Parameter extraction of different fuel cell models with transferred adaptive differential evolution

International Nuclear Information System (INIS)

Gong, Wenyin; Yan, Xuesong; Liu, Xiaobo; Cai, Zhihua

2015-01-01

To improve the design and control of FC (fuel cell) models, it is important to extract their unknown parameters. Generally, the parameter extraction problems of FC models can be transformed as nonlinear and multi-variable optimization problems. To extract the parameters of different FC models exactly and fast, in this paper, we propose a transferred adaptive DE (differential evolution) framework, in which the successful parameters of the adaptive DE solving previous problems are properly transferred to solve new optimization problems in the similar problem-domains. Based on this framework, an improved adaptive DE method (TRADE, in short) is presented as an illustration. To verify the performance of our proposal, TRADE is used to extract the unknown parameters of two types of fuel cell models, i.e., PEMFC (proton exchange membrane fuel cell) and SOFC (solid oxide fuel cell). The results of TRADE are also compared with those of other state-of-the-art EAs (evolutionary algorithms). Even though the modification is very simple, the results indicate that TRADE can extract the parameters of both PEMFC and SOFC models exactly and fast. Moreover, the V–I characteristics obtained by TRADE agree well with the simulated and experimental data in all cases for both types of fuel cell models. Also, it improves the performance of the original adaptive DE significantly in terms of both the quality of final solutions and the convergence speed in all cases. Additionally, TRADE is able to provide better results compared with other EAs. - Highlights: • A framework of transferred adaptive differential evolution is proposed. • Based on the framework, an improved differential evolution (TRADE) is presented. • TRADE obtains very promising results to extract the parameters of PEMFC and SOFC models

Reassessing Domain Architecture Evolution of Metazoan Proteins: The Contribution of Different Evolutionary Mechanisms

Directory of Open Access Journals (Sweden)

Laszlo Patthy

2011-08-01

Full Text Available In the accompanying papers we have shown that sequence errors of public databases and confusion of paralogs and epaktologs (proteins that are related only through the independent acquisition of the same domain types significantly distort the picture that emerges from comparison of the domain architecture (DA of multidomain Metazoan proteins since they introduce a strong bias in favor of terminal over internal DA change. The issue of whether terminal or internal DA changes occur with greater probability has very important implications for the DA evolution of multidomain proteins since gene fusion can add domains only at terminal positions, whereas domain-shuffling is capable of inserting domains both at internal and terminal positions. As a corollary, overestimation of terminal DA changes may be misinterpreted as evidence for a dominant role of gene fusion in DA evolution. In this manuscript we show that in several recent studies of DA evolution of Metazoa the authors used databases that are significantly contaminated with incomplete, abnormal and mispredicted sequences (e.g., UniProtKB/TrEMBL, EnsEMBL and/or the authors failed to separate paralogs and epaktologs, explaining why these studies concluded that the major mechanism for gains of new domains in metazoan proteins is gene fusion. In contrast with the latter conclusion, our studies on high quality orthologous and paralogous Swiss-Prot sequences confirm that shuffling of mobile domains had a major role in the evolution of multidomain proteins of Metazoa and especially those formed in early vertebrates.

Processes of fungal proteome evolution and gain of function: gene duplication and domain rearrangement

International Nuclear Information System (INIS)

Cohen-Gihon, Inbar; Nussinov, Ruth; Sharan, Roded

2011-01-01

During evolution, organisms have gained functional complexity mainly by modifying and improving existing functioning systems rather than creating new ones ab initio. Here we explore the interplay between two processes which during evolution have had major roles in the acquisition of new functions: gene duplication and protein domain rearrangements. We consider four possible evolutionary scenarios: gene families that have undergone none of these event types; only gene duplication; only domain rearrangement, or both events. We characterize each of the four evolutionary scenarios by functional attributes. Our analysis of ten fungal genomes indicates that at least for the fungi clade, species significantly appear to gain complexity by gene duplication accompanied by the expansion of existing domain architectures via rearrangements. We show that paralogs gaining new domain architectures via duplication tend to adopt new functions compared to paralogs that preserve their domain architectures. We conclude that evolution of protein families through gene duplication and domain rearrangement is correlated with their functional properties. We suggest that in general, new functions are acquired via the integration of gene duplication and domain rearrangements rather than each process acting independently

Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.

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Claudia Alvarez-Carreño

Full Text Available The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes.Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role.Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the

Numerical solutions of ordinary and partial differential equations in the frequency domain

International Nuclear Information System (INIS)

Hazi, G.; Por, G.

1997-01-01

Numerical problems during the noise simulation in a nuclear power plant are discussed. The solutions of ordinary and partial differential equations are studied in the frequency domain. Numerical methods by the transfer function method are applied. It is shown that the correctness of the numerical methods is limited for ordinary differential equations in the frequency domain. To overcome the difficulties, step-size selection is suggested. (author)

Stress induced magnetic-domain evolution in magnetoelectric composites

Science.gov (United States)

Trivedi, Harsh; Shvartsman, Vladimir V.; Lupascu, Doru C.; Medeiros, Marco S. A.; Pullar, Robert C.

2018-06-01

Local observation of the stress mediated magnetoelectric (ME) effect in composites has gained a great deal of interest over the last decades. However, there is an apparent lack of rigorous methods for a quantitative characterization of the ME effect at the local scale, especially in polycrystalline microstructures. In the present work, we address this issue by locally probing the surface magnetic state of barium titante–hexagonal barium ferrite (BaTiO3–BaFe12O19) ceramic composites using magnetic force microscopy (MFM). The effect of the piezoelectrically induced local stress on the magnetostrictive component (BaFe12O19, BaM) was observed in the form of the evolution of the magnetic domains. The local piezoelectric stress was induced by applying a voltage to the neighboring BaTiO3 grains, using a conductive atomic force microscopy tip. The resulting stochastic evolution of magnetic domains was studied in the context of the induced magnetoelastic anisotropy. In order to overcome the ambiguity in the domain changes observed by MFM, certain generalizations about the observed MFM contrast are put forward, followed by application of an algorithm for extracting the average micromagnetic changes. An average change in domain wall thickness of 50 nm was extracted, giving a lower limit on the corresponding induced magnetoelastic anisotropy energy. Furthermore, we demonstrate that this induced magnetomechanical energy is approximately equal to the K1 magnetocrystalline anisotropy constant of BaM, and compare it with a modeled value of applied elastic energy density. The comparison allowed us to judge the quality of the interfaces in the composite system, by roughly gauging the energy conversion ratio.

Application of differential evolution algorithm on self-potential data.

Science.gov (United States)

Li, Xiangtao; Yin, Minghao

2012-01-01

Differential evolution (DE) is a population based evolutionary algorithm widely used for solving multidimensional global optimization problems over continuous spaces, and has been successfully used to solve several kinds of problems. In this paper, differential evolution is used for quantitative interpretation of self-potential data in geophysics. Six parameters are estimated including the electrical dipole moment, the depth of the source, the distance from the origin, the polarization angle and the regional coefficients. This study considers three kinds of data from Turkey: noise-free data, contaminated synthetic data, and Field example. The differential evolution and the corresponding model parameters are constructed as regards the number of the generations. Then, we show the vibration of the parameters at the vicinity of the low misfit area. Moreover, we show how the frequency distribution of each parameter is related to the number of the DE iteration. Experimental results show the DE can be used for solving the quantitative interpretation of self-potential data efficiently compared with previous methods.

Automatic Clustering Using FSDE-Forced Strategy Differential Evolution

Science.gov (United States)

Yasid, A.

2018-01-01

Clustering analysis is important in datamining for unsupervised data, cause no adequate prior knowledge. One of the important tasks is defining the number of clusters without user involvement that is known as automatic clustering. This study intends on acquiring cluster number automatically utilizing forced strategy differential evolution (AC-FSDE). Two mutation parameters, namely: constant parameter and variable parameter are employed to boost differential evolution performance. Four well-known benchmark datasets were used to evaluate the algorithm. Moreover, the result is compared with other state of the art automatic clustering methods. The experiment results evidence that AC-FSDE is better or competitive with other existing automatic clustering algorithm.

Comparative Hi-C Reveals that CTCF Underlies Evolution of Chromosomal Domain Architecture

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Matteo Vietri Rudan

2015-03-01

Full Text Available Topological domains are key architectural building blocks of chromosomes, but their functional importance and evolutionary dynamics are not well defined. We performed comparative high-throughput chromosome conformation capture (Hi-C in four mammals and characterized the conservation and divergence of chromosomal contact insulation and the resulting domain architectures within distantly related genomes. We show that the modular organization of chromosomes is robustly conserved in syntenic regions and that this is compatible with conservation of the binding landscape of the insulator protein CTCF. Specifically, conserved CTCF sites are co-localized with cohesin, are enriched at strong topological domain borders, and bind to DNA motifs with orientations that define the directionality of CTCF’s long-range interactions. Conversely, divergent CTCF binding between species is correlated with divergence of internal domain structure, likely driven by local CTCF binding sequence changes, demonstrating how genome evolution can be linked to a continuous flux of local conformation changes. We also show that large-scale domains are reorganized during genome evolution as intact modules.

Dynamical evolution of domain walls in an expanding universe

Science.gov (United States)

Press, William H.; Ryden, Barbara S.; Spergel, David N.

1989-01-01

Whenever the potential of a scalar field has two or more separated, degenerate minima, domain walls form as the universe cools. The evolution of the resulting network of domain walls is calculated for the case of two potential minima in two and three dimensions, including wall annihilation, crossing, and reconnection effects. The nature of the evolution is found to be largely independent of the rate at which the universe expands. Wall annihilation and reconnection occur almost as fast as causality allows, so that the horizon volume is 'swept clean' and contains, at any time, only about one, fairly smooth, wall. Quantitative statistics are given. The total area of wall per volume decreases as the first power of time. The relative slowness of the decrease and the smoothness of the wall on the horizon scale make it impossible for walls to both generate large-scale structure and be consistent with quadrupole microwave background anisotropy limits.

Universal features in the genome-level evolution of protein domains.

Science.gov (United States)

Cosentino Lagomarsino, Marco; Sellerio, Alessandro L; Heijning, Philip D; Bassetti, Bruno

2009-01-01

Protein domains can be used to study proteome evolution at a coarse scale. In particular, they are found on genomes with notable statistical distributions. It is known that the distribution of domains with a given topology follows a power law. We focus on a further aspect: these distributions, and the number of distinct topologies, follow collective trends, or scaling laws, depending on the total number of domains only, and not on genome-specific features. We present a stochastic duplication/innovation model, in the class of the so-called 'Chinese restaurant processes', that explains this observation with two universal parameters, representing a minimal number of domains and the relative weight of innovation to duplication. Furthermore, we study a model variant where new topologies are related to occurrence in genomic data, accounting for fold specificity. Both models have general quantitative agreement with data from hundreds of genomes, which indicates that the domains of a genome are built with a combination of specificity and robust self-organizing phenomena. The latter are related to the basic evolutionary 'moves' of duplication and innovation, and give rise to the observed scaling laws, a priori of the specific evolutionary history of a genome. We interpret this as the concurrent effect of neutral and selective drives, which increase duplication and decrease innovation in larger and more complex genomes. The validity of our model would imply that the empirical observation of a small number of folds in nature may be a consequence of their evolution.

Solving SAT Problem Based on Hybrid Differential Evolution Algorithm

Science.gov (United States)

Liu, Kunqi; Zhang, Jingmin; Liu, Gang; Kang, Lishan

Satisfiability (SAT) problem is an NP-complete problem. Based on the analysis about it, SAT problem is translated equally into an optimization problem on the minimum of objective function. A hybrid differential evolution algorithm is proposed to solve the Satisfiability problem. It makes full use of strong local search capacity of hill-climbing algorithm and strong global search capability of differential evolution algorithm, which makes up their disadvantages, improves the efficiency of algorithm and avoids the stagnation phenomenon. The experiment results show that the hybrid algorithm is efficient in solving SAT problem.

Battery parameterisation based on differential evolution via a boundary evolution strategy

DEFF Research Database (Denmark)

Yang, Guangya

2013-01-01

the advances of evolutionary algorithms (EAs). Differential evolution (DE) is selected and modified to parameterise an equivalent circuit model of lithium-ion batteries. A boundary evolution strategy (BES) is developed and incorporated into the DE to update the parameter boundaries during the parameterisation......, as the equivalent circuit model is an abstract map of the battery electric characteristics, the determination of the possible ranges of parameters can be a challenging task. In this paper, an efficient yet easy to implement method is proposed to parameterise the equivalent circuit model of batteries utilising...

The Cellular Differential Evolution Based on Chaotic Local Search

Directory of Open Access Journals (Sweden)

Qingfeng Ding

2015-01-01

Full Text Available To avoid immature convergence and tune the selection pressure in the differential evolution (DE algorithm, a new differential evolution algorithm based on cellular automata and chaotic local search (CLS or ccDE is proposed. To balance the exploration and exploitation tradeoff of differential evolution, the interaction among individuals is limited in cellular neighbors instead of controlling parameters in the canonical DE. To improve the optimizing performance of DE, the CLS helps by exploring a large region to avoid immature convergence in the early evolutionary stage and exploiting a small region to refine the final solutions in the later evolutionary stage. What is more, to improve the convergence characteristics and maintain the population diversity, the binomial crossover operator in the canonical DE may be instead by the orthogonal crossover operator without crossover rate. The performance of ccDE is widely evaluated on a set of 14 bound constrained numerical optimization problems compared with the canonical DE and several DE variants. The simulation results show that ccDE has better performances in terms of convergence rate and solution accuracy than other optimizers.

Application of differential evolution algorithm on self-potential data.

Directory of Open Access Journals (Sweden)

Xiangtao Li

Full Text Available Differential evolution (DE is a population based evolutionary algorithm widely used for solving multidimensional global optimization problems over continuous spaces, and has been successfully used to solve several kinds of problems. In this paper, differential evolution is used for quantitative interpretation of self-potential data in geophysics. Six parameters are estimated including the electrical dipole moment, the depth of the source, the distance from the origin, the polarization angle and the regional coefficients. This study considers three kinds of data from Turkey: noise-free data, contaminated synthetic data, and Field example. The differential evolution and the corresponding model parameters are constructed as regards the number of the generations. Then, we show the vibration of the parameters at the vicinity of the low misfit area. Moreover, we show how the frequency distribution of each parameter is related to the number of the DE iteration. Experimental results show the DE can be used for solving the quantitative interpretation of self-potential data efficiently compared with previous methods.

Conserved domains and SINE diversity during animal evolution.

Science.gov (United States)

Luchetti, Andrea; Mantovani, Barbara

2013-10-01

Eukaryotic genomes harbour a number of mobile genetic elements (MGEs); moving from one genomic location to another, they are known to impact on the host genome. Short interspersed elements (SINEs) are well-represented, non-autonomous retroelements and they are likely the most diversified MGEs. In some instances, sequence domains conserved across unrelated SINEs have been identified; remarkably, one of these, called Nin, has been conserved since the Radiata-Bilateria splitting. Here we report on two new domains: Inv, derived from Nin, identified in insects and in deuterostomes, and Pln, restricted to polyneopteran insects. The identification of Inv and Pln sequences allowed us to retrieve new SINEs, two in insects and one in a hemichordate. The diverse structural combination of the different domains in different SINE families, during metazoan evolution, offers a clearer view of SINE diversity and their frequent de novo emergence through module exchange, possibly underlying the high evolutionary success of SINEs. © 2013 Elsevier Inc. All rights reserved.

Differential pleiotropy and HOX functional organization.

Science.gov (United States)

Sivanantharajah, Lovesha; Percival-Smith, Anthony

2015-02-01

Key studies led to the idea that transcription factors are composed of defined modular protein motifs or domains, each with separable, unique function. During evolution, the recombination of these modular domains could give rise to transcription factors with new properties, as has been shown using recombinant molecules. This archetypic, modular view of transcription factor organization is based on the analyses of a few transcription factors such as GAL4, which may represent extreme exemplars rather than an archetype or the norm. Recent work with a set of Homeotic selector (HOX) proteins has revealed differential pleiotropy: the observation that highly-conserved HOX protein motifs and domains make small, additive, tissue specific contributions to HOX activity. Many of these differentially pleiotropic HOX motifs may represent plastic sequence elements called short linear motifs (SLiMs). The coupling of differential pleiotropy with SLiMs, suggests that protein sequence changes in HOX transcription factors may have had a greater impact on morphological diversity during evolution than previously believed. Furthermore, differential pleiotropy may be the genetic consequence of an ensemble nature of HOX transcription factor allostery, where HOX proteins exist as an ensemble of states with the capacity to integrate an extensive array of developmental information. Given a new structural model for HOX functional domain organization, the properties of the archetypic TF may require reassessment. Copyright © 2014 Elsevier Inc. All rights reserved.

Algebraic dynamics solutions and algebraic dynamics algorithm for nonlinear partial differential evolution equations of dynamical systems

Institute of Scientific and Technical Information of China (English)

2008-01-01

Using functional derivative technique in quantum field theory, the algebraic dy-namics approach for solution of ordinary differential evolution equations was gen-eralized to treat partial differential evolution equations. The partial differential evo-lution equations were lifted to the corresponding functional partial differential equations in functional space by introducing the time translation operator. The functional partial differential evolution equations were solved by algebraic dynam-ics. The algebraic dynamics solutions are analytical in Taylor series in terms of both initial functions and time. Based on the exact analytical solutions, a new nu-merical algorithm—algebraic dynamics algorithm was proposed for partial differ-ential evolution equations. The difficulty of and the way out for the algorithm were discussed. The application of the approach to and computer numerical experi-ments on the nonlinear Burgers equation and meteorological advection equation indicate that the algebraic dynamics approach and algebraic dynamics algorithm are effective to the solution of nonlinear partial differential evolution equations both analytically and numerically.

Parsing parallel evolution: ecological divergence and differential gene expression in the adaptive radiations of thick-lipped Midas cichlid fishes from Nicaragua.

Science.gov (United States)

Manousaki, Tereza; Hull, Pincelli M; Kusche, Henrik; Machado-Schiaffino, Gonzalo; Franchini, Paolo; Harrod, Chris; Elmer, Kathryn R; Meyer, Axel

2013-02-01

The study of parallel evolution facilitates the discovery of common rules of diversification. Here, we examine the repeated evolution of thick lips in Midas cichlid fishes (the Amphilophus citrinellus species complex)-from two Great Lakes and two crater lakes in Nicaragua-to assess whether similar changes in ecology, phenotypic trophic traits and gene expression accompany parallel trait evolution. Using next-generation sequencing technology, we characterize transcriptome-wide differential gene expression in the lips of wild-caught sympatric thick- and thin-lipped cichlids from all four instances of repeated thick-lip evolution. Six genes (apolipoprotein D, myelin-associated glycoprotein precursor, four-and-a-half LIM domain protein 2, calpain-9, GTPase IMAP family member 8-like and one hypothetical protein) are significantly underexpressed in the thick-lipped morph across all four lakes. However, other aspects of lips' gene expression in sympatric morphs differ in a lake-specific pattern, including the magnitude of differentially expressed genes (97-510). Generally, fewer genes are differentially expressed among morphs in the younger crater lakes than in those from the older Great Lakes. Body shape, lower pharyngeal jaw size and shape, and stable isotopes (δ(13)C and δ(15)N) differ between all sympatric morphs, with the greatest differentiation in the Great Lake Nicaragua. Some ecological traits evolve in parallel (those related to foraging ecology; e.g. lip size, body and head shape) but others, somewhat surprisingly, do not (those related to diet and food processing; e.g. jaw size and shape, stable isotopes). Taken together, this case of parallelism among thick- and thin-lipped cichlids shows a mosaic pattern of parallel and nonparallel evolution. © 2012 Blackwell Publishing Ltd.

Optimizing Transmission Network Expansion Planning With The Mean Of Chaotic Differential Evolution Algorithm

Directory of Open Access Journals (Sweden)

Ahmed R. Abdelaziz

2015-08-01

Full Text Available This paper presents an application of Chaotic differential evolution optimization approach meta-heuristics in solving transmission network expansion planning TNEP using an AC model associated with reactive power planning RPP. The reliabilityredundancy of network analysis optimization problems implicate selection of components with multiple choices and redundancy levels that produce maximum benefits can be subject to the cost weight and volume constraints is presented in this paper. Classical mathematical methods have failed in handling non-convexities and non-smoothness in optimization problems. As an alternative to the classical optimization approaches the meta-heuristics have attracted lot of attention due to their ability to find an almost global optimal solution in reliabilityredundancy optimization problems. Evolutionary algorithms EAs paradigms of evolutionary computation field are stochastic and robust meta-heuristics useful to solve reliabilityredundancy optimization problems. EAs such as genetic algorithm evolutionary programming evolution strategies and differential evolution are being used to find global or near global optimal solution. The Differential Evolution Algorithm DEA population-based algorithm is an optimal algorithm with powerful global searching capability but it is usually in low convergence speed and presents bad searching capability in the later evolution stage. A new Chaotic Differential Evolution algorithm CDE based on the cat map is recommended which combines DE and chaotic searching algorithm. Simulation results and comparisons show that the chaotic differential evolution algorithm using Cat map is competitive and stable in performance with other optimization approaches and other maps.

Existence results for impulsive evolution differential equations with state-dependent delay

OpenAIRE

Eduardo Hernandez M.; Rathinasamy Sakthivel; Sueli Tanaka Aki

2008-01-01

We study the existence of mild solution for impulsive evolution abstract differential equations with state-dependent delay. A concrete application to partial delayed differential equations is considered.

Evolution of SH2 domains and phosphotyrosine signalling networks

Science.gov (United States)

Liu, Bernard A.; Nash, Piers D.

2012-01-01

Src homology 2 (SH2) domains mediate selective protein–protein interactions with tyrosine phosphorylated proteins, and in doing so define specificity of phosphotyrosine (pTyr) signalling networks. SH2 domains and protein-tyrosine phosphatases expand alongside protein-tyrosine kinases (PTKs) to coordinate cellular and organismal complexity in the evolution of the unikont branch of the eukaryotes. Examination of conserved families of PTKs and SH2 domain proteins provides fiduciary marks that trace the evolutionary landscape for the development of complex cellular systems in the proto-metazoan and metazoan lineages. The evolutionary provenance of conserved SH2 and PTK families reveals the mechanisms by which diversity is achieved through adaptations in tissue-specific gene transcription, altered ligand binding, insertions of linear motifs and the gain or loss of domains following gene duplication. We discuss mechanisms by which pTyr-mediated signalling networks evolve through the development of novel and expanded families of SH2 domain proteins and the elaboration of connections between pTyr-signalling proteins. These changes underlie the variety of general and specific signalling networks that give rise to tissue-specific functions and increasingly complex developmental programmes. Examination of SH2 domains from an evolutionary perspective provides insight into the process by which evolutionary expansion and modification of molecular protein interaction domain proteins permits the development of novel protein-interaction networks and accommodates adaptation of signalling networks. PMID:22889907

Solving Partial Differential Equations Using a New Differential Evolution Algorithm

Directory of Open Access Journals (Sweden)

Natee Panagant

2014-01-01

Full Text Available This paper proposes an alternative meshless approach to solve partial differential equations (PDEs. With a global approximate function being defined, a partial differential equation problem is converted into an optimisation problem with equality constraints from PDE boundary conditions. An evolutionary algorithm (EA is employed to search for the optimum solution. For this approach, the most difficult task is the low convergence rate of EA which consequently results in poor PDE solution approximation. However, its attractiveness remains due to the nature of a soft computing technique in EA. The algorithm can be used to tackle almost any kind of optimisation problem with simple evolutionary operation, which means it is mathematically simpler to use. A new efficient differential evolution (DE is presented and used to solve a number of the partial differential equations. The results obtained are illustrated and compared with exact solutions. It is shown that the proposed method has a potential to be a future meshless tool provided that the search performance of EA is greatly enhanced.

Using Differential Evolution to Optimize Learning from Signals and Enhance Network Security

Energy Technology Data Exchange (ETDEWEB)

Harmer, Paul K [Air Force Institute of Technology; Temple, Michael A [Air Force Institute of Technology; Buckner, Mark A [ORNL; Farquhar, Ethan [ORNL

2011-01-01

Computer and communication network attacks are commonly orchestrated through Wireless Access Points (WAPs). This paper summarizes proof-of-concept research activity aimed at developing a physical layer Radio Frequency (RF) air monitoring capability to limit unauthorizedWAP access and mprove network security. This is done using Differential Evolution (DE) to optimize the performance of a Learning from Signals (LFS) classifier implemented with RF Distinct Native Attribute (RF-DNA) fingerprints. Performance of the resultant DE-optimized LFS classifier is demonstrated using 802.11a WiFi devices under the most challenging conditions of intra-manufacturer classification, i.e., using emissions of like-model devices that only differ in serial number. Using identical classifier input features, performance of the DE-optimized LFS classifier is assessed relative to a Multiple Discriminant Analysis / Maximum Likelihood (MDA/ML) classifier that has been used for previous demonstrations. The comparative assessment is made using both Time Domain (TD) and Spectral Domain (SD) fingerprint features. For all combinations of classifier type, feature type, and signal-to-noise ratio considered, results show that the DEoptimized LFS classifier with TD features is uperior and provides up to 20% improvement in classification accuracy with proper selection of DE parameters.

Effects of biases in domain wall network evolution. II. Quantitative analysis

Science.gov (United States)

Correia, J. R. C. C. C.; Leite, I. S. C. R.; Martins, C. J. A. P.

2018-04-01

Domain walls form at phase transitions which break discrete symmetries. In a cosmological context, they often overclose the Universe (contrary to observational evidence), although one may prevent this by introducing biases or forcing anisotropic evolution of the walls. In a previous work [Correia et al., Phys. Rev. D 90, 023521 (2014), 10.1103/PhysRevD.90.023521], we numerically studied the evolution of various types of biased domain wall networks in the early Universe, confirming that anisotropic networks ultimately reach scaling while those with a biased potential or biased initial conditions decay. We also found that the analytic decay law obtained by Hindmarsh was in good agreement with simulations of biased potentials, but not of biased initial conditions, and suggested that the difference was related to the Gaussian approximation underlying the analytic law. Here, we extend our previous work in several ways. For the cases of biased potential and biased initial conditions, we study in detail the field distributions in the simulations, confirming that the validity (or not) of the Gaussian approximation is the key difference between the two cases. For anisotropic walls, we carry out a more extensive set of numerical simulations and compare them to the canonical velocity-dependent one-scale model for domain walls, finding that the model accurately predicts the linear scaling regime after isotropization. Overall, our analysis provides a quantitative description of the cosmological evolution of these networks.

An Enhanced Differential Evolution with Elite Chaotic Local Search

Directory of Open Access Journals (Sweden)

Zhaolu Guo

2015-01-01

Full Text Available Differential evolution (DE is a simple yet efficient evolutionary algorithm for real-world engineering problems. However, its search ability should be further enhanced to obtain better solutions when DE is applied to solve complex optimization problems. This paper presents an enhanced differential evolution with elite chaotic local search (DEECL. In DEECL, it utilizes a chaotic search strategy based on the heuristic information from the elite individuals to promote the exploitation power. Moreover, DEECL employs a simple and effective parameter adaptation mechanism to enhance the robustness. Experiments are conducted on a set of classical test functions. The experimental results show that DEECL is very competitive on the majority of the test functions.

Cloud computing task scheduling strategy based on improved differential evolution algorithm

Science.gov (United States)

Ge, Junwei; He, Qian; Fang, Yiqiu

2017-04-01

In order to optimize the cloud computing task scheduling scheme, an improved differential evolution algorithm for cloud computing task scheduling is proposed. Firstly, the cloud computing task scheduling model, according to the model of the fitness function, and then used improved optimization calculation of the fitness function of the evolutionary algorithm, according to the evolution of generation of dynamic selection strategy through dynamic mutation strategy to ensure the global and local search ability. The performance test experiment was carried out in the CloudSim simulation platform, the experimental results show that the improved differential evolution algorithm can reduce the cloud computing task execution time and user cost saving, good implementation of the optimal scheduling of cloud computing tasks.

Hybridizing Differential Evolution with a Genetic Algorithm for Color Image Segmentation

Directory of Open Access Journals (Sweden)

R. V. V. Krishna

2016-10-01

Full Text Available This paper proposes a hybrid of differential evolution and genetic algorithms to solve the color image segmentation problem. Clustering based color image segmentation algorithms segment an image by clustering the features of color and texture, thereby obtaining accurate prototype cluster centers. In the proposed algorithm, the color features are obtained using the homogeneity model. A new texture feature named Power Law Descriptor (PLD which is a modification of Weber Local Descriptor (WLD is proposed and further used as a texture feature for clustering. Genetic algorithms are competent in handling binary variables, while differential evolution on the other hand is more efficient in handling real parameters. The obtained texture feature is binary in nature and the color feature is a real value, which suits very well the hybrid cluster center optimization problem in image segmentation. Thus in the proposed algorithm, the optimum texture feature centers are evolved using genetic algorithms, whereas the optimum color feature centers are evolved using differential evolution.

Differential Evolution for Many-Particle Adaptive Quantum Metrology

NARCIS (Netherlands)

Lovett, N.B.; Crosnier, C.; Perarnau- Llobet, M.; Sanders, B.

2013-01-01

We devise powerful algorithms based on differential evolution for adaptive many-particle quantum metrology. Our new approach delivers adaptive quantum metrology policies for feedback control that are orders-of-magnitude more efficient and surpass the few-dozen-particle limitation arising in methods

An Efficient Binary Differential Evolution with Parameter Adaptation

Directory of Open Access Journals (Sweden)

Dongli Jia

2013-04-01

Full Text Available Differential Evolution (DE has been applied to many scientific and engineering problems for its simplicity and efficiency. However, the standard DE cannot be used in a binary search space directly. This paper proposes an adaptive binary Differential Evolution algorithm, or ABDE, that has a similar framework as the standard DE but with an improved binary mutation strategy in which the best individual participates. To further enhance the search ability, the parameters of the ABDE are slightly disturbed in an adaptive manner. Experiments have been carried out by comparing ABDE with two binary DE variants, normDE and BDE, and the most used binary search technique, GA, on a set of 13 selected benchmark functions and the classical 0-1 knapsack problem. Results show that the ABDE performs better than, or at least comparable to, the other algorithms in terms of search ability, convergence speed, and solution accuracy.

Homogenization of the evolution Stokes equation in a perforated domain with a stochastic Fourier boundary condition

KAUST Repository

Bessaih, Hakima

2015-04-01

The evolution Stokes equation in a domain containing periodically distributed obstacles subject to Fourier boundary condition on the boundaries is considered. We assume that the dynamic is driven by a stochastic perturbation on the interior of the domain and another stochastic perturbation on the boundaries of the obstacles. We represent the solid obstacles by holes in the fluid domain. The macroscopic (homogenized) equation is derived as another stochastic partial differential equation, defined in the whole non perforated domain. Here, the initial stochastic perturbation on the boundary becomes part of the homogenized equation as another stochastic force. We use the twoscale convergence method after extending the solution with 0 in the holes to pass to the limit. By Itô stochastic calculus, we get uniform estimates on the solution in appropriate spaces. In order to pass to the limit on the boundary integrals, we rewrite them in terms of integrals in the whole domain. In particular, for the stochastic integral on the boundary, we combine the previous idea of rewriting it on the whole domain with the assumption that the Brownian motion is of trace class. Due to the particular boundary condition dealt with, we get that the solution of the stochastic homogenized equation is not divergence free. However, it is coupled with the cell problem that has a divergence free solution. This paper represents an extension of the results of Duan and Wang (Comm. Math. Phys. 275:1508-1527, 2007), where a reaction diffusion equation with a dynamical boundary condition with a noise source term on both the interior of the domain and on the boundary was studied, and through a tightness argument and a pointwise two scale convergence method the homogenized equation was derived. © American Institute of Mathematical Sciences.

Birth and death of protein domains: A simple model of evolution explains power law behavior

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Berezovskaya Faina S

2002-10-01

Full Text Available Abstract Background Power distributions appear in numerous biological, physical and other contexts, which appear to be fundamentally different. In biology, power laws have been claimed to describe the distributions of the connections of enzymes and metabolites in metabolic networks, the number of interactions partners of a given protein, the number of members in paralogous families, and other quantities. In network analysis, power laws imply evolution of the network with preferential attachment, i.e. a greater likelihood of nodes being added to pre-existing hubs. Exploration of different types of evolutionary models in an attempt to determine which of them lead to power law distributions has the potential of revealing non-trivial aspects of genome evolution. Results A simple model of evolution of the domain composition of proteomes was developed, with the following elementary processes: i domain birth (duplication with divergence, ii death (inactivation and/or deletion, and iii innovation (emergence from non-coding or non-globular sequences or acquisition via horizontal gene transfer. This formalism can be described as a birth, death and innovation model (BDIM. The formulas for equilibrium frequencies of domain families of different size and the total number of families at equilibrium are derived for a general BDIM. All asymptotics of equilibrium frequencies of domain families possible for the given type of models are found and their appearance depending on model parameters is investigated. It is proved that the power law asymptotics appears if, and only if, the model is balanced, i.e. domain duplication and deletion rates are asymptotically equal up to the second order. It is further proved that any power asymptotic with the degree not equal to -1 can appear only if the hypothesis of independence of the duplication/deletion rates on the size of a domain family is rejected. Specific cases of BDIMs, namely simple, linear, polynomial and rational

An Orthogonal Learning Differential Evolution Algorithm for Remote Sensing Image Registration

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Wenping Ma

2014-01-01

Full Text Available We introduce an area-based method for remote sensing image registration. We use orthogonal learning differential evolution algorithm to optimize the similarity metric between the reference image and the target image. Many local and global methods have been used to achieve the optimal similarity metric in the last few years. Because remote sensing images are usually influenced by large distortions and high noise, local methods will fail in some cases. For this reason, global methods are often required. The orthogonal learning (OL strategy is efficient when searching in complex problem spaces. In addition, it can discover more useful information via orthogonal experimental design (OED. Differential evolution (DE is a heuristic algorithm. It has shown to be efficient in solving the remote sensing image registration problem. So orthogonal learning differential evolution algorithm (OLDE is efficient for many optimization problems. The OLDE method uses the OL strategy to guide the DE algorithm to discover more useful information. Experiments show that the OLDE method is more robust and efficient for registering remote sensing images.

Contemporary evolution during invasion: evidence for differentiation, natural selection, and local adaptation.

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Colautti, Robert I; Lau, Jennifer A

2015-05-01

Biological invasions are 'natural' experiments that can improve our understanding of contemporary evolution. We evaluate evidence for population differentiation, natural selection and adaptive evolution of invading plants and animals at two nested spatial scales: (i) among introduced populations (ii) between native and introduced genotypes. Evolution during invasion is frequently inferred, but rarely confirmed as adaptive. In common garden studies, quantitative trait differentiation is only marginally lower (~3.5%) among introduced relative to native populations, despite genetic bottlenecks and shorter timescales (i.e. millennia vs. decades). However, differentiation between genotypes from the native vs. introduced range is less clear and confounded by nonrandom geographic sampling; simulations suggest this causes a high false-positive discovery rate (>50%) in geographically structured populations. Selection differentials (¦s¦) are stronger in introduced than in native species, although selection gradients (¦β¦) are not, consistent with introduced species experiencing weaker genetic constraints. This could facilitate rapid adaptation, but evidence is limited. For example, rapid phenotypic evolution often manifests as geographical clines, but simulations demonstrate that nonadaptive trait clines can evolve frequently during colonization (~two-thirds of simulations). Additionally, QST-FST studies may often misrepresent the strength and form of natural selection acting during invasion. Instead, classic approaches in evolutionary ecology (e.g. selection analysis, reciprocal transplant, artificial selection) are necessary to determine the frequency of adaptive evolution during invasion and its influence on establishment, spread and impact of invasive species. These studies are rare but crucial for managing biological invasions in the context of global change. © 2015 John Wiley & Sons Ltd.

Molecular representation of molar domain (volume), evolution equations, and linear constitutive relations for volume transport.

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Eu, Byung Chan

2008-09-07

In the traditional theories of irreversible thermodynamics and fluid mechanics, the specific volume and molar volume have been interchangeably used for pure fluids, but in this work we show that they should be distinguished from each other and given distinctive statistical mechanical representations. In this paper, we present a general formula for the statistical mechanical representation of molecular domain (volume or space) by using the Voronoi volume and its mean value that may be regarded as molar domain (volume) and also the statistical mechanical representation of volume flux. By using their statistical mechanical formulas, the evolution equations of volume transport are derived from the generalized Boltzmann equation of fluids. Approximate solutions of the evolution equations of volume transport provides kinetic theory formulas for the molecular domain, the constitutive equations for molar domain (volume) and volume flux, and the dissipation of energy associated with volume transport. Together with the constitutive equation for the mean velocity of the fluid obtained in a previous paper, the evolution equations for volume transport not only shed a fresh light on, and insight into, irreversible phenomena in fluids but also can be applied to study fluid flow problems in a manner hitherto unavailable in fluid dynamics and irreversible thermodynamics. Their roles in the generalized hydrodynamics will be considered in the sequel.

Parameter identification of PEMFC model based on hybrid adaptive differential evolution algorithm

International Nuclear Information System (INIS)

Sun, Zhe; Wang, Ning; Bi, Yunrui; Srinivasan, Dipti

2015-01-01

In this paper, a HADE (hybrid adaptive differential evolution) algorithm is proposed for the identification problem of PEMFC (proton exchange membrane fuel cell). Inspired by biological genetic strategy, a novel adaptive scaling factor and a dynamic crossover probability are presented to improve the adaptive and dynamic performance of differential evolution algorithm. Moreover, two kinds of neighborhood search operations based on the bee colony foraging mechanism are introduced for enhancing local search efficiency. Through testing the benchmark functions, the proposed algorithm exhibits better performance in convergent accuracy and speed. Finally, the HADE algorithm is applied to identify the nonlinear parameters of PEMFC stack model. Through experimental comparison with other identified methods, the PEMFC model based on the HADE algorithm shows better performance. - Highlights: • We propose a hybrid adaptive differential evolution algorithm (HADE). • The search efficiency is enhanced in low and high dimension search space. • The effectiveness is confirmed by testing benchmark functions. • The identification of the PEMFC model is conducted by adopting HADE.

Differential evolution based method for total transfer capability ...

African Journals Online (AJOL)

The application of Differential Evolution (DE) to compute the Total Transfer Capability (TTC) in deregulated market is proposed in this paper. The objective is to maximize a specific point-to-point power transaction without violating system constraints using DE. This algorithm is based on full ac optimal power flow solution to ...

Reliability-redundancy optimization by means of a chaotic differential evolution approach

International Nuclear Information System (INIS)

Coelho, Leandro dos Santos

2009-01-01

The reliability design is related to the performance analysis of many engineering systems. The reliability-redundancy optimization problems involve selection of components with multiple choices and redundancy levels that produce maximum benefits, can be subject to the cost, weight, and volume constraints. Classical mathematical methods have failed in handling nonconvexities and nonsmoothness in optimization problems. As an alternative to the classical optimization approaches, the meta-heuristics have been given much attention by many researchers due to their ability to find an almost global optimal solution in reliability-redundancy optimization problems. Evolutionary algorithms (EAs) - paradigms of evolutionary computation field - are stochastic and robust meta-heuristics useful to solve reliability-redundancy optimization problems. EAs such as genetic algorithm, evolutionary programming, evolution strategies and differential evolution are being used to find global or near global optimal solution. A differential evolution approach based on chaotic sequences using Lozi's map for reliability-redundancy optimization problems is proposed in this paper. The proposed method has a fast convergence rate but also maintains the diversity of the population so as to escape from local optima. An application example in reliability-redundancy optimization based on the overspeed protection system of a gas turbine is given to show its usefulness and efficiency. Simulation results show that the application of deterministic chaotic sequences instead of random sequences is a possible strategy to improve the performance of differential evolution.

Possible description of domain walls in two-dimensional spin glasses by stochastic Loewner evolutions

International Nuclear Information System (INIS)

Bernard, Denis; Le Doussal, Pierre; Middleton, A. Alan

2007-01-01

Domain walls for spin glasses are believed to be scale invariant; a stronger symmetry, conformal invariance, has the potential to hold. The statistics of zero-temperature Ising spin glass domain walls in two dimensions are used to test the hypothesis that these domain walls are described by a Schramm-Loewner evolution SLE κ . Multiple tests are consistent with SLE κ , where κ=2.32±0.08. Both conformal invariance and the domain Markov property are tested. The latter does not hold in small systems, but detailed numerical evidence suggests that it holds in the continuum limit

Ferroelectric domains and phase evolution in (Fe:) KTa{sub 1−x}Nb{sub x}O{sub 3} crystals

Energy Technology Data Exchange (ETDEWEB)

Zhao, Hongyang; Cai, Kang; Fan, Ziran; Huang, Zhideng [Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Department of Materials Science and Engineering, Wuhan Institute of Technology, 693 Xiongchu Road, Wuhan 430073 (China); Ma, Zhibin, E-mail: mazb@wit.edu.cn [Hubei Key Laboratory of Plasma Chemistry and Advanced Materials, Department of Materials Science and Engineering, Wuhan Institute of Technology, 693 Xiongchu Road, Wuhan 430073 (China); Jia, Tingting; Kimura, Hideo [National Institute for Materials Science, Sengen 1-2-1, Tsukuba 305-0047 (Japan); Yang, Yuguo [New Materials Research Institute, Shandong Academy of Sciences, No. 19, Keyuan Road, Jinan 250014 (China); Matsumoto, Takao; Tohei, Tetsuya; Shibata, Naoya; Ikuhara, Yuichi [Institute of Engineering Innovation, School of Engineering, University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-8656 (Japan)

2017-08-15

Highlights: • Three phase transitions were observed: the R–O, O–T, T–C evolutions. • KTN ferroelectric domain switching is because of the nano-polar-regions. • The domain evolution showed KTN has triangle shape, but Fe: KTN has straight line. - Abstract: The domain structures and phase evolution in mixed ferroelectric (Fe): KTa{sub 1−x}Nb{sub x}O{sub 3} (KTN) crystals were investigated. Temperature dependent Raman spectra show that Curie temperatures of KTN and Fe: KTN are far below room temperature, but the ferroelectric domain switching was still visualized by scanning probe microscopy at room temperature. These observed domains origin from the nano-regions near the grain boundaries. In addition, the intrinsic domains (triangle for KTN and straight line/stripe for Fe: KTN) could only be observed at low temperature by transmission electron microscopy. Three phase transitions in Fe: KTN crystals were found by Raman spectroscopy and dielectric testing: 175 K for Rhombohedral-to-Orthorhombic (R–O), 210 K for Orthorhombic-to-Tetragonal (O–T) and 250 K for Tetragonal-to-Cubic (T–C), which is consistent with the domain behavior.

Focus on Membrane Differentiation and Membrane Domains in the Prokaryotic Cell

NARCIS (Netherlands)

Boekema, Egbert J.; Scheffers, Dirk-Jan; van Bezouwen, Laura S.; Bolhuis, Henk; Folea, I. Mihaela

2013-01-01

A summary is presented of membrane differentiation in the prokaryotic cell, with an emphasis on the organization of proteins in the plasma/cell membrane. Many species belonging to the Eubacteria and Archaea have special membrane domains and/or membrane proliferation, which are vital for different

Parameter Estimation of Damped Compound Pendulum Differential Evolution Algorithm

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Saad Mohd Sazli

2016-01-01

Full Text Available This paper present the parameter identification of damped compound pendulum using differential evolution algorithm. The procedure used to achieve the parameter identification of the experimental system consisted of input output data collection, ARX model order selection and parameter estimation using conventional method least square (LS and differential evolution (DE algorithm. PRBS signal is used to be input signal to regulate the motor speed. Whereas, the output signal is taken from position sensor. Both, input and output data is used to estimate the parameter of the ARX model. The residual error between the actual and predicted output responses of the models is validated using mean squares error (MSE. Analysis showed that, MSE value for LS is 0.0026 and MSE value for DE is 3.6601×10-5. Based results obtained, it was found that DE have lower MSE than the LS method.

Differential Evolution and Particle Swarm Optimization for Partitional Clustering

DEFF Research Database (Denmark)

Krink, Thiemo; Paterlini, Sandra

2006-01-01

for numerical optimisation, which are hardly known outside the search heuristics field, are particle swarm optimisation (PSO) and differential evolution (DE). The performance of GAs for a representative point evolution approach to clustering is compared with PSO and DE. The empirical results show that DE......Many partitional clustering algorithms based on genetic algorithms (GA) have been proposed to tackle the problem of finding the optimal partition of a data set. Very few studies considered alternative stochastic search heuristics other than GAs or simulated annealing. Two promising algorithms...

Characterization of Inclusions in Evolution of Sodium Sulfate Using Terahertz Time-domain Spectroscopy.

Science.gov (United States)

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.

Structure and evolution of N-domains in AAA metalloproteases.

Science.gov (United States)

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

2015-02-27

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

Market-based transmission expansion planning by improved differential evolution

International Nuclear Information System (INIS)

Georgilakis, Pavlos S.

2010-01-01

The restructuring and deregulation has exposed the transmission planner to new objectives and uncertainties. As a result, new criteria and approaches are needed for transmission expansion planning (TEP) in deregulated electricity markets. This paper proposes a new market-based approach for TEP. An improved differential evolution (IDE) model is proposed for the solution of this new market-based TEP problem. The modifications of IDE in comparison to the simple differential evolution method are: (1) the scaling factor F is varied randomly within some range, (2) an auxiliary set is employed to enhance the diversity of the population, (3) the newly generated trial vector is compared with the nearest parent, and (4) the simple feasibility rule is used to treat the constraints. Results from the application of the proposed method on the IEEE 30-bus test system demonstrate the feasibility and practicality of the proposed IDE for the solution of TEP problem. (author)

A Hybrid Backtracking Search Optimization Algorithm with Differential Evolution

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Lijin Wang

2015-01-01

Full Text Available The backtracking search optimization algorithm (BSA is a new nature-inspired method which possesses a memory to take advantage of experiences gained from previous generation to guide the population to the global optimum. BSA is capable of solving multimodal problems, but it slowly converges and poorly exploits solution. The differential evolution (DE algorithm is a robust evolutionary algorithm and has a fast convergence speed in the case of exploitive mutation strategies that utilize the information of the best solution found so far. In this paper, we propose a hybrid backtracking search optimization algorithm with differential evolution, called HBD. In HBD, DE with exploitive strategy is used to accelerate the convergence by optimizing one worse individual according to its probability at each iteration process. A suit of 28 benchmark functions are employed to verify the performance of HBD, and the results show the improvement in effectiveness and efficiency of hybridization of BSA and DE.

RDEL: Restart Differential Evolution algorithm with Local Search Mutation for global numerical optimization

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Ali Wagdy Mohamed

2014-11-01

Full Text Available In this paper, a novel version of Differential Evolution (DE algorithm based on a couple of local search mutation and a restart mechanism for solving global numerical optimization problems over continuous space is presented. The proposed algorithm is named as Restart Differential Evolution algorithm with Local Search Mutation (RDEL. In RDEL, inspired by Particle Swarm Optimization (PSO, a novel local mutation rule based on the position of the best and the worst individuals among the entire population of a particular generation is introduced. The novel local mutation scheme is joined with the basic mutation rule through a linear decreasing function. The proposed local mutation scheme is proven to enhance local search tendency of the basic DE and speed up the convergence. Furthermore, a restart mechanism based on random mutation scheme and a modified Breeder Genetic Algorithm (BGA mutation scheme is combined to avoid stagnation and/or premature convergence. Additionally, an exponent increased crossover probability rule and a uniform scaling factors of DE are introduced to promote the diversity of the population and to improve the search process, respectively. The performance of RDEL is investigated and compared with basic differential evolution, and state-of-the-art parameter adaptive differential evolution variants. It is discovered that the proposed modifications significantly improve the performance of DE in terms of quality of solution, efficiency and robustness.

Stable multi-domain spectral penalty methods for fractional partial differential equations

Science.gov (United States)

Xu, Qinwu; Hesthaven, Jan S.

2014-01-01

We propose stable multi-domain spectral penalty methods suitable for solving fractional partial differential equations with fractional derivatives of any order. First, a high order discretization is proposed to approximate fractional derivatives of any order on any given grids based on orthogonal polynomials. The approximation order is analyzed and verified through numerical examples. Based on the discrete fractional derivative, we introduce stable multi-domain spectral penalty methods for solving fractional advection and diffusion equations. The equations are discretized in each sub-domain separately and the global schemes are obtained by weakly imposed boundary and interface conditions through a penalty term. Stability of the schemes are analyzed and numerical examples based on both uniform and nonuniform grids are considered to highlight the flexibility and high accuracy of the proposed schemes.

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

International Nuclear Information System (INIS)

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

2016-01-01

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

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

Science.gov (United States)

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

2016-04-01

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

Adaptive grid based multi-objective Cauchy differential evolution for stochastic dynamic economic emission dispatch with wind power uncertainty.

Science.gov (United States)

Zhang, Huifeng; Lei, Xiaohui; Wang, Chao; Yue, Dong; Xie, Xiangpeng

2017-01-01

Since wind power is integrated into the thermal power operation system, dynamic economic emission dispatch (DEED) has become a new challenge due to its uncertain characteristics. This paper proposes an adaptive grid based multi-objective Cauchy differential evolution (AGB-MOCDE) for solving stochastic DEED with wind power uncertainty. To properly deal with wind power uncertainty, some scenarios are generated to simulate those possible situations by dividing the uncertainty domain into different intervals, the probability of each interval can be calculated using the cumulative distribution function, and a stochastic DEED model can be formulated under different scenarios. For enhancing the optimization efficiency, Cauchy mutation operation is utilized to improve differential evolution by adjusting the population diversity during the population evolution process, and an adaptive grid is constructed for retaining diversity distribution of Pareto front. With consideration of large number of generated scenarios, the reduction mechanism is carried out to decrease the scenarios number with covariance relationships, which can greatly decrease the computational complexity. Moreover, the constraint-handling technique is also utilized to deal with the system load balance while considering transmission loss among thermal units and wind farms, all the constraint limits can be satisfied under the permitted accuracy. After the proposed method is simulated on three test systems, the obtained results reveal that in comparison with other alternatives, the proposed AGB-MOCDE can optimize the DEED problem while handling all constraint limits, and the optimal scheme of stochastic DEED can decrease the conservation of interval optimization, which can provide a more valuable optimal scheme for real-world applications.

Existence of solutions for quasilinear random impulsive neutral differential evolution equation

Directory of Open Access Journals (Sweden)

B. Radhakrishnan

2018-07-01

Full Text Available This paper deals with the existence of solutions for quasilinear random impulsive neutral functional differential evolution equation in Banach spaces and the results are derived by using the analytic semigroup theory, fractional powers of operators and the Schauder fixed point approach. An application is provided to illustrate the theory. Keywords: Quasilinear differential equation, Analytic semigroup, Random impulsive neutral differential equation, Fixed point theorem, 2010 Mathematics Subject Classification: 34A37, 47H10, 47H20, 34K40, 34K45, 35R12

Evolution of networks for body plan patterning; interplay of modularity, robustness and evolvability.

Directory of Open Access Journals (Sweden)

Kirsten H Ten Tusscher

2011-10-01

Full Text Available A major goal of evolutionary developmental biology (evo-devo is to understand how multicellular body plans of increasing complexity have evolved, and how the corresponding developmental programs are genetically encoded. It has been repeatedly argued that key to the evolution of increased body plan complexity is the modularity of the underlying developmental gene regulatory networks (GRNs. This modularity is considered essential for network robustness and evolvability. In our opinion, these ideas, appealing as they may sound, have not been sufficiently tested. Here we use computer simulations to study the evolution of GRNs' underlying body plan patterning. We select for body plan segmentation and differentiation, as these are considered to be major innovations in metazoan evolution. To allow modular networks to evolve, we independently select for segmentation and differentiation. We study both the occurrence and relation of robustness, evolvability and modularity of evolved networks. Interestingly, we observed two distinct evolutionary strategies to evolve a segmented, differentiated body plan. In the first strategy, first segments and then differentiation domains evolve (SF strategy. In the second scenario segments and domains evolve simultaneously (SS strategy. We demonstrate that under indirect selection for robustness the SF strategy becomes dominant. In addition, as a byproduct of this larger robustness, the SF strategy is also more evolvable. Finally, using a combined functional and architectural approach, we determine network modularity. We find that while SS networks generate segments and domains in an integrated manner, SF networks use largely independent modules to produce segments and domains. Surprisingly, we find that widely used, purely architectural methods for determining network modularity completely fail to establish this higher modularity of SF networks. Finally, we observe that, as a free side effect of evolving segmentation

Battery parameterisation based on differential evolution via a boundary evolution strategy

Science.gov (United States)

Yang, Guangya

2014-01-01

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

Differential evolution-simulated annealing for multiple sequence alignment

Science.gov (United States)

Addawe, R. C.; Addawe, J. M.; Sueño, M. R. K.; Magadia, J. C.

2017-10-01

Multiple sequence alignments (MSA) are used in the analysis of molecular evolution and sequence structure relationships. In this paper, a hybrid algorithm, Differential Evolution - Simulated Annealing (DESA) is applied in optimizing multiple sequence alignments (MSAs) based on structural information, non-gaps percentage and totally conserved columns. DESA is a robust algorithm characterized by self-organization, mutation, crossover, and SA-like selection scheme of the strategy parameters. Here, the MSA problem is treated as a multi-objective optimization problem of the hybrid evolutionary algorithm, DESA. Thus, we name the algorithm as DESA-MSA. Simulated sequences and alignments were generated to evaluate the accuracy and efficiency of DESA-MSA using different indel sizes, sequence lengths, deletion rates and insertion rates. The proposed hybrid algorithm obtained acceptable solutions particularly for the MSA problem evaluated based on the three objectives.

Differential Evolution algorithm applied to FSW model calibration

Science.gov (United States)

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

2014-03-01

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

A POPULATION MEMETICS APPROACH TO CULTURAL EVOLUTION IN CHAFFINCH SONG: DIFFERENTIATION AMONG POPULATIONS.

Science.gov (United States)

Lynch, Alejandro; Baker, Allan J

1994-04-01

We investigated cultural evolution in populations of common chaffinches (Fringilla coelebs) in the Atlantic islands (Azores, Madeira, and Canaries) and neighboring continental regions (Morocco and Iberia) by employing a population-memetic approach. To quantify differentiation, we used the concept of a song meme, defined as a single syllable or a series of linked syllables capable of being transmitted. The levels of cultural differentiation are higher among the Canaries populations than among the Azorean ones, even though the islands are on average closer to each other geographically. This is likely the result of reduced levels of migration, lower population sizes, and bottlenecks (possibly during the colonization of these populations) in the Canaries; all these factors produce a smaller effective population size and therefore accentuate the effects of differentiation by random drift. Significant levels of among-population differentiation in the Azores, in spite of substantial levels of migration, attest to the differentiating effects of high mutation rates of memes, which allow the accumulation of new mutants in different populations before migration can disperse them throughout the entire region. © 1994 The Society for the Study of Evolution.

Evidence of correlated evolution and adaptive differentiation of stem and leaf functional traits in the herbaceous genus, Helianthus.

Science.gov (United States)

Pilote, Alex J; Donovan, Lisa A

2016-12-01

Patterns of plant stem traits are expected to align with a "fast-slow" plant economic spectrum across taxa. Although broad patterns support such tradeoffs in field studies, tests of hypothesized correlated trait evolution and adaptive differentiation are more robust when taxa relatedness and environment are taken into consideration. Here we test for correlated evolution of stem and leaf traits and their adaptive differentiation across environments in the herbaceous genus, Helianthus. Stem and leaf traits of 14 species of Helianthus (28 populations) were assessed in a common garden greenhouse study. Phylogenetically independent contrasts were used to test for evidence of correlated evolution of stem hydraulic and biomechanical properties, correlated evolution of stem and leaf traits, and adaptive differentiation associated with source habitat environments. Among stem traits, there was evidence for correlated evolution of some hydraulic and biomechanical properties, supporting an expected tradeoff between stem theoretical hydraulic efficiency and resistance to bending stress. Population differentiation for suites of stem and leaf traits was found to be consistent with a "fast-slow" resource-use axis for traits related to water transport and use. Associations of population traits with source habitat characteristics supported repeated evolution of a resource-acquisitive "drought-escape" strategy in arid environments. This study provides evidence of correlated evolution of stem and leaf traits consistent with the fast-slow spectrum of trait combinations related to water transport and use along the stem-to-leaf pathway. Correlations of traits with source habitat characteristics further indicate that the correlated evolution is associated, at least in part, with adaptive differentiation of Helianthus populations among native habitats differing in climate. © 2016 Botanical Society of America.

Size evolution of ultrafine particles: Differential signatures of normal and episodic events

International Nuclear Information System (INIS)

Joshi, Manish; Khan, Arshad; Anand, S.; Sapra, B.K.

2016-01-01

The effect of fireworks on the aerosol number characteristics of atmosphere was studied for an urban mega city. Measurements were made at 50 m height to assess the local changes around the festival days. Apart from the increase in total number concentration and characteristic accumulation mode, short-term increase of ultrafine particle concentration was noted. Total number concentration varies an order of magnitude during the measurement period in which peak occurs at a frequency of approximately one per day. On integral scale, it seems not possible to distinguish an episodic (e.g. firework bursting induced aerosol emission) and a normal (ambient atmospheric changes) event. However these events could be differentiated on the basis of size evolution analysis around number concentration peaks. The results are discussed relative to past studies and inferences are drawn towards aerosol signatures of firework bursting. The short-term burst in ultrafine particle concentration can pose an inhalation hazard. - Highlights: • Effect of firework emissions on atmospheric aerosol characteristics was studied. • Significant increase in ultrafine particle concentration was observed during firework bursting. • Size distribution evolution analysis of number concentration peaks has been performed. • Differential signatures of normal and episodic event were noted. - Notable increase in ultrafine particle concentration during firework bursting was seen. Normal and episodic event could be differentiated on the basis of size evolution analysis.

Almost Automorphic and Pseudo-Almost Automorphic Solutions to Semilinear Evolution Equations with Nondense Domain

Directory of Open Access Journals (Sweden)

Bruno de Andrade

2009-01-01

Full Text Available We study the existence and uniqueness of almost automorphic (resp., pseudo-almost automorphic solutions to a first-order differential equation with linear part dominated by a Hille-Yosida type operator with nondense domain.

pSum-SaDE: A Modified p-Median Problem and Self-Adaptive Differential Evolution Algorithm for Text Summarization

Directory of Open Access Journals (Sweden)

Rasim M. Alguliev

2011-01-01

Full Text Available Extractive multidocument summarization is modeled as a modified p-median problem. The problem is formulated with taking into account four basic requirements, namely, relevance, information coverage, diversity, and length limit that should satisfy summaries. To solve the optimization problem a self-adaptive differential evolution algorithm is created. Differential evolution has been proven to be an efficient and robust algorithm for many real optimization problems. However, it still may converge toward local optimum solutions, need to manually adjust the parameters, and finding the best values for the control parameters is a consuming task. In the paper is proposed a self-adaptive scaling factor in original DE to increase the exploration and exploitation ability. This paper has found that self-adaptive differential evolution can efficiently find the best solution in comparison with the canonical differential evolution. We implemented our model on multi-document summarization task. Experiments have shown that the proposed model is competitive on the DUC2006 dataset.

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

Science.gov (United States)

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.

Protein domain evolution is associated with reproductive diversification and adaptive radiation in the genus Eucalyptus.

Science.gov (United States)

Kersting, Anna R; Mizrachi, Eshchar; Bornberg-Bauer, Erich; Myburg, Alexander A

2015-06-01

Eucalyptus is a pivotal genus within the rosid order Myrtales with distinct geographic history and adaptations. Comparative analysis of protein domain evolution in the newly sequenced Eucalyptus grandis genome and other rosid lineages sheds light on the adaptive mechanisms integral to the success of this genus of woody perennials. We reconstructed the ancestral domain content to elucidate the gain, loss and expansion of protein domains and domain arrangements in Eucalyptus in the context of rosid phylogeny. We used functional gene ontology (GO) annotation of genes to investigate the possible biological and evolutionary consequences of protein domain expansion. We found that protein modulation within the angiosperms occurred primarily on the level of expansion of certain domains and arrangements. Using RNA-Seq data from E. grandis, we showed that domain expansions have contributed to tissue-specific expression of tandemly duplicated genes. Our results indicate that tandem duplication of genes, a key feature of the Eucalyptus genome, has played an important role in the expansion of domains, particularly in proteins related to the specialization of reproduction and biotic and abiotic interactions affecting root and floral biology, and that tissue-specific expression of proteins with expanded domains has facilitated subfunctionalization in domain families. © 2014 University of Pretoria New Phytologist © 2014 New Phytologist Trust.

Homogenization of the evolution Stokes equation in a perforated domain with a stochastic Fourier boundary condition

KAUST Repository

Bessaih, Hakima; Efendiev, Yalchin; Maris, Florin

2015-01-01

The evolution Stokes equation in a domain containing periodically distributed obstacles subject to Fourier boundary condition on the boundaries is considered. We assume that the dynamic is driven by a stochastic perturbation on the interior

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

Science.gov (United States)

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

2013-01-01

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

Multiple Active Contours Guided by Differential Evolution for Medical Image Segmentation

Directory of Open Access Journals (Sweden)

I. Cruz-Aceves

2013-01-01

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

Parameter optimization of differential evolution algorithm for automatic playlist generation problem

Science.gov (United States)

Alamag, Kaye Melina Natividad B.; Addawe, Joel M.

2017-11-01

With the digitalization of music, the number of collection of music increased largely and there is a need to create lists of music that filter the collection according to user preferences, thus giving rise to the Automatic Playlist Generation Problem (APGP). Previous attempts to solve this problem include the use of search and optimization algorithms. If a music database is very large, the algorithm to be used must be able to search the lists thoroughly taking into account the quality of the playlist given a set of user constraints. In this paper we perform an evolutionary meta-heuristic optimization algorithm, Differential Evolution (DE) using different combination of parameter values and select the best performing set when used to solve four standard test functions. Performance of the proposed algorithm is then compared with normal Genetic Algorithm (GA) and a hybrid GA with Tabu Search. Numerical simulations are carried out to show better results from Differential Evolution approach with the optimized parameter values.

Optimal Control Problems for Partial Differential Equations on Reticulated Domains

CERN Document Server

Kogut, Peter I

2011-01-01

In the development of optimal control, the complexity of the systems to which it is applied has increased significantly, becoming an issue in scientific computing. In order to carry out model-reduction on these systems, the authors of this work have developed a method based on asymptotic analysis. Moving from abstract explanations to examples and applications with a focus on structural network problems, they aim at combining techniques of homogenization and approximation. Optimal Control Problems for Partial Differential Equations on Reticulated Domains is an excellent reference tool for gradu

Existence of mild solutions of a semilinear evolution differential inclusions with nonlocal conditions

Directory of Open Access Journals (Sweden)

Reem A. Al-Omair

2009-03-01

Full Text Available In this paper we prove the existence of a mild solution for a semilinear evolution differential inclusion with nonlocal condition and governed by a family of linear operators, not necessarily bounded or closed, in a Banach space. No compactness assumption is assumed on the evolution operator generated by the family operators. Also, we prove that the set of mild solutions is compact.

Differential paralog divergence modulates genome evolution across yeast species.

Directory of Open Access Journals (Sweden)

Monica R Sanchez

2017-02-01

Full Text Available Evolutionary outcomes depend not only on the selective forces acting upon a species, but also on the genetic background. However, large timescales and uncertain historical selection pressures can make it difficult to discern such important background differences between species. Experimental evolution is one tool to compare evolutionary potential of known genotypes in a controlled environment. Here we utilized a highly reproducible evolutionary adaptation in Saccharomyces cerevisiae to investigate whether experimental evolution of other yeast species would select for similar adaptive mutations. We evolved populations of S. cerevisiae, S. paradoxus, S. mikatae, S. uvarum, and interspecific hybrids between S. uvarum and S. cerevisiae for ~200-500 generations in sulfate-limited continuous culture. Wild-type S. cerevisiae cultures invariably amplify the high affinity sulfate transporter gene, SUL1. However, while amplification of the SUL1 locus was detected in S. paradoxus and S. mikatae populations, S. uvarum cultures instead selected for amplification of the paralog, SUL2. We measured the relative fitness of strains bearing deletions and amplifications of both SUL genes from different species, confirming that, converse to S. cerevisiae, S. uvarum SUL2 contributes more to fitness in sulfate limitation than S. uvarum SUL1. By measuring the fitness and gene expression of chimeric promoter-ORF constructs, we were able to delineate the cause of this differential fitness effect primarily to the promoter of S. uvarum SUL1. Our data show evidence of differential sub-functionalization among the sulfate transporters across Saccharomyces species through recent changes in noncoding sequence. Furthermore, these results show a clear example of how such background differences due to paralog divergence can drive changes in genome evolution.

Origin and Evolution of Protein Fold Designs Inferred from Phylogenomic Analysis of CATH Domain Structures in Proteomes

Science.gov (United States)

Bukhari, Syed Abbas; Caetano-Anollés, Gustavo

2013-01-01

The spatial arrangements of secondary structures in proteins, irrespective of their connectivity, depict the overall shape and organization of protein domains. These features have been used in the CATH and SCOP classifications to hierarchically partition fold space and define the architectural make up of proteins. Here we use phylogenomic methods and a census of CATH structures in hundreds of genomes to study the origin and diversification of protein architectures (A) and their associated topologies (T) and superfamilies (H). Phylogenies that describe the evolution of domain structures and proteomes were reconstructed from the structural census and used to generate timelines of domain discovery. Phylogenies of CATH domains at T and H levels of structural abstraction and associated chronologies revealed patterns of reductive evolution, the early rise of Archaea, three epochs in the evolution of the protein world, and patterns of structural sharing between superkingdoms. Phylogenies of proteomes confirmed the early appearance of Archaea. While these findings are in agreement with previous phylogenomic studies based on the SCOP classification, phylogenies unveiled sharing patterns between Archaea and Eukarya that are recent and can explain the canonical bacterial rooting typically recovered from sequence analysis. Phylogenies of CATH domains at A level uncovered general patterns of architectural origin and diversification. The tree of A structures showed that ancient structural designs such as the 3-layer (αβα) sandwich (3.40) or the orthogonal bundle (1.10) are comparatively simpler in their makeup and are involved in basic cellular functions. In contrast, modern structural designs such as prisms, propellers, 2-solenoid, super-roll, clam, trefoil and box are not widely distributed and were probably adopted to perform specialized functions. Our timelines therefore uncover a universal tendency towards protein structural complexity that is remarkable. PMID:23555236

Many-Objective Distinct Candidates Optimization using Differential Evolution

DEFF Research Database (Denmark)

Justesen, Peter; Ursem, Rasmus Kjær

2010-01-01

for each objective. The Many-Objective Distinct Candidates Optimization using Differential Evolution (MODCODE) algorithm takes a novel approach by focusing search using a user-defined number of subpopulations each returning a distinct optimal solution within the preferred region of interest. In this paper......, we present the novel MODCODE algorithm incorporating the ROD measure to measure and control candidate distinctiveness. MODCODE is tested against GDE3 on three real world centrifugal pump design problems supplied by Grundfos. Our algorithm outperforms GDE3 on all problems with respect to all...

Differential associations between domains of sibling conflict and adolescent emotional adjustment.

Science.gov (United States)

Campione-Barr, Nicole; Greer, Kelly Bassett; Kruse, Anna

2013-01-01

Issues of equality and fairness and invasion of the personal domain, 2 previously identified topic areas of adolescent sibling conflict (N. Campione-Barr & J. G. Smetana, 2010), were examined in 145 dyads (Mfirst-born = 14.97, SD = 1.69 years; Msecond-born = 12.20, SD = 1.90 years) for their differential effects on youths' emotional adjustment over 1 year. The impact of internalizing symptoms on later sibling conflicts also was tested. Invasion of the personal domain conflicts were associated with higher levels of anxiety and lower self-esteem 1 year later, whereas Equality and Fairness issues were associated with greater depressed mood. Conversely, greater internalizing symptomatology and lower self-esteem predicted more of both types of conflict. Moderating influences of gender and ordinal position were also examined. © 2012 The Authors. Child Development © 2012 Society for Research in Child Development, Inc.

D1/D2 domain of large-subunit ribosomal DNA for differentiation of Orpinomyces spp.

Science.gov (United States)

Dagar, Sumit S; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K

2011-09-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation.

Differential Evolution Algorithm with Self-Adaptive Population Resizing Mechanism

Directory of Open Access Journals (Sweden)

Xu Wang

2013-01-01

Full Text Available A differential evolution (DE algorithm with self-adaptive population resizing mechanism, SapsDE, is proposed to enhance the performance of DE by dynamically choosing one of two mutation strategies and tuning control parameters in a self-adaptive manner. More specifically, more appropriate mutation strategies along with its parameter settings can be determined adaptively according to the previous status at different stages of the evolution process. To verify the performance of SapsDE, 17 benchmark functions with a wide range of dimensions, and diverse complexities are used. Nonparametric statistical procedures were performed for multiple comparisons between the proposed algorithm and five well-known DE variants from the literature. Simulation results show that SapsDE is effective and efficient. It also exhibits much more superiorresultsthan the other five algorithms employed in the comparison in most of the cases.

Differential evolution to enhance localization of mobile robots

DEFF Research Database (Denmark)

Lisowski, Michal; Fan, Zhun; Ravn, Ole

2011-01-01

. In addition, a novel mechanism for effective robot kidnap detection was proposed. Experiments were performed using computer simulations based on the odometer data and laser range finder measurements collected in advance by a robot in real-life. Experimental results showed that integrating DE enables MCL...... to provide more accurate robot pose estimations in shorter time while using fewer particles.......This paper focuses on the mobile robot localization problems: pose tracking, global localization and robot kidnap. Differential Evolution (DE) applied to extend Monte Carlo Localization (MCL) was investigated to better solve localization problem by increasing localization reliability and speed...

Evolution effects of the copper surface morphology on the nucleation density and growth of graphene domains at different growth pressures

Energy Technology Data Exchange (ETDEWEB)

Hedayat, Seyed Mahdi [Transport Phenomena & Nanotechnology Lab., School of Chemical Engineering, College of Engineering, University of Tehran (Iran, Islamic Republic of); Karimi-Sabet, Javad, E-mail: j_karimi@alum.sharif.edu [NFCRS, Nuclear Science and Technology Research Institute, Tehran (Iran, Islamic Republic of); Shariaty-Niassar, Mojtaba, E-mail: mshariat@ut.ac.ir [Transport Phenomena & Nanotechnology Lab., School of Chemical Engineering, College of Engineering, University of Tehran (Iran, Islamic Republic of)

2017-03-31

Highlights: • Manipulation of the Cu surface morphology in a wide range by electropolishing treatment. • Comparison of the nucleation density of graphene at low pressure and atmospheric pressure CVD processes. • Controlling the evolution of the Cu surface morphology inside a novel confined space. • Growth of large-size graphene domains. - Abstract: In this work, we study the influence of the surface morphology of the catalytic copper substrate on the nucleation density and the growth rate of graphene domains at low and atmospheric pressure chemical vapor deposition (LPCVD and APCVD) processes. In order to obtain a wide range of initial surface morphology, precisely controlled electropolishing methods were developed to manipulate the roughntreess value of the as-received Cu substrate (RMS = 30 nm) to ultra-rough (RMS = 130 nm) and ultra-smooth (RMS = 2 nm) surfaces. The nucleation and growth of graphene domains show obviously different trends at LPCVD and APCVD conditions. In contrast to APCVD condition, the nucleation density of graphene domains is almost equal in substrates with different initial roughness values at LPCVD condition. We show that this is due to the evolution of the surface morphology of the Cu substrate during the graphene growth steps. By stopping the surface sublimation of copper substrate in a confined space saturated with Cu atoms, the evolution of the Cu surface was impeded. This results in the reduction of the nucleation density of graphene domains up to 24 times in the pre-smoothed Cu substrates at LPCVD condition.

Evolution effects of the copper surface morphology on the nucleation density and growth of graphene domains at different growth pressures

International Nuclear Information System (INIS)

Hedayat, Seyed Mahdi; Karimi-Sabet, Javad; Shariaty-Niassar, Mojtaba

2017-01-01

Highlights: • Manipulation of the Cu surface morphology in a wide range by electropolishing treatment. • Comparison of the nucleation density of graphene at low pressure and atmospheric pressure CVD processes. • Controlling the evolution of the Cu surface morphology inside a novel confined space. • Growth of large-size graphene domains. - Abstract: In this work, we study the influence of the surface morphology of the catalytic copper substrate on the nucleation density and the growth rate of graphene domains at low and atmospheric pressure chemical vapor deposition (LPCVD and APCVD) processes. In order to obtain a wide range of initial surface morphology, precisely controlled electropolishing methods were developed to manipulate the roughntreess value of the as-received Cu substrate (RMS = 30 nm) to ultra-rough (RMS = 130 nm) and ultra-smooth (RMS = 2 nm) surfaces. The nucleation and growth of graphene domains show obviously different trends at LPCVD and APCVD conditions. In contrast to APCVD condition, the nucleation density of graphene domains is almost equal in substrates with different initial roughness values at LPCVD condition. We show that this is due to the evolution of the surface morphology of the Cu substrate during the graphene growth steps. By stopping the surface sublimation of copper substrate in a confined space saturated with Cu atoms, the evolution of the Cu surface was impeded. This results in the reduction of the nucleation density of graphene domains up to 24 times in the pre-smoothed Cu substrates at LPCVD condition.

Process and domain specificity in regions engaged for face processing: an fMRI study of perceptual differentiation.

Science.gov (United States)

Collins, Heather R; Zhu, Xun; Bhatt, Ramesh S; Clark, Jonathan D; Joseph, Jane E

2012-12-01

The degree to which face-specific brain regions are specialized for different kinds of perceptual processing is debated. This study parametrically varied demands on featural, first-order configural, or second-order configural processing of faces and houses in a perceptual matching task to determine the extent to which the process of perceptual differentiation was selective for faces regardless of processing type (domain-specific account), specialized for specific types of perceptual processing regardless of category (process-specific account), engaged in category-optimized processing (i.e., configural face processing or featural house processing), or reflected generalized perceptual differentiation (i.e., differentiation that crosses category and processing type boundaries). ROIs were identified in a separate localizer run or with a similarity regressor in the face-matching runs. The predominant principle accounting for fMRI signal modulation in most regions was generalized perceptual differentiation. Nearly all regions showed perceptual differentiation for both faces and houses for more than one processing type, even if the region was identified as face-preferential in the localizer run. Consistent with process specificity, some regions showed perceptual differentiation for first-order processing of faces and houses (right fusiform face area and occipito-temporal cortex and right lateral occipital complex), but not for featural or second-order processing. Somewhat consistent with domain specificity, the right inferior frontal gyrus showed perceptual differentiation only for faces in the featural matching task. The present findings demonstrate that the majority of regions involved in perceptual differentiation of faces are also involved in differentiation of other visually homogenous categories.

Process- and Domain-Specificity in Regions Engaged for Face Processing: An fMRI Study of Perceptual Differentiation

Science.gov (United States)

Collins, Heather R.; Zhu, Xun; Bhatt, Ramesh S.; Clark, Jonathan D.; Joseph, Jane E.

2015-01-01

The degree to which face-specific brain regions are specialized for different kinds of perceptual processing is debated. The present study parametrically varied demands on featural, first-order configural or second-order configural processing of faces and houses in a perceptual matching task to determine the extent to which the process of perceptual differentiation was selective for faces regardless of processing type (domain-specific account), specialized for specific types of perceptual processing regardless of category (process-specific account), engaged in category-optimized processing (i.e., configural face processing or featural house processing) or reflected generalized perceptual differentiation (i.e. differentiation that crosses category and processing type boundaries). Regions of interest were identified in a separate localizer run or with a similarity regressor in the face-matching runs. The predominant principle accounting for fMRI signal modulation in most regions was generalized perceptual differentiation. Nearly all regions showed perceptual differentiation for both faces and houses for more than one processing type, even if the region was identified as face-preferential in the localizer run. Consistent with process-specificity, some regions showed perceptual differentiation for first-order processing of faces and houses (right fusiform face area and occipito-temporal cortex, and right lateral occipital complex), but not for featural or second-order processing. Somewhat consistent with domain-specificity, the right inferior frontal gyrus showed perceptual differentiation only for faces in the featural matching task. The present findings demonstrate that the majority of regions involved in perceptual differentiation of faces are also involved in differentiation of other visually homogenous categories. PMID:22849402

Vinayaka : A Semi-Supervised Projected Clustering Method Using Differential Evolution

OpenAIRE

Satish Gajawada; Durga Toshniwal

2012-01-01

Differential Evolution (DE) is an algorithm for evolutionary optimization. Clustering problems have beensolved by using DE based clustering methods but these methods may fail to find clusters hidden insubspaces of high dimensional datasets. Subspace and projected clustering methods have been proposed inliterature to find subspace clusters that are present in subspaces of dataset. In this paper we proposeVINAYAKA, a semi-supervised projected clustering method based on DE. In this method DE opt...

Superdiffusions and positive solutions of nonlinear partial differential equations

CERN Document Server

Dynkin, E B

2004-01-01

This book is devoted to the applications of probability theory to the theory of nonlinear partial differential equations. More precisely, it is shown that all positive solutions for a class of nonlinear elliptic equations in a domain are described in terms of their traces on the boundary of the domain. The main probabilistic tool is the theory of superdiffusions, which describes a random evolution of a cloud of particles. A substantial enhancement of this theory is presented that can be of interest for everybody who works on applications of probabilistic methods to mathematical analysis.

D1/D2 Domain of Large-Subunit Ribosomal DNA for Differentiation of Orpinomyces spp.▿

Science.gov (United States)

Dagar, Sumit S.; Kumar, Sanjay; Mudgil, Priti; Singh, Rameshwar; Puniya, Anil K.

2011-01-01

This study presents the suitability of D1/D2 domain of large-subunit (LSU) ribosomal DNA (rDNA) for differentiation of Orpinomyces joyonii and Orpinomyces intercalaris based on PCR-restriction fragment length polymorphism (RFLP). A variation of G/T in O. intercalaris created an additional restriction site for AluI, which was used as an RFLP marker. The results demonstrate adequate heterogeneity in the LSU rDNA for species-level differentiation. PMID:21784906

Mapping the Landscape of Domain-Wall Pinning in Ferromagnetic Films Using Differential Magneto-Optical Microscopy

Science.gov (United States)

Badea, Robert; Berezovsky, Jesse

2016-06-01

The propagation of domain walls in a ferromagnetic film is largely determined by domain-wall pinning at defects in the material. In this article, we map the effective potential landscape for domain-wall pinning in permalloy films by raster scanning a single ferromagnetic vortex and monitoring the hysteretic vortex displacement vs applied magnetic field. The measurement is carried out using a differential magneto-optical microscopy technique which yields spatial sensitivity of approximately 10 nm. We present a simple algorithm for extracting an effective pinning potential from the measurement of vortex displacement vs applied field. The resulting maps of the pinning potential reveal distinct types of pinning sites, which we attribute to quasi-zero-, one-, and two-dimensional defects in the permalloy film.

Harmony Search Based Parameter Ensemble Adaptation for Differential Evolution

Directory of Open Access Journals (Sweden)

Rammohan Mallipeddi

2013-01-01

Full Text Available In differential evolution (DE algorithm, depending on the characteristics of the problem at hand and the available computational resources, different strategies combined with a different set of parameters may be effective. In addition, a single, well-tuned combination of strategies and parameters may not guarantee optimal performance because different strategies combined with different parameter settings can be appropriate during different stages of the evolution. Therefore, various adaptive/self-adaptive techniques have been proposed to adapt the DE strategies and parameters during the course of evolution. In this paper, we propose a new parameter adaptation technique for DE based on ensemble approach and harmony search algorithm (HS. In the proposed method, an ensemble of parameters is randomly sampled which form the initial harmony memory. The parameter ensemble evolves during the course of the optimization process by HS algorithm. Each parameter combination in the harmony memory is evaluated by testing them on the DE population. The performance of the proposed adaptation method is evaluated using two recently proposed strategies (DE/current-to-pbest/bin and DE/current-to-gr_best/bin as basic DE frameworks. Numerical results demonstrate the effectiveness of the proposed adaptation technique compared to the state-of-the-art DE based algorithms on a set of challenging test problems (CEC 2005.

An Improved Differential Evolution Based Dynamic Economic Dispatch with Nonsmooth Fuel Cost Function

Directory of Open Access Journals (Sweden)

R. Balamurugan

2007-09-01

Full Text Available Dynamic economic dispatch (DED is one of the major operational decisions in electric power systems. DED problem is an optimization problem with an objective to determine the optimal combination of power outputs for all generating units over a certain period of time in order to minimize the total fuel cost while satisfying dynamic operational constraints and load demand in each interval. This paper presents an improved differential evolution (IDE method to solve the DED problem of generating units considering valve-point effects. Heuristic crossover technique and gene swap operator are introduced in the proposed approach to improve the convergence characteristic of the differential evolution (DE algorithm. To illustrate the effectiveness of the proposed approach, two test systems consisting of five and ten generating units have been considered. The results obtained through the proposed method are compared with those reported in the literature.

A Global Multi-Objective Optimization Tool for Design of Mechatronic Components using Generalized Differential Evolution

DEFF Research Database (Denmark)

Bech, Michael Møller; Nørgård, Christian; Roemer, Daniel Beck

2016-01-01

This paper illustrates how the relatively simple constrained multi-objective optimization algorithm Generalized Differential Evolution 3 (GDE3), can assist with the practical sizing of mechatronic components used in e.g. digital displacement fluid power machinery. The studied bi- and tri-objectiv......This paper illustrates how the relatively simple constrained multi-objective optimization algorithm Generalized Differential Evolution 3 (GDE3), can assist with the practical sizing of mechatronic components used in e.g. digital displacement fluid power machinery. The studied bi- and tri...... different optimization control parameter settings and it is concluded that GDE3 is a reliable optimization tool that can assist mechatronic engineers in the design and decision making process....

Improved Differential Evolution Algorithm for Wireless Sensor Network Coverage Optimization

Directory of Open Access Journals (Sweden)

Xing Xu

2014-04-01

Full Text Available In order to serve for the ecological monitoring efficiency of Poyang Lake, an improved hybrid algorithm, mixed with differential evolution and particle swarm optimization, is proposed and applied to optimize the coverage problem of wireless sensor network. And then, the affect of the population size and the number of iterations on the coverage performance are both discussed and analyzed. The four kinds of statistical results about the coverage rate are obtained through lots of simulation experiments.

Identification of fractional-order systems via a switching differential evolution subject to noise perturbations

Energy Technology Data Exchange (ETDEWEB)

Zhu, Wu, E-mail: dtzhuwu@gmail.com [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Fang, Jian-an [College of Information Science and Technology, Donghua University, Shanghai 201620 (China); Tang, Yang, E-mail: yang.tang@pik-potsdam.de [Institute of Physics, Humboldt University, Berlin 12489 (Germany); Potsdam Institute for Climate Impact Research, Potsdam 14415 (Germany); Research Institute for Intelligent Control and System, Harbin Institute of Technology, Harbin 150006 (China); Zhang, Wenbing [Institute of Textiles and Clothing, The Hong Kong Polytechnic University, Hong Kong (China); Xu, Yulong [College of Information Science and Technology, Donghua University, Shanghai 201620 (China)

2012-10-01

In this Letter, a differential evolution variant, called switching DE (SDE), has been employed to estimate the orders and parameters in incommensurate fractional-order chaotic systems. The proposed algorithm includes a switching population utilization strategy, where the population size is adjusted dynamically based on the solution-searching status. Thus, this adaptive control method realizes the identification of fractional-order Lorenz, Lü and Chen systems in both deterministic and stochastic environments, respectively. Numerical simulations are provided, where comparisons are made with five other State-of-the-Art evolutionary algorithms (EAs) to verify the effectiveness of the proposed method. -- Highlights: ► Switching population utilization strategy is applied for differential evolution. ► The parameters are estimated in both deterministic and stochastic environments. ► Comparisons with five other EAs verify the effectiveness of the proposed method.

Identification of fractional-order systems via a switching differential evolution subject to noise perturbations

International Nuclear Information System (INIS)

Zhu, Wu; Fang, Jian-an; Tang, Yang; Zhang, Wenbing; Xu, Yulong

2012-01-01

In this Letter, a differential evolution variant, called switching DE (SDE), has been employed to estimate the orders and parameters in incommensurate fractional-order chaotic systems. The proposed algorithm includes a switching population utilization strategy, where the population size is adjusted dynamically based on the solution-searching status. Thus, this adaptive control method realizes the identification of fractional-order Lorenz, Lü and Chen systems in both deterministic and stochastic environments, respectively. Numerical simulations are provided, where comparisons are made with five other State-of-the-Art evolutionary algorithms (EAs) to verify the effectiveness of the proposed method. -- Highlights: ► Switching population utilization strategy is applied for differential evolution. ► The parameters are estimated in both deterministic and stochastic environments. ► Comparisons with five other EAs verify the effectiveness of the proposed method.

Parameter identification based on modified simulated annealing differential evolution algorithm for giant magnetostrictive actuator

Science.gov (United States)

Gao, Xiaohui; Liu, Yongguang

2018-01-01

There is a serious nonlinear relationship between input and output in the giant magnetostrictive actuator (GMA) and how to establish mathematical model and identify its parameters is very important to study characteristics and improve control accuracy. The current-displacement model is firstly built based on Jiles-Atherton (J-A) model theory, Ampere loop theorem and stress-magnetism coupling model. And then laws between unknown parameters and hysteresis loops are studied to determine the data-taking scope. The modified simulated annealing differential evolution algorithm (MSADEA) is proposed by taking full advantage of differential evolution algorithm's fast convergence and simulated annealing algorithm's jumping property to enhance the convergence speed and performance. Simulation and experiment results shows that this algorithm is not only simple and efficient, but also has fast convergence speed and high identification accuracy.

Identification of time-varying nonlinear systems using differential evolution algorithm

DEFF Research Database (Denmark)

Perisic, Nevena; Green, Peter L; Worden, Keith

2013-01-01

(DE) algorithm for the identification of time-varying systems. DE is an evolutionary optimisation method developed to perform direct search in a continuous space without requiring any derivative estimation. DE is modified so that the objective function changes with time to account for the continuing......, thus identification of time-varying systems with nonlinearities can be a very challenging task. In order to avoid conventional least squares and gradient identification methods which require uni-modal and double differentiable objective functions, this work proposes a modified differential evolution...... inclusion of new data within an error metric. This paper presents results of identification of a time-varying SDOF system with Coulomb friction using simulated noise-free and noisy data for the case of time-varying friction coefficient, stiffness and damping. The obtained results are promising and the focus...

Time-Domain Studies as a Probe of Stellar Evolution

Science.gov (United States)

Miller, Adam Andrew

This dissertation focuses on the use of time-domain techniques to discover and characterize these rare astrophysical gems, while also addressing some gaps in our understanding of the earliest and latest stages of stellar evolution. The observational studies presented herein can be grouped into three parts: (i) the study of stellar death (supernovae); (ii) the study of stellar birth; and (iii) the use of modern machine-learning algorithms to discover and classify variable sources. I present observations of supernova (SN) 2006gy, the most luminous SN ever at the time of discovery, and the even-more luminous SN 2008es. Together, these two supernovae (SNe) demonstrate that core-collapse SNe can be significantly more luminous than thermonuclear type Ia SNe, and that there are multiple channels for producing these brilliant core-collapse explosions. For SN 2006gy I show that the progenitor star experienced violent, eruptive mass loss on multiple occasions during the centuries prior to explosion, a scenario that was completely unexpected within the cannon of massive-star evolution theory. I also present observations of SN 2008iy, one of the most unusual SNe ever discovered. Typical SNe take ≲3 weeks to reach peak luminosity; SN 2008iy exhibited a slow and steady rise for ˜400 days before reaching maximum brightness. The best explanation for such behavior is that the progenitor of SN 2008iy experienced an episodic phase of mass loss ˜100 yr prior to explosion. The three SNe detailed in this dissertation have altered our understanding of massive-star mass loss, namely, these SNe provide distinct evidence that post-main sequence mass loss, for at least some massive stars, occurs in sporatic fits, rather than being steady. They also demonstrate that core collapse is not restricted to the red supergiant and Wolf-Rayet stages of stellar evolution as theory predicted. Instead, some massive stars explode while in a luminous blue variable-like state. I also present

Mycoplasma hyopneumoniae and Mycoplasma flocculare differential domains from orthologous surface proteins induce distinct cellular immune responses in mice.

Science.gov (United States)

Leal, Fernanda Munhoz Dos Anjos; Virginio, Veridiana Gomes; Martello, Carolina Lumertz; Paes, Jéssica Andrade; Borges, Thiago J; Jaeger, Natália; Bonorino, Cristina; Ferreira, Henrique Bunselmeyer

2016-07-15

Mycoplasma hyopneumoniae and Mycoplasma flocculare are two genetically close species found in the swine respiratory tract. Despite their similarities, while M. hyopneumoniae is the causative agent of porcine enzootic pneumonia, M. flocculare is a commensal bacterium. Genomic and transcriptional comparative analyses so far failed to explain the difference in pathogenicity between these two species. We then hypothesized that such difference might be, at least in part, explained by amino acid sequence and immunological or functional differences between ortholog surface proteins. In line with that, it was verified that approximately 85% of the ortholog surface proteins from M. hyopneumoniae 7448 and M. flocculare present one or more differential domains. To experimentally assess possible immunological implications of this kind of difference, the extracellular differential domains from one pair of orthologous surface proteins (MHP7448_0612, from M. hyopneumoniae, and MF_00357, from M. flocculare) were expressed in E. coli and used to immunize mice. The recombinant polypeptides (rMHP61267-169 and rMF35767-196, respectively) induced distinct cellular immune responses. While, rMHP61267-169 induced both Th1 and Th2 responses, rMF35767-196 induced just an early pro-inflammatory response. These results indicate that immunological properties determined by differential domains in orthologous surface protein might play a role in pathogenicity, contributing to elicit specific and differential immune responses against each species. Copyright © 2016 Elsevier B.V. All rights reserved.

Phylogeny of the TRAF/MATH domain.

Science.gov (United States)

Zapata, Juan M; Martínez-García, Vanesa; Lefebvre, Sophie

2007-01-01

The TNF-receptor associated factor (TRAF) domain (TD), also known as the meprin and TRAF-C homology (MATH) domain is a fold of seven anti-parallel p-helices that participates in protein-protein interactions. This fold is broadly represented among eukaryotes, where it is found associated with a discrete set of protein-domains. Virtually all protein families encompassing a TRAF/MATH domain seem to be involved in the regulation of protein processing and ubiquitination, strongly suggesting a parallel evolution of the TRAF/MATH domain and certain proteolysis pathways in eukaryotes. The restricted number of living organisms for which we have information of their genetic and protein make-up limits the scope and analysis of the MATH domain in evolution. However, the available information allows us to get a glimpse on the origins, distribution and evolution of the TRAF/MATH domain, which will be overviewed in this chapter.

Evolution of Parallel Spindles Like genes in plants and highlight of unique domain architecture#

Directory of Open Access Journals (Sweden)

Consiglio Federica M

2011-03-01

Full Text Available Abstract Background Polyploidy has long been recognized as playing an important role in plant evolution. In flowering plants, the major route of polyploidization is suggested to be sexual through gametes with somatic chromosome number (2n. Parallel Spindle1 gene in Arabidopsis thaliana (AtPS1 was recently demonstrated to control spindle orientation in the 2nd division of meiosis and, when mutated, to induce 2n pollen. Interestingly, AtPS1 encodes a protein with a FHA domain and PINc domain putatively involved in RNA decay (i.e. Nonsense Mediated mRNA Decay. In potato, 2n pollen depending on parallel spindles was described long time ago but the responsible gene has never been isolated. The knowledge derived from AtPS1 as well as the availability of genome sequences makes it possible to isolate potato PSLike (PSL and to highlight the evolution of PSL family in plants. Results Our work leading to the first characterization of PSLs in potato showed a greater PSL complexity in this species respect to Arabidopsis thaliana. Indeed, a genomic PSL locus and seven cDNAs affected by alternative splicing have been cloned. In addition, the occurrence of at least two other PSL loci in potato was suggested by the sequence comparison of alternatively spliced transcripts. Phylogenetic analysis on 20 Viridaeplantae showed the wide distribution of PSLs throughout the species and the occurrence of multiple copies only in potato and soybean. The analysis of PSLFHA and PSLPINc domains evidenced that, in terms of secondary structure, a major degree of variability occurred in PINc domain respect to FHA. In terms of specific active sites, both domains showed diversification among plant species that could be related to a functional diversification among PSL genes. In addition, some specific active sites were strongly conserved among plants as supported by sequence alignment and by evidence of negative selection evaluated as difference between non-synonymous and

Composite Differential Evolution with Modified Oracle Penalty Method for Constrained Optimization Problems

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Minggang Dong

2014-01-01

Full Text Available Motivated by recent advancements in differential evolution and constraints handling methods, this paper presents a novel modified oracle penalty function-based composite differential evolution (MOCoDE for constrained optimization problems (COPs. More specifically, the original oracle penalty function approach is modified so as to satisfy the optimization criterion of COPs; then the modified oracle penalty function is incorporated in composite DE. Furthermore, in order to solve more complex COPs with discrete, integer, or binary variables, a discrete variable handling technique is introduced into MOCoDE to solve complex COPs with mix variables. This method is assessed on eleven constrained optimization benchmark functions and seven well-studied engineering problems in real life. Experimental results demonstrate that MOCoDE achieves competitive performance with respect to some other state-of-the-art approaches in constrained optimization evolutionary algorithms. Moreover, the strengths of the proposed method include few parameters and its ease of implementation, rendering it applicable to real life. Therefore, MOCoDE can be an efficient alternative to solving constrained optimization problems.

Evolution of function in the "two dinucleotide binding domains" flavoproteins.

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Sunil Ojha

2007-07-01

Full Text Available Structural and biochemical constraints force some segments of proteins to evolve more slowly than others, often allowing identification of conserved structural or sequence motifs that can be associated with substrate binding properties, chemical mechanisms, and molecular functions. We have assessed the functional and structural constraints imposed by cofactors on the evolution of new functions in a superfamily of flavoproteins characterized by two-dinucleotide binding domains, the "two dinucleotide binding domains" flavoproteins (tDBDF superfamily. Although these enzymes catalyze many different types of oxidation/reduction reactions, each is initiated by a stereospecific hydride transfer reaction between two cofactors, a pyridine nucleotide and flavin adenine dinucleotide (FAD. Sequence and structural analysis of more than 1,600 members of the superfamily reveals new members and identifies details of the evolutionary connections among them. Our analysis shows that in all of the highly divergent families within the superfamily, these cofactors adopt a conserved configuration optimal for stereospecific hydride transfer that is stabilized by specific interactions with amino acids from several motifs distributed among both dinucleotide binding domains. The conservation of cofactor configuration in the active site restricts the pyridine nucleotide to interact with FAD from the re-side, limiting the flow of electrons from the re-side to the si-side. This directionality of electron flow constrains interactions with the different partner proteins of different families to occur on the same face of the cofactor binding domains. As a result, superimposing the structures of tDBDFs aligns not only these interacting proteins, but also their constituent electron acceptors, including heme and iron-sulfur clusters. Thus, not only are specific aspects of the cofactor-directed chemical mechanism conserved across the superfamily, the constraints they impose are

Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event

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Gheysen Godelieve

2008-11-01

Full Text Available Abstract Background Endo-1,4-beta-glucanases or cellulases from the glycosyl hydrolase family 5 (GHF5 have been found in numerous bacteria and fungi, and recently also in higher eukaryotes, particularly in plant-parasitic nematodes (PPN. The origin of these genes has been attributed to horizontal gene transfer from bacteria, although there still is a lot of uncertainty about the origin and structure of the ancestral GHF5 PPN endoglucanase. It is not clear whether this ancestral endoglucanase consisted of the whole gene cassette, containing a catalytic domain and a carbohydrate-binding module (CBM, type 2 in PPN and bacteria or only of the catalytic domain while the CBM2 was retrieved by domain shuffling later in evolution. Previous studies on the evolution of these genes have focused primarily on data of sedentary nematodes, while in this study, extra data from migratory nematodes were included. Results Two new endoglucanases from the migratory nematodes Pratylenchus coffeae and Ditylenchus africanus were included in this study. The latter one is the first gene isolated from a PPN of a different superfamily (Sphaerularioidea; all previously known nematode endoglucanases belong to the superfamily Tylenchoidea (order Rhabditida. Phylogenetic analyses were conducted with the PPN GHF5 endoglucanases and homologous endoglucanases from bacterial and other eukaryotic lineages such as beetles, fungi and plants. No statistical incongruence between the phylogenetic trees deduced from the catalytic domain and the CBM2 was found, which could suggest that both domains have evolved together. Furthermore, based on gene structure data, we inferred a model for the evolution of the GHF5 endoglucanase gene structure in plant-parasitic nematodes. Our data confirm a close relationship between Pratylenchus spp. and the root knot nematodes, while some Radopholus similis endoglucanases are more similar to cyst nematode genes. Conclusion We conclude that the ancestral

Evolution of GHF5 endoglucanase gene structure in plant-parasitic nematodes: no evidence for an early domain shuffling event.

Science.gov (United States)

Kyndt, Tina; Haegeman, Annelies; Gheysen, Godelieve

2008-11-03

Endo-1,4-beta-glucanases or cellulases from the glycosyl hydrolase family 5 (GHF5) have been found in numerous bacteria and fungi, and recently also in higher eukaryotes, particularly in plant-parasitic nematodes (PPN). The origin of these genes has been attributed to horizontal gene transfer from bacteria, although there still is a lot of uncertainty about the origin and structure of the ancestral GHF5 PPN endoglucanase. It is not clear whether this ancestral endoglucanase consisted of the whole gene cassette, containing a catalytic domain and a carbohydrate-binding module (CBM, type 2 in PPN and bacteria) or only of the catalytic domain while the CBM2 was retrieved by domain shuffling later in evolution. Previous studies on the evolution of these genes have focused primarily on data of sedentary nematodes, while in this study, extra data from migratory nematodes were included. Two new endoglucanases from the migratory nematodes Pratylenchus coffeae and Ditylenchus africanus were included in this study. The latter one is the first gene isolated from a PPN of a different superfamily (Sphaerularioidea); all previously known nematode endoglucanases belong to the superfamily Tylenchoidea (order Rhabditida). Phylogenetic analyses were conducted with the PPN GHF5 endoglucanases and homologous endoglucanases from bacterial and other eukaryotic lineages such as beetles, fungi and plants. No statistical incongruence between the phylogenetic trees deduced from the catalytic domain and the CBM2 was found, which could suggest that both domains have evolved together. Furthermore, based on gene structure data, we inferred a model for the evolution of the GHF5 endoglucanase gene structure in plant-parasitic nematodes. Our data confirm a close relationship between Pratylenchus spp. and the root knot nematodes, while some Radopholus similis endoglucanases are more similar to cyst nematode genes. We conclude that the ancestral PPN GHF5 endoglucanase gene most probably consisted of

Evolution, functional differentiation, and co-expression of the RLK gene family revealed in Jilin ginseng, Panax ginseng C.A. Meyer.

Science.gov (United States)

Lin, Yanping; Wang, Kangyu; Li, Xiangyu; Sun, Chunyu; Yin, Rui; Wang, Yanfang; Wang, Yi; Zhang, Meiping

2018-02-21

Most genes in a genome exist in the form of a gene family; therefore, it is necessary to have knowledge of how a gene family functions to comprehensively understand organismal biology. The receptor-like kinase (RLK)-encoding gene family is one of the most important gene families in plants. It plays important roles in biotic and abiotic stress tolerances, and growth and development. However, little is known about the functional differentiation and relationships among the gene members within a gene family in plants. This study has isolated 563 RLK genes (designated as PgRLK genes) expressed in Jilin ginseng (Panax ginseng C.A. Meyer), investigated their evolution, and deciphered their functional diversification and relationships. The PgRLK gene family is highly diverged and formed into eight types. The LRR type is the earliest and most prevalent, while only the Lec type originated after P. ginseng evolved. Furthermore, although the members of the PgRLK gene family all encode receptor-like protein kinases and share conservative domains, they are functionally very diverse, participating in numerous biological processes. The expressions of different members of the PgRLK gene family are extremely variable within a tissue, at a developmental stage and in the same cultivar, but most of the genes tend to express correlatively, forming a co-expression network. These results not only provide a deeper and comprehensive understanding of the evolution, functional differentiation and correlation of a gene family in plants, but also an RLK genic resource useful for enhanced ginseng genetic improvement.

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.

2009-10-28

Cell migration and growth are essential components of the development of multicellular organisms. The role of various cues in directing cell migration is widespread, in particular, the role of signals in the environment in the control of cell motility and directional guidance. In many cases, especially in developmental biology, growth of the domain also plays a large role in the distribution of cells and, in some cases, cell or signal distribution may actually drive domain growth. There is an almost ubiquitous use of partial differential equations (PDEs) for modelling the time evolution of cellular density and environmental cues. In the last 20 years, a lot of attention has been devoted to connecting macroscopic PDEs with more detailed microscopic models of cellular motility, including models of directional sensing and signal transduction pathways. However, domain growth is largely omitted in the literature. In this paper, individual-based models describing cell movement and domain growth are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge by making the lattice size variable over time. A reaction-diffusion master equation formalism is generalised to the case of growing lattices and used in the derivation of the macroscopic PDEs. © 2009 Society for Mathematical Biology.

Hybrid Discrete Differential Evolution Algorithm for Lot Splitting with Capacity Constraints in Flexible Job Scheduling

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Xinli Xu

2013-01-01

Full Text Available A two-level batch chromosome coding scheme is proposed to solve the lot splitting problem with equipment capacity constraints in flexible job shop scheduling, which includes a lot splitting chromosome and a lot scheduling chromosome. To balance global search and local exploration of the differential evolution algorithm, a hybrid discrete differential evolution algorithm (HDDE is presented, in which the local strategy with dynamic random searching based on the critical path and a random mutation operator is developed. The performance of HDDE was experimented with 14 benchmark problems and the practical dye vat scheduling problem. The simulation results showed that the proposed algorithm has the strong global search capability and can effectively solve the practical lot splitting problems with equipment capacity constraints.

Boussinesq evolution equations

DEFF Research Database (Denmark)

Bredmose, Henrik; Schaffer, H.; Madsen, Per A.

2004-01-01

This paper deals with the possibility of using methods and ideas from time domain Boussinesq formulations in the corresponding frequency domain formulations. We term such frequency domain models "evolution equations". First, we demonstrate that the numerical efficiency of the deterministic...... Boussinesq evolution equations of Madsen and Sorensen [Madsen, P.A., Sorensen, O.R., 1993. Bound waves and triad interactions in shallow water. Ocean Eng. 20 359-388] can be improved by using Fast Fourier Transforms to evaluate the nonlinear terms. For a practical example of irregular waves propagating over...... a submerged bar, it is demonstrated that evolution equations utilising FFT can be solved around 100 times faster than the corresponding time domain model. Use of FFT provides an efficient bridge between the frequency domain and the time domain. We utilise this by adapting the surface roller model for wave...

On convergence of differential evolution over a class of continuous functions with unique global optimum.

Science.gov (United States)

Ghosh, Sayan; Das, Swagatam; Vasilakos, Athanasios V; Suresh, Kaushik

2012-02-01

Differential evolution (DE) is arguably one of the most powerful stochastic real-parameter optimization algorithms of current interest. Since its inception in the mid 1990s, DE has been finding many successful applications in real-world optimization problems from diverse domains of science and engineering. This paper takes a first significant step toward the convergence analysis of a canonical DE (DE/rand/1/bin) algorithm. It first deduces a time-recursive relationship for the probability density function (PDF) of the trial solutions, taking into consideration the DE-type mutation, crossover, and selection mechanisms. Then, by applying the concepts of Lyapunov stability theorems, it shows that as time approaches infinity, the PDF of the trial solutions concentrates narrowly around the global optimum of the objective function, assuming the shape of a Dirac delta distribution. Asymptotic convergence behavior of the population PDF is established by constructing a Lyapunov functional based on the PDF and showing that it monotonically decreases with time. The analysis is applicable to a class of continuous and real-valued objective functions that possesses a unique global optimum (but may have multiple local optima). Theoretical results have been substantiated with relevant computer simulations.

Multipass forging of Inconel 718 in the delta-Supersolvus domain: assessing and modeling microstructure evolution

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Zouari Meriem

2014-01-01

Full Text Available This work is focused on the evolution of the microstructure of Inconel 718 during multi-pass forging processes. During the forming process, the material is subjected to several physical phenomena such as work-hardening, recovery, recrystallization and grain growth. In this work, transformation kinetics are modeled in the δ-Supersolvus domain (T>Tsolvus where the alloy is single-phase, all the alloying elements being dissolved into the FCC matrix. Torsion tests were used to simulate the forging process and recrystallization kinetics was modeled using a discontinuous dynamic recrystallization (DDRX two-site mean field model. The microstructure evolution under hot forging conditions is predicted in both dynamic and post-dynamic regimes based on the initial distribution of grain size and the evolution of dislocation density distribution during each step of the process. The model predicts recrystallization kinetics, recrystallized grain size distribution and stress–strain curve for different thermo-mechanical conditions and makes the connection between dynamic and post-dynamic regimes.

Improved Differential Evolution Algorithm for Parameter Estimation to Improve the Production of Biochemical Pathway

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Chuii Khim Chong

2012-06-01

Full Text Available This paper introduces an improved Differential Evolution algorithm (IDE which aims at improving its performance in estimating the relevant parameters for metabolic pathway data to simulate glycolysis pathway for yeast. Metabolic pathway data are expected to be of significant help in the development of efficient tools in kinetic modeling and parameter estimation platforms. Many computation algorithms face obstacles due to the noisy data and difficulty of the system in estimating myriad of parameters, and require longer computational time to estimate the relevant parameters. The proposed algorithm (IDE in this paper is a hybrid of a Differential Evolution algorithm (DE and a Kalman Filter (KF. The outcome of IDE is proven to be superior than Genetic Algorithm (GA and DE. The results of IDE from experiments show estimated optimal kinetic parameters values, shorter computation time and increased accuracy for simulated results compared with other estimation algorithms

General purpose graphics-processing-unit implementation of cosmological domain wall network evolution.

Science.gov (United States)

Correia, J R C C C; Martins, C J A P

2017-10-01

Topological defects unavoidably form at symmetry breaking phase transitions in the early universe. To probe the parameter space of theoretical models and set tighter experimental constraints (exploiting the recent advances in astrophysical observations), one requires more and more demanding simulations, and therefore more hardware resources and computation time. Improving the speed and efficiency of existing codes is essential. Here we present a general purpose graphics-processing-unit implementation of the canonical Press-Ryden-Spergel algorithm for the evolution of cosmological domain wall networks. This is ported to the Open Computing Language standard, and as a consequence significant speedups are achieved both in two-dimensional (2D) and 3D simulations.

General purpose graphics-processing-unit implementation of cosmological domain wall network evolution

Science.gov (United States)

Correia, J. R. C. C. C.; Martins, C. J. A. P.

2017-10-01

Topological defects unavoidably form at symmetry breaking phase transitions in the early universe. To probe the parameter space of theoretical models and set tighter experimental constraints (exploiting the recent advances in astrophysical observations), one requires more and more demanding simulations, and therefore more hardware resources and computation time. Improving the speed and efficiency of existing codes is essential. Here we present a general purpose graphics-processing-unit implementation of the canonical Press-Ryden-Spergel algorithm for the evolution of cosmological domain wall networks. This is ported to the Open Computing Language standard, and as a consequence significant speedups are achieved both in two-dimensional (2D) and 3D simulations.

Optimasi Peletakan Base Transceiver Station Di Kabupaten Mojokerto Menggunakan Algoritma Differential Evolution

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Ahadi Arif Nugraha

2015-03-01

Full Text Available Salah satu aspek penting dalam perencanaan infrastruktur jaringan seluler adalah Base Transceiver Station (BTS yang merupakan sebuah pemancar dan penerima sinyal telephone seluler. Di satu sisi, peningkatan jumlah menara memang akan mendukung tercapainya pemenuhan kebutuhan masyarakat terhadap layanan telekomunikasi. Namun di sisi lain, penempatan menara yang  tanpa perencanaan serta koordinasi yang tepat akan menimbulkan jumlah menara yang berlebih sehingga dapat mengganggu estetika lingkungan, tata ruang suatu wilayah, dan radiasi gelombang radio yang tidak terkontrol sehingga sangat mengganggu. Berdasarkan permasalahan diatas, maka dapat diselesaikan dengan cara menyusun suatu master plan yang lengkap dan rinci tentang penataan lokasi menara di Kabupaten Mojokerto untuk lima tahun mendatang. Penataan lokasi menara dilakukan dengan menggunakan algoritma Differential Evolution (DE untuk menemukan solusi penataan menara yang baik berdasarkan luas cakupan area sel yang dihasilkan, kemudian menggunakan software MapInfo sebagai media visualisasi peta lokasi penempatan menara telekomunikasi. Dalam perancangan menara BTS tahun 2019, Kabupaten Mojokerto membutuhkan 106 menara BTS 2G dan 36 menara BTS 3G. Penempatan menara BTS 2G dan 3G menggunakan algoritma differential evolution mampu mengoptimalkan 2,94% dari luas wilayah Kabupaten Mojokerto

Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Selected Set of Discrete Chaotic Systems

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Roman Senkerik

2014-01-01

Full Text Available Evolutionary technique differential evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of set of different chaotic systems. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used also as the chaotic pseudorandom number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudorandom sequences given by chaotic map to help differential evolution algorithm search for the best controller settings for the very same chaotic system. The optimizations were performed for three different chaotic systems, two types of case studies and developed cost functions.

Does the oxytocin receptor polymorphism (rs2254298 confer 'vulnerability' for psychopathology or 'differential susceptibility'? insights from evolution

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Brüne Martin

2012-04-01

Full Text Available Abstract The diathesis-stress model of psychiatric conditions has recently been challenged by the view that it might be more accurate to speak of 'differential susceptibility' or 'plasticity' genes, rather than one-sidedly focusing on individual vulnerability. That is, the same allelic variation that predisposes to a psychiatric disorder if associated with (developmentally early environmental adversity may lead to a better-than-average functional outcome in the same domain under thriving (or favourable environmental conditions. Studies of polymorphic variations of the serotonin transporter gene, the monoamino-oxidase-inhibitor A coding gene or the dopamine D4 receptor gene indicate that the early environment plays a crucial role in the development of favourable versus unfavourable outcomes. Current evidence is limited, however, to establishing a link between genetic variation and behavioural phenotypes. In contrast, little is known about how plasticity may be expressed at the neuroanatomical level as a 'hard-wired' correlate of observable behaviour. The present review article seeks to further strengthen the argument in favour of the differential susceptibility theory by incorporating findings from behavioural and neuroanatomical studies in relation to genetic variation of the oxytocin receptor gene. It is suggested that polymorphic variation at the oxytocin receptor gene (rs2254298 is associated with sociability, amygdala volume and differential risk for psychiatric conditions including autism, depression and anxiety disorder, depending on the quality of early environmental experiences. Seeing genetic variation at the core of developmental plasticity can explain, in contrast to the diathesis-stress perspective, why evolution by natural selection has maintained such 'risk' alleles in the gene pool of a population. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/37

Tracking the Evolution of the Internet of Things Concept Across Different Application Domains

Science.gov (United States)

Ibarra-Esquer, Jorge E.; González-Navarro, Félix F.; Flores-Rios, Brenda L.; Burtseva, Larysa; Astorga-Vargas, María A.

2017-01-01

Both the idea and technology for connecting sensors and actuators to a network to remotely monitor and control physical systems have been known for many years and developed accordingly. However, a little more than a decade ago the concept of the Internet of Things (IoT) was coined and used to integrate such approaches into a common framework. Technology has been constantly evolving and so has the concept of the Internet of Things, incorporating new terminology appropriate to technological advances and different application domains. This paper presents the changes that the IoT has undertaken since its conception and research on how technological advances have shaped it and fostered the arising of derived names suitable to specific domains. A two-step literature review through major publishers and indexing databases was conducted; first by searching for proposals on the Internet of Things concept and analyzing them to find similarities, differences, and technological features that allow us to create a timeline showing its development; in the second step the most mentioned names given to the IoT for specific domains, as well as closely related concepts were identified and briefly analyzed. The study confirms the claim that a consensus on the IoT definition has not yet been reached, as enabling technology keeps evolving and new application domains are being proposed. However, recent changes have been relatively moderated, and its variations on application domains are clearly differentiated, with data and data technologies playing an important role in the IoT landscape. PMID:28613238

Tracking the Evolution of the Internet of Things Concept Across Different Application Domains

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Jorge E. Ibarra-Esquer

2017-06-01

Full Text Available Both the idea and technology for connecting sensors and actuators to a network to remotely monitor and control physical systems have been known for many years and developed accordingly. However, a little more than a decade ago the concept of the Internet of Things (IoT was coined and used to integrate such approaches into a common framework. Technology has been constantly evolving and so has the concept of the Internet of Things, incorporating new terminology appropriate to technological advances and different application domains. This paper presents the changes that the IoT has undertaken since its conception and research on how technological advances have shaped it and fostered the arising of derived names suitable to specific domains. A two-step literature review through major publishers and indexing databases was conducted; first by searching for proposals on the Internet of Things concept and analyzing them to find similarities, differences, and technological features that allow us to create a timeline showing its development; in the second step the most mentioned names given to the IoT for specific domains, as well as closely related concepts were identified and briefly analyzed. The study confirms the claim that a consensus on the IoT definition has not yet been reached, as enabling technology keeps evolving and new application domains are being proposed. However, recent changes have been relatively moderated, and its variations on application domains are clearly differentiated, with data and data technologies playing an important role in the IoT landscape.

Tracking the Evolution of the Internet of Things Concept Across Different Application Domains.

Science.gov (United States)

Ibarra-Esquer, Jorge E; González-Navarro, Félix F; Flores-Rios, Brenda L; Burtseva, Larysa; Astorga-Vargas, María A

2017-06-14

Both the idea and technology for connecting sensors and actuators to a network to remotely monitor and control physical systems have been known for many years and developed accordingly. However, a little more than a decade ago the concept of the Internet of Things (IoT) was coined and used to integrate such approaches into a common framework. Technology has been constantly evolving and so has the concept of the Internet of Things, incorporating new terminology appropriate to technological advances and different application domains. This paper presents the changes that the IoT has undertaken since its conception and research on how technological advances have shaped it and fostered the arising of derived names suitable to specific domains. A two-step literature review through major publishers and indexing databases was conducted; first by searching for proposals on the Internet of Things concept and analyzing them to find similarities, differences, and technological features that allow us to create a timeline showing its development; in the second step the most mentioned names given to the IoT for specific domains, as well as closely related concepts were identified and briefly analyzed. The study confirms the claim that a consensus on the IoT definition has not yet been reached, as enabling technology keeps evolving and new application domains are being proposed. However, recent changes have been relatively moderated, and its variations on application domains are clearly differentiated, with data and data technologies playing an important role in the IoT landscape.

Long-Term Scheduling of Large-Scale Cascade Hydropower Stations Using Improved Differential Evolution Algorithm

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Xiaohao Wen

2018-03-01

Full Text Available Long-term scheduling of large cascade hydropower stations (LSLCHS is a complex problem of high dimension, nonlinearity, coupling and complex constraint. In view of the above problem, we present an improved differential evolution (iLSHADE algorithm based on LSHADE, a state-of-the-art evolutionary algorithm. iLSHADE uses new mutation strategies “current to pbest/2-rand” to obtain wider search range and accelerate convergence with the preventing individual repeated failure evolution (PIRFE strategy. The handling of complicated constraints strategy of ε-constrained method is presented to handle outflow, water level and output constraints in the cascade reservoir operation. Numerical experiments of 10 benchmark functions have been done, showing that iLSHADE has stable convergence and high efficiency. Furthermore, we demonstrate the performance of the iLSHADE algorithm by comparing it with other improved differential evolution algorithms for LSLCHS in four large hydropower stations of the Jinsha River. With the applications of iLSHADE in reservoir operation, LSLCHS can obtain more power generation benefit than other alternatives in dry, normal, and wet years. The results of numerical experiments and case studies show that the iLSHADE has a distinct optimization effect and good stability, and it is a valid and reliable tool to solve LSLCHS problem.

DSTATCOM allocation in distribution networks considering reconfiguration using differential evolution algorithm

International Nuclear Information System (INIS)

Jazebi, S.; Hosseinian, S.H.; Vahidi, B.

2011-01-01

Highlights: → Reconfiguration and DSTATCOM allocation are implemented for RDS planning. → Differential evolution algorithm is applied to solve the nonlinear problem. → Optimal status of tie switches, DSTATCOM size and location are determined. → The goal is to minimize network losses and to improve voltage profile. → The results show the effectiveness of the proposed method to satisfy objectives. -- Abstract: The main idea in distribution network reconfiguration is usually to reduce loss by changing the status of sectionalizing switches and determining appropriate tie switches. Recently Distribution FACTS (DFACTS) devices such as DSTATCOM also have been planned for loss reduction and voltage profile improvement in steady state conditions. This paper implements a combinatorial process based on reconfiguration and DSTATCOM allocation in order to mitigate losses and improve voltage profile in power distribution networks. The distribution system tie switches, DSTATCOM location and size have been optimally determined to obtain an appropriate operational condition. Differential evolution algorithm (DEA) has been used to solve and overcome the complicity of this combinatorial nonlinear optimization problem. To validate the accuracy of results a comparison with particle swarm optimization (PSO) has been made. Simulations have been applied on 69 and 83 busses distribution test systems. All optimization results show the effectiveness of the combinatorial approach in loss reduction and voltage profile improvement.

Aerodynamic Shape Optimization Using Hybridized Differential Evolution

Science.gov (United States)

Madavan, Nateri K.

2003-01-01

An aerodynamic shape optimization method that uses an evolutionary algorithm known at Differential Evolution (DE) in conjunction with various hybridization strategies is described. DE is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Various hybridization strategies for DE are explored, including the use of neural networks as well as traditional local search methods. A Navier-Stokes solver is used to evaluate the various intermediate designs and provide inputs to the hybrid DE optimizer. The method is implemented on distributed parallel computers so that new designs can be obtained within reasonable turnaround times. Results are presented for the inverse design of a turbine airfoil from a modern jet engine. (The final paper will include at least one other aerodynamic design application). The capability of the method to search large design spaces and obtain the optimal airfoils in an automatic fashion is demonstrated.

Incremental localized boundary-domain integro-differential equations of elastic damage mechanics for inhomogeneous body

OpenAIRE

Mikhailov, SE

2006-01-01

Copyright @ 2006 Tech Science Press A quasi-static mixed boundary value problem of elastic damage mechanics for a continuously inhomogeneous body is considered. Using the two-operator Green-Betti formula and the fundamental solution of an auxiliary homogeneous linear elasticity with frozen initial, secant or tangent elastic coe±cients, a boundary-domain integro-differential formulation of the elasto-plastic problem with respect to the displacement rates and their gradients is derived. Usin...

An Improved Differential Evolution Algorithm for Maritime Collision Avoidance Route Planning

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Yu-xin Zhao

2014-01-01

Full Text Available High accuracy navigation and surveillance systems are pivotal to ensure efficient ship route planning and marine safety. Based on existing ship navigation and maritime collision prevention rules, an improved approach for collision avoidance route planning using a differential evolution algorithm was developed. Simulation results show that the algorithm is capable of significantly enhancing the optimized route over current methods. It has the potential to be used as a tool to generate optimal vessel routing in the presence of conflicts.

Euchromatin islands in large heterochromatin domains are enriched for CTCF binding and differentially DNA-methylated regions

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Wen Bo

2012-10-01

Full Text Available Abstract Background The organization of higher order chromatin is an emerging epigenetic mechanism for understanding development and disease. We and others have previously observed dynamic changes during differentiation and oncogenesis in large heterochromatin domains such as Large Organized Chromatin K (lysine modifications (LOCKs, of histone H3 lysine-9 dimethylation (H3K9me2 or other repressive histone posttranslational modifications. The microstructure of these regions has not previously been explored. Results We analyzed the genome-wide distribution of H3K9me2 in two human pluripotent stem cell lines and three differentiated cells lines. We identified > 2,500 small regions with very low H3K9me2 signals in the body of LOCKs, which were termed as euchromatin islands (EIs. EIs are 6.5-fold enriched for DNase I Hypersensitive Sites and 8-fold enriched for the binding of CTCF, the major organizer of higher-order chromatin. Furthermore, EIs are 2–6 fold enriched for differentially DNA-methylated regions associated with tissue types (T-DMRs, reprogramming (R-DMRs and cancer (C-DMRs. Gene ontology (GO analysis suggests that EI-associated genes are functionally related to organ system development, cell adhesion and cell differentiation. Conclusions We identify the existence of EIs as a finer layer of epigenomic architecture within large heterochromatin domains. Their enrichment for CTCF sites and DNAse hypersensitive sites, as well as association with DMRs, suggest that EIs play an important role in normal epigenomic architecture and its disruption in disease.

Development and evolution of the unique cetacean dentition

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Brooke A. Armfield

2013-02-01

Full Text Available The evolutionary success of mammals is rooted in their high metabolic rate. A high metabolic rate is sustainable thanks to efficient food processing and that in turn is facilitated by precise occlusion of the teeth and the acquisition of rhythmic mastication. These major evolutionary innovations characterize most members of the Class Mammalia. Cetaceans are one of the few groups of mammals in which precise occlusion has been secondarily lost. Most toothed whales have an increased number of simple crowned teeth that are similar along the tooth row. Evolution toward these specializations began immediately after the time cetaceans transitioned from terrestrial-to-marine environments. The fossil record documents the critical aspects of occlusal evolution of cetaceans, and allows us to pinpoint the evolutionary timing of the macroevolutionary events leading to their unusual dental morphology among mammals. The developmental controls of tooth differentiation and tooth number have been studied in a few mammalian clades, but nothing is known about how these controls differ between cetaceans and mammals that retain functional occlusion. Here we show that pigs, a cetacean relative with regionalized tooth morphology and complex tooth crowns, retain the typical mammalian gene expression patterns that control early tooth differentiation, expressing Bmp4 in the rostral (mesial, anterior domain of the jaw, and Fgf8 caudally (distal, posterior. By contrast, dolphins have lost these regional differences in dental morphology and the Bmp4 domain is extended into the caudal region of the developing jaw. We hypothesize that the functional constraints underlying mammalian occlusion have been released in cetaceans, facilitating changes in the genetic control of early dental development. Such major developmental changes drive morphological evolution and are correlated with major shifts in diet and food processing during cetacean evolution.

A Self Adaptive Differential Evolution Algorithm for Global Optimization

Science.gov (United States)

Kumar, Pravesh; Pant, Millie

This paper presents a new Differential Evolution algorithm based on hybridization of adaptive control parameters and trigonometric mutation. First we propose a self adaptive DE named ADE where choice of control parameter F and Cr is not fixed at some constant value but is taken iteratively. The proposed algorithm is further modified by applying trigonometric mutation in it and the corresponding algorithm is named as ATDE. The performance of ATDE is evaluated on the set of 8 benchmark functions and the results are compared with the classical DE algorithm in terms of average fitness function value, number of function evaluations, convergence time and success rate. The numerical result shows the competence of the proposed algorithm.

Differential morphology and image processing.

Science.gov (United States)

Maragos, P

1996-01-01

Image processing via mathematical morphology has traditionally used geometry to intuitively understand morphological signal operators and set or lattice algebra to analyze them in the space domain. We provide a unified view and analytic tools for morphological image processing that is based on ideas from differential calculus and dynamical systems. This includes ideas on using partial differential or difference equations (PDEs) to model distance propagation or nonlinear multiscale processes in images. We briefly review some nonlinear difference equations that implement discrete distance transforms and relate them to numerical solutions of the eikonal equation of optics. We also review some nonlinear PDEs that model the evolution of multiscale morphological operators and use morphological derivatives. Among the new ideas presented, we develop some general 2-D max/min-sum difference equations that model the space dynamics of 2-D morphological systems (including the distance computations) and some nonlinear signal transforms, called slope transforms, that can analyze these systems in a transform domain in ways conceptually similar to the application of Fourier transforms to linear systems. Thus, distance transforms are shown to be bandpass slope filters. We view the analysis of the multiscale morphological PDEs and of the eikonal PDE solved via weighted distance transforms as a unified area in nonlinear image processing, which we call differential morphology, and briefly discuss its potential applications to image processing and computer vision.

An Improved Binary Differential Evolution Algorithm to Infer Tumor Phylogenetic Trees.

Science.gov (United States)

Liang, Ying; Liao, Bo; Zhu, Wen

2017-01-01

Tumourigenesis is a mutation accumulation process, which is likely to start with a mutated founder cell. The evolutionary nature of tumor development makes phylogenetic models suitable for inferring tumor evolution through genetic variation data. Copy number variation (CNV) is the major genetic marker of the genome with more genes, disease loci, and functional elements involved. Fluorescence in situ hybridization (FISH) accurately measures multiple gene copy number of hundreds of single cells. We propose an improved binary differential evolution algorithm, BDEP, to infer tumor phylogenetic tree based on FISH platform. The topology analysis of tumor progression tree shows that the pathway of tumor subcell expansion varies greatly during different stages of tumor formation. And the classification experiment shows that tree-based features are better than data-based features in distinguishing tumor. The constructed phylogenetic trees have great performance in characterizing tumor development process, which outperforms other similar algorithms.

Chaos Enhanced Differential Evolution in the Task of Evolutionary Control of Discrete Chaotic LOZI Map

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Roman Senkerik

2016-01-01

Full Text Available In this paper, evolutionary technique Differential Evolution (DE is used for the evolutionary tuning of controller parameters for the stabilization of selected discrete chaotic system, which is the two-dimensional Lozi map. The novelty of the approach is that the selected controlled discrete dissipative chaotic system is used within Chaos enhanced heuristic concept as the chaotic pseudo-random number generator to drive the mutation and crossover process in the DE. The idea was to utilize the hidden chaotic dynamics in pseudo-random sequences given by chaotic map to help Differential evolution algorithm in searching for the best controller settings for the same chaotic system. The optimizations were performed for three different required final behavior of the chaotic system, and two types of developed cost function. To confirm the robustness of presented approach, comparisons with canonical DE strategy and PSO algorithm have been performed.

SH3 domain tyrosine phosphorylation--sites, role and evolution.

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Zuzana Tatárová

Full Text Available BACKGROUND: SH3 domains are eukaryotic protein domains that participate in a plethora of cellular processes including signal transduction, proliferation, and cellular movement. Several studies indicate that tyrosine phosphorylation could play a significant role in the regulation of SH3 domains. RESULTS: To explore the incidence of the tyrosine phosphorylation within SH3 domains we queried the PhosphoSite Plus database of phosphorylation sites. Over 100 tyrosine phosphorylations occurring on 20 different SH3 domain positions were identified. The tyrosine corresponding to c-Src Tyr-90 was by far the most frequently identified SH3 domain phosphorylation site. A comparison of sequences around this tyrosine led to delineation of a preferred sequence motif ALYD(Y/F. This motif is present in about 15% of human SH3 domains and is structurally well conserved. We further observed that tyrosine phosphorylation is more abundant than serine or threonine phosphorylation within SH3 domains and other adaptor domains, such as SH2 or WW domains. Tyrosine phosphorylation could represent an important regulatory mechanism of adaptor domains. CONCLUSIONS: While tyrosine phosphorylation typically promotes signaling protein interactions via SH2 or PTB domains, its role in SH3 domains is the opposite - it blocks or prevents interactions. The regulatory function of tyrosine phosphorylation is most likely achieved by the phosphate moiety and its charge interfering with binding of polyproline helices of SH3 domain interacting partners.

Multi-objective optimization of p-xylene oxidation process using an improved self-adaptive differential evolution algorithm

Institute of Scientific and Technical Information of China (English)

Lili Tao; Bin Xu; Zhihua Hu; Weimin Zhong

2017-01-01

The rise in the use of global polyester fiber contributed to strong demand of the Terephthalic acid (TPA). The liquid-phase catalytic oxidation of p-xylene (PX) to TPA is regarded as a critical and efficient chemical process in industry [1]. PX oxidation reaction involves many complex side reactions, among which acetic acid combustion and PX combustion are the most important. As the target product of this oxidation process, the quality and yield of TPA are of great concern. However, the improvement of the qualified product yield can bring about the high energy consumption, which means that the economic objectives of this process cannot be achieved simulta-neously because the two objectives are in conflict with each other. In this paper, an improved self-adaptive multi-objective differential evolution algorithm was proposed to handle the multi-objective optimization prob-lems. The immune concept is introduced to the self-adaptive multi-objective differential evolution algorithm (SADE) to strengthen the local search ability and optimization accuracy. The proposed algorithm is successfully tested on several benchmark test problems, and the performance measures such as convergence and divergence metrics are calculated. Subsequently, the multi-objective optimization of an industrial PX oxidation process is carried out using the proposed immune self-adaptive multi-objective differential evolution algorithm (ISADE). Optimization results indicate that application of ISADE can greatly improve the yield of TPA with low combustion loss without degenerating TA quality.

Design of Test Wrapper Scan Chain Based on Differential Evolution

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Aijun Zhu

2013-08-01

Full Text Available Integrated Circuit has entered the era of design of the IP-based SoC (System on Chip, which makes the IP core reuse become a key issue. SoC test wrapper design for scan chain is a NP Hard problem, we propose an algorithm based on Differential Evolution (DE to design wrapper scan chain. Through group’s mutation, crossover and selection operations, the design of test wrapper scan chain is achieved. Experimental verification is carried out according to the international standard benchmark ITC’02. The results show that the algorithm can obtain shorter longest wrapper scan chains, compared with other algorithms.

A DIFFERENTIAL EVOLUTION ALGORITHM DEVELOPED FOR A NURSE SCHEDULING PROBLEM

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Shahnazari-Shahrezaei, P.

2012-11-01

Full Text Available Nurse scheduling is a type of manpower allocation problem that tries to satisfy hospital managers objectives and nurses preferences as much as possible by generating fair shift schedules. This paper presents a nurse scheduling problem based on a real case study, and proposes two meta-heuristics a differential evolution algorithm (DE and a greedy randomised adaptive search procedure (GRASP to solve it. To investigate the efficiency of the proposed algorithms, two problems are solved. Furthermore, some comparison metrics are applied to examine the reliability of the proposed algorithms. The computational results in this paper show that the proposed DE outperforms the GRASP.

Utilization of the Discrete Differential Evolution for Optimization in Multidimensional Point Clouds.

Science.gov (United States)

Uher, Vojtěch; Gajdoš, Petr; Radecký, Michal; Snášel, Václav

2016-01-01

The Differential Evolution (DE) is a widely used bioinspired optimization algorithm developed by Storn and Price. It is popular for its simplicity and robustness. This algorithm was primarily designed for real-valued problems and continuous functions, but several modified versions optimizing both integer and discrete-valued problems have been developed. The discrete-coded DE has been mostly used for combinatorial problems in a set of enumerative variants. However, the DE has a great potential in the spatial data analysis and pattern recognition. This paper formulates the problem as a search of a combination of distinct vertices which meet the specified conditions. It proposes a novel approach called the Multidimensional Discrete Differential Evolution (MDDE) applying the principle of the discrete-coded DE in discrete point clouds (PCs). The paper examines the local searching abilities of the MDDE and its convergence to the global optimum in the PCs. The multidimensional discrete vertices cannot be simply ordered to get a convenient course of the discrete data, which is crucial for good convergence of a population. A novel mutation operator utilizing linear ordering of spatial data based on the space filling curves is introduced. The algorithm is tested on several spatial datasets and optimization problems. The experiments show that the MDDE is an efficient and fast method for discrete optimizations in the multidimensional point clouds.

Analysis of the Sequences, Structures, and Functions of Product-Releasing Enzyme Domains in Fungal Polyketide Synthases

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Lu Liu

2017-09-01

Full Text Available Product-releasing enzyme (PRE domains in fungal non-reducing polyketide synthases (NR-PKSs play a crucial role in catalysis and editing during polyketide biosynthesis, especially accelerating final biosynthetic reactions accompanied with product offloading. However, up to date, the systematic knowledge about PRE domains is deficient. In the present study, the relationships between sequences, structures, and functions of PRE domains were analyzed with 574 NR-PKSs of eight groups (I–VIII. It was found that the PRE domains in NR-PKSs could be mainly classified into three types, thioesterase (TE, reductase (R, and metallo-β-lactamase-type TE (MβL-TE. The widely distributed TE or TE-like domains were involved in NR-PKSs of groups I–IV, VI, and VIII. The R domains appeared in NR-PKSs of groups IV and VII, while the physically discrete MβL-TE domains were employed by most NR-PKSs of group V. The changes of catalytic sites and structural characteristics resulted in PRE functional differentiations. The phylogeny revealed that the evolution of TE domains was accompanied by complex functional divergence. The diverse sequence lengths of TE lid-loops affected substrate specificity with different chain lengths. The volume diversification of TE catalytic pockets contributed to catalytic mechanisms with functional differentiations. The above findings may help to understand the crucial catalysis of fungal aromatic polyketide biosyntheses and govern recombination of NR-PKSs to obtain unnatural target products.

Self-assembled domain structures: From micro- to nanoscale

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Vladimir Shur

2015-06-01

Full Text Available The recent achievements in studying the self-assembled evolution of micro- and nanoscale domain structures in uniaxial single crystalline ferroelectrics lithium niobate and lithium tantalate have been reviewed. The results obtained by visualization of static domain patterns and kinetics of the domain structure by different methods from common optical microscopy to more sophisticated scanning probe microscopy, scanning electron microscopy and confocal Raman microscopy, have been discussed. The kinetic approach based on various nucleation processes similar to the first-order phase transition was used for explanation of the domain structure evolution scenarios. The main mechanisms of self-assembling for nonequilibrium switching conditions caused by screening ineffectiveness including correlated nucleation, domain growth anisotropy, and domain–domain interaction have been considered. The formation of variety of self-assembled domain patterns such as fractal-type, finger and web structures, broad domain boundaries, and dendrites have been revealed at each of all five stages of domain structure evolution during polarization reversal. The possible applications of self-assembling for micro- and nanodomain engineering were reviewed briefly. The review covers mostly the results published by our research group.

Long-term evolution and gravitational wave radiation of neutron stars with differential rotation induced by r-modes

International Nuclear Information System (INIS)

Yu Yunwei; Cao Xiaofeng; Zheng Xiaoping

2009-01-01

In a second-order r-mode theory, Sa and Tome found that the r-mode oscillation in neutron stars (NSs) could induce stellar differential rotation, which naturally leads to a saturated state of the oscillation. Based on a consideration of the coupling of the r-modes and the stellar spin and thermal evolution, we carefully investigate the influences of the differential rotation on the long-term evolution of isolated NSs and NSs in low-mass X-ray binaries, where the viscous damping of the r-modes and its resultant effects are taken into account. The numerical results show that, for both kinds of NSs, the differential rotation can significantly prolong the duration of the r-modes. As a result, the stars can keep nearly a constant temperature and constant angular velocity for over a thousand years. Moreover, the persistent radiation of a quasi-monochromatic gravitational wave would also be predicted due to the long-term steady r-mode oscillation and stellar rotation. This increases the detectability of gravitational waves from both young isolated and old accreting NSs. (research papers)

Difference-frequency generation in the field of a few-cycle laser pulse propagating in a GaAs crystal with a domain structure

International Nuclear Information System (INIS)

Oganesyan, David L; Vardanyan, Aleksandr O; Oganesyan, G D

2013-01-01

Difference-frequency generation in a GaAs crystal with a periodic domain structure in the field of a few-cycle laser pulse is considered for the case of weakly pronounced material dispersion. The straight-line method is used to solve numerically the system of coupled nonlinear partial differential equations describing the evolution of the electric field of this laser pulse in GaAs crystals with periodic and chirped domain structures. It is shown that application of a GaAs crystal with a chirped domain structure makes it possible to control the frequency-modulation law for a broadband differencefrequency pulse. (nonlinear optical phenomena)

Domain shape instabilities and dendrite domain growth in uniaxial ferroelectrics

Science.gov (United States)

Shur, Vladimir Ya.; Akhmatkhanov, Andrey R.

2018-01-01

The effects of domain wall shape instabilities and the formation of nanodomains in front of moving walls obtained in various uniaxial ferroelectrics are discussed. Special attention is paid to the formation of self-assembled nanoscale and dendrite domain structures under highly non-equilibrium switching conditions. All obtained results are considered in the framework of the unified kinetic approach to domain structure evolution based on the analogy with first-order phase transformation. This article is part of the theme issue `From atomistic interfaces to dendritic patterns'.

Co-evolution of intelligent socio-technical systems modelling and applications in large scale emergency and transport domains

CERN Document Server

2013-01-01

As the interconnectivity between humans through technical devices is becoming ubiquitous, the next step is already in the making: ambient intelligence, i.e. smart (technical) environments, which will eventually play the same active role in communication as the human players, leading to a co-evolution in all domains where real-time communication is essential. This topical volume, based on the findings of the Socionical European research project, gives equal attention to two highly relevant domains of applications: transport, specifically traffic, dynamics from the viewpoint of a socio-technical interaction and evacuation scenarios for large-scale emergency situations. Care was taken to investigate as much as possible the limits of scalability and to combine the modeling using complex systems science approaches with relevant data analysis.

SH3 Domains Differentially Stimulate Distinct Dynamin I Assembly Modes and G Domain Activity.

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Sai Krishnan

Full Text Available Dynamin I is a highly regulated GTPase enzyme enriched in nerve terminals which mediates vesicle fission during synaptic vesicle endocytosis. One regulatory mechanism involves its interactions with proteins containing Src homology 3 (SH3 domains. At least 30 SH3 domain-containing proteins bind dynamin at its proline-rich domain (PRD. Those that stimulate dynamin activity act by promoting its oligomerisation. We undertook a systematic parallel screening of 13 glutathione-S-transferase (GST-tagged endocytosis-related SH3 domains on dynamin binding, GTPase activity and oligomerisation. No correlation was found between dynamin binding and their potency to stimulate GTPase activity. There was limited correlation between the extent of their ability to stimulate dynamin activity and the level of oligomerisation, indicating an as yet uncharacterised allosteric coupling of the PRD and G domain. We examined the two variants, dynamin Iab and Ibb, which differ in the alternately splice middle domain α2 helix. They responded differently to the panel of SH3s, with the extent of stimulation between the splice variants varying greatly between the SH3s. This study reveals that SH3 binding can act as a heterotropic allosteric regulator of the G domain via the middle domain α2 helix, suggesting an involvement of this helix in communicating the PRD-mediated allostery. This indicates that SH3 binding both stabilises multiple conformations of the tetrameric building block of dynamin, and promotes assembly of dynamin-SH3 complexes with distinct rates of GTP hydrolysis.

Genome-wide analysis of the Solanum tuberosum (potato) trehalose-6-phosphate synthase (TPS) gene family: evolution and differential expression during development and stress.

Science.gov (United States)

Xu, Yingchun; Wang, Yanjie; Mattson, Neil; Yang, Liu; Jin, Qijiang

2017-12-01

Trehalose-6-phosphate synthase (TPS) serves important functions in plant desiccation tolerance and response to environmental stimuli. At present, a comprehensive analysis, i.e. functional classification, molecular evolution, and expression patterns of this gene family are still lacking in Solanum tuberosum (potato). In this study, a comprehensive analysis of the TPS gene family was conducted in potato. A total of eight putative potato TPS genes (StTPSs) were identified by searching the latest potato genome sequence. The amino acid identity among eight StTPSs varied from 59.91 to 89.54%. Analysis of d N /d S ratios suggested that regions in the TPP (trehalose-6-phosphate phosphatase) domains evolved faster than the TPS domains. Although the sequence of the eight StTPSs showed high similarity (2571-2796 bp), their gene length is highly differentiated (3189-8406 bp). Many of the regulatory elements possibly related to phytohormones, abiotic stress and development were identified in different TPS genes. Based on the phylogenetic tree constructed using TPS genes of potato, and four other Solanaceae plants, TPS genes could be categorized into 6 distinct groups. Analysis revealed that purifying selection most likely played a major role during the evolution of this family. Amino acid changes detected in specific branches of the phylogenetic tree suggests relaxed constraints might have contributed to functional divergence among groups. Moreover, StTPSs were found to exhibit tissue and treatment specific expression patterns upon analysis of transcriptome data, and performing qRT-PCR. This study provides a reference for genome-wide identification of the potato TPS gene family and sets a framework for further functional studies of this important gene family in development and stress response.

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

Science.gov (United States)

Garamszegi, Sara; Franzosa, Eric A; Xia, Yu

2013-01-01

A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1) domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2) domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral-host interactions that are

Differential Evolution-Based PID Control of Nonlinear Full-Car Electrohydraulic Suspensions

Directory of Open Access Journals (Sweden)

Jimoh O. Pedro

2013-01-01

Full Text Available This paper presents a differential-evolution- (DE- optimized, independent multiloop proportional-integral-derivative (PID controller design for full-car nonlinear, electrohydraulic suspension systems. The multiloop PID control stabilises the actuator via force feedback and also improves the system performance. Controller gains are computed using manual tuning and through DE optimization to minimise a performance index, which addresses suspension travel, road holding, vehicle handling, ride comfort, and power consumption constraints. Simulation results showed superior performance of the DE-optimized PID-controlled active vehicle suspension system (AVSS over the manually tuned PID-controlled AVSS and the passive vehicle suspension system (PVSS.

On parametric domain for asymptotic stability with probability one of zero solution of linear Ito stochastic differential equations

International Nuclear Information System (INIS)

Phan Thanh An; Phan Le Na; Ngo Quoc Chung

2004-05-01

We describe a practical implementation for finding parametric domain for asymptotic stability with probability one of zero solution of linear Ito stochastic differential equations based on Korenevskij and Mitropolskij's sufficient condition and our sufficient conditions. Numerical results show that all of these sufficient conditions are crucial in the implementation. (author)

Untangling spider silk evolution with spidroin terminal domains

Directory of Open Access Journals (Sweden)

Garb Jessica E

2010-08-01

Full Text Available Abstract Background Spidroins are a unique family of large, structural proteins that make up the bulk of spider silk fibers. Due to the highly variable nature of their repetitive sequences, spidroin evolutionary relationships have principally been determined from their non-repetitive carboxy (C-terminal domains, though they offer limited character data. The few known spidroin amino (N-terminal domains have been difficult to obtain, but potentially contain critical phylogenetic information for reconstructing the diversification of spider silks. Here we used silk gland expression data (ESTs from highly divergent species to evaluate the functional significance and phylogenetic utility of spidroin N-terminal domains. Results We report 11 additional spidroin N-termini found by sequencing ~1,900 silk gland cDNAs from nine spider species that shared a common ancestor > 240 million years ago. In contrast to their hyper-variable repetitive regions, spidroin N-terminal domains have retained striking similarities in sequence identity, predicted secondary structure, and hydrophobicity. Through separate and combined phylogenetic analyses of N-terminal domains and their corresponding C-termini, we find that combined analysis produces the most resolved trees and that N-termini contribute more support and less conflict than the C-termini. These analyses show that paralogs largely group by silk gland type, except for the major ampullate spidroins. Moreover, spidroin structural motifs associated with superior tensile strength arose early in the history of this gene family, whereas a motif conferring greater extensibility convergently evolved in two distantly related paralogs. Conclusions A non-repetitive N-terminal domain appears to be a universal attribute of spidroin proteins, likely retained from the origin of spider silk production. Since this time, spidroin N-termini have maintained several features, consistent with this domain playing a key role in silk

Enhanced performance for differential detection in coherent Brillouin optical time-domain analysis sensors

Science.gov (United States)

Shao, Liyang; Zhang, Yunpeng; Li, Zonglei; Zhang, Zhiyong; Zou, Xihua; Luo, Bin; Pan, Wei; Yan, Lianshan

2016-11-01

Logarithmic detectors (LogDs) have been used in coherent Brillouin optical time-domain analysis (BOTDA) sensors to reduce the effect of phase fluctuation, demodulation complexities, and measurement time. However, because of the inherent properties of LogDs, a DC component at the level of hundreds of millivolts that prohibits high-gain signal amplification (SA) could be generated, resulting in unacceptable data acquisition (DAQ) inaccuracies and decoding errors in the process of prototype integration. By generating a reference light at a level similar to the probe light, differential detection can be applied to remove the DC component automatically using a differential amplifier before the DAQ process. Therefore, high-gain SA can be employed to reduce quantization errors. The signal-to-noise ratio of the weak Brillouin gain signal is improved from ˜11.5 to ˜21.8 dB. A BOTDA prototype is implemented based on the proposed scheme. The experimental results show that the measurement accuracy of the Brillouin frequency shift (BFS) is improved from ±1.9 to ±0.8 MHz at the end of a 40-km sensing fiber.

Differential Evolution between Monotocous and Polytocous Species

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Hyeonju Ahn

2014-04-01

Full Text Available One of the most important traits for both animal science and livestock production is the number of offspring for a species. This study was performed to identify differentially evolved genes and their distinct functions that influence the number of offspring at birth by comparative analysis of eight monotocous mammals and seven polytocous mammals in a number of scopes: specific amino acid substitution with site-wise adaptive evolution, gene expansion and specific orthologous group. The mutually exclusive amino acid substitution among the 16 mammalian species identified five candidate genes. These genes were both directly and indirectly related to ovulation. Furthermore, in monotocous mammals, the EPH gene family was found to have undergone expansion. Previously, the EPHA4 gene was found to positively affect litter size in pigs and supports the possibility of the EPH gene playing a role in determining the number of offspring per birth. The identified genes in this study offer a basis from which the differences between monotocous and polytocous species can be studied. Furthermore, these genes may harbor some clues to the underlying mechanism, which determines litter size and may prove useful for livestock breeding strategies.

Improved differential evolution algorithms for handling economic dispatch optimization with generator constraints

International Nuclear Information System (INIS)

Coelho, Leandro dos Santos; Mariani, Viviana Cocco

2007-01-01

Global optimization based on evolutionary algorithms can be used as the important component for many engineering optimization problems. Evolutionary algorithms have yielded promising results for solving nonlinear, non-differentiable and multi-modal optimization problems in the power systems area. Differential evolution (DE) is a simple and efficient evolutionary algorithm for function optimization over continuous spaces. It has reportedly outperformed search heuristics when tested over both benchmark and real world problems. This paper proposes improved DE algorithms for solving economic load dispatch problems that take into account nonlinear generator features such as ramp rate limits and prohibited operating zones in the power system operation. The DE algorithms and its variants are validated for two test systems consisting of 6 and 15 thermal units. Various DE approaches outperforms other state of the art algorithms reported in the literature in solving load dispatch problems with generator constraints

Pulse Retrieval Algorithm for Interferometric Frequency-Resolved Optical Gating Based on Differential Evolution

OpenAIRE

Hyyti, Janne; Escoto, Esmerando; Steinmeyer, Günter

2017-01-01

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 robustness of the algorithm against experimental artifacts and noise. These tests show that the i...

Multi-objective optimization of coal-fired power plants using differential evolution

International Nuclear Information System (INIS)

Wang, Ligang; Yang, Yongping; Dong, Changqing; Morosuk, Tatiana; Tsatsaronis, George

2014-01-01

Highlights: • Multi-objective optimization of large-scale coal-fired power plants using differential evolution. • A newly-proposed algorithm for searching the fronts of decision space in a single run. • A reduction of cost of electricity by 2–4% with an optimal efficiency increase up to 2% points. • The uncertainty comes mainly from temperature- and reheat-related cost factors of steam generator. • An exergoeconomic analysis and comparison between optimal designs and one real industrial design. - Abstract: The design trade-offs between thermodynamics and economics for thermal systems can be studied with the aid of multi-objective optimization techniques. The investment costs usually increase with increasing thermodynamic performance of a system. In this paper, an enhanced differential evolution with diversity-preserving and density-adjusting mechanisms, and a newly-proposed algorithm for searching the decision space frontier in a single run were used, to conduct the multi-objective optimization of large-scale, supercritical coal-fired plants. The uncertainties associated with cost functions were discussed by analyzing the sensitivity of the decision space frontier to some significant parameters involved in cost functions. Comparisons made with the aid of an exergoeconomic analysis between the cost minimum designs and a real industrial design demonstrated how the plant improvement was achieved. It is concluded that the cost of electricity could be reduced by a 2–4%, whereas the efficiency could be increased by up to two percentage points. The largest uncertainty is introduced by the temperature-related and reheat-related cost coefficients of the steam generator. More reliable data on the price prediction of future advanced materials should be used to obtain more accurate fronts of the objective space

Mantle differentiation and thermal evolution of Mars, Mercury, and Venus

International Nuclear Information System (INIS)

Spohn, T.

1991-01-01

In the present models for the thermal evolution of Mercury, Venus, and Mars encompass core and mantle chemical differentiation, lithospheric growth, and volcanic heat-transfer processes. Calculation results indicate that crust and lithosphere thicknesses are primarily dependent on planet size as well as the bulk concentration of planetary radiogenic elements and the lithosphere's thermal conductivity. The evidence for Martian volcanism for at least 3.5 Gyr, and in Mercury for up to 1 Gyr, in conjunction with the presence of a magnetic field on Mercury and its absence on Mars, suggest the dominance of a lithospheric conduction heat-transfer mechanism in these planets for most of their thermal history; by contrast, volcanic heat piping may have been an important heat-transfer mechanism on Venus. 50 refs

Signatures of pleiotropy, economy and convergent evolution in a domain-resolved map of human-virus protein-protein interaction networks.

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Sara Garamszegi

Full Text Available A central challenge in host-pathogen systems biology is the elucidation of general, systems-level principles that distinguish host-pathogen interactions from within-host interactions. Current analyses of host-pathogen and within-host protein-protein interaction networks are largely limited by their resolution, treating proteins as nodes and interactions as edges. Here, we construct a domain-resolved map of human-virus and within-human protein-protein interaction networks by annotating protein interactions with high-coverage, high-accuracy, domain-centric interaction mechanisms: (1 domain-domain interactions, in which a domain in one protein binds to a domain in a second protein, and (2 domain-motif interactions, in which a domain in one protein binds to a short, linear peptide motif in a second protein. Analysis of these domain-resolved networks reveals, for the first time, significant mechanistic differences between virus-human and within-human interactions at the resolution of single domains. While human proteins tend to compete with each other for domain binding sites by means of sequence similarity, viral proteins tend to compete with human proteins for domain binding sites in the absence of sequence similarity. Independent of their previously established preference for targeting human protein hubs, viral proteins also preferentially target human proteins containing linear motif-binding domains. Compared to human proteins, viral proteins participate in more domain-motif interactions, target more unique linear motif-binding domains per residue, and contain more unique linear motifs per residue. Together, these results suggest that viruses surmount genome size constraints by convergently evolving multiple short linear motifs in order to effectively mimic, hijack, and manipulate complex host processes for their survival. Our domain-resolved analyses reveal unique signatures of pleiotropy, economy, and convergent evolution in viral

Multiple wall-reflection effect in adaptive-array differential-phase reflectometry on QUEST

International Nuclear Information System (INIS)

Idei, H.; Fujisawa, A.; Nagashima, Y.; Onchi, T.; Hanada, K.; Zushi, H.; Mishra, K.; Hamasaki, M.; Hayashi, Y.; Yamamoto, M.K.

2016-01-01

A phased array antenna and Software-Defined Radio (SDR) heterodyne-detection systems have been developed for adaptive array approaches in reflectometry on the QUEST. In the QUEST device considered as a large oversized cavity, standing wave (multiple wall-reflection) effect was significantly observed with distorted amplitude and phase evolution even if the adaptive array analyses were applied. The distorted fields were analyzed by Fast Fourier Transform (FFT) in wavenumber domain to treat separately the components with and without wall reflections. The differential phase evolution was properly obtained from the distorted field evolution by the FFT procedures. A frequency derivative method has been proposed to overcome the multiple-wall reflection effect, and SDR super-heterodyned components with small frequency difference for the derivative method were correctly obtained using the FFT analysis

Kinematic evolution of the Mbakop Pan-African granitoids (western Cameroon domain): An integrated AMS and EBSD approach

Science.gov (United States)

Bella Nké, B. E.; Njanko, T.; Mamtani, M. A.; Njonfang, E.; Rochette, P.

2018-06-01

This study integrates anisotropy of magnetic susceptibility, microstructural and crystallographic preferred orientation (CPO) data from the Mbakop granitic pluton (MGP; Pan-African age) in order to decipher its kinematic evolution. The MGP lies close to NE-SW branch of Central Cameroon Shear Zone (CCSZ) and is emplaced in gneissic basement. High mean magnetic susceptibility and presence of multi-domain magnetite are recorded. Quartz CPO measured using Electron Backscatter diffraction reveals dominance of rhomb , prism and prism slip in different samples, which is consistent with microstructures developed under upper greenschist/amphibolite facies conditions. Quartz CPO along with other kinematic indicators (feldspar porphyroclasts/mineral fish) indicate non-coaxial deformation was important during tectonic evolution of the MGP. Contrasting sense of shear is recorded implying multi-stage mylonitization in the Western Cameroon Domain. Top-towards-south sense of shear is related to regional D2 deformation (613-585 Ma), while top-towards-north is related to D3 (585-540 Ma). The magnetic fabric in MGP records D3. The obliquity between mean orientation of magnetic foliation (N12°E) and the NE-SW CCSZ branch (N48°E) gives kinematic vorticity number of 0.95. This indicates dominantly simple shear with a minor pure shear component. It is concluded that regional transpression was important during MGP emplacement.

Spectral analysis of point-vortex dynamics: first application to vortex polygons in a circular domain

International Nuclear Information System (INIS)

Speetjens, M F M; Meleshko, V V; Van Heijst, G J F

2014-01-01

The present study addresses the classical problem of the dynamics and stability of a cluster of N-point vortices of equal strength arranged in a polygonal configuration (‘N-vortex polygons’). In unbounded domains, such N-vortex polygons are unconditionally stable for N⩽7. Confinement in a circular domain tightens the stability conditions to N⩽6 and a maximum polygon size relative to the domain radius. This work expands on existing studies on stability and integrability by a first giving an exploratory spectral analysis of the dynamics of N vortex polygons in circular domains. Key to this is that the spectral signature of the time evolution of vortex positions reflects their qualitative behaviour. Expressing vortex motion by a generic evolution operator (the so-called Koopman operator) provides a rigorous framework for such spectral analyses. This paves the way to further differentiation and classification of point-vortex behaviour beyond stability and integrability. The concept of Koopman-based spectral analysis is demonstrated for N-vortex polygons. This reveals that conditional stability can be seen as a local form of integrability and confirms an important generic link between spectrum and dynamics: discrete spectra imply regular (quasi-periodic) motion; continuous (sub-)spectra imply chaotic motion. Moreover, this exposes rich nonlinear dynamics as intermittency between regular and chaotic motion and quasi-coherent structures formed by chaotic vortices. (ss 1)

Towards a Differentiated and Domain-Specific View of Educational Technology: An Exploratory Study of History Teachers' Technology Use

Science.gov (United States)

Voet, Michiel; De Wever, Bram

2017-01-01

Adopting a differentiated and domain-specific view of educational technology, the present study focuses on the case of school history. It argues that, in this particular context, one of technology's main assets is its ability to support inquiry-based learning activities, during which students interpret the past through historical reasoning. As…

Characterization and Evolution of the Cell Cycle-Associated Mob Domain-Containing Proteins in Eukaryotes

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Nicola Vitulo

2007-01-01

Full Text Available The MOB family includes a group of cell cycle-associated proteins highly conserved throughout eukaryotes, whose founding members are implicated in mitotic exit and co-ordination of cell cycle progression with cell polarity and morphogenesis. Here we report the characterization and evolution of the MOB domain-containing proteins as inferred from the 43 eukaryotic genomes so far sequenced. We show that genes for Mob-like proteins are present in at least 41 of these genomes, confi rming the universal distribution of this protein family and suggesting its prominent biological function. The phylogenetic analysis reveals fi ve distinct MOB domain classes, showing a progressive expansion of this family from unicellular to multicellular organisms, reaching the highest number in mammals. Plant Mob genes appear to have evolved from a single ancestor, most likely after the loss of one or more genes during the early stage of Viridiplantae evolutionary history. Three of the Mob classes are widespread among most of the analyzed organisms. The possible biological and molecular function of Mob proteins and their role in conserved signaling pathways related to cell proliferation, cell death and cell polarity are also presented and critically discussed.

A Domain Specific Embedded Language in C++ for Automatic Differentiation, Projection, Integration and Variational Formulations

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Christophe Prud'homme

2006-01-01

Full Text Available In this article, we present a domain specific embedded language in C++ that can be used in various contexts such as numerical projection onto a functional space, numerical integration, variational formulations and automatic differentiation. Albeit these tools operate in different ways, the language overcomes this difficulty by decoupling expression constructions from evaluation. The language is implemented using expression templates and meta-programming techniques and uses various Boost libraries. The language is exercised on a number of non-trivial examples and a benchmark presents the performance behavior on a few test problems.

Differential and Domain-Specific Associations Among Right-Wing Authoritarianism, Social Dominance Orientation, and Adolescent Delinquency.

Science.gov (United States)

Oosterhoff, Benjamin; Shook, Natalie J; Clay, Russ; Metzger, Aaron

2017-09-01

Using a dual-process model (DPM) framework, this research examined whether right-wing authoritarianism (RWA) and social dominance orientation (SDO) are differentially associated with adolescent delinquency. In Study 1 ( N = 847; M age = 15.96) and Study 2 ( N = 340; M age = 16.64), adolescents completed measures of RWA, SDO, and engagement in different forms of delinquency. In Study 2, adolescents also reported their beliefs about obeying different laws. Across both studies, adolescents who endorsed greater RWA engaged in lower levels of delinquency and those who endorsed greater SDO engaged in higher levels of delinquency. Findings from Study 2 suggest that these associations are contingent on the domain-specific purpose of the law being violated and are also present with adolescents' beliefs about their obligation to obey laws. These results extend the DPM, demonstrating that RWA and SDO are differentially linked with youth delinquency.

Accelerating Markov chain Monte Carlo simulation by differential evolution with self-adaptive randomized subspace sampling

Energy Technology Data Exchange (ETDEWEB)

Vrugt, Jasper A [Los Alamos National Laboratory; Hyman, James M [Los Alamos National Laboratory; Robinson, Bruce A [Los Alamos National Laboratory; Higdon, Dave [Los Alamos National Laboratory; Ter Braak, Cajo J F [NETHERLANDS; Diks, Cees G H [UNIV OF AMSTERDAM

2008-01-01

Markov chain Monte Carlo (MCMC) methods have found widespread use in many fields of study to estimate the average properties of complex systems, and for posterior inference in a Bayesian framework. Existing theory and experiments prove convergence of well constructed MCMC schemes to the appropriate limiting distribution under a variety of different conditions. In practice, however this convergence is often observed to be disturbingly slow. This is frequently caused by an inappropriate selection of the proposal distribution used to generate trial moves in the Markov Chain. Here we show that significant improvements to the efficiency of MCMC simulation can be made by using a self-adaptive Differential Evolution learning strategy within a population-based evolutionary framework. This scheme, entitled DiffeRential Evolution Adaptive Metropolis or DREAM, runs multiple different chains simultaneously for global exploration, and automatically tunes the scale and orientation of the proposal distribution in randomized subspaces during the search. Ergodicity of the algorithm is proved, and various examples involving nonlinearity, high-dimensionality, and multimodality show that DREAM is generally superior to other adaptive MCMC sampling approaches. The DREAM scheme significantly enhances the applicability of MCMC simulation to complex, multi-modal search problems.

Expansion of protein domain repeats.

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Asa K Björklund

2006-08-01

Full Text Available Many proteins, especially in eukaryotes, contain tandem repeats of several domains from the same family. These repeats have a variety of binding properties and are involved in protein-protein interactions as well as binding to other ligands such as DNA and RNA. The rapid expansion of protein domain repeats is assumed to have evolved through internal tandem duplications. However, the exact mechanisms behind these tandem duplications are not well-understood. Here, we have studied the evolution, function, protein structure, gene structure, and phylogenetic distribution of domain repeats. For this purpose we have assigned Pfam-A domain families to 24 proteomes with more sensitive domain assignments in the repeat regions. These assignments confirmed previous findings that eukaryotes, and in particular vertebrates, contain a much higher fraction of proteins with repeats compared with prokaryotes. The internal sequence similarity in each protein revealed that the domain repeats are often expanded through duplications of several domains at a time, while the duplication of one domain is less common. Many of the repeats appear to have been duplicated in the middle of the repeat region. This is in strong contrast to the evolution of other proteins that mainly works through additions of single domains at either terminus. Further, we found that some domain families show distinct duplication patterns, e.g., nebulin domains have mainly been expanded with a unit of seven domains at a time, while duplications of other domain families involve varying numbers of domains. Finally, no common mechanism for the expansion of all repeats could be detected. We found that the duplication patterns show no dependence on the size of the domains. Further, repeat expansion in some families can possibly be explained by shuffling of exons. However, exon shuffling could not have created all repeats.

Alternative splicing targeting the hTAF4-TAFH domain of TAF4 represses proliferation and accelerates chondrogenic differentiation of human mesenchymal stem cells.

Directory of Open Access Journals (Sweden)

Jekaterina Kazantseva

Full Text Available Transcription factor IID (TFIID activity can be regulated by cellular signals to specifically alter transcription of particular subsets of genes. Alternative splicing of TFIID subunits is often the result of external stimulation of upstream signaling pathways. We studied tissue distribution and cellular expression of different splice variants of TFIID subunit TAF4 mRNA and biochemical properties of its isoforms in human mesenchymal stem cells (hMSCs to reveal the role of different isoforms of TAF4 in the regulation of proliferation and differentiation. Expression of TAF4 transcripts with exons VI or VII deleted, which results in a structurally modified hTAF4-TAFH domain, increases during early differentiation of hMSCs into osteoblasts, adipocytes and chondrocytes. Functional analysis data reveals that TAF4 isoforms with the deleted hTAF4-TAFH domain repress proliferation of hMSCs and preferentially promote chondrogenic differentiation at the expense of other developmental pathways. This study also provides initial data showing possible cross-talks between TAF4 and TP53 activity and switching between canonical and non-canonical WNT signaling in the processes of proliferation and differentiation of hMSCs. We propose that TAF4 isoforms generated by the alternative splicing participate in the conversion of the cellular transcriptional programs from the maintenance of stem cell state to differentiation, particularly differentiation along the chondrogenic pathway.

Optimization Shape of Variable Capacitance Micromotor Using Differential Evolution Algorithm

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A. Ketabi

2010-01-01

Full Text Available A new method for optimum shape design of variable capacitance micromotor (VCM using Differential Evolution (DE, a stochastic search algorithm, is presented. In this optimization exercise, the objective function aims to maximize torque value and minimize the torque ripple, where the geometric parameters are considered to be the variables. The optimization process is carried out using a combination of DE algorithm and FEM analysis. Fitness value is calculated by FEM analysis using COMSOL3.4, and the DE algorithm is realized by MATLAB7.4. The proposed method is applied to a VCM with 8 poles at the stator and 6 poles at the rotor. The results show that the optimized micromotor using DE algorithm had higher torque value and lower torque ripple, indicating the validity of this methodology for VCM design.

Evolution Inclusions and Variation Inequalities for Earth Data Processing II Differential-operator Inclusions and Evolution Variation Inequalities for Earth Data Processing

CERN Document Server

Zgurovsky, Mikhail Z; Kasyanov, Pavlo O

2011-01-01

Here, the authors present modern mathematical methods to solve problems of differential-operator inclusions and evolution variation inequalities which may occur in fields such as geophysics, aerohydrodynamics, or fluid dynamics. For the first time, they describe the detailed generalization of various approaches to the analysis of fundamentally nonlinear models and provide a toolbox of mathematical equations. These new mathematical methods can be applied to a broad spectrum of problems. Examples of these are phase changes, diffusion of electromagnetic, acoustic, vibro-, hydro- and seismoacousti

Crustal-Scale Fault Interaction at Rifted Margins and the Formation of Domain-Bounding Breakaway Complexes: Insights From Offshore Norway

Science.gov (United States)

Osmundsen, P. T.; Péron-Pinvidic, G.

2018-03-01

The large-magnitude faults that control crustal thinning and excision at rifted margins combine into laterally persistent structural boundaries that separate margin domains of contrasting morphology and structure. We term them breakaway complexes. At the Mid-Norwegian margin, we identify five principal breakaway complexes that separate the proximal, necking, distal, and outer margin domains. Downdip and lateral interactions between the faults that constitute breakaway complexes became fundamental to the evolution of the 3-D margin architecture. Different types of fault interaction are observed along and between these faults, but simple models for fault growth will not fully describe their evolution. These structures operate on the crustal scale, cut large thicknesses of heterogeneously layered lithosphere, and facilitate fundamental margin processes such as deformation coupling and exhumation. Variations in large-magnitude fault geometry, erosional footwall incision, and subsequent differential subsidence along the main breakaway complexes likely record the variable efficiency of these processes.

Estimating Traffic Accidents in Turkey Using Differential Evolution Algorithm

Science.gov (United States)

Akgüngör, Ali Payıdar; Korkmaz, Ersin

2017-06-01

Estimating traffic accidents play a vital role to apply road safety procedures. This study proposes Differential Evolution Algorithm (DEA) models to estimate the number of accidents in Turkey. In the model development, population (P) and the number of vehicles (N) are selected as model parameters. Three model forms, linear, exponential and semi-quadratic models, are developed using DEA with the data covering from 2000 to 2014. Developed models are statistically compared to select the best fit model. The results of the DE models show that the linear model form is suitable to estimate the number of accidents. The statistics of this form is better than other forms in terms of performance criteria which are the Mean Absolute Percentage Errors (MAPE) and the Root Mean Square Errors (RMSE). To investigate the performance of linear DE model for future estimations, a ten-year period from 2015 to 2024 is considered. The results obtained from future estimations reveal the suitability of DE method for road safety applications.

Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

KAUST Repository

Horiuchi, Youko

2015-12-23

Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis-eQTLs. Expression

Differential gene expression in porcine SK6 cells infected with wild-type and SAP domain-mutant foot-and-mouth disease virus.

Science.gov (United States)

Ni, Zixin; Yang, Fan; Cao, Weijun; Zhang, Xiangle; Jin, Ye; Mao, Ruoqing; Du, Xiaoli; Li, Weiwei; Guo, Jianhong; Liu, Xiangtao; Zhu, Zixiang; Zheng, Haixue

2016-06-01

Foot-and-mouth disease virus (FMDV) is the causative agent of a highly contagious disease in livestock. The viral proteinase L(pro) of FMDV is involved in pathogenicity, and mutation of the L(pro) SAP domain reduces FMDV pathogenicity in pigs. To determine the gene expression profiles associated with decreased pathogenicity in porcine cells, we performed transcriptome analysis using next-generation sequencing technology and compared differentially expressed genes in SK6 cells infected with FMDV containing L(pro) with either a wild-type or mutated version of the SAP domain. This analysis yielded 1,853 genes that exhibited a ≥ 2-fold change in expression and was validated by real-time quantitative PCR detection of several differentially expressed genes. Many of the differentially expressed genes correlated with antiviral responses corresponded to genes associated with transcription factors, immune regulation, cytokine production, inflammatory response, and apoptosis. Alterations in gene expression profiles may be responsible for the variations in pathogenicity observed between the two FMDV variants. Our results provided genes of interest for the further study of antiviral pathways and pathogenic mechanisms related to FMDV L(pro).

Application of plurigaussian simulation to delineate the layout of alteration domains in Sungun copper deposit

Science.gov (United States)

Talebi, Hassan; Asghari, Omid; Emery, Xavier

2013-12-01

An accurate estimation of mineral grades in ore deposits with heterogeneous spatial variations requires defining geological domains that differentiate the types of mineralogy, alteration and lithology. Deterministic models define the layout of the domains based on the interpretation of the drill holes and do not take into account the uncertainty in areas with fewer data. Plurigaussian simulation (PGS) can be an alternative to generate multiple numerical models of the ore body, with the aim of assessing the uncertainty in the domain boundaries and improving the geological controls in the characterization of quantitative attributes. This study addresses the application of PGS to Sungun porphyry copper deposit (Iran), in order to simulate the layout of four hypogene alteration zones: potassic, phyllic, propylitic and argillic. The aim of this study is to construct numerical models in which the alteration structures reflect the evolution observed in the geology.

Study of magnetic domain evolution in an auxetic plane of Galfenol using Kerr microscopy

Science.gov (United States)

Raghunath, Ganesh; Flatau, Alison B.

2015-05-01

Galfenol (FexGa100-x), a magnetostrictive alloy (3/2λ 110-400 ppm) of Iron and Gallium exhibits an in-plane auxetic response in the ⟨110⟩ crystallographic direction. Negative Poisson's ratios have been observed in response to application of stress fields, where values of as low as -0.7 have been reported for compositions of greater than roughly 20% Ga [Zhang et al., J. Appl. Phys. 108(2), 023513 (2010)] and in response to application of magnetic fields, where values of as low as -2.5 have been reported to be expected for compositions of less than roughly 20% Ga [G. Raghunath and A. B. Flatau, IEEE Trans. Magn. (in press)]. Several models have been proposed to understand these two distinct phenomena. Galfenol samples with less than 20% Ga also exhibit an unusual response to an increasing magnetic field applied along the ⟨110⟩ direction. The longitudinal strain which increases initially with applied field experiences a dip (until ˜10 mT) before increasing again to reach saturation. The transverse strain increases and reaches a maximum value (at the same field of ˜10 mT) and then drops from the maximum by 5%-10% as magnetic saturation is approached [G. Raghunath and A. B. Flatau, IEEE Trans. Magn. (in press)].This work deals with discussing the evolution of magnetic domains in a 16 at. % Ga single crystal Galfenol sample when subjected to magnetic fields in the ⟨110⟩ direction in the (100) plane. The magnetic domains on the surface of mechanically polished Galfenol samples were imaged using Magneto-Optic Kerr Effect microscopy. Simultaneously, the strains along the longitudinal and transverse ⟨110⟩ directions were recorded using a bi-directional strain gauge rosette mounted on the unpolished bottom surface of the planar samples. The energy from the applied magnetic field is expected to grow the ⟨110⟩ oriented domains at the expense of domains oriented along all other directions. But since the plane has an easy ⟨100⟩ axis, we expect the

Analysis of chitin-binding proteins from Manduca sexta provides new insights into evolution of peritrophin A-type chitin-binding domains in insects.

Science.gov (United States)

Tetreau, Guillaume; Dittmer, Neal T; Cao, Xiaolong; Agrawal, Sinu; Chen, Yun-Ru; Muthukrishnan, Subbaratnam; Haobo, Jiang; Blissard, Gary W; Kanost, Michael R; Wang, Ping

2015-07-01

In insects, chitin is a major structural component of the cuticle and the peritrophic membrane (PM). In nature, chitin is always associated with proteins among which chitin-binding proteins (CBPs) are the most important for forming, maintaining and regulating the functions of these extracellular structures. In this study, a genome-wide search for genes encoding proteins with ChtBD2-type (peritrophin A-type) chitin-binding domains (CBDs) was conducted. A total of 53 genes encoding 56 CBPs were identified, including 15 CPAP1s (cuticular proteins analogous to peritrophins with 1 CBD), 11 CPAP3s (CPAPs with 3 CBDs) and 17 PMPs (PM proteins) with a variable number of CBDs, which are structural components of cuticle or of the PM. CBDs were also identified in enzymes of chitin metabolism including 6 chitinases and 7 chitin deacetylases encoded by 6 and 5 genes, respectively. RNA-seq analysis confirmed that PMP and CPAP genes have differential spatial expression patterns. The expression of PMP genes is midgut-specific, while CPAP genes are widely expressed in different cuticle forming tissues. Phylogenetic analysis of CBDs of proteins in insects belonging to different orders revealed that CPAP1s from different species constitute a separate family with 16 different groups, including 6 new groups identified in this study. The CPAP3s are clustered into a separate family of 7 groups present in all insect orders. Altogether, they reveal that duplication events of CBDs in CPAP1s and CPAP3s occurred prior to the evolutionary radiation of insect species. In contrast to the CPAPs, all CBDs from individual PMPs are generally clustered and distinct from other PMPs in the same species in phylogenetic analyses, indicating that the duplication of CBDs in each of these PMPs occurred after divergence of insect species. Phylogenetic analysis of these three CBP families showed that the CBDs in CPAP1s form a clearly separate family, while those found in PMPs and CPAP3s were clustered

Evolution of magnetized, differentially rotating neutron stars: Simulations in full general relativity

International Nuclear Information System (INIS)

Duez, Matthew D.; Liu, Yuk Tung; Shapiro, Stuart L.; Stephens, Branson C.; Shibata, Masaru

2006-01-01

We study the effects of magnetic fields on the evolution of differentially rotating neutron stars, which can be formed in stellar core collapse or binary neutron star coalescence. Magnetic braking and the magnetorotational instability (MRI) both act on differentially rotating stars to redistribute angular momentum. Simulations of these stars are carried out in axisymmetry using our recently developed codes which integrate the coupled Einstein-Maxwell-MHD equations. We consider stars with two different equations of state (EOS), a gamma-law EOS with Γ=2, and a more realistic hybrid EOS, and we evolve them adiabatically. Our simulations show that the fate of the star depends on its mass and spin. For initial data, we consider three categories of differentially rotating, equilibrium configurations, which we label normal, hypermassive and ultraspinning. Normal configurations have rest masses below the maximum achievable with uniform rotation, and angular momentum below the maximum for uniform rotation at the same rest mass. Hypermassive stars have rest masses exceeding the mass limit for uniform rotation. Ultraspinning stars are not hypermassive, but have angular momentum exceeding the maximum for uniform rotation at the same rest mass. We show that a normal star will evolve to a uniformly rotating equilibrium configuration. An ultraspinning star evolves to an equilibrium state consisting of a nearly uniformly rotating central core, surrounded by a differentially rotating torus with constant angular velocity along magnetic field lines, so that differential rotation ceases to wind the magnetic field. In addition, the final state is stable against the MRI, although it has differential rotation. For a hypermassive neutron star, the MHD-driven angular momentum transport leads to catastrophic collapse of the core. The resulting rotating black hole is surrounded by a hot, massive, magnetized torus undergoing quasistationary accretion, and a magnetic field collimated along

Late replicating domains are highly recombining in females but have low male recombination rates: implications for isochore evolution.

Directory of Open Access Journals (Sweden)

Catherine J Pink

Full Text Available In mammals sequences that are either late replicating or highly recombining have high rates of evolution at putatively neutral sites. As early replicating domains and highly recombining domains both tend to be GC rich we a priori expect these two variables to covary. If so, the relative contribution of either of these variables to the local neutral substitution rate might have been wrongly estimated owing to covariance with the other. Against our expectations, we find that sex-averaged recombination rates show little or no correlation with replication timing, suggesting that they are independent determinants of substitution rates. However, this result masks significant sex-specific complexity: late replicating domains tend to have high recombination rates in females but low recombination rates in males. That these trends are antagonistic explains why sex-averaged recombination is not correlated with replication timing. This unexpected result has several important implications. First, although both male and female recombination rates covary significantly with intronic substitution rates, the magnitude of this correlation is moderately underestimated for male recombination and slightly overestimated for female recombination, owing to covariance with replicating timing. Second, the result could explain why male recombination is strongly correlated with GC content but female recombination is not. If to explain the correlation between GC content and replication timing we suppose that late replication forces reduced GC content, then GC promotion by biased gene conversion during female recombination is partly countered by the antagonistic effect of later replicating sequence tending increase AT content. Indeed, the strength of the correlation between female recombination rate and local GC content is more than doubled by control for replication timing. Our results underpin the need to consider sex-specific recombination rates and potential covariates in

Efficient receiver tuning using differential evolution strategies

Science.gov (United States)

Wheeler, Caleb H.; Toland, Trevor G.

2016-08-01

Differential evolution (DE) is a powerful and computationally inexpensive optimization strategy that can be used to search an entire parameter space or to converge quickly on a solution. The Kilopixel Array Pathfinder Project (KAPPa) is a heterodyne receiver system delivering 5 GHz of instantaneous bandwidth in the tuning range of 645-695 GHz. The fully automated KAPPa receiver test system finds optimal receiver tuning using performance feedback and DE. We present an adaptation of DE for use in rapid receiver characterization. The KAPPa DE algorithm is written in Python 2.7 and is fully integrated with the KAPPa instrument control, data processing, and visualization code. KAPPa develops the technologies needed to realize heterodyne focal plane arrays containing 1000 pixels. Finding optimal receiver tuning by investigating large parameter spaces is one of many challenges facing the characterization phase of KAPPa. This is a difficult task via by-hand techniques. Characterizing or tuning in an automated fashion without need for human intervention is desirable for future large scale arrays. While many optimization strategies exist, DE is ideal for time and performance constraints because it can be set to converge to a solution rapidly with minimal computational overhead. We discuss how DE is utilized in the KAPPa system and discuss its performance and look toward the future of 1000 pixel array receivers and consider how the KAPPa DE system might be applied.

Boundary Control of Linear Evolution PDEs - Continuous and Discrete

DEFF Research Database (Denmark)

Rasmussen, Jan Marthedal

2004-01-01

Consider a partial di erential equation (PDE) of evolution type, such as the wave equation or the heat equation. Assume now that you can influence the behavior of the solution by setting the boundary conditions as you please. This is boundary control in a broad sense. A substantial amount...... of literature exists in the area of theoretical results concerning control of partial differential equations. The results have included existence and uniqueness of controls, minimum time requirements, regularity of domains, and many others. Another huge research field is that of control theory for ordinary di...... erential equations. This field has mostly concerned engineers and others with practical applications in mind. This thesis makes an attempt to bridge the two research areas. More specifically, we make finite dimensional approximations to certain evolution PDEs, and analyze how properties of the discrete...

The architectural design of networks of protein domain architectures.

Science.gov (United States)

Hsu, Chia-Hsin; Chen, Chien-Kuo; Hwang, Ming-Jing

2013-08-23

Protein domain architectures (PDAs), in which single domains are linked to form multiple-domain proteins, are a major molecular form used by evolution for the diversification of protein functions. However, the design principles of PDAs remain largely uninvestigated. In this study, we constructed networks to connect domain architectures that had grown out from the same single domain for every single domain in the Pfam-A database and found that there are three main distinctive types of these networks, which suggests that evolution can exploit PDAs in three different ways. Further analysis showed that these three different types of PDA networks are each adopted by different types of protein domains, although many networks exhibit the characteristics of more than one of the three types. Our results shed light on nature's blueprint for protein architecture and provide a framework for understanding architectural design from a network perspective.

Reptile Toll-like receptor 5 unveils adaptive evolution of bacterial flagellin recognition.

Science.gov (United States)

Voogdt, Carlos G P; Bouwman, Lieneke I; Kik, Marja J L; Wagenaar, Jaap A; van Putten, Jos P M

2016-01-07

Toll-like receptors (TLR) are ancient innate immune receptors crucial for immune homeostasis and protection against infection. TLRs are present in mammals, birds, amphibians and fish but have not been functionally characterized in reptiles despite the central position of this animal class in vertebrate evolution. Here we report the cloning, characterization, and function of TLR5 of the reptile Anolis carolinensis (Green Anole lizard). The receptor (acTLR5) displays the typical TLR protein architecture with 22 extracellular leucine rich repeats flanked by a N- and C-terminal leucine rich repeat domain, a membrane-spanning region, and an intracellular TIR domain. The receptor is phylogenetically most similar to TLR5 of birds and most distant to fish TLR5. Transcript analysis revealed acTLR5 expression in multiple lizard tissues. Stimulation of acTLR5 with TLR ligands demonstrated unique responsiveness towards bacterial flagellin in both reptile and human cells. Comparison of acTLR5 and human TLR5 using purified flagellins revealed differential sensitivity to Pseudomonas but not Salmonella flagellin, indicating development of species-specific flagellin recognition during the divergent evolution of mammals and reptiles. Our discovery of reptile TLR5 fills the evolutionary gap regarding TLR conservation across vertebrates and provides novel insights in functional evolution of host-microbe interactions.

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

Science.gov (United States)

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

2016-06-01

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

The inverse F-BAR domain protein srGAP2 acts through srGAP3 to modulate neuronal differentiation and neurite outgrowth of mouse neuroblastoma cells.

Directory of Open Access Journals (Sweden)

Yue Ma

Full Text Available The inverse F-BAR (IF-BAR domain proteins srGAP1, srGAP2 and srGAP3 are implicated in neuronal development and may be linked to mental retardation, schizophrenia and seizure. A partially overlapping expression pattern and highly similar protein structures indicate a functional redundancy of srGAPs in neuronal development. Our previous study suggests that srGAP3 negatively regulates neuronal differentiation in a Rac1-dependent manner in mouse Neuro2a cells. Here we show that exogenously expressed srGAP1 and srGAP2 are sufficient to inhibit valporic acid (VPA-induced neurite initiation and growth in the mouse Neuro2a cells. While ectopic- or over-expression of RhoGAP-defective mutants, srGAP1(R542A and srGAP2(R527A exert a visible inhibitory effect on neuronal differentiation. Unexpectedly, knockdown of endogenous srGAP2 fails to facilitate the neuronal differentiation induced by VPA, but promotes neurite outgrowth of differentiated cells. All three IF-BAR domains from srGAP1-3 can induce filopodia formation in Neuro2a, but the isolated IF-BAR domain from srGAP2, not from srGAP1 and srGAP3, can promote VPA-induced neurite initiation and neuronal differentiation. We identify biochemical and functional interactions of the three srGAPs family members. We propose that srGAP3-Rac1 signaling may be required for the effect of srGAP1 and srGAP2 on attenuating neuronal differentiation. Furthermore, inhibition of Slit-Robo interaction can phenocopy a loss-of-function of srGAP3, indicating that srGAP3 may be dedicated to the Slit-Robo pathway. Our results demonstrate the interplay between srGAP1, srGAP2 and srGAP3 regulates neuronal differentiation and neurite outgrowth. These findings may provide us new insights into the possible roles of srGAPs in neuronal development and a potential mechanism for neurodevelopmental diseases.

Differential Item Functioning of the Psychological Domain of the Menopause Rating Scale

Science.gov (United States)

Portela-Buelvas, Katherin; Oviedo, Heidi C.; Herazo, Edwin; Campo-Arias, Adalberto

2016-01-01

Introduction. Quality of life could be quantified with the Menopause Rating Scale (MRS), which evaluates the severity of somatic, psychological, and urogenital symptoms in menopause. However, differential item functioning (DIF) analysis has not been applied previously. Objective. To establish the DIF of the psychological domain of the MRS in Colombian women. Methods. 4,009 women aged between 40 and 59 years, who participated in the CAVIMEC (Calidad de Vida en la Menopausia y Etnias Colombianas) project, were included. Average age was 49.0 ± 5.9 years. Women were classified in mestizo, Afro-Colombian, and indigenous. The results were presented as averages and standard deviation (X ± SD). A p value <0.001 was considered statistically significant. Results. In mestizo women, the highest X ± SD were obtained in physical and mental exhaustion (PME) (0.86 ± 0.93) and the lowest ones in anxiety (0.44 ± 0.79). In Afro-Colombian women, an average score of 0.99 ± 1.07 for PME and 0.63 ± 0.88 for anxiety was gotten. Indigenous women obtained an increased average score for PME (1.33 ± 0.93). The lowest score was evidenced in depressive mood (0.50 ± 0.81), which is different from other Colombian women (p < 0.001). Conclusions. The psychological items of the MRS show differential functioning according to the ethnic group, which may induce systematic error in the measurement of the construct. PMID:27847825

Differential Item Functioning of the Psychological Domain of the Menopause Rating Scale.

Science.gov (United States)

Monterrosa-Castro, Alvaro; Portela-Buelvas, Katherin; Oviedo, Heidi C; Herazo, Edwin; Campo-Arias, Adalberto

2016-01-01

Introduction. Quality of life could be quantified with the Menopause Rating Scale (MRS), which evaluates the severity of somatic, psychological, and urogenital symptoms in menopause. However, differential item functioning (DIF) analysis has not been applied previously. Objective . To establish the DIF of the psychological domain of the MRS in Colombian women. Methods . 4,009 women aged between 40 and 59 years, who participated in the CAVIMEC (Calidad de Vida en la Menopausia y Etnias Colombianas) project, were included. Average age was 49.0 ± 5.9 years. Women were classified in mestizo, Afro-Colombian, and indigenous. The results were presented as averages and standard deviation ( X ± SD). A p value <0.001 was considered statistically significant. Results . In mestizo women, the highest X ± SD were obtained in physical and mental exhaustion (PME) (0.86 ± 0.93) and the lowest ones in anxiety (0.44 ± 0.79). In Afro-Colombian women, an average score of 0.99 ± 1.07 for PME and 0.63 ± 0.88 for anxiety was gotten. Indigenous women obtained an increased average score for PME (1.33 ± 0.93). The lowest score was evidenced in depressive mood (0.50 ± 0.81), which is different from other Colombian women ( p < 0.001). Conclusions . The psychological items of the MRS show differential functioning according to the ethnic group, which may induce systematic error in the measurement of the construct.

Requirement of the coiled-coil domain of PML-RARα oncoprotein for localization, sumoylation, and inhibition of monocyte differentiation

International Nuclear Information System (INIS)

Kim, Young-Eui; Kim, Dong-Yeon; Lee, Jang-Mi; Kim, Seong-Tae; Han, Tae-Hee; Ahn, Jin-Hyun

2005-01-01

Homo-oligomerization via a coiled-coil (C-C) domain has been shown to be necessary for the promyelocytic leukemia (PML)-retinoic acid receptor-α (RARα) fusion protein to acquire oncogenic potential in acute promyelocytic leukemia. We show here that PML(ΔC-C)-RARα, which contains a deletion in its C-C domain, is neither localized as characteristic microspeckles nor modified by small ubiquitin-like modifiers (SUMO). The absence of sumoylation of the ΔC-C mutant was due to the lack of binding to Ubc9, a SUMO conjugation enzyme. The integrity of RING finger domain was also needed for both sumoylation and microspeckle formation. In GAL4-DNA tethering assays, the ΔC-C mutant completely lost the inhibitory effect on retinoic acid (RA)-mediated transactivation. Furthermore, the expression of CD14 in U937 cells expressing the ΔC-C mutant in response to vitamin D3 was markedly higher than in cells expressing PML-RARα. However, the RA-mediated induction of C/EBPβ in cells expressing the ΔC-C mutant was comparable to that of control cells. Thus, our results suggest that the C-C domain-associated functions of sumoylation, localization as microspeckles, and the inhibition of monocyte differentiation all contribute to the oncogenic activity of PML-RARα

On the adaptivity and complexity embedded into differential evolution

International Nuclear Information System (INIS)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman; Zelinka, Ivan

2016-01-01

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

On the adaptivity and complexity embedded into differential evolution

Energy Technology Data Exchange (ETDEWEB)

Senkerik, Roman; Pluhacek, Michal; Jasek, Roman [Tomas Bata University in Zlin, Faculty of Applied Informatics, Nam T.G. Masaryka 5555, 760 01 Zlin, Czech Republic, senkerik@fai.utb.cz,pluhacek@fai.utb.cz (Czech Republic); Zelinka, Ivan [Technical University of Ostrava, Faculty of Electrical Engineering and Computer Science, 17. listopadu 15,708 33 Ostrava-Poruba, Czech Republic, ivan.zelinka@vsb.cz (Czech Republic)

2016-06-08

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

On the adaptivity and complexity embedded into differential evolution

Science.gov (United States)

Senkerik, Roman; Pluhacek, Michal; Zelinka, Ivan; Jasek, Roman

2016-06-01

This research deals with the comparison of the two modern approaches for evolutionary algorithms, which are the adaptivity and complex chaotic dynamics. This paper aims on the investigations on the chaos-driven Differential Evolution (DE) concept. This paper is aimed at the embedding of discrete dissipative chaotic systems in the form of chaotic pseudo random number generators for the DE and comparing the influence to the performance with the state of the art adaptive representative jDE. This research is focused mainly on the possible disadvantages and advantages of both compared approaches. Repeated simulations for Lozi map driving chaotic systems were performed on the simple benchmark functions set, which are more close to the real optimization problems. Obtained results are compared with the canonical not-chaotic and not adaptive DE. Results show that with used simple test functions, the performance of ChaosDE is better in the most cases than jDE and Canonical DE, furthermore due to the unique sequencing in CPRNG given by the hidden chaotic dynamics, thus better and faster selection of unique individuals from population, ChaosDE is faster.

On Improving Efficiency of Differential Evolution for Aerodynamic Shape Optimization Applications

Science.gov (United States)

Madavan, Nateri K.

2004-01-01

Differential Evolution (DE) is a simple and robust evolutionary strategy that has been proven effective in determining the global optimum for several difficult optimization problems. Although DE offers several advantages over traditional optimization approaches, its use in applications such as aerodynamic shape optimization where the objective function evaluations are computationally expensive is limited by the large number of function evaluations often required. In this paper various approaches for improving the efficiency of DE are reviewed and discussed. These approaches are implemented in a DE-based aerodynamic shape optimization method that uses a Navier-Stokes solver for the objective function evaluations. Parallelization techniques on distributed computers are used to reduce turnaround times. Results are presented for the inverse design of a turbine airfoil. The efficiency improvements achieved by the different approaches are evaluated and compared.

Domain walls in the extensions of the Standard Model

Science.gov (United States)

Krajewski, Tomasz; Lalak, Zygmunt; Lewicki, Marek; Olszewski, Paweł

2018-05-01

Our main interest is the evolution of domain walls of the Higgs field in the early Universe. The aim of this paper is to understand how dynamics of Higgs domain walls could be influenced by yet unknown interactions from beyond the Standard Model. We assume that the Standard Model is valid up to certain, high, energy scale Λ and use the framework of the effective field theory to describe physics below that scale. Performing numerical simulations with different values of the scale Λ we are able to extend our previous analysis [1]. Our recent numerical simulations show that evolution of Higgs domain walls is rather insensitive to interactions beyond the Standard Model as long as masses of new particles are grater than 1012 GeV. For lower values of Λ the RG improved effective potential is strongly modified at field strengths crucial to the evolution of domain walls. However, we find that even for low values of Λ, Higgs domain walls decayed shortly after their formation for generic initial conditions. On the other hand, in simulations with specifically chosen initial conditions Higgs domain walls can live longer and enter the scaling regime. We also determine the energy spectrum of gravitational waves produced by decaying domain walls of the Higgs field. For generic initial field configurations the amplitude of the signal is too small to be observed in planned detectors.

A Markov Chain Monte Carlo version of the genetic algorithm Differential Evolution: easy Bayesian computing for real parameter spaces

NARCIS (Netherlands)

Braak, ter C.J.F.

2006-01-01

Differential Evolution (DE) is a simple genetic algorithm for numerical optimization in real parameter spaces. In a statistical context one would not just want the optimum but also its uncertainty. The uncertainty distribution can be obtained by a Bayesian analysis (after specifying prior and

Scaling properties of domain wall networks

International Nuclear Information System (INIS)

Leite, A. M. M.; Martins, C. J. A. P.

2011-01-01

We revisit the cosmological evolution of domain wall networks, taking advantage of recent improvements in computing power. We carry out high-resolution field theory simulations in two, three and four spatial dimensions to study the effects of dimensionality and damping on the evolution of the network. Our results are consistent with the expected scale-invariant evolution of the network, which suggests that previous hints of deviations from this behavior may have been due to the limited dynamical range of those simulations. We also use the results of very large (1024 3 ) simulations in three cosmological epochs to provide a calibration for the velocity-dependent one-scale model for domain walls: we numerically determine the two free model parameters to have the values c w =0.5±0.2 and k w =1.1±0.3.

Evolution of EF-hand calcium-modulated proteins. IV. Exon shuffling did not determine the domain compositions of EF-hand proteins

Science.gov (United States)

Kretsinger, R. H.; Nakayama, S.

1993-01-01

In the previous three reports in this series we demonstrated that the EF-hand family of proteins evolved by a complex pattern of gene duplication, transposition, and splicing. The dendrograms based on exon sequences are nearly identical to those based on protein sequences for troponin C, the essential light chain myosin, the regulatory light chain, and calpain. This validates both the computational methods and the dendrograms for these subfamilies. The proposal of congruence for calmodulin, troponin C, essential light chain, and regulatory light chain was confirmed. There are, however, significant differences in the calmodulin dendrograms computed from DNA and from protein sequences. In this study we find that introns are distributed throughout the EF-hand domain and the interdomain regions. Further, dendrograms based on intron type and distribution bear little resemblance to those based on protein or on DNA sequences. We conclude that introns are inserted, and probably deleted, with relatively high frequency. Further, in the EF-hand family exons do not correspond to structural domains and exon shuffling played little if any role in the evolution of this widely distributed homolog family. Calmodulin has had a turbulent evolution. Its dendrograms based on protein sequence, exon sequence, 3'-tail sequence, intron sequences, and intron positions all show significant differences.

Differential Equations as Actions

DEFF Research Database (Denmark)

Ronkko, Mauno; Ravn, Anders P.

1997-01-01

We extend a conventional action system with a primitive action consisting of a differential equation and an evolution invariant. The semantics is given by a predicate transformer. The weakest liberal precondition is chosen, because it is not always desirable that steps corresponding to differential...... actions shall terminate. It is shown that the proposed differential action has a semantics which corresponds to a discrete approximation when the discrete step size goes to zero. The extension gives action systems the power to model real-time clocks and continuous evolutions within hybrid systems....

Constructing HVS-Based Optimal Substitution Matrix Using Enhanced Differential Evolution

Directory of Open Access Journals (Sweden)

Shu-Fen Tu

2013-01-01

Full Text Available Least significant bit (LSB substitution is a method of information hiding. The secret message is embedded into the last k bits of a cover-image in order to evade the notice of hackers. The security and stego-image quality are two main limitations of the LSB substitution method. Therefore, some researchers have proposed an LSB substitution matrix to address these two issues. Finding the optimal LSB substitution matrix can be conceptualized as a problem of combinatorial optimization. In this paper, we adopt a different heuristic method based on other researchers’ method, called enhanced differential evolution (EDE, to construct an optimal LSB substitution matrix. Differing from other researchers, we adopt an HVS-based measurement as a fitness function and embed the secret by modifying the pixel to a closest value rather than simply substituting the LSBs. Our scheme extracts the secret by modular operations as simple LSB substitution does. The experimental results show that the proposed embedding algorithm indeed improves imperceptibility of stego-images substantially.

Generalized vector calculus on convex domain

Science.gov (United States)

Agrawal, Om P.; Xu, Yufeng

2015-06-01

In this paper, we apply recently proposed generalized integral and differential operators to develop generalized vector calculus and generalized variational calculus for problems defined over a convex domain. In particular, we present some generalization of Green's and Gauss divergence theorems involving some new operators, and apply these theorems to generalized variational calculus. For fractional power kernels, the formulation leads to fractional vector calculus and fractional variational calculus for problems defined over a convex domain. In special cases, when certain parameters take integer values, we obtain formulations for integer order problems. Two examples are presented to demonstrate applications of the generalized variational calculus which utilize the generalized vector calculus developed in the paper. The first example leads to a generalized partial differential equation and the second example leads to a generalized eigenvalue problem, both in two dimensional convex domains. We solve the generalized partial differential equation by using polynomial approximation. A special case of the second example is a generalized isoperimetric problem. We find an approximate solution to this problem. Many physical problems containing integer order integrals and derivatives are defined over arbitrary domains. We speculate that future problems containing fractional and generalized integrals and derivatives in fractional mechanics will be defined over arbitrary domains, and therefore, a general variational calculus incorporating a general vector calculus will be needed for these problems. This research is our first attempt in that direction.

Non-dominated sorting binary differential evolution for the multi-objective optimization of cascading failures protection in complex networks

International Nuclear Information System (INIS)

Li, Y.F.; Sansavini, G.; Zio, E.

2013-01-01

A number of research works have been devoted to the optimization of protection strategies (e.g. transmission line switch off) of critical infrastructures (e.g. power grids, telecommunication networks, computer networks, etc) to avoid cascading failures. This work aims at improving a previous optimization approach proposed by some of the authors [1], based on the modified binary differential evolution (MBDE) algorithm. The improvements are three-fold: (1) in the optimization problem formulation, we introduce a third objective function to minimize the impacts of the switching off operations onto the existing network topology; (2) in the optimization problem formulation, we use the final results of cascades, rather than only a short horizon of one step cascading, to evaluate the effects of the switching off strategies; (3) in the optimization algorithm, the fast non-dominated sorting mechanisms are incorporated into the MBDE algorithm: a new algorithm, namely non-dominated sorting binary differential evolution algorithm (NSBDE) is then proposed. The numerical application to the topological structure of the 380 kV Italian power transmission network proves the benefits of the improvements.

Differential evolution and simulated annealing algorithms for mechanical systems design

Directory of Open Access Journals (Sweden)

H. Saruhan

2014-09-01

Full Text Available In this study, nature inspired algorithms – the Differential Evolution (DE and the Simulated Annealing (SA – are utilized to seek a global optimum solution for ball bearings link system assembly weight with constraints and mixed design variables. The Genetic Algorithm (GA and the Evolution Strategy (ES will be a reference for the examination and validation of the DE and the SA. The main purpose is to minimize the weight of an assembly system composed of a shaft and two ball bearings. Ball bearings link system is used extensively in many machinery applications. Among mechanical systems, designers pay great attention to the ball bearings link system because of its significant industrial importance. The problem is complex and a time consuming process due to mixed design variables and inequality constraints imposed on the objective function. The results showed that the DE and the SA performed and obtained convergence reliability on the global optimum solution. So the contribution of the DE and the SA application to the mechanical system design can be very useful in many real-world mechanical system design problems. Beside, the comparison confirms the effectiveness and the superiority of the DE over the others algorithms – the SA, the GA, and the ES – in terms of solution quality. The ball bearings link system assembly weight of 634,099 gr was obtained using the DE while 671,616 gr, 728213.8 gr, and 729445.5 gr were obtained using the SA, the ES, and the GA respectively.

Solution structure of a DNA mimicking motif of an RNA aptamer against transcription factor AML1 Runt domain.

Science.gov (United States)

Nomura, Yusuke; Tanaka, Yoichiro; Fukunaga, Jun-ichi; Fujiwara, Kazuya; Chiba, Manabu; Iibuchi, Hiroaki; Tanaka, Taku; Nakamura, Yoshikazu; Kawai, Gota; Kozu, Tomoko; Sakamoto, Taiichi

2013-12-01

AML1/RUNX1 is an essential transcription factor involved in the differentiation of hematopoietic cells. AML1 binds to the Runt-binding double-stranded DNA element (RDE) of target genes through its N-terminal Runt domain. In a previous study, we obtained RNA aptamers against the AML1 Runt domain by systematic evolution of ligands by exponential enrichment and revealed that RNA aptamers exhibit higher affinity for the Runt domain than that for RDE and possess the 5'-GCGMGNN-3' and 5'-N'N'CCAC-3' conserved motif (M: A or C; N and N' form Watson-Crick base pairs) that is important for Runt domain binding. In this study, to understand the structural basis of recognition of the Runt domain by the aptamer motif, the solution structure of a 22-mer RNA was determined using nuclear magnetic resonance. The motif contains the AH(+)-C mismatch and base triple and adopts an unusual backbone structure. Structural analysis of the aptamer motif indicated that the aptamer binds to the Runt domain by mimicking the RDE sequence and structure. Our data should enhance the understanding of the structural basis of DNA mimicry by RNA molecules.

Assessing the performance of a differential evolution algorithm in structural damage detection by varying the objective function

OpenAIRE

Villalba-Morales, Jesús Daniel; Laier, José Elias

2014-01-01

Structural damage detection has become an important research topic in certain segments of the engineering community. These methodologies occasionally formulate an optimization problem by defining an objective function based on dynamic parameters, with metaheuristics used to find the solution. In this study, damage localization and quantification is performed by an Adaptive Differential Evolution algorithm, which solves the associated optimization problem. Furthermore, this paper looks at the ...

Basis adaptation and domain decomposition for steady-state partial differential equations with random coefficients

Energy Technology Data Exchange (ETDEWEB)

Tipireddy, R.; Stinis, P.; Tartakovsky, A. M.

2017-12-01

We present a novel approach for solving steady-state stochastic partial differential equations (PDEs) with high-dimensional random parameter space. The proposed approach combines spatial domain decomposition with basis adaptation for each subdomain. The basis adaptation is used to address the curse of dimensionality by constructing an accurate low-dimensional representation of the stochastic PDE solution (probability density function and/or its leading statistical moments) in each subdomain. Restricting the basis adaptation to a specific subdomain affords finding a locally accurate solution. Then, the solutions from all of the subdomains are stitched together to provide a global solution. We support our construction with numerical experiments for a steady-state diffusion equation with a random spatially dependent coefficient. Our results show that highly accurate global solutions can be obtained with significantly reduced computational costs.

Cloud computing task scheduling strategy based on differential evolution and ant colony optimization

Science.gov (United States)

Ge, Junwei; Cai, Yu; Fang, Yiqiu

2018-05-01

This paper proposes a task scheduling strategy DEACO based on the combination of Differential Evolution (DE) and Ant Colony Optimization (ACO), aiming at the single problem of optimization objective in cloud computing task scheduling, this paper combines the shortest task completion time, cost and load balancing. DEACO uses the solution of the DE to initialize the initial pheromone of ACO, reduces the time of collecting the pheromone in ACO in the early, and improves the pheromone updating rule through the load factor. The proposed algorithm is simulated on cloudsim, and compared with the min-min and ACO. The experimental results show that DEACO is more superior in terms of time, cost, and load.

Design of 2-D Recursive Filters Using Self-adaptive Mutation Differential Evolution Algorithm

Directory of Open Access Journals (Sweden)

Lianghong Wu

2011-08-01

Full Text Available This paper investigates a novel approach to the design of two-dimensional recursive digital filters using differential evolution (DE algorithm. The design task is reformulated as a constrained minimization problem and is solved by an Self-adaptive Mutation DE algorithm (SAMDE, which adopts an adaptive mutation operator that combines with the advantages of the DE/rand/1/bin strategy and the DE/best/2/bin strategy. As a result, its convergence performance is improved greatly. Numerical experiment results confirm the conclusion. The proposedSAMDE approach is effectively applied to test a numerical example and is compared with previous design methods. The computational experiments show that the SAMDE approach can obtain better results than previous design methods.

Supplementary Material for: Global expression differences and tissue specific expression differences in rice evolution result in two contrasting types of differentially expressed genes

KAUST Repository

Horiuchi, Youko; Harushima, Yoshiaki; Fujisawa, Hironori; Mochizuki, Takako; Fujita, Masahiro; Ohyanagi, Hajime; Kurata, Nori

2015-01-01

Abstract Background Since the development of transcriptome analysis systems, many expression evolution studies characterized evolutionary forces acting on gene expression, without explicit discrimination between global expression differences and tissue specific expression differences. However, different types of gene expression alteration should have different effects on an organism, the evolutionary forces that act on them might be different, and different types of genes might show different types of differential expression between species. To confirm this, we studied differentially expressed (DE) genes among closely related groups that have extensive gene expression atlases, and clarified characteristics of different types of DE genes including the identification of regulating loci for differential expression using expression quantitative loci (eQTL) analysis data. Results We detected differentially expressed (DE) genes between rice subspecies in five homologous tissues that were verified using japonica and indica transcriptome atlases in public databases. Using the transcriptome atlases, we classified DE genes into two types, global DE genes and changed-tissues DE genes. Global type DE genes were not expressed in any tissues in the atlas of one subspecies, however changed-tissues type DE genes were expressed in both subspecies with different tissue specificity. For the five tissues in the two japonica-indica combinations, 4.6 ± 0.8 and 5.9 ± 1.5 % of highly expressed genes were global and changed-tissues DE genes, respectively. Changed-tissues DE genes varied in number between tissues, increasing linearly with the abundance of tissue specifically expressed genes in the tissue. Molecular evolution of global DE genes was rapid, unlike that of changed-tissues DE genes. Based on gene ontology, global and changed-tissues DE genes were different, having no common GO terms. Expression differences of most global DE genes were regulated by cis

Aerodynamic optimization of supersonic compressor cascade using differential evolution on GPU

Energy Technology Data Exchange (ETDEWEB)

Aissa, Mohamed Hasanine; Verstraete, Tom [Von Karman Institute for Fluid Dynamics (VKI) 1640 Sint-Genesius-Rode (Belgium); Vuik, Cornelis [Delft University of Technology 2628 CD Delft (Netherlands)

2016-06-08

Differential Evolution (DE) is a powerful stochastic optimization method. Compared to gradient-based algorithms, DE is able to avoid local minima but requires at the same time more function evaluations. In turbomachinery applications, function evaluations are performed with time-consuming CFD simulation, which results in a long, non affordable, design cycle. Modern High Performance Computing systems, especially Graphic Processing Units (GPUs), are able to alleviate this inconvenience by accelerating the design evaluation itself. In this work we present a validated CFD Solver running on GPUs, able to accelerate the design evaluation and thus the entire design process. An achieved speedup of 20x to 30x enabled the DE algorithm to run on a high-end computer instead of a costly large cluster. The GPU-enhanced DE was used to optimize the aerodynamics of a supersonic compressor cascade, achieving an aerodynamic loss minimization of 20%.

SH2 Domain Histochemistry.

Science.gov (United States)

Buhs, Sophia; Nollau, Peter

2017-01-01

Among posttranslational modifications, the phosphorylation of tyrosine residues is a key modification in cell signaling. Because of its biological importance, characterization of the cellular state of tyrosine phosphorylation is of great interest. Based on the unique properties of endogenously expressed SH2 domains recognizing tyrosine phosphorylated signaling proteins with high specificity we have developed an alternative approach, coined SH2 profiling, enabling us to decipher complex patterns of tyrosine phosphorylation in various normal and cancerous tissues. So far, SH2 profiling has largely been applied for the analysis of protein extracts with the limitation that information on spatial distribution and intensity of tyrosine phosphorylation within a tissue is lost. Here, we describe a novel SH2 domain based strategy for differential characterization of the state of tyrosine phosphorylation in formaldehyde-fixed and paraffin-embedded tissues. This approach demonstrates that SH2 domains may serve as very valuable tools for the analysis of the differential state of tyrosine phosphorylation in primary tissues fixed and processed under conditions frequently applied by routine pathology laboratories.

Evolutionary dynamics of protein domain architecture in plants

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Zhang Xue-Cheng

2012-01-01

Full Text Available Abstract Background Protein domains are the structural, functional and evolutionary units of the protein. Protein domain architectures are the linear arrangements of domain(s in individual proteins. Although the evolutionary history of protein domain architecture has been extensively studied in microorganisms, the evolutionary dynamics of domain architecture in the plant kingdom remains largely undefined. To address this question, we analyzed the lineage-based protein domain architecture content in 14 completed green plant genomes. Results Our analyses show that all 14 plant genomes maintain similar distributions of species-specific, single-domain, and multi-domain architectures. Approximately 65% of plant domain architectures are universally present in all plant lineages, while the remaining architectures are lineage-specific. Clear examples are seen of both the loss and gain of specific protein architectures in higher plants. There has been a dynamic, lineage-wise expansion of domain architectures during plant evolution. The data suggest that this expansion can be largely explained by changes in nuclear ploidy resulting from rounds of whole genome duplications. Indeed, there has been a decrease in the number of unique domain architectures when the genomes were normalized into a presumed ancestral genome that has not undergone whole genome duplications. Conclusions Our data show the conservation of universal domain architectures in all available plant genomes, indicating the presence of an evolutionarily conserved, core set of protein components. However, the occurrence of lineage-specific domain architectures indicates that domain architecture diversity has been maintained beyond these core components in plant genomes. Although several features of genome-wide domain architecture content are conserved in plants, the data clearly demonstrate lineage-wise, progressive changes and expansions of individual protein domain architectures, reinforcing

Numerical simulation for Jeffery-Hamel flow and heat transfer of micropolar fluid based on differential evolution algorithm

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Ara, Asmat; Khan, Najeeb Alam; Naz, Farah; Raja, Muhammad Asif Zahoor; Rubbab, Qammar

2018-01-01

This article explores the Jeffery-Hamel flow of an incompressible non-Newtonian fluid inside non-parallel walls and observes the influence of heat transfer in the flow field. The fluid is considered to be micropolar fluid that flows in a convergent/divergent channel. The governing nonlinear partial differential equations (PDEs) are converted to nonlinear coupled ordinary differential equations (ODEs) with the help of a suitable similarity transformation. The resulting nonlinear analysis is determined analytically with the utilization of the Taylor optimization method based on differential evolution (DE) algorithm. In order to understand the flow field, the effects of pertinent parameters such as the coupling parameter, spin gradient viscosity parameter and the Reynolds number have been examined on velocity and temperature profiles. It concedes that the good results can be attained by an implementation of the proposed method. Ultimately, the accuracy of the method is confirmed by comparing the present results with the results obtained by Runge-Kutta method.

Numerical simulation for Jeffery-Hamel flow and heat transfer of micropolar fluid based on differential evolution algorithm

Directory of Open Access Journals (Sweden)

Asmat Ara

2018-01-01

Full Text Available This article explores the Jeffery-Hamel flow of an incompressible non-Newtonian fluid inside non-parallel walls and observes the influence of heat transfer in the flow field. The fluid is considered to be micropolar fluid that flows in a convergent/divergent channel. The governing nonlinear partial differential equations (PDEs are converted to nonlinear coupled ordinary differential equations (ODEs with the help of a suitable similarity transformation. The resulting nonlinear analysis is determined analytically with the utilization of the Taylor optimization method based on differential evolution (DE algorithm. In order to understand the flow field, the effects of pertinent parameters such as the coupling parameter, spin gradient viscosity parameter and the Reynolds number have been examined on velocity and temperature profiles. It concedes that the good results can be attained by an implementation of the proposed method. Ultimately, the accuracy of the method is confirmed by comparing the present results with the results obtained by Runge-Kutta method.

Improved control for distributed parameter systems with time-dependent spatial domains utilizing mobile sensor–actuator networks

International Nuclear Information System (INIS)

Zhang Jian-Zhong; Cui Bao-Tong; Zhuang Bo

2017-01-01

A guidance policy for controller performance enhancement utilizing mobile sensor–actuator networks (MSANs) is proposed for a class of distributed parameter systems (DPSs), which are governed by diffusion partial differential equations (PDEs) with time-dependent spatial domains. Several sufficient conditions for controller performance enhancement are presented. First, the infinite dimensional operator theory is used to derive an abstract evolution equation of the systems under some rational assumptions on the operators, and a static output feedback controller is designed to control the spatial process. Then, based on Lyapunov stability arguments, guidance policies for collocated and non-collocated MSANs are provided to enhance the performance of the proposed controller, which show that the time-dependent characteristic of the spatial domains can significantly affect the design of the mobile scheme. Finally, a simulation example illustrates the effectiveness of the proposed policy. (paper)

Evolution of Src Homology 2 (SH2) Domain to Recognize Sulfotyrosine.

Science.gov (United States)

Ju, Tong; Niu, Wei; Guo, Jiantao

2016-09-16

Protein tyrosine O-sulfation is considered as the most common type of post-translational tyrosine modification in nature and plays important roles in extracellular biomolecular interactions. To facilitate the mapping, biological study, and medicinal application of this type of post-translational modification, we seek to evolve a small protein scaffold that recognizes sulfotyrosine with high affinity. We focused our efforts on the engineering of the Src Homology 2 (SH2) domain, which represents the largest class of known phosphotyrosine-recognition domain in nature and has a highly evolvable binding pocket. By using phage display, we successfully engineered the SH2 domain to recognize sulfotyrosine with high affinity. The best mutant, SH2-60.1, displayed more than 1700 fold higher sulfotyrosine-binding affinity than that of the wild-type SH2 domain. We also demonstrated that the evolved SH2 domain mutants could be used to detect sulfoprotein levels on the cell surface. These evolved SH2 domain mutants can be potentially applied to the study of protein tyrosine O-sulfation with proper experimental designs.

Protein domain organisation: adding order.

Science.gov (United States)

Kummerfeld, Sarah K; Teichmann, Sarah A

2009-01-29

Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected degree of clustering and more domain pairs in forward and

Protein domain organisation: adding order

Directory of Open Access Journals (Sweden)

Kummerfeld Sarah K

2009-01-01

Full Text Available Abstract Background Domains are the building blocks of proteins. During evolution, they have been duplicated, fused and recombined, to produce proteins with novel structures and functions. Structural and genome-scale studies have shown that pairs or groups of domains observed together in a protein are almost always found in only one N to C terminal order and are the result of a single recombination event that has been propagated by duplication of the multi-domain unit. Previous studies of domain organisation have used graph theory to represent the co-occurrence of domains within proteins. We build on this approach by adding directionality to the graphs and connecting nodes based on their relative order in the protein. Most of the time, the linear order of domains is conserved. However, using the directed graph representation we have identified non-linear features of domain organization that are over-represented in genomes. Recognising these patterns and unravelling how they have arisen may allow us to understand the functional relationships between domains and understand how the protein repertoire has evolved. Results We identify groups of domains that are not linearly conserved, but instead have been shuffled during evolution so that they occur in multiple different orders. We consider 192 genomes across all three kingdoms of life and use domain and protein annotation to understand their functional significance. To identify these features and assess their statistical significance, we represent the linear order of domains in proteins as a directed graph and apply graph theoretical methods. We describe two higher-order patterns of domain organisation: clusters and bi-directionally associated domain pairs and explore their functional importance and phylogenetic conservation. Conclusion Taking into account the order of domains, we have derived a novel picture of global protein organization. We found that all genomes have a higher than expected

A comparative analysis of particle swarm optimization and differential evolution algorithms for parameter estimation in nonlinear dynamic systems

International Nuclear Information System (INIS)

Banerjee, Amit; Abu-Mahfouz, Issam

2014-01-01

The use of evolutionary algorithms has been popular in recent years for solving the inverse problem of identifying system parameters given the chaotic response of a dynamical system. The inverse problem is reformulated as a minimization problem and population-based optimizers such as evolutionary algorithms have been shown to be efficient solvers of the minimization problem. However, to the best of our knowledge, there has been no published work that evaluates the efficacy of using the two most popular evolutionary techniques – particle swarm optimization and differential evolution algorithm, on a wide range of parameter estimation problems. In this paper, the two methods along with their variants (for a total of seven algorithms) are applied to fifteen different parameter estimation problems of varying degrees of complexity. Estimation results are analyzed using nonparametric statistical methods to identify if an algorithm is statistically superior to others over the class of problems analyzed. Results based on parameter estimation quality suggest that there are significant differences between the algorithms with the newer, more sophisticated algorithms performing better than their canonical versions. More importantly, significant differences were also found among variants of the particle swarm optimizer and the best performing differential evolution algorithm

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

Science.gov (United States)

Dong, Zheng; Zhou, Hongyu; Tao, Peng

2018-02-01

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

Partial Differential Equations

CERN Document Server

1988-01-01

The volume contains a selection of papers presented at the 7th Symposium on differential geometry and differential equations (DD7) held at the Nankai Institute of Mathematics, Tianjin, China, in 1986. Most of the contributions are original research papers on topics including elliptic equations, hyperbolic equations, evolution equations, non-linear equations from differential geometry and mechanics, micro-local analysis.

Cloud Particles Differential Evolution Algorithm: A Novel Optimization Method for Global Numerical Optimization

Directory of Open Access Journals (Sweden)

Wei Li

2015-01-01

Full Text Available We propose a new optimization algorithm inspired by the formation and change of the cloud in nature, referred to as Cloud Particles Differential Evolution (CPDE algorithm. The cloud is assumed to have three states in the proposed algorithm. Gaseous state represents the global exploration. Liquid state represents the intermediate process from the global exploration to the local exploitation. Solid state represents the local exploitation. The best solution found so far acts as a nucleus. In gaseous state, the nucleus leads the population to explore by condensation operation. In liquid state, cloud particles carry out macrolocal exploitation by liquefaction operation. A new mutation strategy called cloud differential mutation is introduced in order to solve a problem that the misleading effect of a nucleus may cause the premature convergence. In solid state, cloud particles carry out microlocal exploitation by solidification operation. The effectiveness of the algorithm is validated upon different benchmark problems. The results have been compared with eight well-known optimization algorithms. The statistical analysis on performance evaluation of the different algorithms on 10 benchmark functions and CEC2013 problems indicates that CPDE attains good performance.

The diversity and evolution of Wolbachia ankyrin repeat domain genes.

Directory of Open Access Journals (Sweden)

Stefanos Siozios

Full Text Available Ankyrin repeat domain-encoding genes are common in the eukaryotic and viral domains of life, but they are rare in bacteria, the exception being a few obligate or facultative intracellular Proteobacteria species. Despite having a reduced genome, the arthropod strains of the alphaproteobacterium Wolbachia contain an unusually high number of ankyrin repeat domain-encoding genes ranging from 23 in wMel to 60 in wPip strain. This group of genes has attracted considerable attention for their astonishing large number as well as for the fact that ankyrin proteins are known to participate in protein-protein interactions, suggesting that they play a critical role in the molecular mechanism that determines host-Wolbachia symbiotic interactions. We present a comparative evolutionary analysis of the wMel-related ankyrin repeat domain-encoding genes present in different Drosophila-Wolbachia associations. Our results show that the ankyrin repeat domain-encoding genes change in size by expansion and contraction mediated by short directly repeated sequences. We provide examples of intra-genic recombination events and show that these genes are likely to be horizontally transferred between strains with the aid of bacteriophages. These results confirm previous findings that the Wolbachia genomes are evolutionary mosaics and illustrate the potential that these bacteria have to generate diversity in proteins potentially involved in the symbiotic interactions.

Optimization of ultrasonic arrays design and setting using a differential evolution

International Nuclear Information System (INIS)

Puel, B.; Chatillon, S.; Calmon, P.; Lesselier, D.

2011-01-01

Optimization of both design and setting of phased arrays could be not so easy when they are performed manually via parametric studies. An optimization method based on an Evolutionary Algorithm and numerical simulation is proposed and evaluated. The Randomized Adaptive Differential Evolution has been adapted to meet the specificities of the non-destructive testing applications. In particular, the solution of multi-objective problems is aimed at with the implementation of the concept of pareto-optimal sets of solutions. The algorithm has been implemented and connected to the ultrasonic simulation modules of the CIVA software used as forward model. The efficiency of the method is illustrated on two realistic cases of application: optimization of the position and delay laws of a flexible array inspecting a nozzle, considered as a mono-objective problem; and optimization of the design of a surrounded array and its delay laws, considered as a constrained bi-objective problem. (authors)

A SLAM based on auxiliary marginalised particle filter and differential evolution

Science.gov (United States)

Havangi, R.; Nekoui, M. A.; Teshnehlab, M.; Taghirad, H. D.

2014-09-01

FastSLAM is a framework for simultaneous localisation and mapping (SLAM) using a Rao-Blackwellised particle filter. In FastSLAM, particle filter is used for the robot pose (position and orientation) estimation, and parametric filter (i.e. EKF and UKF) is used for the feature location's estimation. However, in the long term, FastSLAM is an inconsistent algorithm. In this paper, a new approach to SLAM based on hybrid auxiliary marginalised particle filter and differential evolution (DE) is proposed. In the proposed algorithm, the robot pose is estimated based on auxiliary marginal particle filter that operates directly on the marginal distribution, and hence avoids performing importance sampling on a space of growing dimension. In addition, static map is considered as a set of parameters that are learned using DE. Compared to other algorithms, the proposed algorithm can improve consistency for longer time periods and also, improve the estimation accuracy. Simulations and experimental results indicate that the proposed algorithm is effective.

Insights into function of PSI domains from structure of the Met receptor PSI domain

International Nuclear Information System (INIS)

Kozlov, Guennadi; Perreault, Audrey; Schrag, Joseph D.; Park, Morag; Cygler, Miroslaw; Gehring, Kalle; Ekiel, Irena

2004-01-01

PSI domains are cysteine-rich modules found in extracellular fragments of hundreds of signaling proteins, including plexins, semaphorins, integrins, and attractins. Here, we report the solution structure of the PSI domain from the human Met receptor, a receptor tyrosine kinase critical for proliferation, motility, and differentiation. The structure represents a cysteine knot with short regions of secondary structure including a three-stranded antiparallel β-sheet and two α-helices. All eight cysteines are involved in disulfide bonds with the pattern consistent with that for the PSI domain from Sema4D. Comparison with the Sema4D structure identifies a structurally conserved core comprising the N-terminal half of the PSI domain. Interestingly, this part links adjacent SEMA and immunoglobulin domains in the Sema4D structure, suggesting that the PSI domain serves as a wedge between propeller and immunoglobulin domains and is responsible for the correct positioning of the ligand-binding site of the receptor

Differential evolution algorithm-based kernel parameter selection for Fukunaga-Koontz Transform subspaces construction

Science.gov (United States)

Binol, Hamidullah; Bal, Abdullah; Cukur, Huseyin

2015-10-01

The performance of the kernel based techniques depends on the selection of kernel parameters. That's why; suitable parameter selection is an important problem for many kernel based techniques. This article presents a novel technique to learn the kernel parameters in kernel Fukunaga-Koontz Transform based (KFKT) classifier. The proposed approach determines the appropriate values of kernel parameters through optimizing an objective function constructed based on discrimination ability of KFKT. For this purpose we have utilized differential evolution algorithm (DEA). The new technique overcomes some disadvantages such as high time consumption existing in the traditional cross-validation method, and it can be utilized in any type of data. The experiments for target detection applications on the hyperspectral images verify the effectiveness of the proposed method.

Differential evolution enhanced with multiobjective sorting-based mutation operators.

Science.gov (United States)

Wang, Jiahai; Liao, Jianjun; Zhou, Ying; Cai, Yiqiao

2014-12-01

Differential evolution (DE) is a simple and powerful population-based evolutionary algorithm. The salient feature of DE lies in its mutation mechanism. Generally, the parents in the mutation operator of DE are randomly selected from the population. Hence, all vectors are equally likely to be selected as parents without selective pressure at all. Additionally, the diversity information is always ignored. In order to fully exploit the fitness and diversity information of the population, this paper presents a DE framework with multiobjective sorting-based mutation operator. In the proposed mutation operator, individuals in the current population are firstly sorted according to their fitness and diversity contribution by nondominated sorting. Then parents in the mutation operators are proportionally selected according to their rankings based on fitness and diversity, thus, the promising individuals with better fitness and diversity have more opportunity to be selected as parents. Since fitness and diversity information is simultaneously considered for parent selection, a good balance between exploration and exploitation can be achieved. The proposed operator is applied to original DE algorithms, as well as several advanced DE variants. Experimental results on 48 benchmark functions and 12 real-world application problems show that the proposed operator is an effective approach to enhance the performance of most DE algorithms studied.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

Science.gov (United States)

Liu, Bernard A

2017-01-01

Today there exists a rapidly expanding number of sequenced genomes. Cataloging protein interaction domains such as the Src Homology 2 (SH2) domain across these various genomes can be accomplished with ease due to existing algorithms and predictions models. An evolutionary analysis of SH2 domains provides a step towards understanding how SH2 proteins integrated with existing signaling networks to position phosphotyrosine signaling as a crucial driver of robust cellular communication networks in metazoans. However organizing and tracing SH2 domain across organisms and understanding their evolutionary trajectory remains a challenge. This chapter describes several methodologies towards analyzing the evolutionary trajectory of SH2 domains including a global SH2 domain classification system, which facilitates annotation of new SH2 sequences essential for tracing the lineage of SH2 domains throughout eukaryote evolution. This classification utilizes a combination of sequence homology, protein domain architecture and the boundary positions between introns and exons within the SH2 domain or genes encoding these domains. Discrete SH2 families can then be traced across various genomes to provide insight into its origins. Furthermore, additional methods for examining potential mechanisms for divergence of SH2 domains from structural changes to alterations in the protein domain content and genome duplication will be discussed. Therefore a better understanding of SH2 domain evolution may enhance our insight into the emergence of phosphotyrosine signaling and the expansion of protein interaction domains.

Equivalent construction of the infinitesimal time translation operator in algebraic dynamics algorithm for partial differential evolution equation

Institute of Scientific and Technical Information of China (English)

无

2010-01-01

We give an equivalent construction of the infinitesimal time translation operator for partial differential evolution equation in the algebraic dynamics algorithm proposed by Shun-Jin Wang and his students. Our construction involves only simple partial differentials and avoids the derivative terms of δ function which appear in the course of computation by means of Wang-Zhang operator. We prove Wang’s equivalent theorem which says that our construction and Wang-Zhang’s are equivalent. We use our construction to deal with several typical equations such as nonlinear advection equation, Burgers equation, nonlinear Schrodinger equation, KdV equation and sine-Gordon equation, and obtain at least second order approximate solutions to them. These equations include the cases of real and complex field variables and the cases of the first and the second order time derivatives.

Chemical Shift Assignments of the C-terminal Eps15 Homology Domain-3 EH Domain*

Science.gov (United States)

Caplan, Steve; Sorgen, Paul L.

2013-01-01

The C-terminal Eps15 homology (EH) domain 3 (EHD3) belongs to a eukaryotic family of endocytic regulatory proteins and is involved in the recycling of various receptors from the early endosome to the endocytic recycling compartment or in retrograde transport from the endosomes to the Golgi. EH domains are highly conserved in the EHD family and function as protein-protein interaction units that bind to Asn-Pro-Phe (NPF) motif-containing proteins. The EH domain of EHD1 was the first C-terminal EH domain from the EHD family to be solved by NMR. The differences observed between this domain and proteins with N-terminal EH domains helped describe a mechanism for the differential binding of NPF-containing proteins. Here, structural studies were expanded to include the EHD3 EH domain. While the EHD1 and EHD3 EH domains are highly homologous, they have different protein partners. A comparison of these structures will help determine the selectivity in protein binding between the EHD family members and lead to a better understanding of their unique roles in endocytic regulation. PMID:23754701

Ultrafast carrier dynamics unravel role of surface ligands and metal domain size on the photocatalytic hydrogen evolution efficiency of Au-tipped CdS nanorods: an ultrafast transient absorption spectroscopy study

Science.gov (United States)

Ben-Shahar, Yuval; Kriegel, Ilka; Scotognella, Francesco; Waiskopf, Nir; Dal Conte, Stefano; Moretti, Luca; Cerullo, Giulio; Rabani, Eran; Banin, Uri

2017-02-01

Semiconductor-metal hybrid nanostructures are interesting materials for photocatalysis. Their tunable properties offer a highly controllable platform to design light-induced charge separation, a key to their function in photocatalytic water splitting. Hydrogen evolution quantum yields are influenced by factors as size, shape, material and morphology of the system, additionally the surface coating or the metal domain size play a dominant role. In this paper we present a study on a well-defined model system of Au-tipped CdS nanorods. We use transient absorption spectroscopy to get insights into the charge carrier dynamics after photoexcitation of the bandgap of CdS nanorods. The study of charge transfer processes combined with the hydrogen evolution efficiency unravels the effects of surface coating and the gold tip size on the photocatalytic efficiency. Differences in efficiency with various surface ligands are primarily ascribed to the effects of surface passivation. Surface trapping of charge carriers is competing with effective charge separation, a prerequisite for photocatalysis, leading to the observed lower hydrogen production quantum yields. Interestingly, non-monotonic hydrogen evolution efficiency with size of the gold tip is observed, resulting in an optimal metal domain size for the most efficient photocatalysis. These results are explained by the sizedependent interplay of the metal domain charging and the relative band-alignments. Taken together our findings are of major importance for the potential application of hybrid nanoparticles as photocatalysts.

Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains.

Science.gov (United States)

Vishwanath, Sneha; de Brevern, Alexandre G; Srinivasan, Narayanaswamy

2018-02-01

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in

Neogene palaeogeography and basin evolution of the Western Carpathians, Northern Pannonian domain and adjoining areas

Science.gov (United States)

Kováč, Michal; Márton, Emő; Oszczypko, Nestor; Vojtko, Rastislav; Hók, Jozef; Králiková, Silvia; Plašienka, Dušan; Klučiar, Tomáš; Hudáčková, Natália; Oszczypko-Clowes, Marta

2017-08-01

The data on the Neogene geodynamics, palaeogeography, and basin evolution of the Western Carpathians, Northern Pannonian domain and adjoining areas (ALCAPA Mega-unit) are summarized, re-evaluated, supplemented, and newly interpreted. The proposed concept is illustrated by a series of palinspastic and palaeotopographic maps. The Miocene development of the Outer Carpathians reflects the vanishing subduction of the residual oceanic and/or thinned continental crust. A compression perpendicular to the front of the orogenic system led to the closing of residual flysch troughs and to accretionary wedge growth, as well as to the development of a foredeep on the margin of the European Platform. Docking of the Outer Western Carpathians accretionary wedge, together with the Central Western Carpathians and Northern Pannonian domain, was accompanied by stretching of the overriding microplate. An orogen parallel and perpendicular extension was associated with the opening and subsidence of the Early and Middle Miocene hinterland (back-arc) basin system that compensated counter-clockwise rotations of the individual crustal fragments of ALCAPA. The Late Miocene development relates to the opening of the Pannonian Basin System. This process was coupled with common stretching of both ALCAPA and Tisza-Dacia Mega-units due to the pull exerted by subduction rollback in front of the Eastern Carpathians. The filling up of the hinterland basin system was associated with thermal subsidence and was followed by the Pliocene tectonic inversion and consequent erosion of the basin system margins, as well as part of the interior.

Identification of the kinase that activates a nonmetazoan STAT gives insights into the evolution of phosphotyrosine-SH2 domain signaling.

Science.gov (United States)

Araki, Tsuyoshi; Kawata, Takefumi; Williams, Jeffrey G

2012-07-10

SH2 domains are integral to many animal signaling pathways. By interacting with specific phosphotyrosine residues, they provide regulatable protein-protein interaction domains. Dictyostelium is the only nonmetazoan with functionally characterized SH2 domains, but the cognate tyrosine kinases are unknown. There are no orthologs of the animal tyrosine kinases, but there are very many tyrosine kinase-like kinases (TKLs), a group of kinases which, despite their family name, are classified mainly as serine-threonine kinases. STATs are transcription factors that dimerize via phosphotyrosine-SH2 domain interactions. STATc is activated by phosphorylation on Tyr922 when cells are exposed to the prestalk inducer differentiation inducing factor (DIF-1), a chlorinated hexaphenone. We show that in a null mutant for Pyk2, a tyrosine-specific TKL, exposure to DIF-1 does not activate STATc. Conversely, overexpression of Pyk2 causes constitutive STATc activation. Pyk2 phosphorylates STATc on Tyr922 in vitro and complexes with STATc both in vitro and in vivo. This demonstration that a TKL directly activates a STAT has significant implications for understanding the evolutionary origins of SH2 domain-phosphotyrosine signaling. It also has mechanistic implications. Our previous work suggested that a predicted constitutive STATc tyrosine kinase activity is counterbalanced in vivo by the DIF-1-regulated activity of PTP3, a Tyr922 phosphatase. Here we show that the STATc-Pyk2 complex is formed constitutively by an interaction between the STATc SH2 domain and phosphotyrosine residues on Pyk2 that are generated by autophosphorylation. Also, as predicted, Pyk2 is constitutively active as a STATc kinase. This observation provides further evidence for this highly atypical, possibly ancestral, STAT regulation mechanism.

A Hybrid Multiobjective Differential Evolution Algorithm and Its Application to the Optimization of Grinding and Classification

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Yalin Wang

2013-01-01

Full Text Available The grinding-classification is the prerequisite process for full recovery of the nonrenewable minerals with both production quality and quantity objectives concerned. Its natural formulation is a constrained multiobjective optimization problem of complex expression since the process is composed of one grinding machine and two classification machines. In this paper, a hybrid differential evolution (DE algorithm with multi-population is proposed. Some infeasible solutions with better performance are allowed to be saved, and they participate randomly in the evolution. In order to exploit the meaningful infeasible solutions, a functionally partitioned multi-population mechanism is designed to find an optimal solution from all possible directions. Meanwhile, a simplex method for local search is inserted into the evolution process to enhance the searching strategy in the optimization process. Simulation results from the test of some benchmark problems indicate that the proposed algorithm tends to converge quickly and effectively to the Pareto frontier with better distribution. Finally, the proposed algorithm is applied to solve a multiobjective optimization model of a grinding and classification process. Based on the technique for order performance by similarity to ideal solution (TOPSIS, the satisfactory solution is obtained by using a decision-making method for multiple attributes.

Domain Walls and Matter-Antimatter Domains in the Early Universe

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Dolgov A.D.

2017-01-01

Full Text Available We suggest a scenario of spontaneous (or dynamical C and CP violation according to which it is possible to generate domains of matter and antimatter separated by cosmologically large distances. Such C(CP violation existed only in the early universe and later it disappeared with the only trace of generated matter and antimatter domains. So this scenario does not suffer from the problem of domain walls. According to this scenario the width of the domain wall should grow exponentially to prevent annihilation at the domain boundaries. Though there is a classical result obtained by Basu and Vilenkin that the width of the wall tends to the one of the stationary solution (constant physical width. That is why we considered thick domain walls in a de Sitter universe following paper by Basu and Vilenkin. However, we were interested not only in stationary solutions found therein, but also investigated the general case of domain wall evolution with time. When the wall thickness parameter, δ0 , is smaller than H−1/2 where H is the Hubble parameter in de Sitter space-time, then the stationary solutions exist, and initial field configurations tend with time to the stationary ones. However, there are no stationary solutions for δ0>H−1/2 We have calculated numerically the rate of the wall expansion in this case and have found that the width of the wall grows exponentially fast for δ0≫H−1 An explanation for the critical value δ0c=H−1/2 is also proposed.

Polyphase tectono-magmatic and fluid history related to mantle exhumation in an ultra-distal rift domain: example of the fossil Platta domain, SE Switzerland

Science.gov (United States)

Epin, Marie-Eva; Manatschal, Gianreto; Amann, Méderic; Lescanne, Marc

2017-04-01

Despite the fact that many studies have investigated mantle exhumation at magma-poor rifted margins, there are still numerous questions concerning the 3D architecture, magmatic, fluid and thermal evolution of these ultra-distal domains that remain unexplained. Indeed, it has been observed in seismic data from ultra-distal magma-poor rifted margins that top basement is heavily structured and complex, however, the processes controlling the morpho-tectonic and magmatic evolution of these domains remain unknown. The aim of this study is to describe the 3D top basement morphology of an exhumed mantle domain, exposed over 200 km2 in the fossil Platta domain in SE Switzerland, and to define the timing and processes controlling its evolution. The examined Platta nappe corresponds to a remnant of the former ultra-distal Adriatic margin of the Alpine Tethys. The rift-structures are relatively well preserved due to the weak Alpine tectonic and metamorphic overprint during the emplacement in the Alpine nappe stack. Detailed mapping of parts of the Platta nappe enabled us to document the top basement architecture of an exhumed mantle domain and to investigate its link to later, rift/oceanic structures, magmatic additions and fluids. Our observations show a polyphase and/or complex: 1) deformation history associated with mantle exhumation along low-angle exhumation faults overprinted by later high-angle normal faults, 2) top basement morphology capped by magmato-sedimentary rocks, 3) tectono-magmatic evolution that includes gabbros, emplaced at deeper levels and subsequently exhumed and overlain by younger extrusive magmatic additions, and 4) fluid history including serpentinization, calcification, hydrothermal vent, rodingitization and spilitization affecting exhumed mantle and associated magmatic rocks. The overall observations provide important information on the temporal and spatial evolution of the tectonic, magmatic and fluid systems controlling the formation of ultra

Domain Wall Evolution in Phase Transforming Oxides

Science.gov (United States)

2015-01-14

Chemically Derived PZT Thin Films on Pt Substrates, Journal of the American Ceramic Society, (09 2014): 2973. doi: 10.1111/jace.13007 Jacob L. Jones...Mari-Ann Einarsrud, D. Johnson. Piezoelectric K0.5Na0.5NbO3 ceramics textured using needle-like K0.5Na0.5NbO3 templates, Journal of the American...Jones. Quantitative comparison between the degree of domain orientation and nonlinear properties of a PZT ceramic during electrical and mechanical

A Convergent Differential Evolution Algorithm with Hidden Adaptation Selection for Engineering Optimization

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Zhongbo Hu

2014-01-01

Full Text Available Many improved differential Evolution (DE algorithms have emerged as a very competitive class of evolutionary computation more than a decade ago. However, few improved DE algorithms guarantee global convergence in theory. This paper developed a convergent DE algorithm in theory, which employs a self-adaptation scheme for the parameters and two operators, that is, uniform mutation and hidden adaptation selection (haS operators. The parameter self-adaptation and uniform mutation operator enhance the diversity of populations and guarantee ergodicity. The haS can automatically remove some inferior individuals in the process of the enhancing population diversity. The haS controls the proposed algorithm to break the loop of current generation with a small probability. The breaking probability is a hidden adaptation and proportional to the changes of the number of inferior individuals. The proposed algorithm is tested on ten engineering optimization problems taken from IEEE CEC2011.

Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

Science.gov (United States)

Culbertson, Jennifer; Kirby, Simon

2016-01-01

The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

Co-evolution of affinity and stability of grafted amyloid-motif domain antibodies.

Science.gov (United States)

Julian, Mark C; Lee, Christine C; Tiller, Kathryn E; Rabia, Lilia A; Day, Evan K; Schick, Arthur J; Tessier, Peter M

2015-10-01

An attractive approach for designing lead antibody candidates is to mimic natural protein interactions by grafting peptide recognition motifs into the complementarity-determining regions (CDRs). We are using this approach to generate single-domain (VH) antibodies specific for amyloid-forming proteins such as the Alzheimer's Aβ peptide. Here, we use random mutagenesis and yeast surface display to improve the binding affinity of a lead VH domain grafted with Aβ residues 33-42 in CDR3. Interestingly, co-selection for improved Aβ binding and VH display on the surface of yeast yields antibody domains with improved affinity and reduced stability. The highest affinity VH domains were strongly destabilized on the surface of yeast as well as unfolded when isolated as autonomous domains. In contrast, stable VH domains with improved affinity were reliably identified using yeast surface display by replacing the display antibody that recognizes a linear epitope tag at the terminus of both folded and unfolded VH domains with a conformational ligand (Protein A) that recognizes a discontinuous epitope on the framework of folded VH domains. Importantly, we find that selection for improved stability using Protein A without simultaneous co-selection for improved Aβ binding leads to strong enrichment for stabilizing mutations that reduce antigen binding. Our findings highlight the importance of simultaneously optimizing affinity and stability to improve the rapid isolation of well-folded and specific antibody fragments. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Application of enhanced discrete differential evolution approach to unit commitment problem

International Nuclear Information System (INIS)

Yuan Xiaohui; Su Anjun; Nie Hao; Yuan Yanbin; Wang Liang

2009-01-01

This paper proposes a discrete binary differential evolution (DBDE) approach to solve the unit commitment problem (UCP). The proposed method is enhanced by priority list based on the unit characteristics and heuristic search strategies to handle constraints effectively. The implementation of the proposed method for UCP consists of three stages. Firstly, the DBDE based on priority list is applied for unit scheduling when neglecting the minimum up/down time constraints. Secondly, repairing strategies are used to handle the minimum up/down time constraints and decommit excess spinning reserve units. Finally, heuristic unit substitution search and gray zone modification algorithm are used to improve optimal solution further. Furthermore, the effects of two crucial parameters on performance of the DBDE for solving UCP are studied as well. To verify the advantages of the method, the proposed method is tested and compared to the other methods on the systems with the number of units in the range of 10-100. Numerical results demonstrate that the proposed method is superior to other methods reported in the literature.

A software for parameter optimization with Differential Evolution Entirely Parallel method

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Konstantin Kozlov

2016-08-01

Full Text Available Summary. Differential Evolution Entirely Parallel (DEEP package is a software for finding unknown real and integer parameters in dynamical models of biological processes by minimizing one or even several objective functions that measure the deviation of model solution from data. Numerical solutions provided by the most efficient global optimization methods are often problem-specific and cannot be easily adapted to other tasks. In contrast, DEEP allows a user to describe both mathematical model and objective function in any programming language, such as R, Octave or Python and others. Being implemented in C, DEEP demonstrates as good performance as the top three methods from CEC-2014 (Competition on evolutionary computation benchmark and was successfully applied to several biological problems. Availability. DEEP method is an open source and free software distributed under the terms of GPL licence version 3. The sources are available at http://deepmethod.sourceforge.net/ and binary packages for Fedora GNU/Linux are provided for RPM package manager at https://build.opensuse.org/project/repositories/home:mackoel:compbio.

Myeloma Cell Dynamics in Response to Treatment Supports a Model of Hierarchical Differentiation and Clonal Evolution.

Science.gov (United States)

Tang, Min; Zhao, Rui; van de Velde, Helgi; Tross, Jennifer G; Mitsiades, Constantine; Viselli, Suzanne; Neuwirth, Rachel; Esseltine, Dixie-Lee; Anderson, Kenneth; Ghobrial, Irene M; San Miguel, Jesús F; Richardson, Paul G; Tomasson, Michael H; Michor, Franziska

2016-08-15

Since the pioneering work of Salmon and Durie, quantitative measures of tumor burden in multiple myeloma have been used to make clinical predictions and model tumor growth. However, such quantitative analyses have not yet been performed on large datasets from trials using modern chemotherapy regimens. We analyzed a large set of tumor response data from three randomized controlled trials of bortezomib-based chemotherapy regimens (total sample size n = 1,469 patients) to establish and validate a novel mathematical model of multiple myeloma cell dynamics. Treatment dynamics in newly diagnosed patients were most consistent with a model postulating two tumor cell subpopulations, "progenitor cells" and "differentiated cells." Differential treatment responses were observed with significant tumoricidal effects on differentiated cells and less clear effects on progenitor cells. We validated this model using a second trial of newly diagnosed patients and a third trial of refractory patients. When applying our model to data of relapsed patients, we found that a hybrid model incorporating both a differentiation hierarchy and clonal evolution best explains the response patterns. The clinical data, together with mathematical modeling, suggest that bortezomib-based therapy exerts a selection pressure on myeloma cells that can shape the disease phenotype, thereby generating further inter-patient variability. This model may be a useful tool for improving our understanding of disease biology and the response to chemotherapy regimens. Clin Cancer Res; 22(16); 4206-14. ©2016 AACR. ©2016 American Association for Cancer Research.

Conical differentiability for evolution variational inequalities

Czech Academy of Sciences Publication Activity Database

Jarušek, Jiří; Krbec, Miroslav; Rao, M.; Sokolowski, J.

2003-01-01

Roč. 193, č. 1 (2003), s. 131-146 ISSN 0022-0396 R&D Projects: GA AV ČR IAA1075005; GA ČR GA201/01/1201 Institutional research plan: CEZ:AV0Z1019905; CEZ:AV0Z1019905 Keywords : parabolic variational inequality * Lipschitz domain * tangent cone Subject RIV: BA - General Mathematics Impact factor: 0.862, year: 2003

A Comparative Study of Differential Evolution, Particle Swarm Optimization, and Evolutionary Algorithms on Numerical Benchmark Problems

DEFF Research Database (Denmark)

Vesterstrøm, Jacob Svaneborg; Thomsen, Rene

2004-01-01

Several extensions to evolutionary algorithms (EAs) and particle swarm optimization (PSO) have been suggested during the last decades offering improved performance on selected benchmark problems. Recently, another search heuristic termed differential evolution (DE) has shown superior performance...... in several real-world applications. In this paper, we evaluate the performance of DE, PSO, and EAs regarding their general applicability as numerical optimization techniques. The comparison is performed on a suite of 34 widely used benchmark problems. The results from our study show that DE generally...... outperforms the other algorithms. However, on two noisy functions, both DE and PSO were outperformed by the EA....

Many-Objective Optimization Using Adaptive Differential Evolution with a New Ranking Method

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Xiaoguang He

2014-01-01

Full Text Available Pareto dominance is an important concept and is usually used in multiobjective evolutionary algorithms (MOEAs to determine the nondominated solutions. However, for many-objective problems, using Pareto dominance to rank the solutions even in the early generation, most obtained solutions are often the nondominated solutions, which results in a little selection pressure of MOEAs toward the optimal solutions. In this paper, a new ranking method is proposed for many-objective optimization problems to verify a relatively smaller number of representative nondominated solutions with a uniform and wide distribution and improve the selection pressure of MOEAs. After that, a many-objective differential evolution with the new ranking method (MODER for handling many-objective optimization problems is designed. At last, the experiments are conducted and the proposed algorithm is compared with several well-known algorithms. The experimental results show that the proposed algorithm can guide the search to converge to the true PF and maintain the diversity of solutions for many-objective problems.

Size evolution of ultrafine particles: Differential signatures of normal and episodic events.

Science.gov (United States)

Joshi, Manish; Khan, Arshad; Anand, S; Sapra, B K

2016-01-01

The effect of fireworks on the aerosol number characteristics of atmosphere was studied for an urban mega city. Measurements were made at 50 m height to assess the local changes around the festival days. Apart from the increase in total number concentration and characteristic accumulation mode, short-term increase of ultrafine particle concentration was noted. Total number concentration varies an order of magnitude during the measurement period in which peak occurs at a frequency of approximately one per day. On integral scale, it seems not possible to distinguish an episodic (e.g. firework bursting induced aerosol emission) and a normal (ambient atmospheric changes) event. However these events could be differentiated on the basis of size evolution analysis around number concentration peaks. The results are discussed relative to past studies and inferences are drawn towards aerosol signatures of firework bursting. The short-term burst in ultrafine particle concentration can pose an inhalation hazard. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gene duplication and the evolution of hemoglobin isoform differentiation in birds.

Science.gov (United States)

Grispo, Michael T; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E; Storz, Jay F

2012-11-02

The majority of bird species co-express two functionally distinct hemoglobin (Hb) isoforms in definitive erythrocytes as follows: HbA (the major adult Hb isoform, with α-chain subunits encoded by the α(A)-globin gene) and HbD (the minor adult Hb isoform, with α-chain subunits encoded by the α(D)-globin gene). The α(D)-globin gene originated via tandem duplication of an embryonic α-like globin gene in the stem lineage of tetrapod vertebrates, which suggests the possibility that functional differentiation between the HbA and HbD isoforms may be attributable to a retained ancestral character state in HbD that harkens back to a primordial, embryonic function. To investigate this possibility, we conducted a combined analysis of protein biochemistry and sequence evolution to characterize the structural and functional basis of Hb isoform differentiation in birds. Functional experiments involving purified HbA and HbD isoforms from 11 different bird species revealed that HbD is characterized by a consistently higher O(2) affinity in the presence of allosteric effectors such as organic phosphates and Cl(-) ions. In the case of both HbA and HbD, analyses of oxygenation properties under the two-state Monod-Wyman-Changeux allosteric model revealed that the pH dependence of Hb-O(2) affinity stems primarily from changes in the O(2) association constant of deoxy (T-state)-Hb. Ancestral sequence reconstructions revealed that the amino acid substitutions that distinguish the adult-expressed Hb isoforms are not attributable to the retention of an ancestral (pre-duplication) character state in the α(D)-globin gene that is shared with the embryonic α-like globin gene.

Gene Duplication and the Evolution of Hemoglobin Isoform Differentiation in Birds*

Science.gov (United States)

Grispo, Michael T.; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E.; Storz, Jay F.

2012-01-01

The majority of bird species co-express two functionally distinct hemoglobin (Hb) isoforms in definitive erythrocytes as follows: HbA (the major adult Hb isoform, with α-chain subunits encoded by the αA-globin gene) and HbD (the minor adult Hb isoform, with α-chain subunits encoded by the αD-globin gene). The αD-globin gene originated via tandem duplication of an embryonic α-like globin gene in the stem lineage of tetrapod vertebrates, which suggests the possibility that functional differentiation between the HbA and HbD isoforms may be attributable to a retained ancestral character state in HbD that harkens back to a primordial, embryonic function. To investigate this possibility, we conducted a combined analysis of protein biochemistry and sequence evolution to characterize the structural and functional basis of Hb isoform differentiation in birds. Functional experiments involving purified HbA and HbD isoforms from 11 different bird species revealed that HbD is characterized by a consistently higher O2 affinity in the presence of allosteric effectors such as organic phosphates and Cl− ions. In the case of both HbA and HbD, analyses of oxygenation properties under the two-state Monod-Wyman-Changeux allosteric model revealed that the pH dependence of Hb-O2 affinity stems primarily from changes in the O2 association constant of deoxy (T-state)-Hb. Ancestral sequence reconstructions revealed that the amino acid substitutions that distinguish the adult-expressed Hb isoforms are not attributable to the retention of an ancestral (pre-duplication) character state in the αD-globin gene that is shared with the embryonic α-like globin gene. PMID:22962007

Optimal Location and Sizing of UPQC in Distribution Networks Using Differential Evolution Algorithm

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Seyed Abbas Taher

2012-01-01

Full Text Available Differential evolution (DE algorithm is used to determine optimal location of unified power quality conditioner (UPQC considering its size in the radial distribution systems. The problem is formulated to find the optimum location of UPQC based on an objective function (OF defined for improving of voltage and current profiles, reducing power loss and minimizing the investment costs considering the OF's weighting factors. Hence, a steady-state model of UPQC is derived to set in forward/backward sweep load flow. Studies are performed on two IEEE 33-bus and 69-bus standard distribution networks. Accuracy was evaluated by reapplying the procedures using both genetic (GA and immune algorithms (IA. Comparative results indicate that DE is capable of offering a nearer global optimal in minimizing the OF and reaching all the desired conditions than GA and IA.

A mixed finite element domain decomposition method for nearly elastic wave equations in the frequency domain

Energy Technology Data Exchange (ETDEWEB)

Feng, Xiaobing [Univ. of Tennessee, Knoxville, TN (United States)

1996-12-31

A non-overlapping domain decomposition iterative method is proposed and analyzed for mixed finite element methods for a sequence of noncoercive elliptic systems with radiation boundary conditions. These differential systems describe the motion of a nearly elastic solid in the frequency domain. The convergence of the iterative procedure is demonstrated and the rate of convergence is derived for the case when the domain is decomposed into subdomains in which each subdomain consists of an individual element associated with the mixed finite elements. The hybridization of mixed finite element methods plays a important role in the construction of the discrete procedure.

Adaptor proteins intersectin 1 and 2 bind similar proline-rich ligands but are differentially recognized by SH2 domain-containing proteins.

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Olga Novokhatska

Full Text Available BACKGROUND: Scaffolding proteins of the intersectin (ITSN family, ITSN1 and ITSN2, are crucial for the initiation stage of clathrin-mediated endocytosis. These proteins are closely related but have implications in distinct pathologies. To determine how these proteins could be separated in certain cell pathways we performed a comparative study of ITSNs. METHODOLOGY/PRINCIPAL FINDINGS: We have shown that endogenous ITSN1 and ITSN2 colocalize and form a complex in cells. A structural comparison of five SH3 domains, which mediated most ITSNs protein-protein interactions, demonstrated a similarity of their ligand-binding sites. We showed that the SH3 domains of ITSN2 bound well-established interactors of ITSN1 as well as newly identified ITSNs protein partners. A search for a novel interacting interface revealed multiple tyrosines that could be phosphorylated in ITSN2. Phosphorylation of ITSN2 isoforms but not ITSN1 short isoform was observed in various cell lines. EGF stimulation of HeLa cells enhanced tyrosine phosphorylation of ITSN2 isoforms and enabled their recognition by the SH2 domains of the Fyn, Fgr and Abl1 kinases, the regulatory subunit of PI3K, the adaptor proteins Grb2 and Crk, and phospholipase C gamma. The SH2 domains mentioned were unable to bind ITSN1 short isoform. CONCLUSIONS/SIGNIFICANCE: Our results indicate that during evolution of vertebrates ITSN2 acquired a novel protein-interaction interface that allows its specific recognition by the SH2 domains of signaling proteins. We propose that these data could be important to understand the functional diversity of paralogous ITSN proteins.

Abstract methods in partial differential equations

CERN Document Server

Carroll, Robert W

2012-01-01

Detailed, self-contained treatment examines modern abstract methods in partial differential equations, especially abstract evolution equations. Suitable for graduate students with some previous exposure to classical partial differential equations. 1969 edition.

Accelerating parameter identification of proton exchange membrane fuel cell model with ranking-based differential evolution

International Nuclear Information System (INIS)

Gong, Wenyin; Cai, Zhihua

2013-01-01

Parameter identification of PEM (proton exchange membrane) fuel cell model is a very active area of research. Generally, it can be treated as a numerical optimization problem with complex nonlinear and multi-variable features. DE (differential evolution), which has been successfully used in various fields, is a simple yet efficient evolutionary algorithm for global numerical optimization. In this paper, with the objective of accelerating the process of parameter identification of PEM fuel cell models and reducing the necessary computational efforts, we firstly present a generic and simple ranking-based mutation operator for the DE algorithm. Then, the ranking-based mutation operator is incorporated into five highly-competitive DE variants to solve the PEM fuel cell model parameter identification problems. The main contributions of this work are the proposed ranking-based DE variants and their application to the parameter identification problems of PEM fuel cell models. Experiments have been conducted by using both the simulated voltage–current data and the data obtained from the literature to validate the performance of our approach. The results indicate that the ranking-based DE methods provide better results with respect to the solution quality, the convergence rate, and the success rate compared with their corresponding original DE methods. In addition, the voltage–current characteristics obtained by our approach are in good agreement with the original voltage–current curves in all cases. - Highlights: • A simple and generic ranking-based mutation operator is presented in this paper. • Several DE (differential evolution) variants are used to solve the parameter identification of PEMFC (proton exchange membrane fuel cells) model. • Results show that our method accelerates the process of parameter identification. • The V–I characteristics are in very good agreement with experimental data

An implementation of differential evolution algorithm for inversion of geoelectrical data

Science.gov (United States)

Balkaya, Çağlayan

2013-11-01

Differential evolution (DE), a population-based evolutionary algorithm (EA) has been implemented to invert self-potential (SP) and vertical electrical sounding (VES) data sets. The algorithm uses three operators including mutation, crossover and selection similar to genetic algorithm (GA). Mutation is the most important operator for the success of DE. Three commonly used mutation strategies including DE/best/1 (strategy 1), DE/rand/1 (strategy 2) and DE/rand-to-best/1 (strategy 3) were applied together with a binomial type crossover. Evolution cycle of DE was realized without boundary constraints. For the test studies performed with SP data, in addition to both noise-free and noisy synthetic data sets two field data sets observed over the sulfide ore body in the Malachite mine (Colorado) and over the ore bodies in the Neem-Ka Thana cooper belt (India) were considered. VES test studies were carried out using synthetically produced resistivity data representing a three-layered earth model and a field data set example from Gökçeada (Turkey), which displays a seawater infiltration problem. Mutation strategies mentioned above were also extensively tested on both synthetic and field data sets in consideration. Of these, strategy 1 was found to be the most effective strategy for the parameter estimation by providing less computational cost together with a good accuracy. The solutions obtained by DE for the synthetic cases of SP were quite consistent with particle swarm optimization (PSO) which is a more widely used population-based optimization algorithm than DE in geophysics. Estimated parameters of SP and VES data were also compared with those obtained from Metropolis-Hastings (M-H) sampling algorithm based on simulated annealing (SA) without cooling to clarify uncertainties in the solutions. Comparison to the M-H algorithm shows that DE performs a fast approximate posterior sampling for the case of low-dimensional inverse geophysical problems.

A Model Parameter Extraction Method for Dielectric Barrier Discharge Ozone Chamber using Differential Evolution

Science.gov (United States)

Amjad, M.; Salam, Z.; Ishaque, K.

2014-04-01

In order to design an efficient resonant power supply for ozone gas generator, it is necessary to accurately determine the parameters of the ozone chamber. In the conventional method, the information from Lissajous plot is used to estimate the values of these parameters. However, the experimental setup for this purpose can only predict the parameters at one operating frequency and there is no guarantee that it results in the highest ozone gas yield. This paper proposes a new approach to determine the parameters using a search and optimization technique known as Differential Evolution (DE). The desired objective function of DE is set at the resonance condition and the chamber parameter values can be searched regardless of experimental constraints. The chamber parameters obtained from the DE technique are validated by experiment.

A Hybrid Differential Evolution and Tree Search Algorithm for the Job Shop Scheduling Problem

Directory of Open Access Journals (Sweden)

Rui Zhang

2011-01-01

Full Text Available The job shop scheduling problem (JSSP is a notoriously difficult problem in combinatorial optimization. In terms of the objective function, most existing research has been focused on the makespan criterion. However, in contemporary manufacturing systems, due-date-related performances are more important because they are essential for maintaining a high service reputation. Therefore, in this study we aim at minimizing the total weighted tardiness in JSSP. Considering the high complexity, a hybrid differential evolution (DE algorithm is proposed for the problem. To enhance the overall search efficiency, a neighborhood property of the problem is discovered, and then a tree search procedure is designed and embedded into the DE framework. According to the extensive computational experiments, the proposed approach is efficient in solving the job shop scheduling problem with total weighted tardiness objective.

Ordinary differential equations with applications in molecular biology.

Science.gov (United States)

Ilea, M; Turnea, M; Rotariu, M

2012-01-01

Differential equations are of basic importance in molecular biology mathematics because many biological laws and relations appear mathematically in the form of a differential equation. In this article we presented some applications of mathematical models represented by ordinary differential equations in molecular biology. The vast majority of quantitative models in cell and molecular biology are formulated in terms of ordinary differential equations for the time evolution of concentrations of molecular species. Assuming that the diffusion in the cell is high enough to make the spatial distribution of molecules homogenous, these equations describe systems with many participating molecules of each kind. We propose an original mathematical model with small parameter for biological phospholipid pathway. All the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. If we reduce the size of the solution region the same small epsilon will result in a different condition number. It is clear that the solution for a smaller region is less difficult. We introduce the mathematical technique known as boundary function method for singular perturbation system. In this system, the small parameter is an asymptotic variable, different from the independent variable. In general, the solutions of such equations exhibit multiscale phenomena. Singularly perturbed problems form a special class of problems containing a small parameter which may tend to zero. Many molecular biology processes can be quantitatively characterized by ordinary differential equations. Mathematical cell biology is a very active and fast growing interdisciplinary area in which mathematical concepts, techniques, and models are applied to a variety of problems in developmental medicine and bioengineering. Among the different modeling approaches, ordinary differential equations (ODE) are particularly important and have led to significant advances

The origin and evolution of Basigin(BSG) gene: A comparative genomic and phylogenetic analysis.

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Zhu, Xinyan; Wang, Shenglan; Shao, Mingjie; Yan, Jie; Liu, Fei

2017-07-01

Basigin (BSG), also known as extracellular matrix metalloproteinase inducer (EMMPRIN) or cluster of differentiation 147 (CD147), plays various fundamental roles in the intercellular recognition involved in immunologic phenomena, differentiation, and development. In this study, we aimed to compare the similarities and differences of BSG among organisms and explore possible evolutionary relationships based on the comparison result. We used the extensive BLAST tool to search the metazoan genomes, N-glycosylation sites, the transmembrane region and other functional sites. We then identified BSG homologs from genomic sequences and analyzed their phylogenetic relationships. We identified that BSG genes exist not only in the vertebrate metazoans but also in the invertebrate metazoans such as Amphioxus B. floridae, D. melanogaster, A. mellifera, S. japonicum, C. gigas, and T. patagoniensis. After sequence analysis, we confirmed that only vertebrate metazoans and Cephalochordate (amphioxus B. floridae) have the classic structure (a signal peptide, two Ig-like domains (IgC2 and IgI), a transmembrane region, and an intracellular domain). The invertebrate metazoans (excluding amphioxus B. floridae) lack the N-terminal signal peptides and IgC2 domain. We then generated a phylogenetic tree, genome organization comparison, and chromosomal disposition analysis based on the biological information obtained from the NCBI and Ensembl databases. Finally, we established the possible evolutionary scenario of the BSG gene, which showed the restricted exon rearrangement that has occurred during evolution, forming the present-day BSG gene. Copyright © 2017 Elsevier Ltd. All rights reserved.

Advanced functional evolution equations and inclusions

CERN Document Server

Benchohra, Mouffak

2015-01-01

This book presents up-to-date results on abstract evolution equations and differential inclusions in infinite dimensional spaces. It covers equations with time delay and with impulses, and complements the existing literature in functional differential equations and inclusions. The exposition is devoted to both local and global mild solutions for some classes of functional differential evolution equations and inclusions, and other densely and non-densely defined functional differential equations and inclusions in separable Banach spaces or in Fréchet spaces. The tools used include classical fixed points theorems and the measure-of non-compactness, and each chapter concludes with a section devoted to notes and bibliographical remarks. This monograph is particularly useful for researchers and graduate students studying pure and applied mathematics, engineering, biology and all other applied sciences.

Adaptive Differential Evolution Approach for Constrained Economic Power Dispatch with Prohibited Operating Zones

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Abdellatif HAMOUDA

2011-12-01

Full Text Available Economic power dispatch (EPD is one of the main tools for optimal operation and planning of modern power systems. To solve effectively the EPD problem, most of the conventional calculus methods rely on the assumption that the fuel cost characteristic of a generating unit is a continuous and convex function, resulting in inaccurate dispatch. This paper presents the design and application of efficient adaptive differential evolution (ADE algorithm for the solution of the economic power dispatch problem, where the non-convex characteristics of the generators, such us prohibited operating zones and ramp rate limits of the practical generator operation are considered. The 26 bus benchmark test system with 6 units having prohibited operating zones and ramp rate limits was used for testing and validation purposes. The results obtained demonstrate the effectiveness of the proposed method for solving the non-convex economic dispatch problem.

Lifetime monogamy and the evolution of eusociality

DEFF Research Database (Denmark)

Boomsma, Jacobus J

2009-01-01

and termites is thus analogous to the evolution of multicellularity. Focusing on lifetime monogamy as a universal precondition for the evolution of obligate eusociality simplifies the theory and may help to resolve controversies about levels of selection and targets of adaptation. The monogamy window...... underlines that cooperative breeding and eusociality are different domains of social evolution, characterized by different sectors of parameter space for Hamilton's rule....

Differential expression of a novel seven transmembrane domain protein in epididymal fat from aged and diabetic mice.

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Yang, H; Egan, J M; Rodgers, B D; Bernier, M; Montrose-Rafizadeh, C

1999-06-01

To identify novel seven transmembrane domain proteins from 3T3-L1 adipocytes, we used PCR to amplify 3T3-L1 adipocyte complementary DNA (cDNA) with primers homologous to the N- and C-termini of pancreatic glucagon-like peptide-1 (GLP-1) receptor. We screened a cDNA library prepared from fully differentiated 3T3-L1 adipocytes using a 500-bp cDNA PCR product probe. Herein describes the isolation and characterization of a 1.6-kb cDNA clone that encodes a novel 298-amino acid protein that we termed TPRA40 (transmembrane domain protein of 40 kDa regulated in adipocytes). TPRA40 has seven putative transmembrane domains and shows little homology with the known GLP-1 receptor or with other G protein-coupled receptors. The levels of TPRA40 mRNA and protein were higher in 3T3-L1 adipocytes than in 3T3-L1 fibroblasts. TPRA40 is present in a number of mouse and human tissues. Interestingly, TPRA40 mRNA levels were significantly increased by 2- to 3-fold in epididymal fat of 24-month-old mice vs. young controls as well as in db/db and ob/ob mice vs. nondiabetic control littermates. No difference in TPRA40 mRNA levels was observed in brain, heart, skeletal muscle, liver, or kidney. Furthermore, no difference in TPRA40 expression was detected in brown fat of ob/ob mice when compared with age-matched controls. Taken together, these data suggest that TPRA40 represents a novel membrane-associated protein whose expression in white adipose tissue is altered with aging and type 2 diabetes.

Poorly Differentiated Thyroid Carcinoma.

Science.gov (United States)

Setia, Namrata; Barletta, Justine A

2014-12-01

Poorly differentiated thyroid carcinoma (PDTC) has been recognized for the past 30 years as an entity showing intermediate differentiation and clinical behavior between well-differentiated thyroid carcinomas (ie, papillary thyroid carcinoma and follicular thyroid carcinoma) and anaplastic thyroid carcinoma; however, there has been considerable controversy around the definition of PDTC. In this review, the evolution in the definition of PDTC, current diagnostic criteria, differential diagnoses, potentially helpful immunohistochemical studies, and molecular alterations are discussed with the aim of highlighting where the diagnosis of PDTC currently stands. Published by Elsevier Inc.

Optimal Decision Fusion for Urban Land-Use/Land-Cover Classification Based on Adaptive Differential Evolution Using Hyperspectral and LiDAR Data

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Yanfei Zhong

2017-08-01

Full Text Available Hyperspectral images and light detection and ranging (LiDAR data have, respectively, the high spectral resolution and accurate elevation information required for urban land-use/land-cover (LULC classification. To combine the respective advantages of hyperspectral and LiDAR data, this paper proposes an optimal decision fusion method based on adaptive differential evolution, namely ODF-ADE, for urban LULC classification. In the ODF-ADE framework the normalized difference vegetation index (NDVI, gray-level co-occurrence matrix (GLCM and digital surface model (DSM are extracted to form the feature map. The three different classifiers of the maximum likelihood classifier (MLC, support vector machine (SVM and multinomial logistic regression (MLR are used to classify the extracted features. To find the optimal weights for the different classification maps, weighted voting is used to obtain the classification result and the weights of each classification map are optimized by the differential evolution algorithm which uses a self-adaptive strategy to obtain the parameter adaptively. The final classification map is obtained after post-processing based on conditional random fields (CRF. The experimental results confirm that the proposed algorithm is very effective in urban LULC classification.

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

Science.gov (United States)

Li, Jing; Hong, Wenxue

2014-12-01

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

Fixation times in differentiation and evolution in the presence of bottlenecks, deserts, and oases.

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Chou, Tom; Wang, Yu

2015-05-07

Cellular differentiation and evolution are stochastic processes that can involve multiple types (or states) of particles moving on a complex, high-dimensional state-space or "fitness" landscape. Cells of each specific type can thus be quantified by their population at a corresponding node within a network of states. Their dynamics across the state-space network involve genotypic or phenotypic transitions that can occur upon cell division, such as during symmetric or asymmetric cell differentiation, or upon spontaneous mutation. Here, we use a general multi-type branching processes to study first passage time statistics for a single cell to appear in a specific state. Our approach readily allows for nonexponentially distributed waiting times between transitions, reflecting, e.g., the cell cycle. For simplicity, we restrict most of our detailed analysis to exponentially distributed waiting times (Poisson processes). We present results for a sequential evolutionary process in which L successive transitions propel a population from a "wild-type" state to a given "terminally differentiated," "resistant," or "cancerous" state. Analytic and numeric results are also found for first passage times across an evolutionary chain containing a node with increased death or proliferation rate, representing a desert/bottleneck or an oasis. Processes involving cell proliferation are shown to be "nonlinear" (even though mean-field equations for the expected particle numbers are linear) resulting in first passage time statistics that depend on the position of the bottleneck or oasis. Our results highlight the sensitivity of stochastic measures to cell division fate and quantify the limitations of using certain approximations (such as the fixed-population and mean-field assumptions) in evaluating fixation times. Published by Elsevier Ltd.

Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans.

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Alisha K Holloway

2007-10-01

Full Text Available Adaptive protein evolution is pervasive in Drosophila. Genomic studies, thus far, have analyzed each protein as a single entity. However, the targets of adaptive events may be localized to particular parts of proteins, such as protein domains or regions involved in protein folding. We compared the population genetic mechanisms driving sequence polymorphism and divergence in defined protein domains and non-domain regions. Interestingly, we find that non-domain regions of proteins are more frequent targets of directional selection. Protein domains are also evolving under directional selection, but appear to be under stronger purifying selection than non-domain regions. Non-domain regions of proteins clearly play a major role in adaptive protein evolution on a genomic scale and merit future investigations of their functional properties.

Managing Software Process Evolution

DEFF Research Database (Denmark)

This book focuses on the design, development, management, governance and application of evolving software processes that are aligned with changing business objectives, such as expansion to new domains or shifting to global production. In the context of an evolving business world, it examines...... the complete software process lifecycle, from the initial definition of a product to its systematic improvement. In doing so, it addresses difficult problems, such as how to implement processes in highly regulated domains or where to find a suitable notation system for documenting processes, and provides...... essential insights and tips to help readers manage process evolutions. And last but not least, it provides a wealth of examples and cases on how to deal with software evolution in practice. Reflecting these topics, the book is divided into three parts. Part 1 focuses on software business transformation...

Cognitive Function, Origin, and Evolution of Musical Emotions

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Leonid Perlovsky

2013-12-01

Full Text Available Cognitive function of music, its origin, and evolution has been a mystery until recently. Here we discuss a theory of a fundamental function of music in cognition and culture. Music evolved in parallel with language. The evolution of language toward a semantically powerful tool required freeing from uncontrolled emotions. Knowledge evolved fast along with language. This created cognitive dissonances, contradictions among knowledge and instincts, which differentiated consciousness. To sustain evolution of language and culture, these contradictions had to be unified. Music was the mechanism of unification. Differentiated emotions are needed for resolving cognitive dissonances. As knowledge has been accumulated, contradictions multiplied and correspondingly more varied emotions had to evolve. While language differentiated psyche, music unified it. Thus the need for refined musical emotions in the process of cultural evolution is grounded in fundamental mechanisms of cognition. This is why today's human mind and cultures cannot exist without today's music.

The evolution of mollusc shells.

Science.gov (United States)

McDougall, Carmel; Degnan, Bernard M

2018-05-01

Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains. Outside a few conserved genes, such as carbonic anhydrase, a so-called "biomineralization toolkit" has yet to be discovered. Despite this, a common suite of protein domains, which are often associated with the extracellular matrix and immunity, appear to have been independently and often uniquely co-opted into the mantle secretomes of different species. The evolvability of the mantle secretome provides a molecular explanation for the evolution and diversity of molluscan shells. These genomic processes are likely to underlie the evolution of other animal biominerals, including coral and echinoderm skeletons. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties. © 2018 Wiley Periodicals, Inc.

Koordinasi Optimal Capacitive Energy Storage (CES dan Kontroler PID Menggunakan Differential Evolution Algorithm (DEA pada Sistem Tenaga Listrik

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Akbar Swandaru

2012-09-01

Full Text Available Peningkatan suplai daya listrik diperlukan untuk memenuhi kebutuhan daya listrik. Generator cenderung beroperasi dalam beban penuh.Hal ini berpengaruh pada keamanan generator dalam operasi sistem tenaga listrik.Salah satu masalah adalah osilasi frekuensi.Bila perubahan beban terjadi, kontroler diperlukan untuk meredam osilasi frekuensi ini.Pada tugas akhir ini diusulkan sebuah koordinasi antara Kontroler Capacitive Energy Storage (CES dan Kontroler PID. CES disini berfungsi untuk membantu kinerja Governor agar meredam osilasi frekuensi dengan cepat. Kontroler CES ini digunakan bersama dengan PID controller yang dioptimalkan dengan  Differential Evolution Algorithm (DEA.

Thermal evolution of magma reservoirs in the shallow crust and incidence on magma differentiation: the St-Jean-du-Doigt layered intrusion (Brittany, France)

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Barboni, M.; Bussy, F.; Ovtcharova, M.; Schoene, B.

2009-12-01

Understanding the emplacement and growth of intrusive bodies in terms of mechanism, duration, thermal evolution and rates are fundamental aspects of crustal evolution. Recent studies show that many plutons grow in several Ma by in situ accretion of discrete magma pulses, which constitute small-scale magmatic reservoirs. The residence time of magmas, and hence their capacities to interact and differentiate, are controlled by the local thermal environment. The latter is highly dependant on 1) the emplacement depth, 2) the magmas and country rock composition, 3) the country rock thermal conductivity, 4) the rate of magma injection and 5) the geometry of the intrusion. In shallow level plutons, where magmas solidify quickly, evidence for magma mixing and/or differentiation processes is considered by many authors to be inherited from deeper levels. We show however that in-situ differentiation and magma interactions occurred within basaltic and felsic sills at shallow depth (0.3 GPa) in the St-Jean-du-Doigt bimodal intrusion, France. Field evidence coupled to high precision zircon U-Pb dating document progressive thermal maturation within the incrementally built laccolith. Early m-thick mafic sills are homogeneous and fine-grained with planar contacts with neighbouring felsic sills; within a minimal 0.5 Ma time span, the system gets warmer, adjacent sills interact and mingle, and mafic sills are differentiating in the top 40 cm of the layer. Rheological and thermal modelling show that observed in-situ differentiation-accumulation processes may be achieved in less than 10 years at shallow depth, provided that (1) the differentiating sills are injected beneath consolidated, yet still warm basalt sills, which act as low conductive insulating screens, (2) the early mafic sills accreted under the roof of the laccolith as a 100m thick top layer within 0.5 My, and (3) subsequent and sustained magmatic activity occurred on a short time scale (years) at an injection rate of ca. 0

Network evolution: rewiring and signatures of conservation in signaling.

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Mark G F Sun

Full Text Available The analysis of network evolution has been hampered by limited availability of protein interaction data for different organisms. In this study, we investigate evolutionary mechanisms in Src Homology 3 (SH3 domain and kinase interaction networks using high-resolution specificity profiles. We constructed and examined networks for 23 fungal species ranging from Saccharomyces cerevisiae to Schizosaccharomyces pombe. We quantify rates of different rewiring mechanisms and show that interaction change through binding site evolution is faster than through gene gain or loss. We found that SH3 interactions evolve swiftly, at rates similar to those found in phosphoregulation evolution. Importantly, we show that interaction changes are sufficiently rapid to exhibit saturation phenomena at the observed timescales. Finally, focusing on the SH3 interaction network, we observe extensive clustering of binding sites on target proteins by SH3 domains and a strong correlation between the number of domains that bind a target protein (target in-degree and interaction conservation. The relationship between in-degree and interaction conservation is driven by two different effects, namely the number of clusters that correspond to interaction interfaces and the number of domains that bind to each cluster leads to sequence specific conservation, which in turn results in interaction conservation. In summary, we uncover several network evolution mechanisms likely to generalize across peptide recognition modules.

Algebraic aspects of evolution partial differential equation arising in the study of constant elasticity of variance model from financial mathematics

Science.gov (United States)

Motsepa, Tanki; Aziz, Taha; Fatima, Aeeman; Khalique, Chaudry Masood

2018-03-01

The optimal investment-consumption problem under the constant elasticity of variance (CEV) model is investigated from the perspective of Lie group analysis. The Lie symmetry group of the evolution partial differential equation describing the CEV model is derived. The Lie point symmetries are then used to obtain an exact solution of the governing model satisfying a standard terminal condition. Finally, we construct conservation laws of the underlying equation using the general theorem on conservation laws.

Building Measures of Instructional Differentiation from Teacher Checklists

Science.gov (United States)

Williams, Ryan; Swanlund, Andrew; Miller, Shazia; Konstantopoulos, Spyros; van der Ploeg, Arie

2012-01-01

Differentiated instruction is commonly believed to be critical to improving the quality and efficiency of teachers' instructional repertoires (Fischer & Rose, 2001; Tomlinson, 2004). Tomlinson (2000) describes differentiation in four domains: content, process, product, and learning environment. Content differentiation involves varying…

Thickness-dependent a_1/a_2 domain evolution in ferroelectric PbTiO_3 films

International Nuclear Information System (INIS)

Li, S.; Zhu, Y.L.; Tang, Y.L.; Liu, Y.; Zhang, S.R.; Wang, Y.J.; Ma, X.L.

2017-01-01

Ferroelectric a_1/a_2 domain structure has great potentials in high dielectric capacitors and tunable microwave devices. Understanding its structure is crucial to better control the domain configurations for future applications. In this paper, PbTiO_3 thin films with variant thicknesses are deposited on (110)-oriented GdScO_3 substrates by Pulsed Laser Deposition (PLD) and investigated by using conventional transmission electron microscopy (TEM) and Cs-corrected Scanning TEM. Contrast analysis and electron diffractions reveal that PbTiO_3 films are domain oriented consisting of a_1/a_2 and a/c domain structure. The a_1/a_2 domains are found to distribute periodically and its width increases with increasing film thickness following square root rule. Cs-corrected STEM imaging demonstrates that the domain walls of a_1/a_2 domain structure have the rotation characteristic of 90° ferroelastic domain wall. The interchange of a_1/a_2 domains induces the formation of vertex domains composed of two 90° and one 180° domain walls. Strains are mainly concentrated on the domain walls. The formation of this complex domain configuration is discussed in terms of the effect of the misfit strain, film thickness and cooling rate. These results provide novel information about a_1/a_2 domain structures and are expected to shed some light on modulating a_1/a_2 ferroelectric domain patterns in the design of ferroelectric-based devices.

Using some results about the Lie evolution of differential operators to obtain the Fokker-Planck equation for non-Hamiltonian dynamical systems of interest

Science.gov (United States)

Bianucci, Marco

2018-05-01

Finding the generalized Fokker-Planck Equation (FPE) for the reduced probability density function of a subpart of a given complex system is a classical issue of statistical mechanics. Zwanzig projection perturbation approach to this issue leads to the trouble of resumming a series of commutators of differential operators that we show to correspond to solving the Lie evolution of first order differential operators along the unperturbed Liouvillian of the dynamical system of interest. In this paper, we develop in a systematic way the procedure to formally solve this problem. In particular, here we show which the basic assumptions are, concerning the dynamical system of interest, necessary for the Lie evolution to be a group on the space of first order differential operators, and we obtain the coefficients of the so-evolved operators. It is thus demonstrated that if the Liouvillian of the system of interest is not a first order differential operator, in general, the FPE structure breaks down and the master equation contains all the power of the partial derivatives, up to infinity. Therefore, this work shed some light on the trouble of the ubiquitous emergence of both thermodynamics from microscopic systems and regular regression laws at macroscopic scales. However these results are very general and can be applied also in other contexts that are non-Hamiltonian as, for example, geophysical fluid dynamics, where important events, like El Niño, can be considered as large time scale phenomena emerging from the observation of few ocean degrees of freedom of a more complex system, including the interaction with the atmosphere.

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

Science.gov (United States)

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

2018-03-01

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

Differential rates of genic and chromosomal evolution in bats of the family Rhinolophidae.

Science.gov (United States)

Qumsiyeh, M B; Owen, R D; Chesser, R K

1988-06-01

Data for nondifferentially stained chromosomes from 10 species of Rhinolophus (Chiroptera: Rhinolophidae) suggest a conserved chromosomal evolution. G-banded chromosomes for three well differentiated species (Rhinolophus hipposideros, Rhinolophus blasii, and Rhinolophus acuminatus) corroborate a low level of gross chromosomal rearrangements. Additionally, a comparison between G-banded chromosomes of Rhinolophus (Rhinolophidae) and Hipposideros (Hipposideridae) suggests extreme conservatism in chromosomal arms between these two distantly related groups. On the other hand, we report extensive genic divergence as assayed by starch gel electrophoresis among these 10 species, and between Rhinolophus and two hipposiderid genera (Hipposideros and Aselliscus). The present chromosomal data are not sufficient for phylogenetic analysis. Phylogenies based on electrophoretic data are in many aspects discordant with those based on the classical morphological criteria. Different (and as yet not clearly understood) evolutionary forces affecting chromosomal, morphologic, and electrophoretic variation may be the reason for the apparent lack of concordance in these independent data sets.

T cell activation and differentiation is modulated by a CD6 domain 1 antibody Itolizumab.

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Usha Bughani

Full Text Available CD6 is associated with T-cell modulation and is implicated in several autoimmune diseases. We previously demonstrated that Itolizumab, a CD6 domain 1 (CD6D1 specific humanized monoclonal antibody, inhibited the proliferation and cytokine production by T lymphocytes stimulated with anti-CD3 antibody or when co-stimulated with ALCAM. Aberrant IL-17 producing CD4+ helper T-cells (Th17 have been identified as pivotal for the pathogenesis of certain inflammatory autoimmune disorders, including psoriasis. Itolizumab has demonstrated efficacy in human diseases known to have an IL-17 driven pathogenesis. Here, in in vitro experiments we show that by day 3 of human PBMC activation using anti-CD3 and anti-CD28 co-stimulation in a Th17 polarizing milieu, 15-35% of CD4+ T-cells overexpress CD6 and there is an establishment of differentiated Th17 cells. Addition of Itolizumab reduces the activation and differentiation of T cells to Th17 cells and decreases production of IL-17. These effects are associated with the reduction of key transcription factors pSTAT3 and RORγT. Further, transcription analysis studies in these conditions indicate that Itolizumab suppressed T cell activation by primarily reducing cell cycle, DNA transcription and translation associated genes. To understand the mechanism of this inhibition, we evaluated the effect of this anti-human CD6D1 mAb on ALCAM-CD6 as well as TCR-mediated T cell activation. We show that Itolizumab but not its F(ab'2 fragment directly inhibits CD6 receptor hyper-phosphorylation and leads to subsequent decrease in associated ZAP70 kinase and docking protein SLP76. Since Itolizumab binds to CD6 expressed only on human and chimpanzee, we developed an antibody binding specifically to mouse CD6D1. This antibody successfully ameliorated the incidence of experimental autoimmune encephalitis in the mice model. These results position CD6 as a key molecule in sustaining the activation and differentiation of T cells and an

KCNK10, a Tandem Pore Domain Potassium Channel, Is a Regulator of Mitotic Clonal Expansion during the Early Stage of Adipocyte Differentiation

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Makoto Nishizuka

2014-12-01

Full Text Available KCNK10, a member of tandem pore domain potassium channel family, gives rise to leak K+ currents. It plays important roles in stabilizing the negative resting membrane potential and in counterbalancing depolarization. We previously demonstrated that kcnk10 expression is quickly elevated during the early stage of adipogenesis of 3T3-L1 cells and that reduction of kcnk10 expression inhibits adipocyte differentiation. However, the molecular mechanism of KCNK10 in adipocyte differentiation remains unclear. Here we revealed that kcnk10 is induced by 3-isobutyl-1-methylxanthine, a cyclic nucleotide phosphodiesterase inhibitor and a potent inducer of adipogenesis, during the early stage of adipocyte differentiation. We also demonstrated that KCNK10 functions as a positive regulator of mitotic clonal expansion (MCE, a necessary process for terminal differentiation. The reduction of kcnk10 expression repressed the expression levels of CCAAT/enhancer-binding protein β (C/EBPβ and C/EBPδ as well as the phosphorylation level of Akt during the early phase of adipogenesis. In addition, knockdown of kcnk10 expression suppressed insulin-induced Akt phosphorylation. These results indicate that KCNK10 contributes to the regulation of MCE through the control of C/EBPβ and C/EBPδ expression and insulin signaling.

Evolution of plant P-type ATPases

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Christian N.S. Pedersen

2012-02-01

Full Text Available Five organisms having completely sequenced genomes and belonging to all major branches of green plants (Viridiplantae were analyzed with respect to their content of P-type ATPases encoding genes. These were the chlorophytes Ostreococcus tauria and Chlamydomonas reinhardtii, and the streptophytes Physcomitrella patens (a moss, Selaginella moellendorffii (a primitive vascular plant, and Arabidopsis thaliana (a model flowering plant. Each organism contained sequences for all five subfamilies of P-type ATPases. Our analysis demonstrates when specific subgroups of P-type ATPases disappeared in the evolution of Angiosperms. Na/K-pump related P2C ATPases were lost with the evolution of streptophytes whereas Na+ or K+ pumping P2D ATPases and secretory pathway Ca2+-ATPases remained until mosses. An N-terminally located calmodulin binding domain in P2B ATPases can only be detected in pumps from Streptophytae, whereas, like in animals, a C-terminally localized calmodulin binding domain might be present in chlorophyte P2B Ca2+-ATPases. Chlorophyte genomes encode P3A ATPases resembling protist plasma membrane H+-ATPases and a C-terminal regulatory domain is missing. The complete inventory of P-type ATPases in the major branches of Viridiplantae is an important starting point for elucidating the evolution in plants of these important pumps.

Differential Evolution Based IDWNN Controller for Fault Ride-Through of Grid-Connected Doubly Fed Induction Wind Generators.

Science.gov (United States)

Manonmani, N; Subbiah, V; Sivakumar, L

2015-01-01

The key objective of wind turbine development is to ensure that output power is continuously increased. It is authenticated that wind turbines (WTs) supply the necessary reactive power to the grid at the time of fault and after fault to aid the flowing grid voltage. At this juncture, this paper introduces a novel heuristic based controller module employing differential evolution and neural network architecture to improve the low-voltage ride-through rate of grid-connected wind turbines, which are connected along with doubly fed induction generators (DFIGs). The traditional crowbar-based systems were basically applied to secure the rotor-side converter during the occurrence of grid faults. This traditional controller is found not to satisfy the desired requirement, since DFIG during the connection of crowbar acts like a squirrel cage module and absorbs the reactive power from the grid. This limitation is taken care of in this paper by introducing heuristic controllers that remove the usage of crowbar and ensure that wind turbines supply necessary reactive power to the grid during faults. The controller is designed in this paper to enhance the DFIG converter during the grid fault and this controller takes care of the ride-through fault without employing any other hardware modules. The paper introduces a double wavelet neural network controller which is appropriately tuned employing differential evolution. To validate the proposed controller module, a case study of wind farm with 1.5 MW wind turbines connected to a 25 kV distribution system exporting power to a 120 kV grid through a 30 km 25 kV feeder is carried out by simulation.

Differential Evolution Based IDWNN Controller for Fault Ride-Through of Grid-Connected Doubly Fed Induction Wind Generators

Directory of Open Access Journals (Sweden)

N. Manonmani

2015-01-01

Full Text Available The key objective of wind turbine development is to ensure that output power is continuously increased. It is authenticated that wind turbines (WTs supply the necessary reactive power to the grid at the time of fault and after fault to aid the flowing grid voltage. At this juncture, this paper introduces a novel heuristic based controller module employing differential evolution and neural network architecture to improve the low-voltage ride-through rate of grid-connected wind turbines, which are connected along with doubly fed induction generators (DFIGs. The traditional crowbar-based systems were basically applied to secure the rotor-side converter during the occurrence of grid faults. This traditional controller is found not to satisfy the desired requirement, since DFIG during the connection of crowbar acts like a squirrel cage module and absorbs the reactive power from the grid. This limitation is taken care of in this paper by introducing heuristic controllers that remove the usage of crowbar and ensure that wind turbines supply necessary reactive power to the grid during faults. The controller is designed in this paper to enhance the DFIG converter during the grid fault and this controller takes care of the ride-through fault without employing any other hardware modules. The paper introduces a double wavelet neural network controller which is appropriately tuned employing differential evolution. To validate the proposed controller module, a case study of wind farm with 1.5 MW wind turbines connected to a 25 kV distribution system exporting power to a 120 kV grid through a 30 km 25 kV feeder is carried out by simulation.

Optimal Control for Stochastic Delay Evolution Equations

Energy Technology Data Exchange (ETDEWEB)

Meng, Qingxin, E-mail: mqx@hutc.zj.cn [Huzhou University, Department of Mathematical Sciences (China); Shen, Yang, E-mail: skyshen87@gmail.com [York University, Department of Mathematics and Statistics (Canada)

2016-08-15

In this paper, we investigate a class of infinite-dimensional optimal control problems, where the state equation is given by a stochastic delay evolution equation with random coefficients, and the corresponding adjoint equation is given by an anticipated backward stochastic evolution equation. We first prove the continuous dependence theorems for stochastic delay evolution equations and anticipated backward stochastic evolution equations, and show the existence and uniqueness of solutions to anticipated backward stochastic evolution equations. Then we establish necessary and sufficient conditions for optimality of the control problem in the form of Pontryagin’s maximum principles. To illustrate the theoretical results, we apply stochastic maximum principles to study two examples, an infinite-dimensional linear-quadratic control problem with delay and an optimal control of a Dirichlet problem for a stochastic partial differential equation with delay. Further applications of the two examples to a Cauchy problem for a controlled linear stochastic partial differential equation and an optimal harvesting problem are also considered.

Functional Properties at Domain Walls in BiFeO3: Electrical, Magnetic, and Structural investigations

Science.gov (United States)

He, Qing; Yang, C.-H.; Yu, P.; Gajek, M.; Seidel, J.; Ramesh, R.; Wang, F.; Chu, Y.-H.; Martin, L. W.; Spaldin, N.; Rother, A.

2009-03-01

BiFeO3 (BFO) is a widely studied robust ferroelectric, antiferromagnetic multiferroic. Conducting-atomic force microscopy studies reveal the presence of enhanced conductivity at certain types of domain walls in BFO. We have completed detailed TEM studies of the physical structure at these domain walls as well as in-depth DFT calculations of the evolution of electronic structure at these domain walls. These studies reveal two major contributions to the observed conduction: the formation of an electrostatic potential at the domain walls as well as a structurally-driven change in the electronic structure (i.e., a lower band gap locally) at the domain walls. We will discuss the use of optical characterization techniques as a way of probing this change in electronic structure at domain walls as well as detailed IV characterization both in atmospheric and UHV environments. Finally, the evolution of magnetism at these domain walls has been studied through the use of photoemission measurements. Initial findings point to a significant change in the magnetic order at these domain walls in BFO.

Study of domain structure in segmented polyether polyurethaneureas by PAT

International Nuclear Information System (INIS)

Yin Chuanyuan; Xu Weizheng; Gu Qingchao

1990-01-01

The domain structure of segmented polyether polyurethaneureas is investigated by means of positron annihilation technique, small angle X-ray scattering and differential scanning calorimetry. The experimental results show that the decrease of domain volume and free volume results from the increase of hard segment contents, and that the increase of domain volume and free volume results from the increase of molecular weight of soft segments

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers.

Science.gov (United States)

Finnerty, John R; Mazza, Maureen E; Jezewski, Peter A

2009-01-20

Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx) in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal), were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

Domain duplication, divergence, and loss events in vertebrate Msx paralogs reveal phylogenomically informed disease markers

Directory of Open Access Journals (Sweden)

Finnerty John R

2009-01-01

Full Text Available Abstract Background Msx originated early in animal evolution and is implicated in human genetic disorders. To reconstruct the functional evolution of Msx and inform the study of human mutations, we analyzed the phylogeny and synteny of 46 metazoan Msx proteins and tracked the duplication, diversification and loss of conserved motifs. Results Vertebrate Msx sequences sort into distinct Msx1, Msx2 and Msx3 clades. The sister-group relationship between MSX1 and MSX2 reflects their derivation from the 4p/5q chromosomal paralogon, a derivative of the original "MetaHox" cluster. We demonstrate physical linkage between Msx and other MetaHox genes (Hmx, NK1, Emx in a cnidarian. Seven conserved domains, including two Groucho repression domains (N- and C-terminal, were present in the ancestral Msx. In cnidarians, the Groucho domains are highly similar. In vertebrate Msx1, the N-terminal Groucho domain is conserved, while the C-terminal domain diverged substantially, implying a novel function. In vertebrate Msx2 and Msx3, the C-terminal domain was lost. MSX1 mutations associated with ectodermal dysplasia or orofacial clefting disorders map to conserved domains in a non-random fashion. Conclusion Msx originated from a MetaHox ancestor that also gave rise to Tlx, Demox, NK, and possibly EHGbox, Hox and ParaHox genes. Duplication, divergence or loss of domains played a central role in the functional evolution of Msx. Duplicated domains allow pleiotropically expressed proteins to evolve new functions without disrupting existing interaction networks. Human missense sequence variants reside within evolutionarily conserved domains, likely disrupting protein function. This phylogenomic evaluation of candidate disease markers will inform clinical and functional studies.

Distribution and evolution of stable single α-helices (SAH domains in myosin motor proteins.

Directory of Open Access Journals (Sweden)

Dominic Simm

Full Text Available Stable single-alpha helices (SAHs are versatile structural elements in many prokaryotic and eukaryotic proteins acting as semi-flexible linkers and constant force springs. This way SAH-domains function as part of the lever of many different myosins. Canonical myosin levers consist of one or several IQ-motifs to which light chains such as calmodulin bind. SAH-domains provide flexibility in length and stiffness to the myosin levers, and may be particularly suited for myosins working in crowded cellular environments. Although the function of the SAH-domains in human class-6 and class-10 myosins has well been characterised, the distribution of the SAH-domain in all myosin subfamilies and across the eukaryotic tree of life remained elusive. Here, we analysed the largest available myosin sequence dataset consisting of 7919 manually annotated myosin sequences from 938 species representing all major eukaryotic branches using the SAH-prediction algorithm of Waggawagga, a recently developed tool for the identification of SAH-domains. With this approach we identified SAH-domains in more than one third of the supposed 79 myosin subfamilies. Depending on the myosin class, the presence of SAH-domains can range from a few to almost all class members indicating complex patterns of independent and taxon-specific SAH-domain gain and loss.

The early thermal evolution of Mars

Science.gov (United States)

Bhatia, G. K.; Sahijpal, S.

2016-01-01

Hf-W isotopic systematics of Martian meteorites have provided evidence for the early accretion and rapid core formation of Mars. We present the results of numerical simulations performed to study the early thermal evolution and planetary scale differentiation of Mars. The simulations are confined to the initial 50 Myr (Ma) of the formation of solar system. The accretion energy produced during the growth of Mars and the decay energy due to the short-lived radio-nuclides 26Al, 60Fe, and the long-lived nuclides, 40K, 235U, 238U, and 232Th are incorporated as the heat sources for the thermal evolution of Mars. During the core-mantle differentiation of Mars, the molten metallic blobs were numerically moved using Stoke's law toward the center with descent velocity that depends on the local acceleration due to gravity. Apart from the accretion and the radioactive heat energies, the gravitational energy produced during the differentiation of Mars and the associated heat transfer is also parametrically incorporated in the present work to make an assessment of its contribution to the early thermal evolution of Mars. We conclude that the accretion energy alone cannot produce widespread melting and differentiation of Mars even with an efficient consumption of the accretion energy. This makes 26Al the prime source for the heating and planetary scale differentiation of Mars. We demonstrate a rapid accretion and core-mantle differentiation of Mars within the initial ~1.5 Myr. This is consistent with the chronological records of Martian meteorites.

Artificial boundary conditions for certain evolution PDEs with cubic nonlinearity for non-compactly supported initial data

Science.gov (United States)

Vaibhav, V.

2011-04-01

The paper addresses the problem of constructing non-reflecting boundary conditions for two types of one dimensional evolution equations, namely, the cubic nonlinear Schrödinger (NLS) equation, ∂tu+Lu-iχ|u|2u=0 with L≡-i∂x2, and the equation obtained by letting L≡∂x3. The usual restriction of compact support of the initial data is relaxed by allowing it to have a constant amplitude along with a linear phase variation outside a compact domain. We adapt the pseudo-differential approach developed by Antoine et al. (2006) [5] for the NLS equation to the second type of evolution equation, and further, extend the scheme to the aforementioned class of initial data for both of the equations. In addition, we discuss efficient numerical implementation of our scheme and produce the results of several numerical experiments demonstrating its effectiveness.

Functional analysis of SH3 domain containing ring finger 2 during the myogenic differentiation of quail myoblast cells

Directory of Open Access Journals (Sweden)

Si Won Kim

2017-08-01

Full Text Available Objective Owing to the public availability of complete genome sequences, including avian species, massive bioinformatics analyses may be conducted for computational gene prediction and the identification of gene regulatory networks through various informatics tools. However, to evaluate the biofunctional activity of a predicted target gene, in vivo and in vitro functional genomic analyses should be a prerequisite. Methods Due to a lack of quail genomic sequence information, we first identified the partial genomic structure and sequences of the quail SH3 domain containing ring finger 2 (SH3RF2 gene. Subsequently, SH3RF2 was knocked out using clustered regularly interspaced short palindromic repeat/Cas9 technology and single cell-derived SH3RF2 mutant sublines were established to study the biofunctional activity of SH3RF2 in quail myoblast (QM7 cells during muscle differentiation. Results Through a T7 endonuclease I assay and genotyping analysis, we established an SH3RF2 knockout (KO QM7#4 subline with 61 and 155 nucleotide deletion mutations in SH3RF2. After the induction of myotube differentiation, the expression profiles were analyzed and compared between regular QM7 and SH3RF2 KO QM7#4 cells by global RNA sequencing and bioinformatics analysis. Conclusion We did not detect any statistically significant role of SH3RF2 during myotube differentiation in QM7 myoblast cells. However, additional experiments are necessary to examine the biofunctional activity of SH3RF2 in cell proliferation and muscle growth.

Gravitational waves from domain walls and their implications

Directory of Open Access Journals (Sweden)

Kazunori Nakayama

2017-07-01

Full Text Available We evaluate the impact of domain-wall annihilation on the currently ongoing and planned gravitational wave experiments, including a case in which domain walls experience a frictional force due to interactions with the ambient plasma. We show the sensitivity reach in terms of physical parameters, namely, the wall tension and the annihilation temperature. We find that a Higgs portal scalar, which stabilizes the Higgs potential at high energy scales, can form domain walls whose annihilation produces a large amount of gravitational waves within the reach of the advanced LIGO experiment (O5. Domain wall annihilation can also generate baryon asymmetry if the scalar is coupled to either SU(2L gauge fields or the (B−L current. This is a variant of spontaneous baryogenesis, but it naturally avoids the isocurvature constraint due to the scaling behavior of the domain-wall evolution. We delineate the parameter space where the domain-wall baryogenesis works successfully and discuss its implications for the gravitational wave experiments.

Genome-Wide Identification and Evolution of HECT Genes in Soybean

Directory of Open Access Journals (Sweden)

Xianwen Meng

2015-04-01

Full Text Available Proteins containing domains homologous to the E6-associated protein (E6-AP carboxyl terminus (HECT are an important class of E3 ubiquitin ligases involved in the ubiquitin proteasome pathway. HECT-type E3s play crucial roles in plant growth and development. However, current understanding of plant HECT genes and their evolution is very limited. In this study, we performed a genome-wide analysis of the HECT domain-containing genes in soybean. Using high-quality genome sequences, we identified 19 soybean HECT genes. The predicted HECT genes were distributed unevenly across 15 of 20 chromosomes. Nineteen of these genes were inferred to be segmentally duplicated gene pairs, suggesting that in soybean, segmental duplications have made a significant contribution to the expansion of the HECT gene family. Phylogenetic analysis showed that these HECT genes can be divided into seven groups, among which gene structure and domain architecture was relatively well-conserved. The Ka/Ks ratios show that after the duplication events, duplicated HECT genes underwent purifying selection. Moreover, expression analysis reveals that 15 of the HECT genes in soybean are differentially expressed in 14 tissues, and are often highly expressed in the flowers and roots. In summary, this work provides useful information on which further functional studies of soybean HECT genes can be based.

Ordinary differential equations introduction to the theory of ordinary differential equations in the real domain

CERN Document Server

Kurzweil, J

1986-01-01

The author, Professor Kurzweil, is one of the world's top experts in the area of ordinary differential equations - a fact fully reflected in this book. Unlike many classical texts which concentrate primarily on methods of integration of differential equations, this book pursues a modern approach: the topic is discussed in full generality which, at the same time, permits us to gain a deep insight into the theory and to develop a fruitful intuition. The basic framework of the theory is expanded by considering further important topics like stability, dependence of a solution on a parameter, Car

Noise Analysis of Single-Ended Input Differential Amplifier using Stochastic Differential Equation

OpenAIRE

Tarun Kumar Rawat; Abhirup Lahiri; Ashish Gupta

2008-01-01

In this paper, we analyze the effect of noise in a single- ended input differential amplifier working at high frequencies. Both extrinsic and intrinsic noise are analyzed using time domain method employing techniques from stochastic calculus. Stochastic differential equations are used to obtain autocorrelation functions of the output noise voltage and other solution statistics like mean and variance. The analysis leads to important design implications and suggests changes in the device parame...

Calibration of three-axis magnetometers with differential evolution algorithm

International Nuclear Information System (INIS)

Pang, Hongfeng; Zhang, Qi; Wang, Wei; Wang, Junya; Li, Ji; Luo, Shitu; Wan, Chengbiao; Chen, Dixiang; Pan, Mengchun; Luo, Feilu

2013-01-01

The accuracy of three-axis magnetometers is influenced by different scale and bias of each axis and nonorthogonality between axes. One limitation of traditional iteration methods is that initial parameters influence the calibration, thus leading to the local optimal or wrong results. In this paper, a new method is proposed to calibrate three-axis magnetometers. To employ this method, a nonmagnetic rotation platform, a proton magnetometer, a DM-050 three-axis magnetometer and the differential evolution (DE) algorithm are used. The performance of this calibration method is analyzed with simulation and experiment. In simulation, the calibration results of DE, unscented Kalman filter (UKF), recursive least squares (RLS) and genetic algorithm (GA) are compared. RMS error using DE is least, which is reduced from 81.233 nT to 1.567 nT. Experimental results show that comparing with UKF, RLS and GA, the DE algorithm has not only the least calibration error but also the best robustness. After calibration, RMS error is reduced from 68.914 nT to 2.919 nT. In addition, the DE algorithm is not sensitive to initial parameters, which is an important advantage compared with traditional iteration algorithms. The proposed algorithm can avoid the troublesome procedure to select suitable initial parameters, thus it can improve the calibration performance of three-axis magnetometers. - Highlights: • The calibration results and robustness of UKF, GA, RLS and DE algorithm are analyzed. • Calibration error of DE is the least in simulation and experiment. • Comparing with traditional calibration algorithms, DE is not sensitive to initial parameters. • It can improve the calibration performance of three-axis magnetometers

Aerobic exercise training differentially affects ACE C- and N-domain activities in humans: Interactions with ACE I/D polymorphism and association with vascular reactivity.

Science.gov (United States)

Alves, Cléber Rene; Fernandes, Tiago; Lemos, José Ribeiro; Magalhães, Flávio de Castro; Trombetta, Ivani Credidio; Alves, Guilherme Barreto; Mota, Glória de Fátima Alves da; Dias, Rodrigo Gonçalves; Pereira, Alexandre Costa; Krieger, José Eduardo; Negrão, Carlos Eduardo; Oliveira, Edilamar Menezes

2018-01-01

genotype. AET differentially affects the ACE C- and N-domain activities, and the N-domain activity is dependent on ACE polymorphism.

The evolution of the DLK1-DIO3 imprinted domain in mammals.

Directory of Open Access Journals (Sweden)

Carol A Edwards

2008-06-01

Full Text Available A comprehensive, domain-wide comparative analysis of genomic imprinting between mammals that imprint and those that do not can provide valuable information about how and why imprinting evolved. The imprinting status, DNA methylation, and genomic landscape of the Dlk1-Dio3 cluster were determined in eutherian, metatherian, and prototherian mammals including tammar wallaby and platypus. Imprinting across the whole domain evolved after the divergence of eutherian from marsupial mammals and in eutherians is under strong purifying selection. The marsupial locus at 1.6 megabases, is double that of eutherians due to the accumulation of LINE repeats. Comparative sequence analysis of the domain in seven vertebrates determined evolutionary conserved regions common to particular sub-groups and to all vertebrates. The emergence of Dlk1-Dio3 imprinting in eutherians has occurred on the maternally inherited chromosome and is associated with region-specific resistance to expansion by repetitive elements and the local introduction of noncoding transcripts including microRNAs and C/D small nucleolar RNAs. A recent mammal-specific retrotransposition event led to the formation of a completely new gene only in the eutherian domain, which may have driven imprinting at the cluster.

Socio-cognitive influences on the domain-specificity of prosocial behavior in the second year.

Science.gov (United States)

Kärtner, Joscha; Schuhmacher, Nils; Collard, Jenny

2014-11-01

The main aim of this study was to explain the domain-specificity of early prosocial behavior in different domains (i.e., helping, comforting, and cooperation) by simultaneously assessing specific socio-cognitive factors (i.e., self-other-differentiation and joint attentional skills) that were hypothesized to be differentially related to the three domains of prosocial behavior. Based on a longitudinal study design, observational and parental report data were collected when toddlers (N=42) from German urban middle-class families were 15 and 18 months of age. At 15 months, regression analyses indicated differential relationships between socio-cognitive development and prosocial behavior (i.e., joint attentional skills were positively related with helping and, as hypothesized, both joint attentional skills and self-other differentiation were positively related with cooperation). Furthermore, self-other differentiation at 15 months predicted increases in coordination between 15 and 18 months. Finally, between 15 and 18 months, parental reports of socio-cognitive measures increased significantly while behavioral measures of both socio-cognitive concepts and prosocial behavior were stable across time. In sum, these results support the theoretical assumption of domain-specific socio-cognitive influences that constitute differential development of prosocial behavior. Implications of the results for theory and future studies are discussed from different perspectives with a focus on an interference interpretation calling for the integration of socialization approaches to the study of prosocial development. Copyright © 2014 Elsevier Inc. All rights reserved.

Image-domain full waveform inversion

KAUST Repository

Zhang, Sanzong

2013-08-20

The main difficulty with the data-domain full waveform inversion (FWI) is that it tends to get stuck in the local minima associated with the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in velocity model. To reduce this nonlinearity, we define the image-domain objective function to minimize the difference of the suboffset-domain common image gathers (CIGs) obtained by migrating the observed data and the calculated data. The derivation shows that the gradient of this new objective function is the combination of the gradient of the conventional FWI and the image-domain differential semblance optimization (DSO). Compared to the conventional FWI, the imagedomain FWI is immune to cycle skipping problems by smearing the nonzero suboffset images along wavepath. It also can avoid the edge effects and the gradient artifacts that are inherent in DSO due to the falsely over-penalized focused images. This is achieved by subtracting the focused image associated with the calculated data from the unfocused image associated with the observed data in the image-domain misfit function. The numerical results of the Marmousi model show that image-domain FWI is less sensitive the initial model than the conventional FWI. © 2013 SEG.

Image-domain full waveform inversion

KAUST Repository

Zhang, Sanzong; Schuster, Gerard T.

2013-01-01

The main difficulty with the data-domain full waveform inversion (FWI) is that it tends to get stuck in the local minima associated with the waveform misfit function. This is because the waveform misfit function is highly nonlinear with respect to changes in velocity model. To reduce this nonlinearity, we define the image-domain objective function to minimize the difference of the suboffset-domain common image gathers (CIGs) obtained by migrating the observed data and the calculated data. The derivation shows that the gradient of this new objective function is the combination of the gradient of the conventional FWI and the image-domain differential semblance optimization (DSO). Compared to the conventional FWI, the imagedomain FWI is immune to cycle skipping problems by smearing the nonzero suboffset images along wavepath. It also can avoid the edge effects and the gradient artifacts that are inherent in DSO due to the falsely over-penalized focused images. This is achieved by subtracting the focused image associated with the calculated data from the unfocused image associated with the observed data in the image-domain misfit function. The numerical results of the Marmousi model show that image-domain FWI is less sensitive the initial model than the conventional FWI. © 2013 SEG.

Polygons of differential equations for finding exact solutions

International Nuclear Information System (INIS)

Kudryashov, Nikolai A.; Demina, Maria V.

2007-01-01

A method for finding exact solutions of nonlinear differential equations is presented. Our method is based on the application of polygons corresponding to nonlinear differential equations. It allows one to express exact solutions of the equation studied through solutions of another equation using properties of the basic equation itself. The ideas of power geometry are used and developed. Our approach has a pictorial interpretation, which is illustrative and effective. The method can be also applied for finding transformations between solutions of differential equations. To demonstrate the method application exact solutions of several equations are found. These equations are: the Korteveg-de Vries-Burgers equation, the generalized Kuramoto-Sivashinsky equation, the fourth-order nonlinear evolution equation, the fifth-order Korteveg-de Vries equation, the fifth-order modified Korteveg-de Vries equation and the sixth-order nonlinear evolution equation describing turbulent processes. Some new exact solutions of nonlinear evolution equations are given

Birth and upgrowth of the Hox topological domains during evolution

NARCIS (Netherlands)

Deschamps, Jacqueline

The recently discovered chromatin compartments called topologically associating domains (TADs) are essential for the three-dimensional organization of regulatory interactions driving gene expression. A new study documents the emergence of a TAD flanking the amphioxus Hox cluster, prefiguring the

Birth and upgrowth of the Hox topological domains during evolution

NARCIS (Netherlands)

Deschamps, J.

2016-01-01

The recently discovered chromatin compartments called topologically associating domains (TADs) are essential for the three-dimensional organization of regulatory interactions driving gene expression. A new study documents the emergence of a TAD flanking the amphioxus Hox cluster, prefiguring the

Optimization of heliostat field layout in solar central receiver systems on annual basis using differential evolution algorithm

International Nuclear Information System (INIS)

Atif, Maimoon; Al-Sulaiman, Fahad A.

2015-01-01

Highlights: • Differential evolution optimization model was developed to optimize the heliostat field. • Five optical parameters were considered for the optimization of the optical efficiency. • Optimization using insolation weighted and un-weighted annual efficiency are developed. • The daily averaged annual optical efficiency was calculated to be 0.5023 while the monthly was 0.5025. • The insolation weighted daily averaged annual efficiency was 0.5634. - Abstract: Optimization of a heliostat field is an essential task to make a solar central receiver system effective because major optical losses are associated with the heliostat fields. In this study, a mathematical model was developed to effectively optimize the heliostat field on annual basis using differential evolution, which is an evolutionary algorithm. The heliostat field layout optimization is based on the calculation of five optical performance parameters: the mirror or the heliostat reflectivity, the cosine factor, the atmospheric attenuation factor, the shadowing and blocking factor, and the intercept factor. This model calculates all the aforementioned performance parameters at every stage of the optimization, until the best heliostat field layout based on annual performance is obtained. Two different approaches were undertaken to optimize the heliostat field layout: one with optimizing insolation weighted annual efficiency and the other with optimizing the un-weighted annual efficiency. Moreover, an alternate approach was also proposed to efficiently optimize the heliostat field in which the number of computational time steps was considerably reduced. It was observed that the daily averaged annual optical efficiency was calculated to be 0.5023 as compared to the monthly averaged annual optical efficiency, 0.5025. Moreover, the insolation weighted daily averaged annual efficiency of the heliostat field was 0.5634 for Dhahran, Saudi Arabia. The code developed can be used for any other

Multimedia applications in differential services

International Nuclear Information System (INIS)

Mahfooz, S.; Merabti, M.; Pereira, R.

2003-01-01

In this paper we present a mechanism to provide Quality of Service (QoS) guarantees to different multimedia applications that share link bandwidth in IP-based differential services domain. In this mechanism weights are associated with each and to individual users according to their priorities. In order to evaluate the performance of our scheme we conducted simulations. The test data used portray different multimedia applications i.e. MPEG-2, IP telephony. The simulation results obtained show the effectiveness of our scheme for multimedia applications by allocating link share to each multimedia application and minimising end-to-end transmission delay 9Y bringing them in line with the recommended standard acceptable transmission delay for multimedia applications. This paper also presents extension to our proposed Relative Bandwidth Sharing (RES) scheme for differential services. We have identified and highlighted the role of border routers and core routers in differential services domain. Exploring features of Internet Protocol IPv6 in our architecture. (author)

Black holes escaping from domain walls

International Nuclear Information System (INIS)

Flachi, Antonino; Sasaki, Misao; Pujolas, Oriol; Tanaka, Takahiro

2006-01-01

Previous studies concerning the interaction of branes and black holes suggested that a small black hole intersecting a brane may escape via a mechanism of reconnection. Here we consider this problem by studying the interaction of a small black hole and a domain wall composed of a scalar field and simulate the evolution of this system when the black hole acquires an initial recoil velocity. We test and confirm previous results, however, unlike the cases previously studied, in the more general set-up considered here, we are able to follow the evolution of the system also during the separation, and completely illustrate how the escape of the black hole takes place

A modified differential evolution approach for dynamic economic dispatch with valve-point effects

International Nuclear Information System (INIS)

Yuan Xiaohui; Wang Liang; Yuan Yanbin; Zhang Yongchuan; Cao Bo; Yang Bo

2008-01-01

Dynamic economic dispatch (DED) plays an important role in power system operation, which is a complicated non-linear constrained optimization problem. It has nonsmooth and nonconvex characteristic when generation unit valve-point effects are taken into account. This paper proposes a modified differential evolution approach (MDE) to solve DED problem with valve-point effects. In the proposed MDE method, feasibility-based selection comparison techniques and heuristic search rules are devised to handle constraints effectively. In contrast to the penalty function method, the constraints-handling method does not require penalty factors or any extra parameters and can guide the population to the feasible region quickly. Especially, it can be satisfied equality constraints of DED problem precisely. Moreover, the effects of two crucial parameters on the performance of the MDE for DED problem are studied as well. The feasibility and effectiveness of the proposed method is demonstrated for application example and the test results are compared with those of other methods reported in literature. It is shown that the proposed method is capable of yielding higher quality solutions

Vector domain decomposition schemes for parabolic equations

Science.gov (United States)

Vabishchevich, P. N.

2017-09-01

A new class of domain decomposition schemes for finding approximate solutions of timedependent problems for partial differential equations is proposed and studied. A boundary value problem for a second-order parabolic equation is used as a model problem. The general approach to the construction of domain decomposition schemes is based on partition of unity. Specifically, a vector problem is set up for solving problems in individual subdomains. Stability conditions for vector regionally additive schemes of first- and second-order accuracy are obtained.

Differential Regulation of Disheveled in a Novel Vegetal Cortical Domain in Sea Urchin Eggs and Embryos: Implications for the Localized Activation of Canonical Wnt Signaling

Science.gov (United States)

Peng, ChiehFu Jeff; Wikramanayake, Athula H.

2013-01-01

Pattern formation along the animal-vegetal (AV) axis in sea urchin embryos is initiated when canonical Wnt (cWnt) signaling is activated in vegetal blastomeres. The mechanisms that restrict cWnt signaling to vegetal blastomeres are not well understood, but there is increasing evidence that the egg’s vegetal cortex plays a critical role in this process by mediating localized “activation” of Disheveled (Dsh). To investigate how Dsh activity is regulated along the AV axis, sea urchin-specific Dsh antibodies were used to examine expression, subcellular localization, and post-translational modification of Dsh during development. Dsh is broadly expressed during early sea urchin development, but immunolocalization studies revealed that this protein is enriched in a punctate pattern in a novel vegetal cortical domain (VCD) in the egg. Vegetal blastomeres inherit this VCD during embryogenesis, and at the 60-cell stage Dsh puncta are seen in all cells that display nuclear β-catenin. Analysis of Dsh post-translational modification using two-dimensional Western blot analysis revealed that compared to Dsh pools in the bulk cytoplasm, this protein is differentially modified in the VCD and in the 16-cell stage micromeres that partially inherit this domain. Dsh localization to the VCD is not directly affected by disruption of microfilaments and microtubules, but unexpectedly, microfilament disruption led to degradation of all the Dsh pools in unfertilized eggs over a period of incubation suggesting that microfilament integrity is required for maintaining Dsh stability. These results demonstrate that a pool of differentially modified Dsh in the VCD is selectively inherited by the vegetal blastomeres that activate cWnt signaling in early embryos, and suggests that this domain functions as a scaffold for localized Dsh activation. Localized cWnt activation regulates AV axis patterning in many metazoan embryos. Hence, it is possible that the VCD is an evolutionarily conserved

Casimir forces in the time domain: Theory

International Nuclear Information System (INIS)

Rodriguez, Alejandro W.; McCauley, Alexander P.; Joannopoulos, John D.; Johnson, Steven G.

2009-01-01

We present a method to compute Casimir forces in arbitrary geometries and for arbitrary materials based on the finite-difference time-domain (FDTD) scheme. The method involves the time evolution of electric and magnetic fields in response to a set of current sources, in a modified medium with frequency-independent conductivity. The advantage of this approach is that it allows one to exploit existing FDTD software, without modification, to compute Casimir forces. In this paper, we focus on the derivation, implementation choices, and essential properties of the time-domain algorithm, both considered analytically and illustrated in the simplest parallel-plate geometry.

Structural models of zebrafish (Danio rerio NOD1 and NOD2 NACHT domains suggest differential ATP binding orientations: insights from computational modeling, docking and molecular dynamics simulations.

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Jitendra Maharana

Full Text Available Nucleotide-binding oligomerization domain-containing protein 1 (NOD1 and NOD2 are cytosolic pattern recognition receptors playing pivotal roles in innate immune signaling. NOD1 and NOD2 recognize bacterial peptidoglycan derivatives iE-DAP and MDP, respectively and undergoes conformational alternation and ATP-dependent self-oligomerization of NACHT domain followed by downstream signaling. Lack of structural adequacy of NACHT domain confines our understanding about the NOD-mediated signaling mechanism. Here, we predicted the structure of NACHT domain of both NOD1 and NOD2 from model organism zebrafish (Danio rerio using computational methods. Our study highlighted the differential ATP binding modes in NOD1 and NOD2. In NOD1, γ-phosphate of ATP faced toward the central nucleotide binding cavity like NLRC4, whereas in NOD2 the cavity was occupied by adenine moiety. The conserved 'Lysine' at Walker A formed hydrogen bonds (H-bonds and Aspartic acid (Walker B formed electrostatic interaction with ATP. At Sensor 1, Arg328 of NOD1 exhibited an H-bond with ATP, whereas corresponding Arg404 of NOD2 did not. 'Proline' of GxP motif (Pro386 of NOD1 and Pro464 of NOD2 interacted with adenine moiety and His511 at Sensor 2 of NOD1 interacted with γ-phosphate group of ATP. In contrast, His579 of NOD2 interacted with the adenine moiety having a relatively inverted orientation. Our findings are well supplemented with the molecular interaction of ATP with NLRC4, and consistent with mutagenesis data reported for human, which indicates evolutionary shared NOD signaling mechanism. Together, this study provides novel insights into ATP binding mechanism, and highlights the differential ATP binding modes in zebrafish NOD1 and NOD2.

Nonlinear evolution equations

CERN Document Server

Uraltseva, N N

1995-01-01

This collection focuses on nonlinear problems in partial differential equations. Most of the papers are based on lectures presented at the seminar on partial differential equations and mathematical physics at St. Petersburg University. Among the topics explored are the existence and properties of solutions of various classes of nonlinear evolution equations, nonlinear imbedding theorems, bifurcations of solutions, and equations of mathematical physics (Navier-Stokes type equations and the nonlinear Schrödinger equation). The book will be useful to researchers and graduate students working in p

The Evolution of the Scavenger Receptor Cysteine-Rich Domain of the Class A Scavenger Receptors

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Nicholas eYap

2015-07-01

Full Text Available The class A Scavenger Receptor (cA-SR family is a group of five evolutionarily related innate immune receptors. The cA-SRs are known for their promiscuous ligand binding; as they have been shown to bind bacteria such as Streptococcus pneumoniae, and Escherichia coli, as well as different modified forms of low-density lipoprotein. Three of the five family members possess a Scavenger Receptor Cysteine Rich (SRCR domain while the remaining two receptors lack the domain. Previous work has suggested that the Macrophage Associated Receptor with COllagenous structure (MARCO shares a recent common ancestor with the non-SRCR-containing receptors; however the origin of the SRCR domain within the cA-SRs remains unknown. We hypothesize that the SRCR domains of the cA-SRs have a common origin that predates teleost fish. Using the newly available sequence data from sea lamprey and ghost shark genome projects, we have shown that MARCO shares a common ancestor with the SRCR-containing proteins. In addition, we explored the evolutionary relationships within the SRCR domain by reconstructing the ancestral SRCR domains of the cA-SRs. We identified a motif that is highly conserved between the cA-SR SRCR domains and the ancestral SRCR domain that consist of WGTVCDD. We also show that the GRAEVYY motif, a functionally important motif within MARCO, is poorly conserved in the other cA-SRs and in the reconstructed ancestral domain. Further, we identified three sites within MARCO’s SRCR domain which are under positive selection. Two of these sites lie adjacent to the conserved WGTVCDD motif, and may indicate a potential biological function for these sites. Together these findings indicate a common origin of the SRCR domain within the cA-SRs; however different selective pressures between the proteins may have caused MARCOs SRCR domain to evolve to contain different functional motifs when compared to the other SRCR-containing cA-SRs.

Heterogeneous Ferroelectric Solid Solutions Phases and Domain States

CERN Document Server

Topolov, Vitaly

2012-01-01

The book deals with perovskite-type ferroelectric solid solutions for modern materials science and applications, solving problems of complicated heterophase/domain structures near the morphotropic phase boundary and applications to various systems with morphotropic phases. In this book domain state–interface diagrams are presented for the interpretation of heterophase states in perovskite-type ferroelectric solid solutions. It allows to describe the stress relief in the presence of polydomain phases, the behavior of unit-cell parameters of coexisting phases and the effect of external electric fields. The novelty of the book consists in (i) the first systematization of data about heterophase states and their evolution in ferroelectric solid solutions (ii) the general interpretation of heterophase and domain structures at changing temperature, composition or electric field (iii) the complete analysis of interconnection domain structures, unit-cell parameters changes, heterophase structures and stress relief.

Non-dense domain operator matrices and Cauchy problems

International Nuclear Information System (INIS)

Lalaoui Rhali, S.

2002-12-01

In this work, we study Cauchy problems with non-dense domain operator matrices. By assuming that the entries of an unbounded operator matrix are Hille-Yosida operators, we give a necessary and sufficient condition ensuring that the part of this operator matrix generates a semigroup in the closure of its domain. This allows us to prove the well-posedness of the corresponding Cauchy problem. Our results are applied to delay and neutral differential equations. (author)

Solving Bi-Objective Optimal Power Flow using Hybrid method of Biogeography-Based Optimization and Differential Evolution Algorithm: A case study of the Algerian Electrical Network

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Ouafa Herbadji

2016-03-01

Full Text Available This paper proposes a new hybrid metaheuristique algorithm based on the hybridization of Biogeography-based optimization with the Differential Evolution for solving the optimal power flow problem with emission control. The biogeography-based optimization (BBO algorithm is strongly influenced by equilibrium theory of island biogeography, mainly through two steps: Migration and Mutation. Differential Evolution (DE is one of the best Evolutionary Algorithms for global optimization. The hybridization of these two methods is used to overcome traps of local optimal solutions and problems of time consumption. The objective of this paper is to minimize the total fuel cost of generation, total emission, total real power loss and also maintain an acceptable system performance in terms of limits on generator real power, bus voltages and power flow of transmission lines. In the present work, BBO/DE has been applied to solve the optimal power flow problems on IEEE 30-bus test system and the Algerian electrical network 114 bus. The results obtained from this method show better performances compared with DE, BBO and other well known metaheuristique and evolutionary optimization methods.

Remote-sensing image encryption in hybrid domains

Science.gov (United States)

Zhang, Xiaoqiang; Zhu, Guiliang; Ma, Shilong

2012-04-01

Remote-sensing technology plays an important role in military and industrial fields. Remote-sensing image is the main means of acquiring information from satellites, which always contain some confidential information. To securely transmit and store remote-sensing images, we propose a new image encryption algorithm in hybrid domains. This algorithm makes full use of the advantages of image encryption in both spatial domain and transform domain. First, the low-pass subband coefficients of image DWT (discrete wavelet transform) decomposition are sorted by a PWLCM system in transform domain. Second, the image after IDWT (inverse discrete wavelet transform) reconstruction is diffused with 2D (two-dimensional) Logistic map and XOR operation in spatial domain. The experiment results and algorithm analyses show that the new algorithm possesses a large key space and can resist brute-force, statistical and differential attacks. Meanwhile, the proposed algorithm has the desirable encryption efficiency to satisfy requirements in practice.

Domain engineering product lines, languages, and conceptual models

CERN Document Server

Reinhartz-Berger, Iris; Clark, Tony

2013-01-01

Domain engineering is a set of activities intended to develop, maintain, and manage the creation and evolution of an area of knowledge suitable for processing by a range of software systems.  It is of considerable practical significance, as it provides methods and techniques that help reduce time-to-market, development costs, and project risks on one hand, and helps improve system quality and performance on a consistent basis on the other. In this book, the editors present a collection of invited chapters from various fields related to domain engineering. The individual chapters pres

Multi-Objective Differential Evolution for Voltage Security Constrained Optimal Power Flow in Deregulated Power Systems

Science.gov (United States)

Roselyn, J. Preetha; Devaraj, D.; Dash, Subhransu Sekhar

2013-11-01

Voltage stability is an important issue in the planning and operation of deregulated power systems. The voltage stability problems is a most challenging one for the system operators in deregulated power systems because of the intense use of transmission line capabilities and poor regulation in market environment. This article addresses the congestion management problem avoiding offline transmission capacity limits related to voltage stability by considering Voltage Security Constrained Optimal Power Flow (VSCOPF) problem in deregulated environment. This article presents the application of Multi Objective Differential Evolution (MODE) algorithm to solve the VSCOPF problem in new competitive power systems. The maximum of L-index of the load buses is taken as the indicator of voltage stability and is incorporated in the Optimal Power Flow (OPF) problem. The proposed method in hybrid power market which also gives solutions to voltage stability problems by considering the generation rescheduling cost and load shedding cost which relieves the congestion problem in deregulated environment. The buses for load shedding are selected based on the minimum eigen value of Jacobian with respect to the load shed. In the proposed approach, real power settings of generators in base case and contingency cases, generator bus voltage magnitudes, real and reactive power demands of selected load buses using sensitivity analysis are taken as the control variables and are represented as the combination of floating point numbers and integers. DE/randSF/1/bin strategy scheme of differential evolution with self-tuned parameter which employs binomial crossover and difference vector based mutation is used for the VSCOPF problem. A fuzzy based mechanism is employed to get the best compromise solution from the pareto front to aid the decision maker. The proposed VSCOPF planning model is implemented on IEEE 30-bus system, IEEE 57 bus practical system and IEEE 118 bus system. The pareto optimal

Research on the Compression Algorithm of the Infrared Thermal Image Sequence Based on Differential Evolution and Double Exponential Decay Model

Science.gov (United States)

Zhang, Jin-Yu; Meng, Xiang-Bing; Xu, Wei; Zhang, Wei; Zhang, Yong

2014-01-01

This paper has proposed a new thermal wave image sequence compression algorithm by combining double exponential decay fitting model and differential evolution algorithm. This study benchmarked fitting compression results and precision of the proposed method was benchmarked to that of the traditional methods via experiment; it investigated the fitting compression performance under the long time series and improved model and validated the algorithm by practical thermal image sequence compression and reconstruction. The results show that the proposed algorithm is a fast and highly precise infrared image data processing method. PMID:24696649

Research on the Compression Algorithm of the Infrared Thermal Image Sequence Based on Differential Evolution and Double Exponential Decay Model

Directory of Open Access Journals (Sweden)

Jin-Yu Zhang

2014-01-01

Full Text Available This paper has proposed a new thermal wave image sequence compression algorithm by combining double exponential decay fitting model and differential evolution algorithm. This study benchmarked fitting compression results and precision of the proposed method was benchmarked to that of the traditional methods via experiment; it investigated the fitting compression performance under the long time series and improved model and validated the algorithm by practical thermal image sequence compression and reconstruction. The results show that the proposed algorithm is a fast and highly precise infrared image data processing method.

Polarization of concave domains by traveling wave pinning.

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Slawomir Bialecki

Full Text Available Pattern formation is one of the most fundamental yet puzzling phenomena in physics and biology. We propose that traveling front pinning into concave portions of the boundary of 3-dimensional domains can serve as a generic gradient-maintaining mechanism. Such a mechanism of domain polarization arises even for scalar bistable reaction-diffusion equations, and, depending on geometry, a number of stationary fronts may be formed leading to complex spatial patterns. The main advantage of the pinning mechanism, with respect to the Turing bifurcation, is that it allows for maintaining gradients in the specific regions of the domain. By linking the instant domain shape with the spatial pattern, the mechanism can be responsible for cellular polarization and differentiation.

The Differential Effects of Task Complexity on Domain-Specific and Peer Assessment Skills

Science.gov (United States)

van Zundert, Marjo J.; Sluijsmans, Dominique M. A.; Konings, Karen D.; van Merrienboer, Jeroen J. G.

2012-01-01

In this study the relationship between domain-specific skills and peer assessment skills as a function of task complexity is investigated. We hypothesised that peer assessment skills were superposed on domain-specific skills and will therefore suffer more when higher cognitive load is induced by increased task complexity. In a mixed factorial…

Directed evolution of the TALE N-terminal domain for recognition of all 5' bases.

Science.gov (United States)

Lamb, Brian M; Mercer, Andrew C; Barbas, Carlos F

2013-11-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5'-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5' T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5' T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes.

Hybrid Differential Evolution Optimisation for Earth Observation Satellite Scheduling with Time-Dependent Earliness-Tardiness Penalties

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Guoliang Li

2017-01-01

Full Text Available We study the order acceptance and scheduling (OAS problem with time-dependent earliness-tardiness penalties in a single agile earth observation satellite environment where orders are defined by their release dates, available processing time windows ranging from earliest start date to deadline, processing times, due dates, sequence-dependent setup times, and revenues. The objective is to maximise total revenue, where the revenue from an order is a piecewise linear function of its earliness and tardiness with reference to its due date. We formulate this problem as a mixed integer linear programming model and develop a novel hybrid differential evolution (DE algorithm under self-adaptation framework to solve this problem. Compared with classical DE, hybrid DE employs two mutation operations, scaling factor adaptation and crossover probability adaptation. Computational tests indicate that the proposed algorithm outperforms classical DE in addition to two other variants of DE.

Partial differential equations for scientists and engineers

CERN Document Server

Farlow, Stanley J

1993-01-01

Most physical phenomena, whether in the domain of fluid dynamics, electricity, magnetism, mechanics, optics, or heat flow, can be described in general by partial differential equations. Indeed, such equations are crucial to mathematical physics. Although simplifications can be made that reduce these equations to ordinary differential equations, nevertheless the complete description of physical systems resides in the general area of partial differential equations.This highly useful text shows the reader how to formulate a partial differential equation from the physical problem (constructing th

Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization.

Science.gov (United States)

González-Romero, Rodrigo; Eirín-López, José M; Ausió, Juan

2015-01-01

High mobility group (HMG)-N proteins are a family of small nonhistone proteins that bind to nucleosomes (N). Despite the amount of information available on their structure and function, there is an almost complete lack of information on the molecular evolutionary mechanisms leading to their exclusive differentiation. In the present work, we provide evidence suggesting that HMGN lineages constitute independent monophyletic groups derived from a common ancestor prior to the diversification of vertebrates. Based on observations of the functional diversification across vertebrate HMGN proteins and on the extensive silent nucleotide divergence, our results suggest that the long-term evolution of HMGNs occurs under strong purifying selection, resulting from the lineage-specific functional constraints of their different protein domains. Selection analyses on independent lineages suggest that their functional specialization was mediated by bursts of adaptive selection at specific evolutionary times, in a small subset of codons with functional relevance-most notably in HMGN1, and in the rapidly evolving HMGN5. This work provides useful information to our understanding of the specialization imparted on chromatin metabolism by HMGNs, especially on the evolutionary mechanisms underlying their functional differentiation in vertebrates. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Differential evolution algorithm based automatic generation control for interconnected power systems with

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Banaja Mohanty

2014-09-01

Full Text Available This paper presents the design and performance analysis of Differential Evolution (DE algorithm based Proportional–Integral (PI and Proportional–Integral–Derivative (PID controllers for Automatic Generation Control (AGC of an interconnected power system. Initially, a two area thermal system with governor dead-band nonlinearity is considered for the design and analysis purpose. In the proposed approach, the design problem is formulated as an optimization problem control and DE is employed to search for optimal controller parameters. Three different objective functions are used for the design purpose. The superiority of the proposed approach has been shown by comparing the results with a recently published Craziness based Particle Swarm Optimization (CPSO technique for the same interconnected power system. It is noticed that, the dynamic performance of DE optimized PI controller is better than CPSO optimized PI controllers. Additionally, controller parameters are tuned at different loading conditions so that an adaptive gain scheduling control strategy can be employed. The study is further extended to a more realistic network of two-area six unit system with different power generating units such as thermal, hydro, wind and diesel generating units considering boiler dynamics for thermal plants, Generation Rate Constraint (GRC and Governor Dead Band (GDB non-linearity.

Optimal trajectory planning of free-floating space manipulator using differential evolution algorithm

Science.gov (United States)

Wang, Mingming; Luo, Jianjun; Fang, Jing; Yuan, Jianping

2018-03-01

The existence of the path dependent dynamic singularities limits the volume of available workspace of free-floating space robot and induces enormous joint velocities when such singularities are met. In order to overcome this demerit, this paper presents an optimal joint trajectory planning method using forward kinematics equations of free-floating space robot, while joint motion laws are delineated with application of the concept of reaction null-space. Bézier curve, in conjunction with the null-space column vectors, are applied to describe the joint trajectories. Considering the forward kinematics equations of the free-floating space robot, the trajectory planning issue is consequently transferred to an optimization issue while the control points to construct the Bézier curve are the design variables. A constrained differential evolution (DE) scheme with premature handling strategy is implemented to find the optimal solution of the design variables while specific objectives and imposed constraints are satisfied. Differ from traditional methods, we synthesize null-space and specialized curve to provide a novel viewpoint for trajectory planning of free-floating space robot. Simulation results are presented for trajectory planning of 7 degree-of-freedom (DOF) kinematically redundant manipulator mounted on a free-floating spacecraft and demonstrate the feasibility and effectiveness of the proposed method.

Insight into molecular interactions between two PB1 domains

NARCIS (Netherlands)

van Drogen-Petit, A.; Zwahlen, C.; Peter, M.; Bonvin, A.M.J.J.

2004-01-01

Specific protein–protein interactions play crucial roles in the regulation of any biological process. Recently, a new protein–protein interaction domain termed PB1 (Phox and Bem1) was identified, which is conserved throughout evolution and present in diverse proteins functioning in signal

Modeling growth and dissemination of lymphoma in a co-evolving lymph node: a diffuse-domain approach

Science.gov (United States)

Chuang, Yao-Li; Cristini, Vittorio; Chen, Ying; Li, Xiangrong; Frieboes, Hermann; Lowengrub, John

2013-03-01

While partial differential equation models of tumor growth have successfully described various spatiotemporal phenomena observed for in-vitro tumor spheroid experiments, one challenge towards taking these models to further study in-vivo tumors is that instead of relatively static tissue culture with regular boundary conditions, in-vivo tumors are often confined in organ tissues that co-evolve with the tumor growth. Here we adopt a recently developed diffuse-domain method to account for the co-evolving domain boundaries, adapting our previous in-vitro tumor model for the development of lymphoma encapsulated in a lymph node, which may swell or shrink due to proliferation and dissemination of lymphoma cells and treatment by chemotherapy. We use the model to study the induced spatial heterogeneity, which may arise as an emerging phenomenon in experimental observations and model analysis. Spatial heterogeneity is believed to lead to tumor infiltration patterns and reduce the efficacy of chemotherapy, leaving residuals that cause cancer relapse after the treatment. Understanding the spatiotemporal evolution of in-vivo tumors can be an essential step towards more effective strategies of curing cancer. Supported by NIH-PSOC grant 1U54CA143907-01.

Autonomic Differentiation Map: A Novel Statistical Tool for Interpretation of Heart Rate Variability

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Daniela Lucini

2018-04-01

Full Text Available In spite of the large body of evidence suggesting Heart Rate Variability (HRV alone or combined with blood pressure variability (providing an estimate of baroreflex gain as a useful technique to assess the autonomic regulation of the cardiovascular system, there is still an ongoing debate about methodology, interpretation, and clinical applications. In the present investigation, we hypothesize that non-parametric and multivariate exploratory statistical manipulation of HRV data could provide a novel informational tool useful to differentiate normal controls from clinical groups, such as athletes, or subjects affected by obesity, hypertension, or stress. With a data-driven protocol in 1,352 ambulant subjects, we compute HRV and baroreflex indices from short-term data series as proxies of autonomic (ANS regulation. We apply a three-step statistical procedure, by first removing age and gender effects. Subsequently, by factor analysis, we extract four ANS latent domains that detain the large majority of information (86.94%, subdivided in oscillatory (40.84%, amplitude (18.04%, pressure (16.48%, and pulse domains (11.58%. Finally, we test the overall capacity to differentiate clinical groups vs. control. To give more practical value and improve readability, statistical results concerning individual discriminant ANS proxies and ANS differentiation profiles are displayed through peculiar graphical tools, i.e., significance diagram and ANS differentiation map, respectively. This approach, which simultaneously uses all available information about the system, shows what domains make up the difference in ANS discrimination. e.g., athletes differ from controls in all domains, but with a graded strength: maximal in the (normalized oscillatory and in the pulse domains, slightly less in the pressure domain and minimal in the amplitude domain. The application of multiple (non-parametric and exploratory statistical and graphical tools to ANS proxies defines

Differential susceptibility to plasticity: a 'missing link' between gene-culture co-evolution and neuropsychiatric spectrum disorders?

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Wurzman Rachel

2012-04-01

Full Text Available Abstract Brüne's proposal that erstwhile 'vulnerability' genes need to be reconsidered as 'plasticity' genes, given the potential for certain environments to yield increased positive function in the same domain as potential dysfunction, has implications for psychiatric nosology as well as a more dynamic understanding of the relationship between genes and culture. In addition to validating neuropsychiatric spectrum disorder nosologies by calling for similar methodological shifts in gene-environment-interaction studies, Brüne's position elevates the importance of environmental contexts - inclusive of socio-cultural variables - as mechanisms that contribute to clinical presentation. We assert that when models of susceptibility to plasticity and neuropsychiatric spectrum disorders are concomitantly considered, a new line of inquiry emerges into the co-evolution and co-determination of socio-cultural contexts and endophenotypes. This presents potentially unique opportunities, benefits, challenges, and responsibilities for research and practice in psychiatry. Please see related manuscript: http://www.biomedcentral.com/1741-7015/10/38

Domain decomposition methods and deflated Krylov subspace iterations

NARCIS (Netherlands)

Nabben, R.; Vuik, C.

2006-01-01

The balancing Neumann-Neumann (BNN) and the additive coarse grid correction (BPS) preconditioner are fast and successful preconditioners within domain decomposition methods for solving partial differential equations. For certain elliptic problems these preconditioners lead to condition numbers which

Assembly constraints drive co-evolution among ribosomal constituents.

Science.gov (United States)

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

Ribosome biogenesis, a central and essential cellular process, occurs through sequential association and mutual co-folding of protein-RNA constituents in a well-defined assembly pathway. Here, we construct a network of co-evolving nucleotide/amino acid residues within the ribosome and demonstrate that assembly constraints are strong predictors of co-evolutionary patterns. Predictors of co-evolution include a wide spectrum of structural reconstitution events, such as cooperativity phenomenon, protein-induced rRNA reconstitutions, molecular packing of different rRNA domains, protein-rRNA recognition, etc. A correlation between folding rate of small globular proteins and their topological features is known. We have introduced an analogous topological characteristic for co-evolutionary network of ribosome, which allows us to differentiate between rRNA regions subjected to rapid reconstitutions from those hindered by kinetic traps. Furthermore, co-evolutionary patterns provide a biological basis for deleterious mutation sites and further allow prediction of potential antibiotic targeting sites. Understanding assembly pathways of multicomponent macromolecules remains a key challenge in biophysics. Our study provides a 'proof of concept' that directly relates co-evolution to biophysical interactions during multicomponent assembly and suggests predictive power to identify candidates for critical functional interactions as well as for assembly-blocking antibiotic target sites. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Domain decomposition methods for solving an image problem

Energy Technology Data Exchange (ETDEWEB)

Tsui, W.K.; Tong, C.S. [Hong Kong Baptist College (Hong Kong)

1994-12-31

The domain decomposition method is a technique to break up a problem so that ensuing sub-problems can be solved on a parallel computer. In order to improve the convergence rate of the capacitance systems, pre-conditioned conjugate gradient methods are commonly used. In the last decade, most of the efficient preconditioners are based on elliptic partial differential equations which are particularly useful for solving elliptic partial differential equations. In this paper, the authors apply the so called covering preconditioner, which is based on the information of the operator under investigation. Therefore, it is good for various kinds of applications, specifically, they shall apply the preconditioned domain decomposition method for solving an image restoration problem. The image restoration problem is to extract an original image which has been degraded by a known convolution process and additive Gaussian noise.

Time domain calculation of connector loads of a very large floating structure

Science.gov (United States)

Gu, Jiayang; Wu, Jie; Qi, Enrong; Guan, Yifeng; Yuan, Yubo

2015-06-01

Loads generated after an air crash, ship collision, and other accidents may destroy very large floating structures (VLFSs) and create additional connector loads. In this study, the combined effects of ship collision and wave loads are considered to establish motion differential equations for a multi-body VLFS. A time domain calculation method is proposed to calculate the connector load of the VLFS in waves. The Longuet-Higgins model is employed to simulate the stochastic wave load. Fluid force and hydrodynamic coefficient are obtained with DNV Sesam software. The motion differential equation is calculated by applying the time domain method when the frequency domain hydrodynamic coefficient is converted into the memory function of the motion differential equation of the time domain. As a result of the combined action of wave and impact loads, high-frequency oscillation is observed in the time history curve of the connector load. At wave directions of 0° and 75°, the regularities of the time history curves of the connector loads in different directions are similar and the connector loads of C1 and C2 in the X direction are the largest. The oscillation load is observed in the connector in the Y direction at a wave direction of 75° and not at 0°. This paper presents a time domain calculation method of connector load to provide a certain reference function for the future development of Chinese VLFS

Vacuum tension effects on the evolution of domain walls in the early universe

International Nuclear Information System (INIS)

Aurilia, A.

1984-06-01

The ''vacuum pressure'' mechanism of the hadronic bag model is taken as a guide to formulate the dynamics of closed domain walls in the cosmological case. The effective action functional suggested by this analogy is a straightforward generalization of the Einstein-Maxwell action: it involves a 3-index antisymmetric potential whose coupling to matter generates two effective cosmological constants, one inside and one outside the domain wall. It is suggested that this mechanism, which is alternative to the introduction of a Higgs potential, is the source of the bubble nucleation process envisaged in the New Inflationary Cosmology. The dynamics of a spherical domain in a de Sitter phase is analyzed and is consistent with the geometrical formulation of shell dynamics proposed long ago by Israel. (author)

A Differential Evolution Based MPPT Method for Photovoltaic Modules under Partial Shading Conditions

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Kok Soon Tey

2014-01-01

Full Text Available Partially shaded photovoltaic (PV modules have multiple peaks in the power-voltage (P-V characteristic curve and conventional maximum power point tracking (MPPT algorithm, such as perturbation and observation (P&O, which is unable to track the global maximum power point (GMPP accurately due to its localized search space. Therefore, this paper proposes a differential evolution (DE based optimization algorithm to provide the globalized search space to track the GMPP. The direction of mutation in the DE algorithm is modified to ensure that the mutation always converges to the best solution among all the particles in the generation. This helps to provide the rapid convergence of the algorithm. Simulation of the proposed PV system is carried out in PSIM and the results are compared to P&O algorithm. In the hardware implementation, a high step-up DC-DC converter is employed to verify the proposed algorithm experimentally on partial shading conditions, load variation, and solar intensity variation. The experimental results show that the proposed algorithm is able to converge to the GMPP within 1.2 seconds with higher efficiency than P&O.

Genome differentiation of Drosophila melanogaster from a microclimate contrast in Evolution Canyon, Israel

Science.gov (United States)

Hübner, Sariel; Rashkovetsky, Eugenia; Kim, Young Bun; Oh, Jung Hun; Michalak, Katarzyna; Weiner, Dmitry; Korol, Abraham B.; Nevo, Eviatar; Michalak, Pawel

2013-01-01

The opposite slopes of “Evolution Canyon” in Israel have served as a natural model system of adaptation to a microclimate contrast. Long-term studies of Drosophila melanogaster populations inhabiting the canyon have exhibited significant interslope divergence in thermal and drought stress resistance, candidate genes, mobile elements, habitat choice, mating discrimination, and wing-shape variation, all despite close physical proximity of the contrasting habitats, as well as substantial interslope migration. To examine patterns of genetic differentiation at the genome-wide level, we used high coverage sequencing of the flies’ genomes. A total of 572 genes were significantly different in allele frequency between the slopes, 106 out of which were associated with 74 significantly overrepresented gene ontology (GO) terms, particularly so with response to stimulus and developmental and reproductive processes, thus corroborating previous observations of interslope divergence in stress response, life history, and mating functions. There were at least 37 chromosomal “islands” of interslope divergence and low sequence polymorphism, plausible signatures of selective sweeps, more abundant in flies derived from one (north-facing) of the slopes. Positive correlation between local recombination rate and the level of nucleotide polymorphism was also found. PMID:24324170

The PR/SET Domain Zinc Finger Protein Prdm4 Regulates Gene Expression in Embryonic Stem Cells but Plays a Nonessential Role in the Developing Mouse Embryo

Science.gov (United States)

Bogani, Debora; Morgan, Marc A. J.; Nelson, Andrew C.; Costello, Ita; McGouran, Joanna F.; Kessler, Benedikt M.

2013-01-01

Prdm4 is a highly conserved member of the Prdm family of PR/SET domain zinc finger proteins. Many well-studied Prdm family members play critical roles in development and display striking loss-of-function phenotypes. Prdm4 functional contributions have yet to be characterized. Here, we describe its widespread expression in the early embryo and adult tissues. We demonstrate that DNA binding is exclusively mediated by the Prdm4 zinc finger domain, and we characterize its tripartite consensus sequence via SELEX (systematic evolution of ligands by exponential enrichment) and ChIP-seq (chromatin immunoprecipitation-sequencing) experiments. In embryonic stem cells (ESCs), Prdm4 regulates key pluripotency and differentiation pathways. Two independent strategies, namely, targeted deletion of the zinc finger domain and generation of a EUCOMM LacZ reporter allele, resulted in functional null alleles. However, homozygous mutant embryos develop normally and adults are healthy and fertile. Collectively, these results strongly suggest that Prdm4 functions redundantly with other transcriptional partners to cooperatively regulate gene expression in the embryo and adult animal. PMID:23918801

Optimization of dynamic economic dispatch with valve-point effect using chaotic sequence based differential evolution algorithms

International Nuclear Information System (INIS)

He Dakuo; Dong Gang; Wang Fuli; Mao Zhizhong

2011-01-01

A chaotic sequence based differential evolution (DE) approach for solving the dynamic economic dispatch problem (DEDP) with valve-point effect is presented in this paper. The proposed method combines the DE algorithm with the local search technique to improve the performance of the algorithm. DE is the main optimizer, while an approximated model for local search is applied to fine tune in the solution of the DE run. To accelerate convergence of DE, a series of constraints handling rules are adopted. An initial population obtained by using chaotic sequence exerts optimal performance of the proposed algorithm. The combined algorithm is validated for two test systems consisting of 10 and 13 thermal units whose incremental fuel cost function takes into account the valve-point loading effects. The proposed combined method outperforms other algorithms reported in literatures for DEDP considering valve-point effects.

Epochs of radioactivity in historical evolution of the earth with reference to evolution of biosphere

International Nuclear Information System (INIS)

Neruchev, S.G.

1976-01-01

Periodic epochs of intense contamination of the medium by uranium in the course of the Earth's evolution and the biogene mechanism of uranium accumulation in sediments during the lifetime are established. Global differentiation of the radioactivity epochs and essential effect of periodic radiation on the evolution of biosphere are shown. Radiational-mutational mechanism in shown to be extremely nonuniform during the evolution of the organic kingdom. It has been found that the intermittency in radioactive epochs is responsible for peculiarities in the stratigraphic distribution of sedimentary uranium, sapropelic shales, phosphorites, oil-producing rocks and other minerals

Collision of domain walls in asymptotically anti-de Sitter spacetime

International Nuclear Information System (INIS)

Takamizu, Yu-ichi; Maeda, Kei-ichi

2006-01-01

We study collision of two domain walls in five-dimensional asymptotically anti-de Sitter spacetime. This may provide the reheating mechanism of an ekpyrotic (or cyclic) brane universe, in which two Bogomol'nyi-Prasad-Sommerfield branes collide and evolve into a hot big bang universe. We evaluate a change of scalar field making the domain wall and can investigate the effect of a negative cosmological term in the bulk to the collision process and the evolution of our universe

Transverse field-induced nucleation pad switching modes during domain wall injection

Energy Technology Data Exchange (ETDEWEB)

Bryan, M. T.; Fry, P. W.; Schrefl, T.; Gibbs, M. R. J.; Allwood, D. A.; Im, M.-Y.; Fischer, P.

2010-03-12

We have used magnetic transmission X-ray microscopy (M-TXM) to image in-field magnetization configurations of patterned Ni{sub 80}Fe{sub 20} domain wall 'injection pads' and attached planar nanowires. Comparison with micromagnetic simulations suggests that the evolution of magnetic domains in rectangular injection pads depends on the relative orientation of closure domains in the remanent state. The magnetization reversal pathway is also altered by the inclusion of transverse magnetic fields. These different modes explain previous results of domain wall injection into nanowires. Even more striking was the observation of domain walls injecting halfway across the width of wider (>400 nm wide) wires but over wire lengths of several micrometers. These extended Neel walls can interact with adjacent nanowires and cause a switching in the side of the wire undergoing reversal as the domain wall continues to expand.

Iterative Splitting Methods for Differential Equations

CERN Document Server

Geiser, Juergen

2011-01-01

Iterative Splitting Methods for Differential Equations explains how to solve evolution equations via novel iterative-based splitting methods that efficiently use computational and memory resources. It focuses on systems of parabolic and hyperbolic equations, including convection-diffusion-reaction equations, heat equations, and wave equations. In the theoretical part of the book, the author discusses the main theorems and results of the stability and consistency analysis for ordinary differential equations. He then presents extensions of the iterative splitting methods to partial differential

NONLINEAR EVOLUTION OF GLOBAL HYDRODYNAMIC SHALLOW-WATER INSTABILITY IN THE SOLAR TACHOCLINE

International Nuclear Information System (INIS)

Dikpati, Mausumi

2012-01-01

We present a fully nonlinear hydrodynamic 'shallow-water' model of the solar tachocline. The model consists of a global spherical shell of differentially rotating fluid, which has a deformable top, thus allowing motions in radial directions along with latitudinal and longitudinal directions. When the system is perturbed, in the course of its nonlinear evolution it can generate unstable low-frequency shallow-water shear modes from the differential rotation, high-frequency gravity waves, and their interactions. Radiative and overshoot tachoclines are characterized in this model by high and low effective gravity values, respectively. Building a semi-implicit spectral scheme containing very low numerical diffusion, we perform nonlinear evolution of shallow-water modes. Our first results show that (1) high-latitude jets or polar spin-up occurs due to nonlinear evolution of unstable hydrodynamic shallow-water disturbances and differential rotation, (2) Reynolds stresses in the disturbances together with changing shell thickness and meridional flow are responsible for the evolution of differential rotation, (3) disturbance energy primarily remains concentrated in the lowest longitudinal wavenumbers, (4) an oscillation in energy between perturbed and unperturbed states occurs due to evolution of these modes in a nearly dissipation-free system, and (5) disturbances are geostrophic, but occasional nonadjustment in geostrophic balance can occur, particularly in the case of high effective gravity, leading to generation of gravity waves. We also find that a linearly stable differential rotation profile remains nonlinearly stable.

Collage-type approach to inverse problems for elliptic PDEs on perforated domains

Directory of Open Access Journals (Sweden)

Herb E. Kunze

2015-02-01

Full Text Available We present a collage-based method for solving inverse problems for elliptic partial differential equations on a perforated domain. The main results of this paper establish a link between the solution of an inverse problem on a perforated domain and the solution of the same model on a domain with no holes. The numerical examples at the end of the paper show the goodness of this approach.

The Origin and Early Evolution of Membrane Proteins

Science.gov (United States)

Pohorille, Andrew; Schweighofter, Karl; Wilson, Michael A.

2006-01-01

The origin and early evolution of membrane proteins, and in particular ion channels, are considered from the point of view that the transmembrane segments of membrane proteins are structurally quite simple and do not require specific sequences to fold. We argue that the transport of solute species, especially ions, required an early evolution of efficient transport mechanisms, and that the emergence of simple ion channels was protobiologically plausible. We also argue that, despite their simple structure, such channels could possess properties that, at the first sight, appear to require markedly larger complexity. These properties can be subtly modulated by local modifications to the sequence rather than global changes in molecular architecture. In order to address the evolution and development of ion channels, we focus on identifying those protein domains that are commonly associated with ion channel proteins and are conserved throughout the three main domains of life (Eukarya, Prokarya, and Archaea). We discuss the potassium-sodium-calcium superfamily of voltage-gated ion channels, mechanosensitive channels, porins, and ABC-transporters and argue that these families of membrane channels have sufficiently universal architectures that they can readily adapt to the diverse functional demands arising during evolution.

Analysis of the Diffuse Domain Method for Second Order Elliptic Boundary Value Problems

NARCIS (Netherlands)

Burger, Martin; Elvetun, Ole; Schlottbom, Matthias

2017-01-01

The diffuse domain method for partial differential equations on complicated geometries recently received strong attention in particular from practitioners, but many fundamental issues in the analysis are still widely open. In this paper, we study the diffuse domain method for approximating second

Conservation and diversification of Msx protein in metazoan evolution.

Science.gov (United States)

Takahashi, Hirokazu; Kamiya, Akiko; Ishiguro, Akira; Suzuki, Atsushi C; Saitou, Naruya; Toyoda, Atsushi; Aruga, Jun

2008-01-01

Msx (/msh) family genes encode homeodomain (HD) proteins that control ontogeny in many animal species. We compared the structures of Msx genes from a wide range of Metazoa (Porifera, Cnidaria, Nematoda, Arthropoda, Tardigrada, Platyhelminthes, Mollusca, Brachiopoda, Annelida, Echiura, Echinodermata, Hemichordata, and Chordata) to gain an understanding of the role of these genes in phylogeny. Exon-intron boundary analysis suggested that the position of the intron located N-terminally to the HDs was widely conserved in all the genes examined, including those of cnidarians. Amino acid (aa) sequence comparison revealed 3 new evolutionarily conserved domains, as well as very strong conservation of the HDs. Two of the three domains were associated with Groucho-like protein binding in both a vertebrate and a cnidarian Msx homolog, suggesting that the interaction between Groucho-like proteins and Msx proteins was established in eumetazoan ancestors. Pairwise comparison among the collected HDs and their C-flanking aa sequences revealed that the degree of sequence conservation varied depending on the animal taxa from which the sequences were derived. Highly conserved Msx genes were identified in the Vertebrata, Cephalochordata, Hemichordata, Echinodermata, Mollusca, Brachiopoda, and Anthozoa. The wide distribution of the conserved sequences in the animal phylogenetic tree suggested that metazoan ancestors had already acquired a set of conserved domains of the current Msx family genes. Interestingly, although strongly conserved sequences were recovered from the Vertebrata, Cephalochordata, and Anthozoa, the sequences from the Urochordata and Hydrozoa showed weak conservation. Because the Vertebrata-Cephalochordata-Urochordata and Anthozoa-Hydrozoa represent sister groups in the Chordata and Cnidaria, respectively, Msx sequence diversification may have occurred differentially in the course of evolution. We speculate that selective loss of the conserved domains in Msx family

Evolution of the vertebrate neurocranium: problems of the premandibular domain and the origin of the trabecula.

Science.gov (United States)

Kuratani, Shigeru; Ahlberg, Per E

2018-01-01

The subdivision of the gnathostome neurocranium into an anterior neural crest-derived moiety and a posterior mesodermal moiety has attracted the interest of researchers for nearly two centuries. We present a synthetic scenario for the evolution of this structure, uniting developmental data from living cyclostomes and gnathostomes with morphological data from fossil stem gnathostomes in a common phylogenetic framework. Ancestrally, vertebrates had an anteroposteriorly short forebrain, and the neurocranium was essentially mesodermal; skeletal structures derived from premandibular ectomesenchyme were mostly anterior to the brain and formed part of the visceral arch skeleton. The evolution of a one-piece neurocranial 'head shield' in jawless stem gnathostomes, such as galeaspids and osteostracans, caused this mesenchyme to become incorporated into the neurocranium, but its position relative to the brain and nasohypophyseal duct remained unchanged. Basically similar distribution of the premandibular ectomesenchyme is inferred, even in placoderms, the earliest jawed vertebrates, in which the separation of hypophyseal and nasal placodes obliterated the nasohypophyseal duct, leading to redeployment of this ectomesenchyme between the separate placodes and permitting differentiation of the crown gnathostome trabecula that floored the forebrain. Initially this region was very short, and the bulk of the premandibular cranial part projected anteroventral to the nasal capsule, as in jawless stem gnathostomes. Due to the lengthening of the forebrain, the anteriorly projecting 'upper lip' was lost, resulting in the modern gnathostome neurocranium with a long forebrain cavity floored by the trabeculae.

Evolution of defect signatures at ferroelectric domain walls in Mg-doped LiNbO3

International Nuclear Information System (INIS)

Nataf, Guillaume F.; Guennou, Mael; Haussmann, Alexander; Barrett, Nick; Kreisel, Jens

2016-01-01

The domain structure of uniaxial ferroelectric lithium niobate single crystals is investigated using Raman spectroscopy mapping. The influence of doping with magnesium and poling at room temperature is studied by analysing frequency shifts at domain walls and their variations with dopant concentration and annealing conditions. It is shown that defects are stabilized at domain walls and that changes in the defect structures with Mg concentration can be probed by the shift of Raman modes. We show that the signatures of polar defects in the bulk and at the domain walls differ. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Shapes of isolated domains and field induced evolution of regular and random 2D domain structures in LiNbO3 and LiTaO3

International Nuclear Information System (INIS)

Chernykh, A.; Shur, V.; Nikolaeva, E.; Shishkin, E.; Shur, A.; Terabe, K.; Kurimura, S.; Kitamura, K.; Gallo, K.

2005-01-01

The variety of the shapes of isolated domains, revealed in congruent and stoichiometric LiTaO 3 and LiNbO 3 by chemical etching and visualized by optical and scanning probe microscopy, was obtained by computer simulation. The kinetic nature of the domain shape was clearly demonstrated. The kinetics of domain structure with the dominance of the growth of the steps formed at the domain walls as a result of domain merging was investigated experimentally in slightly distorted artificial regular two-dimensional (2D) hexagonal domain structure and random natural one. The artificial structure has been realized in congruent LiNbO 3 by 2D electrode pattern produced by photolithography. The polarization reversal in congruent LiTaO 3 was investigated as an example of natural domain growth limited by merging. The switching process defined by domain merging was studied by computer simulation. The crucial dependence of the switching kinetics on the nuclei concentration has been revealed

Lie symmetries for systems of evolution equations

Science.gov (United States)

Paliathanasis, Andronikos; Tsamparlis, Michael

2018-01-01

The Lie symmetries for a class of systems of evolution equations are studied. The evolution equations are defined in a bimetric space with two Riemannian metrics corresponding to the space of the independent and dependent variables of the differential equations. The exact relation of the Lie symmetries with the collineations of the bimetric space is determined.

Conical differentiability for evolution variational inequalities

Science.gov (United States)

Jarušek, Jiří; Krbec, Miroslav; Rao, Murali; Sokołowski, Jan

The conical differentiability of solutions to the parabolic variational inequality with respect to the right-hand side is proved in the paper. From one side the result is based on the Lipschitz continuity in H {1}/{2},1 (Q) of solutions to the variational inequality with respect to the right-hand side. On the other side, in view of the polyhedricity of the convex cone K={v∈ H;v |Σ c⩾0,v |Σ d=0}, we prove new results on sensitivity analysis of parabolic variational inequalities. Therefore, we have a positive answer to the question raised by Fulbert Mignot (J. Funct. Anal. 22 (1976) 25-32).

Classical solutions of mixed problems for quasilinear first order PFDEs on a cylindrical domain

Directory of Open Access Journals (Sweden)

Wojciech Czernous

2014-01-01

Full Text Available We abandon the setting of the domain as a Cartesian product of real intervals, customary for first order PFDEs (partial functional differential equations with initial boundary conditions. We give a new set of conditions on the possibly unbounded domain \\(\\Omega\\ with Lipschitz differentiable boundary. Well-posedness is then reliant on a variant of the normal vector condition. There is a neighbourhood of \\(\\partial\\Omega\\ with the property that if a characteristic trajectory has a point therein, then its every earlier point lies there as well. With local assumptions on coefficients and on the free term, we prove existence and Lipschitz dependence on data of classical solutions on \\((0,c\\times\\Omega\\ to the initial boundary value problem, for small \\(c\\. Regularity of solutions matches this domain, and the proof uses the Banach fixed-point theorem. Our general model of functional dependence covers problems with deviating arguments and integro-differential equations.

Mantle flow influence on subduction evolution

Science.gov (United States)

Chertova, Maria V.; Spakman, Wim; Steinberger, Bernhard

2018-05-01

The impact of remotely forced mantle flow on regional subduction evolution is largely unexplored. Here we investigate this by means of 3D thermo-mechanical numerical modeling using a regional modeling domain. We start with simplified models consisting of a 600 km (or 1400 km) wide subducting plate surrounded by other plates. Mantle inflow of ∼3 cm/yr is prescribed during 25 Myr of slab evolution on a subset of the domain boundaries while the other side boundaries are open. Our experiments show that the influence of imposed mantle flow on subduction evolution is the least for trench-perpendicular mantle inflow from either the back or front of the slab leading to 10-50 km changes in slab morphology and trench position while no strong slab dip changes were observed, as compared to a reference model with no imposed mantle inflow. In experiments with trench-oblique mantle inflow we notice larger effects of slab bending and slab translation of the order of 100-200 km. Lastly, we investigate how subduction in the western Mediterranean region is influenced by remotely excited mantle flow that is computed by back-advection of a temperature and density model scaled from a global seismic tomography model. After 35 Myr of subduction evolution we find 10-50 km changes in slab position and slab morphology and a slight change in overall slab tilt. Our study shows that remotely forced mantle flow leads to secondary effects on slab evolution as compared to slab buoyancy and plate motion. Still these secondary effects occur on scales, 10-50 km, typical for the large-scale deformation of the overlying crust and thus may still be of large importance for understanding geological evolution.

Differential structural properties of GLP-1 and exendin-4 determine their relative affinity for the GLP-1 receptor N-terminal extracellular domain.

Science.gov (United States)

Runge, Steffen; Schimmer, Susann; Oschmann, Jan; Schiødt, Christine Bruun; Knudsen, Sanne Möller; Jeppesen, Claus Bekker; Madsen, Kjeld; Lau, Jesper; Thøgersen, Henning; Rudolph, Rainer

2007-05-15

Glucagon-like peptide-1 (GLP-1) and exendin-4 (Ex4) are homologous peptides with established potential for treatment of type 2 diabetes. They bind and activate the pancreatic GLP-1 receptor (GLP-1R) with similar affinity and potency and thereby promote insulin secretion in a glucose-dependent manner. GLP-1R belongs to family B of the seven transmembrane G-protein coupled receptors. The N-terminal extracellular domain (nGLP-1R) is a ligand binding domain with differential affinity for Ex4 and GLP-1: low affinity for GLP-1 and high affinity for exendin-4. The superior affinity of nGLP-1R for Ex4 was previously explained by an additional interaction between nGLP-1R and the C-terminal Trp-cage of Ex4. In this study we have combined biophysical and pharmacological approaches thus relating structural properties of the ligands in solution to their relative binding affinity for nGLP-1R. We used both a tracer competition assay and ligand-induced thermal stabilization of nGLP-1R to measure the relative affinity of full length, truncated, and chimeric ligands for soluble refolded nGLP-1R. The ligands in solution and the conformational consequences of ligand binding to nGLP-1R were characterized by circular dichroism and fluorescence spectroscopy. We found a correlation between the helical content of the free ligands and their relative binding affinity for nGLP-1R, supporting the hypothesis that the ligands are helical at least in the segment that binds to nGLP-1R. The Trp-cage of Ex4 was not necessary to maintain a superior helicity of Ex4 compared to GLP-1. The results suggest that the differential affinity of nGLP-1R is explained almost entirely by divergent residues in the central part of the ligands: Leu10-Gly30 of Ex4 and Val16-Arg36 of GLP-1. In view of our results it appears that the Trp-cage plays only a minor role for the interaction between Ex4 and nGLP-1R and for the differential affinity of nGLP-1R for GLP-1 and Ex4.

The Successor Function and Pareto Optimal Solutions of Cooperative Differential Systems with Concavity. I

DEFF Research Database (Denmark)

Andersen, Kurt Munk; Sandqvist, Allan

1997-01-01

We investigate the domain of definition and the domain of values for the successor function of a cooperative differential system x'=f(t,x), where the coordinate functions are concave in x for any fixed value of t. Moreover, we give a characterization of a weakly Pareto optimal solution.......We investigate the domain of definition and the domain of values for the successor function of a cooperative differential system x'=f(t,x), where the coordinate functions are concave in x for any fixed value of t. Moreover, we give a characterization of a weakly Pareto optimal solution....

Developmental and evolutionary significance of the mandibular arch and prechordal/premandibular cranium in vertebrates: revising the heterotopy scenario of gnathostome jaw evolution

Science.gov (United States)

Kuratani, Shigeru; Adachi, Noritaka; Wada, Naoyuki; Oisi, Yasuhiro; Sugahara, Fumiaki

2013-01-01

The cephalic neural crest produces streams of migrating cells that populate pharyngeal arches and a more rostral, premandibular domain, to give rise to an extensive ectomesenchyme in the embryonic vertebrate head. The crest cells forming the trigeminal stream are the major source of the craniofacial skeleton; however, there is no clear distinction between the mandibular arch and the premandibular domain in this ectomesenchyme. The question regarding the evolution of the gnathostome jaw is, in part, a question about the differentiation of the mandibular arch, the rostralmost component of the pharynx, and in part a question about the developmental fate of the premandibular domain. We address the developmental definition of the mandibular arch in connection with the developmental origin of the trabeculae, paired cartilaginous elements generally believed to develop in the premandibular domain, and also of enigmatic cartilaginous elements called polar cartilages. Based on comparative embryology, we propose that the mandibular arch ectomesenchyme in gnathostomes can be defined as a Dlx1-positive domain, and that the polar cartilages, which develop from the Dlx1-negative premandibular ectomesenchyme, would represent merely posterior parts of the trabeculae. We also show, in the lamprey embryo, early migration of mandibular arch mesenchyme into the premandibular domain, and propose an updated version of the heterotopy theory on the origin of the jaw. PMID:22500853

Online transition matrix identification of the state evolution model for the extended Kalman filter in electrical impedance tomography

International Nuclear Information System (INIS)

Moura, Fernando S; Aya, Julio C C; Lima, Raul G; Fleury, Agenor T

2008-01-01

One of the electrical impedance tomography objectives is to estimate the electrical resistivity distribution in a domain based only on contour electrical potential measurements caused by an imposed electrical current distribution into the boundary. In biomedical applications, the random walk model is frequently used as evolution model and, under this conditions, it is observed poor tracking ability of the Extended Kalman Filter (EKF). An analytically developed evolution model is not feasible at this moment. The present work investigates the possibility of identifying the evolution model in parallel to the EKF and updating the evolution model with certain periodicity. The evolution model is identified using the history of resistivity distribution obtained by a sensitivity matrix based algorithm. To numerically identify the linear evolution model, it is used the Ibrahim Time Domain Method, normally used to identify the transition matrix on structural dynamics. The investigation was performed by numerical simulations of a time varying domain with the addition of noise. Numerical dificulties to compute the transition matrix were solved using a Tikhonov regularization. The EKF numerical simulations suggest that the tracking ability is significantly improved.

The evolution of alliance capabilities

NARCIS (Netherlands)

Heimeriks, K.H.; Duysters, G.M.; Vanhaverbeke, W.P.M.

2004-01-01

This paper assesses the effectiveness and differential performance effects of learning mechanisms on the evolution of alliance capabilities. Relying on the concept of capability lifecycles, prior research has suggested that different capability levels could be identified in which different

Overcoming Deception in Evolution of Cognitive Behaviors

DEFF Research Database (Denmark)

Lehman, Joel; Miikkulainen, Risto

2014-01-01

When scaling neuroevolution to complex behaviors, cognitive capabilities such as learning, communication, and memory become increasingly important. However, successfully evolving such cognitive abilities remains difficult. This paper argues that a main cause for such difficulty is deception, i.......e. evolution converges to a behavior unrelated to the desired solution. More specifically, cognitive behaviors often require accumulating neural structure that provides no immediate fitness benefit, and evolution often thus converges to non-cognitive solutions. To investigate this hypothesis, a common...... evolutionary robotics T-Maze domain is adapted in three separate ways to require agents to communicate, remember, and learn. Indicative of deception, evolution driven by objective-based fitness often converges upon simple non- cognitive behaviors. In contrast, evolution driven to explore novel behaviors, i...

Algebraic dynamics solutions and algebraic dynamics algorithm for nonlinear ordinary differential equations

Institute of Scientific and Technical Information of China (English)

WANG; Shunjin; ZHANG; Hua

2006-01-01

The problem of preserving fidelity in numerical computation of nonlinear ordinary differential equations is studied in terms of preserving local differential structure and approximating global integration structure of the dynamical system.The ordinary differential equations are lifted to the corresponding partial differential equations in the framework of algebraic dynamics,and a new algorithm-algebraic dynamics algorithm is proposed based on the exact analytical solutions of the ordinary differential equations by the algebraic dynamics method.In the new algorithm,the time evolution of the ordinary differential system is described locally by the time translation operator and globally by the time evolution operator.The exact analytical piece-like solution of the ordinary differential equations is expressd in terms of Taylor series with a local convergent radius,and its finite order truncation leads to the new numerical algorithm with a controllable precision better than Runge Kutta Algorithm and Symplectic Geometric Algorithm.

An accurate modelling of the two-diode model of PV module using a hybrid solution based on differential evolution

International Nuclear Information System (INIS)

Chin, Vun Jack; Salam, Zainal; Ishaque, Kashif

2016-01-01

Highlights: • An accurate computational method for the two-diode model of PV module is proposed. • The hybrid method employs analytical equations and Differential Evolution (DE). • I PV , I o1 , and R p are computed analytically, while a 1 , a 2 , I o2 and R s are optimized. • This allows the model parameters to be computed without using costly assumptions. - Abstract: This paper proposes an accurate computational technique for the two-diode model of PV module. Unlike previous methods, it does not rely on assumptions that cause the accuracy to be compromised. The key to this improvement is the implementation of a hybrid solution, i.e. by incorporating the analytical method with the differential evolution (DE) optimization technique. Three parameters, i.e. I PV , I o1 , and R p are computed analytically, while the remaining, a 1 , a 2 , I o2 and R s are optimized using the DE. To validate its accuracy, the proposed method is tested on three PV modules of different technologies: mono-crystalline, poly-crystalline and thin film. Furthermore, its performance is evaluated against two popular computational methods for the two-diode model. The proposed method is found to exhibit superior accuracy for the variation in irradiance and temperature for all module types. In particular, the improvement in accuracy is evident at low irradiance conditions; the root-mean-square error is one order of magnitude lower than that of the other methods. In addition, the values of the model parameters are consistent with the physics of PV cell. It is envisaged that the method can be very useful for PV simulation, in which accuracy of the model is of prime concern.

The evolution of WRKY transcription factors.

Science.gov (United States)

Rinerson, Charles I; Rabara, Roel C; Tripathi, Prateek; Shen, Qingxi J; Rushton, Paul J

2015-02-27

The availability of increasing numbers of sequenced genomes has necessitated a re-evaluation of the evolution of the WRKY transcription factor family. Modern day plants descended from a charophyte green alga that colonized the land between 430 and 470 million years ago. The first charophyte genome sequence from Klebsormidium flaccidum filled a gap in the available genome sequences in the plant kingdom between unicellular green algae that typically have 1-3 WRKY genes and mosses that contain 30-40. WRKY genes have been previously found in non-plant species but their occurrence has been difficult to explain. Only two WRKY genes are present in the Klebsormidium flaccidum genome and the presence of a Group IIb gene was unexpected because it had previously been thought that Group IIb WRKY genes first appeared in mosses. We found WRKY transcription factor genes outside of the plant lineage in some diplomonads, social amoebae, fungi incertae sedis, and amoebozoa. This patchy distribution suggests that lateral gene transfer is responsible. These lateral gene transfer events appear to pre-date the formation of the WRKY groups in flowering plants. Flowering plants contain proteins with domains typical for both resistance (R) proteins and WRKY transcription factors. R protein-WRKY genes have evolved numerous times in flowering plants, each type being restricted to specific flowering plant lineages. These chimeric proteins contain not only novel combinations of protein domains but also novel combinations and numbers of WRKY domains. Once formed, R protein WRKY genes may combine different components of signalling pathways that may either create new diversity in signalling or accelerate signalling by short circuiting signalling pathways. We propose that the evolution of WRKY transcription factors includes early lateral gene transfers to non-plant organisms and the occurrence of algal WRKY genes that have no counterparts in flowering plants. We propose two alternative hypotheses

Time-domain Green's Function Method for three-dimensional nonlinear subsonic flows

Science.gov (United States)

Tseng, K.; Morino, L.

1978-01-01

The Green's Function Method for linearized 3D unsteady potential flow (embedded in the computer code SOUSSA P) is extended to include the time-domain analysis as well as the nonlinear term retained in the transonic small disturbance equation. The differential-delay equations in time, as obtained by applying the Green's Function Method (in a generalized sense) and the finite-element technique to the transonic equation, are solved directly in the time domain. Comparisons are made with both linearized frequency-domain calculations and existing nonlinear results.

Positive and purifying selection influence the evolution of doublesex in the Anastrepha fraterculus species group.

Directory of Open Access Journals (Sweden)

Iderval S Sobrinho

Full Text Available The gene doublesex (dsx is considered to be under strong selective constraint along its evolutionary history because of its central role in somatic sex differentiation in insects. However, previous studies of dsx used global estimates of evolutionary rates to investigate its molecular evolution, which potentially miss signals of adaptive changes in generally conserved genes. In this work, we investigated the molecular evolution of dsx in the Anastrepha fraterculus species group (Diptera, Tephritidae, and test the hypothesis that this gene evolved solely by purifying selection using divergence-based and population-based methods. In the first approach, we compared sequences from Anastrepha and other Tephritidae with other Muscomorpha species, analyzed variation in nonsynonymous to synonymous rate ratios (dN/dS in the Tephritidae, and investigated radical and conservative changes in amino acid physicochemical properties. We show a general selective constraint on dsx, but with signs of positive selection mainly in the common region. Such changes were localized in alpha-helices previously reported to be involved in dimer formation in the OD2 domain and near the C-terminal of the OD1 domain. In the population-based approach, we amplified a region of 540 bp that spanned almost all of the region common to both sexes from 32 different sites in Brazil. We investigated patterns of selection using neutrality tests based on the frequency spectrum and locations of synonymous and nonsynonymous mutations in a haplotype network. As in the divergence-based approach, these analyses showed that dsx has evolved under an overall selective constraint, but with some events of positive selection. In contrast to previous studies, our analyses indicate that even though dsx has indeed evolved as a conserved gene, the common region of dsx has also experienced bouts of positive selection, perhaps driven by sexual selection, during its evolution.

Multi-objective optimization of in-situ bioremediation of groundwater using a hybrid metaheuristic technique based on differential evolution, genetic algorithms and simulated annealing

Directory of Open Access Journals (Sweden)

Kumar Deepak

2015-12-01

Full Text Available Groundwater contamination due to leakage of gasoline is one of the several causes which affect the groundwater environment by polluting it. In the past few years, In-situ bioremediation has attracted researchers because of its ability to remediate the contaminant at its site with low cost of remediation. This paper proposed the use of a new hybrid algorithm to optimize a multi-objective function which includes the cost of remediation as the first objective and residual contaminant at the end of the remediation period as the second objective. The hybrid algorithm was formed by combining the methods of Differential Evolution, Genetic Algorithms and Simulated Annealing. Support Vector Machines (SVM was used as a virtual simulator for biodegradation of contaminants in the groundwater flow. The results obtained from the hybrid algorithm were compared with Differential Evolution (DE, Non Dominated Sorting Genetic Algorithm (NSGA II and Simulated Annealing (SA. It was found that the proposed hybrid algorithm was capable of providing the best solution. Fuzzy logic was used to find the best compromising solution and finally a pumping rate strategy for groundwater remediation was presented for the best compromising solution. The results show that the cost incurred for the best compromising solution is intermediate between the highest and lowest cost incurred for other non-dominated solutions.

From Microscopic to Macroscopic Descriptions of Cell Migration on Growing Domains

KAUST Repository

Baker, Ruth E.; Yates, Christian A.; Erban, Radek

2009-01-01

are studied, and correspondence with a macroscopic-level PDE describing the evolution of cell density is demonstrated. The individual-based models are formulated in terms of random walkers on a lattice. Domain growth provides an extra mathematical challenge

Finite difference method and algebraic polynomial interpolation for numerically solving Poisson's equation over arbitrary domains

Directory of Open Access Journals (Sweden)

Tsugio Fukuchi

2014-06-01

Full Text Available The finite difference method (FDM based on Cartesian coordinate systems can be applied to numerical analyses over any complex domain. A complex domain is usually taken to mean that the geometry of an immersed body in a fluid is complex; here, it means simply an analytical domain of arbitrary configuration. In such an approach, we do not need to treat the outer and inner boundaries differently in numerical calculations; both are treated in the same way. Using a method that adopts algebraic polynomial interpolations in the calculation around near-wall elements, all the calculations over irregular domains reduce to those over regular domains. Discretization of the space differential in the FDM is usually derived using the Taylor series expansion; however, if we use the polynomial interpolation systematically, exceptional advantages are gained in deriving high-order differences. In using the polynomial interpolations, we can numerically solve the Poisson equation freely over any complex domain. Only a particular type of partial differential equation, Poisson's equations, is treated; however, the arguments put forward have wider generality in numerical calculations using the FDM.

Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

KAUST Repository

Li, Ping; Jiang, Li Jun; Bagci, Hakan

2018-01-01

It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

Discontinuous Galerkin Time-Domain Modeling of Graphene Nano-Ribbon Incorporating the Spatial Dispersion Effects

KAUST Repository

Li, Ping

2018-04-13

It is well known that graphene demonstrates spatial dispersion properties, i.e., its conductivity is nonlocal and a function of spectral wave number (momentum operator) q. In this paper, to account for effects of spatial dispersion on transmission of high speed signals along graphene nano-ribbon (GNR) interconnects, a discontinuous Galerkin time-domain (DGTD) algorithm is proposed. The atomically-thick GNR is modeled using a nonlocal transparent surface impedance boundary condition (SIBC) incorporated into the DGTD scheme. Since the conductivity is a complicated function of q (and one cannot find an analytical Fourier transform pair between q and spatial differential operators), an exact time domain SIBC model cannot be derived. To overcome this problem, the conductivity is approximated by its Taylor series in spectral domain under low-q assumption. This approach permits expressing the time domain SIBC in the form of a second-order partial differential equation (PDE) in current density and electric field intensity. To permit easy incorporation of this PDE with the DGTD algorithm, three auxiliary variables, which degenerate the second-order (temporal and spatial) differential operators to first-order ones, are introduced. Regarding to the temporal dispersion effects, the auxiliary differential equation (ADE) method is utilized to eliminates the expensive temporal convolutions. To demonstrate the applicability of the proposed scheme, numerical results, which involve characterization of spatial dispersion effects on the transfer impedance matrix of GNR interconnects, are presented.

SmPL: A Domain-Specific Language for Specifying Collateral Evolutions in Linux Device Drivers

DEFF Research Database (Denmark)

Padioleau, Yoann; Lawall, Julia Laetitia; Muller, Gilles

2007-01-01

identifying the affected files and modifying all of the code fragments in these files that in some way depend on the changed interface. We have studied the collateral evolution problem in the context of Linux device drivers. Currently, collateral evolutions in Linux are mostly done manually using a text...

Equivalence of linear canonical transform domains to fractional Fourier domains and the bicanonical width product: a generalization of the space-bandwidth product.

Science.gov (United States)

Oktem, Figen S; Ozaktas, Haldun M

2010-08-01

Linear canonical transforms (LCTs) form a three-parameter family of integral transforms with wide application in optics. We show that LCT domains correspond to scaled fractional Fourier domains and thus to scaled oblique axes in the space-frequency plane. This allows LCT domains to be labeled and ordered by the corresponding fractional order parameter and provides insight into the evolution of light through an optical system modeled by LCTs. If a set of signals is highly confined to finite intervals in two arbitrary LCT domains, the space-frequency (phase space) support is a parallelogram. The number of degrees of freedom of this set of signals is given by the area of this parallelogram, which is equal to the bicanonical width product but usually smaller than the conventional space-bandwidth product. The bicanonical width product, which is a generalization of the space-bandwidth product, can provide a tighter measure of the actual number of degrees of freedom, and allows us to represent and process signals with fewer samples.

Differential recognition of syk-binding sites by each of the two phosphotyrosine-binding pockets of the Vav SH2 domain.

Science.gov (United States)

Chen, Chih-Hong; Piraner, Dan; Gorenstein, Nina M; Geahlen, Robert L; Beth Post, Carol

2013-11-01

The association of spleen tyrosine kinase (Syk), a central tyrosine kinase in B cell signaling, with Vav SH2 domain is controlled by phosphorylation of two closely spaced tyrosines in Syk linker B: Y342 and Y346. Previous studies established both singly phosphorylated and doubly phosphorylated forms play a role in signaling. The structure of the doubly phosphorylated form identified a new recognition of phosphotyrosine whereby two phosphotyrosines bind simultaneously to the Vav SH2 domain, one in the canonical pTyr pocket and one in the specificity pocket on the opposite side of the central β-sheet. It is unknown if the specificity pocket can bind phosphotyrosine independent of phosphotyrosine binding the pTyr pocket. To address this gap in knowledge, we determined the structure of the complex between Vav1 SH2 and a peptide (SykLB-YpY) modeling the singly phosphorylated-Y346 form of Syk with unphosphorylated Y342. The nuclear magnetic resonance (NMR) data conclusively establish that recognition of phosphotyrosine is swapped between the two pockets; phosphorylated pY346 binds the specificity pocket of Vav1 SH2, and unphosphorylated Y342 occupies what is normally the pTyr binding pocket. Nearly identical changes in chemical shifts occurred upon binding all three forms of singly and doubly phosphorylated peptides; however, somewhat smaller shift perturbations for SykLB-YpY from residues in regions of high internal mobility suggest that internal motions are coupled to binding affinity. The differential recognition that includes this swapped binding of phosphotyrosine to the specificity pocket of Vav SH2 increases the repertoire of possible phosphotyrosine binding by SH2 domains in regulating protein-protein interactions in cellular signaling. Copyright © 2013 Wiley Periodicals, Inc.

Frequency-Domain Tomography for Single-shot, Ultrafast Imaging of Evolving Laser-Plasma Accelerators

Science.gov (United States)

Li, Zhengyan; Zgadzaj, Rafal; Wang, Xiaoming; Downer, Michael

2011-10-01

Intense laser pulses propagating through plasma create plasma wakefields that often evolve significantly, e.g. by expanding and contracting. However, such dynamics are known in detail only through intensive simulations. Laboratory visualization of evolving plasma wakes in the ``bubble'' regime is important for optimizing and scaling laser-plasma accelerators. Recently snap-shots of quasi-static wakes were recorded using frequency-domain holography (FDH). To visualize the wake's evolution, we have generalized FDH to frequency-domain tomography (FDT), which uses multiple probes propagating at different angles with respect to the pump pulse. Each probe records a phase streak, imprinting a partial record of the evolution of pump-created structures. We then topographically reconstruct the full evolution from all phase streaks. To prove the concept, a prototype experiment visualizing nonlinear index evolution in glass is demonstrated. Four probes propagating at 0, 0.6, 2, 14 degrees to the index ``bubble'' are angularly and temporally multiplexed to a single spectrometer to achieve cost-effective FDT. From these four phase streaks, an FDT algorithm analogous to conventional CT yields a single-shot movie of the pump's self-focusing dynamics.

Coronary artery segmentation in X-ray angiogram using Gabor filters and differential evolution

International Nuclear Information System (INIS)

Cervantes S, F.; Hernandez A, A.; Cruz A, I.; Solorio M, S.; Cordova F, T.; Avina C, J. G.

2016-10-01

Segmentation of coronary arteries in X-ray angiograms represents an essential task for computer-aided diagnosis, since it can help cardiologists in diagnosing and monitoring vascular abnormalities. Due to the main disadvantages of the X-ray angiograms are the nonuniform illumination, and the weak contrast between blood vessels and image background, different vessel enhancement methods have been introduced. In this paper, a novel method for blood vessel enhancement based on Gabor filters tuned using the optimization strategy of Differential evolution (De) is proposed. Because the Gabor filters are governed by three different parameters, the optimal selection of those parameters is highly desirable in order to maximize the vessel detection rate while reducing the computational cost of the training stage. To obtain the optimal set of parameters for the Gabor filters, the area (Az) under the receiver operating characteristic curve is used as objective function. In the experimental results, the proposed method obtained the highest detection performance with Az = 0.956 using a test set of 60 angiograms, and Az = 0.934 with a training set of 20 angiograms compared with different state-of-the-art vessel detection methods. In addition, the experimental results in terms of computational time have also shown that the proposed method can be highly suitable for clinical decision support. (Author)

Coronary artery segmentation in X-ray angiogram using Gabor filters and differential evolution

Energy Technology Data Exchange (ETDEWEB)

Cervantes S, F.; Hernandez A, A.; Cruz A, I. [Centro de Investigacion en Matematicas, A. C., Jalisco s/n, Col. Valenciana, 36240 Guanajuato, Gto. (Mexico); Solorio M, S. [IMSS, Unidad de Investigacion, UMAE Hospital de Especialidades No. 1 del Centro Medico Nacional del Bajio, 37260 Leon, Guanajuato (Mexico); Cordova F, T. [Universidad de Guanajuato, Departamento de Ingenieria Fisica, 37150 Leon, Guanajuato (Mexico); Avina C, J. G., E-mail: ivan.cruz@cimat.mx [Universidad de Guanajuato, Departamento de Electronica, 36885 Salamanca, Guanajuato (Mexico)

2016-10-15

Segmentation of coronary arteries in X-ray angiograms represents an essential task for computer-aided diagnosis, since it can help cardiologists in diagnosing and monitoring vascular abnormalities. Due to the main disadvantages of the X-ray angiograms are the nonuniform illumination, and the weak contrast between blood vessels and image background, different vessel enhancement methods have been introduced. In this paper, a novel method for blood vessel enhancement based on Gabor filters tuned using the optimization strategy of Differential evolution (De) is proposed. Because the Gabor filters are governed by three different parameters, the optimal selection of those parameters is highly desirable in order to maximize the vessel detection rate while reducing the computational cost of the training stage. To obtain the optimal set of parameters for the Gabor filters, the area (Az) under the receiver operating characteristic curve is used as objective function. In the experimental results, the proposed method obtained the highest detection performance with Az = 0.956 using a test set of 60 angiograms, and Az = 0.934 with a training set of 20 angiograms compared with different state-of-the-art vessel detection methods. In addition, the experimental results in terms of computational time have also shown that the proposed method can be highly suitable for clinical decision support. (Author)

Integrated model of multiple kernel learning and differential evolution for EUR/USD trading.

Science.gov (United States)

Deng, Shangkun; Sakurai, Akito

2014-01-01

Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL) with differential evolution (DE) for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI), while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX) currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Integrated Model of Multiple Kernel Learning and Differential Evolution for EUR/USD Trading

Directory of Open Access Journals (Sweden)

Shangkun Deng

2014-01-01

Full Text Available Currency trading is an important area for individual investors, government policy decisions, and organization investments. In this study, we propose a hybrid approach referred to as MKL-DE, which combines multiple kernel learning (MKL with differential evolution (DE for trading a currency pair. MKL is used to learn a model that predicts changes in the target currency pair, whereas DE is used to generate the buy and sell signals for the target currency pair based on the relative strength index (RSI, while it is also combined with MKL as a trading signal. The new hybrid implementation is applied to EUR/USD trading, which is the most traded foreign exchange (FX currency pair. MKL is essential for utilizing information from multiple information sources and DE is essential for formulating a trading rule based on a mixture of discrete structures and continuous parameters. Initially, the prediction model optimized by MKL predicts the returns based on a technical indicator called the moving average convergence and divergence. Next, a combined trading signal is optimized by DE using the inputs from the prediction model and technical indicator RSI obtained from multiple timeframes. The experimental results showed that trading using the prediction learned by MKL yielded consistent profits.

Extraordinary molecular evolution in the PRDM9 fertility gene.

Directory of Open Access Journals (Sweden)

James H Thomas

2009-12-01

Full Text Available Recent work indicates that allelic incompatibility in the mouse PRDM9 (Meisetz gene can cause hybrid male sterility, contributing to genetic isolation and potentially speciation. The only phenotype of mouse PRDM9 knockouts is a meiosis I block that causes sterility in both sexes. The PRDM9 gene encodes a protein with histone H3(K4 trimethyltransferase activity, a KRAB domain, and a DNA-binding domain consisting of multiple tandem C2H2 zinc finger (ZF domains. We have analyzed human coding polymorphism and interspecies evolutionary changes in the PRDM9 gene. The ZF domains of PRDM9 are evolving very rapidly, with compelling evidence of positive selection in primates. Positively selected amino acids are predominantly those known to make nucleotide specific contacts in C2H2 zinc fingers. These results suggest that PRDM9 is subject to recurrent selection to change DNA-binding specificity. The human PRDM9 protein is highly polymorphic in its ZF domains and nearly all polymorphisms affect the same nucleotide contact residues that are subject to positive selection. ZF domain nucleotide sequences are strongly homogenized within species, indicating that interfinger recombination contributes to their evolution. PRDM9 has previously been assumed to be a transcription factor required to induce meiosis specific genes, a role that is inconsistent with its molecular evolution. We suggest instead that PRDM9 is involved in some aspect of centromere segregation conflict and that rapidly evolving centromeric DNA drives changes in PRDM9 DNA-binding domains.

Directed evolution of the TALE N-terminal domain for recognition of all 5′ bases

Science.gov (United States)

Lamb, Brian M.; Mercer, Andrew C.; Barbas, Carlos F.

2013-01-01

Transcription activator-like effector (TALE) proteins can be designed to bind virtually any DNA sequence. General guidelines for design of TALE DNA-binding domains suggest that the 5′-most base of the DNA sequence bound by the TALE (the N0 base) should be a thymine. We quantified the N0 requirement by analysis of the activities of TALE transcription factors (TALE-TF), TALE recombinases (TALE-R) and TALE nucleases (TALENs) with each DNA base at this position. In the absence of a 5′ T, we observed decreases in TALE activity up to >1000-fold in TALE-TF activity, up to 100-fold in TALE-R activity and up to 10-fold reduction in TALEN activity compared with target sequences containing a 5′ T. To develop TALE architectures that recognize all possible N0 bases, we used structure-guided library design coupled with TALE-R activity selections to evolve novel TALE N-terminal domains to accommodate any N0 base. A G-selective domain and broadly reactive domains were isolated and characterized. The engineered TALE domains selected in the TALE-R format demonstrated modularity and were active in TALE-TF and TALEN architectures. Evolved N-terminal domains provide effective and unconstrained TALE-based targeting of any DNA sequence as TALE binding proteins and designer enzymes. PMID:23980031

Source Reconstruction of Brain Potentials Using Bayesian Model Averaging to Analyze Face Intra-Domain vs. Face-Occupation Cross-Domain Processing.

Science.gov (United States)

Olivares, Ela I; Lage-Castellanos, Agustín; Bobes, María A; Iglesias, Jaime

2018-01-01

We investigated the neural correlates of the access to and retrieval of face structure information in contrast to those concerning the access to and retrieval of person-related verbal information, triggered by faces. We experimentally induced stimulus familiarity via a systematic learning procedure including faces with and without associated verbal information. Then, we recorded event-related potentials (ERPs) in both intra-domain (face-feature) and cross-domain (face-occupation) matching tasks while N400-like responses were elicited by incorrect eyes-eyebrows completions and occupations, respectively. A novel Bayesian source reconstruction approach plus conjunction analysis of group effects revealed that in both cases the generated N170s were of similar amplitude but had different neural origin. Thus, whereas the N170 of faces was associated predominantly to right fusiform and occipital regions (the so-called "Fusiform Face Area", "FFA" and "Occipital Face Area", "OFA", respectively), the N170 of occupations was associated to a bilateral very posterior activity, suggestive of basic perceptual processes. Importantly, the right-sided perceptual P200 and the face-related N250 were evoked exclusively in the intra-domain task, with sources in OFA and extensively in the fusiform region, respectively. Regarding later latencies, the intra-domain N400 seemed to be generated in right posterior brain regions encompassing mainly OFA and, to some extent, the FFA, likely reflecting neural operations triggered by structural incongruities. In turn, the cross-domain N400 was related to more anterior left-sided fusiform and temporal inferior sources, paralleling those described previously for the classic verbal N400. These results support the existence of differentiated neural streams for face structure and person-related verbal processing triggered by faces, which can be activated differentially according to specific task demands.

Source Reconstruction of Brain Potentials Using Bayesian Model Averaging to Analyze Face Intra-Domain vs. Face-Occupation Cross-Domain Processing

Directory of Open Access Journals (Sweden)

Ela I. Olivares

2018-03-01

Full Text Available We investigated the neural correlates of the access to and retrieval of face structure information in contrast to those concerning the access to and retrieval of person-related verbal information, triggered by faces. We experimentally induced stimulus familiarity via a systematic learning procedure including faces with and without associated verbal information. Then, we recorded event-related potentials (ERPs in both intra-domain (face-feature and cross-domain (face-occupation matching tasks while N400-like responses were elicited by incorrect eyes-eyebrows completions and occupations, respectively. A novel Bayesian source reconstruction approach plus conjunction analysis of group effects revealed that in both cases the generated N170s were of similar amplitude but had different neural origin. Thus, whereas the N170 of faces was associated predominantly to right fusiform and occipital regions (the so-called “Fusiform Face Area”, “FFA” and “Occipital Face Area”, “OFA”, respectively, the N170 of occupations was associated to a bilateral very posterior activity, suggestive of basic perceptual processes. Importantly, the right-sided perceptual P200 and the face-related N250 were evoked exclusively in the intra-domain task, with sources in OFA and extensively in the fusiform region, respectively. Regarding later latencies, the intra-domain N400 seemed to be generated in right posterior brain regions encompassing mainly OFA and, to some extent, the FFA, likely reflecting neural operations triggered by structural incongruities. In turn, the cross-domain N400 was related to more anterior left-sided fusiform and temporal inferior sources, paralleling those described previously for the classic verbal N400. These results support the existence of differentiated neural streams for face structure and person-related verbal processing triggered by faces, which can be activated differentially according to specific task demands.

The cysteine-rich core domain of REIC/Dkk-3 is critical for its effect on monocyte differentiation and tumor regression.

Science.gov (United States)

Kinoshita, Rie; Watanabe, Masami; Huang, Peng; Li, Shun-Ai; Sakaguchi, Masakiyo; Kumon, Hiromi; Futami, Junichiro

2015-06-01

Reduced expression in immortalized cells (REIC)/Dickkopf (Dkk)-3 is a tumor-suppressor gene and has been studied as a promising therapeutic gene for cancer gene therapy. Intratumoral injection of an adenovirus vector carrying the human REIC/Dkk-3 gene (Ad-REIC) elicits cancer cell-specific apoptosis and anticancer immune responses. The cytokine-like effect of secretory REIC/Dkk-3 on the induction of dendritic cell (DC)-like cell differentiation from monocytes plays a role in systemic anticancer immunity. In the present study, we generated recombinant full-length and N-terminally truncated REIC/Dkk-3 to characterize the biological activity of the protein. During the purification procedure, we identified a 17 kDa cysteine-rich stable product (C17-REIC) showing limited degradation. Further analysis showed that the C17-REIC domain was sufficient for the induction of DC-like cell differentiation from monocytes. Concomitant with the differentiation of DCs, the REIC/Dkk-3 protein induced the phosphorylation of glycogen synthase kinase 3β (GSK-3β) and signal transducers and activators of transcription (STAT) at a level comparable to that of granulocyte/macrophage colony-stimulating factor. In a mouse model of subcutaneous renal adenocarcinoma, intraperitoneal injection of full-length and C17-REIC proteins exerted anticancer effects in parallel with the activation of immunocompetent cells such as DCs and cytotoxic T lymphocytes in peripheral blood. Taken together, our results indicate that the stable cysteine-rich core region of REIC/Dkk-3 is responsible for the induction of anticancer immune responses. Because REIC/Dkk-3 is a naturally circulating serum protein, the upregulation REIC/Dkk-3 protein expression could be a promising option for cancer therapy.

The metaphysics of evolution.

Science.gov (United States)

Dupré, John

2017-10-06

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. It then explores the implications of process metaphysics for conceptualizing evolution. After explaining what it is for an organism to be a process, the paper takes up the Hull/Ghiselin thesis of species as individuals and explores the conditions under which a species or lineage could constitute an individual process. It is argued that only sexual species satisfy these conditions, and that within sexual species the degree of organization varies. This, in turn, has important implications for species' evolvability. One important moral is that evolution will work differently in different biological domains.

A Novel Discrete Differential Evolution Algorithm for the Vehicle Routing Problem in B2C E-Commerce

Science.gov (United States)

Xia, Chao; Sheng, Ying; Jiang, Zhong-Zhong; Tan, Chunqiao; Huang, Min; He, Yuanjian

2015-12-01

In this paper, a novel discrete differential evolution (DDE) algorithm is proposed to solve the vehicle routing problems (VRP) in B2C e-commerce, in which VRP is modeled by the incomplete graph based on the actual urban road system. First, a variant of classical VRP is described and a mathematical programming model for the variant is given. Second, the DDE is presented, where individuals are represented as the sequential encoding scheme, and a novel reparation operator is employed to repair the infeasible solutions. Furthermore, a FLOYD operator for dealing with the shortest route is embedded in the proposed DDE. Finally, an extensive computational study is carried out in comparison with the predatory search algorithm and genetic algorithm, and the results show that the proposed DDE is an effective algorithm for VRP in B2C e-commerce.

Ferroelectric Polarization Switching Dynamics and Domain Growth of Triglycine Sulfate and Imidazolium Perchlorate

KAUST Repository

Ma, He

2016-04-10

The weak bond energy and large anisotropic domain wall energy induce many special characteristics of the domain nucleation, growth, and polarization switch in triglycine sulfate (TGS) and imidazolium perchlorate (IM), two typical molecular ferroelectrics. Their domain nucleation and polarization switch are rather slower than those of conventional oxide ferroelectrics, which may be due to the weaker bond energy of hydrogen bond or van der Waals bond than that of ionic bond. These chemical bonds dominate the elastic energy, with the latter being an important component of domain wall energy and playing an important role in domain nucleation and domain growth. The ratio of anisotropic domain wall energy to Gibbs free energy is large in TGS and IM, which allows a favorable domain shape and a special domain evolution under a certain electric field. Therefore, this study not only sheds light on the physical nature but also indicates the application direction for molecular ferroelectrics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

Rolling Force Prediction in Heavy Plate Rolling Based on Uniform Differential Neural Network

Directory of Open Access Journals (Sweden)

Fei Zhang

2016-01-01

Full Text Available Accurate prediction of the rolling force is critical to assuring the quality of the final product in steel manufacturing. Exit thickness of plate for each pass is calculated from roll gap, mill spring, and predicted roll force. Ideal pass scheduling is dependent on a precise prediction of the roll force in each pass. This paper will introduce a concept that allows obtaining the material model parameters directly from the rolling process on an industrial scale by the uniform differential neural network. On the basis of the characteristics that the uniform distribution can fully characterize the solution space and enhance the diversity of the population, uniformity research on differential evolution operator is made to get improved crossover with uniform distribution. When its original function is transferred with a transfer function, the uniform differential evolution algorithms can quickly solve complex optimization problems. Neural network structure and weights threshold are optimized by uniform differential evolution algorithm, and a uniform differential neural network is formed to improve rolling force prediction accuracy in process control system.

Differential sensitivity of Src-family kinases to activation by SH3 domain displacement.

Directory of Open Access Journals (Sweden)

Jamie A Moroco

Full Text Available Src-family kinases (SFKs are non-receptor protein-tyrosine kinases involved in a variety of signaling pathways in virtually every cell type. The SFKs share a common negative regulatory mechanism that involves intramolecular interactions of the SH3 domain with the PPII helix formed by the SH2-kinase linker as well as the SH2 domain with a conserved phosphotyrosine residue in the C-terminal tail. Growing evidence suggests that individual SFKs may exhibit distinct activation mechanisms dictated by the relative strengths of these intramolecular interactions. To elucidate the role of the SH3:linker interaction in the regulation of individual SFKs, we used a synthetic SH3 domain-binding peptide (VSL12 to probe the sensitivity of downregulated c-Src, Hck, Lyn and Fyn to SH3-based activation in a kinetic kinase assay. All four SFKs responded to VSL12 binding with enhanced kinase activity, demonstrating a conserved role for SH3:linker interaction in the control of catalytic function. However, the sensitivity and extent of SH3-based activation varied over a wide range. In addition, autophosphorylation of the activation loops of c-Src and Hck did not override regulatory control by SH3:linker displacement, demonstrating that these modes of activation are independent. Our results show that despite the similarity of their downregulated conformations, individual Src-family members show diverse responses to activation by domain displacement which may reflect their adaptation to specific signaling environments in vivo.

Modeling evolution of the mind and cultures: emotional Sapir-Whorf hypothesis

Science.gov (United States)

Perlovsky, Leonid I.

2009-05-01

Evolution of cultures is ultimately determined by mechanisms of the human mind. The paper discusses the mechanisms of evolution of language from primordial undifferentiated animal cries to contemporary conceptual contents. In parallel with differentiation of conceptual contents, the conceptual contents were differentiated from emotional contents of languages. The paper suggests the neural brain mechanisms involved in these processes. Experimental evidence and theoretical arguments are discussed, including mathematical approaches to cognition and language: modeling fields theory, the knowledge instinct, and the dual model connecting language and cognition. Mathematical results are related to cognitive science, linguistics, and psychology. The paper gives an initial mathematical formulation and mean-field equations for the hierarchical dynamics of both the human mind and culture. In the mind heterarchy operation of the knowledge instinct manifests through mechanisms of differentiation and synthesis. The emotional contents of language are related to language grammar. The conclusion is an emotional version of Sapir-Whorf hypothesis. Cultural advantages of "conceptual" pragmatic cultures, in which emotionality of language is diminished and differentiation overtakes synthesis resulting in fast evolution at the price of self doubts and internal crises are compared to those of traditional cultures where differentiation lags behind synthesis, resulting in cultural stability at the price of stagnation. Multi-language, multi-ethnic society might combine the benefits of stability and fast differentiation. Unsolved problems and future theoretical and experimental directions are discussed.

Environmental/economic dispatch problem of power system by using an enhanced multi-objective differential evolution algorithm

International Nuclear Information System (INIS)

Lu Youlin; Zhou Jianzhong; Qin Hui; Wang Ying; Zhang Yongchuan

2011-01-01

An enhanced multi-objective differential evolution algorithm (EMODE) is proposed in this paper to solve environmental/economic dispatch (EED) problem by considering the minimal of fuel cost and emission effects synthetically. In the proposed algorithm, an elitist archive technique is adopted to retain the non-dominated solutions obtained during the evolutionary process, and the operators of DE are modified according to the characteristics of multi-objective optimization problems. Moreover, in order to avoid premature convergence, a local random search (LRS) operator is integrated with the proposed method to improve the convergence performance. In view of the difficulties of handling the complicated constraints of EED problem, a new heuristic constraints handling method without any penalty factor settings is presented. The feasibility and effectiveness of the proposed EMODE method is demonstrated for a test power system. Compared with other methods, EMODE can get higher quality solutions by reducing the fuel cost and the emission effects synthetically.

Thermal response of domains in cardiolipin content bilayers

Energy Technology Data Exchange (ETDEWEB)

Domenech, Oscar [Departament de Quimica-Fisica, Facultat de Quimica, U.B. 08028 (Spain); Morros, Antoni [Unitat de Biofisica, Departament de Bioquimica i Biologia Molecular, Facultat de Medicina (Spain); Servei de Ressonancia Magnetica Nuclear (SeRMN), U.A.B., 08193 Bellaterra, Barcelona (Spain); Cabanas, Miquel E. [Servei de Ressonancia Magnetica Nuclear (SeRMN), U.A.B., 08193 Bellaterra, Barcelona (Spain); Montero, M. Teresa [Departament de Fisicoquimica, Facultat de Farmacia, U.B. 08028 (Spain); Hernandez-Borrell, Jordi [Departament de Fisicoquimica, Facultat de Farmacia, U.B. 08028 (Spain)], E-mail: jordihernandezborrell@ub.edu

2007-10-15

In the study described here, supported planar bilayers (SPBs) of 1-palmitoy-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE):cardiolipin (CL) (0.8:0.2, mol/mol) were examined using atomic force microscopy (AFM). SPBs were formed from suspensions of POPE:CL (0.8:0.2, mol/mol) in inverted hexagonal (H{sub II}) phases (buffer containing Ca{sup 2+}). Three laterally segregated domains which differ in height were observed at 24 degC. Based on the area accounted for each domain and the nominal composition of the mixture, we interpret that the higher domain is formed by CL, while the intermediate and lower domains (LDs) are formed by POPE. The three domains respond to temperature increase with relative changes in their area. At 37 degC, we observed that the increase in the area of the intermediate domain occurs at the expense of the LD. {sup 31}P-nuclear magnetic resonance ({sup 31}P-NMR) and Differential scanning calorimetry (DSC) were used in combination with AFM to characterize the phase behavior of the suspensions and to elucidate the nature of the structures observed.

Differential equations with applications in cancer diseases.

Science.gov (United States)

Ilea, M; Turnea, M; Rotariu, M

2013-01-01

Mathematical modeling is a process by which a real world problem is described by a mathematical formulation. The cancer modeling is a highly challenging problem at the frontier of applied mathematics. A variety of modeling strategies have been developed, each focusing on one or more aspects of cancer. The vast majority of mathematical models in cancer diseases biology are formulated in terms of differential equations. We propose an original mathematical model with small parameter for the interactions between these two cancer cell sub-populations and the mathematical model of a vascular tumor. We work on the assumption that, the quiescent cells' nutrient consumption is long. One the equations system includes small parameter epsilon. The smallness of epsilon is relative to the size of the solution domain. MATLAB simulations obtained for transition rate from the quiescent cells' nutrient consumption is long, we show a similar asymptotic behavior for two solutions of the perturbed problem. In this system, the small parameter is an asymptotic variable, different from the independent variable. The graphical output for a mathematical model of a vascular tumor shows the differences in the evolution of the tumor populations of proliferating, quiescent and necrotic cells. The nutrient concentration decreases sharply through the viable rim and tends to a constant level in the core due to the nearly complete necrosis in this region. Many mathematical models can be quantitatively characterized by ordinary differential equations or partial differential equations. The use of MATLAB in this article illustrates the important role of informatics in research in mathematical modeling. The study of avascular tumor growth cells is an exciting and important topic in cancer research and will profit considerably from theoretical input. Interpret these results to be a permanent collaboration between math's and medical oncologists.

Direct approach for solving nonlinear evolution and two-point

Indian Academy of Sciences (India)

Time-delayed nonlinear evolution equations and boundary value problems have a wide range of applications in science and engineering. In this paper, we implement the differential transform method to solve the nonlinear delay differential equation and boundary value problems. Also, we present some numerical examples ...

Evolution of magnetic islands in tokamaks

International Nuclear Information System (INIS)

Dubois, M.; Samain, A.

1980-01-01

The evolution of magnetic islands is studied by a variational method on the assumption that it consists of a sequence of equilibria. The characteristic time of the evolution is then a resistive time. The sequence may, however, reach a configuration where the angle of the flux lines at the X-point vanishes. This behaviour is plausible in the case of q=1 islands, in contrast to the case of q>1. The subsequent evolution must assign a certain role to inertia. It is shown that this role cannot consist of a rapid displacement of the separatrix preserving its topology, but must be due to the onset of small-grain kinetic and magnetic turbulence extending from the separatrix in a large domain. (author)

Study of the evolution of nitrogen compounds during grape ripening. application to differentiate grape varieties and cultivated systems.

Science.gov (United States)

Garde-Cerdán, Teresa; Lorenzo, Cándida; Lara, José Félix; Pardo, Francisco; Ancín-Azpilicueta, Carmen; Salinas, M Rosario

2009-03-25

The aim of this work was to study the evolution of amino acids and ammonium during grape ripening and to evaluate its application to differentiate grape varieties and cultivated systems (organic and nonorganic). For this purpose, Monastrell, Syrah, Merlot, and Petit Verdot grapes produced using conventional agriculture and Monastrell grape cultivated using organic agriculture, collected during two consecutive harvests at different stages of ripening, were studied. These years of harvest were very different climatic years; even so, the grape varieties presented similar qualitative compositions. Therefore, the percentage of amino acids at harvest moment allowed differentiation of grapes according to variety and cultivated system, regardless of the year. The nitrogen composition could allow estimation of the fermentative aroma potential of grapes. Thus, Syrah was the grape with the greatest aroma potential at harvest. Monastrell nonorganic grape had a concentration of nitrogen compounds superior to that of Monastrell organic grape. In Monastrell, Syrah, and Merlot, traditional varieties in the area, the highest concentration of nitrogen compounds coincided with the highest degrees Baume/total acidity ratio and color index during 2007. Consequently, technological and phenolic maturity of these grape varieties coincided with the maximum composition of nitrogen compounds. However, in 2008, this did not happen because grape ripening was irregular as a consequence of different climatological conditions.

Evolution of the RNase P RNA structural domain in Leptospira spp

NARCIS (Netherlands)

Ravishankar, Vigneshwaran; Ahmed, Ahmed; Sivagnanam, Ulaganathan; Muthuraman, Krishnaraja; Karthikaichamy, Anbarasu; Wilson, Herald A.; Devendran, Ajay; Hartskeerl, Rudy A.; Raj, Stephen M. L.

2014-01-01

We have employed the RNase P RNA (RPR) gene, which is present as single copy in chromosome I of Leptospira spp. to investigate the phylogeny of structural domains present in the RNA subunit of the tRNA processing enzyme, RNase P. RPR gene sequences of 150 strains derived from NCBI database along

Pan-Domain Analysis of ZIP Zinc Transporters

Directory of Open Access Journals (Sweden)

Laura E. Lehtovirta-Morley

2017-12-01

Full Text Available The ZIP (Zrt/Irt-like protein family of zinc transporters is found in all three domains of life. However, little is known about the phylogenetic relationship amongst ZIP transporters, their distribution, or their origin. Here we employed phylogenetic analysis to explore the evolution of ZIP transporters, with a focus on the major human fungal pathogen, Candida albicans. Pan-domain analysis of bacterial, archaeal, fungal, and human proteins revealed a complex relationship amongst the ZIP family members. Here we report (i a eukaryote-wide group of cellular zinc importers, (ii a fungal-specific group of zinc importers having genetic association with the fungal zincophore, and, (iii a pan-kingdom supercluster made up of two distinct subgroups with orthologues in bacterial, archaeal, and eukaryotic phyla.

[Structure and evolution of the eukaryotic FANCJ-like proteins].

Science.gov (United States)

Wuhe, Jike; Zefeng, Wu; Sanhong, Fan; Xuguang, Xi

2015-02-01

The FANCJ-like protein family is a class of ATP-dependent helicases that can catalytically unwind duplex DNA along the 5'-3' direction. It is involved in the processes of DNA damage repair, homologous recombination and G-quadruplex DNA unwinding, and plays a critical role in maintaining genome integrity. In this study, we systemically analyzed FNACJ-like proteins from 47 eukaryotic species and discussed their sequences diversity, origin and evolution, motif organization patterns and spatial structure differences. Four members of FNACJ-like proteins, including XPD, CHL1, RTEL1 and FANCJ, were found in eukaryotes, but some of them were seriously deficient in most fungi and some insects. For example, the Zygomycota fungi lost RTEL1, Basidiomycota and Ascomycota fungi lost RTEL1 and FANCJ, and Diptera insect lost FANCJ. FANCJ-like proteins contain canonical motor domains HD1 and HD2, and the HD1 domain further integrates with three unique domains Fe-S, Arch and Extra-D. Fe-S and Arch domains are relatively conservative in all members of the family, but the Extra-D domain is lost in XPD and differs from one another in rest members. There are 7, 10 and 2 specific motifs found from the three unique domains respectively, while 5 and 12 specific motifs are found from HD1 and HD2 domains except the conserved motifs reported previously. By analyzing the arrangement pattern of these specific motifs, we found that RTEL1 and FANCJ are more closer and share two specific motifs Vb2 and Vc in HD2 domain, which are likely related with their G-quadruplex DNA unwinding activity. The evidence of evolution showed that FACNJ-like proteins were originated from a helicase, which has a HD1 domain inserted by extra Fe-S domain and Arch domain. By three continuous gene duplication events and followed specialization, eukaryotes finally possessed the current four members of FANCJ-like proteins.

A role for chromatin topology in imprinted domain regulation.

Science.gov (United States)

MacDonald, William A; Sachani, Saqib S; White, Carlee R; Mann, Mellissa R W

2016-02-01

Recently, many advancements in genome-wide chromatin topology and nuclear architecture have unveiled the complex and hidden world of the nucleus, where chromatin is organized into discrete neighbourhoods with coordinated gene expression. This includes the active and inactive X chromosomes. Using X chromosome inactivation as a working model, we utilized publicly available datasets together with a literature review to gain insight into topologically associated domains, lamin-associated domains, nucleolar-associating domains, scaffold/matrix attachment regions, and nucleoporin-associated chromatin and their role in regulating monoallelic expression. Furthermore, we comprehensively review for the first time the role of chromatin topology and nuclear architecture in the regulation of genomic imprinting. We propose that chromatin topology and nuclear architecture are important regulatory mechanisms for directing gene expression within imprinted domains. Furthermore, we predict that dynamic changes in chromatin topology and nuclear architecture play roles in tissue-specific imprint domain regulation during early development and differentiation.

Evolution of defect signatures at ferroelectric domain walls in Mg-doped LiNbO{sub 3}

Energy Technology Data Exchange (ETDEWEB)

Nataf, Guillaume F. [Materials, Research and Technology Department, Luxembourg Institute of Science and Technology, 41 Rue du Brill, 4422, Belvaux (Luxembourg); Service de Physique de l' Etat Condense, DSM/IRAMIS/SPEC, CNRS UMR 3680, CEA Saclay, 91191, Gif sur Yvette cedex (France); Guennou, Mael [Materials, Research and Technology Department, Luxembourg Institute of Science and Technology, 41 Rue du Brill, 4422, Belvaux (Luxembourg); Haussmann, Alexander [Institut fuer Angewandte Photophysik, Technische Universitaet Dresden, George-Baehr-Str. 1, 01069, Dresden (Germany); Barrett, Nick [Service de Physique de l' Etat Condense, DSM/IRAMIS/SPEC, CNRS UMR 3680, CEA Saclay, 91191, Gif sur Yvette cedex (France); Kreisel, Jens [Materials, Research and Technology Department, Luxembourg Institute of Science and Technology, 41 Rue du Brill, 4422, Belvaux (Luxembourg); Physics and Materials Science Research Unit, University of Luxembourg, 41 Rue du Brill, 4422, Belvaux (Luxembourg)

2016-03-15

The domain structure of uniaxial ferroelectric lithium niobate single crystals is investigated using Raman spectroscopy mapping. The influence of doping with magnesium and poling at room temperature is studied by analysing frequency shifts at domain walls and their variations with dopant concentration and annealing conditions. It is shown that defects are stabilized at domain walls and that changes in the defect structures with Mg concentration can be probed by the shift of Raman modes. We show that the signatures of polar defects in the bulk and at the domain walls differ. (copyright 2016 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

An information theory framework for dynamic functional domain connectivity.

Science.gov (United States)

Vergara, Victor M; Miller, Robyn; Calhoun, Vince

2017-06-01

Dynamic functional network connectivity (dFNC) analyzes time evolution of coherent activity in the brain. In this technique dynamic changes are considered for the whole brain. This paper proposes an information theory framework to measure information flowing among subsets of functional networks call functional domains. Our method aims at estimating bits of information contained and shared among domains. The succession of dynamic functional states is estimated at the domain level. Information quantity is based on the probabilities of observing each dynamic state. Mutual information measurement is then obtained from probabilities across domains. Thus, we named this value the cross domain mutual information (CDMI). Strong CDMIs were observed in relation to the subcortical domain. Domains related to sensorial input, motor control and cerebellum form another CDMI cluster. Information flow among other domains was seldom found. Other methods of dynamic connectivity focus on whole brain dFNC matrices. In the current framework, information theory is applied to states estimated from pairs of multi-network functional domains. In this context, we apply information theory to measure information flow across functional domains. Identified CDMI clusters point to known information pathways in the basal ganglia and also among areas of sensorial input, patterns found in static functional connectivity. In contrast, CDMI across brain areas of higher level cognitive processing follow a different pattern that indicates scarce information sharing. These findings show that employing information theory to formally measured information flow through brain domains reveals additional features of functional connectivity. Copyright © 2017 Elsevier B.V. All rights reserved.

A highly accurate spectral method for the Navier–Stokes equations in a semi-infinite domain with flexible boundary conditions

Energy Technology Data Exchange (ETDEWEB)

Matsushima, Toshiki; Ishioka, Keiichi, E-mail: matsushima@kugi.kyoto-u.ac.jp, E-mail: ishioka@gfd-dennou.org [Graduate School of Science, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto 606-8502 (Japan)

2017-04-15

This paper presents a spectral method for numerically solving the Navier–Stokes equations in a semi-infinite domain bounded by a flat plane: the aim is to obtain high accuracy with flexible boundary conditions. The proposed use is for numerical simulations of small-scale atmospheric phenomena near the ground. We introduce basis functions that fit the semi-infinite domain, and an integral condition for vorticity is used to reduce the computational cost when solving the partial differential equations that appear when the viscosity term is treated implicitly. Furthermore, in order to ensure high accuracy, two iteration techniques are applied when solving the system of linear equations and in determining boundary values. This significantly reduces numerical errors, and the proposed method enables high-resolution numerical experiments. This is demonstrated by numerical experiments showing the collision of a vortex ring into a wall; these were performed using numerical models based on the proposed method. It is shown that the time evolution of the flow field is successfully obtained not only near the boundary, but also in a region far from the boundary. The applicability of the proposed method and the integral condition is discussed. (paper)

Differentiation of illicit drugs with THz time-domain spectroscopy

International Nuclear Information System (INIS)

Liu Guifeng; Ma Shihua; Ji Te; Zhao Hongwei; Wang Wenfeng

2010-01-01

The tera hertz time-domain spectroscopy (THz-TDS) was used for sensing and identifying illicit drugs. The absorption spectra of seven illicit drug samples(morphine and its hydrochloride, cocaine hydrochloride, codeine phosphate, papaverine hydrochloride, pethidine hydrochloride, and thebaine) were studied by THz-TDS at 0.3-2.0 THz at room temperature. The geometric structure and vibration frequencies of morphine were calculated by density functional theory. The four absorption features were dominated by intra-/inter-molecular collective or lattice vibration modes. Each illicit drug has a distinct signature in its THz spectra. The results indicate that the THz-TDS can be used to identify and discriminate illicit drugs by their characteristic fingerprints. (authors)

Thermal-driven evolution of magnetic domain structures in ultrathin films

Czech Academy of Sciences Publication Activity Database

Zablotskyy, Vitaliy A.; Maziewski, A.; Polyakova, T.

2006-01-01

Roč. 112, - (2006), s. 101-108 ISSN 1012-0394. [International School on Physics and Chemistry of Condensed Matter /17./ and International Symposium on Physics in Material Science /5./. Bialoweza, 21.06.2005-29.06.2005] EU Projects: European Commission(XE) 3177 - NANOMAG- LAB Grant - others:PSCSR(PL) 4T11B00624 Institutional research plan: CEZ:AV0Z10100520 Keywords : ultrathin magnetic films * magnetic domain * phase transitions Subject RIV: BM - Solid Matter Physics ; Magnetism Impact factor: 0.493, year: 2005

Software evolution and maintenance

CERN Document Server

Tripathy, Priyadarshi

2014-01-01

Software Evolution and Maintenance: A Practitioner's Approach is an accessible textbook for students and professionals, which collates the advances in software development and provides the most current models and techniques in maintenance.Explains two maintenance standards: IEEE/EIA 1219 and ISO/IEC14764Discusses several commercial reverse and domain engineering toolkitsSlides for instructors are available onlineInformation is based on the IEEE SWEBOK (Software Engineering Body of Knowledge)

Optimization of seasonal ARIMA models using differential evolution - simulated annealing (DESA) algorithm in forecasting dengue cases in Baguio City

Science.gov (United States)

Addawe, Rizavel C.; Addawe, Joel M.; Magadia, Joselito C.

2016-10-01

Accurate forecasting of dengue cases would significantly improve epidemic prevention and control capabilities. This paper attempts to provide useful models in forecasting dengue epidemic specific to the young and adult population of Baguio City. To capture the seasonal variations in dengue incidence, this paper develops a robust modeling approach to identify and estimate seasonal autoregressive integrated moving average (SARIMA) models in the presence of additive outliers. Since the least squares estimators are not robust in the presence of outliers, we suggest a robust estimation based on winsorized and reweighted least squares estimators. A hybrid algorithm, Differential Evolution - Simulated Annealing (DESA), is used to identify and estimate the parameters of the optimal SARIMA model. The method is applied to the monthly reported dengue cases in Baguio City, Philippines.

MUPBED - interworking challenges in a multi-domain and multi-technology network environment

DEFF Research Database (Denmark)

Foisel, Hans-Martin; Spaeth, Jan; Cavazzoni, Carlo

2007-01-01

Todays data transport networks are evolving continuously towards customer oriented and application aware networks. This evolution happens in Europe in a highly diverse network environment, covering multiple network domains, layers, technologies, control and management approaches. In this paper...

Mechanism of Dynamic Recrystallization and Evolution of Texture in the Hot Working Domains of the Processing Map for Mg-4Al-2Ba-2Ca Alloy

Directory of Open Access Journals (Sweden)

Kalidass Suresh

2017-12-01

Full Text Available The occurrence of dynamic recrystallization (DRX and its effect on the evolution of texture during uniaxial compression of a creep-resistant cast Mg-4Al-2Ba-2Ca alloy in the temperature range of 260–500 °C and strain rate range of 0.0003–10 s−1 has been studied using transmission electron microscopy and electron backscatter diffraction techniques with a view to understand its mechanism. For this purpose, a processing map has been developed for this alloy, which revealed two domains of DRX in the temperature and strain rate ranges of: (1 300–390 °C/0.0003–0.001 s−1 and (2 400–500 °C/0.0003–0.5 s−1. In Domain 1, DRX occurs by basal slip and recovery by dislocation climb, as indicated by the presence of planar slip bands and high dislocation density leading to tilt boundary formation and a low-intensity basal texture. On the other hand, DRX in Domain 2 occurs by second order pyramidal slip and recovery by cross-slip since the microstructure revealed tangled dislocation structure with twist boundaries and randomized texture. The high volume content of intermetallic phases Mg21Al3Ba2 and (Al,Mg2Ca eutectic phase is considered to be responsible for the observed hot deformation behavior.

Efficient Power Scheduling in Smart Homes Using Hybrid Grey Wolf Differential Evolution Optimization Technique with Real Time and Critical Peak Pricing Schemes

Directory of Open Access Journals (Sweden)

Muqaddas Naz

2018-02-01

Full Text Available With the emergence of automated environments, energy demand by consumers is increasing rapidly. More than 80% of total electricity is being consumed in the residential sector. This brings a challenging task of maintaining the balance between demand and generation of electric power. In order to meet such challenges, a traditional grid is renovated by integrating two-way communication between the consumer and generation unit. To reduce electricity cost and peak load demand, demand side management (DSM is modeled as an optimization problem, and the solution is obtained by applying meta-heuristic techniques with different pricing schemes. In this paper, an optimization technique, the hybrid gray wolf differential evolution (HGWDE, is proposed by merging enhanced differential evolution (EDE and gray wolf optimization (GWO scheme using real-time pricing (RTP and critical peak pricing (CPP. Load shifting is performed from on-peak hours to off-peak hours depending on the electricity cost defined by the utility. However, there is a trade-off between user comfort and cost. To validate the performance of the proposed algorithm, simulations have been carried out in MATLAB. Results illustrate that using RTP, the peak to average ratio (PAR is reduced to 53.02%, 29.02% and 26.55%, while the electricity bill is reduced to 12.81%, 12.012% and 12.95%, respectively, for the 15-, 30- and 60-min operational time interval (OTI. On the other hand, the PAR and electricity bill are reduced to 47.27%, 22.91%, 22% and 13.04%, 12%, 11.11% using the CPP tariff.

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

Science.gov (United States)

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.

CIME course on Control of Partial Differential Equations

CERN Document Server

Alabau-Boussouira, Fatiha; Glass, Olivier; Le Rousseau, Jérôme; Zuazua, Enrique

2012-01-01

The term “control theory” refers to the body of results - theoretical, numerical and algorithmic - which have been developed to influence the evolution of the state of a given system in order to meet a prescribed performance criterion. Systems of interest to control theory may be of very different natures. This monograph is concerned with models that can be described by partial differential equations of evolution. It contains five major contributions and is connected to the CIME Course on Control of Partial Differential Equations that took place in Cetraro (CS, Italy), July 19 - 23, 2010.  Specifically, it covers the stabilization of evolution equations, control of the Liouville equation, control in fluid mechanics, control and numerics for the wave equation, and Carleman estimates for elliptic and parabolic equations with application to control. We are confident this work will provide an authoritative reference work for all scientists who are interested in this field, representing at the same time a fri...

Evolution of electrical properties and domain configuration of Mn modified Pb(In1/2Nb1/2)O3-PbTiO3 single crystals

Science.gov (United States)

Qiao, Huimin; He, Chao; Yuan, Feifei; Wang, Zujian; Li, Xiuzhi; Liu, Ying; Guo, Haiyan; Long, Xifa

2018-04-01

The acceptor doped relaxor-based ferroelectric materials are useful for high power applications such as probes in ultrasound-guided high intensity focused ultrasound therapy. In addition, a high Curie temperature is desired because of wider temperature usage and improved temperature stability. Previous investigations have focused on Pb(Mg1/3Nb2/3)O3-PbTiO3 and Pb(Zn1/3Nb2/3)O3-PbTiO3 systems, which have a ultrahigh piezoelectric coefficient and dielectric constant, but a relatively low Curie temperature. It is desirable to study the binary relaxor-based system with a high Curie temperature. Therefore, Pb(In1/2Nb1/2)O3-PbTiO3 (PINT) single crystals were chosen to study the Mn-doped influence on their electrical properties and domain configuration. The evolution of ferroelectric hysteresis loops for doped and virgin samples exhibit the pinning effect in Mn-doped PINT crystals. The relaxation behaviors of doped and virgin samples are studied by fit of the modified Curie-Weiss law and Volgel-Fucher relation. In addition, a short-range correlation length was fitted to study the behavior of polar nanoregions based on the domain configuration obtained by piezoresponse force microscopy. Complex domain structures and smaller short-range correlation lengths (100-150 nm for Mn-doped PINT and >400 nm for pure PINT) were obtained in the Mn-doped PINT single crystals.

Predicting Community Evolution in Social Networks

Directory of Open Access Journals (Sweden)

Stanisław Saganowski

2015-05-01

Full Text Available Nowadays, sustained development of different social media can be observed worldwide. One of the relevant research domains intensively explored recently is analysis of social communities existing in social media as well as prediction of their future evolution taking into account collected historical evolution chains. These evolution chains proposed in the paper contain group states in the previous time frames and its historical transitions that were identified using one out of two methods: Stable Group Changes Identification (SGCI and Group Evolution Discovery (GED. Based on the observed evolution chains of various length, structural network features are extracted, validated and selected as well as used to learn classification models. The experimental studies were performed on three real datasets with different profile: DBLP, Facebook and Polish blogosphere. The process of group prediction was analysed with respect to different classifiers as well as various descriptive feature sets extracted from evolution chains of different length. The results revealed that, in general, the longer evolution chains the better predictive abilities of the classification models. However, chains of length 3 to 7 enabled the GED-based method to almost reach its maximum possible prediction quality. For SGCI, this value was at the level of 3–5 last periods.

Changing the cubic ferrimagnetic domain structure in temperature region of spin flip transition

International Nuclear Information System (INIS)

Djuraev, D.R.; Niyazov, L.N.; Saidov, K.S.; Sokolov, B.Yu.

2011-01-01

The transformation of cubic ferrimagnetic Tb 0.2 Y 2.8 Fe 5 O 12 domain structure has been studied by magneto optic method in the temperature region of spontaneous spin flip phase transition (SPT). It has been found that SPT occurs in a finite temperature interval where the coexistence of low- and high- temperature magnetic phase domains has observed. A character of domain structure evolution in temperature region of spin flip essentially depends on the presence of mechanical stresses in crystal. Interpretation of experimental results has been carried out within the framework of SPT theory for a cubic crystal. (authors)

Evolution of the snake body form reveals homoplasy in amniote Hox gene function.

Science.gov (United States)

Head, Jason J; Polly, P David

2015-04-02

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

Mixed-integer evolution strategies for parameter optimization and their applications to medical image analysis

NARCIS (Netherlands)

Li, Rui

2009-01-01

The target of this work is to extend the canonical Evolution Strategies (ES) from traditional real-valued parameter optimization domain to mixed-integer parameter optimization domain. This is necessary because there exist numerous practical optimization problems from industry in which the set of

Eps homology domain endosomal transport proteins differentially localize to the neuromuscular junction

Directory of Open Access Journals (Sweden)

Mate Suzanne E

2012-09-01

Full Text Available Abstract Background Recycling of endosomes is important for trafficking and maintenance of proteins at the neuromuscular junction (NMJ. We have previously shown high expression of the endocytic recycling regulator Eps15 homology domain-containing (EHD1 proteinin the Torpedo californica electric organ, a model tissue for investigating a cholinergic synapse. In this study, we investigated the localization of EHD1 and its paralogs EHD2, EHD3, and EHD4 in mouse skeletal muscle, and assessed the morphological changes in EHD1−/− NMJs. Methods Localization of the candidate NMJ protein EHD1 was assessed by confocal microscopy analysis of whole-mount mouse skeletal muscle fibers after direct gene transfer and immunolabeling. The potential function of EHD1 was assessed by specific force measurement and α-bungarotoxin-based endplate morphology mapping in EHD1−/− mouse skeletal muscle. Results Endogenous EHD1 localized to primary synaptic clefts of murine NMJ, and this localization was confirmed by expression of recombinant green fluorescent protein labeled-EHD1 in murine skeletal muscle in vivo. EHD1−/− mouse skeletal muscle had normal histology and NMJ morphology, and normal specific force generation during muscle contraction. The EHD 1–4 proteins showed differential localization in skeletal muscle: EHD2 to muscle vasculature, EHD3 to perisynaptic regions, and EHD4 to perinuclear regions and to primary synaptic clefts, but at lower levels than EHD1. Additionally, specific antibodies raised against mammalian EHD1-4 recognized proteins of the expected mass in the T. californica electric organ. Finally, we found that EHD4 expression was more abundant in EHD1−/− mouse skeletal muscle than in wild-type skeletal muscle. Conclusion EHD1 and EHD4 localize to the primary synaptic clefts of the NMJ. Lack of obvious defects in NMJ structure and muscle function in EHD1−/− muscle may be due to functional compensation by other EHD paralogs.

Domain-Specific Impulsivity in School-Age Children

Science.gov (United States)

Tsukayama, Eli; Duckworth, Angela Lee; Kim, Betty

2013-01-01

Impulsivity is a salient individual difference in children with well-established predictive validity for life outcomes. The current investigation proposes that impulsive behaviors vary systematically by domain. In a series of studies with ethnically and socioeconomically diverse samples of middle school students, we find that schoolwork-related and interpersonal-related impulsivity, as observed by teachers, parents, and the students themselves, are distinct, moderately correlated behavioral tendencies. Each demonstrates differentiated relationships with dimensions of childhood temperament, Big Five personality factors, and outcomes, such as sociometric popularity, report card grades, and classroom conduct. Implications for theoretical conceptions of impulsivity as well as for practical applications (e.g., domain-specific interventions) are discussed. PMID:24118714

Artificial domain duplication replicates evolutionary history of ketol-acid reductoisomerases.

Science.gov (United States)

Cahn, Jackson K B; Brinkmann-Chen, Sabine; Buller, Andrew R; Arnold, Frances H

2016-07-01

The duplication of protein structural domains has been proposed as a common mechanism for the generation of new protein folds. A particularly interesting case is the class II ketol-acid reductoisomerase (KARI), which putatively arose from an ancestral class I KARI by duplication of the C-terminal domain and corresponding loss of obligate dimerization. As a result, the class II enzymes acquired a deeply embedded figure-of-eight knot. To test this evolutionary hypothesis we constructed a novel class II KARI by duplicating the C-terminal domain of a hyperthermostable class I KARI. The new protein is monomeric, as confirmed by gel filtration and X-ray crystallography, and has the deeply knotted class II KARI fold. Surprisingly, its catalytic activity is nearly unchanged from the parent KARI. This provides strong evidence in support of domain duplication as the mechanism for the evolution of the class II KARI fold and demonstrates the ability of domain duplication to generate topological novelty in a function-neutral manner. © 2015 The Protein Society.

The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes

Science.gov (United States)

Liu, Shengyi; Liu, Yumei; Yang, Xinhua; Tong, Chaobo; Edwards, David; Parkin, Isobel A. P.; Zhao, Meixia; Ma, Jianxin; Yu, Jingyin; Huang, Shunmou; Wang, Xiyin; Wang, Junyi; Lu, Kun; Fang, Zhiyuan; Bancroft, Ian; Yang, Tae-Jin; Hu, Qiong; Wang, Xinfa; Yue, Zhen; Li, Haojie; Yang, Linfeng; Wu, Jian; Zhou, Qing; Wang, Wanxin; King, Graham J; Pires, J. Chris; Lu, Changxin; Wu, Zhangyan; Sampath, Perumal; Wang, Zhuo; Guo, Hui; Pan, Shengkai; Yang, Limei; Min, Jiumeng; Zhang, Dong; Jin, Dianchuan; Li, Wanshun; Belcram, Harry; Tu, Jinxing; Guan, Mei; Qi, Cunkou; Du, Dezhi; Li, Jiana; Jiang, Liangcai; Batley, Jacqueline; Sharpe, Andrew G; Park, Beom-Seok; Ruperao, Pradeep; Cheng, Feng; Waminal, Nomar Espinosa; Huang, Yin; Dong, Caihua; Wang, Li; Li, Jingping; Hu, Zhiyong; Zhuang, Mu; Huang, Yi; Huang, Junyan; Shi, Jiaqin; Mei, Desheng; Liu, Jing; Lee, Tae-Ho; Wang, Jinpeng; Jin, Huizhe; Li, Zaiyun; Li, Xun; Zhang, Jiefu; Xiao, Lu; Zhou, Yongming; Liu, Zhongsong; Liu, Xuequn; Qin, Rui; Tang, Xu; Liu, Wenbin; Wang, Yupeng; Zhang, Yangyong; Lee, Jonghoon; Kim, Hyun Hee; Denoeud, France; Xu, Xun; Liang, Xinming; Hua, Wei; Wang, Xiaowu; Wang, Jun; Chalhoub, Boulos; Paterson, Andrew H

2014-01-01

Polyploidization has provided much genetic variation for plant adaptive evolution, but the mechanisms by which the molecular evolution of polyploid genomes establishes genetic architecture underlying species differentiation are unclear. Brassica is an ideal model to increase knowledge of polyploid evolution. Here we describe a draft genome sequence of Brassica oleracea, comparing it with that of its sister species B. rapa to reveal numerous chromosome rearrangements and asymmetrical gene loss in duplicated genomic blocks, asymmetrical amplification of transposable elements, differential gene co-retention for specific pathways and variation in gene expression, including alternative splicing, among a large number of paralogous and orthologous genes. Genes related to the production of anticancer phytochemicals and morphological variations illustrate consequences of genome duplication and gene divergence, imparting biochemical and morphological variation to B. oleracea. This study provides insights into Brassica genome evolution and will underpin research into the many important crops in this genus. PMID:24852848

Pod systems: an equivariant ordinary differential equation approach to dynamical systems on a spatial domain

International Nuclear Information System (INIS)

Elmhirst, Toby; Stewart, Ian; Doebeli, Michael

2008-01-01

We present a class of systems of ordinary differential equations (ODEs), which we call 'pod systems', that offers a new perspective on dynamical systems defined on a spatial domain. Such systems are typically studied as partial differential equations, but pod systems bring the analytic techniques of ODE theory to bear on the problems, and are thus able to study behaviours and bifurcations that are not easily accessible to the standard methods. In particular, pod systems are specifically designed to study spatial dynamical systems that exhibit multi-modal solutions. A pod system is essentially a linear combination of parametrized functions in which the coefficients and parameters are variables whose dynamics are specified by a system of ODEs. That is, pod systems are concerned with the dynamics of functions of the form Ψ(s, t) = y 1 (t) φ(s; x 1 (t)) + ··· + y N (t) φ(s; x N (t)), where s in R n is the spatial variable and φ: R n × R d → R. The parameters x i in R d and coefficients y i in R are dynamic variables which evolve according to some system of ODEs, x-dot i = G i (x, y) and y-dot i = H i (x, y), for i = 1, ..., N. The dynamics of Ψ in function space can then be studied through the dynamics of the x and y in finite dimensions. A vital feature of pod systems is that the ODEs that specify the dynamics of the x and y variables are not arbitrary; restrictions on G i and H i are required to guarantee that the dynamics of Ψ in function space are well defined (that is, that trajectories are unique). One important restriction is symmetry in the ODEs which arises because Ψ is invariant under permutations of the indices of the (x i , y i ) pairs. However, this is not the whole story, and the primary goal of this paper is to determine the necessary structure of the ODEs explicitly to guarantee that the dynamics of Ψ are well defined

Quasi-Newton methods for parameter estimation in functional differential equations

Science.gov (United States)

Brewer, Dennis W.

1988-01-01

A state-space approach to parameter estimation in linear functional differential equations is developed using the theory of linear evolution equations. A locally convergent quasi-Newton type algorithm is applied to distributed systems with particular emphasis on parameters that induce unbounded perturbations of the state. The algorithm is computationally implemented on several functional differential equations, including coefficient and delay estimation in linear delay-differential equations.

Pseudo-differential operators on manifolds with singularities

CERN Document Server

Schulze, B-W

1991-01-01

The analysis of differential equations in domains and on manifolds with singularities belongs to the main streams of recent developments in applied and pure mathematics. The applications and concrete models from engineering and physics are often classical but the modern structure calculus was only possible since the achievements of pseudo-differential operators. This led to deep connections with index theory, topology and mathematical physics. The present book is devoted to elliptic partial differential equations in the framework of pseudo-differential operators. The first chapter contains the Mellin pseudo-differential calculus on R+ and the functional analysis of weighted Sobolev spaces with discrete and continuous asymptotics. Chapter 2 is devoted to the analogous theory on manifolds with conical singularities, Chapter 3 to manifolds with edges. Employed are pseudo-differential operators along edges with cone-operator-valued symbols.

Decomposition of a hierarchy of nonlinear evolution equations

International Nuclear Information System (INIS)

Geng Xianguo

2003-01-01

The generalized Hamiltonian structures for a hierarchy of nonlinear evolution equations are established with the aid of the trace identity. Using the nonlinearization approach, the hierarchy of nonlinear evolution equations is decomposed into a class of new finite-dimensional Hamiltonian systems. The generating function of integrals and their generator are presented, based on which the finite-dimensional Hamiltonian systems are proved to be completely integrable in the Liouville sense. As an application, solutions for the hierarchy of nonlinear evolution equations are reduced to solving the compatible Hamiltonian systems of ordinary differential equations

The analysis of decimation and interpolation in the linear canonical transform domain.

Science.gov (United States)

Xu, Shuiqing; Chai, Yi; Hu, Youqiang; Huang, Lei; Feng, Li

2016-01-01

Decimation and interpolation are the two basic building blocks in the multirate digital signal processing systems. As the linear canonical transform (LCT) has been shown to be a powerful tool for optics and signal processing, it is worthwhile and interesting to analyze the decimation and interpolation in the LCT domain. In this paper, the definition of equivalent filter in the LCT domain have been given at first. Then, by applying the definition, the direct implementation structure and polyphase networks for decimator and interpolator in the LCT domain have been proposed. Finally, the perfect reconstruction expressions for differential filters in the LCT domain have been presented as an application. The proposed theorems in this study are the bases for generalizations of the multirate signal processing in the LCT domain, which can advance the filter banks theorems in the LCT domain.

Topological structure of the solution set for evolution inclusions

CERN Document Server

Zhou, Yong; Peng, Li

2017-01-01

This book systematically presents the topological structure of solution sets and attractability for nonlinear evolution inclusions, together with its relevant applications in control problems and partial differential equations. It provides readers the background material needed to delve deeper into the subject and explore the rich research literature.  In addition, the book addresses many of the basic techniques and results recently developed in connection with this theory, including the structure of solution sets for evolution inclusions with m-dissipative operators; quasi-autonomous and non-autonomous evolution inclusions and control systems;evolution inclusions with the Hille-Yosida operator; functional evolution inclusions; impulsive evolution inclusions; and stochastic evolution inclusions. Several applications of evolution inclusions and control systems are also discussed in detail.  Based on extensive research work conducted by the authors and other experts over the past four years, the information p...