Roediger, E.; ZuHone, J. A.

2012-01-01

We present a simplified and fast method for simulating minor mergers between galaxy clusters. Instead of following the evolution of the dark matter halos directly by the N-body method, we employ a rigid potential approximation for both clusters. The simulations are run in the rest frame of the more massive cluster and account for the resulting inertial accelerations in an optimised way. We test the reliability of this method for studies of minor merger induced gas sloshing by performing a one-to-one comparison between our simulations and hydro+N-body ones. We find that the rigid potential approximation reproduces the sloshing-related features well except for two artifacts: the temperature just outside the cold fronts is slightly over-predicted, and the outward motion of the cold fronts is delayed by typically 200 Myr. We discuss reasons for both artifacts.

Analytic Evolution of Singular Distribution Amplitudes in QCD

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

Tandogan Kunkel, Asli

2014-08-01

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

Chemical evolution and the origin of life: cumulative keyword subject index 1970-1986

NASA Technical Reports Server (NTRS)

Roy, A. C.; Powers, J. V.; Rummel, J. D. (Principal Investigator)

1990-01-01

This cumulative subject index encompasses the subject indexes of the bibliographies on Chemical Evolution and the Origin of Life that were first published in 1970 and have continued through publication of the 1986 bibliography supplement. Early bibliographies focused on experimental and theoretical material dealing directly with the concepts of chemical evolution and the origin of life, excluding the broader areas of exobiology, biological evolution, and geochemistry. In recent years, these broader subject areas have also been incorporated as they appear in literature searches relating to chemical evolution and the origin of life, although direct attempts have not been made to compile all of the citations in these broad areas. The keyword subject indexes have also undergone an analogous change in scope. Compilers of earlier bibliographies used the most specific term available in producing the subject index. Compilers of recent bibliographies have used a number of broad terms relating to the overall subject content of each citation and specific terms where appropriate. The subject indexes of these 17 bibliographies have, in general, been cumulatively compiled exactly as they originally appeared. However, some changes have been made in an attempt to correct errors, combine terms, and provide more meaningful terms.

Structuring evolution: biochemical networks and metabolic diversification in birds.

PubMed

Morrison, Erin S; Badyaev, Alexander V

2016-08-25

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

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

ERIC Educational Resources Information Center

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

2009-01-01

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

76 FR 11940 - Airworthiness Directives; Turbomeca Model Arriel 1E2, 1S, and 1S1 Turboshaft Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-04

... discrepancies led to a ``one-off'' abnormal evolution of gas generator (NG) rating during engine starting. In... evolution of gas generator (NG) rating during engine starting. In one of these cases, this resulted in an...

Animal Foraging and the Evolution of Goal-Directed Cognition

ERIC Educational Resources Information Center

Hills, Thomas T.

2006-01-01

Foraging-and feeding-related behaviors across eumetazoans share similar molecular mechanisms, suggesting the early evolution of an optimal foraging behavior called area-restricted search (ARS), involving mechanisms of dopamine and glutamate in the modulation of behavioral focus. Similar mechanisms in the vertebrate basal ganglia control motor…

Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea?

PubMed

Nielsen, Claus

2013-08-16

Two theories for the origin of animal life cycles with planktotrophic larvae are now discussed seriously: The terminal addition theory proposes a holopelagic, planktotrophic gastraea as the ancestor of the eumetazoans with addition of benthic adult stages and retention of the planktotrophic stages as larvae, i.e. the ancestral life cycles were indirect. The intercalation theory now proposes a benthic, deposit-feeding gastraea as the bilaterian ancestor with a direct development, and with planktotrophic larvae evolving independently in numerous lineages through specializations of juveniles. Information from the fossil record, from mapping of developmental types onto known phylogenies, from occurrence of apical organs, and from genetics gives no direct information about the ancestral eumetazoan life cycle; however, there are plenty of examples of evolution from an indirect development to direct development, and no unequivocal example of evolution in the opposite direction. Analyses of scenarios for the two types of evolution are highly informative. The evolution of the indirect spiralian life cycle with a trochophora larva from a planktotrophic gastraea is explained by the trochophora theory as a continuous series of ancestors, where each evolutionary step had an adaptational advantage. The loss of ciliated larvae in the ecdysozoans is associated with the loss of outer ciliated epithelia. A scenario for the intercalation theory shows the origin of the planktotrophic larvae of the spiralians through a series of specializations of the general ciliation of the juvenile. The early steps associated with the enhancement of swimming seem probable, but the following steps which should lead to the complicated downstream-collecting ciliary system are without any advantage, or even seem disadvantageous, until the whole structure is functional. None of the theories account for the origin of the ancestral deuterostome (ambulacrarian) life cycle. All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value.

3-D direct numerical model for failure of non-cohesive granular soils with upward seepage flow

NASA Astrophysics Data System (ADS)

Fukumoto, Yutaka; Ohtsuka, Satoru

2017-12-01

The paper reports the application of a 3-D direct particle-fluid simulation model to the seepage failure of granular soils. The goal of this study is to numerically capture the process of the failure which is induced by the seepage flow from the micromechanical aspects with no macroscopic assumptions. In order to accomplish this goal, non-cohesive granular assemblies with an upward seepage flow and a variety of pressure gradients are investigated. The motion and the collision of the soil particles are calculated by a soft sphere model, such as the discrete element method, and the flow of the pore fluid is directly solved at a smaller scale than the diameter of the soil particles by the lattice Boltzmann method. By coupling these methods, the interaction between the soil particles and the seepage flow is also considered. As a result of the series of analyses, the numerically predicted value for the critical hydraulic gradient is found to be in good agreement with the theoretical value. In addition, the rapid change in the flow pattern around the critical hydraulic gradient can be microscopically captured. By observing the evolution of the force chains inside the soils, it is demonstrated that the failure process of the contact networks can also be reproduced by the simulation model presented here.

Directional selection in the evolution of elongated upper canines in clouded leopards and sabre-toothed cats.

PubMed

Harano, Tomohiro; Kutsukake, Nobuyuki

2018-06-14

Extremely developed or specialised traits such as the elongated upper canines of extinct sabre-toothed cats are often not analogous to those of any extant species, which limits our understanding of their evolutionary cause. However, an extant species may have undergone directional selection for a similar extreme phenotype. Among living felids, the clouded leopard, Neofelis nebulosa, has exceptionally long upper canines for its body size. We hypothesised that directional selection generated the elongated upper canines of clouded leopards in a manner similar to the process in extinct sabre-toothed cats. To test this, we developed an approach that compared the effect of directional selection among lineages in a phylogeny using a simulation of trait evolution and approximate Bayesian computation. This approach was applied to analyse the evolution of upper canine length in the Felidae phylogeny. Our analyses consistently showed directional selection favouring longer upper canines in the clouded leopard lineage and a lineage leading to the sabre-toothed cat with the longest upper canines, Smilodon. Most of our analyses detected an effect of directional selection for longer upper canines in the lineage leading to another sabre-toothed cat, Homotherium, although this selection may have occurred exclusively in the primitive species. In all the analyses, the clouded leopard and Smilodon lineages showed comparable directional selection. This implies that clouded leopards share a selection advantage with sabre-toothed cats in having elongated upper canines. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Publications of the Exobiology Program for 1988: A special bibliography

NASA Technical Reports Server (NTRS)

1990-01-01

The 1988 publications resulting from research pursued under the auspices of NASA's Exobiology Program are listed. The Exobiology Program is an integrated program designed to investigate those processes that may have been responsible for or related to the origin, evolution, and distribution of life in the universe. Research supported by this program is in the areas of cosmic evolution of biogenic compounds, prebiotic evolution, early evolution of life, and evolution of advanced life. Pre-mission and pre-project activities supporting these areas are included in the areas of solar system exploration and the search for extraterrestrial intelligence. A planetary protection subject area is also included because of its direct relevance to the Exobiology program.

Real-time non-rigid target tracking for ultrasound-guided clinical interventions

NASA Astrophysics Data System (ADS)

Zachiu, C.; Ries, M.; Ramaekers, P.; Guey, J.-L.; Moonen, C. T. W.; de Senneville, B. Denis

2017-10-01

Biological motion is a problem for non- or mini-invasive interventions when conducted in mobile/deformable organs due to the targeted pathology moving/deforming with the organ. This may lead to high miss rates and/or incomplete treatment of the pathology. Therefore, real-time tracking of the target anatomy during the intervention would be beneficial for such applications. Since the aforementioned interventions are often conducted under B-mode ultrasound (US) guidance, target tracking can be achieved via image registration, by comparing the acquired US images to a separate image established as positional reference. However, such US images are intrinsically altered by speckle noise, introducing incoherent gray-level intensity variations. This may prove problematic for existing intensity-based registration methods. In the current study we address US-based target tracking by employing the recently proposed EVolution registration algorithm. The method is, by construction, robust to transient gray-level intensities. Instead of directly matching image intensities, EVolution aligns similar contrast patterns in the images. Moreover, the displacement is computed by evaluating a matching criterion for image sub-regions rather than on a point-by-point basis, which typically provides more robust motion estimates. However, unlike similar previously published approaches, which assume rigid displacements in the image sub-regions, the EVolution algorithm integrates the matching criterion in a global functional, allowing the estimation of an elastic dense deformation. The approach was validated for soft tissue tracking under free-breathing conditions on the abdomen of seven healthy volunteers. Contact echography was performed on all volunteers, while three of the volunteers also underwent standoff echography. Each of the two modalities is predominantly specific to a particular type of non- or mini-invasive clinical intervention. The method demonstrated on average an accuracy of  ˜1.5 mm and submillimeter precision. This, together with a computational performance of 20 images per second make the proposed method an attractive solution for real-time target tracking during US-guided clinical interventions.

Real-time non-rigid target tracking for ultrasound-guided clinical interventions.

PubMed

Zachiu, C; Ries, M; Ramaekers, P; Guey, J-L; Moonen, C T W; de Senneville, B Denis

2017-10-04

Biological motion is a problem for non- or mini-invasive interventions when conducted in mobile/deformable organs due to the targeted pathology moving/deforming with the organ. This may lead to high miss rates and/or incomplete treatment of the pathology. Therefore, real-time tracking of the target anatomy during the intervention would be beneficial for such applications. Since the aforementioned interventions are often conducted under B-mode ultrasound (US) guidance, target tracking can be achieved via image registration, by comparing the acquired US images to a separate image established as positional reference. However, such US images are intrinsically altered by speckle noise, introducing incoherent gray-level intensity variations. This may prove problematic for existing intensity-based registration methods. In the current study we address US-based target tracking by employing the recently proposed EVolution registration algorithm. The method is, by construction, robust to transient gray-level intensities. Instead of directly matching image intensities, EVolution aligns similar contrast patterns in the images. Moreover, the displacement is computed by evaluating a matching criterion for image sub-regions rather than on a point-by-point basis, which typically provides more robust motion estimates. However, unlike similar previously published approaches, which assume rigid displacements in the image sub-regions, the EVolution algorithm integrates the matching criterion in a global functional, allowing the estimation of an elastic dense deformation. The approach was validated for soft tissue tracking under free-breathing conditions on the abdomen of seven healthy volunteers. Contact echography was performed on all volunteers, while three of the volunteers also underwent standoff echography. Each of the two modalities is predominantly specific to a particular type of non- or mini-invasive clinical intervention. The method demonstrated on average an accuracy of  ∼1.5 mm and submillimeter precision. This, together with a computational performance of 20 images per second make the proposed method an attractive solution for real-time target tracking during US-guided clinical interventions.

Origins of native vascular plants of Antarctica: comments from a historical phytogeography viewpoint.

PubMed

Mosyakin, S L; Bezusko, L G; Mosyakin, A S

2007-01-01

The article provides an overview of the problem of origin of the only native vascular plants of Antarctica, Deschampsia antartica (Poaceae) and Colobanthus quitensis (Caryophyllaceae), from the viewpoint of modern historical phytogeography and related fields of science. Some authors suggested the Tertiary relict status of these plants in Antarctica, while others favour their recent Holocene immigration. Direct data (fossil or molecular genetic ones) for solving this controversy is still lacking. However, there is no convincing evidence supporting the Tertiary relict status of these plants in Antarctica. Most probably D. antarctica and C. quitensis migrated to Antarctica in the Holocene or Late Pleistocene (last interglacial?) through bird-aided long-distance dispersal. It should be critically tested by (1) appropriate methods of molecular phylogeography, (2) molecular clock methods, if feasible, (3) direct paleobotanical studies, (4) paleoclimatic reconstructions, and (5) comparison with cases of taxa with similar distribution/dispersal patterns. The problem of the origin of Antarctic vascular plants is a perfect model for integration of modern methods of molecular phylogeography and phylogenetics, population biology, paleobiology and paleogeography for solving a long-standing enigma of historical plant geography and evolution.

Distribution and evolution of genes responsible for biosynthesis of mycotoxins in Fusarium

USDA-ARS?s Scientific Manuscript database

Fusarium secondary metabolites (SMs) include some of the mycotoxins of greatest concern to food and feed safety. In fungi, genes directly involved in synthesis of the same SM are typically located adjacent to one another in gene clusters. To better understand the distribution and evolution of mycoto...

Amino acid Alphabet Size in Protein Evolution Experiments: Better to Search a Small library Thoroughly or a Large Library Sparsely?

PubMed Central

Muñoz, Enrique

2015-01-01

We compare the results obtained from searching a smaller library thoroughly versus searching a more diverse, larger library sparsely. We study protein evolution with reduced amino acid alphabets, by simulating directed evolution experiments at three different alphabet sizes: 20, 5 and 2. We employ a physical model for evolution, the generalized NK model, that has proved successful in modeling protein evolution, antibody evolution, and T cell selection. We find that antibodies with higher affinity are found by searching a library with a larger alphabet sparsely than by searching a smaller library thoroughly, even with well-designed reduced libraries. We find ranked amino acid usage frequencies in agreement with observations of the CDR-H3 variable region of human antibodies. PMID:18375453

Phenotypic variability and selection of lipid-producing microalgae in a microfluidic centrifuge

NASA Astrophysics Data System (ADS)

Estévez-Torres, André.; Mestler, Troy; Austin, Robert H.

2010-03-01

Isogenic cells are known to display various expression levels that may result in different phenotypes within a population. Here we focus on the phenotypic variability of a species of unicellular algae that produce neutral lipids. Lipid-producing algae are one of the most promising sources of biofuel. We have implemented a simple microfluidic method to assess lipid-production variability in a population of algae that relays on density differences. We will discuss the reasons of this variability and address the promising avenues of this technique for directing the evolution of algae towards high lipid productivity.

Preliminary study of the three-dimensional deformation of the vortex in Karman vortex street

NASA Astrophysics Data System (ADS)

Ling, Guocan; Guo, Liang; Wu, Zuobin; Ma, Huiyang

1992-03-01

The mechanism for 3D evolution of the isolated Karman vortex and the thin-vortex filament in a circular cylinder wake is studied numerically using the LIA method. The results show that the vortex motion is unstable for small 3D disturbances in the separated wake of a circular cylinder. Karman vortex in the time-averaged wake flowfield wolves into a horseshoe-spoon-like 3D structure. The thin vortex filament deforms three-dimensionally in the braid and generates streamwise vortex structures which incline to the region maximum-deformation direction of the flowfield.

Microstructural comparison of the kinematics of discrete and continuum dislocations models

NASA Astrophysics Data System (ADS)

Sandfeld, Stefan; Po, Giacomo

2015-12-01

The Continuum Dislocation Dynamics (CDD) theory and the Discrete Dislocation Dynamics (DDD) method are compared based on concise mathematical formulations of the coarse graining of discrete data. A numerical tool for converting from a discrete to a continuum representation of a given dislocation configuration is developed, which allows to directly compare both simulation approaches based on continuum quantities (e.g. scalar density, geometrically necessary densities, mean curvature). Investigating the evolution of selected dislocation configurations within analytically given velocity fields for both DDD and CDD reveals that CDD contains a surprising number of important microstructural details.

Diagnostic methods for CW laser damage testing

NASA Astrophysics Data System (ADS)

Stewart, Alan F.; Shah, Rashmi S.

2004-06-01

High performance optical coatings are an enabling technology for many applications - navigation systems, telecom, fusion, advanced measurement systems of many types as well as directed energy weapons. The results of recent testing of superior optical coatings conducted at high flux levels will be presented. The diagnostics used in this type of nondestructive testing and the analysis of the data demonstrates the evolution of test methodology. Comparison of performance data under load to the predictions of thermal and optical models shows excellent agreement. These tests serve to anchor the models and validate the performance of the materials and coatings.

Extracting joint weak values with local, single-particle measurements.

PubMed

Resch, K J; Steinberg, A M

2004-04-02

Weak measurement is a new technique which allows one to describe the evolution of postselected quantum systems. It appears to be useful for resolving a variety of thorny quantum paradoxes, particularly when used to study properties of pairs of particles. Unfortunately, such nonlocal or joint observables often prove difficult to measure directly in practice (for instance, in optics-a common testing ground for this technique-strong photon-photon interactions would be needed to implement an appropriate von Neumann interaction). Here we derive a general, experimentally feasible, method for extracting these joint weak values from correlations between single-particle observables.

INTERDISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: Estimating Topology of Discrete Dynamical Networks

NASA Astrophysics Data System (ADS)

Guo, Shu-Juan; Fu, Xin-Chu

2010-07-01

In this paper, by applying Lasalle's invariance principle and some results about the trace of a matrix, we propose a method for estimating the topological structure of a discrete dynamical network based on the dynamical evolution of the network. The network concerned can be directed or undirected, weighted or unweighted, and the local dynamics of each node can be nonidentical. The connections among the nodes can be all unknown or partially known. Finally, two examples, including a Hénon map and a central network, are illustrated to verify the theoretical results.

Echo movement and evolution from real-time processing.

NASA Technical Reports Server (NTRS)

Schaffner, M. R.

1972-01-01

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

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template.

PubMed

Gouran, Hossein; Chakraborty, Sandeep; Rao, Basuthkar J; Asgeirsson, Bjarni; Dandekar, Abhaya

2014-01-01

Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction.

Directed evolution induces tributyrin hydrolysis in a virulence factor of Xylella fastidiosa using a duplicated gene as a template

PubMed Central

Rao, Basuthkar J.; Asgeirsson, Bjarni; Dandekar, Abhaya

2014-01-01

Duplication of genes is one of the preferred ways for natural selection to add advantageous functionality to the genome without having to reinvent the wheel with respect to catalytic efficiency and protein stability. The duplicated secretory virulence factors of Xylella fastidiosa (LesA, LesB and LesC), implicated in Pierce's disease of grape and citrus variegated chlorosis of citrus species, epitomizes the positive selection pressures exerted on advantageous genes in such pathogens. A deeper insight into the evolution of these lipases/esterases is essential to develop resistance mechanisms in transgenic plants. Directed evolution, an attempt to accelerate the evolutionary steps in the laboratory, is inherently simple when targeted for loss of function. A bigger challenge is to specify mutations that endow a new function, such as a lost functionality in a duplicated gene. Previously, we have proposed a method for enumerating candidates for mutations intended to transfer the functionality of one protein into another related protein based on the spatial and electrostatic properties of the active site residues (DECAAF). In the current work, we present in vivo validation of DECAAF by inducing tributyrin hydrolysis in LesB based on the active site similarity to LesA. The structures of these proteins have been modeled using RaptorX based on the closely related LipA protein from Xanthomonas oryzae. These mutations replicate the spatial and electrostatic conformation of LesA in the modeled structure of the mutant LesB as well, providing in silico validation before proceeding to the laborious in vivo work. Such focused mutations allows one to dissect the relevance of the duplicated genes in finer detail as compared to gene knockouts, since they do not interfere with other moonlighting functions, protein expression levels or protein-protein interaction. PMID:25717364

A multi-pixel InSAR time series analysis method: Simultaneous estimation of atmospheric noise, orbital errors and deformation

NASA Astrophysics Data System (ADS)

Jolivet, R.; Simons, M.

2016-12-01

InSAR time series analysis allows reconstruction of ground deformation with meter-scale spatial resolution and high temporal sampling. For instance, the ESA Sentinel-1 Constellation is capable of providing 6-day temporal sampling, thereby opening a new window on the spatio-temporal behavior of tectonic processes. However, due to computational limitations, most time series methods rely on a pixel-by-pixel approach. This limitation is a concern because (1) accounting for orbital errors requires referencing all interferograms to a common set of pixels before reconstruction of the time series and (2) spatially correlated atmospheric noise due to tropospheric turbulence is ignored. Decomposing interferograms into statistically independent wavelets will mitigate issues of correlated noise, but prior estimation of orbital uncertainties will still be required. Here, we explore a method that considers all pixels simultaneously when solving for the spatio-temporal evolution of interferometric phase Our method is based on a massively parallel implementation of a conjugate direction solver. We consider an interferogram as the sum of the phase difference between 2 SAR acquisitions and the corresponding orbital errors. In addition, we fit the temporal evolution with a physically parameterized function while accounting for spatially correlated noise in the data covariance. We assume noise is isotropic for any given InSAR pair with a covariance described by an exponential function that decays with increasing separation distance between pixels. We regularize our solution in space using a similar exponential function as model covariance. Given the problem size, we avoid matrix multiplications of the full covariances by computing convolutions in the Fourier domain. We first solve the unregularized least squares problem using the LSQR algorithm to approach the final solution, then run our conjugate direction solver to account for data and model covariances. We present synthetic tests showing the efficiency of our method. We then reconstruct a 20-year continuous time series covering Northern Chile. Without input from any additional GNSS data, we recover the secular deformation rate, seasonal oscillations and the deformation fields from the 2005 Mw 7.8 Tarapaca and 2007 Mw 7.7 Tocopilla earthquakes.

Uncovering the origins of spiral structure through the measurement of pattern speeds and their radial variation

NASA Astrophysics Data System (ADS)

Meidt, Sharon E.

At the intersection of galactic dynamics, evolution and global structure, unresolved issues in the nature and origin of spirals can be addressed through the characterization of the angular speeds of the patterns and their possible radial variation. In this thesis I describe the development, testing, and application of the Radial Tremaine-Weinberg (TWR) Method, a generalized version of the continuity-based TW method wherein the pattern speed is allowed to vary arbitrarily with radius. I will address the utility of, and caveats in applying, the TWR calculation together with a standard regularization technique in a series of tests on N- body simulations. The regularization, which smooths otherwise intrinsically noisy solutions based on a priori assumptions for the radial dependence of the pattern speed, proves to be essential for achieving the radial precision necessary for accurate measurement. I also present results from applications of the TWR method to observations of real galaxies, where the possible sources and sinks in the continuity equation are well understood. Using CO observations of the grand design galaxy M51, the TWR method reveals a heretofore un-measured inner spiral pattern speed for the bright two-armed spiral structure, with a value significantly higher than conventional estimates. In addition, the radial dependence implied in the TWR solution suggests a possible resonant link between the inner and outer regions of the bright spiral arms. These findings signify an advance in observational investigations into the nature and origin of grand-design spiral structure. By analyzing high-quality HI and CO data cubes available for four other spiral galaxies, the characteristic signatures of the processes that drive spiral structure are likewise identifiable; within this small sample, the first direct evidence for the presence of resonant coupling of multiple distinct patterns is found in some galaxies, while a simple single pattern speed is measured in others. I conclude with a summary of future avenues for investigation with the TWR method and propose additional modifications of the TW calculation with which the influence of bar and spiral structure on the evolution of galaxy disks can be directly characterized.

A direct Primitive Variable Recovery Scheme for hyperbolic conservative equations: The case of relativistic hydrodynamics.

PubMed

Aguayo-Ortiz, A; Mendoza, S; Olvera, D

2018-01-01

In this article we develop a Primitive Variable Recovery Scheme (PVRS) to solve any system of coupled differential conservative equations. This method obtains directly the primitive variables applying the chain rule to the time term of the conservative equations. With this, a traditional finite volume method for the flux is applied in order avoid violation of both, the entropy and "Rankine-Hugoniot" jump conditions. The time evolution is then computed using a forward finite difference scheme. This numerical technique evades the recovery of the primitive vector by solving an algebraic system of equations as it is often used and so, it generalises standard techniques to solve these kind of coupled systems. The article is presented bearing in mind special relativistic hydrodynamic numerical schemes with an added pedagogical view in the appendix section in order to easily comprehend the PVRS. We present the convergence of the method for standard shock-tube problems of special relativistic hydrodynamics and a graphical visualisation of the errors using the fluctuations of the numerical values with respect to exact analytic solutions. The PVRS circumvents the sometimes arduous computation that arises from standard numerical methods techniques, which obtain the desired primitive vector solution through an algebraic polynomial of the charges.

A direct Primitive Variable Recovery Scheme for hyperbolic conservative equations: The case of relativistic hydrodynamics

PubMed Central

Mendoza, S.; Olvera, D.

2018-01-01

In this article we develop a Primitive Variable Recovery Scheme (PVRS) to solve any system of coupled differential conservative equations. This method obtains directly the primitive variables applying the chain rule to the time term of the conservative equations. With this, a traditional finite volume method for the flux is applied in order avoid violation of both, the entropy and “Rankine-Hugoniot” jump conditions. The time evolution is then computed using a forward finite difference scheme. This numerical technique evades the recovery of the primitive vector by solving an algebraic system of equations as it is often used and so, it generalises standard techniques to solve these kind of coupled systems. The article is presented bearing in mind special relativistic hydrodynamic numerical schemes with an added pedagogical view in the appendix section in order to easily comprehend the PVRS. We present the convergence of the method for standard shock-tube problems of special relativistic hydrodynamics and a graphical visualisation of the errors using the fluctuations of the numerical values with respect to exact analytic solutions. The PVRS circumvents the sometimes arduous computation that arises from standard numerical methods techniques, which obtain the desired primitive vector solution through an algebraic polynomial of the charges. PMID:29659602

Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways.

PubMed

Orlenko, Alena; Chi, Peter B; Liberles, David A

2017-05-25

Understanding the genotype-phenotype map is fundamental to our understanding of genomes. Genes do not function independently, but rather as part of networks or pathways. In the case of metabolic pathways, flux through the pathway is an important next layer of biological organization up from the individual gene or protein. Flux control in metabolic pathways, reflecting the importance of mutation to individual enzyme genes, may be evolutionarily variable due to the role of mutation-selection-drift balance. The evolutionary stability of rate limiting steps and the patterns of inter-molecular co-evolution were evaluated in a simulated pathway with a system out of equilibrium due to fluctuating selection, population size, or positive directional selection, to contrast with those under stabilizing selection. Depending upon the underlying population genetic regime, fluctuating population size was found to increase the evolutionary stability of rate limiting steps in some scenarios. This result was linked to patterns of local adaptation of the population. Further, during positive directional selection, as with more complex mutational scenarios, an increase in the observation of inter-molecular co-evolution was observed. Differences in patterns of evolution when systems are in and out of equilibrium, including during positive directional selection may lead to predictable differences in observed patterns for divergent evolutionary scenarios. In particular, this result might be harnessed to detect differences between compensatory processes and directional processes at the pathway level based upon evolutionary observations in individual proteins. Detecting functional shifts in pathways reflects an important milestone in predicting when changes in genotypes result in changes in phenotypes.

Major regulatory factors in the evolution of development: the roles of goosecoid and Msx in the evolution of the direct-developing sea urchin Heliocidaris erythrogramma.

PubMed

Wilson, Keen A; Andrews, Mary E; Rudolf Turner, F; Raff, Rudolf A

2005-01-01

The transcription factors Gsc and Msx are expressed in the oral ectoderm of the indirect-developing sea urchin Heliocidaris tuberculata. Their patterns of expression are highly modified in the direct developer Heliocidaris erythrogramma, which lacks an oral ectoderm. We here test the hypothesis that they are large effect genes responsible for the loss of the oral ectoderm module in the direct-developing larva of H. erythrogramma as well as for the restoration of an overt oral ectoderm in H.e. xH.t. hybrids. We undertook misexpression/overexpression and knockdown assays in the two species and in hybrids by mRNA injection. The results indicate that dramatic changes of function of these transcription factors has occurred. One of these genes, Gsc, has the ability when misexpressed to partially restore oral ectoderm in H. erythrogramma. On the other hand, Msx has lost any oral function and instead has a role in mesoderm proliferation and patterning. In addition, we found that the H. tuberculataGsc is up regulated in H.e. xH.t. hybrids, showing a preferential use of the indirect developing parental gene in the development of the hybrid. We suggest that Gsc qualifies as a gene of large evolutionary effect and is partially responsible for the evolution of direct development of H. erythrogramma. We discuss these results in light of modularity and genetic networks in development, as well as in their implications for the rapid evolution of large morphological changes in development.

Human genetics: measuring the raw material of evolution.

PubMed

Armour, John A L

2009-09-15

By direct sequencing of two Y chromosomes inherited from the same paternal ancestor, a landmark study has derived a good direct estimate for the rate of base substitution mutations on the human Y chromosome.

Phase and Texture Evolution in Chemically Derived PZT Thin Films on Pt Substrates

DTIC Science & Technology

2014-09-01

function of heating rate. The FWHM of the Ill PZT texture components is sim 2978 Journal of the American Ceramic Society Mhin et al. Vol. 97, No. 9...Z39.18 ABSTRACT Phase and Texture Evolution in Chemically Derived PZT Thin Films on Pt Substrates Report Title The crystallization of lead zirconate...phase influencing texture evolution. The results suggest that PZT nucleates directly on Pt, which explains the observation of a more highly oriented

Nonlinear evolution of three-dimensional instabilities of thin and thick electron scale current sheets: Plasmoid formation and current filamentation

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

Jain, Neeraj; Büchner, Jörg; Max Planck Institute for Solar System Research, Justus-Von-Liebig-Weg-3, Göttingen

Nonlinear evolution of three dimensional electron shear flow instabilities of an electron current sheet (ECS) is studied using electron-magnetohydrodynamic simulations. The dependence of the evolution on current sheet thickness is examined. For thin current sheets (half thickness =d{sub e}=c/ω{sub pe}), tearing mode instability dominates. In its nonlinear evolution, it leads to the formation of oblique current channels. Magnetic field lines form 3-D magnetic spirals. Even in the absence of initial guide field, the out-of-reconnection-plane magnetic field generated by the tearing instability itself may play the role of guide field in the growth of secondary finite-guide-field instabilities. For thicker current sheetsmore » (half thickness ∼5 d{sub e}), both tearing and non-tearing modes grow. Due to the non-tearing mode, current sheet becomes corrugated in the beginning of the evolution. In this case, tearing mode lets the magnetic field reconnect in the corrugated ECS. Later thick ECS develops filamentary structures and turbulence in which reconnection occurs. This evolution of thick ECS provides an example of reconnection in self-generated turbulence. The power spectra for both the thin and thick current sheets are anisotropic with respect to the electron flow direction. The cascade towards shorter scales occurs preferentially in the direction perpendicular to the electron flow.« less

Assessment of the further improved (G'/G)-expansion method and the extended tanh-method in probing exact solutions of nonlinear PDEs.

PubMed

Akbar, M Ali; Ali, Norhashidah Hj Mohd; Mohyud-Din, Syed Tauseef

2013-01-01

The (G'/G)-expansion method is one of the most direct and effective method for obtaining exact solutions of nonlinear partial differential equations (PDEs). In the present article, we construct the exact traveling wave solutions of nonlinear evolution equations in mathematical physics via the (2 + 1)-dimensional breaking soliton equation by using two methods: namely, a further improved (G'/G)-expansion method, where G(ξ) satisfies the auxiliary ordinary differential equation (ODE) [G'(ξ)](2) = p G (2)(ξ) + q G (4)(ξ) + r G (6)(ξ); p, q and r are constants and the well known extended tanh-function method. We demonstrate, nevertheless some of the exact solutions bring out by these two methods are analogous, but they are not one and the same. It is worth mentioning that the first method has not been exercised anybody previously which gives further exact solutions than the second one. PACS numbers 02.30.Jr, 05.45.Yv, 02.30.Ik.

Microstructural Rearrangements and their Rheological Implications in a Model Thixotropic Elastoviscoplastic Fluid

NASA Astrophysics Data System (ADS)

Jamali, Safa; McKinley, Gareth H.; Armstrong, Robert C.

2017-01-01

We identify the sequence of microstructural changes that characterize the evolution of an attractive particulate gel under flow and discuss their implications on macroscopic rheology. Dissipative particle dynamics is used to monitor shear-driven evolution of a fabric tensor constructed from the ensemble spatial configuration of individual attractive constituents within the gel. By decomposing this tensor into isotropic and nonisotropic components we show that the average coordination number correlates directly with the flow curve of the shear stress versus shear rate, consistent with theoretical predictions for attractive systems. We show that the evolution in nonisotropic local particle rearrangements are primarily responsible for stress overshoots (strain-hardening) at the inception of steady shear flow and also lead, at larger times and longer scales, to microstructural localization phenomena such as shear banding flow-induced structure formation in the vorticity direction.

Multiphysics of bone remodeling: A 2D mesoscale activation simulation.

PubMed

Spingarn, C; Wagner, D; Rémond, Y; George, D

2017-01-01

In this work, we present an evolutive trabecular model for bone remodeling based on a boundary detection algorithm accounting for both biology and applied mechanical forces, known to be an important factor in bone evolution. A finite element (FE) numerical model using the Abaqus/Standard® software was used with a UMAT subroutine to solve the governing coupled mechanical-biological non-linear differential equations of the bone evolution model. The simulations present cell activation on a simplified trabeculae configuration organization with trabecular thickness of 200µm. For this activation process, the results confirm that the trabeculae are mainly oriented in the active direction of the principal mechanical stresses and according to the principal applied mechanical load directions. The trabeculae surface activation is clearly identified and can provide understanding of the different bone cell activations in more complex geometries and load conditions.

Directed evolution of artificial metalloenzymes for in vivo metathesis

NASA Astrophysics Data System (ADS)

Jeschek, Markus; Reuter, Raphael; Heinisch, Tillmann; Trindler, Christian; Klehr, Juliane; Panke, Sven; Ward, Thomas R.

2016-09-01

The field of biocatalysis has advanced from harnessing natural enzymes to using directed evolution to obtain new biocatalysts with tailor-made functions. Several tools have recently been developed to expand the natural enzymatic repertoire with abiotic reactions. For example, artificial metalloenzymes, which combine the versatile reaction scope of transition metals with the beneficial catalytic features of enzymes, offer an attractive means to engineer new reactions. Three complementary strategies exist: repurposing natural metalloenzymes for abiotic transformations; in silico metalloenzyme (re-)design; and incorporation of abiotic cofactors into proteins. The third strategy offers the opportunity to design a wide variety of artificial metalloenzymes for non-natural reactions. However, many metal cofactors are inhibited by cellular components and therefore require purification of the scaffold protein. This limits the throughput of genetic optimization schemes applied to artificial metalloenzymes and their applicability in vivo to expand natural metabolism. Here we report the compartmentalization and in vivo evolution of an artificial metalloenzyme for olefin metathesis, which represents an archetypal organometallic reaction without equivalent in nature. Building on previous work on an artificial metallohydrolase, we exploit the periplasm of Escherichia coli as a reaction compartment for the ‘metathase’ because it offers an auspicious environment for artificial metalloenzymes, mainly owing to low concentrations of inhibitors such as glutathione, which has recently been identified as a major inhibitor. This strategy facilitated the assembly of a functional metathase in vivo and its directed evolution with substantially increased throughput compared to conventional approaches that rely on purified protein variants. The evolved metathase compares favourably with commercial catalysts, shows activity for different metathesis substrates and can be further evolved in different directions by adjusting the workflow. Our results represent the systematic implementation and evolution of an artificial metalloenzyme that catalyses an abiotic reaction in vivo, with potential applications in, for example, non-natural metabolism.

Self-evolving atomistic kinetic Monte Carlo simulations of defects in materials

DOE PAGES

Xu, Haixuan; Beland, Laurent K.; Stoller, Roger E.; ...

2015-01-29

The recent development of on-the-fly atomistic kinetic Monte Carlo methods has led to an increased amount attention on the methods and their corresponding capabilities and applications. In this review, the framework and current status of Self-Evolving Atomistic Kinetic Monte Carlo (SEAKMC) are discussed. SEAKMC particularly focuses on defect interaction and evolution with atomistic details without assuming potential defect migration/interaction mechanisms and energies. The strength and limitation of using an active volume, the key concept introduced in SEAKMC, are discussed. Potential criteria for characterizing an active volume are discussed and the influence of active volume size on saddle point energies ismore » illustrated. A procedure starting with a small active volume followed by larger active volumes was found to possess higher efficiency. Applications of SEAKMC, ranging from point defect diffusion, to complex interstitial cluster evolution, to helium interaction with tungsten surfaces, are summarized. A comparison of SEAKMC with molecular dynamics and conventional object kinetic Monte Carlo is demonstrated. Overall, SEAKMC is found to be complimentary to conventional molecular dynamics, especially when the harmonic approximation of transition state theory is accurate. However it is capable of reaching longer time scales than molecular dynamics and it can be used to systematically increase the accuracy of other methods such as object kinetic Monte Carlo. Furthermore, the challenges and potential development directions are also outlined.« less

Directed Evolution to Engineer Monobody for FRET Biosensor Assembly and Imaging at Live-Cell Surface.

PubMed

Limsakul, Praopim; Peng, Qin; Wu, Yiqian; Allen, Molly E; Liang, Jing; Remacle, Albert G; Lopez, Tyler; Ge, Xin; Kay, Brian K; Zhao, Huimin; Strongin, Alex Y; Yang, Xiang-Lei; Lu, Shaoying; Wang, Yingxiao

2018-04-19

Monitoring enzymatic activities at the cell surface is challenging due to the poor efficiency of transport and membrane integration of fluorescence resonance energy transfer (FRET)-based biosensors. Therefore, we developed a hybrid biosensor with separate donor and acceptor that assemble in situ. The directed evolution and sequence-function analysis technologies were integrated to engineer a monobody variant (PEbody) that binds to R-phycoerythrin (R-PE) dye. PEbody was used for visualizing the dynamic formation/separation of intercellular junctions. We further fused PEbody with the enhanced CFP and an enzyme-specific peptide at the extracellular surface to create a hybrid FRET biosensor upon R-PE capture for monitoring membrane-type-1 matrix metalloproteinase (MT1-MMP) activities. This biosensor revealed asymmetric distribution of MT1-MMP activities, which were high and low at loose and stable cell-cell contacts, respectively. Therefore, directed evolution and rational design are promising tools to engineer molecular binders and hybrid FRET biosensors for monitoring molecular regulations at the surface of living cells. Copyright © 2018 Elsevier Ltd. All rights reserved.

Characterization of Inclusions in Evolution of Sodium Sulfate Using Terahertz Time-domain Spectroscopy.

PubMed

Bao, Rima; Wu, Zhikui; Li, Hao; Wang, Fang; Miao, Xinyang; Feng, Chengjing

2017-01-01

The study of fluid inclusion is one of the important means to understanding the evolution of mineral crystals, and can therefore provide original information of mineral evolution. In the process of evolution, outside factors such as temperature and pressure, directly affect the number and size of inclusions, and thus are related to the properties of crystals. In this paper, terahertz time-domain spectroscopy (THz-TDS) was used to detect sodium sulfate crystals with different growth temperatures, and absorption coefficient spectra of the samples were obtained. It is suggested that the evolution of sodium sulfate could be divided into two stages, and 80°C was the turning point. X-ray diffraction (XRD) and polarizing microscopy were used to support this conclusion. The research showed that THz-TDS could characterize the evolution of mineral crystals, and it had a unique advantage in terms of crystal evolution.

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

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

Xu, Zhijie; Li, Dongsheng; Xu, Wei

2015-04-01

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

TTLEM - an implicit-explicit (IMEX) scheme for modelling landscape evolution in MATLAB

NASA Astrophysics Data System (ADS)

Campforts, Benjamin; Schwanghart, Wolfgang

2016-04-01

Landscape evolution models (LEM) are essential to unravel interdependent earth surface processes. They are proven very useful to bridge several temporal and spatial timescales and have been successfully used to integrate existing empirical datasets. There is a growing consensus that landscapes evolve at least as much in the horizontal as in the vertical direction urging for an efficient implementation of dynamic drainage networks. Here we present a spatially explicit LEM, which is based on the object-oriented function library TopoToolbox 2 (Schwanghart and Scherler, 2014). Similar to other LEMs, rivers are considered to be the main drivers for simulated landscape evolution as they transmit pulses of tectonic perturbations and set the base level of surrounding hillslopes. Highly performant graph algorithms facilitate efficient updates of the flow directions to account for planform changes in the river network and the calculation of flow-related terrain attributes. We implement the model using an implicit-explicit (IMEX) scheme, i.e. different integrators are used for different terms in the diffusion-incision equation. While linear diffusion is solved using an implicit scheme, we calculate incision explicitly. Contrary to previously published LEMS, however, river incision is solved using a total volume method which is total variation diminishing in order to prevent numerical diffusion when solving the stream power law (Campforts and Govers, 2015). We show that the use of this updated numerical scheme alters both landscape topography and catchment wide erosion rates at a geological time scale. Finally, the availability of a graphical user interface facilitates user interaction, making the tool very useful both for research and didactical purposes. References Campforts, B., Govers, G., 2015. Keeping the edge: A numerical method that avoids knickpoint smearing when solving the stream power law. J. Geophys. Res. Earth Surf. 120, 1189-1205. doi:10.1002/2014JF003376 Schwanghart, W., Scherler, D., 2014. TopoToolbox 2 - MATLAB-based software for topographic analysis and modeling in Earth surface sciences. Earth Surf. Dyn. 2, 1-7. doi:10.5194/esurf-2-1-2014

COMBINED MULTIPOINT REMOTE AND IN SITU OBSERVATIONS OF THE ASYMMETRIC EVOLUTION OF A FAST SOLAR CORONAL MASS EJECTION

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

Rollett, T.; Möstl, C.; Temmer, M.

2014-07-20

We present an analysis of the fast coronal mass ejection (CME) of 2012  March 7, which was imaged by both STEREO spacecraft and observed in situ by MESSENGER, Venus Express, Wind, and Mars Express. Based on detected arrivals at four different positions in interplanetary space, it was possible to strongly constrain the kinematics and the shape of the ejection. Using the white-light heliospheric imagery from STEREO-A and B, we derived two different kinematical profiles for the CME by applying the novel constrained self-similar expansion method. In addition, we used a drag-based model to investigate the influence of the ambient solarmore » wind on the CME's propagation. We found that two preceding CMEs heading in different directions disturbed the overall shape of the CME and influenced its propagation behavior. While the Venus-directed segment underwent a gradual deceleration (from ∼2700 km s{sup –1} at 15 R {sub ☉} to ∼1500 km s{sup –1} at 154 R {sub ☉}), the Earth-directed part showed an abrupt retardation below 35 R {sub ☉} (from ∼1700 to ∼900 km s{sup –1}). After that, it was propagating with a quasi-constant speed in the wake of a preceding event. Our results highlight the importance of studies concerning the unequal evolution of CMEs. Forecasting can only be improved if conditions in the solar wind are properly taken into account and if attention is also paid to large events preceding the one being studied.« less

Novel in situ resistance measurement for the investigation of CIGS growth in a selenization process

NASA Astrophysics Data System (ADS)

Liu, Wei; Tian, Jian-Guo; Li, Zu-Bin; He, Qing; Li, Feng-Yan; Li, Chang-Jian; Sun, Yun

2009-03-01

During the selenization process of CIGS thin films, the relation between the element loss rate and the precursor depositions are analyzed. The growth of the CIGS thin films during the selenization process is investigated by the novel in situ resistance measurement, by which the formation of compound semiconductors can be observed directly and simultaneously. Their structures, phase evolutions and element losses are analyzed by XRD and XRF. Based on the experimental results, it can be concluded that the phase transforms have nothing to do with the deposition sequences of precursors, while the element loss rates are related to the deposition sequences in this process. In addition, element loss mechanisms of CIGS thin films prepared by the selenization process are analyzed by the phase evolutions and chemical combined path in the In, Ga-Se reaction processes. Moreover it is verified that the element losses are depressed by increasing the ramping-up rate finally. The results provide effective methods to fabricate high-quality CIGS thin films with low element losses.

Regio- and stereoselectivity of P450-catalysed hydroxylation of steroids controlled by laboratory evolution

NASA Astrophysics Data System (ADS)

Kille, Sabrina; Zilly, Felipe E.; Acevedo, Juan P.; Reetz, Manfred T.

2011-09-01

A current challenge in synthetic organic chemistry is the development of methods that allow the regio- and stereoselective oxidative C-H activation of natural or synthetic compounds with formation of the corresponding alcohols. Cytochrome P450 enzymes enable C-H activation at non-activated positions, but the simultaneous control of both regio- and stereoselectivity is problematic. Here, we demonstrate that directed evolution using iterative saturation mutagenesis provides a means to solve synthetic problems of this kind. Using P450 BM3(F87A) as the starting enzyme and testosterone as the substrate, which results in a 1:1 mixture of the 2β- and 15β-alcohols, mutants were obtained that are 96-97% selective for either of the two regioisomers, each with complete diastereoselectivity. The mutants can be used for selective oxidative hydroxylation of other steroids without performing additional mutagenesis experiments. Molecular dynamics simulations and docking experiments shed light on the origin of regio- and stereoselectivity.

Improving care and wellness in bipolar disorder: origins, evolution and future directions of a collaborative knowledge exchange network

PubMed Central

2012-01-01

The Collaborative RESearch team to study psychosocial factors in bipolar disorder (CREST.BD) is a multidisciplinary, cross-sectoral network dedicated to both fundamental research and knowledge exchange on bipolar disorder (BD). The core mission of the network is to advance the science and understanding of psychological and social issues associated with BD, improve the care and wellness of people living with BD, and strengthen services and supports for these individuals. CREST.BD bridges traditional and newer research approaches, particularly embracing community-based participatory research (CBPR) methods. Membership of CREST is broad, including academic researchers, people with BD, their family members and supports, and a variety of health care providers. Here, we describe the origins, evolution, approach to planning and evaluation and future vision for our network within the landscape of CBPR and integrated knowledge translation (KT), and explore the keys and challenges to success we have encountered working within this framework. PMID:22963889

On dangerous ground: the evolution of body armour in cordyline lizards.

PubMed

Broeckhoven, Chris; El Adak, Yousri; Hui, Cang; Van Damme, Raoul; Stankowich, Theodore

2018-06-13

Animal body armour is often considered an adaptation that protects prey against predatory attacks, yet comparative studies that link the diversification of these allegedly protective coverings to differential predation risk or pressure are scarce. Here, we examine the evolution of body armour, including spines and osteoderms, in Cordylinae, a radiation of southern African lizards. Using phylogenetic comparative methods, we attempt to identify the ecological and environmental correlates of body armour that may hint at the selective pressures responsible for defensive trait diversification. Our results show that species inhabiting arid environments are more likely to possess elaborated body armour, specifically osteoderms. We did not find any effect of estimated predation pressure or risk on the degree of body armour. These findings suggest that body armour might not necessarily evolve in response to direct interactions with predators, but rather as a result of increased habitat-mediated predation risk. Furthermore, we discuss the possibility that osteoderms might have been shaped by factors unrelated to predation. © 2018 The Author(s).

Bell-polynomial approach and Wronskian determinant solutions for three sets of differential-difference nonlinear evolution equations with symbolic computation

NASA Astrophysics Data System (ADS)

Qin, Bo; Tian, Bo; Wang, Yu-Feng; Shen, Yu-Jia; Wang, Ming

2017-10-01

Under investigation in this paper are the Belov-Chaltikian (BC), Leznov and Blaszak-Marciniak (BM) lattice equations, which are associated with the conformal field theory, UToda(m_1,m_2) system and r-matrix, respectively. With symbolic computation, the Bell-polynomial approach is developed to directly bilinearize those three sets of differential-difference nonlinear evolution equations (NLEEs). This Bell-polynomial approach does not rely on any dependent variable transformation, which constitutes the key step and main difficulty of the Hirota bilinear method, and thus has the advantage in the bilinearization of the differential-difference NLEEs. Based on the bilinear forms obtained, the N-soliton solutions are constructed in terms of the N × N Wronskian determinant. Graphic illustrations demonstrate that those solutions, more general than the existing results, permit some new properties, such as the solitonic propagation and interactions for the BC lattice equations, and the nonnegative dark solitons for the BM lattice equations.