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Sample records for dynamic evolutionary hybrid

  1. A dynamic hybrid framework for constrained evolutionary optimization.

    Science.gov (United States)

    Wang, Yong; Cai, Zixing

    2012-02-01

    Based on our previous work, this paper presents a dynamic hybrid framework, called DyHF, for solving constrained optimization problems. This framework consists of two major steps: global search model and local search model. In the global and local search models, differential evolution serves as the search engine, and Pareto dominance used in multiobjective optimization is employed to compare the individuals in the population. Unlike other existing methods, the above two steps are executed dynamically according to the feasibility proportion of the current population in this paper, with the purpose of reasonably distributing the computational resource for the global and local search during the evolution. The performance of DyHF is tested on 22 benchmark test functions. The experimental results clearly show that the overall performance of DyHF is highly competitive with that of a number of state-of-the-art approaches from the literature.

  2. Evolutionary Design of Both Topologies and Parameters of a Hybrid Dynamical System

    DEFF Research Database (Denmark)

    Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

    2012-01-01

    This paper investigates the issue of evolutionary design of open-ended plants for hybrid dynamical systems--i.e. both their topologies and parameters. Hybrid bond graphs are used to represent dynamical systems involving both continuous and discrete system dynamics. Genetic programming, with some...... special mechanisms incorporated, is used as a search tool to explore the open-ended design space of hybrid bond graphs. Combination of these two tools--i.e., hybrid bond graphs (HGBs) and genetic programming (GP)--leads to an approach called HBGGP that can automatically generate viable design candidates...... of hybrid dynamical systems that fulfill predefined design specifications. A comprehensive investigation of a case study of DC-DC converter design demonstrates the feasibility and effectiveness of the HBGGP approach. Important characteristics of the approach are also discussed, with some future research...

  3. A Hybrid Chaotic Quantum Evolutionary Algorithm

    DEFF Research Database (Denmark)

    Cai, Y.; Zhang, M.; Cai, H.

    2010-01-01

    A hybrid chaotic quantum evolutionary algorithm is proposed to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm. The proposed algorithm adopts the chaotic initialization method to generate initial population which will form...... and enhance the global search ability. A large number of tests show that the proposed algorithm has higher convergence speed and better optimizing ability than quantum evolutionary algorithm, real-coded quantum evolutionary algorithm and hybrid quantum genetic algorithm. Tests also show that when chaos...... is introduced to quantum evolutionary algorithm, the hybrid chaotic search strategy is superior to the carrier chaotic strategy, and has better comprehensive performance than the chaotic mutation strategy in most of cases. Especially, the proposed algorithm is the only one that has 100% convergence rate in all...

  4. Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

    Science.gov (United States)

    Ferriere, Regis; Legendre, Stéphane

    2013-01-01

    Adaptive dynamics theory has been devised to account for feedbacks between ecological and evolutionary processes. Doing so opens new dimensions to and raises new challenges about evolutionary rescue. Adaptive dynamics theory predicts that successive trait substitutions driven by eco-evolutionary feedbacks can gradually erode population size or growth rate, thus potentially raising the extinction risk. Even a single trait substitution can suffice to degrade population viability drastically at once and cause ‘evolutionary suicide’. In a changing environment, a population may track a viable evolutionary attractor that leads to evolutionary suicide, a phenomenon called ‘evolutionary trapping’. Evolutionary trapping and suicide are commonly observed in adaptive dynamics models in which the smooth variation of traits causes catastrophic changes in ecological state. In the face of trapping and suicide, evolutionary rescue requires that the population overcome evolutionary threats generated by the adaptive process itself. Evolutionary repellors play an important role in determining how variation in environmental conditions correlates with the occurrence of evolutionary trapping and suicide, and what evolutionary pathways rescue may follow. In contrast with standard predictions of evolutionary rescue theory, low genetic variation may attenuate the threat of evolutionary suicide and small population sizes may facilitate escape from evolutionary traps. PMID:23209163

  5. Optimal Control of Evolutionary Dynamics

    CERN Document Server

    Chakrabarti, Raj; McLendon, George

    2008-01-01

    Elucidating the fitness measures optimized during the evolution of complex biological systems is a major challenge in evolutionary theory. We present experimental evidence and an analytical framework demonstrating how biochemical networks exploit optimal control strategies in their evolutionary dynamics. Optimal control theory explains a striking pattern of extremization in the redox potentials of electron transport proteins, assuming only that their fitness measure is a control objective functional with bounded controls.

  6. Evolutionary Dynamics of Biological Games

    Science.gov (United States)

    Nowak, Martin A.; Sigmund, Karl

    2004-02-01

    Darwinian dynamics based on mutation and selection form the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short- and long-term evolution in phenotype space and have found applications ranging from animal behavior and ecology to speciation, macroevolution, and human language. Evolutionary game theory is an essential component of a mathematical and computational approach to biology.

  7. Neuronal boost to evolutionary dynamics.

    Science.gov (United States)

    de Vladar, Harold P; Szathmáry, Eörs

    2015-12-06

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild.

  8. Neuronal boost to evolutionary dynamics

    Science.gov (United States)

    de Vladar, Harold P.; Szathmáry, Eörs

    2015-01-01

    Standard evolutionary dynamics is limited by the constraints of the genetic system. A central message of evolutionary neurodynamics is that evolutionary dynamics in the brain can happen in a neuronal niche in real time, despite the fact that neurons do not reproduce. We show that Hebbian learning and structural synaptic plasticity broaden the capacity for informational replication and guided variability provided a neuronally plausible mechanism of replication is in place. The synergy between learning and selection is more efficient than the equivalent search by mutation selection. We also consider asymmetric landscapes and show that the learning weights become correlated with the fitness gradient. That is, the neuronal complexes learn the local properties of the fitness landscape, resulting in the generation of variability directed towards the direction of fitness increase, as if mutations in a genetic pool were drawn such that they would increase reproductive success. Evolution might thus be more efficient within evolved brains than among organisms out in the wild. PMID:26640653

  9. Evolutionary dynamics of mammalian karyotypes

    Directory of Open Access Journals (Sweden)

    Carlo Alberto Redi

    2012-12-01

    Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....

  10. Evolutionary Dynamics of Biological Games

    OpenAIRE

    Nowak, M. A.; Sigmund, K.

    2004-01-01

    Darwinian dynamics based on mutation and selection from the core of mathematical models for adaptation and coevolution of biological populations. The evolutionary outcome is often not a fitness-maximizing equilibrium but can include oscillations and chaos. For studying frequency-dependent selection, game-theoretic arguments are more appropriate than optimization algorithms. Replicator and adaptive dynamics describe short-and long-term evolution in phenotype space and have found applications r...

  11. for hybrid dynamical systems

    Directory of Open Access Journals (Sweden)

    Wassim M. Haddad

    2001-01-01

    Full Text Available In this paper we develop a unified dynamical systems framework for a general class of systems possessing left-continuous flows; that is, left-continuous dynamical systems. These systems are shown to generalize virtually all existing notions of dynamical systems and include hybrid, impulsive, and switching dynamical systems as special cases. Furthermore, we generalize dissipativity, passivity, and nonexpansivity theory to left-continuous dynamical systems. Specifically, the classical concepts of system storage functions and supply rates are extended to left-continuous dynamical systems providing a generalized hybrid system energy interpretation in terms of stored energy, dissipated energy over the continuous-time dynamics, and dissipated energy over the resetting events. Finally, the generalized dissipativity notions are used to develop general stability criteria for feedback interconnections of left-continuous dynamical systems. These results generalize the positivity and small gain theorems to the case of left-continuous, hybrid, and impulsive dynamical systems.

  12. Organisations’ evolutionary dynamics: a group dynamics approach

    Directory of Open Access Journals (Sweden)

    Germán Eduardo Vargas

    2010-04-01

    Full Text Available Colombian entrepreneurs’ straggling, reactionary and inertial orientation has been inconsistently lustified by the availability of internal and leveraged resources, a concept intensifying deficient technological capacity. Company activity (seen as being a socioeconomic unit has been integrally orientated within an evolutionary framework by company identity and cohesion as well as adaptation and evolutionary mechanisms. The present document uses a group dynamics’ model to illustrate how knowledge-based strategic orientation and integration for innovation have become an imperative for development, from slight leverage, distinguishing between two evolutionary company forms: traditional economic (inertial, as they introduce sporadic incremental improvements and modern companies (dynamic and radical innovators. Revealing conclusions obtained from such model may be used for intervening in and modernising company activity.

  13. Unifying evolutionary and network dynamics

    Science.gov (United States)

    Swarup, Samarth; Gasser, Les

    2007-06-01

    Many important real-world networks manifest small-world properties such as scale-free degree distributions, small diameters, and clustering. The most common model of growth for these networks is preferential attachment, where nodes acquire new links with probability proportional to the number of links they already have. We show that preferential attachment is a special case of the process of molecular evolution. We present a single-parameter model of network growth that unifies varieties of preferential attachment with the quasispecies equation (which models molecular evolution), and also with the Erdős-Rényi random graph model. We suggest some properties of evolutionary models that might be applied to the study of networks. We also derive the form of the degree distribution resulting from our algorithm, and we show through simulations that the process also models aspects of network growth. The unification allows mathematical machinery developed for evolutionary dynamics to be applied in the study of network dynamics, and vice versa.

  14. Cost Optimization Using Hybrid Evolutionary Algorithm in Cloud Computing

    Directory of Open Access Journals (Sweden)

    B. Kavitha

    2015-07-01

    Full Text Available The main aim of this research is to design the hybrid evolutionary algorithm for minimizing multiple problems of dynamic resource allocation in cloud computing. The resource allocation is one of the big problems in the distributed systems when the client wants to decrease the cost for the resource allocation for their task. In order to assign the resource for the task, the client must consider the monetary cost and computational cost. Allocation of resources by considering those two costs is difficult. To solve this problem in this study, we make the main task of client into many subtasks and we allocate resources for each subtask instead of selecting the single resource for the main task. The allocation of resources for the each subtask is completed through our proposed hybrid optimization algorithm. Here, we hybrid the Binary Particle Swarm Optimization (BPSO and Binary Cuckoo Search algorithm (BCSO by considering monetary cost and computational cost which helps to minimize the cost of the client. Finally, the experimentation is carried out and our proposed hybrid algorithm is compared with BPSO and BCSO algorithms. Also we proved the efficiency of our proposed hybrid optimization algorithm.

  15. Evolutionary computation for dynamic optimization problems

    CERN Document Server

    Yao, Xin

    2013-01-01

    This book provides a compilation on the state-of-the-art and recent advances of evolutionary computation for dynamic optimization problems. The motivation for this book arises from the fact that many real-world optimization problems and engineering systems are subject to dynamic environments, where changes occur over time. Key issues for addressing dynamic optimization problems in evolutionary computation, including fundamentals, algorithm design, theoretical analysis, and real-world applications, are presented. "Evolutionary Computation for Dynamic Optimization Problems" is a valuable reference to scientists, researchers, professionals and students in the field of engineering and science, particularly in the areas of computational intelligence, nature- and bio-inspired computing, and evolutionary computation.

  16. Evolutionary approaches of economic dynamics (In French)

    OpenAIRE

    Yildizoglu, Murat

    2009-01-01

    This chapter presents the methods and contributions of evolutionary approach to economic dynamics. First, we expose why economic dynamics can indeed be considered as evolutionary. Second, we discuss sources of diversity and selection mechanisms that drive these dynamics, in the context of industrial dynamics. Third, we expose the main methods of this approach. Last, we give a partial survey of this approach’s contributions in economic systems covering a full spectrum, from organizational to m...

  17. Evolutionary dynamics of group fairness.

    Science.gov (United States)

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

    2015-08-07

    The emergence and impact of fairness is commonly studied in the context of 2-person games, notably the Ultimatum Game. Often, however, humans face problems of collective action involving more than two individuals where fairness is known to play a very important role, and whose dynamics cannot be inferred from what is known from 2-person games. Here, we propose a generalization of the Ultimatum Game for an arbitrary number of players--the Multiplayer Ultimatum Game. Proposals are made to a group of responders who must individually reject or accept the proposal. If the total number of individual acceptances stands below a given threshold, the offer will be rejected; otherwise, the offer will be accepted, and equally shared by all responders. We investigate the evolution of fairness in populations of individuals by means of evolutionary game theory, providing both analytical insights and results from numerical simulations. We show how imposing stringent consensuses significantly increases the value of the proposals, leading to fairer outcomes and more tolerant players. Furthermore, we show how stochastic effects--such as imitation errors and/or errors when assessing the fitness of others--may further enhance the overall success in reaching fair collective action. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Improved Evolutionary Hybrids for Flexible Ligand Docking in Autodock

    Energy Technology Data Exchange (ETDEWEB)

    Belew, R.K.; Hart, W.E.; Morris, G.M.; Rosin, C.

    1999-01-27

    In this paper we evaluate the design of the hybrid evolutionary algorithms (EAs) that are currently used to perform flexible ligand binding in the Autodock docking software. Hybrid EAs incorporate specialized operators that exploit domain-specific features to accelerate an EA's search. We consider hybrid EAs that use an integrated local search operator to reline individuals within each iteration of the search. We evaluate several factors that impact the efficacy of a hybrid EA, and we propose new hybrid EAs that provide more robust convergence to low-energy docking configurations than the methods currently available in Autodock.

  19. Evolutionary design of discrete controllers for hybrid mechatronic systems

    DEFF Research Database (Denmark)

    Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik

    2015-01-01

    This paper investigates the issue of evolutionary design of controllers for hybrid mechatronic systems. Finite State Automaton (FSA) is selected as the representation for a discrete controller due to its interpretability, fast execution speed and natural extension to a statechart, which is very...... popular in industrial applications. A case study of a two-tank system is used to demonstrate that the proposed evolutionary approach can lead to a successful design of an FSA controller for the hybrid mechatronic system, represented by a hybrid bond graph. Generalisation of the evolved FSA controller...... of the evolutionary design of controllers for hybrid mechatronic systems. Finally, some important future research directions are pointed out, leading to the major work of the succeeding part of the research....

  20. On evolutionary ray-projection dynamics

    NARCIS (Netherlands)

    Joosten, Reinoud; Roorda, Berend

    2011-01-01

    We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman (Econome

  1. A Hybrid Evolutionary Algorithm for Discrete Optimization

    Directory of Open Access Journals (Sweden)

    J. Bhuvana

    2015-03-01

    Full Text Available Most of the real world multi-objective problems demand us to choose one Pareto optimal solution out of a finite set of choices. Flexible job shop scheduling problem is one such problem whose solutions are required to be selected from a discrete solution space. In this study we have designed a hybrid genetic algorithm to solve this scheduling problem. Hybrid genetic algorithms combine both the aspects of the search, exploration and exploitation of the search space. Proposed algorithm, Hybrid GA with Discrete Local Search, performs global search through the GA and exploits the locality through discrete local search. Proposed hybrid algorithm not only has the ability to generate Pareto optimal solutions and also identifies them with less computation. Five different benchmark test instances are used to evaluate the performance of the proposed algorithm. Results observed shown that the proposed algorithm has produced the known Pareto optimal solutions through exploration and exploitation of the search space with less number of functional evaluations.

  2. Evolutionary Dynamics of Digitized Organizational Routines

    Science.gov (United States)

    Liu, Peng

    2013-01-01

    This dissertation explores the effects of increased digitization on the evolutionary dynamics of organizational routines. Do routines become more flexible, or more rigid, as the mix of digital technologies and human actors changes? What are the mechanisms that govern the evolution of routines? The dissertation theorizes about the effects of…

  3. Hybridizing Evolutionary Algorithms with Opportunistic Local Search

    DEFF Research Database (Denmark)

    Gießen, Christian

    2013-01-01

    There is empirical evidence that memetic algorithms (MAs) can outperform plain evolutionary algorithms (EAs). Recently the first runtime analyses have been presented proving the aforementioned conjecture rigorously by investigating Variable-Depth Search, VDS for short (Sudholt, 2008). Sudholt...... raised the question if there are problems where VDS performs badly. We answer this question in the affirmative in the following way. We analyze MAs with VDS, which is also known as Kernighan-Lin for the TSP, on an artificial problem and show that MAs with a simple first-improvement local search...... outperform VDS. Moreover, we show that the performance gap is exponential. We analyze the features leading to a failure of VDS and derive a new local search operator, coined Opportunistic Local Search, that can easily overcome regions of the search space where local optima are clustered. The power...

  4. Chaotic Dynamics in Hybrid Systems

    NARCIS (Netherlands)

    P.J. Collins (Pieter)

    2008-01-01

    htmlabstractIn this paper we give an overview of some aspects of chaotic dynamics in hybrid systems, which comprise different types of behaviour. Hybrid systems may exhibit discontinuous dependence on initial conditions leading to new dynamical phenomena. We indicate how methods from topological

  5. Chaotic dynamics in hybrid systems

    NARCIS (Netherlands)

    P.J. Collins (Pieter)

    2008-01-01

    htmlabstractIn this paper we give an overview of some aspects of chaotic dynamics in hybrid systems, which comprise different types of behaviour. Hybrid systems may exhibit discontinuous dependence on initial conditions leading to new dynamical phenomena. We indicate how methods from topological

  6. A HYBRID DYNAMIC PROGRAM SLICING

    Institute of Scientific and Technical Information of China (English)

    Yi Tong; Wu Fangjun

    2005-01-01

    This letter proposes a hybrid method for computing dynamic program slicing. The key element is to construct a Coverage-Testing-based Dynamic Dependence Graph (CTDDG),which makes use of both dynamic and static information to get execution status. The approach overcomes the limitations of previous dynamic slicing methods, which have to redo slicing if slice criterion changes.

  7. Multiscale structure in eco-evolutionary dynamics

    Science.gov (United States)

    Stacey, Blake C.

    In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of interdependency lead to structure at multiple scales of organization. Evolution excels at producing such complex structures. In turn, the existence of these complex interrelationships within a biological system affects the evolutionary dynamics of that system. I present a mathematical formalism for multiscale structure, grounded in information theory, which makes these intuitions quantitative, and I show how dynamics defined in terms of population genetics or evolutionary game theory can lead to multiscale organization. For complex systems, "more is different," and I address this from several perspectives. Spatial host--consumer models demonstrate the importance of the structures which can arise due to dynamical pattern formation. Evolutionary game theory reveals the novel effects which can result from multiplayer games, nonlinear payoffs and ecological stochasticity. Replicator dynamics in an environment with mesoscale structure relates to generalized conditionalization rules in probability theory. The idea of natural selection "acting at multiple levels" has been mathematized in a variety of ways, not all of which are equivalent. We will face down the confusion, using the experience developed over the course of this thesis to clarify the situation.

  8. The Evolutionary Dynamics of Biofuel Value Chains

    DEFF Research Database (Denmark)

    Ponte, Stefano

    2014-01-01

    and multipolarity. Empirically, I do so by examining the evolutionary dynamics of governance in biofuel value chains, with specific focus on the key regulatory and institutional features that facilitated their emergence and expansion. First, I examine the formation, evolution, and governance of three national....../regional value chains (in Brazil, the US, and the EU); then, I provide evidence to support a trend towards the increasing but still partial formation of a global biofuel value chain and examine its governance traits....

  9. A Simple General Model of Evolutionary Dynamics

    Science.gov (United States)

    Thurner, Stefan

    Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense

  10. Stochastic evolutionary dynamics of direct reciprocity.

    Science.gov (United States)

    Imhof, Lorens A; Nowak, Martin A

    2010-02-01

    Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the resident population is calculated. The new mutant takes over the population with this probability. In this case, the mutant becomes the new resident. Otherwise, the existing resident remains. Then, another mutant is generated. These dynamics lead to a stationary distribution over the entire strategy space. Our new approach generalizes classical adaptive dynamics in three ways: (i) the population size is finite; (ii) mutants can be drawn non-locally and (iii) the dynamics are stochastic. We explore reactive strategies in the repeated Prisoner's Dilemma. We perform 'knock-out experiments' to study how various strategies affect the evolution of cooperation. We find that 'tit-for-tat' is a weak catalyst for the emergence of cooperation, while 'always cooperate' is a strong catalyst for the emergence of defection. Our analysis leads to a new understanding of the optimal level of forgiveness that is needed for the evolution of cooperation under direct reciprocity.

  11. Hybrid multiobjective evolutionary design for artificial neural networks.

    Science.gov (United States)

    Goh, Chi-Keong; Teoh, Eu-Jin; Tan, Kay Chen

    2008-09-01

    Evolutionary algorithms are a class of stochastic search methods that attempts to emulate the biological process of evolution, incorporating concepts of selection, reproduction, and mutation. In recent years, there has been an increase in the use of evolutionary approaches in the training of artificial neural networks (ANNs). While evolutionary techniques for neural networks have shown to provide superior performance over conventional training approaches, the simultaneous optimization of network performance and architecture will almost always result in a slow training process due to the added algorithmic complexity. In this paper, we present a geometrical measure based on the singular value decomposition (SVD) to estimate the necessary number of neurons to be used in training a single-hidden-layer feedforward neural network (SLFN). In addition, we develop a new hybrid multiobjective evolutionary approach that includes the features of a variable length representation that allow for easy adaptation of neural networks structures, an architectural recombination procedure based on the geometrical measure that adapts the number of necessary hidden neurons and facilitates the exchange of neuronal information between candidate designs, and a microhybrid genetic algorithm ( microHGA) with an adaptive local search intensity scheme for local fine-tuning. In addition, the performances of well-known algorithms as well as the effectiveness and contributions of the proposed approach are analyzed and validated through a variety of data set types.

  12. Hybrid Disease Diagnosis Using Multiobjective Optimization with Evolutionary Parameter Optimization

    Directory of Open Access Journals (Sweden)

    MadhuSudana Rao Nalluri

    2017-01-01

    Full Text Available With the widespread adoption of e-Healthcare and telemedicine applications, accurate, intelligent disease diagnosis systems have been profoundly coveted. In recent years, numerous individual machine learning-based classifiers have been proposed and tested, and the fact that a single classifier cannot effectively classify and diagnose all diseases has been almost accorded with. This has seen a number of recent research attempts to arrive at a consensus using ensemble classification techniques. In this paper, a hybrid system is proposed to diagnose ailments using optimizing individual classifier parameters for two classifier techniques, namely, support vector machine (SVM and multilayer perceptron (MLP technique. We employ three recent evolutionary algorithms to optimize the parameters of the classifiers above, leading to six alternative hybrid disease diagnosis systems, also referred to as hybrid intelligent systems (HISs. Multiple objectives, namely, prediction accuracy, sensitivity, and specificity, have been considered to assess the efficacy of the proposed hybrid systems with existing ones. The proposed model is evaluated on 11 benchmark datasets, and the obtained results demonstrate that our proposed hybrid diagnosis systems perform better in terms of disease prediction accuracy, sensitivity, and specificity. Pertinent statistical tests were carried out to substantiate the efficacy of the obtained results.

  13. Evolutionary Dynamic Multiobjective Optimization Via Kalman Filter Prediction.

    Science.gov (United States)

    Muruganantham, Arrchana; Tan, Kay Chen; Vadakkepat, Prahlad

    2016-12-01

    Evolutionary algorithms are effective in solving static multiobjective optimization problems resulting in the emergence of a number of state-of-the-art multiobjective evolutionary algorithms (MOEAs). Nevertheless, the interest in applying them to solve dynamic multiobjective optimization problems has only been tepid. Benchmark problems, appropriate performance metrics, as well as efficient algorithms are required to further the research in this field. One or more objectives may change with time in dynamic optimization problems. The optimization algorithm must be able to track the moving optima efficiently. A prediction model can learn the patterns from past experience and predict future changes. In this paper, a new dynamic MOEA using Kalman filter (KF) predictions in decision space is proposed to solve the aforementioned problems. The predictions help to guide the search toward the changed optima, thereby accelerating convergence. A scoring scheme is devised to hybridize the KF prediction with a random reinitialization method. Experimental results and performance comparisons with other state-of-the-art algorithms demonstrate that the proposed algorithm is capable of significantly improving the dynamic optimization performance.

  14. Mate Choice Drives Evolutionary Stability in a Hybrid Complex.

    Directory of Open Access Journals (Sweden)

    Miguel Morgado-Santos

    Full Text Available Previous studies have shown that assortative mating acts as a driver of speciation by countering hybridization between two populations of the same species (pre-zygotic isolation or through mate choice among the hybrids (hybrid speciation. In both speciation types, assortative mating promotes speciation over a transient hybridization stage. We studied mate choice in a hybrid vertebrate complex, the allopolyploid fish Squalius alburnoides. This complex is composed by several genomotypes connected by an intricate reproductive dynamics. We developed a model that predicts the hybrid complex can persist when females exhibit particular mate choice patterns. Our model is able to reproduce the diversity of population dynamic outcomes found in nature, namely the dominance of the triploids and the dominance of the tetraploids, depending on female mate choice patterns and frequency of the parental species. Experimental mate choice trials showed that females exhibit the preferences predicted by the model. Thus, despite the known role of assortative mating in driving speciation, our findings suggest that certain mate choice patterns can instead hinder speciation and support the persistence of hybrids over time without speciation or extinction.

  15. Mate Choice Drives Evolutionary Stability in a Hybrid Complex

    Science.gov (United States)

    Morgado-Santos, Miguel; Pereira, Henrique Miguel

    2015-01-01

    Previous studies have shown that assortative mating acts as a driver of speciation by countering hybridization between two populations of the same species (pre-zygotic isolation) or through mate choice among the hybrids (hybrid speciation). In both speciation types, assortative mating promotes speciation over a transient hybridization stage. We studied mate choice in a hybrid vertebrate complex, the allopolyploid fish Squalius alburnoides. This complex is composed by several genomotypes connected by an intricate reproductive dynamics. We developed a model that predicts the hybrid complex can persist when females exhibit particular mate choice patterns. Our model is able to reproduce the diversity of population dynamic outcomes found in nature, namely the dominance of the triploids and the dominance of the tetraploids, depending on female mate choice patterns and frequency of the parental species. Experimental mate choice trials showed that females exhibit the preferences predicted by the model. Thus, despite the known role of assortative mating in driving speciation, our findings suggest that certain mate choice patterns can instead hinder speciation and support the persistence of hybrids over time without speciation or extinction. PMID:26181664

  16. A hybrid evolutionary algorithm for distribution feeder reconfiguration

    Indian Academy of Sciences (India)

    Taher Niknam; Reza Khorshidi; Bahman Bahmani Firouzi

    2010-04-01

    Distribution feeder reconfiguration (DFR) is formulated as a multiobjective optimization problem which minimizes real power losses, deviation of the node voltages and the number of switching operations and also balances the loads on the feeders. In the proposed method, the distance ($\\lambda_2$ norm) between the vectorvalued objective function and the worst-case vector-valued objective function in the feasible set is maximized. In the algorithm, the status of tie and sectionalizing switches are considered as the control variables. The proposed DFR problem is a non-differentiable optimization problem. Therefore, a new hybrid evolutionary algorithm based on combination of fuzzy adaptive particle swarm optimization (FAPSO) and ant colony optimization (ACO), called HFAPSO, is proposed to solve it. The performance of HFAPSO is evaluated and compared with other methods such as genetic algorithm (GA), ACO, the original PSO, Hybrid PSO and ACO (HPSO) considering different distribution test systems.

  17. Evolutionary epistemology and dynamical virtual learning networks.

    Science.gov (United States)

    Giani, Umberto

    2004-01-01

    This paper is an attempt to define the main features of a new educational model aimed at satisfying the needs of a rapidly changing society. The evolutionary epistemology paradigm of culture diffusion in human groups could be the conceptual ground for the development of this model. Multidimensionality, multi-disciplinarity, complexity, connectivity, critical thinking, creative thinking, constructivism, flexible learning, contextual learning, are the dimensions that should characterize distance learning models aimed at increasing the epistemological variability of learning communities. Two multimedia educational software, Dynamic Knowledge Networks (DKN) and Dynamic Virtual Learning Networks (DVLN) are described. These two complementary tools instantiate these dimensions, and were tested in almost 150 online courses. Even if the examples are framed in the medical context, the analysis of the shortcomings of the traditional educational systems and the proposed solutions can be applied to the vast majority of the educational contexts.

  18. Classical vs Quantum Games: Continuous-time Evolutionary Strategy Dynamics

    CERN Document Server

    Leung, Ming Lam

    2011-01-01

    This paper unifies the concepts of evolutionary games and quantum strategies. First, we state the formulation and properties of classical evolutionary strategies, with focus on the destinations of evolution in 2-player 2-strategy games. We then introduce a new formalism of quantum evolutionary dynamics, and give an example where an evolving quantum strategy gives reward if played against its classical counterpart.

  19. Form of an evolutionary tradeoff affects eco-evolutionary dynamics in a predator-prey system.

    Science.gov (United States)

    Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

    2014-11-11

    Evolution on a time scale similar to ecological dynamics has been increasingly recognized for the last three decades. Selection mediated by ecological interactions can change heritable phenotypic variation (i.e., evolution), and evolution of traits, in turn, can affect ecological interactions. Hence, ecological and evolutionary dynamics can be tightly linked and important to predict future dynamics, but our understanding of eco-evolutionary dynamics is still in its infancy and there is a significant gap between theoretical predictions and empirical tests. Empirical studies have demonstrated that the presence of genetic variation can dramatically change ecological dynamics, whereas theoretical studies predict that eco-evolutionary dynamics depend on the details of the genetic variation, such as the form of a tradeoff among genotypes, which can be more important than the presence or absence of the genetic variation. Using a predator-prey (rotifer-algal) experimental system in laboratory microcosms, we studied how different forms of a tradeoff between prey defense and growth affect eco-evolutionary dynamics. Our experimental results show for the first time to our knowledge that different forms of the tradeoff produce remarkably divergent eco-evolutionary dynamics, including near fixation, near extinction, and coexistence of algal genotypes, with quantitatively different population dynamics. A mathematical model, parameterized from completely independent experiments, explains the observed dynamics. The results suggest that knowing the details of heritable trait variation and covariation within a population is essential for understanding how evolution and ecology will interact and what form of eco-evolutionary dynamics will result.

  20. The Evolutionary Dynamics of Biofuel Value Chains

    DEFF Research Database (Denmark)

    Ponte, Stefano

    2014-01-01

    In this paper I propose to push the frontier of global value chain (GVC) governance analysis through the concept of ‘polarity’. Much of the existing GVC literature has focused on ‘unipolar’ value chains, where one group of ‘lead firms’ inhabiting a specific function in a chain plays a dominant role...... and multipolarity. Empirically, I do so by examining the evolutionary dynamics of governance in biofuel value chains, with specific focus on the key regulatory and institutional features that facilitated their emergence and expansion. First, I examine the formation, evolution, and governance of three national....../regional value chains (in Brazil, the US, and the EU); then, I provide evidence to support a trend towards the increasing but still partial formation of a global biofuel value chain and examine its governance traits....

  1. Evolutionary dynamics with fluctuating population sizes and strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David R.

    2015-08-01

    Game theory ideas provide a useful framework for studying evolutionary dynamics in a well-mixed environment. This approach, however, typically enforces a strictly fixed overall population size, deemphasizing natural growth processes. We study a competitive Lotka-Volterra model, with number fluctuations, that accounts for natural population growth and encompasses interaction scenarios typical of evolutionary games. We show that, in an appropriate limit, the model describes standard evolutionary games with both genetic drift and overall population size fluctuations. However, there are also regimes where a varying population size can strongly influence the evolutionary dynamics. We focus on the strong mutualism scenario and demonstrate that standard evolutionary game theory fails to describe our simulation results. We then analytically and numerically determine fixation probabilities as well as mean fixation times using matched asymptotic expansions, taking into account the population size degree of freedom. These results elucidate the interplay between population dynamics and evolutionary dynamics in well-mixed systems.

  2. Evolutionary dynamics of nationalism and migration

    Science.gov (United States)

    Barreira da Silva Rocha, André

    2013-08-01

    I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.

  3. Passivity analysis of higher order evolutionary dynamics and population games

    KAUST Repository

    Mabrok, Mohamed

    2017-01-05

    Evolutionary dynamics describe how the population composition changes in response to the fitness levels, resulting in a closed-loop feedback system. Recent work established a connection between passivity theory and certain classes of population games, namely so-called “stable games”. In particular, it was shown that a combination of stable games and (an analogue of) passive evolutionary dynamics results in stable convergence to Nash equilibrium. This paper considers the converse question of necessary conditions for evolutionary dynamics to exhibit stable behaviors for all generalized stable games. Using methods from robust control analysis, we show that if an evolutionary dynamic does not satisfy a passivity property, then it is possible to construct a generalized stable game that results in instability. The results are illustrated on selected evolutionary dynamics with particular attention to replicator dynamics, which are also shown to be lossless, a special class of passive systems.

  4. Evolving Quantum Oracles with Hybrid Quantum-inspired Evolutionary Algorithm

    CERN Document Server

    Ding, S; Yang, Q; Ding, Shengchao; Jin, Zhi; Yang, Qing

    2006-01-01

    Quantum oracles play key roles in the studies of quantum computation and quantum information. But implementing quantum oracles efficiently with universal quantum gates is a hard work. Motivated by genetic programming, this paper proposes a novel approach to evolve quantum oracles with a hybrid quantum-inspired evolutionary algorithm. The approach codes quantum circuits with numerical values and combines the cost and correctness of quantum circuits into the fitness function. To speed up the calculation of matrix multiplication in the evaluation of individuals, a fast algorithm of matrix multiplication with Kronecker product is also presented. The experiments show the validity and the effects of some parameters of the presented approach. And some characteristics of the novel approach are discussed too.

  5. The genomic basis of eco-evolutionary dynamics.

    Science.gov (United States)

    Rodríguez-Verdugo, Alejandra; Buckley, James; Stapley, Jessica

    2017-03-01

    Recent recognition that ecological and evolutionary processes can operate on similar timescales has led to a rapid increase in theoretical and empirical studies on eco-evolutionary dynamics. Progress in the fields of evolutionary biology, genomics and ecology is greatly enhancing our understanding of rapid adaptive processes, the predictability of adaptation and the genetics of ecologically important traits. However, progress in these fields has proceeded largely independently of one another. In an attempt to better integrate these fields, the centre for 'Adaptation to a Changing Environment' organized a conference entitled 'The genomic basis of eco-evolutionary change' and brought together experts in ecological genomics and eco-evolutionary dynamics. In this review, we use the work of the invited speakers to summarize eco-evolutionary dynamics and discuss how they are relevant for understanding and predicting responses to contemporary environmental change. Then, we show how recent advances in genomics are contributing to our understanding of eco-evolutionary dynamics. Finally, we highlight the gaps in our understanding of eco-evolutionary dynamics and recommend future avenues of research in eco-evolutionary dynamics. © 2017 John Wiley & Sons Ltd.

  6. Eco-evolutionary dynamics in an urbanizing planet.

    Science.gov (United States)

    Alberti, Marina

    2015-02-01

    A great challenge for ecology in the coming decades is to understand the role humans play in eco-evolutionary dynamics. If, as emerging evidence shows, rapid evolutionary change affects ecosystem functioning and stability, current rapid environmental change and its evolutionary effects might have significant implications for ecological and human wellbeing on a relatively short time scale. Humans are major selective agents with potential for unprecedented evolutionary consequences for Earth's ecosystems, especially as cities expand rapidly. In this review, I identify emerging hypotheses on how urbanization drives eco-evolutionary dynamics. Studying how human-driven micro-evolutionary changes interact with ecological processes offers us the chance to advance our understanding of eco-evolutionary feedbacks and will provide new insights for maintaining biodiversity and ecosystem function over the long term. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Hybridization between pollination syndromes as an ecological and evolutionary resource.

    Science.gov (United States)

    Cronk, Quentin; Yang, Ji Yong

    2016-12-01

    In plants, pollination syndromes (the correlated presence of many features of relevance to pollination mode, for instance pollination by a particular animal clade) are a striking feature of plant biodiversity, providing great floral phenotypic diversity (Fenster et al. ). Adaptation to a particular animal pollinator provides an explanation for why recently diverged plants can have such extreme differentiation in floral form. One might expect such elaborate adaptations to provide a high degree of pollinator specificity and hence reproductive isolation, but there are many cases where substantial gene flow exists between extreme floral morphs (see Table 1), and the resulting hybrids may be highly fertile. This gene flow provides tremendous opportunities to study the genetics and biology of the pollination syndromes by providing intermediate forms and segregating genotypes. If it is true that pollination syndromes result from adaptation under strong selection, we will expect such flowers to be crucibles of natural selection. If strong selection for particular floral phenotypes can be shown, then this, when coupled with hybridization, will give us one of the most valuable of all experimental systems for evolutionary research: gene flow and selection in balance. In this issue of Molecular Ecology, the paper of Milano et al. () delivers this. It shows that in populations of the Ipomopsis aggregata complex, gene flow between pollination morphs is high and selection to stabilize those morphs is also high: a probable case of gene flow-selection balance. © 2016 John Wiley & Sons Ltd.

  8. Hybrid swarms : catalysts for multiple evolutionary events in Senecio in the British Isles

    OpenAIRE

    Lowe, A. J.; Abbott, R J

    2015-01-01

    Background: Introgressive hybridisation is an evolutionary catalyst producing novel variants able to explore new ecological niches and evolve as new hybrid taxa. However, the role of ‘hybrid swarms’ – highly variable populations produced following interspecific hybridisation – in generating this evolutionary novelty has been poorly studied. Aims: We examine the alternative origins of tetraploid hybrid derivatives of Senecio vulgaris and S. squalidus, via local polytopic formation or long-dist...

  9. Evolutionary dynamics of prokaryotic transcriptional regulatory networks.

    Science.gov (United States)

    Madan Babu, M; Teichmann, Sarah A; Aravind, L

    2006-04-28

    The structure of complex transcriptional regulatory networks has been studied extensively in certain model organisms. However, the evolutionary dynamics of these networks across organisms, which would reveal important principles of adaptive regulatory changes, are poorly understood. We use the known transcriptional regulatory network of Escherichia coli to analyse the conservation patterns of this network across 175 prokaryotic genomes, and predict components of the regulatory networks for these organisms. We observe that transcription factors are typically less conserved than their target genes and evolve independently of them, with different organisms evolving distinct repertoires of transcription factors responding to specific signals. We show that prokaryotic transcriptional regulatory networks have evolved principally through widespread tinkering of transcriptional interactions at the local level by embedding orthologous genes in different types of regulatory motifs. Different transcription factors have emerged independently as dominant regulatory hubs in various organisms, suggesting that they have convergently acquired similar network structures approximating a scale-free topology. We note that organisms with similar lifestyles across a wide phylogenetic range tend to conserve equivalent interactions and network motifs. Thus, organism-specific optimal network designs appear to have evolved due to selection for specific transcription factors and transcriptional interactions, allowing responses to prevalent environmental stimuli. The methods for biological network analysis introduced here can be applied generally to study other networks, and these predictions can be used to guide specific experiments.

  10. Quantifying the evolutionary dynamics of language.

    Science.gov (United States)

    Lieberman, Erez; Michel, Jean-Baptiste; Jackson, Joe; Tang, Tina; Nowak, Martin A

    2007-10-11

    Human language is based on grammatical rules. Cultural evolution allows these rules to change over time. Rules compete with each other: as new rules rise to prominence, old ones die away. To quantify the dynamics of language evolution, we studied the regularization of English verbs over the past 1,200 years. Although an elaborate system of productive conjugations existed in English's proto-Germanic ancestor, Modern English uses the dental suffix, '-ed', to signify past tense. Here we describe the emergence of this linguistic rule amidst the evolutionary decay of its exceptions, known to us as irregular verbs. We have generated a data set of verbs whose conjugations have been evolving for more than a millennium, tracking inflectional changes to 177 Old-English irregular verbs. Of these irregular verbs, 145 remained irregular in Middle English and 98 are still irregular today. We study how the rate of regularization depends on the frequency of word usage. The half-life of an irregular verb scales as the square root of its usage frequency: a verb that is 100 times less frequent regularizes 10 times as fast. Our study provides a quantitative analysis of the regularization process by which ancestral forms gradually yield to an emerging linguistic rule.

  11. The evolutionary dynamics of grammar acquisition.

    Science.gov (United States)

    Komarova, N L; Niyogi, P; Nowak, M A

    2001-03-07

    Grammar is the computational system of language. It is a set of rules that specifies how to construct sentences out of words. Grammar is the basis of the unlimited expressibility of human language. Children acquire the grammar of their native language without formal education simply by hearing a number of sample sentences. Children could not solve this learning task if they did not have some pre-formed expectations. In other words, children have to evaluate the sample sentences and choose one grammar out of a limited set of candidate grammars. The restricted search space and the mechanism which allows to evaluate the sample sentences is called universal grammar. Universal grammar cannot be learned; it must be in place when the learning process starts. In this paper, we design a mathematical theory that places the problem of language acquisition into an evolutionary context. We formulate equations for the population dynamics of communication and grammar learning. We ask how accurate children have to learn the grammar of their parents' language for a population of individuals to evolve and maintain a coherent grammatical system. It turns out that there is a maximum error tolerance for which a predominant grammar is stable. We calculate the maximum size of the search space that is compatible with coherent communication in a population. Thus, we specify the conditions for the evolution of universal grammar.

  12. Bridging developmental systems theory and evolutionary psychology using dynamic optimization.

    Science.gov (United States)

    Frankenhuis, Willem E; Panchanathan, Karthik; Clark Barrett, H

    2013-07-01

    Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic optimization integrates developmental systems theorists' focus on dynamics and contingency with the 'design stance' of evolutionary psychology. It provides a theoretical framework as well as a set of tools for exploring the properties of developmental systems that natural selection might favor, given particular evolutionary ecologies. We also discuss limitations of the approach.

  13. Evolutionary insights into scleractinian corals using comparative genomic hybridizations

    Directory of Open Access Journals (Sweden)

    Aranda Manuel

    2012-09-01

    Full Text Available Abstract Background Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization. Results Our results showed that the current microarray platform for A. palmata is able to provide biological relevant information for a wide variety of coral species covering both the complex clade as well the robust clade. Analysis of the fraction of highly diverged genes showed a significantly higher amount of genes without annotation corroborating previous findings that point towards a higher rate of divergence for taxonomically restricted genes. Among the genes with annotation, we found many mitochondrial genes to be highly diverged in M. faveolata when compared to A. palmata, while the majority of nuclear encoded genes maintained an average divergence rate. Conclusions The use of present microarray platforms for transcriptional analyses in different coral species will greatly enhance the understanding of the molecular basis of stress and health and highlight evolutionary differences between scleractinian coral species. On a genomic basis, we show that cDNA arrays can be used to identify patterns of divergence. Mitochondrion-encoded genes seem to have diverged faster than

  14. Global Analysis of an Expectations Augmented Evolutionary Dynamics

    OpenAIRE

    Angelo Antoci; Antonio Gay; Massimiliano Landi; Pier Luigi Sacco

    2007-01-01

    We consider a deterministic evolutionary model where players form expectations about future play. Players are not fully rational and have expectations that change over time in response to current payoffs and feedback from the past. We provide a complete characterization of the qualitative dynamics so induced for a two strategies population game,and relate our findings to standard evolutionary dynamics and equilibrium selection when agents have rational forward looking expectations

  15. Evolution in Mind: Evolutionary Dynamics, Cognitive Processes, and Bayesian Inference.

    Science.gov (United States)

    Suchow, Jordan W; Bourgin, David D; Griffiths, Thomas L

    2017-07-01

    Evolutionary theory describes the dynamics of population change in settings affected by reproduction, selection, mutation, and drift. In the context of human cognition, evolutionary theory is most often invoked to explain the origins of capacities such as language, metacognition, and spatial reasoning, framing them as functional adaptations to an ancestral environment. However, evolutionary theory is useful for understanding the mind in a second way: as a mathematical framework for describing evolving populations of thoughts, ideas, and memories within a single mind. In fact, deep correspondences exist between the mathematics of evolution and of learning, with perhaps the deepest being an equivalence between certain evolutionary dynamics and Bayesian inference. This equivalence permits reinterpretation of evolutionary processes as algorithms for Bayesian inference and has relevance for understanding diverse cognitive capacities, including memory and creativity. Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Dynamical characteristics of software trustworthiness and their evolutionary complexity

    Institute of Scientific and Technical Information of China (English)

    ZHENG ZhiMing; MA ShiLong; LI Wei; WEI Wei; JIANG Xin; ZHANG ZhanLi; GUO BingHui

    2009-01-01

    Developing trusted $oftwares has become an important trend and a natural choice In the development of software technology and applications, and software trustworthiness modeling has become a prerequisite and necessary means. To discuss and explain the basic scientific problems in software trustworthiness and to establish theoretical foundations for software trustworthiness measurement, combining the Ideas of dynamical system study, this paper studies evolutionary laws of software trustworthiness and the dynamical mechanism under the effect of various internal and external factors, and proposes dynamical models for software trustworthiness, thus, software trustworthiness can be considered as the statistical characteristics of behaviors of software systems in the dynamical and open environment. By analyzing two simple examples, the paper explains the relationship between the limit evolutionary behaviors of software trustworthiness attributes and dynamical system characteristics, and interprets the dynamical characteristics of software trustworthiness and their evolutionary complexity.

  17. Hybrid Dynamical Systems Modeling, Stability, and Robustness

    CERN Document Server

    Goebel, Rafal; Teel, Andrew R

    2012-01-01

    Hybrid dynamical systems exhibit continuous and instantaneous changes, having features of continuous-time and discrete-time dynamical systems. Filled with a wealth of examples to illustrate concepts, this book presents a complete theory of robust asymptotic stability for hybrid dynamical systems that is applicable to the design of hybrid control algorithms--algorithms that feature logic, timers, or combinations of digital and analog components. With the tools of modern mathematical analysis, Hybrid Dynamical Systems unifies and generalizes earlier developments in continuous-time and discret

  18. An evolutionary dynamics model adapted to eusocial insects.

    Directory of Open Access Journals (Sweden)

    Louise van Oudenhove

    Full Text Available This study aims to better understand the evolutionary processes allowing species coexistence in eusocial insect communities. We develop a mathematical model that applies adaptive dynamics theory to the evolutionary dynamics of eusocial insects, focusing on the colony as the unit of selection. The model links long-term evolutionary processes to ecological interactions among colonies and seasonal worker production within the colony. Colony population dynamics is defined by both worker production and colony reproduction. Random mutations occur in strategies, and mutant colonies enter the community. The interactions of colonies at the ecological timescale drive the evolution of strategies at the evolutionary timescale by natural selection. This model is used to study two specific traits in ants: worker body size and the degree of collective foraging. For both traits, trade-offs in competitive ability and other fitness components allows to determine conditions in which selection becomes disruptive. Our results illustrate that asymmetric competition underpins diversity in ant communities.

  19. Dynamical investigation of macromolecular hybridization bioassays

    CERN Document Server

    Bittner, R; Wixforth, A

    2002-01-01

    A novel sensoric technique for the dynamical in situ investigation of a hybridization bio assay is presented, which utilizes a metal bead labeling method. Therein, hybridization results in an increased metal coverage on parts of a substrate, where it takes place. Our sensing principle relies on the measurement of the radio frequency impedance of the hybridization spots. We propose several examples for sensor devices.

  20. A New Dynamical Evolutionary Algorithm Based on Statistical Mechanics

    Institute of Scientific and Technical Information of China (English)

    LI YuanXiang(李元香); ZOU XiuFen(邹秀芬); KANG LiShan(康立山); Zbigniew Michalewicz

    2003-01-01

    In this paper, a new dynamical evolutionary algorithm (DEA) is presented basedon the theory of statistical mechanics. The novelty of this kind of dynamical evolutionary algorithmis that all individuals in a population (called particles in a dynamical system) are running andsearching with their population evolving driven by a nev selecting mechanism. This mechanismsimulates the principle of molecular dynamics, which is easy to design and implement. A basictheoretical analysis for the dynamical evolutionary algorithm is given and as a consequence twostopping criteria of the algorithm are derived from the principle of energy minimization and the lawof entropy increasing. In order to verify the effectiveness of the scheme, DEA is applied to solvingsome typical numerical function minimization problems which are poorly solved by traditionalevolutionary algorithms. The experimental results show that DEA is fast and reliable.

  1. Optimization of Evolutionary Neural Networks Using Hybrid Learning Algorithms

    OpenAIRE

    Abraham, Ajith

    2004-01-01

    Evolutionary artificial neural networks (EANNs) refer to a special class of artificial neural networks (ANNs) in which evolution is another fundamental form of adaptation in addition to learning. Evolutionary algorithms are used to adapt the connection weights, network architecture and learning algorithms according to the problem environment. Even though evolutionary algorithms are well known as efficient global search algorithms, very often they miss the best local solutions in the complex s...

  2. An evolutionary economics approach to ecosystem dynamics

    NARCIS (Netherlands)

    Blijleven, V.B; Angeren, van J.; Brinkkemper, S.

    2013-01-01

    Biology and evolution lie at the heart of the ecosystem metaphor that is recurrently applied in the digital era. Although the evolution and analogy with evolutionary biology is acknowledged within the research domains of business ecosystems and digital ecosystems, several key definitions and self-or

  3. An evolutionary economics approach to ecosystem dynamics

    NARCIS (Netherlands)

    Blijleven, V.B; Angeren, van J.; Brinkkemper, S.

    2013-01-01

    Biology and evolution lie at the heart of the ecosystem metaphor that is recurrently applied in the digital era. Although the evolution and analogy with evolutionary biology is acknowledged within the research domains of business ecosystems and digital ecosystems, several key definitions and

  4. Hybrid fitness, adaptation and evolutionary diversification: lessons learned from Louisiana Irises.

    Science.gov (United States)

    Arnold, M L; Ballerini, E S; Brothers, A N

    2012-03-01

    Estimates of hybrid fitness have been used as either a platform for testing the potential role of natural hybridization in the evolution of species and species complexes or, alternatively, as a rationale for dismissing hybridization events as being of any evolutionary significance. From the time of Darwin's publication of The Origin, through the neo-Darwinian synthesis, to the present day, the observation of variability in hybrid fitness has remained a challenge for some models of speciation. Yet, Darwin and others have reported the elevated fitness of hybrid genotypes under certain environmental conditions. In modern scientific terminology, this observation reflects the fact that hybrid genotypes can demonstrate genotype × environment interactions. In the current review, we illustrate the development of one plant species complex, namely the Louisiana Irises, into a 'model system' for investigating hybrid fitness and the role of genetic exchange in adaptive evolution and diversification. In particular, we will argue that a multitude of approaches, involving both experimental and natural environments, and incorporating both manipulative analyses and surveys of natural populations, are necessary to adequately test for the evolutionary significance of introgressive hybridization. An appreciation of the variability of hybrid fitness leads to the conclusion that certain genetic signatures reflect adaptive evolution. Furthermore, tests of the frequency of allopatric versus sympatric/parapatric divergence (that is, divergence with ongoing gene flow) support hybrid genotypes as a mechanism of evolutionary diversification in numerous species complexes.

  5. An Evolutionary Mobility Aware Multi-Objective Hybrid Routing Algorithm for Heterogeneous Wireless Sensor Networks

    DEFF Research Database (Denmark)

    Kulkarni, Nandkumar P.; Prasad, Neeli R.; Prasad, Ramjee

    Researchers have faced numerous challenges while designing WSNs and protocols in many applications such as object tracking in military, detection of disastrous events, environment and health monitoring etc. Amongst all sustaining connectivity and capitalizing on the network lifetime is a serious...... deliberation. To tackle these two problems, Mobile Wireless Sensor Networks (MWSNs) is a better choice. In MWSN, Sensor nodes move freely to a target area without the need for any special infrastructure. Due to mobility, the routing process in MWSN has become more complicated as connections in the network can...... change dynamically. In this paper, the authors put forward an Evolutionary Mobility aware multi-objective hybrid Routing Protocol for heterogeneous wireless sensor networks (EMRP). EMRP uses two-level hierarchical clustering. EMRP selects the optimal path from source to sink using multiple metrics...

  6. Effective hybrid evolutionary computational algorithms for global optimization and applied to construct prion AGAAAAGA fibril models

    CERN Document Server

    Zhang, Jiapu

    2010-01-01

    Evolutionary algorithms are parallel computing algorithms and simulated annealing algorithm is a sequential computing algorithm. This paper inserts simulated annealing into evolutionary computations and successful developed a hybrid Self-Adaptive Evolutionary Strategy $\\mu+\\lambda$ method and a hybrid Self-Adaptive Classical Evolutionary Programming method. Numerical results on more than 40 benchmark test problems of global optimization show that the hybrid methods presented in this paper are very effective. Lennard-Jones potential energy minimization is another benchmark for testing new global optimization algorithms. It is studied through the amyloid fibril constructions by this paper. To date, there is little molecular structural data available on the AGAAAAGA palindrome in the hydrophobic region (113-120) of prion proteins.This region belongs to the N-terminal unstructured region (1-123) of prion proteins, the structure of which has proved hard to determine using NMR spectroscopy or X-ray crystallography ...

  7. Evolutionary genetics of hybrid breakdown in the marine copepod Tigriopus californicus

    OpenAIRE

    Ellison, Christopher K

    2008-01-01

    Populations of the supra-littoral marine copepod Tigriopus californicus are known to be highly divergent and to exhibit a pattern of hybrid breakdown when crossed under laboratory conditions. This dissertation examines the genetic mechanisms involved in hybrid breakdown in T. californicus, particularly those involving integration of the nuclear and mitochondrial genomes. In Chapter I, I summarize some of the relevant literature concerning the importance of hybrid breakdown to evolutionary bio...

  8. The evolutionary rate dynamically tracks changes in HIV-1 epidemics

    Energy Technology Data Exchange (ETDEWEB)

    Maljkovic-berry, Irina [Los Alamos National Laboratory; Athreya, Gayathri [Los Alamos National Laboratory; Daniels, Marcus [Los Alamos National Laboratory; Bruno, William [Los Alamos National Laboratory; Korber, Bette [Los Alamos National Laboratory; Kuiken, Carla [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory

    2009-01-01

    Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.

  9. Finding Global Minima with a New Dynamical Evolutionary Algorithm

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    A new dynamical evolutionary algorithm (DEA) based on the theory of statistical mechanics is presented. This algorithm is very different from the traditional evolutionary algorithm and the two novel fe-atures are the unique of selecting strategy and the determination of individuals that are selected to crossover and mutate. We use DEA to solve a lot of global optimization problems that are nonlinear, multimodal and multidimensional and obtain satisfactory results.

  10. Optimization of Conformational Dynamics in an Epistatic Evolutionary Trajectory.

    Science.gov (United States)

    González, Mariano M; Abriata, Luciano A; Tomatis, Pablo E; Vila, Alejandro J

    2016-07-01

    The understanding of protein evolution depends on the ability to relate the impact of mutations on molecular traits to organismal fitness. Biological activity and robustness have been regarded as important features in shaping protein evolutionary landscapes. Conformational dynamics, which is essential for protein function, has received little attention in the context of evolutionary analyses. Here we employ NMR spectroscopy, the chief experimental tool to describe protein dynamics at atomic level in solution at room temperature, to study the intrinsic dynamic features of a metallo- Β: -lactamase enzyme and three variants identified during a directed evolution experiment that led to an expanded substrate profile. We show that conformational dynamics in the catalytically relevant microsecond to millisecond timescale is optimized along the favored evolutionary trajectory. In addition, we observe that the effects of mutations on dynamics are epistatic. Mutation Gly262Ser introduces slow dynamics on several residues that surround the active site when introduced in the wild-type enzyme. Mutation Asn70Ser removes the slow dynamics observed for few residues of the wild-type enzyme, but increases the number of residues that undergo slow dynamics when introduced in the Gly262Ser mutant. These effects on dynamics correlate with the epistatic interaction between these two mutations on the bacterial phenotype. These findings indicate that conformational dynamics is an evolvable trait, and that proteins endowed with more dynamic active sites also display a larger potential for promoting evolution.

  11. Cross-species amplification of 41 microsatellites in European cyprinids: A tool for evolutionary, population genetics and hybridization studies

    Directory of Open Access Journals (Sweden)

    Gilles André

    2010-05-01

    Full Text Available Abstract Background Cyprinids display the most abundant and widespread species among the European freshwater Teleostei and are known to hybridize quite commonly. Nevertheless, a limited number of markers for conducting comparative differentiation, evolutionary and hybridization dynamics studies are available to date. Findings Five multiplex PCR sets were optimized in order to assay 41 cyprinid-specific polymorphic microsatellite loci (including 10 novel loci isolated from Chondrostoma nasus nasus, Chondrostoma toxostoma toxostoma and Leuciscus leuciscus for 503 individuals (440 purebred specimens and 63 hybrids from 15 European cyprinid species. The level of genetic diversity was assessed in Alburnus alburnus, Alburnoides bipunctatus, C. genei, C. n. nasus, C. soetta, C. t. toxostoma, L. idus, L. leuciscus, Pachychilon pictum, Rutilus rutilus, Squalius cephalus and Telestes souffia. The applicability of the markers was also tested on Abramis brama, Blicca bjoerkna and Scardinius erythrophtalmus specimens. Overall, between 24 and 37 of these markers revealed polymorphic for the investigated species and 23 markers amplified for all the 15 European cyprinid species. Conclusions The developed set of markers demonstrated its performance in discriminating European cyprinid species. Furthermore, it allowed detecting and characterizing hybrid individuals. These microsatellites will therefore be useful to perform comparative evolutionary and population genetics studies dealing with European cyprinids, what is of particular interest in conservation issues and constitutes a tool of choice to conduct hybridization studies.

  12. Evolutionary dynamics of group interactions on structured populations: A review

    CERN Document Server

    Perc, Matjaz; Szolnoki, Attila; Floría, Luis M; Moreno, Yamir; 10.1098/rsif.2012.0997

    2013-01-01

    Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and nonliving matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proven valuable for studying pattern formation, equilibrium selection, and self-organisation in evolutionary games. Here we review recent advances in the study of evolutionary dynamics of group interactions on structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory...

  13. Emergence of structured communities through evolutionary dynamics.

    Science.gov (United States)

    Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M

    2015-10-21

    Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. Copyright © 2015 Elsevier Ltd. All rights reserved.

  14. Hybrid Airy Plasmons with Dynamically Steerable Trajectories

    CERN Document Server

    Li, Rujiang; Lin, Xiao; Wang, Huaping; Xu, Zhiwei; Chen, Hongsheng

    2016-01-01

    With the intriguing properties of diffraction-free, self-accelerating, and self-healing, Airy plasmons are promising to be used in the trapping, transporting, and sorting of micro-objects, imaging, and chip scale signal processing. However, the high dissipative loss and the lack of dynamical steerability restrict the implementation of Airy plasmons in these applications. Here we reveal the hybrid Airy plasmons for the first time by taking a hybrid graphene-based plasmonic waveguide in the terahertz (THz) domain as an example. Due to the coupling between an optical mode and a plasmonic mode, the hybrid Airy plasmons can have large propagation lengths and effective transverse deflections, where the transverse waveguide confinements are governed by the hybrid modes with moderate quality factors. Meanwhile, the propagation trajectories of hybrid Airy plasmons are dynamically steerable by changing the chemical potential of graphene. These hybrid Airy plasmons may promote the further discovery of non-diffracting be...

  15. Hybrid Airy plasmons with dynamically steerable trajectories.

    Science.gov (United States)

    Li, Rujiang; Imran, Muhammad; Lin, Xiao; Wang, Huaping; Xu, Zhiwei; Chen, Hongsheng

    2017-01-26

    With their intriguing diffraction-free, self-accelerating, and self-healing properties, Airy plasmons show promise for use in the trapping, transporting, and sorting of micro-objects, imaging, and chip scale signal processing. However, high dissipative loss and lack of dynamical steerability restrict the implementation of Airy plasmons in these applications. Here we reveal hybrid Airy plasmons for the first time by taking a hybrid graphene-based plasmonic waveguide in the terahertz (THz) domain as an example. Due to coupling between optical modes and plasmonic modes, the hybrid Airy plasmons can have large propagation lengths and effective transverse deflections, where the transverse waveguide confinements are governed by the hybrid modes with moderate quality factors. Meanwhile, the propagation trajectories of the hybrid Airy plasmons are dynamically steerable by changing the chemical potential of graphene. These hybrid Airy plasmons may promote the further discovery of non-diffracting beams along with the emerging developments of optical tweezers and tractor beams.

  16. An Allele Real-Coded Quantum Evolutionary Algorithm Based on Hybrid Updating Strategy.

    Science.gov (United States)

    Zhang, Yu-Xian; Qian, Xiao-Yi; Peng, Hui-Deng; Wang, Jian-Hui

    2016-01-01

    For improving convergence rate and preventing prematurity in quantum evolutionary algorithm, an allele real-coded quantum evolutionary algorithm based on hybrid updating strategy is presented. The real variables are coded with probability superposition of allele. A hybrid updating strategy balancing the global search and local search is presented in which the superior allele is defined. On the basis of superior allele and inferior allele, a guided evolutionary process as well as updating allele with variable scale contraction is adopted. And H ε gate is introduced to prevent prematurity. Furthermore, the global convergence of proposed algorithm is proved by Markov chain. Finally, the proposed algorithm is compared with genetic algorithm, quantum evolutionary algorithm, and double chains quantum genetic algorithm in solving continuous optimization problem, and the experimental results verify the advantages on convergence rate and search accuracy.

  17. An Allele Real-Coded Quantum Evolutionary Algorithm Based on Hybrid Updating Strategy

    Directory of Open Access Journals (Sweden)

    Yu-Xian Zhang

    2016-01-01

    Full Text Available For improving convergence rate and preventing prematurity in quantum evolutionary algorithm, an allele real-coded quantum evolutionary algorithm based on hybrid updating strategy is presented. The real variables are coded with probability superposition of allele. A hybrid updating strategy balancing the global search and local search is presented in which the superior allele is defined. On the basis of superior allele and inferior allele, a guided evolutionary process as well as updating allele with variable scale contraction is adopted. And Hε gate is introduced to prevent prematurity. Furthermore, the global convergence of proposed algorithm is proved by Markov chain. Finally, the proposed algorithm is compared with genetic algorithm, quantum evolutionary algorithm, and double chains quantum genetic algorithm in solving continuous optimization problem, and the experimental results verify the advantages on convergence rate and search accuracy.

  18. A SAA-based Novel Hybrid Intelligent Evolutionary Algorithm for Job Shop Scheduling Problem

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Through systematic analysis and comparison of the common features of SAA, ES and traditional LS (local search) algorithm, a new hybrid strategy of mixing SA, ES with LS, namely HIEA (Hybrid Intelligent Evolutionary Algorithm), is proposed in this paper. Viewed as a whole, the hybrid strategy is also an intelligent heuristic searching procedure. But it has some characteristics such as generality, robustness, etc., because it synthesizes advantages of SA, ES and LS, while the shortages of the three methods are overcome. This paper applies Markov chain theory to describe the hybrid strategy mathematically, and proves that the algorithm possesses the global asymptotical convergence and analyzes the performance of HIEA.

  19. Constrained Optimization Based on Hybrid Evolutionary Algorithm and Adaptive Constraint-Handling Technique

    DEFF Research Database (Denmark)

    Wang, Yong; Cai, Zixing; Zhou, Yuren

    2009-01-01

    A novel approach to deal with numerical and engineering constrained optimization problems, which incorporates a hybrid evolutionary algorithm and an adaptive constraint-handling technique, is presented in this paper. The hybrid evolutionary algorithm simultaneously uses simplex crossover and two...... mutation operators to generate the offspring population. Additionally, the adaptive constraint-handling technique consists of three main situations. In detail, at each situation, one constraint-handling mechanism is designed based on current population state. Experiments on 13 benchmark test functions...... and four well-known constrained design problems verify the effectiveness and efficiency of the proposed method. The experimental results show that integrating the hybrid evolutionary algorithm with the adaptive constraint-handling technique is beneficial, and the proposed method achieves competitive...

  20. Evolutionary psychology: toward a unifying theory and a hybrid science.

    Science.gov (United States)

    Caporael, L R

    2001-01-01

    Although evolutionary psychology is typically associated with "selfish gene theory," numerous other approaches to the study of mind and behavior provide a wealth of concepts for theorizing about psychology, culture, and development. These include general evolutionary approaches and theories focused on sociality, dual inheritance, multilevel selection, and developmental systems. Most evolutionary accounts use the same methods as Darwin-the "fit among facts"-to use natural selection as an explanation for behavior. Scientific standards for constraining and evaluating such accounts, research into the mutual influence of science and society on the understanding of evolution, and computational technologies for modeling species-typical processes are important considerations. Coevolutionary theories and developmental systems theories may eventually give rise to unification in a broad and general sense. Such a unification would be interdisciplinary and problem centered rather than discipline centered.

  1. Evolutionary dynamics of altruism and cheating among social amoebas.

    Science.gov (United States)

    Brännström, A; Dieckmann, U

    2005-08-01

    Dictyostelium discoideum is a eukaryotic amoeba, which, when starvation is imminent, aggregates to form fruiting bodies consisting of a stalk of reproductively dead cells that supports spores. Because different clones may be involved in such aggregations, cheater strategies may emerge that allocate a smaller fraction of cells to stalk formation, thus gaining a reproductive advantage. In this paper, we model the evolutionary dynamics of allocation strategies in Dictyostelium under the realistic assumption that the number of clones involved in aggregations follows a random distribution. By determining the full course of evolutionary dynamics, we show that evolutionary branching in allocation strategies may occur, resulting in dimorphic populations that produce stalkless and stalked fruiting bodies. We also demonstrate that such dimorphisms are more likely to emerge when the variation in the number of clones involved in aggregations is large.

  2. Modeling hybrid perovskites by molecular dynamics.

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  3. Modeling hybrid perovskites by molecular dynamics

    Science.gov (United States)

    Mattoni, Alessandro; Filippetti, Alessio; Caddeo, Claudia

    2017-02-01

    The topical review describes the recent progress in the modeling of hybrid perovskites by molecular dynamics simulations. Hybrid perovskites and in particular methylammonium lead halide (MAPI) have a tremendous technological relevance representing the fastest-advancing solar material to date. They also represent the paradigm of an organic-inorganic crystalline material with some conceptual peculiarities: an inorganic semiconductor for what concerns the electronic and absorption properties with a hybrid and solution processable organic-inorganic body. After briefly explaining the basic concepts of ab initio and classical molecular dynamics, the model potential recently developed for hybrid perovskites is described together with its physical motivation as a simple ionic model able to reproduce the main dynamical properties of the material. Advantages and limits of the two strategies (either ab initio or classical) are discussed in comparison with the time and length scales (from pico to microsecond scale) necessary to comprehensively study the relevant properties of hybrid perovskites from molecular reorientations to electrocaloric effects. The state-of-the-art of the molecular dynamics modeling of hybrid perovskites is reviewed by focusing on a selection of showcase applications of methylammonium lead halide: molecular cations disorder; temperature evolution of vibrations; thermally activated defects diffusion; thermal transport. We finally discuss the perspectives in the modeling of hybrid perovskites by molecular dynamics.

  4. Evolutionary programming for goal-driven dynamic planning

    Science.gov (United States)

    Vaccaro, James M.; Guest, Clark C.; Ross, David O.

    2002-03-01

    one step closer to solving more difficult real-world AI problems. Using a hybrid approach that includes adaptation via evolutionary computation for the intelligent planning of a Risk player's turn provides better dynamic intelligent planning than more uniform approaches.

  5. Evolutionary dynamics of Newcastle disease virus

    Science.gov (United States)

    Miller, P.J.; Kim, L.M.; Ip, H.S.; Afonso, C.L.

    2009-01-01

    A comprehensive dataset of NDV genome sequences was evaluated using bioinformatics to characterize the evolutionary forces affecting NDV genomes. Despite evidence of recombination in most genes, only one event in the fusion gene of genotype V viruses produced evolutionarily viable progenies. The codon-associated rate of change for the six NDV proteins revealed that the highest rate of change occurred at the fusion protein. All proteins were under strong purifying (negative) selection; the fusion protein displayed the highest number of amino acids under positive selection. Regardless of the phylogenetic grouping or the level of virulence, the cleavage site motif was highly conserved implying that mutations at this site that result in changes of virulence may not be favored. The coding sequence of the fusion gene and the genomes of viruses from wild birds displayed higher yearly rates of change in virulent viruses than in viruses of low virulence, suggesting that an increase in virulence may accelerate the rate of NDV evolution. ?? 2009 Elsevier Inc.

  6. A stochastic evolutionary model for survival dynamics

    CERN Document Server

    Fenner, Trevor; Loizou, George

    2014-01-01

    The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. In our model, the only implicit assumption made is that the longer an actor has been in the system, the more likely it is to have failed. We derive a power-law distribution for the process and provide preliminary empirical evidence for the validity of the model from two well-known survival analysis data sets.

  7. Evolutionary dynamics of a smoothed war of attrition game.

    Science.gov (United States)

    Iyer, Swami; Killingback, Timothy

    2016-05-07

    In evolutionary game theory the War of Attrition game is intended to model animal contests which are decided by non-aggressive behavior, such as the length of time that a participant will persist in the contest. The classical War of Attrition game assumes that no errors are made in the implementation of an animal׳s strategy. However, it is inevitable in reality that such errors must sometimes occur. Here we introduce an extension of the classical War of Attrition game which includes the effect of errors in the implementation of an individual׳s strategy. This extension of the classical game has the important feature that the payoff is continuous, and as a consequence admits evolutionary behavior that is fundamentally different from that possible in the original game. We study the evolutionary dynamics of this new game in well-mixed populations both analytically using adaptive dynamics and through individual-based simulations, and show that there are a variety of possible outcomes, including simple monomorphic or dimorphic configurations which are evolutionarily stable and cannot occur in the classical War of Attrition game. In addition, we study the evolutionary dynamics of this extended game in a variety of spatially and socially structured populations, as represented by different complex network topologies, and show that similar outcomes can also occur in these situations. Copyright © 2016 Elsevier Ltd. All rights reserved.

  8. Strategy selection in evolutionary game dynamics on group interaction networks.

    Science.gov (United States)

    Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao

    2014-11-01

    Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.

  9. Reconstructing the Nonlinear Dynamical Systems by Evolutionary Computation Techniques

    Institute of Scientific and Technical Information of China (English)

    LIU Minzhong; KANG Lishan

    2006-01-01

    We introduce a new dynamical evolutionary algorithm(DEA) based on the theory of statistical mechanics and investigate the reconstruction problem for the nonlinear dynamical systems using observation data. The convergence of the algorithm is discussed. We make the numerical experiments and test our model using the two famous chaotic systems (mainly the Lorenz and Chen systems ). The results show the relatively accurate reconstruction of these chaotic systems based on observational data can be obtained. Therefore we may conclude that there are broad prospects using our method to model the nonlinear dynamical systems.

  10. Hybrid Predictive Control for Dynamic Transport Problems

    CERN Document Server

    Núñez, Alfredo A; Cortés, Cristián E

    2013-01-01

    Hybrid Predictive Control for Dynamic Transport Problems develops methods for the design of predictive control strategies for nonlinear-dynamic hybrid discrete-/continuous-variable systems. The methodology is designed for real-time applications, particularly the study of dynamic transport systems. Operational and service policies are considered, as well as cost reduction. The control structure is based on a sound definition of the key variables and their evolution. A flexible objective function able to capture the predictive behaviour of the system variables is described. Coupled with efficient algorithms, mainly drawn from the area of computational intelligence, this is shown to optimize performance indices for real-time applications. The framework of the proposed predictive control methodology is generic and, being able to solve nonlinear mixed-integer optimization problems dynamically, is readily extendable to other industrial processes. The main topics of this book are: ●hybrid predictive control (HPC) ...

  11. Evolutionary insights into scleractinian corals using comparative genomic hybridizations.

    KAUST Repository

    Aranda, Manuel

    2012-09-21

    Coral reefs belong to the most ecologically and economically important ecosystems on our planet. Yet, they are under steady decline worldwide due to rising sea surface temperatures, disease, and pollution. Understanding the molecular impact of these stressors on different coral species is imperative in order to predict how coral populations will respond to this continued disturbance. The use of molecular tools such as microarrays has provided deep insight into the molecular stress response of corals. Here, we have performed comparative genomic hybridizations (CGH) with different coral species to an Acropora palmata microarray platform containing 13,546 cDNA clones in order to identify potentially rapidly evolving genes and to determine the suitability of existing microarray platforms for use in gene expression studies (via heterologous hybridization).

  12. Hybrid Dynamic Network Data Envelopment Analysis

    Directory of Open Access Journals (Sweden)

    Ling Li

    2015-01-01

    Full Text Available Conventional DEA models make no hypothesis concerning the internal operations in a static situation. To open the “black box” and work with dynamic assessment issues synchronously, we put forward a hybrid model for evaluating the relative efficiencies of a set of DMUs over an observed time period with a composite of network DEA and dynamic DEA. We vertically deal with intermediate products between divisions with assignable inputs in the network structure and, horizontally, we extend network structure by means of a dynamic pattern with unrelated activities between two succeeding periods. The hybrid dynamic network DEA model proposed in this paper enables us to (i pry into the internal operations of DEA by another network structure, (ii obtain dynamic change of period efficiency, and (iii gain the overall dynamic efficiency of DMUs over the entire observed periods. We finally illustrate the calculation procedure of the proposed approach by a numerical example.

  13. Hybrid dynamical systems observation and control

    CERN Document Server

    Defoort, Michael

    2015-01-01

    This book is a collection of contributions defining the state of current knowledge and new trends in hybrid systems – systems involving both continuous dynamics and discrete events – as described by the work of several well-known groups of researchers. Hybrid Dynamical Systems presents theoretical advances in such areas as diagnosability, observability and stabilization for various classes of system. Continuous and discrete state estimation and self-triggering control of nonlinear systems are advanced. The text employs various methods, among them, high-order sliding modes, Takagi–Sugeno representation and sampled-data switching to achieve its ends. The many applications of hybrid systems from power converters to computer science are not forgotten; studies of flexible-joint robotic arms and – as representative biological systems – the behaviour of the human heart and vasculature, demonstrate the wide-ranging practical significance of control in hybrid systems. The cross-disciplinary origins of study ...

  14. Hybrid Airy Plasmons with Dynamically Steerable Trajectories

    OpenAIRE

    Li, Rujiang; Imran, Muhammad; Lin, Xiao; Wang, Huaping; Xu, Zhiwei; Chen, Hongsheng

    2016-01-01

    With the intriguing properties of diffraction-free, self-accelerating, and self-healing, Airy plasmons are promising to be used in the trapping, transporting, and sorting of micro-objects, imaging, and chip scale signal processing. However, the high dissipative loss and the lack of dynamical steerability restrict the implementation of Airy plasmons in these applications. Here we reveal the hybrid Airy plasmons for the first time by taking a hybrid graphene-based plasmonic waveguide in the ter...

  15. Gillespie eco‐evolutionary models (GEMs) reveal the role of heritable trait variation in eco‐evolutionary dynamics

    OpenAIRE

    DeLong, John P.; Gibert, Jean P.

    2016-01-01

    Abstract Heritable trait variation is a central and necessary ingredient of evolution. Trait variation also directly affects ecological processes, generating a clear link between evolutionary and ecological dynamics. Despite the changes in variation that occur through selection, drift, mutation, and recombination, current eco‐evolutionary models usually fail to track how variation changes through time. Moreover, eco‐evolutionary models assume fitness functions for each trait and each ecologic...

  16. Evolutionary dynamics of time-resolved social interactions

    Science.gov (United States)

    Cardillo, Alessio; Petri, Giovanni; Nicosia, Vincenzo; Sinatra, Roberta; Gómez-Gardeñes, Jesús; Latora, Vito

    2014-11-01

    Cooperation among unrelated individuals is frequently observed in social groups when their members combine efforts and resources to obtain a shared benefit that is unachievable by an individual alone. However, understanding why cooperation arises despite the natural tendency of individuals toward selfish behavior is still an open problem and represents one of the most fascinating challenges in evolutionary dynamics. Recently, the structural characterization of the networks in which social interactions take place has shed some light on the mechanisms by which cooperative behavior emerges and eventually overcomes the natural temptation to defect. In particular, it has been found that the heterogeneity in the number of social ties and the presence of tightly knit communities lead to a significant increase in cooperation as compared with the unstructured and homogeneous connection patterns considered in classical evolutionary dynamics. Here, we investigate the role of social-ties dynamics for the emergence of cooperation in a family of social dilemmas. Social interactions are in fact intrinsically dynamic, fluctuating, and intermittent over time, and they can be represented by time-varying networks. By considering two experimental data sets of human interactions with detailed time information, we show that the temporal dynamics of social ties has a dramatic impact on the evolution of cooperation: the dynamics of pairwise interactions favors selfish behavior.

  17. Evolutionary dynamics of fairness on graphs with migration.

    Science.gov (United States)

    Wang, Xiaofeng; Chen, Xiaojie; Wang, Long

    2015-09-07

    Individual migration plays a crucial role in evolutionary dynamics of population on networks. In this paper, we generalize the networked ultimatum game by diluting population structures as well as endowing individuals with migration ability, and investigate evolutionary dynamics of fairness on graphs with migration in the ultimatum game. We first revisit the impact of node degree on the evolution of fairness. Interestingly, numerical simulations reveal that there exists an optimal value of node degree resulting in the maximal offer level of populations. Then we explore the effects of dilution and migration on the evolution of fairness, and find that both the dilution of population structures and the endowment of migration ability to individuals would lead to the drop of offer level, while the rise of acceptance level of populations. Notably, natural selection even favors the evolution of self-incompatible strategies, when either vacancy rate or migration rate exceeds a critical threshold. To confirm our simulation results, we also propose an analytical method to study the evolutionary dynamics of fairness on graphs with migration. This method can be applied to explore any games governed by pairwise interactions in finite populations. Copyright © 2015 Elsevier Ltd. All rights reserved.

  18. Uncertainty Quantification in Hybrid Dynamical Systems

    CERN Document Server

    Sahai, Tuhin

    2011-01-01

    Uncertainty quantification (UQ) techniques are frequently used to ascertain output variability in systems with parametric uncertainty. Traditional algorithms for UQ are either system-agnostic and slow (such as Monte Carlo) or fast with stringent assumptions on smoothness (such as polynomial chaos and Quasi-Monte Carlo). In this work, we develop a fast UQ approach for hybrid dynamical systems by extending the polynomial chaos methodology to these systems. To capture discontinuities, we use a wavelet-based Wiener-Haar expansion. We develop a boundary layer approach to propagate uncertainty through separable reset conditions. We also introduce a transport theory based approach for propagating uncertainty through hybrid dynamical systems. Here the expansion yields a set of hyperbolic equations that are solved by integrating along characteristics. The solution of the partial differential equation along the characteristics allows one to quantify uncertainty in hybrid or switching dynamical systems. The above method...

  19. Uncertainty quantification in hybrid dynamical systems

    Science.gov (United States)

    Sahai, Tuhin; Pasini, José Miguel

    2013-03-01

    Uncertainty quantification (UQ) techniques are frequently used to ascertain output variability in systems with parametric uncertainty. Traditional algorithms for UQ are either system-agnostic and slow (such as Monte Carlo) or fast with stringent assumptions on smoothness (such as polynomial chaos and Quasi-Monte Carlo). In this work, we develop a fast UQ approach for hybrid dynamical systems by extending the polynomial chaos methodology to these systems. To capture discontinuities, we use a wavelet-based Wiener-Haar expansion. We develop a boundary layer approach to propagate uncertainty through separable reset conditions. We also introduce a transport theory based approach for propagating uncertainty through hybrid dynamical systems. Here the expansion yields a set of hyperbolic equations that are solved by integrating along characteristics. The solution of the partial differential equation along the characteristics allows one to quantify uncertainty in hybrid or switching dynamical systems. The above methods are demonstrated on example problems.

  20. Gillespie eco-evolutionary models (GEMs) reveal the role of heritable trait variation in eco-evolutionary dynamics.

    Science.gov (United States)

    DeLong, John P; Gibert, Jean P

    2016-02-01

    Heritable trait variation is a central and necessary ingredient of evolution. Trait variation also directly affects ecological processes, generating a clear link between evolutionary and ecological dynamics. Despite the changes in variation that occur through selection, drift, mutation, and recombination, current eco-evolutionary models usually fail to track how variation changes through time. Moreover, eco-evolutionary models assume fitness functions for each trait and each ecological context, which often do not have empirical validation. We introduce a new type of model, Gillespie eco-evolutionary models (GEMs), that resolves these concerns by tracking distributions of traits through time as eco-evolutionary dynamics progress. This is done by allowing change to be driven by the direct fitness consequences of model parameters within the context of the underlying ecological model, without having to assume a particular fitness function. GEMs work by adding a trait distribution component to the standard Gillespie algorithm - an approach that models stochastic systems in nature that are typically approximated through ordinary differential equations. We illustrate GEMs with the Rosenzweig-MacArthur consumer-resource model. We show not only how heritable trait variation fuels trait evolution and influences eco-evolutionary dynamics, but also how the erosion of variation through time may hinder eco-evolutionary dynamics in the long run. GEMs can be developed for any parameter in any ordinary differential equation model and, furthermore, can enable modeling of multiple interacting traits at the same time. We expect GEMs will open the door to a new direction in eco-evolutionary and evolutionary modeling by removing long-standing modeling barriers, simplifying the link between traits, fitness, and dynamics, and expanding eco-evolutionary treatment of a greater diversity of ecological interactions. These factors make GEMs much more than a modeling advance, but an important

  1. Dynamical systems revisited : Hybrid systems with Zeno executions

    OpenAIRE

    ZHANG, JUN; Johansson, Karl Henrik; Lygeros, John; Sastry, Shankar

    2000-01-01

    Results from classical dynamical systems are generalized to hybrid dynamical systems. The concept of omega limit set is introduced for hybrid systems and is used to prove new results on invariant sets and stability, where Zeno and non-Zeno hybrid systems can be treated within the same framework. As an example, LaSalle's Invariance Principle is extended to hybrid systems. Zeno hybrid systems are discussed in detail. The omega limit set of a Zeno execution is characterized for classes of hybrid...

  2. Unpredictability induced by unfocused games in evolutionary game dynamics.

    Science.gov (United States)

    Hashimoto, Koh

    2006-08-07

    Evolutionary game theory is a basis of replicator systems and has applications ranging from animal behavior and human language to ecosystems and other hierarchical network systems. Most studies in evolutionary game dynamics have focused on a single game, but, in many situations, we see that many games are played simultaneously. We construct a replicator equation with plural games by assuming that a reward of a player is a simple summation of the reward of each game. Even if the numbers of the strategies of the games are different, its dynamics can be described in one replicator equation. We here show that when players play several games at the same time, the fate of a single game cannot be determined without knowing the structures of the whole other games. The most absorbing fact is that even if a single game has a ESS (evolutionary stable strategy), the relative frequencies of strategies in the game does not always converge to the ESS point when other games are played simultaneously.

  3. Evolutionary principles underlying structure and response dynamics of cellular networks.

    Science.gov (United States)

    Steinacher, Arno; Soyer, Orkun S

    2012-01-01

    The network view in systems biology, in conjunction with the continuing development of experimental technologies, is providing us with the key structural and dynamical features of both cell-wide and pathway-level regulatory, signaling and metabolic systems. These include for example modularity and presence of hub proteins at the structural level and ultrasensitivity and feedback control at the level of dynamics. The uncovering of such features, and the seeming commonality of some of them, makes many systems biologists believe that these could represent design principles that underpin cellular systems across organisms. Here, we argue that such claims on any observed feature requires an understanding of how it has emerged in evolution and how it can shape subsequent evolution. We review recent and past studies that aim to achieve such evolutionary understanding for observed features of cellular networks. We argue that this evolutionary framework could lead to deciphering evolutionary origin and relevance of proposed design principles, thereby allowing to predict their presence or absence in an organism based on its environment and biochemistry and their effect on its future evolution.

  4. Genome size as a key to evolutionary complex aquatic plants: polyploidy and hybridization in Callitriche (Plantaginaceae.

    Directory of Open Access Journals (Sweden)

    Jan Prančl

    Full Text Available Despite their complex evolutionary histories, aquatic plants are highly underrepresented in contemporary biosystematic studies. Of them, the genus Callitriche is particularly interesting because of such evolutionary features as wide variation in chromosome numbers and pollination systems. However, taxonomic difficulties have prevented broader investigation of this genus. In this study we applied flow cytometry to Callitriche for the first time in order to gain an insight into evolutionary processes and genome size differentiation in the genus. Flow cytometry complemented by confirmation of chromosome counts was applied to an extensive dataset of 1077 Callitriche individuals from 495 localities in 11 European countries and the USA. Genome size was determined for 12 taxa. The results suggest that many important processes have interacted in the evolution of the genus, including polyploidization and hybridization. Incongruence between genome size and ploidy level, intraspecific variation in genome size, formation of autotriploid and hybridization between species with different pollination systems were also detected. Hybridization takes place particularly in the diploid-tetraploid complex C. cophocarpa-C. platycarpa, for which the triploid hybrids were frequently recorded in the area of co-occurrence of its parents. A hitherto unknown hybrid (probably C. hamulata × C. cophocarpa with a unique chromosome number was discovered in the Czech Republic. However, hybridization occurs very rarely among most of the studied species. The main ecological preferences were also compared among the taxa collected. Although Callitriche taxa often grow in mixed populations, the ecological preferences of individual species are distinctly different in some cases. Anyway, flow cytometry is a very efficient method for taxonomic delimitation, determination and investigation of Callitriche species, and is even able to distinguish homoploid taxa and identify introduced

  5. Iterative Dynamic Diversity Evolutionary Algorithm for Constrained Optimization

    Institute of Scientific and Technical Information of China (English)

    GAO Wei-Shang; SHAO Cheng

    2014-01-01

    Evolutionary algorithms (EAs) were shown to be effective for complex constrained optimization problems. However, inflexible exploration in general EAs would lead to losing the global optimum nearby the ill-convergence regions. In this paper, we propose an iterative dynamic diversity evolutionary algorithm (IDDEA) with contractive subregions guiding exploitation through local extrema to the global optimum in suitable steps. In IDDEA, a novel optimum estimation strategy with multi-agents evolving diversely is suggested to efficiently compute dominance trend and establish a subregion. In addition, a subregion converging iteration is designed to redistrict a smaller subregion in current subregion for next iteration, which is based on a special dominance estimation scheme. Meanwhile, an infimum penalty function is embedded into IDDEA to judge agents and penalize adaptively the unfeasible agents with the lowest fitness of feasible agents. Furthermore, several engineering design optimization problems taken from the specialized literature are successfully solved by the present algorithm with high reliable solutions.

  6. An Evolutionary Comparison of the Handicap Principle and Hybrid Equilibrium Theories of Signaling.

    Science.gov (United States)

    Kane, Patrick; Zollman, Kevin J S

    2015-01-01

    The handicap principle has come under significant challenge both from empirical studies and from theoretical work. As a result, a number of alternative explanations for honest signaling have been proposed. This paper compares the evolutionary plausibility of one such alternative, the "hybrid equilibrium," to the handicap principle. We utilize computer simulations to compare these two theories as they are instantiated in Maynard Smith's Sir Philip Sidney game. We conclude that, when both types of communication are possible, evolution is unlikely to lead to handicap signaling and is far more likely to result in the partially honest signaling predicted by hybrid equilibrium theory.

  7. Dynamics of 3-DOF Hybrid Robot Manipulator

    Institute of Scientific and Technical Information of China (English)

    周兵; 毛泰祥; 杨汝清

    2004-01-01

    This paper introduces a 3-dof hybrid robotic manipulator which is constructed by combming a parallel mechanism and a pantograph to increase stiffness as well as workspace. And by analyzing its kinematics and dynamics with Lagrange's method, the dynamic model is obtained which is essential for feed-forward control of the manipulator. An explicit solution is given out. Finally, a simulation test is carried out on computers.

  8. Hybrid Robust Multi-Objective Evolutionary Optimization Algorithm

    Science.gov (United States)

    2009-03-10

    has been successfully run on Microsoft Windows workstations, Linux workstations and Beowulf style clusters . The software can run in two modes...on a processor (the cluster server in this case) and the objective function evaluations are then made into jobs that are submitted to the job manager...of the cluster in question. This architecture is preferred by the authors to allow for large parallelized computational fluid dynamics and finite

  9. Filtering in hybrid dynamic Bayesian networks

    DEFF Research Database (Denmark)

    Andersen, Morten Nonboe; Andersen, Rasmus Ørum; Wheeler, Kevin

    2004-01-01

    We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2-Time Slice DBN (2T-DBN) from (Koller & Lerner, 2000) to model fault detection in a watertank system. In (Koller & Lerner, 2000) a generic Particle Filter (PF) is used for infere...

  10. Filtering in hybrid dynamic Bayesian networks (left)

    DEFF Research Database (Denmark)

    Andersen, Morten Nonboe; Andersen, Rasmus Ørum; Wheeler, Kevin

    We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2-Time Slice DBN (2T-DBN) from (Koller & Lerner, 2000) to model fault detection in a watertank system. In (Koller & Lerner, 2000) a generic Particle Filter (PF) is used for infere...

  11. Filtering in hybrid dynamic Bayesian networks (center)

    DEFF Research Database (Denmark)

    Andersen, Morten Nonboe; Andersen, Rasmus Ørum; Wheeler, Kevin

    We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2-Time Slice DBN (2T-DBN) from (Koller & Lerner, 2000) to model fault detection in a watertank system. In (Koller & Lerner, 2000) a generic Particle Filter (PF) is used for infere...

  12. Evolutionary dynamics of time-resolved social interactions

    CERN Document Server

    Cardillo, Alessio; Nicosia, Vincenzo; Sinatra, Roberta; Gómez-Gardeñes, Jesús; Latora, Vito

    2013-01-01

    Cooperation among unrelated individuals is frequently observed in social groups when their members join efforts and resources to obtain a shared benefit which is unachievable by singles. However, understanding why cooperation arises despite the natural tendency of individuals towards selfish behaviors is still an open problem and represents one of the most fascinating challenges in volutionary dynamics. Very recently, the structural characterization of the networks upon which social interactions take place has shed some light on the mechanisms by which cooperative behaviours emerge and eventually overcome the individual temptation to defect. In particular, it has been found that the heterogeneity in the number of social ties and the presence of tightly-knit communities lead to a significant increase of cooperation as compared with the unstructured and homogeneous connection patterns considered in classical evolutionary dynamics. Here we investigate the role of social ties dynamics for the emergence of coopera...

  13. Evolutionary network games: Imitation and Best-Response dynamics

    CERN Document Server

    Cimini, Giulio; Sánchez, Angel

    2014-01-01

    We consider games of strategic substitutes and strategic complements on networks. We introduce two different evolutionary dynamics in order to refine their multiplicity of equilibria, that can be related to alternative informational contexts. We find that for the best-shot game, taken as a model for substitutes, a replicator-like dynamics does not lead to Nash equilibria, whereas it leads to unique equilibria (full cooperation or full defection, depending on the initial condition and the game parameter) for complements, represented by a coordination game. On the other hand, when the dynamics becomes more cognitively demanding in the form of a best response evolution, predictions are always Nash equilibria (at least when individuals are fully rational): For the best-shot game we find equilibria with a definite value of the fraction of contributors, whereas for the coordination game symmetric equilibria arise only for low or high initial fractions of cooperators. We also consider extensions of the natural incom...

  14. Stationary Stability for Evolutionary Dynamics in Finite Populations

    Directory of Open Access Journals (Sweden)

    Marc Harper

    2016-08-01

    Full Text Available We demonstrate a vast expansion of the theory of evolutionary stability to finite populations with mutation, connecting the theory of the stationary distribution of the Moran process with the Lyapunov theory of evolutionary stability. We define the notion of stationary stability for the Moran process with mutation and generalizations, as well as a generalized notion of evolutionary stability that includes mutation called an incentive stable state (ISS candidate. For sufficiently large populations, extrema of the stationary distribution are ISS candidates and we give a family of Lyapunov quantities that are locally minimized at the stationary extrema and at ISS candidates. In various examples, including for the Moran and Wright–Fisher processes, we show that the local maxima of the stationary distribution capture the traditionally-defined evolutionarily stable states. The classical stability theory of the replicator dynamic is recovered in the large population limit. Finally we include descriptions of possible extensions to populations of variable size and populations evolving on graphs.

  15. Kinetics and dynamics of DNA hybridization.

    Science.gov (United States)

    Yin, Yandong; Zhao, Xin Sheng

    2011-11-15

    DNA hybridization, wherein strands of DNA form duplex or larger hybrids through noncovalent, sequence-specific interactions, is one of the most fundamental processes in biology. Developing a better understanding of the kinetic and dynamic properties of DNA hybridization will thus help in the elucidation of molecular mechanisms involved in numerous biochemical processes. Moreover, because DNA hybridization has been widely adapted in biotechnology, its study is invaluable to the development of a range of commercially important processes. In this Account, we examine recent studies of the kinetics and dynamics of DNA hybridization, including (i) intramolecular collision of random coil, single-stranded DNA (ssDNA), (ii) nucleic acid hairpin folding, and (iii) considerations of DNA hybridization from both a global view and a detailed base-by-base view. We also examine the spontaneous single-base-pair flipping in duplex DNA because of its importance to both DNA hybridization and repair. Intramolecular collision of random coil ssDNA, with chemical relaxation times ranging from hundreds of nanoseconds to a few microseconds, is investigated both theoretically and experimentally. The first passage time theory of Szabo, Schulten, and Schulten, which determines the average reaction time of the intrachain collision, was tested. Although it was found to provide an acceptable approximation, a more sophisticated theoretical treatment is desirable. Nucleic acid hairpin folding has been extensively investigated as an important model system of DNA hybridization. The relaxation time of hairpin folding and unfolding strongly depends on the stem length, and it may range from hundreds of microseconds to hundreds of milliseconds. The traditional two-state model has been revised to a multistate model as a result of new experimental observations and theoretical study, and partially folded intermediate states have been introduced to the folding energy landscape. On the other hand, new

  16. A hybrid artificial bee colony optimization and quantum evolutionary algorithm for continuous optimization problems.

    Science.gov (United States)

    Duan, Hai-Bin; Xu, Chun-Fang; Xing, Zhi-Hui

    2010-02-01

    In this paper, a novel hybrid Artificial Bee Colony (ABC) and Quantum Evolutionary Algorithm (QEA) is proposed for solving continuous optimization problems. ABC is adopted to increase the local search capacity as well as the randomness of the populations. In this way, the improved QEA can jump out of the premature convergence and find the optimal value. To show the performance of our proposed hybrid QEA with ABC, a number of experiments are carried out on a set of well-known Benchmark continuous optimization problems and the related results are compared with two other QEAs: the QEA with classical crossover operation, and the QEA with 2-crossover strategy. The experimental comparison results demonstrate that the proposed hybrid ABC and QEA approach is feasible and effective in solving complex continuous optimization problems.

  17. A hybrid multi-objective evolutionary algorithm for wind-turbine blade optimization

    Science.gov (United States)

    Sessarego, M.; Dixon, K. R.; Rival, D. E.; Wood, D. H.

    2015-08-01

    A concurrent-hybrid non-dominated sorting genetic algorithm (hybrid NSGA-II) has been developed and applied to the simultaneous optimization of the annual energy production, flapwise root-bending moment and mass of the NREL 5 MW wind-turbine blade. By hybridizing a multi-objective evolutionary algorithm (MOEA) with gradient-based local search, it is believed that the optimal set of blade designs could be achieved in lower computational cost than for a conventional MOEA. To measure the convergence between the hybrid and non-hybrid NSGA-II on a wind-turbine blade optimization problem, a computationally intensive case was performed using the non-hybrid NSGA-II. From this particular case, a three-dimensional surface representing the optimal trade-off between the annual energy production, flapwise root-bending moment and blade mass was achieved. The inclusion of local gradients in the blade optimization, however, shows no improvement in the convergence for this three-objective problem.

  18. Trust Dynamics in WSNs: An Evolutionary Game-Theoretic Approach

    Directory of Open Access Journals (Sweden)

    Shigen Shen

    2016-01-01

    Full Text Available A sensor node (SN in Wireless Sensor Networks (WSNs can decide whether to collaborate with others based on a trust management system (TMS by making a trust decision. In this paper, we study the trust decision and its dynamics that play a key role to stabilize the whole network using evolutionary game theory. When SNs are making their decisions to select action Trust or Mistrust, a WSNs trust game is created to reflect their utilities. An incentive mechanism bound with one SN’s trust degree is incorporated into this trust game and effectively promotes SNs to select action Trust. The replicator dynamics of SNs’ trust evolution, illustrating the evolutionary process of SNs selecting their actions, are given. We then propose and prove the theorems indicating that evolutionarily stable strategies can be attained under different parameter values, which supply theoretical foundations to devise a TMS for WSNs. Moreover, we can find out the conditions that will lead SNs to choose action Trust as their final behavior. In this manner, we can assure WSNs’ security and stability by introducing a trust mechanism to satisfy these conditions. Experimental results have confirmed the proposed theorems and the effects of the incentive mechanism.

  19. Bidirectional Dynamic Diversity Evolutionary Algorithm for Constrained Optimization

    Directory of Open Access Journals (Sweden)

    Weishang Gao

    2013-01-01

    Full Text Available Evolutionary algorithms (EAs were shown to be effective for complex constrained optimization problems. However, inflexible exploration-exploitation and improper penalty in EAs with penalty function would lead to losing the global optimum nearby or on the constrained boundary. To determine an appropriate penalty coefficient is also difficult in most studies. In this paper, we propose a bidirectional dynamic diversity evolutionary algorithm (Bi-DDEA with multiagents guiding exploration-exploitation through local extrema to the global optimum in suitable steps. In Bi-DDEA potential advantage is detected by three kinds of agents. The scale and the density of agents will change dynamically according to the emerging of potential optimal area, which play an important role of flexible exploration-exploitation. Meanwhile, a novel double optimum estimation strategy with objective fitness and penalty fitness is suggested to compute, respectively, the dominance trend of agents in feasible region and forbidden region. This bidirectional evolving with multiagents can not only effectively avoid the problem of determining penalty coefficient but also quickly converge to the global optimum nearby or on the constrained boundary. By examining the rapidity and veracity of Bi-DDEA across benchmark functions, the proposed method is shown to be effective.

  20. Developmental dynamics: toward a biologically plausible evolutionary psychology.

    Science.gov (United States)

    Lickliter, Robert; Honeycutt, Hunter

    2003-11-01

    There has been a conceptual revolution in the biological sciences over the past several decades. Evidence from genetics, embryology, and developmental biology has converged to offer a more epigenetic, contingent, and dynamic view of how organisms develop. Despite these advances, arguments for the heuristic value of a gene-centered, predeterministic approach to the study of human behavior and development have become increasingly evident in the psychological sciences during this time. In this article, the authors review recent advances in genetics, embryology, and developmental biology that have transformed contemporary developmental and evolutionary theory and explore how these advances challenge gene-centered explanations of human behavior that ignore the complex, highly coordinated system of regulatory dynamics involved in development and evolution.

  1. Disease processes as hybrid dynamical systems

    Directory of Open Access Journals (Sweden)

    Pietro Liò

    2012-08-01

    Full Text Available We investigate the use of hybrid techniques in complex processes of infectious diseases. Since predictive disease models in biomedicine require a multiscale approach for understanding the molecule-cell-tissue-organ-body interactions, heterogeneous methodologies are often employed for describing the different biological scales. Hybrid models provide effective means for complex disease modelling where the action and dosage of a drug or a therapy could be meaningfully investigated: the infection dynamics can be classically described in a continuous fashion, while the scheduling of multiple treatment discretely. We define an algebraic language for specifying general disease processes and multiple treatments, from which a semantics in terms of hybrid dynamical system can be derived. Then, the application of control-theoretic tools is proposed in order to compute the optimal scheduling of multiple therapies. The potentialities of our approach are shown in the case study of the SIR epidemic model and we discuss its applicability on osteomyelitis, a bacterial infection affecting the bone remodelling system in a specific and multiscale manner. We report that formal languages are helpful in giving a general homogeneous formulation for the different scales involved in a multiscale disease process; and that the combination of hybrid modelling and control theory provides solid grounds for computational medicine.

  2. The pachytene checkpoint and its relationship to evolutionary patterns of polyploidization and hybrid sterility.

    Science.gov (United States)

    Li, X C; Barringer, B C; Barbash, D A

    2009-01-01

    Sterility is a commonly observed phenotype in interspecific hybrids. Sterility may result from chromosomal or genic incompatibilities, and much progress has been made toward understanding the genetic basis of hybrid sterility in various taxa. The underlying mechanisms causing hybrid sterility, however, are less well known. The pachytene checkpoint is a meiotic surveillance system that many organisms use to detect aberrant meiotic products, in order to prevent the production of defective gametes. We suggest that activation of the pachytene checkpoint may be an important mechanism contributing to two types of hybrid sterility. First, the pachytene checkpoint may form the mechanistic basis of some gene-based hybrid sterility phenotypes. Second, the pachytene checkpoint may be an important mechanism that mediates chromosomal-based hybrid sterility phenotypes involving gametes with non-haploid (either non-reduced or aneuploid) chromosome sets. Studies in several species suggest that the strength of the pachytene checkpoint is sexually dimorphic, observations that warrant future investigation into whether such variation may contribute to differences in patterns of sterility between male and female interspecific hybrids. In addition, plants seem to lack the pachytene checkpoint, which correlates with increased production of unreduced gametes and a higher incidence of polyploid species in plants versus animals. Although the pachytene checkpoint occurs in many animals and in fungi, at least some of the genes that execute the pachytene checkpoint are different among organisms. This finding suggests that the penetrance of the pachytene checkpoint, and even its presence or absence can evolve rapidly. The surprising degree of evolutionary flexibility in this meiotic surveillance system may contribute to the observed variation in patterns of hybrid sterility and in rates of polyploidization.

  3. A Dynamical Simulation Facility for Hybrid Systems

    CERN Document Server

    Back, A; Myers, M; Back, Allen; Guckenheimer, John; Myers, Mark

    1993-01-01

    Abstract: This paper establishes a general framework for describing hybrid dynamical systems which is particularly suitable for numerical simulation. In this context, the data structures used to describe the sets and functions which comprise the dynamical system are crucial since they provide the link between a natural mathematical formulation of a problem and the correct application of standard numerical algorithms. We describe a partial implementation of the design methodology and use this simulation tool for a specific control problem in robotics as an illustration of the utility of the approach for practical applications.

  4. Hybrid Differential Dynamic Programming with Stochastic Search

    Science.gov (United States)

    Aziz, Jonathan; Parker, Jeffrey; Englander, Jacob

    2016-01-01

    Differential dynamic programming (DDP) has been demonstrated as a viable approach to low-thrust trajectory optimization, namely with the recent success of NASAs Dawn mission. The Dawn trajectory was designed with the DDP-based Static Dynamic Optimal Control algorithm used in the Mystic software. Another recently developed method, Hybrid Differential Dynamic Programming (HDDP) is a variant of the standard DDP formulation that leverages both first-order and second-order state transition matrices in addition to nonlinear programming (NLP) techniques. Areas of improvement over standard DDP include constraint handling, convergence properties, continuous dynamics, and multi-phase capability. DDP is a gradient based method and will converge to a solution nearby an initial guess. In this study, monotonic basin hopping (MBH) is employed as a stochastic search method to overcome this limitation, by augmenting the HDDP algorithm for a wider search of the solution space.

  5. Contrasting views over a hybrid complex: Between speciation and evolutionary "dead-end".

    Science.gov (United States)

    Pala, I; Coelho, M M

    2005-03-14

    The Squalius alburnoides complex, of hybrid origin, comprises diploid, triploid and tetraploid forms and has a widespread distribution in the Iberian waters. The southern populations of this complex, sympatric with S. pyrenaicus, show high genetic variability, diversity of forms and reproductive modes which create pathways that may allow for the establishment of a new species in the future. Here we report a contrasting view over the S. alburnoides complex: in the Mondego River basin (northern Portugal), nuclear "non-hybrid" and tetraploid forms are absent and a clearly impoverished genetic diversity is observed, contributing to a general scarcity of possibilities of generating novel genetic material. Moreover, the bisexual species involved in the maintenance of the complex in this basin (S. carolitertii) exhibits a considerably lower genetic variability, when compared with S. pyrenaicus. The observed differences suggest that, despite being originated by similar hybridization events and maintained by analogous reproductive mechanisms, different populations of the complex were exposed to distinct evolutionary constrains, which in some cases resulted in diversification and speciation while in others led to a compromising situation in terms of evolutionary potential. Additionally, and for the first time all forms were used in the calculation of genetic distances and diversity indices, widening the possibilities of analysis of the complex by allowing the inclusion of a large part of the available data, irrespective of ploidy level.

  6. Functional diversity and evolutionary dynamics of thermoTRP channels.

    Science.gov (United States)

    Saito, Shigeru; Tominaga, Makoto

    2015-03-01

    Animals have evolved sophisticated physiological systems for sensing ambient temperature since changes in environmental temperatures affect various biological processes. Thermosensitive transient receptor potential (thermoTRP) channels serve as thermal sensors in diverse animal species. They are multimodal receptors that are activated by temperature as well as other physical and chemical stimuli. Since thermoTRP channels are calcium permeable non-selective cation channels, their activation leads to an influx of calcium and sodium ions into the cell and triggers downstream signal transduction. ThermoTRP channels have been characterized in diverse animal species over the past several years, illuminating the diversification of thermoTRP channels in the course of evolution. The gene repertoires of thermoTRP channels differ among animal species. Additionally, in some cases, the temperature and chemical sensitivities among orthologous thermoTRP channels vary among species. The evolutionary flexibility of thermoTRP channels enabled them to contribute to unique physiological systems such as infrared sensation in snakes and bats and seasonal adaptation in silk moth. On the other hand, the functional differences of thermoTRP channels among species have been utilized for understanding the molecular basis for their activation (or inhibition) mechanisms, and amino acid residues (or domains) responsible for the respective channel properties have been identified in various thermoTRP channels. Here we summarize the current understanding of the functional diversity and evolutionary dynamics of thermoTRP channels.

  7. Home and away- the evolutionary dynamics of homing endonucleases

    Directory of Open Access Journals (Sweden)

    Barzel Adi

    2011-11-01

    Full Text Available Abstract Background Homing endonucleases (HEases are a large and diverse group of site-specific DNAases. They reside within self-splicing introns and inteins, and promote their horizontal dissemination. In recent years, HEases have been the focus of extensive research due to their promising potential use in gene targeting procedures for the treatment of genetic diseases and for the genetic engineering of crop, animal models and cell lines. Results Using mathematical analysis and computational modeling, we present here a novel account for the evolution and population dynamics of HEase genes (HEGs. We describe HEGs as paradoxical selfish elements whose long-term persistence in a single population relies on low transmission rates and a positive correlation between transmission efficiency and toxicity. Conclusion Plausible conditions allow HEGs to sustain at high frequency through long evolutionary periods, with the endonuclease frequency being either at equilibrium or periodically oscillating. The predictions of our model may prove important not only for evolutionary theory but also for gene therapy and bio-engineering applications of HEases.

  8. Evolutionary dynamics of bacteria in a human host environment

    DEFF Research Database (Denmark)

    Yang, Lei; Jelsbak, Lars; Marvig, Rasmus Lykke;

    2011-01-01

    . In contrast to predictions based on in vitro evolution experiments, we document limited diversification of the evolving lineage despite a highly structured and complex host environment. Notably, the lineage went through an initial period of rapid adaptation caused by a small number of mutations......Laboratory evolution experiments have led to important findings relating organism adaptation and genomic evolution. However, continuous monitoring of long-term evolution has been lacking for natural systems, limiting our understanding of these processes in situ. Here we characterize...... the evolutionary dynamics of a lineage of a clinically important opportunistic bacterial pathogen, Pseudomonas aeruginosa, as it adapts to the airways of several individual cystic fibrosis patients over 200,000 bacterial generations, and provide estimates of mutation rates of bacteria in a natural environment...

  9. pedagog: software for simulating eco-evolutionary population dynamics.

    Science.gov (United States)

    Coombs, Jason A; Letcher, B H; Nislow, K H

    2010-05-01

    pedagog is a Windows program that can be used to determine power for, and validate inferences drawn from, eco-evolutionary studies. It models dynamics of multiple populations and their interactions through individual-based simulations while simultaneously recording genotype, pedigree and trait information at the individual level. pedagog also allows for specification of heritable traits, natural and sexual selection acting upon those traits, population sampling schemes and incorporation of genetic and demographic errors into the output. Overall, parameters can be specified for genetic diversity, demographics, mating design, genetic and demographic errors, individual growth models, trait heritability and selection, and output formatting. Demographic parameters can be either age or function based, and all parameters can be drawn from 12 statistical distributions where appropriate. Simulation results can be automatically formatted for 57 existing software programs to facilitate postsimulation analyses. pedagog is freely available for download at https://bcrc.bio.umass.edu/pedigreesoftware/.

  10. The mathematical law of evolutionary information dynamics and an observer's evolution regularities

    CERN Document Server

    Lerner, Vladimir S

    2011-01-01

    An interactive stochastics, evaluated by an entropy functional (EF) of a random field and informational process' path functional (IPF), allows us modeling the evolutionary information processes and revealing regularities of evolution dynamics. Conventional Shannon's information measure evaluates a sequence of the process' static events for each information state and do not reveal hidden dynamic connections between these events. The paper formulates the mathematical forms of the information regularities, based on a minimax variation principle (VP) for IPF, applied to the evolution's both random microprocesses and dynamic macroprocesses. The paper shows that the VP single form of the mathematical law leads to the following evolutionary regularities: -creation of the order from stochastics through the evolutionary macrodynamics, described by a gradient of dynamic potential, evolutionary speed and the evolutionary conditions of a fitness and diversity; -the evolutionary hierarchy with growing information values a...

  11. General linear dynamics - quantum, classical or hybrid

    CERN Document Server

    Elze, H-T; Vallone, F

    2011-01-01

    We describe our recent proposal of a path integral formulation of classical Hamiltonian dynamics. Which leads us here to a new attempt at hybrid dynamics, which concerns the direct coupling of classical and quantum mechanical degrees of freedom. This is of practical as well as of foundational interest and no fully satisfactory solution of this problem has been established to date. Related aspects will be observed in a general linear ensemble theory, which comprises classical and quantum dynamics in the form of Liouville and von Neumann equations, respectively, as special cases. Considering the simplest object characterized by a two-dimensional state-space, we illustrate how quantum mechanics is special in several respects among possible linear generalizations.

  12. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Directory of Open Access Journals (Sweden)

    Linbin Zhang

    2015-03-01

    Full Text Available Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  13. Sex ratio meiotic drive as a plausible evolutionary mechanism for hybrid male sterility.

    Science.gov (United States)

    Zhang, Linbin; Sun, Tianai; Woldesellassie, Fitsum; Xiao, Hailian; Tao, Yun

    2015-03-01

    Biological diversity on Earth depends on the multiplication of species or speciation, which is the evolution of reproductive isolation such as hybrid sterility between two new species. An unsolved puzzle is the exact mechanism(s) that causes two genomes to diverge from their common ancestor so that some divergent genes no longer function properly in the hybrids. Here we report genetic analyses of divergent genes controlling male fertility and sex ratio in two very young fruitfly species, Drosophila albomicans and D. nasuta. A majority of the genetic divergence for both traits is mapped to the same regions by quantitative trait loci mappings. With introgressions, six major loci are found to contribute to both traits. This genetic colocalization implicates that genes for hybrid male sterility have evolved primarily for controlling sex ratio. We propose that genetic conflicts over sex ratio may operate as a perpetual dynamo for genome divergence. This particular evolutionary mechanism may largely contribute to the rapid evolution of hybrid male sterility and the disproportionate enrichment of its underlying genes on the X chromosome--two patterns widely observed across animals.

  14. Ribosome dynamics and the evolutionary history of ribosomes

    Science.gov (United States)

    Fox, George E.; Paci, Maxim; Tran, Quyen; Petrov, Anton S.; Williams, Loren D.

    2015-09-01

    The ribosome is a dynamic nanomachine responsible for coded protein synthesis. Its major subsystems were essentially in place at the time of the last universal common ancestor (LUCA). Ribosome evolutionary history thus potentially provides a window into the pre- LUCA world. This history begins with the origins of the peptidyl transferase center where the actual peptide is synthesized and then continues over an extended timeframe as additional functional centers including the GTPase center are added. The large ribosomal RNAs (rRNAs) have grown over time by an accretion process and a model exists that proposes a relative age of each accreted element. We have compared atomic resolution ribosome structures before and after EF-G bound GTP hydrolysis and thereby identified the location of 23 pivot points in the large rRNAs that facilitate ribosome dynamics. Pivots in small subunit helices h28 and h44 appear to be especially central to the process and according to the accretion model significantly older than the other helices containing pivots. Overall, the results suggest that ribosomal dynamics occurred in two phases. In the first phase, an inherently mobile h28/h44 combination provided the flexibility needed to create a dynamic ribosome that was essentially a Brownian machine. This addition likely made coded peptide synthesis possible by facilitating movement of a primitive mRNA. During the second phase, addition of pivoting elements and the creation of a factor binding site allowed the regulation of the inherent motion created by h28/h44. All of these events likely occurred before LUCA.

  15. Characterizing Phase Transitions in a Model of Neutral Evolutionary Dynamics

    Science.gov (United States)

    Scott, Adam; King, Dawn; Bahar, Sonya

    2013-03-01

    An evolutionary model was recently introduced for sympatric, phenotypic evolution over a variable fitness landscape with assortative mating (Dees & Bahar 2010). Organisms in the model are described by coordinates in a two-dimensional phenotype space, born at random coordinates with limited variation from their parents as determined by a mutation parameter, mutability. The model has been extended to include both neutral evolution and asexual reproduction in Scott et al (submitted). It has been demonstrated that a second order, non-equilibrium phase transition occurs for the temporal dynamics as the mutability is varied, for both the original model and for neutral conditions. This transition likely belongs to the directed percolation universality class. In contrast, the spatial dynamics of the model shows characteristics of an ordinary percolation phase transition. Here, we characterize the phase transitions exhibited by this model by determining critical exponents for the relaxation times, characteristic lengths, and cluster (species) mass distributions. Missouri Research Board; J.S. McDonnell Foundation

  16. Modeling Evolutionary Dynamics of Lurking in Social Networks

    CERN Document Server

    Javarone, Marco Alberto; Tagarelli, Andrea

    2016-01-01

    Lurking is a complex user-behavioral phenomenon that occurs in all large-scale online communities and social networks. It generally refers to the behavior characterizing users that benefit from the information produced by others in the community without actively contributing back to the production of social content. The amount and evolution of lurkers may strongly affect an online social environment, therefore understanding the lurking dynamics and identifying strategies to curb this trend are relevant problems. In this regard, we introduce the Lurker Game, i.e., a model for analyzing the transitions from a lurking to a non-lurking (i.e., active) user role, and vice versa, in terms of evolutionary game theory. We evaluate the proposed Lurker Game by arranging agents on complex networks and analyzing the system evolution, seeking relations between the network topology and the final equilibrium of the game. Results suggest that the Lurker Game is suitable to model the lurking dynamics, showing how the adoption ...

  17. Differential dynamic logics - automated theorem proving for hybrid systems

    OpenAIRE

    Platzer, André

    2008-01-01

    Hybrid systems are models for complex physical systems and are defined as dynamical systems with interacting discrete transitions and continuous evolutions along differential equations. With the goal of developing a theoretical and practical foundation for deductive verification of hybrid systems, we introduce differential dynamic logic as a new logic with which correctness properties of hybrid systems with parameterized system dynamics can be specified and verified naturally. As a verificati...

  18. Hybrid modeling and prediction of dynamical systems

    Science.gov (United States)

    Lloyd, Alun L.; Flores, Kevin B.

    2017-01-01

    Scientific analysis often relies on the ability to make accurate predictions of a system’s dynamics. Mechanistic models, parameterized by a number of unknown parameters, are often used for this purpose. Accurate estimation of the model state and parameters prior to prediction is necessary, but may be complicated by issues such as noisy data and uncertainty in parameters and initial conditions. At the other end of the spectrum exist nonparametric methods, which rely solely on data to build their predictions. While these nonparametric methods do not require a model of the system, their performance is strongly influenced by the amount and noisiness of the data. In this article, we consider a hybrid approach to modeling and prediction which merges recent advancements in nonparametric analysis with standard parametric methods. The general idea is to replace a subset of a mechanistic model’s equations with their corresponding nonparametric representations, resulting in a hybrid modeling and prediction scheme. Overall, we find that this hybrid approach allows for more robust parameter estimation and improved short-term prediction in situations where there is a large uncertainty in model parameters. We demonstrate these advantages in the classical Lorenz-63 chaotic system and in networks of Hindmarsh-Rose neurons before application to experimentally collected structured population data. PMID:28692642

  19. Hybrid grammar-based approach to nonlinear dynamical system identification from biological time series

    Science.gov (United States)

    McKinney, B. A.; Crowe, J. E., Jr.; Voss, H. U.; Crooke, P. S.; Barney, N.; Moore, J. H.

    2006-02-01

    We introduce a grammar-based hybrid approach to reverse engineering nonlinear ordinary differential equation models from observed time series. This hybrid approach combines a genetic algorithm to search the space of model architectures with a Kalman filter to estimate the model parameters. Domain-specific knowledge is used in a context-free grammar to restrict the search space for the functional form of the target model. We find that the hybrid approach outperforms a pure evolutionary algorithm method, and we observe features in the evolution of the dynamical models that correspond with the emergence of favorable model components. We apply the hybrid method to both artificially generated time series and experimentally observed protein levels from subjects who received the smallpox vaccine. From the observed data, we infer a cytokine protein interaction network for an individual’s response to the smallpox vaccine.

  20. Evolutionary origins and dynamics of octoploid strawberry subgenomes revealed by dense targeted capture linkage maps.

    Science.gov (United States)

    Tennessen, Jacob A; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron

    2014-12-04

    Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.

  1. Hybrid chaotic quantum evolutionary algorithm%混合混沌量子进化算法

    Institute of Scientific and Technical Information of China (English)

    蔡延光; 张敏捷; 蔡颢; 章云

    2012-01-01

    针对量子进化算法计算量大、收敛速度慢以及容易出现早熟等问题,提出混合混沌量子进化算法.该算法采用混沌初始化方法产生初始种群,使种群具有较好的多样性;采用简单量子旋转门更新当前种群中的非最优个体,降低算法的计算量;提出混合混沌搜索策略以提高算法的收敛速度和全局搜索能力.大量的测试表明,与量子进化算法、实数编码量子进化算法和混合量子遗传算法相比,所提出的算法具有较快的收敛速度和较好的寻优能力.大量的测试也表明,若将混沌引入量子进化算法,则混合混沌搜索策略的综合性能明显优于载波混沌策略,在大多数情况下优于混沌变异策略.本文提出的算法是惟一的每次测试都收敛的算法,且实现简单,便于工程应用.将其用于求解城市道路的交通信号配时优化问题,实际效果令人满意.%In order to reduce amount of computation, speed up convergence and restrain premature phenomena of quantum evolutionary algorithm, a hybrid chaotic quantum evolutionary algorithm is presented. The algorithm uses the chaotic initialization method to generate initial population that have better diversity, the simple quantum rotation gate to update non-optimal individuals of population to reduce amount of computation, and the hybrid chaotic search strategy to speed up its convergence and enhance its global search ability. A large number of tests show that the proposed algorithm has higher convergence speed and better optimizing ability than quantum evolutionary algorithm, real-coded quantum evolutionary algorithm and hybrid quantum genetic algorithm. Tests also show that when chaos is introduced to quantum evolutionary algorithm, the hybrid chaotic search strategy is superior to the carrier chaotic strategy, and has better comprehensive performance than the chaotic mutation strategy in most of cases. The proposed algorithm is the only one all

  2. Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature

    Science.gov (United States)

    Ma, Zhanshan (Sam)

    In evolutionary computing (EC), population size is one of the critical parameters that a researcher has to deal with. Hence, it was no surprise that the pioneers of EC, such as De Jong (1975) and Holland (1975), had already studied the population sizing from the very beginning of EC. What is perhaps surprising is that more than three decades later, we still largely depend on the experience or ad-hoc trial-and-error approach to set the population size. For example, in a recent monograph, Eiben and Smith (2003) indicated: "In almost all EC applications, the population size is constant and does not change during the evolutionary search." Despite enormous research on this issue in recent years, we still lack a well accepted theory for population sizing. In this paper, I propose to develop a population dynamics theory forEC with the inspiration from the population dynamics theory of biological populations in nature. Essentially, the EC population is considered as a dynamic system over time (generations) and space (search space or fitness landscape), similar to the spatial and temporal dynamics of biological populations in nature. With this conceptual mapping, I propose to 'transplant' the biological population dynamics theory to EC via three steps: (i) experimentally test the feasibility—whether or not emulating natural population dynamics improves the EC performance; (ii) comparatively study the underlying mechanisms—why there are improvements, primarily via statistical modeling analysis; (iii) conduct theoretical analysis with theoretical models such as percolation theory and extended evolutionary game theory that are generally applicable to both EC and natural populations. This article is a summary of a series of studies we have performed to achieve the general goal [27][30]-[32]. In the following, I start with an extremely brief introduction on the theory and models of natural population dynamics (Sections 1 & 2). In Sections 4 to 6, I briefly discuss three

  3. Computational complexity of ecological and evolutionary spatial dynamics.

    Science.gov (United States)

    Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A

    2015-12-22

    There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP).

  4. Cognitive Architecture with Evolutionary Dynamics Solves Insight Problem

    Science.gov (United States)

    Fedor, Anna; Zachar, István; Szilágyi, András; Öllinger, Michael; de Vladar, Harold P.; Szathmáry, Eörs

    2017-01-01

    In this paper, we show that a neurally implemented a cognitive architecture with evolutionary dynamics can solve the four-tree problem. Our model, called Darwinian Neurodynamics, assumes that the unconscious mechanism of problem solving during insight tasks is a Darwinian process. It is based on the evolution of patterns that represent candidate solutions to a problem, and are stored and reproduced by a population of attractor networks. In our first experiment, we used human data as a benchmark and showed that the model behaves comparably to humans: it shows an improvement in performance if it is pretrained and primed appropriately, just like human participants in Kershaw et al. (2013)'s experiment. In the second experiment, we further investigated the effects of pretraining and priming in a two-by-two design and found a beginner's luck type of effect: solution rate was highest in the condition that was primed, but not pretrained with patterns relevant for the task. In the third experiment, we showed that deficits in computational capacity and learning abilities decreased the performance of the model, as expected. We conclude that Darwinian Neurodynamics is a promising model of human problem solving that deserves further investigation. PMID:28405191

  5. Behavioral variability in an evolutionary theory of behavior dynamics.

    Science.gov (United States)

    Popa, Andrei; McDowell, J J

    2016-03-01

    McDowell's evolutionary theory of behavior dynamics (McDowell, 2004) instantiates populations of behaviors (abstractly represented by integers) that evolve under the selection pressure of the environment in the form of positive reinforcement. Each generation gives rise to the next via low-level Darwinian processes of selection, recombination, and mutation. The emergent patterns can be analyzed and compared to those produced by biological organisms. The purpose of this project was to explore the effects of high mutation rates on behavioral variability in environments that arranged different reinforcer rates and magnitudes. Behavioral variability increased with the rate of mutation. High reinforcer rates and magnitudes reduced these effects; low reinforcer rates and magnitudes augmented them. These results are in agreement with live-organism research on behavioral variability. Various combinations of mutation rates, reinforcer rates, and reinforcer magnitudes produced similar high-level outcomes (equifinality). These findings suggest that the independent variables that describe an experimental condition interact; that is, they do not influence behavior independently. These conclusions have implications for the interpretation of high levels of variability, mathematical undermatching, and the matching theory. The last part of the discussion centers on a potential biological counterpart for the rate of mutation, namely spontaneous fluctuations in the brain's default mode network.

  6. Evolutionary game dynamics of controlled and automatic decision-making

    Science.gov (United States)

    Toupo, Danielle F. P.; Strogatz, Steven H.; Cohen, Jonathan D.; Rand, David G.

    2015-07-01

    We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.

  7. A Hybrid Model for the Mid-Long Term Runoff Forecasting by Evolutionary Computaion Techniques

    Institute of Scientific and Technical Information of China (English)

    Zou Xiu-fen; Kang Li-shan; Cae Hong-qing; Wu Zhi-jian

    2003-01-01

    The mid-long term hydrology forecasting is one of most challenging problems in hydrological studies. This paper proposes an efficient dynamical system prediction model using evolutionary computation techniques. The new model overcomes some disadvantages of conventional hydrology fore casting ones. The observed data is divided into two parts: the slow "smooth and steady" data, and the fast "coarse and fluctuation" data. Under the divide and conquer strategy, the behavior of smooth data is modeled by ordinary differential equations based on evolutionary modeling, and that of the coarse data is modeled using gray correlative forecasting method. Our model is verified on the test data of the mid-long term hydrology forecast in tbe northeast region of China. The experimental results show that the model is superior to gray system prediction model (GSPM).

  8. Nash equilibrium and evolutionary dynamics in semifinalists' dilemma

    Science.gov (United States)

    Baek, Seung Ki; Son, Seung-Woo; Jeong, Hyeong-Chai

    2015-04-01

    We consider a tournament among four equally strong semifinalists. The players have to decide how much stamina to use in the semifinals, provided that the rest is available in the final and the third-place playoff. We investigate optimal strategies for allocating stamina to the successive matches when players' prizes (payoffs) are given according to the tournament results. From the basic assumption that the probability to win a match follows a nondecreasing function of stamina difference, we present symmetric Nash equilibria for general payoff structures. We find three different phases of the Nash equilibria in the payoff space. First, when the champion wins a much bigger payoff than the others, any pure strategy can constitute a Nash equilibrium as long as all four players adopt it in common. Second, when the first two places are much more valuable than the other two, the only Nash equilibrium is such that everyone uses a pure strategy investing all stamina in the semifinal. Third, when the payoff for last place is much smaller than the others, a Nash equilibrium is formed when every player adopts a mixed strategy of using all or none of its stamina in the semifinals. In a limiting case that only last place pays the penalty, this mixed-strategy profile can be proved to be a unique symmetric Nash equilibrium, at least when the winning probability follows a Heaviside step function. Moreover, by using this Heaviside step function, we study the tournament by using evolutionary replicator dynamics to obtain analytic solutions, which reproduces the corresponding Nash equilibria on the population level and gives information on dynamic aspects.

  9. Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.

    Directory of Open Access Journals (Sweden)

    Andrea Sottoriva

    2011-05-01

    Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.

  10. Dissipative dynamics of superconducting hybrid qubit systems

    Energy Technology Data Exchange (ETDEWEB)

    Montes, Enrique; Calero, Jesus M; Reina, John H, E-mail: enriquem@univalle.edu.c, E-mail: j.reina-estupinan@physics.ox.ac.u [Departamento de Fisica, Universidad del Valle, A.A. 25360, Cali (Colombia)

    2009-05-01

    We perform a theoretical study of composed superconducting qubit systems for the case of a coupled qubit configuration based on a hybrid qubit circuit made of both charge and phase qubits, which are coupled via a sigma{sub x} x sigma{sub z} interaction. We compute the system's eigen-energies in terms of the qubit transition frequencies and the strength of the inter-qubit coupling, and describe the sensitivity of the energy crossing/anti-crossing features to such coupling. We compute the hybrid system's dissipative dynamics for the cases of i) collective and ii) independent decoherence, whereby the system interacts with one common and two different baths of harmonic oscillators, respectively. The calculations have been performed within the Bloch-Redfield formalism and we report the solutions for the populations and the coherences of the system's reduced density matrix. The dephasing and relaxation rates are explicitly calculated as a function of the heat bath temperature.

  11. Filtering in Hybrid Dynamic Bayesian Networks

    Science.gov (United States)

    Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin

    2000-01-01

    We implement a 2-time slice dynamic Bayesian network (2T-DBN) framework and make a 1-D state estimation simulation, an extension of the experiment in (v.d. Merwe et al., 2000) and compare different filtering techniques. Furthermore, we demonstrate experimentally that inference in a complex hybrid DBN is possible by simulating fault detection in a watertank system, an extension of the experiment in (Koller & Lerner, 2000) using a hybrid 2T-DBN. In both experiments, we perform approximate inference using standard filtering techniques, Monte Carlo methods and combinations of these. In the watertank simulation, we also demonstrate the use of 'non-strict' Rao-Blackwellisation. We show that the unscented Kalman filter (UKF) and UKF in a particle filtering framework outperform the generic particle filter, the extended Kalman filter (EKF) and EKF in a particle filtering framework with respect to accuracy in terms of estimation RMSE and sensitivity with respect to choice of network structure. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. Furthermore, we investigate the influence of data noise in the watertank simulation using UKF and PFUKD and show that the algorithms are more sensitive to changes in the measurement noise level that the process noise level. Theory and implementation is based on (v.d. Merwe et al., 2000).

  12. A Hybrid Multiobjective Evolutionary Approach for Flexible Job-Shop Scheduling Problems

    Directory of Open Access Journals (Sweden)

    Jian Xiong

    2012-01-01

    Full Text Available This paper addresses multiobjective flexible job-shop scheduling problem (FJSP with three simultaneously considered objectives: minimizing makespan, minimizing total workload, and minimizing maximal workload. A hybrid multiobjective evolutionary approach (H-MOEA is developed to solve the problem. According to the characteristic of FJSP, a modified crowding distance measure is introduced to maintain the diversity of individuals. In the proposed H-MOEA, well-designed chromosome representation and genetic operators are developed for FJSP. Moreover, a local search procedure based on critical path theory is incorporated in H-MOEA to improve the convergence ability of the algorithm. Experiment results on several well-known benchmark instances demonstrate the efficiency and stability of the proposed algorithm. The comparison with other recently published approaches validates that H-MOEA can obtain Pareto-optimal solutions with better quality and/or diversity.

  13. Hybridization of Evolutionary Mechanisms for Feature Subset Selection in Unsupervised Learning

    Science.gov (United States)

    Torres, Dolores; Ponce-de-León, Eunice; Torres, Aurora; Ochoa, Alberto; Díaz, Elva

    Feature subset selection for unsupervised learning, is a very important topic in artificial intelligence because it is the base for saving computational resources. In this implementation we use a typical testor’s methodology in order to incorporate an importance index for each variable. This paper presents the general framework and the way two hybridized meta-heuristics work in this NP-complete problem. The evolutionary mechanisms are based on the Univariate Marginal Distribution Algorithm (UMDA) and the Genetic Algorithm (GA). GA and UMDA - Estimation of Distribution Algorithm (EDA) use a very useful rapid operator implemented for finding typical testors on a very large dataset and also, both algorithms, have a local search mechanism for improving time and fitness. Experiments show that EDA is faster than GA because it has a better exploitation performance; nevertheless, GA’ solutions are more consistent.

  14. An efficient hybrid evolutionary optimization algorithm based on PSO and SA for clustering

    Institute of Scientific and Technical Information of China (English)

    Taher NIKNAM; Babak AMIRI; Javad OLAMAEI; Ali AREFI

    2009-01-01

    The K-means algorithm is one of the most popular techniques in clustering. Nevertheless, the performance of the Kmeans algorithm depends highly on initial cluster centers and converges to local minima. This paper proposes a hybrid evolutionary programming based clustering algorithm, called PSO-SA, by combining particle swarm optimization (PSO) and simulated annealing (SA). The basic idea is to search around the global solution by SA and to increase the information exchange among particles using a mutation operator to escape local optima. Three datasets, Iris, Wisconsin Breast Cancer, and Riplcy's Glass, have been considered to show the effectiveness of the proposed clustering algorithm in providing optimal clusters. The simulation results show that the PSO-SA clustering algorithm not only has a better response but also converges more quickly than the K-means, PSO, and SA algorithms.

  15. The Impact of Mutation Rate on the Computation Time of Evolutionary Dynamic Optimization

    CERN Document Server

    Chen, Tianshi; Tang, Ke; Chen, Guoliang; Yao, Xin

    2011-01-01

    Mutation has traditionally been regarded as an important operator in evolutionary algorithms. In particular, there have been many experimental studies which showed the effectiveness of adapting mutation rates for various static optimization problems. Given the perceived effectiveness of adaptive and self-adaptive mutation for static optimization problems, there have been speculations that adaptive and self-adaptive mutation can benefit dynamic optimization problems even more since adaptation and self-adaptation are capable of following a dynamic environment. However, few theoretical results are available in analyzing rigorously evolutionary algorithms for dynamic optimization problems. It is unclear when adaptive and self-adaptive mutation rates are likely to be useful for evolutionary algorithms in solving dynamic optimization problems. This paper provides the first rigorous analysis of adaptive mutation and its impact on the computation times of evolutionary algorithms in solving certain dynamic optimizatio...

  16. Hybrid Evolutionary Approaches to Maximum Lifetime Routing and Energy Efficiency in Sensor Mesh Networks.

    Science.gov (United States)

    Rahat, Alma A M; Everson, Richard M; Fieldsend, Jonathan E

    2015-01-01

    Mesh network topologies are becoming increasingly popular in battery-powered wireless sensor networks, primarily because of the extension of network range. However, multihop mesh networks suffer from higher energy costs, and the routing strategy employed directly affects the lifetime of nodes with limited energy resources. Hence when planning routes there are trade-offs to be considered between individual and system-wide battery lifetimes. We present a multiobjective routing optimisation approach using hybrid evolutionary algorithms to approximate the optimal trade-off between the minimum lifetime and the average lifetime of nodes in the network. In order to accomplish this combinatorial optimisation rapidly, our approach prunes the search space using k-shortest path pruning and a graph reduction method that finds candidate routes promoting long minimum lifetimes. When arbitrarily many routes from a node to the base station are permitted, optimal routes may be found as the solution to a well-known linear program. We present an evolutionary algorithm that finds good routes when each node is allowed only a small number of paths to the base station. On a real network deployed in the Victoria & Albert Museum, London, these solutions, using only three paths per node, are able to achieve minimum lifetimes of over 99% of the optimum linear program solution's time to first sensor battery failure.

  17. Stability properties of nonlinear dynamical systems and evolutionary stable states

    Energy Technology Data Exchange (ETDEWEB)

    Gleria, Iram, E-mail: iram@fis.ufal.br [Instituto de Física, Universidade Federal de Alagoas, 57072-970 Maceió-AL (Brazil); Brenig, Leon [Faculté des Sciences, Université Libre de Bruxelles, 1050 Brussels (Belgium); Rocha Filho, Tarcísio M.; Figueiredo, Annibal [Instituto de Física and International Center for Condensed Matter Physics, Universidade de Brasília, 70919-970 Brasília-DF (Brazil)

    2017-03-18

    Highlights: • We address the problem of equilibrium stability in a general class of non-linear systems. • We link Evolutionary Stable States (ESS) to stable fixed points of square quasi-polynomial (QP) systems. • We show that an interior ES point may be related to stable interior fixed points of QP systems. - Abstract: In this paper we address the problem of stability in a general class of non-linear systems. We establish a link between the concepts of asymptotic stable interior fixed points of square Quasi-Polynomial systems and evolutionary stable states, a property of some payoff matrices arising from evolutionary games.

  18. Evolutionary dynamics of satellite DNA repeats from Phaseolus beans.

    Science.gov (United States)

    Ribeiro, Tiago; Dos Santos, Karla G B; Richard, Manon M S; Sévignac, Mireille; Thareau, Vincent; Geffroy, Valérie; Pedrosa-Harand, Andrea

    2017-03-01

    Common bean (Phaseolus vulgaris) subtelomeres are highly enriched for khipu, the main satellite DNA identified so far in this genome. Here, we comparatively investigate khipu genomic organization in Phaseolus species from different clades. Additionally, we identified and characterized another satellite repeat, named jumper, associated to khipu. A mixture of P. vulgaris khipu clones hybridized in situ confirmed the presence of khipu-like sequences on subterminal chromosome regions in all Phaseolus species, with differences in the number and intensity of signals between species and when species-specific clones were used. Khipu is present as multimers of ∼500 bp and sequence analyses of cloned fragments revealed close relationship among khipu repeats. The new repeat, named jumper, is a 170-bp satellite sequence present in all Phaseolus species and inserted into the nontranscribed spacer (NTS) of the 5S rDNA in the P. vulgaris genome. Nevertheless, jumper was found as a high-copy repeat at subtelomeres and/or pericentromeres in the Phaseolus microcarpus lineage only. Our data argue for khipu as an important subtelomeric satellite DNA in the genus and for a complex satellite repeat composition of P. microcarpus subtelomeres, which also contain jumper. Furthermore, the differential amplification of these repeats in subtelomeres or pericentromeres reinforces the presence of a dynamic satellite DNA library in Phaseolus.

  19. HYEI: A New Hybrid Evolutionary Imperialist Competitive Algorithm for Fuzzy Knowledge Discovery

    Directory of Open Access Journals (Sweden)

    D. Jalal Nouri

    2014-01-01

    Full Text Available In recent years, imperialist competitive algorithm (ICA, genetic algorithm (GA, and hybrid fuzzy classification systems have been successfully and effectively employed for classification tasks of data mining. Due to overcoming the gaps related to ineffectiveness of current algorithms for analysing high-dimension independent datasets, a new hybrid approach, named HYEI, is presented to discover generic rule-based systems in this paper. This proposed approach consists of three stages and combines an evolutionary-based fuzzy system with two ICA procedures to generate high-quality fuzzy-classification rules. Initially, the best feature subset is selected by using the embedded ICA feature selection, and then these features are used to generate basic fuzzy-classification rules. Finally, all rules are optimized by using an ICA algorithm to reduce their length or to eliminate some of them. The performance of HYEI has been evaluated by using several benchmark datasets from the UCI machine learning repository. The classification accuracy attained by the proposed algorithm has the highest classification accuracy in 6 out of the 7 dataset problems and is comparative to the classification accuracy of the 5 other test problems, as compared to the best results previously published.

  20. An alternative hybrid evolutionary technique focused on allocating machines and sequencing operations

    Directory of Open Access Journals (Sweden)

    Mariano Frutos

    2016-09-01

    Full Text Available We present here a hybrid algorithm for the Flexible Job-Shop Scheduling Problem (FJSSP. This problem involves the optimal use of resources in a flexible production environment in which each operation can be carried out by more than a single machine. Our algorithm allocates, in a first step, the machines to operations and in a second stage it sequences them by integrating a Multi-Objective Evolutionary Algorithm (MOEA and a path-dependent search algorithm (Multi-Objective Simulated Annealing, which is enacted at the genetic phase of the procedure. The joint interaction of those two components yields a very efficient procedure for solving the FJSSP. An important step in the development of the algorithm was the selection of the right MOEA. Candidates were tested on problems of low, medium and high complexity. Further analyses showed the relevance of the search algorithm in the hybrid structure. Finally, comparisons with other algorithms in the literature indicate that the performance of our alternative is good.

  1. Eco-evolutionary dynamics of agricultural networks : implications for sustainable management

    OpenAIRE

    Loeuille, N.; Barot, Sébastien; Georgelin, E.; Kylafis, G.; Lavigne, C.

    2013-01-01

    Community and ecosystem ecology are paying increasing attention to evolutionary dynamics, offering a means of attaining a more comprehensive understanding of ecological networks and more efficient and sustainable agroecosystems. Here, we review how such approaches can be applied, and we provide theoretical models to illustrate how eco-evolutionary dynamics can profoundly change our understanding of agricultural issues. We show that community evolution models can be used in seve...

  2. Engineering microbial systems to explore ecological and evolutionary dynamics.

    Science.gov (United States)

    Tanouchi, Yu; Smith, Robert P; You, Lingchong

    2012-10-01

    A major goal of biological research is to provide a mechanistic understanding of diverse biological processes. To this end, synthetic biology offers a powerful approach, whereby biological questions can be addressed in a well-defined framework. By constructing simple gene circuits, such studies have generated new insights into the design principles of gene regulatory networks. Recently, this strategy has been applied to analyze ecological and evolutionary questions, where population-level interactions are critical. Here, we highlight recent development of such systems and discuss how they were used to address problems in ecology and evolutionary biology. As illustrated by these examples, synthetic ecosystems provide a unique platform to study ecological and evolutionary phenomena that are challenging to study in their natural contexts.

  3. Filtering in Hybrid Dynamic Bayesian Networks

    Science.gov (United States)

    Andersen, Morten Nonboe; Andersen, Rasmus Orum; Wheeler, Kevin

    2004-01-01

    We demonstrate experimentally that inference in a complex hybrid Dynamic Bayesian Network (DBN) is possible using the 2 - T i e Slice DBN (2T-DBN) from [Koller & Lerner, 20001 to model fault detection in a watertank system. In [Koller & Lerner, 20001 a generic Particle Filter (PF) is used for inference. We extend the experiment and perform approximate inference using The Extended Kalman Filter (EKF) and the Unscented Kalman Filter (UKF). Furthermore, we combine these techniques in a 'non-strict' Rao-Blackwellisation framework and apply it to the watertank system. We show that UKF and UKF in a PF framework outperfom the generic PF, EKF and EKF in a PF framework with respect to accuracy and robustness in terms of estimation RMSE. Especially we demonstrate the superiority of UKF in a PF framework when our beliefs of how data was generated are wrong. We also show that the choice of network structure is very important for the performance of the generic PF and the EKF algorithms, but not for the UKF algorithms. Furthermore, we investigate the influence of data noise in the water[ank simulation. Theory and implementation is based on the theory presented.

  4. EVOLUTIONARY DYNAMIC MODEL OF POPULATION WITH NICHE CONSTRUCTION AND ITS APPLICATION RESEARCH

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    Based on the theories and approaches in biomechanics, the mechanism and pattern of niche construction were discussed systematically. Through establishing the spatial pattern of niche and its measuring-fitness formula, and the dynamic system models of single- and two-population with niche construction, including corresponding theoretical analysis and numerical simulation on their evolutionary dynamics of population and the mechanism of competitive coexistence, the co-evolutionary relationship between organisms and their environments was revealed. The results indicate that population dynamics is governed by positive feedback between primary ecological factors and resource content.Niche construction generates an evolutionary effect in system by influencing the fitness of population. A threshold effect exists in single population dynamic system. In dynamic system of two competitive populations, niche construction can lead to alternative competitive consequences, which may be a potential mechanism to explain the competitive coexistence of species.

  5. Parallel dynamics and evolution: Protein conformational fluctuations and assembly reflect evolutionary changes in sequence and structure.

    Science.gov (United States)

    Marsh, Joseph A; Teichmann, Sarah A

    2014-02-01

    Protein structure is dynamic: the intrinsic flexibility of polypeptides facilitates a range of conformational fluctuations, and individual protein chains can assemble into complexes. Proteins are also dynamic in evolution: significant variations in secondary, tertiary and quaternary structure can be observed among divergent members of a protein family. Recent work has highlighted intriguing similarities between these structural and evolutionary dynamics occurring at various levels. Here we review evidence showing how evolutionary changes in protein sequence and structure are often closely related to local protein flexibility and disorder, large-scale motions and quaternary structure assembly. We suggest that these correspondences can be largely explained by neutral evolution, while deviations between structural and evolutionary dynamics can provide valuable functional insights. Finally, we address future prospects for the field and practical applications that arise from a deeper understanding of the intimate relationship between protein structure, dynamics, function and evolution.

  6. Eco-evolutionary dynamics in a coevolving host-virus system.

    Science.gov (United States)

    Frickel, Jens; Sieber, Michael; Becks, Lutz

    2016-04-01

    Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations.

  7. Hybrid dynamics in a species group of swallowtail butterflies.

    Science.gov (United States)

    Dupuis, J R; Sperling, F A H

    2016-10-01

    Hybrid zones provide unique natural laboratories for studying mechanisms of evolution. But identification and classification of hybrid individuals (F1, F2, backcross, etc.) can be complicated by real population changes over time as well as by use of different marker types, both of which challenge documentation of hybrid dynamics. Here, we use multiple genetic markers (mitochondrial DNA, microsatellites and genomewide single nucleotide polymorphisms) to re-examine population structure in a hybrid zone between two species of swallowtail butterflies in western Canada, Papilio machaon and P. zelicaon. Our aim was to test whether their hybrid dynamics remain the same as found 30 years ago using morphology and allozymes, and we compared different genetic data sets as well as alternative hybrid identification and classification methods. Overall, we found high differentiation between the two parental species, corroborating previous research from the 1980s. We identified fewer hybrid individuals in the main zone of hybridization in recent years, but this finding depended on the genetic markers considered. Comparison of methods with simulated data sets generated from our data showed that single nucleotide polymorphisms were more powerful than microsatellites for both hybrid identification and classification. Moreover, substantial variation among comparisons underlined the value of multiple markers and methods for documenting evolutionarily dynamic systems.

  8. Design games: A conceptual framework for dynamic evolutionary design

    NARCIS (Netherlands)

    Sönmez, N.O.; Erdem, A.

    2014-01-01

    Most evolutionary computation (EC) applications in design fields either assume simplified, static, performance-oriented procedures for design or focus on well-defined sub-problems, to be able to impose problem-solving and optimization schemes on design tasks, which render known EC techniques directl

  9. New MPPT algorithm based on hybrid dynamical theory

    KAUST Repository

    Elmetennani, Shahrazed

    2014-11-01

    This paper presents a new maximum power point tracking algorithm based on the hybrid dynamical theory. A multiceli converter has been considered as an adaptation stage for the photovoltaic chain. The proposed algorithm is a hybrid automata switching between eight different operating modes, which has been validated by simulation tests under different working conditions. © 2014 IEEE.

  10. Quantifying the spatiotemporal dynamics in a chorus frog (Pseudacris) hybrid zone over 30 years.

    Science.gov (United States)

    Engebretsen, Kristin N; Barrow, Lisa N; Rittmeyer, Eric N; Brown, Jeremy M; Moriarty Lemmon, Emily

    2016-07-01

    Although theory suggests that hybrid zones can move or change structure over time, studies supported by direct empirical evidence for these changes are relatively limited. We present a spatiotemporal genetic study of a hybrid zone between Pseudacris nigrita and P. fouquettei across the Pearl River between Louisiana and Mississippi. This hybrid zone was initially characterized in 1980 as a narrow and steep "tension zone," in which hybrid populations were inferior to parentals and were maintained through a balance between selection and dispersal. We reanalyzed historical tissue samples and compared them to samples of recently collected individuals using microsatellites. Clinal analyses indicate that the cline has not shifted in roughly 30 years but has widened significantly. Anthropogenic and natural changes may have affected selective pressure or dispersal, and our results suggest that the zone may no longer best be described as a tension zone. To the best of our knowledge, this study provides the first evidence of significant widening of a hybrid cline but stasis of its center. Continued empirical study of dynamic hybrid zones will provide insight into the forces shaping their structure and the evolutionary potential they possess for the elimination or generation of species.

  11. Evolutionary dynamics of the traveler's dilemma and minimum-effort coordination games on complex networks.

    Science.gov (United States)

    Iyer, Swami; Killingback, Timothy

    2014-10-01

    The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.

  12. Stochastic evolutionary dynamics of minimum-effort coordination games

    CERN Document Server

    Li, Kun; Wang, Long

    2016-01-01

    The minimum-effort coordination game, having potentially important implications in both evolutionary biology and sociology, draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classic game theory. In the framework of classic game theory, any common effort level is a strict and trembling hand perfect Nash equilibrium, so that no desideratum is provided for selecting among them. Behavior experiments, however, show that the effort levels employed by subjects are inversely related to the effort costs. Here, we combine coalescence theory and evolutionary game theory to investigate this game in finite populations. Both analytic results and individual-based simulations show that effort costs play a key role in the evolution of contribution levels, which is in good agreement with those observed experimentally. Besides well-mixed populations, set structured populations, where the population structure itself is a consequence of the evolutio...

  13. The stability concept of evolutionary game theory a dynamic approach

    CERN Document Server

    1992-01-01

    These Notes grew from my research in evolutionary biology, specifically on the theory of evolutionarily stable strategies (ESS theory), over the past ten years. Personally, evolutionary game theory has given me the opportunity to transfer my enthusiasm for abstract mathematics to more practical pursuits. I was fortunate to have entered this field in its infancy when many biologists recognized its potential but were not prepared to grant it general acceptance. This is no longer the case. ESS theory is now a rapidly expanding (in both applied and theoretical directions) force that no evolutionary biologist can afford to ignore. Perhaps, to continue the life-cycle metaphor, ESS theory is now in its late adolescence and displays much of the optimism and exuberance of this exciting age. There are dangers in writing a text about a theory at this stage of development. A comprehensive treatment would involve too many loose ends for the reader to appreciate the central message. On the other hand, the current central m...

  14. Evolutionary game dynamics in populations with heterogenous structures.

    Directory of Open Access Journals (Sweden)

    Wes Maciejewski

    2014-04-01

    Full Text Available Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours. In this article we show that such a conclusion largely depends on the individual-level interactions that take place. In particular, averaging payoffs garnered through game interactions rather than accumulating the payoffs can altogether remove the cooperative advantage of heterogeneous graphs while such a difference does not affect the outcome on homogeneous structures. In addition, the rate at which game interactions occur can alter the evolutionary outcome. Less interactions allow heterogeneous graphs to support more cooperation than homogeneous graphs, while higher rates of interactions make homogeneous and heterogeneous graphs virtually indistinguishable in their ability to support cooperation. Most importantly, we show that common measures of evolutionary advantage used in homogeneous populations, such as a comparison of the fixation probability of a rare mutant to that of the resident type, are no longer valid in heterogeneous populations. Heterogeneity causes a bias in where mutations occur in the population which affects the mutant's fixation probability. We derive the appropriate measures for heterogeneous populations that account for this bias.

  15. Evolutionary game dynamics in populations with heterogenous structures.

    Science.gov (United States)

    Maciejewski, Wes; Fu, Feng; Hauert, Christoph

    2014-04-01

    Evolutionary graph theory is a well established framework for modelling the evolution of social behaviours in structured populations. An emerging consensus in this field is that graphs that exhibit heterogeneity in the number of connections between individuals are more conducive to the spread of cooperative behaviours. In this article we show that such a conclusion largely depends on the individual-level interactions that take place. In particular, averaging payoffs garnered through game interactions rather than accumulating the payoffs can altogether remove the cooperative advantage of heterogeneous graphs while such a difference does not affect the outcome on homogeneous structures. In addition, the rate at which game interactions occur can alter the evolutionary outcome. Less interactions allow heterogeneous graphs to support more cooperation than homogeneous graphs, while higher rates of interactions make homogeneous and heterogeneous graphs virtually indistinguishable in their ability to support cooperation. Most importantly, we show that common measures of evolutionary advantage used in homogeneous populations, such as a comparison of the fixation probability of a rare mutant to that of the resident type, are no longer valid in heterogeneous populations. Heterogeneity causes a bias in where mutations occur in the population which affects the mutant's fixation probability. We derive the appropriate measures for heterogeneous populations that account for this bias.

  16. INVERSE DYNAMIC FORMULATION OF A NOVEL HYBRID MACHINE TOOL

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    In recent years, hybrid devices have increasingly received more research.However, few of researchers studied the dynamic analysis.The inverse dynamic analysis of a novel hybrid machine tool designed in Tsinghua University is presented.The hybrid machine tool under consideration consists of parallel and serial structures, which is based on a new 2-DOF parallel platform and serial orientations.The kinematics and the dynamic equations are studied first for the parallel structure through Newton-Euler approach.And then, the dynamic analysis for serial structures is conducted.Finally, a closed-form inverse dynamic formulation is derived by using some elimination techniques.Some simulation results are also given.

  17. Stochastic evolutionary dynamics in minimum-effort coordination games

    Science.gov (United States)

    Li, Kun; Cong, Rui; Wang, Long

    2016-08-01

    The minimum-effort coordination game draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classical game theory. Here, we combine evolutionary game theory and coalescence theory to investigate this game in finite populations. Both analytic results and individual-based simulations show that effort costs play a key role in the evolution of contribution levels, which is in good agreement with those observed experimentally. Besides well-mixed populations, set structured populations have also been taken into consideration. Therein we find that large number of sets and moderate migration rate greatly promote effort levels, especially for high effort costs.

  18. Evolutionary dynamics of fluctuating populations with strong mutualism

    Science.gov (United States)

    Chotibut, Thiparat; Nelson, David

    2013-03-01

    Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.

  19. Evolutionary Dynamics of Rhodopsin Type 2 Opsins in Vertebrates

    Science.gov (United States)

    Yokoyama, Shozo; Tada, Takashi

    2010-01-01

    Among the five groups of visual pigments in vertebrates, the rhodopsin type 2 (RH2) group shows the largest number of gene duplication events. We have isolated three intact and one nonfunctional RH2 opsin genes each from Northern lampfish (Stenobrachius leucopsarus) and scabbardfish (Lepidopus fitchi). Using the deduced amino acid sequences of these and other representative RH2 opsin genes in vertebrates, we have estimated the divergence times and evolutionary rates of amino acid substitution at various stages of RH2 opsin evolution. The results show that the duplications of the lampfish and scabbardfish RH2 opsins have occurred ∼60 and ∼30 million years ago (Ma), respectively. The evolutionary rates of RH2 opsins in the early vertebrate ancestors were ∼0.25 × 10−9/site/year, which increased to ∼1 × 10−9 to 3 × 10−9/site/year in euteleost lineages and to ∼0.3 × 10−9 to 0.5 × 10−9/site/year in coelacanth and tetrapods. PMID:19759234

  20. Impulsive and hybrid dynamical systems stability, dissipativity, and control

    CERN Document Server

    Haddad, Wassim M; Nersesov, Sergey G

    2014-01-01

    This book develops a general analysis and synthesis framework for impulsive and hybrid dynamical systems. Such a framework is imperative for modern complex engineering systems that involve interacting continuous-time and discrete-time dynamics with multiple modes of operation that place stringent demands on controller design and require implementation of increasing complexity--whether advanced high-performance tactical fighter aircraft and space vehicles, variable-cycle gas turbine engines, or air and ground transportation systems. Impulsive and Hybrid Dynamical Systems goes beyond similar

  1. Mechanical sensitivity and the dynamics of evolutionary rate shifts in biomechanical systems.

    Science.gov (United States)

    Muñoz, Martha M; Anderson, Philip S L; Patek, S N

    2017-01-25

    The influence of biophysical relationships on rates of morphological evolution is a cornerstone of evolutionary theory. Mechanical sensitivity-the correlation strength between mechanical output and the system's underlying morphological components-is thought to impact the evolutionary dynamics of form-function relationships, yet has rarely been examined. Here, we compare the evolutionary rates of the mechanical components of the four-bar linkage system in the raptorial appendage of mantis shrimp (Order Stomatopoda). This system's mechanical output (kinematic transmission (KT)) is highly sensitive to variation in its output link, and less sensitive to its input and coupler links. We found that differential mechanical sensitivity is associated with variation in evolutionary rate: KT and the output link exhibit faster rates of evolution than the input and coupler links to which KT is less sensitive. Furthermore, for KT and, to a lesser extent, the output link, rates of evolution were faster in 'spearing' stomatopods than 'smashers', indicating that mechanical sensitivity may influence trait-dependent diversification. Our results suggest that mechanical sensitivity can impact morphological evolution and guide the process of phenotypic diversification. The connection between mechanical sensitivity and evolutionary rates provides a window into the interaction between physical rules and the evolutionary dynamics of morphological diversification. © 2017 The Author(s).

  2. Falsification of Matching Theory and Confirmation of an Evolutionary Theory of Behavior Dynamics in a Critical Experiment.

    Science.gov (United States)

    McDowell, J J; Calvin, Olivia L; Hackett, Ryan; Klapes, Bryan

    2017-03-31

    Two competing predictions of matching theory and an evolutionary theory of behavior dynamics, and one additional prediction of the evolutionary theory, were tested in a critical experiment in which human participants worked on concurrent schedules for money (Dallery, Soto, and McDowell, 2005). The three predictions concerned the descriptive adequacy of matching theory equations, and of equations describing emergent equilibria of the evolutionary theory. Tests of the predictions falsified matching theory and supported the evolutionary theory.

  3. Evolutionary dynamics of rDNA genes on chromosomes of the Eucinostomus fishes: cytotaxonomic and karyoevolutive implications.

    Science.gov (United States)

    Calado, L L; Bertollo, L A C; Cioffi, M B; Costa, G W W F; Jacobina, U P; Molina, W F

    2014-11-27

    Several chromosomal features of Gerreidae fish have been found to be conserved. In this group, it is unclear whether the high degree of chromosomal stasis is maintained when analyzing more dynamic regions of chromosomes, such as rDNA sites that generally show a higher level of variability. Thus, cytogenetic analyses were performed on 3 Atlantic species of the genus Eucinostomus using conventional banding (C-banding, Ag-NOR), AT- and GC-specific fluorochromes, and fluorescence in situ hybridization mapping of telomeric sequences and 5S and 18S rDNA sites. The results showed that although the karyotypical macrostructure of these species is similar (2n = 48 chromosomes, simple Ag-NORs seemingly located on homeologous chromosomes and centromeric heterochromatin pattern), there are differences in the positions of rDNA subunits 5S and 18S. Thus, the ribosomal sites have demonstrated to be effective cytotaxonomic markers in Eucinostomus, presenting a different evolutionary dynamics in relation to other chromosomal regions and allowing access to important evolutionary changes in this group.

  4. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

    Science.gov (United States)

    Sanchez, Alvaro; Gore, Jeff

    2013-01-01

    The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the demographic fate of

  5. feedback between population and evolutionary dynamics determines the fate of social microbial populations.

    Directory of Open Access Journals (Sweden)

    Alvaro Sanchez

    Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the

  6. Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes1[OPEN

    Science.gov (United States)

    Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu

    2016-01-01

    Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883

  7. Abrupt community transitions and cyclic evolutionary dynamics in complex food webs☆

    Science.gov (United States)

    Takahashi, Daisuke; Brännström, Åke; Mazzucco, Rupert; Yamauchi, Atsushi; Dieckmann, Ulf

    2013-01-01

    Understanding the emergence and maintenance of biodiversity ranks among the most fundamental challenges in evolutionary ecology. While processes of community assembly have frequently been analyzed from an ecological perspective, their evolutionary dimensions have so far received less attention. To elucidate the eco-evolutionary processes underlying the long-term build-up and potential collapse of community diversity, here we develop and examine an individual-based model describing coevolutionary dynamics driven by trophic interactions and interference competition, of a pair of quantitative traits determining predator and prey niches. Our results demonstrate the (1) emergence of communities with multiple trophic levels, shown here for the first time for stochastic models with linear functional responses, and (2) intermittent and cyclic evolutionary transitions between two alternative community states. In particular, our results indicate that the interplay of ecological and evolutionary dynamics often results in extinction cascades that remove the entire trophic level of consumers from a community. Finally, we show the (3) robustness of our results under variations of model assumptions, underscoring that processes of consumer collapse and subsequent rebound could be important elements of understanding biodiversity dynamics in natural communities. PMID:23948552

  8. Fixation, transient landscape, and diffusion dilemma in stochastic evolutionary game dynamics.

    Science.gov (United States)

    Zhou, Da; Qian, Hong

    2011-09-01

    Agent-based stochastic models for finite populations have recently received much attention in the game theory of evolutionary dynamics. Both the ultimate fixation and the pre-fixation transient behavior are important to a full understanding of the dynamics. In this paper, we study the transient dynamics of the well-mixed Moran process through constructing a landscape function. It is shown that the landscape playing a central theoretical "device" that integrates several lines of inquiries: the stable behavior of the replicator dynamics, the long-time fixation, and continuous diffusion approximation associated with asymptotically large population. Several issues relating to the transient dynamics are discussed: (i) multiple time scales phenomenon associated with intra- and inter-attractoral dynamics; (ii) discontinuous transition in stochastically stationary process akin to Maxwell construction in equilibrium statistical physics; and (iii) the dilemma diffusion approximation facing as a continuous approximation of the discrete evolutionary dynamics. It is found that rare events with exponentially small probabilities, corresponding to the uphill movements and barrier crossing in the landscape with multiple wells that are made possible by strong nonlinear dynamics, plays an important role in understanding the origin of the complexity in evolutionary, nonlinear biological systems.

  9. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes.

    Science.gov (United States)

    DiBattista, Joseph D; Whitney, Jonathan; Craig, Matthew T; Hobbs, Jean-Paul A; Rocha, Luiz A; Feldheim, Kevin A; Berumen, Michael L; Bowen, Brian W

    2016-08-01

    Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N=141) and A. nigricans (N=412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N=54) and A. japonicus (N=49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000-2.25million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr≈0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST=0.6533, P<0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mtDNA lineage and

  10. Surgeons and suture zones: Hybridization among four surgeonfish species in the Indo-Pacific with variable evolutionary outcomes

    KAUST Repository

    DiBattista, Joseph

    2016-04-30

    Closely related species can provide valuable insights into evolutionary processes through comparison of their ecology, geographic distribution and the history recorded in their genomes. In the Indo-Pacific, many reef fishes are divided into sister species that come into secondary contact at biogeographic borders, most prominently where Indian Ocean and Pacific Ocean faunas meet. It is unclear whether hybridization in this contact zone represents incomplete speciation, secondary contact, an evolutionary dead-end (for hybrids) or some combination of the above. To address these issues, we conducted comprehensive surveys of two widely-distributed surgeonfish species, Acanthurus leucosternon (N = 141) and A. nigricans (N = 412), with mtDNA cytochrome b sequences and ten microsatellite loci. These surgeonfishes are found primarily in the Indian and Pacific Oceans, respectively, but overlap at the Christmas and Cocos-Keeling Islands hybrid zone in the eastern Indian Ocean. We also sampled the two other Pacific members of this species complex, A. achilles (N = 54) and A. japonicus (N = 49), which are known to hybridize with A. nigricans where their ranges overlap. Our results indicate separation between the four species that range from the recent Pleistocene to late Pliocene (235,000 to 2.25 million years ago). The Pacific A. achilles is the most divergent (and possibly ancestral) species with mtDNA dcorr ≈ 0.04, whereas the other two Pacific species (A. japonicus and A. nigricans) are distinguishable only at a population or subspecies level (ΦST = 0.6533, P < 0.001). Little population structure was observed within species, with evidence of recent population expansion across all four geographic ranges. We detected sharing of mtDNA haplotypes between species and extensive hybridization based on microsatellites, consistent with later generation hybrids but also the effects of allele homoplasy. Despite extensive introgression, 98% of specimens had concordance between mt

  11. Does hybridization increase evolutionary rate? Data from the 28S-rDNA D8 domain in echinoderms.

    Science.gov (United States)

    Chenuil, Anne; Egea, Emilie; Rocher, Caroline; Touzet, Hélène; Féral, Jean-Pierre

    2008-11-01

    The divergent domain D8 of the large ribosomal RNA is very variable and extended in vertebrates compared to other eukaryotes. We provide data from 31 species of echinoderms and present the first comparative analysis of the D8 in nonvertebrate deuterostomes. In addition, we obtained 16S mitochondrial DNA sequences for the sea urchin taxa and analyzed single-strand conformation polymorphism (SSCP) of D8 in several populations within the species complex Echinocardium cordatum. A common secondary structure supported by compensatory substitutions and indels is inferred for echinoderms. Variation mostly arises at the tip of the longest stem (D8a), and the most variable taxa also display the longest and most stable D8. The most stable variants are the only ones displaying bulges in the terminal part of the stem, suggesting that selection, rather than maximizing stability of the D8 secondary structure, maintains it in a given range. Striking variation in D8 evolutionary rates was evidenced among sea urchins, by comparison with both 16S mitochondrial DNA and paleontological data. In Echinocardium cordatum and Strongylocentrotus pallidus and S. droebachiensis, belonging to very distant genera, the increase in D8 evolutionary rate is extreme. Their highly stable D8 secondary structures rule out the possibility of pseudogenes. These taxa are the only ones in which interspecific hybridization was reported. We discuss how evolutionary rates may be affected in nuclear relative to mitochondrial genes after hybridization, by selective or mutational processes such as gene silencing and concerted evolution.

  12. Nuclear Hybrid Energy System Modeling: RELAP5 Dynamic Coupling Capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Piyush Sabharwall; Nolan Anderson; Haihua Zhao; Shannon Bragg-Sitton; George Mesina

    2012-09-01

    The nuclear hybrid energy systems (NHES) research team is currently developing a dynamic simulation of an integrated hybrid energy system. A detailed simulation of proposed NHES architectures will allow initial computational demonstration of a tightly coupled NHES to identify key reactor subsystem requirements, identify candidate reactor technologies for a hybrid system, and identify key challenges to operation of the coupled system. This work will provide a baseline for later coupling of design-specific reactor models through industry collaboration. The modeling capability addressed in this report focuses on the reactor subsystem simulation.

  13. Quantum-classical hybrid dynamics - a summary

    CERN Document Server

    Elze, Hans-Thomas

    2013-01-01

    A summary of a recently proposed description of quantum-classical hybrids is presented, which concerns quantum and classical degrees of freedom of a composite object that interact directly with each other. This is based on notions of classical Hamiltonian mechanics suitably extended to quantum mechanics.

  14. HYBRID EVOLUTIONARY ALGORITHMS FOR FREQUENCY AND VOLTAGE CONTROL IN POWER GENERATING SYSTEM

    Directory of Open Access Journals (Sweden)

    A. Soundarrajan

    2010-10-01

    Full Text Available Power generating system has the responsibility to ensure that adequate power is delivered to the load, both reliably and economically. Any electrical system must be maintained at the desired operating level characterized by nominal frequency and voltage profile. But the ability of the power system to track the load is limited due to physical and technical consideration. Hence, a Power System Control is required to maintain a continuous balance between power generation and load demand. The quality of power supply is affected due to continuous and random changes in load during the operation of the power system. Load Frequency Controller (LFC and Automatic Voltage Regulator (AVR play an important role in maintaining constant frequency and voltage in order to ensure the reliability of electric power. The fixed gain PID controllers used for this application fail to perform under varying load conditions and hence provide poor dynamic characteristics with large settling time, overshoot and oscillations. In this paper, Evolutionary Algorithms (EA like, Enhanced Particle Swarm Optimization (EPSO, Multi Objective Particle Swarm Optimization (MOPSO, and Stochastic Particle Swarm Optimization (SPSO are proposed to overcome the premature convergence problem in a standard PSO. These algorithms reduce transient oscillations and also increase the computational efficiency. Simulation results demonstrate that the proposed controller adapt themselves appropriate to varying loads and hence provide better performance characteristics with respect to settling time, oscillations and overshoot.

  15. Role of finite populations in determining evolutionary dynamics

    Science.gov (United States)

    Ray, Tane S.; Payne, Karl A.; Moseley, L. Leo

    2008-02-01

    The connection between the finite size of an evolving population and its dynamical behavior is examined through analytical and computational studies of a simple model of evolution. The infinite population limit of the model is shown to be governed by a special case of the quasispecies equations. A flat fitness landscape yields identical results for the dynamics of infinite and finite populations. On the other hand, a monotonically increasing fitness landscape shows “epochs” in the dynamics of finite populations that become more pronounced as the rate of mutation decreases. The details of the dynamics are profoundly different for any two simulation runs in that events arising from the stochastic noise in the pseudorandom number sequence are amplified. As the population size is increased or, equivalently, the mutation rate is increased, these epochs become smaller but do not entirely disappear.

  16. Evolutionary dynamics of cooperation on interdependent networks with Prisoner's Dilemma and Snowdrift Game

    CERN Document Server

    Wang, Baokui; Wang, Long

    2014-01-01

    The world in which we are living is a huge network of networks and should be described by interdependent networks. The interdependence between networks significantly affects the evolutionary dynamics of cooperation on them. Meanwhile, due to the diversity and complexity of social and biological systems, players on different networks may not interact with each other by the same way, which should be described by multiple models in evolutionary game theory, such as the Prisoner's Dilemma and Snowdrift Game. We therefore study the evolutionary dynamics of cooperation on two interdependent networks playing different games respectively. We clearly evidence that, with the increment of network interdependence, the evolution of cooperation is dramatically promoted on the network playing Prisoner's Dilemma. The cooperation level of the network playing Snowdrift Game reduces correspondingly, although it is almost invisible. In particular, there exists an optimal intermediate region of network interdependence maximizing ...

  17. A Hybrid Evolutionary Algorithm to Quadratic Three-Dimensional Assignment Problem with Local Search for Many-Core Graphics Processors

    Science.gov (United States)

    Lipinski, Piotr

    This paper concerns the quadratic three-dimensional assignment problem (Q3AP), an extension of the quadratic assignment problem (QAP), and proposes an efficient hybrid evolutionary algorithm combining stochastic optimization and local search with a number of crossover operators, a number of mutation operators and an auto-adaptation mechanism. Auto-adaptation manages the pool of evolutionary operators applying different operators in different computation phases to better explore the search space and to avoid premature convergence. Local search additionally optimizes populations of candidate solutions and accelerates evolutionary search. It uses a many-core graphics processor to optimize a number of solutions in parallel, which enables its incorporation into the evolutionary algorithm without excessive increases in the computation time. Experiments performed on benchmark Q3AP instances derived from the classic QAP instances proposed by Nugent et al. confirmed that the proposed algorithm is able to find optimal solutions to Q3AP in a reasonable time and outperforms best known results found in the literature.

  18. Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system.

    Science.gov (United States)

    Hiltunen, Teppo; Ayan, Gökçe B; Becks, Lutz

    2015-06-01

    Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria-ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.

  19. Non-Payoff Monotonic Dynamics in an Evolutionary Game of Courtship

    CERN Document Server

    Chacoma, Andrés; Zanette, Damián H

    2015-01-01

    We propose an evolutionary coordination game to formalize a simplified model of the evolution of strategies during human courtship. The dynamics, derived from the consideration of experimental observations on human social behavior driven by self-esteem, turns out to be non-payoff monotonic. This property gives rise to nontrivial evolution in the players' strategies, which we study both numerically and analytically.

  20. System dynamics of behaviour-evolutionary mix-game models

    Science.gov (United States)

    Gou, Cheng-Ling; Gao, Jie-Ping; Chen, Fang

    2010-11-01

    In real financial markets there are two kinds of traders: one is fundamentalist, and the other is a trend-follower. The mix-game model is proposed to mimic such phenomena. In a mix-game model there are two groups of agents: Group 1 plays the majority game and Group 2 plays the minority game. In this paper, we investigate such a case that some traders in real financial markets could change their investment behaviours by assigning the evolutionary abilities to agents: if the winning rates of agents are smaller than a threshold, they will join the other group; and agents will repeat such an evolution at certain time intervals. Through the simulations, we obtain the following findings: (i) the volatilities of systems increase with the increase of the number of agents in Group 1 and the times of behavioural changes of all agents; (ii) the performances of agents in both groups and the stabilities of systems become better if all agents take more time to observe their new investment behaviours; (iii) there are two-phase zones of market and non-market and two-phase zones of evolution and non-evolution; (iv) parameter configurations located within the cross areas between the zones of markets and the zones of evolution are suited for simulating the financial markets.

  1. Mechanical sensitivity reveals evolutionary dynamics of mechanical systems.

    Science.gov (United States)

    Anderson, P S L; Patek, S N

    2015-04-07

    A classic question in evolutionary biology is how form-function relationships promote or limit diversification. Mechanical metrics, such as kinematic transmission (KT) in linkage systems, are useful tools for examining the evolution of form and function in a comparative context. The convergence of disparate systems on equivalent metric values (mechanical equivalence) has been highlighted as a source of potential morphological diversity under the assumption that morphology can evolve with minimal impact on function. However, this assumption does not account for mechanical sensitivity-the sensitivity of the metric to morphological changes in individual components of a structure. We examined the diversification of a four-bar linkage system in mantis shrimp (Stomatopoda), and found evidence for both mechanical equivalence and differential mechanical sensitivity. KT exhibited variable correlations with individual linkage components, highlighting the components that influence KT evolution, and the components that are free to evolve independently from KT and thereby contribute to the observed pattern of mechanical equivalence. Determining the mechanical sensitivity in a system leads to a deeper understanding of both functional convergence and morphological diversification. This study illustrates the importance of multi-level analyses in delineating the factors that limit and promote diversification in form-function systems. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

  2. System dynamics of behaviour-evolutionary mix-game models

    Institute of Scientific and Technical Information of China (English)

    Gou Cheng-Ling; Gao Jie-Ping; Chen Fang

    2010-01-01

    In real financial markets there are two kinds of traders:one is fundamentalist,and the other is a trend-follower.The mix-game model is proposed to mimic such phenomena.In a mix-game model there are two groups of agents:Group 1 plays the majority game and Group 2 plays the minority game.In this paper,we investigate such a case that some traders in real financial markets could change their investment behaviours by assigning the evolutionary abilities to agents:if the winning rates of agents are smaller than a threshold,they will join the other group;and agents will repeat such an evolution at certain time intervals.Through the simulations,we obtain the following findings:(i) the volatilities of systems increase with the increase of the number of agents in Group 1 and the times of behavioural changes of all agents;(ii) the performances of agents in both groups and the stabilities of systems become better if all agents take more time to observe their new investment behaviours;(iii) there are two-phase zones of market and non-market and two-phase zones of evolution and non-evolution;(iv) parameter configurations located within the cross areas between the zones of markets and the zones of evolution are suited for simulating the financial markets.

  3. Adaptation to fragmentation: evolutionary dynamics driven by human influences.

    Science.gov (United States)

    Cheptou, Pierre-Olivier; Hargreaves, Anna L; Bonte, Dries; Jacquemyn, Hans

    2017-01-19

    Fragmentation-the process by which habitats are transformed into smaller patches isolated from each other-has been identified as a major threat for biodiversity. Fragmentation has well-established demographic and population genetic consequences, eroding genetic diversity and hindering gene flow among patches. However, fragmentation should also select on life history, both predictably through increased isolation, demographic stochasticity and edge effects, and more idiosyncratically via altered biotic interactions. While species have adapted to natural fragmentation, adaptation to anthropogenic fragmentation has received little attention. In this review, we address how and whether organisms might adapt to anthropogenic fragmentation. Drawing on selected case studies and evolutionary ecology models, we show that anthropogenic fragmentation can generate selection on traits at both the patch and landscape scale, and affect the adaptive potential of populations. We suggest that dispersal traits are likely to experience especially strong selection, as dispersal both enables migration among patches and increases the risk of landing in the inhospitable matrix surrounding them. We highlight that suites of associated traits are likely to evolve together. Importantly, we show that adaptation will not necessarily rescue populations from the negative effects of fragmentation, and may even exacerbate them, endangering the entire metapopulation.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

  4. A stochastic evolutionary model for capturing human dynamics

    CERN Document Server

    Fenner, Trevor; Loizou, George

    2015-01-01

    The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in various contexts. Here we propose a generative model to capture the dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. We derive a general solution for the model in the form of a product, and then a continuous approximation to the solution via the renewal equation describing age-structured population dynamics. This enables us to model a wide rage of survival distributions, according to the choice of the mortality distribution. We provide empirical evidence for the validity of the model from a longitudinal data set of popular search engine queries over 114 months, showing that the survival function of these queries is closely matched by the solution for our model with power-law mortality.

  5. The Tangled Nature Model of evolutionary dynamics reconsidered

    DEFF Research Database (Denmark)

    Andersen, Christian Walther; Sibani, Paolo

    2016-01-01

    . To bring out the structural and dynamical effects of trait inheritance , we introduce and numerically analyze a family of TNM models where a positive integer $K$ parametrises correlations between the interactions of an agent and those of its mutated offspring. For $K=1$ a single point mutation randomizes....../t_{\\rm w}$, similarity to the pure aging behaviour approximately describing glassy systems of physical origin. Increasing the value of $K$ decreases the numerical value of the decay exponent of the power law, which is a clear quantitative dynamical effect of trait inheritance....

  6. Catalysis of Protein Folding by Chaperones Accelerates Evolutionary Dynamics in Adapting Cell Populations

    OpenAIRE

    Murat Cetinbaş; Shakhnovich, Eugene I.

    2013-01-01

    Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly f...

  7. Evolutionary dynamics of sporophytic self-incompatibility alleles in plants

    DEFF Research Database (Denmark)

    Schierup, M H; Vekemans, X; Christiansen, F B

    1997-01-01

    The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act c...

  8. Evolutionary dynamics of insertion sequences in Helicobacter pylori.

    Science.gov (United States)

    Kalia, Awdhesh; Mukhopadhyay, Asish K; Dailide, Giedrius; Ito, Yoshiyki; Azuma, Takeshi; Wong, Benjamin C Y; Berg, Douglas E

    2004-11-01

    Prokaryotic insertion sequence (IS) elements behave like parasites in terms of their ability to invade and proliferate in microbial gene pools and like symbionts when they coevolve with their bacterial hosts. Here we investigated the evolutionary history of IS605 and IS607 of Helicobacter pylori, a genetically diverse gastric pathogen. These elements contain unrelated transposase genes (orfA) and also a homolog of the Salmonella virulence gene gipA (orfB). A total of 488 East Asian, Indian, Peruvian, and Spanish isolates were screened, and 18 and 14% of them harbored IS605 and IS607, respectively. IS605 nucleotide sequence analysis (n = 42) revealed geographic subdivisions similar to those of H. pylori; the geographic subdivision was blurred, however, due in part to homologous recombination, as indicated by split decomposition and homoplasy tests (homoplasy ratio, 0.56). In contrast, the IS607 populations (n = 44) showed strong geographic subdivisions with less homologous recombination (homoplasy ratio, 0.2). Diversifying selection (ratio of nonsynonymous change to synonymous change, >1) was evident in approximately 15% of the IS605 orfA codons analyzed but not in the IS607 orfA codons. Diversifying selection was also evident in approximately 2% of the IS605 orfB and approximately 10% of the IS607 orfB codons analyzed. We suggest that the evolution of these elements reflects selection for optimal transposition activity in the case of IS605 orfA and for interactions between the OrfB proteins and other cellular constituents that potentially contribute to bacterial fitness. Taken together, similarities in IS elements and H. pylori population genetic structures and evidence of adaptive evolution in IS elements suggest that there is coevolution between these elements and their bacterial hosts.

  9. The formation of the polyploid hybrids from different subfamily fish crossings and its evolutionary significance.

    Science.gov (United States)

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-06-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp x blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (female symbol) x blunt snout bream (BSB) (male symbol) as well as their pentaploid hybrids. The triploid hybrids possessed 124 chromosomes with two sets from RCC and one set from BSB; the tetraploid hybrids had 148 chromosomes with two sets from RCC and two sets from BSB. The females of tetraploid hybrids produced unreduced tetraploid eggs that were fertilized with the haploid sperm of BSB to generate pentaploid hybrids with 172 chromosomes with three sets from BSB and two sets from RCC. The ploidy levels of triploid, tetraploid, and pentaploid hybrids were confirmed by counting chromosomal number, forming chromosomal karyotype, and measuring DNA content and erythrocyte nuclear volume. The similar and different DNA fragments were PCR amplified and sequenced in triploid, tetraploid hybrids, and their parents, indicating their molecular genetic relationship and genetic markers. In addition, this study also presents results about the phenotypes and feeding habits of polyploid hybrids and discusses the formation mechanism of the polyploid hybrids. It is the first report on the formation of the triploid, tetraploid, and pentaploid hybrids by crossing parents with a different chromosome number in vertebrates. The formation of the polyploid hybrids is potentially interesting in both evolution and fish genetic breeding.

  10. Application of Hybrid Dynamical Theory to the Cardiovascular System

    KAUST Repository

    Laleg-Kirati, Taous-Meriem

    2014-10-14

    In hybrid dynamical systems, the state evolves in continuous time as well as in discrete modes activated by internal conditions or by external events. In the recent years, hybrid systems modeling has been used to represent the dynamics of biological systems. In such systems, discrete behaviors might originate from unexpected changes in normal performance, e.g., a transition from a healthy to an abnormal condition. Simplifications, model assumptions, and/or modeled (and ignored) nonlinearities can be represented by sudden changes in the state. Modeling cardiovascular system (CVS), one of the most fascinating but most complex human physiological systems, with a hybrid approach, is the focus of this chapter. The hybrid property appears naturally in the CVS thanks to the presence of valves which, depending on their state (closed or open), divide the cardiac cycle into four phases. This chapter shows how hybrid models can be used for modeling the CVS. In addition, it describes a preliminary study on the detection of some cardiac anomalies based on the hybrid model and using the standard observer-based approach.

  11. Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

    Science.gov (United States)

    Huizhong, Dong; Hongli, Song

    An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.

  12. A Hybrid Data Association Approach for SLAM in Dynamic Environments

    Directory of Open Access Journals (Sweden)

    Baifan Chen

    2013-02-01

    Full Text Available Data association is critical for Simultaneous Localization and Mapping (SLAM. In a real environment, dynamic obstacles will lead to false data associations which compromise SLAM results. This paper presents a simple and effective data association method for SLAM in dynamic environments. A hybrid approach of data association based on local maps by combining ICNN and JCBB algorithms is used initially. Secondly, we set a judging condition of outlier features in association assumptions and then the static and dynamic features are detected according to spatial and temporal difference. Finally, association assumptions are updated by filtering out the dynamic features. Simulations and experimental results show that this method is feasible.

  13. Biophysical connection between evolutionary dynamics and thermodynamics in in vitro evolution.

    Science.gov (United States)

    Aita, Takuyo; Husimi, Yuzuru

    2012-02-07

    We analyzed a mathematical model of in vitro evolution conducted by repetition of mutagenesis and selection processes. The selection process consists of the selective enrichment and subsequent sampling as follows: each mutant with fitness W is amplified by the Boltzmann factor exp(rW/k(B)T(the)), where the fitness W is defined as the negative Gibbs free energy (-ΔG) in a reaction of the phenotypic molecules and r is the round number of the selective enrichment; then, an arbitrary mutant is randomly chosen from the resulting mutant population and it becomes a new parent in the next generation. As a result, we found that the evolutionary dynamics is described in a mathematical framework similar to thermodynamics: the "evolution constant" k(E) and "evolutionary temperature" T(evo) play key roles similar to the Boltzmann constant k(B) and thermodynamic temperature T(the), respectively. In the stationary state of the evolutionary dynamics, the attractor of the fitness is in inverse proportion to k(E)T(evo). Furthermore, beyond the mathematical analogy, we obtained a biophysical connection between evolutionary dynamics and thermodynamics. Particularly, we found that T(evo) and T(the) are connected by k(E)T(evo)≈k(B)T(the)/2r. These results suggest that we can predict the fitness value in the stationary state by the thermodynamic temperature T(the) in the experimental setup.

  14. Influence of Topological Features on Spatially-Structured Evolutionary Algorithms Dynamics

    CERN Document Server

    DeFelice, Matteo; Panzieri, Stefano

    2012-01-01

    In the last decades, complex networks theory significantly influenced other disciplines on the modeling of both static and dynamic aspects of systems observed in nature. This work aims to investigate the effects of networks' topological features on the dynamics of an evolutionary algorithm, considering in particular the ability to find a large number of optima on multi-modal problems. We introduce a novel spatially-structured evolutionary algorithm and we apply it on two combinatorial problems: ONEMAX and the multi-modal NMAX. Considering three different network models we investigate the relationships between their features, algorithm's convergence and its ability to find multiple optima (for the multi-modal problem). In order to perform a deeper analysis we investigate the introduction of weighted graphs with time-varying weights. The results show that networks with a large Average Path Length lead to an higher number of optima and a consequent slow exploration dynamics (i.e. low First Hitting Time). Further...

  15. How the Magnitude of Prey Genetic Variation Alters Predator-Prey Eco-Evolutionary Dynamics.

    Science.gov (United States)

    Cortez, Michael H

    2016-09-01

    Evolution can alter the stability and dynamics of ecological communities; for example, prey evolution can drive cyclic dynamics in predator-prey systems that are not possible in the absence of evolution. However, it is unclear how the magnitude of additive genetic variation in the evolving species mediates those effects. In this study, I explore how the magnitude of prey additive genetic variation determines what effects prey evolution has on the dynamics and stability of predator-prey systems. I use linear stability analysis to decompose the stability of a general eco-evolutionary predator-prey model into components representing the stabilities of the ecological and evolutionary subsystems as well as the interactions between those subsystems. My results show that with low genetic variation, the cyclic dynamics and stability of the system are determined by the ecological subsystem. With increased genetic variation, disruptive selection always destabilizes stable communities, stabilizing selection can stabilize or destabilize communities, and prey evolution can alter predator-prey phase lags. Stability changes occur approximately when the magnitude of genetic variation balances the (in)stabilities of the ecological and evolutionary subsystems. I discuss the connections between my stability results and prior results from the theory of adaptive dynamics.

  16. An evolutionary computational approach for the dynamic Stackelberg competition problems

    Directory of Open Access Journals (Sweden)

    Lorena Arboleda-Castro

    2016-06-01

    Full Text Available Stackelberg competition models are an important family of economical decision problems from game theory, in which the main goal is to find optimal strategies between two competitors taking into account their hierarchy relationship. Although these models have been widely studied in the past, it is important to note that very few works deal with uncertainty scenarios, especially those that vary over time. In this regard, the present research studies this topic and proposes a computational method for solving efficiently dynamic Stackelberg competition models. The computational experiments suggest that the proposed approach is effective for problems of this nature.

  17. The Formation of the Polyploid Hybrids From Different Subfamily Fish Crossings and Its Evolutionary Significance

    OpenAIRE

    Liu, Shaojun; Qin, Qinbo; Xiao, Jun; Lu, Wenting; Shen, Jiamin; Li, Wei; Liu, Jifang; Duan, Wei; Zhang, Chun; Tao, De Min; Zhao, Rurong; Yan, Jinpeng; Liu, Yun

    2007-01-01

    This study provides genetic evidences at the chromosome, DNA content, DNA fragment and sequence, and morphological levels to support the successful establishment of the polyploid hybrids of red crucian carp × blunt snout bream, which belonged to a different subfamily of fish (Cyprininae subfamily and Cultrinae subfamily) in the catalog. We successfully obtained the sterile triploid hybrids and bisexual fertile tetraploid hybrids of red crucian carp (RCC) (♀) × blunt snout bream (BSB) (♂) as w...

  18. Study of optimal control problems for hybrid dynamical systems

    Institute of Scientific and Technical Information of China (English)

    Gao Rui; Wang Lei; Wang Yuzhen

    2006-01-01

    From the viewpoint of continuous systems, optimal control problem is proposed for a class of controlled Hybrid dynamical systems. Then a mathematical method- HDS minimum principle is put forward, which can solve the above problem. The HDS minimum principle is proved by means of Ekeland's variational principle.

  19. Study on system dynamics of evolutionary mix-game models

    Science.gov (United States)

    Gou, Chengling; Guo, Xiaoqian; Chen, Fang

    2008-11-01

    Mix-game model is ameliorated from an agent-based MG model, which is used to simulate the real financial market. Different from MG, there are two groups of agents in Mix-game: Group 1 plays a majority game and Group 2 plays a minority game. These two groups of agents have different bounded abilities to deal with historical information and to count their own performance. In this paper, we modify Mix-game model by assigning the evolution abilities to agents: if the winning rates of agents are smaller than a threshold, they will copy the best strategies the other agent has; and agents will repeat such evolution at certain time intervals. Through simulations this paper finds: (1) the average winning rates of agents in Group 1 and the mean volatilities increase with the increases of the thresholds of Group 1; (2) the average winning rates of both groups decrease but the mean volatilities of system increase with the increase of the thresholds of Group 2; (3) the thresholds of Group 2 have greater impact on system dynamics than the thresholds of Group 1; (4) the characteristics of system dynamics under different time intervals of strategy change are similar to each other qualitatively, but they are different quantitatively; (5) As the time interval of strategy change increases from 1 to 20, the system behaves more and more stable and the performances of agents in both groups become better also.

  20. A Hybrid Immigrants Scheme for Genetic Algorithms in Dynamic Environments

    Institute of Scientific and Technical Information of China (English)

    Shengxiang Yang; Renato Tinós

    2007-01-01

    Dynamic optimization problems are a kind of optimization problems that involve changes over time. They pose a serious challenge to traditional optimization methods as well as conventional genetic algorithms since the goal is no longer to search for the optimal solution(s) of a fixed problem but to track the moving optimum over time. Dynamic optimization problems have attracted a growing interest from the genetic algorithm community in recent years. Several approaches have been developed to enhance the performance of genetic algorithms in dynamic environments. One approach is to maintain the diversity of the population via random immigrants. This paper proposes a hybrid immigrants scheme that combines the concepts of elitism, dualism and random immigrants for genetic algorithms to address dynamic optimization problems. In this hybrid scheme, the best individual, i.e., the elite, from the previous generation and its dual individual are retrieved as the bases to create immigrants via traditional mutation scheme. These elitism-based and dualism-based immigrants together with some random immigrants are substituted into the current population, replacing the worst individuals in the population. These three kinds of immigrants aim to address environmental changes of slight, medium and significant degrees respectively and hence efficiently adapt genetic algorithms to dynamic environments that are subject to different severities of changes. Based on a series of systematically constructed dynamic test problems, experiments are carried out to investigate the performance of genetic algorithms with the hybrid immigrants scheme and traditional random immigrants scheme. Experimental results validate the efficiency of the proposed hybrid immigrants scheme for improving the performance of genetic algorithms in dynamic environments.

  1. An efficient hybrid evolutionary algorithm based on PSO and HBMO algorithms for multi-objective Distribution Feeder Reconfiguration

    Energy Technology Data Exchange (ETDEWEB)

    Niknam, Taher [Electronic and Electrical Engineering Department, Shiraz University of Technology, Shiraz (Iran)

    2009-08-15

    This paper introduces a robust searching hybrid evolutionary algorithm to solve the multi-objective Distribution Feeder Reconfiguration (DFR). The main objective of the DFR is to minimize the real power loss, deviation of the nodes' voltage, the number of switching operations, and balance the loads on the feeders. Because of the fact that the objectives are different and no commensurable, it is difficult to solve the problem by conventional approaches that may optimize a single objective. This paper presents a new approach based on norm3 for the DFR problem. In the proposed method, the objective functions are considered as a vector and the aim is to maximize the distance (norm2) between the objective function vector and the worst objective function vector while the constraints are met. Since the proposed DFR is a multi objective and non-differentiable optimization problem, a new hybrid evolutionary algorithm (EA) based on the combination of the Honey Bee Mating Optimization (HBMO) and the Discrete Particle Swarm Optimization (DPSO), called DPSO-HBMO, is implied to solve it. The results of the proposed reconfiguration method are compared with the solutions obtained by other approaches, the original DPSO and HBMO over different distribution test systems. (author)

  2. A Self-adaptive Dynamic Evaluation Model for Diabetes Mellitus, Based on Evolutionary Strategies

    Directory of Open Access Journals (Sweden)

    An-Jiang Lu

    2016-03-01

    Full Text Available In order to evaluate diabetes mellitus objectively and accurately, this paper builds a self-adaptive dynamic evaluation model for diabetes mellitus, based on evolutionary strategies. First of all, on the basis of a formalized description of the evolutionary process of diabetes syndromes, using a state transition function, it judges whether a disease is evolutionary, through an excitation parameter. It then, provides evidence for the rebuilding of the evaluation index system. After that, by abstracting and rebuilding the composition of evaluation indexes, it makes use of a heuristic algorithm to determine the composition of the evolved evaluation index set of diabetes mellitus, It then, calculates the weight of each index in the evolved evaluation index set of diabetes mellitus by building a dependency matrix and realizes the self-adaptive dynamic evaluation of diabetes mellitus under an evolutionary environment. Using this evaluation model, it is possible to, quantify all kinds of diagnoses and treatment experiences of diabetes and finally to adopt ideal diagnoses and treatment measures for different patients with diabetics.

  3. Evolutionary dynamics of HBV-D7 subgenotype in Tunisia.

    Science.gov (United States)

    Ciccozzi, Massimo; Chaouch, Houda; Lo Presti, Alessandra; Taffon, Stefania; Villano, Umbertina; Equestre, Michele; Bruni, Roberto; Marcantonio, Cinzia; Tritarelli, Elena; Cella, Eleonora; Blasi, Aletheia; Aouni, Mahjoub; Letaief, Amel; Ciccaglione, Anna Rita

    2017-03-01

    Hepatitis B virus (HBV) is the main cause of diseases liver related infecting more than 200 milion persons worldwide. HBV infection shows high level of prevalence in South-East Europe and in Mediterranean basin. In Tunisia, a country with an intermediate level endemicity, HbsAg prevalence ranges from 2 to 5%. Most of the HBV isolates from Tunisia were classified as subgenotype D7 whose circulation is restricted to a specific area of North Africa including Maghreb region. In this paper, the phylogeny of HBV-D7 isolated from 38 Tunisian patients was investigated by analyzing the S gene region of HBV. A Bayesian coalescent-based framework was used to estimate the origin of the HBV-D7 in the country. The Tunisian D7 isolates were found to share a common ancestor whose origin was traced back to 1958. Population dynamics indicated that HBV-D7 epidemic in Tunisia grew exponentially from 1960s to 1990s. After that, the curve reached a plateau around the years 2000 likely due to the implementation of the infant vaccination program in 1996. Epidemiological data suggested that the exponential growth phase was likely sustained by intra-familial transmission events occurring during infancy. Further characterization of HBV-D7 isolates should be performed to evaluate, in the post-vaccination era, the emergence of new transmission routes, and to monitor the efficacy of the vaccination program. J. Med. Virol. 89:469-475, 2017. © 2016 Wiley Periodicals, Inc.

  4. Key Questions on the Role of Phenotypic Plasticity in Eco-Evolutionary Dynamics.

    Science.gov (United States)

    Hendry, Andrew P

    2016-01-01

    Ecology and evolution have long been recognized as reciprocally influencing each other, with recent research emphasizing how such interactions can occur even on very short (contemporary) time scales. Given that these interactions are mediated by organismal phenotypes, they can be variously shaped by genetic variation, phenotypic plasticity, or both. I here address 8 key questions relevant to the role of plasticity in eco-evolutionary dynamics. Focusing on empirical evidence, especially from natural populations, I offer the following conclusions. 1) Plasticity is--not surprisingly--sometimes adaptive, sometimes maladaptive, and sometimes neutral. 2) Plasticity has costs and limits but these constraints are highly variable, often weak, and hard to detect. 3) Variable environments favor the evolution of increased trait plasticity, which can then buffer fitness/performance (i.e., tolerance). 4) Plasticity sometimes aids colonization of new environments (Baldwin Effect) and responses to in situ environmental change. However, plastic responses are not always necessary or sufficient in these contexts. 5) Plasticity will sometimes promote and sometimes constrain genetic evolution. 6) Plasticity will sometimes help and sometimes hinder ecological speciation but, at present, empirical tests are limited. 7) Plasticity can show considerable evolutionary change in contemporary time, although the rates of this reaction norm evolution are highly variable among taxa and traits. 8) Plasticity appears to have considerable influences on ecological dynamics at the community and ecosystem levels, although many more studies are needed. In summary, plasticity needs to be an integral part of any conceptual framework and empirical investigation of eco-evolutionary dynamics.

  5. Ab initio molecular dynamics using hybrid density functionals

    Science.gov (United States)

    Guidon, Manuel; Schiffmann, Florian; Hutter, Jürg; Vandevondele, Joost

    2008-06-01

    Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.

  6. Next-generation sequencing analysis of lager brewing yeast strains reveals the evolutionary history of interspecies hybridization.

    Science.gov (United States)

    Okuno, Miki; Kajitani, Rei; Ryusui, Rie; Morimoto, Hiroya; Kodama, Yukiko; Itoh, Takehiko

    2016-02-01

    The lager beer yeast Saccharomyces pastorianus is considered an allopolyploid hybrid species between S. cerevisiae and S. eubayanus. Many S. pastorianus strains have been isolated and classified into two groups according to geographical origin, but this classification remains controversial. Hybridization analyses and partial PCR-based sequence data have indicated a separate origin of these two groups, whereas a recent intertranslocation analysis suggested a single origin. To clarify the evolutionary history of this species, we analysed 10 S. pastorianus strains and the S. eubayanus type strain as a likely parent by Illumina next-generation sequencing. In addition to assembling the genomes of five of the strains, we obtained information on interchromosomal translocation, ploidy, and single-nucleotide variants (SNVs). Collectively, these results indicated that the two groups of strains share S. cerevisiae haploid chromosomes. We therefore conclude that both groups of S. pastorianus strains share at least one interspecific hybridization event and originated from a common parental species and that differences in ploidy and SNVs between the groups can be explained by chromosomal deletion or loss of heterozygosity.

  7. Evolutionary constrained optimization

    CERN Document Server

    Deb, Kalyanmoy

    2015-01-01

    This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...

  8. A computer lab exploring evolutionary aspects of chromatin structure and dynamics for an undergraduate chromatin course*.

    Science.gov (United States)

    Eirín-López, José M

    2013-01-01

    The study of chromatin constitutes one of the most active research fields in life sciences, being subject to constant revisions that continuously redefine the state of the art in its knowledge. As every other rapidly changing field, chromatin biology requires clear and straightforward educational strategies able to efficiently translate such a vast body of knowledge to the classroom. With this aim, the present work describes a multidisciplinary computer lab designed to introduce undergraduate students to the dynamic nature of chromatin, within the context of the one semester course "Chromatin: Structure, Function and Evolution." This exercise is organized in three parts including (a) molecular evolutionary biology of histone families (using the H1 family as example), (b) histone structure and variation across different animal groups, and (c) effect of histone diversity on nucleosome structure and chromatin dynamics. By using freely available bioinformatic tools that can be run on common computers, the concept of chromatin dynamics is interactively illustrated from a comparative/evolutionary perspective. At the end of this computer lab, students are able to translate the bioinformatic information into a biochemical context in which the relevance of histone primary structure on chromatin dynamics is exposed. During the last 8 years this exercise has proven to be a powerful approach for teaching chromatin structure and dynamics, allowing students a higher degree of independence during the processes of learning and self-assessment. Copyright © 2013 International Union of Biochemistry and Molecular Biology, Inc.

  9. Scalable and balanced dynamic hybrid data assimilation

    Science.gov (United States)

    Kauranne, Tuomo; Amour, Idrissa; Gunia, Martin; Kallio, Kari; Lepistö, Ahti; Koponen, Sampsa

    2017-04-01

    Scalability of complex weather forecasting suites is dependent on the technical tools available for implementing highly parallel computational kernels, but to an equally large extent also on the dependence patterns between various components of the suite, such as observation processing, data assimilation and the forecast model. Scalability is a particular challenge for 4D variational assimilation methods that necessarily couple the forecast model into the assimilation process and subject this combination to an inherently serial quasi-Newton minimization process. Ensemble based assimilation methods are naturally more parallel, but large models force ensemble sizes to be small and that results in poor assimilation accuracy, somewhat akin to shooting with a shotgun in a million-dimensional space. The Variational Ensemble Kalman Filter (VEnKF) is an ensemble method that can attain the accuracy of 4D variational data assimilation with a small ensemble size. It achieves this by processing a Gaussian approximation of the current error covariance distribution, instead of a set of ensemble members, analogously to the Extended Kalman Filter EKF. Ensemble members are re-sampled every time a new set of observations is processed from a new approximation of that Gaussian distribution which makes VEnKF a dynamic assimilation method. After this a smoothing step is applied that turns VEnKF into a dynamic Variational Ensemble Kalman Smoother VEnKS. In this smoothing step, the same process is iterated with frequent re-sampling of the ensemble but now using past iterations as surrogate observations until the end result is a smooth and balanced model trajectory. In principle, VEnKF could suffer from similar scalability issues as 4D-Var. However, this can be avoided by isolating the forecast model completely from the minimization process by implementing the latter as a wrapper code whose only link to the model is calling for many parallel and totally independent model runs, all of them

  10. Energy-Efficient Scheduling Problem Using an Effective Hybrid Multi-Objective Evolutionary Algorithm

    Directory of Open Access Journals (Sweden)

    Lvjiang Yin

    2016-12-01

    Full Text Available Nowadays, manufacturing enterprises face the challenge of just-in-time (JIT production and energy saving. Therefore, study of JIT production and energy consumption is necessary and important in manufacturing sectors. Moreover, energy saving can be attained by the operational method and turn off/on idle machine method, which also increases the complexity of problem solving. Thus, most researchers still focus on small scale problems with one objective: a single machine environment. However, the scheduling problem is a multi-objective optimization problem in real applications. In this paper, a single machine scheduling model with controllable processing and sequence dependence setup times is developed for minimizing the total earliness/tardiness (E/T, cost, and energy consumption simultaneously. An effective multi-objective evolutionary algorithm called local multi-objective evolutionary algorithm (LMOEA is presented to tackle this multi-objective scheduling problem. To accommodate the characteristic of the problem, a new solution representation is proposed, which can convert discrete combinational problems into continuous problems. Additionally, a multiple local search strategy with self-adaptive mechanism is introduced into the proposed algorithm to enhance the exploitation ability. The performance of the proposed algorithm is evaluated by instances with comparison to other multi-objective meta-heuristics such as Nondominated Sorting Genetic Algorithm II (NSGA-II, Strength Pareto Evolutionary Algorithm 2 (SPEA2, Multiobjective Particle Swarm Optimization (OMOPSO, and Multiobjective Evolutionary Algorithm Based on Decomposition (MOEA/D. Experimental results demonstrate that the proposed LMOEA algorithm outperforms its counterparts for this kind of scheduling problems.

  11. Application of network methods for understanding evolutionary dynamics in discrete habitats.

    Science.gov (United States)

    Greenbaum, Gili; Fefferman, Nina H

    2017-02-16

    In populations occupying discrete habitat patches, gene flow between habitat patches may form an intricate population structure. In such structures, the evolutionary dynamics resulting from interaction of gene flow patterns with other evolutionary forces may be exceedingly complex. Several models describing gene flow between discrete habitat patches have been presented in the population genetics literature; however, these models have usually addressed relatively simple settings of habitable patches, and have stopped short of providing general methodologies for addressing non-trivial gene flow patterns. In the last decades, network theory - a branch of discrete mathematics concerned with complex interactions between discrete elements - has been applied to address several problems in population genetics by modeling gene flow between habitat patches using networks. Here we present the idea and concepts of modeling complex gene flows in discrete habitats using networks. Our goal is to raise awareness to existing network-theory applications in molecular ecology studies, as well as to outline the current and potential contribution of network methods to the understanding of evolutionary dynamics in discrete habitats. We review the main branches of network theory that have been, or that we believe potentially could be, applied to population genetics and molecular ecology research. We address applications to theoretical modelling and to empirical population-genetic studies, and we highlight future directions for extending the integration of network science with molecular ecology. This article is protected by copyright. All rights reserved.

  12. Hybrid simulation theory for a classical nonlinear dynamical system

    Science.gov (United States)

    Drazin, Paul L.; Govindjee, Sanjay

    2017-03-01

    Hybrid simulation is an experimental and computational technique which allows one to study the time evolution of a system by physically testing a subset of it while the remainder is represented by a numerical model that is attached to the physical portion via sensors and actuators. The technique allows one to study large or complicated mechanical systems while only requiring a subset of the complete system to be present in the laboratory. This results in vast cost savings as well as the ability to study systems that simply can not be tested due to scale. However, the errors that arise from splitting the system in two requires careful attention, if a valid simulation is to be guaranteed. To date, efforts to understand the theoretical limitations of hybrid simulation have been restricted to linear dynamical systems. In this work we consider the behavior of hybrid simulation when applied to nonlinear dynamical systems. As a model problem, we focus on the damped, harmonically-driven nonlinear pendulum. This system offers complex nonlinear characteristics, in particular periodic and chaotic motions. We are able to show that the application of hybrid simulation to nonlinear systems requires a careful understanding of what one expects from such an experiment. In particular, when system response is chaotic we advocate the need for the use of multiple metrics to characterize the difference between two chaotic systems via Lyapunov exponents and Lyapunov dimensions, as well as correlation exponents. When system response is periodic we advocate the use of L2 norms. Further, we are able to show that hybrid simulation can falsely predict chaotic or periodic response when the true system has the opposite characteristic. In certain cases, we are able to show that control system parameters can mitigate this issue.

  13. Disease ecology. Ecological and evolutionary effects of fragmentation on infectious disease dynamics.

    Science.gov (United States)

    Jousimo, Jussi; Tack, Ayco J M; Ovaskainen, Otso; Mononen, Tommi; Susi, Hanna; Tollenaere, Charlotte; Laine, Anna-Liisa

    2014-06-13

    Ecological theory predicts that disease incidence increases with increasing density of host networks, yet evolutionary theory suggests that host resistance increases accordingly. To test the combined effects of ecological and evolutionary forces on host-pathogen systems, we analyzed the spatiotemporal dynamics of a plant (Plantago lanceolata)-fungal pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000 host populations. Disease prevalence at the metapopulation level was low, with high annual pathogen extinction rates balanced by frequent (re-)colonizations. Highly connected host populations experienced less pathogen colonization and higher pathogen extinction rates than expected; a laboratory assay confirmed that this phenomenon was caused by higher levels of disease resistance in highly connected host populations.

  14. Against matching theory: predictions of an evolutionary theory of behavior dynamics.

    Science.gov (United States)

    McDowell, J J; Calvin, Nicholas T

    2015-05-01

    A selectionist theory of adaptive behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of resource acquisition or threat escape or avoidance. The theory is implemented by a computer program that creates an artificial organism and animates it with a population of potential behaviors. The population undergoes selection, recombination, and mutation across generations, or ticks of time, which produces a continuous stream of behavior that can be studied as if it were the behavior of a live organism. Novel predictions of the evolutionary theory can be compared to predictions of matching theory in a critical experiment that arranges concurrent schedules with reinforcer magnitudes that vary across conditions in one component of the schedules but not the other. Matching theory and the evolutionary theory make conflicting predictions about the outcome of this critical experiment, such that the results must disconfirm at least one of the theories.

  15. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Science.gov (United States)

    Cetinbaş, Murat; Shakhnovich, Eugene I

    2013-01-01

    Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI) network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  16. Catalysis of protein folding by chaperones accelerates evolutionary dynamics in adapting cell populations.

    Directory of Open Access Journals (Sweden)

    Murat Cetinbaş

    Full Text Available Although molecular chaperones are essential components of protein homeostatic machinery, their mechanism of action and impact on adaptation and evolutionary dynamics remain controversial. Here we developed a physics-based ab initio multi-scale model of a living cell for population dynamics simulations to elucidate the effect of chaperones on adaptive evolution. The 6-loci genomes of model cells encode model proteins, whose folding and interactions in cellular milieu can be evaluated exactly from their genome sequences. A genotype-phenotype relationship that is based on a simple yet non-trivially postulated protein-protein interaction (PPI network determines the cell division rate. Model proteins can exist in native and molten globule states and participate in functional and all possible promiscuous non-functional PPIs. We find that an active chaperone mechanism, whereby chaperones directly catalyze protein folding, has a significant impact on the cellular fitness and the rate of evolutionary dynamics, while passive chaperones, which just maintain misfolded proteins in soluble complexes have a negligible effect on the fitness. We find that by partially releasing the constraint on protein stability, active chaperones promote a deeper exploration of sequence space to strengthen functional PPIs, and diminish the non-functional PPIs. A key experimentally testable prediction emerging from our analysis is that down-regulation of chaperones that catalyze protein folding significantly slows down the adaptation dynamics.

  17. Ancient Origin of the Tryptophan Operon and the Dynamics of Evolutionary Change†

    Science.gov (United States)

    Xie, Gary; Keyhani, Nemat O.; Bonner; Jensen, Roy A.

    2003-01-01

    The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting

  18. Classification of Medical Datasets Using SVMs with Hybrid Evolutionary Algorithms Based on Endocrine-Based Particle Swarm Optimization and Artificial Bee Colony Algorithms.

    Science.gov (United States)

    Lin, Kuan-Cheng; Hsieh, Yi-Hsiu

    2015-10-01

    The classification and analysis of data is an important issue in today's research. Selecting a suitable set of features makes it possible to classify an enormous quantity of data quickly and efficiently. Feature selection is generally viewed as a problem of feature subset selection, such as combination optimization problems. Evolutionary algorithms using random search methods have proven highly effective in obtaining solutions to problems of optimization in a diversity of applications. In this study, we developed a hybrid evolutionary algorithm based on endocrine-based particle swarm optimization (EPSO) and artificial bee colony (ABC) algorithms in conjunction with a support vector machine (SVM) for the selection of optimal feature subsets for the classification of datasets. The results of experiments using specific UCI medical datasets demonstrate that the accuracy of the proposed hybrid evolutionary algorithm is superior to that of basic PSO, EPSO and ABC algorithms, with regard to classification accuracy using subsets with a reduced number of features.

  19. Dynamic Garment Simulation based on Hybrid Bounding Volume Hierarchy

    Directory of Open Access Journals (Sweden)

    Zhu Dongyong

    2016-12-01

    Full Text Available In order to solve the computing speed and efficiency problem of existing dynamic clothing simulation, this paper presents a dynamic garment simulation based on a hybrid bounding volume hierarchy. It firstly uses MCASG graph theory to do the primary segmentation for a given three-dimensional human body model. And then it applies K-means cluster to do the secondary segmentation to collect the human body’s upper arms, lower arms, upper legs, lower legs, trunk, hip and woman’s chest as the elementary units of dynamic clothing simulation. According to different shapes of these elementary units, it chooses the closest and most efficient hybrid bounding box to specify these units, such as cylinder bounding box and elliptic cylinder bounding box. During the process of constructing these bounding boxes, it uses the least squares method and slices of the human body to get the related parameters. This approach makes it possible to use the least amount of bounding boxes to create close collision detection regions for the appearance of the human body. A spring-mass model based on a triangular mesh of the clothing model is finally constructed for dynamic simulation. The simulation result shows the feasibility and superiority of the method described.

  20. Evolutionary game theory for physical and biological scientists. I. Training and validating population dynamics equations.

    Science.gov (United States)

    Liao, David; Tlsty, Thea D

    2014-08-06

    Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.

  1. Gamete production patterns, ploidy, and population genetics reveal evolutionary significant units in hybrid water frogs (Pelophylax esculentus).

    Science.gov (United States)

    Pruvost, Nicolas B M; Hoffmann, Alexandra; Reyer, Heinz-Ulrich

    2013-09-01

    The European water frog Pelophylax esculentus is a natural hybrid between P. lessonae (genotype LL) and P. ridibundus (RR). It reproduces through hybridogenesis, eliminating one parental genome from its germline and producing gametes containing the genome of the other parental species. According to previous studies, this elimination and transmission pattern is very diverse. In mixed populations, where only diploid hybrids (LR) live in sympatry and mate with one or both parental species, the excluded genome varies among regions, and the remaining genome is transmitted clonally to haploid gametes. In all-hybrid populations consisting of diploid (LR) and triploid (LLR and/or LRR) frogs, diploid individuals also produce gametes clonally (1n in males, 2n in females), whereas triploids eliminate the genome they have in single copy and produce haploid gametes containing the recombined other genome. However, here, too, regional differences seem to exist, and some triploids have been reported to produce diploid gametes. In order to systematically study such regional and genotype differences in gamete production, their potential origin, and their consequences for the breeding system, we sampled frogs from five populations in three European countries, performed crossing experiments, and investigated the genetic variation through microsatellite analysis. For four populations, one in Poland, two in Germany, and one in Slovakia, our results confirmed the elimination and transmission pattern described above. In one Slovakian population, however, we found a totally different pattern. Here, triploid males (LLR) produce sperm with a clonally transmitted diploid LL genome, rather than a haploid recombined L genome, and LR females clonally produce haploid R eggs, rather than diploid LR eggs. These differences among the populations in gamete production go along with differences in genomotype composition, breeding system (i.e., the way triploids are produced), and genetic variation

  2. A semiclassical hybrid approach to many particle quantum dynamics

    Science.gov (United States)

    Grossmann, Frank

    2006-07-01

    We analytically derive a correlated approach for a mixed semiclassical many particle dynamics, treating a fraction of the degrees of freedom by the multitrajectory semiclassical initial value method of Herman and Kluk [Chem. Phys. 91, 27 (1984)] while approximately treating the dynamics of the remaining degrees of freedom with fixed initial phase space variables, analogously to the thawed Gaussian wave packet dynamics of Heller [J. Chem. Phys. 62, 1544 (1975)]. A first application of this hybrid approach to the well studied Secrest-Johnson [J. Chem. Phys. 45, 4556 (1966)] model of atom-diatomic collisions is promising. Results close to the quantum ones for correlation functions as well as scattering probabilities could be gained with considerably reduced numerical effort as compared to the full semiclassical Herman-Kluk approach. Furthermore, the harmonic nature of the different degrees of freedom can be determined a posteriori by comparing results with and without the additional approximation.

  3. Dynamics, morphogenesis and convergence of evolutionary quantum Prisoner's Dilemma games on networks.

    Science.gov (United States)

    Li, Angsheng; Yong, Xi

    2016-02-01

    The authors proposed a quantum Prisoner's Dilemma (PD) game as a natural extension of the classic PD game to resolve the dilemma. Here, we establish a new Nash equilibrium principle of the game, propose the notion of convergence and discover the convergence and phase-transition phenomena of the evolutionary games on networks. We investigate the many-body extension of the game or evolutionary games in networks. For homogeneous networks, we show that entanglement guarantees a quick convergence of super cooperation, that there is a phase transition from the convergence of defection to the convergence of super cooperation, and that the threshold for the phase transitions is principally determined by the Nash equilibrium principle of the game, with an accompanying perturbation by the variations of structures of networks. For heterogeneous networks, we show that the equilibrium frequencies of super-cooperators are divergent, that entanglement guarantees emergence of super-cooperation and that there is a phase transition of the emergence with the threshold determined by the Nash equilibrium principle, accompanied by a perturbation by the variations of structures of networks. Our results explore systematically, for the first time, the dynamics, morphogenesis and convergence of evolutionary games in interacting and competing systems.

  4. An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game.

    Science.gov (United States)

    Hoffman, Moshe; Suetens, Sigrid; Gneezy, Uri; Nowak, Martin A

    2015-03-06

    Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium (NE), which is motivated by perfect rationality. NE specifies a strategy for everyone, such that no one would benefit by deviating unilaterally from his/her strategy. Another powerful tool available to game theorists are evolutionary dynamics (ED). Motivated by evolutionary and learning processes, ED specify changes in strategies over time in a population, such that more successful strategies typically become more frequent. A simple game that illustrates interesting ED is the generalized Rock-Paper-Scissors (RPS) game. The RPS game extends the children's game to situations where winning or losing can matter more or less relative to tying. Here we investigate experimentally three RPS games, where the NE is always to randomize with equal probability, but the evolutionary stability of this strategy changes. Consistent with the prediction of ED we find that aggregate behavior is far away from NE when it is evolutionarily unstable. Our findings add to the growing literature that demonstrates the predictive validity of ED in large-scale incentivized laboratory experiments with human subjects.

  5. Microsatellite landscape evolutionary dynamics across 450 million years of vertebrate genome evolution.

    Science.gov (United States)

    Adams, Richard H; Blackmon, Heath; Reyes-Velasco, Jacobo; Schield, Drew R; Card, Daren C; Andrew, Audra L; Waynewood, Nyimah; Castoe, Todd A

    2016-05-01

    The evolutionary dynamics of simple sequence repeats (SSRs or microsatellites) across the vertebrate tree of life remain largely undocumented and poorly understood. In this study, we analyzed patterns of genomic microsatellite abundance and evolution across 71 vertebrate genomes. The highest abundances of microsatellites exist in the genomes of ray-finned fishes, squamate reptiles, and mammals, while crocodilian, turtle, and avian genomes exhibit reduced microsatellite landscapes. We used comparative methods to infer evolutionary rates of change in microsatellite abundance across vertebrates and to highlight particular lineages that have experienced unusually high or low rates of change in genomic microsatellite abundance. Overall, most variation in microsatellite content, abundance, and evolutionary rate is observed among major lineages of reptiles, yet we found that several deeply divergent clades (i.e., squamate reptiles and mammals) contained relatively similar genomic microsatellite compositions. Archosauromorph reptiles (turtles, crocodilians, and birds) exhibit reduced genomic microsatellite content and the slowest rates of microsatellite evolution, in contrast to squamate reptile genomes that have among the highest rates of microsatellite evolution. Substantial branch-specific shifts in SSR content in primates, monotremes, rodents, snakes, and fish are also evident. Collectively, our results support multiple major shifts in microsatellite genomic landscapes among vertebrates.

  6. Variation within Limits: An Evolutionary Approach to the Structure and Dynamics of the Multiform

    Directory of Open Access Journals (Sweden)

    Michael D. C. Drout

    2011-10-01

    Full Text Available This essay draws upon research in evolutionary biology and cognitive psychology to explain the evolution and stability of the oral-traditional multiform. The mind tends to categorize variable entities in terms of cognitive _prototypes_. The dynamics of human mnemonic and communicative processes then generate both variability (in the absence of written texts and contrasting selection pressure on multiform oral-traditional forms to evolve towards these mental abstractions, thereby producing the variability of the multiform. By visualizing the variation spaces of such cultural entities as _adaptive landscapes_, we see that variation-within-limits of the multiform, rather than being paradoxical, results from universal processes of replication and selection.

  7. Differential Dynamic Evolutionary Model of Emergency Financial Service Supply Chain in Natural Disaster Risk Management

    Directory of Open Access Journals (Sweden)

    Shujian Ma

    2016-01-01

    Full Text Available A government-market-public partnership (GMPP could be a feasible arrangement for providing insurance coverage for natural disaster. Firstly, we put forward GMPP management mode. Secondly, the emergency financial service supply chain for natural disaster risk is built from the view of supply chain. Finally, the objective of this paper is to obtain insights into the cooperative and competitive relationship in GMPP system. We establish the cooperative and competitive differential dynamic evolutionary models and prove the existence of equilibrium solutions in order to solve the coordination problems. In conclusion, the equilibrium solutions can be achieved among the insurers, the operating governments, and the public.

  8. Innovation dynamics of Salvadoran agri-food industry from an evolutionary perspective

    Energy Technology Data Exchange (ETDEWEB)

    Peraza Castaneda, E.H.; Aleixandre Mendizábal, G.

    2016-07-01

    This paper presents a holistic approach to analyse the dynamics of innovation of a low-tech sector in a less developed economy, the agri-food industry in El Salvador, in the context of evolutionary economy. This requires using complementary quantitative and qualitative data and methodologies to better understand how Salvadoran agri-food industry innovation system works and how STI public policies can improve the performance of a key sector in terms of national socioeconomic development. The work already done shows a concentrated and vigorous sector with some upstream and downstream connections that innovate depending on firm size, age, R&D activities and use of industrial property rights. (Author)

  9. Key questions in the genetics and genomics of eco-evolutionary dynamics.

    Science.gov (United States)

    Hendry, A P

    2013-12-01

    Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be--to a large extent--the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.

  10. Evolutionary dynamics of public goods games with diverse contributions in finite populations.

    Science.gov (United States)

    Wang, Jing; Wu, Bin; Chen, Xiaojie; Wang, Long

    2010-05-01

    The public goods game is a powerful metaphor for exploring the maintenance of social cooperative behavior in a group of interactional selfish players. Here we study the emergence of cooperation in the public goods games with diverse contributions in finite populations. The theory of stochastic process is innovatively adopted to investigate the evolutionary dynamics of the public goods games involving a diversity of contributions. In the limit of rare mutations, the general stationary distribution of this stochastic process can be analytically approximated by means of diffusion theory. Moreover, we demonstrate that increasing the diversity of contributions greatly reduces the probability of finding the population in a homogeneous state full of defectors. This increase also raises the expectation of the total contribution in the entire population and thus promotes social cooperation. Furthermore, by investigating the evolutionary dynamics of optional public goods games with diverse contributions, we find that nonparticipation can assist players who contribute more in resisting invasion and taking over individuals who contribute less. In addition, numerical simulations are performed to confirm our analytical results. Our results may provide insight into the effect of diverse contributions on cooperative behaviors in the real world.

  11. Stochastic win-stay-lose-shift strategy with dynamic aspirations in evolutionary social dilemmas

    Science.gov (United States)

    Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.

    2016-09-01

    In times of plenty expectations rise, just as in times of crisis they fall. This can be mathematically described as a win-stay-lose-shift strategy with dynamic aspiration levels, where individuals aspire to be as wealthy as their average neighbor. Here we investigate this model in the realm of evolutionary social dilemmas on the square lattice and scale-free networks. By using the master equation and Monte Carlo simulations, we find that cooperators coexist with defectors in the whole phase diagram, even at high temptations to defect. We study the microscopic mechanism that is responsible for the striking persistence of cooperative behavior and find that cooperation spreads through second-order neighbors, rather than by means of network reciprocity that dominates in imitation-based models. For the square lattice the master equation can be solved analytically in the large temperature limit of the Fermi function, while for other cases the resulting differential equations must be solved numerically. Either way, we find good qualitative agreement with the Monte Carlo simulation results. Our analysis also reveals that the evolutionary outcomes are to a large degree independent of the network topology, including the number of neighbors that are considered for payoff determination on lattices, which further corroborates the local character of the microscopic dynamics. Unlike large-scale spatial patterns that typically emerge due to network reciprocity, here local checkerboard-like patterns remain virtually unaffected by differences in the macroscopic properties of the interaction network.

  12. A New Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Complex Networks

    Directory of Open Access Journals (Sweden)

    Guoqiang Chen

    2013-01-01

    Full Text Available Community detection in dynamic networks is an important research topic and has received an enormous amount of attention in recent years. Modularity is selected as a measure to quantify the quality of the community partition in previous detection methods. But, the modularity has been exposed to resolution limits. In this paper, we propose a novel multiobjective evolutionary algorithm for dynamic networks community detection based on the framework of nondominated sorting genetic algorithm. Modularity density which can address the limitations of modularity function is adopted to measure the snapshot cost, and normalized mutual information is selected to measure temporal cost, respectively. The characteristics knowledge of the problem is used in designing the genetic operators. Furthermore, a local search operator was designed, which can improve the effectiveness and efficiency of community detection. Experimental studies based on synthetic datasets show that the proposed algorithm can obtain better performance than the compared algorithms.

  13. Evolutionary systemic risk: Fisher information flow metric in financial network dynamics

    Science.gov (United States)

    Khashanah, Khaldoun; Yang, Hanchao

    2016-03-01

    Recently the topic of financial network dynamics has gained renewed interest from researchers in the field of empirical systemic risk measurements. We refer to this type of network analysis as information flow networks analysis (IFNA). This paper proposes a new method that applies Fisher information metric to the evolutionary dynamics of financial networks using IFNA. Our paper is the first to apply the Fisher information metric to a set of financial time series. We introduce Evolution Index (EI) as a measure of systemic risk in financial networks. It is shown, for concrete networks with actual data of several stock markets, that the EI can be implemented as a measure of fitness of the stock market and as a leading indicator of systemic risk.

  14. The dynamics of hybrid metabolic-genetic oscillators

    Science.gov (United States)

    Reznik, Ed; Kaper, Tasso J.; Segrè, Daniel

    2013-03-01

    The synthetic construction of intracellular circuits is frequently hindered by a poor knowledge of appropriate kinetics and precise rate parameters. Here, we use generalized modeling (GM) to study the dynamical behavior of topological models of a family of hybrid metabolic-genetic circuits known as "metabolators." Under mild assumptions on the kinetics, we use GM to analytically prove that all explicit kinetic models which are topologically analogous to one such circuit, the "core metabolator," cannot undergo Hopf bifurcations. Then, we examine more detailed models of the metabolator. Inspired by the experimental observation of a Hopf bifurcation in a synthetically constructed circuit related to the core metabolator, we apply GM to identify the critical components of the synthetically constructed metabolator which must be reintroduced in order to recover the Hopf bifurcation. Next, we study the dynamics of a re-wired version of the core metabolator, dubbed the "reverse" metabolator, and show that it exhibits a substantially richer set of dynamical behaviors, including both local and global oscillations. Prompted by the observation of relaxation oscillations in the reverse metabolator, we study the role that a separation of genetic and metabolic time scales may play in its dynamics, and find that widely separated time scales promote stability in the circuit. Our results illustrate a generic pipeline for vetting the potential success of a circuit design, simply by studying the dynamics of the corresponding generalized model.

  15. Evolutionary dynamics of finite populations in games with polymorphic fitness equilibria.

    Science.gov (United States)

    Ficici, Sevan G; Pollack, Jordan B

    2007-08-07

    The hawk-dove (HD) game, as defined by Maynard Smith [1982. Evolution and the Theory of Games. Cambridge University Press, Cambridge], allows for a polymorphic fitness equilibrium (PFE) to exist between its two pure strategies; this polymorphism is the attractor of the standard replicator dynamics [Taylor, P.D., Jonker, L., 1978. Evolutionarily stable strategies and game dynamics. Math. Biosci. 40, 145-156; Hofbauer, J., Sigmund, K., 1998. Evolutionary Games and Population Dynamics. Cambridge University Press, Cambridge] operating on an infinite population of pure-strategists. Here, we consider stochastic replicator dynamics, operating on a finite population of pure-strategists playing games similar to HD; in particular, we examine the transient behavior of the system, before it enters an absorbing state due to sampling error. Though stochastic replication prevents the population from fixing onto the PFE, selection always favors the under-represented strategy. Thus, we may naively expect that the mean population state (of the pre-absorption transient) will correspond to the PFE. The empirical results of Fogel et al. [1997. On the instability of evolutionary stable states. BioSystems 44, 135-152] show that the mean population state, in fact, deviates from the PFE with statistical significance. We provide theoretical results that explain their observations. We show that such deviation away from the PFE occurs when the selection pressures that surround the fitness-equilibrium point are asymmetric. Further, we analyze a Markov model to prove that a finite population will generate a distribution over population states that equilibrates selection-pressure asymmetry; the mean of this distribution is generally not the fitness-equilibrium state.

  16. The complex evolutionary dynamics of Hsp70s: a genomic and functional perspective.

    Science.gov (United States)

    Kominek, Jacek; Marszalek, Jaroslaw; Neuvéglise, Cécile; Craig, Elizabeth A; Williams, Barry L

    2013-01-01

    Hsp70 molecular chaperones are ubiquitous. By preventing aggregation, promoting folding, and regulating degradation, Hsp70s are major factors in the ability of cells to maintain proteostasis. Despite a wealth of functional information, little is understood about the evolutionary dynamics of Hsp70s. We undertook an analysis of Hsp70s in the fungal clade Ascomycota. Using the well-characterized 14 Hsp70s of Saccharomyces cerevisiae, we identified 491 orthologs from 53 genomes. Saccharomyces cerevisiae Hsp70s fall into seven subfamilies: four canonical-type Hsp70 chaperones (SSA, SSB, KAR, and SSC) and three atypical Hsp70s (SSE, SSZ, and LHS) that play regulatory roles, modulating the activity of canonical Hsp70 partners. Each of the 53 surveyed genomes harbored at least one member of each subfamily, and thus establishing these seven Hsp70s as units of function and evolution. Genomes of some species contained only one member of each subfamily that is only seven Hsp70s. Overall, members of each subfamily formed a monophyletic group, suggesting that each diversified from their corresponding ancestral gene present in the common ancestor of all surveyed species. However, the pattern of evolution varied across subfamilies. At one extreme, members of the SSB subfamily evolved under concerted evolution. At the other extreme, SSA and SSC subfamilies exhibited a high degree of copy number dynamics, consistent with a birth-death mode of evolution. KAR, SSE, SSZ, and LHS subfamilies evolved in a simple divergent mode with little copy number dynamics. Together, our data revealed that the evolutionary history of this highly conserved and ubiquitous protein family was surprising complex and dynamic.

  17. Hybrid control and motion planning of dynamical legged locomotion

    CERN Document Server

    2012-01-01

    "This book provides a comprehensive presentation of issues and challenges faced by researchers and practicing engineers in motion planning and hybrid control of dynamical legged locomotion. The major features range from offline and online motion planning algorithms to generate desired feasible periodic walking and running motions and tow-level control schemes, including within-stride feedback laws, continuous time update laws and event-based update laws, to asymptotically stabilize the generated desired periodic orbits. This book describes the current state of the art and future directions across all domains of dynamical legged locomotion so that readers can extend proposed motion planning algorithms and control methodologies to other types of planar and 3D legged robots".

  18. A Hybrid Dynamic Programming Method for Concave Resource Allocation Problems

    Institute of Scientific and Technical Information of China (English)

    姜计荣; 孙小玲

    2005-01-01

    Concave resource allocation problem is an integer programming problem of minimizing a nonincreasing concave function subject to a convex nondecreasing constraint and bounded integer variables. This class of problems are encountered in optimization models involving economies of scale. In this paper, a new hybrid dynamic programming method was proposed for solving concave resource allocation problems. A convex underestimating function was used to approximate the objective function and the resulting convex subproblem was solved with dynamic programming technique after transforming it into a 0-1 linear knapsack problem. To ensure the convergence, monotonicity and domain cut technique was employed to remove certain integer boxes and partition the revised domain into a union of integer boxes. Computational results were given to show the efficiency of the algorithm.

  19. An Optimization Framework for Dynamic Hybrid Energy Systems

    Energy Technology Data Exchange (ETDEWEB)

    Wenbo Du; Humberto E Garcia; Christiaan J.J. Paredis

    2014-03-01

    A computational framework for the efficient analysis and optimization of dynamic hybrid energy systems (HES) is developed. A microgrid system with multiple inputs and multiple outputs (MIMO) is modeled using the Modelica language in the Dymola environment. The optimization loop is implemented in MATLAB, with the FMI Toolbox serving as the interface between the computational platforms. Two characteristic optimization problems are selected to demonstrate the methodology and gain insight into the system performance. The first is an unconstrained optimization problem that optimizes the dynamic properties of the battery, reactor and generator to minimize variability in the HES. The second problem takes operating and capital costs into consideration by imposing linear and nonlinear constraints on the design variables. The preliminary optimization results obtained in this study provide an essential step towards the development of a comprehensive framework for designing HES.

  20. A hybrid Evolutionary Functional Link Artificial Neural Network for Data mining and Classification

    Directory of Open Access Journals (Sweden)

    Faissal MILI

    2012-08-01

    Full Text Available This paper presents a specific structure of neural network as the functional link artificial neural network (FLANN. This technique has been employed for classification tasks of data mining. In fact, there are a few studies that used this tool for solving classification problems. In this present research, we propose a hybrid FLANN (HFLANN model, where the optimization process is performed using 3 known population based techniques such as genetic algorithms, particle swarm and differential evolution. This model will be empirically compared to FLANN based back-propagation algorithm and to others classifiers as decision tree, multilayer perceptron based back-propagation algorithm, radical basic function, support vector machine, and K-nearest Neighbor. Our results proved that the proposed model outperforms the other single model. (Abstract

  1. Dynamic Resource Allocation in Hybrid Access Femtocell Network

    Directory of Open Access Journals (Sweden)

    Afaz Uddin Ahmed

    2014-01-01

    Full Text Available Intercell interference is one of the most challenging issues in femtocell deployment under the coverage of existing macrocell. Allocation of resources between femtocell and macrocell is essential to counter the effects of interference in dense femtocell networks. Advances in resource management strategies have improved the control mechanism for interference reduction at lower node density, but most of them are ineffective at higher node density. In this paper, a dynamic resource allocation management algorithm (DRAMA for spectrum shared hybrid access OFDMA femtocell network is proposed. To reduce the macro-femto-tier interference and to improve the quality of service, the proposed algorithm features a dynamic resource allocation scheme by controlling them both centrally and locally. The proposed scheme focuses on Femtocell Access Point (FAP owners’ satisfaction and allows maximum utilization of available resources based on congestion in the network. A simulation environment is developed to study the quantitative performance of DRAMA in hybrid access-control femtocell network and compare it to closed and open access mechanisms. The performance analysis shows that higher number of random users gets connected to the FAP without compromising FAP owners’ satisfaction allowing the macrocell to offload a large number of users in a dense heterogeneous network.

  2. Comparative evolutionary diversity and phylogenetic structure across multiple forest dynamics plots: a mega-phylogeny approach

    Science.gov (United States)

    Erickson, David L.; Jones, Frank A.; Swenson, Nathan G.; Pei, Nancai; Bourg, Norman A.; Chen, Wenna; Davies, Stuart J.; Ge, Xue-jun; Hao, Zhanqing; Howe, Robert W.; Huang, Chun-Lin; Larson, Andrew J.; Lum, Shawn K. Y.; Lutz, James A.; Ma, Keping; Meegaskumbura, Madhava; Mi, Xiangcheng; Parker, John D.; Fang-Sun, I.; Wright, S. Joseph; Wolf, Amy T.; Ye, W.; Xing, Dingliang; Zimmerman, Jess K.; Kress, W. John

    2014-01-01

    Forest dynamics plots, which now span longitudes, latitudes, and habitat types across the globe, offer unparalleled insights into the ecological and evolutionary processes that determine how species are assembled into communities. Understanding phylogenetic relationships among species in a community has become an important component of assessing assembly processes. However, the application of evolutionary information to questions in community ecology has been limited in large part by the lack of accurate estimates of phylogenetic relationships among individual species found within communities, and is particularly limiting in comparisons between communities. Therefore, streamlining and maximizing the information content of these community phylogenies is a priority. To test the viability and advantage of a multi-community phylogeny, we constructed a multi-plot mega-phylogeny of 1347 species of trees across 15 forest dynamics plots in the ForestGEO network using DNA barcode sequence data (rbcL, matK, and psbA-trnH) and compared community phylogenies for each individual plot with respect to support for topology and branch lengths, which affect evolutionary inference of community processes. The levels of taxonomic differentiation across the phylogeny were examined by quantifying the frequency of resolved nodes throughout. In addition, three phylogenetic distance (PD) metrics that are commonly used to infer assembly processes were estimated for each plot [PD, Mean Phylogenetic Distance (MPD), and Mean Nearest Taxon Distance (MNTD)]. Lastly, we examine the partitioning of phylogenetic diversity among community plots through quantification of inter-community MPD and MNTD. Overall, evolutionary relationships were highly resolved across the DNA barcode-based mega-phylogeny, and phylogenetic resolution for each community plot was improved when estimated within the context of the mega-phylogeny. Likewise, when compared with phylogenies for individual plots, estimates of

  3. A master-slave parallel hybrid multi-objective evolutionary algorithm for groundwater remediation design under general hydrogeological conditions

    Science.gov (United States)

    Wu, J.; Yang, Y.; Luo, Q.; Wu, J.

    2012-12-01

    This study presents a new hybrid multi-objective evolutionary algorithm, the niched Pareto tabu search combined with a genetic algorithm (NPTSGA), whereby the global search ability of niched Pareto tabu search (NPTS) is improved by the diversification of candidate solutions arose from the evolving nondominated sorting genetic algorithm II (NSGA-II) population. Also, the NPTSGA coupled with the commonly used groundwater flow and transport codes, MODFLOW and MT3DMS, is developed for multi-objective optimal design of groundwater remediation systems. The proposed methodology is then applied to a large-scale field groundwater remediation system for cleanup of large trichloroethylene (TCE) plume at the Massachusetts Military Reservation (MMR) in Cape Cod, Massachusetts. Furthermore, a master-slave (MS) parallelization scheme based on the Message Passing Interface (MPI) is incorporated into the NPTSGA to implement objective function evaluations in distributed processor environment, which can greatly improve the efficiency of the NPTSGA in finding Pareto-optimal solutions to the real-world application. This study shows that the MS parallel NPTSGA in comparison with the original NPTS and NSGA-II can balance the tradeoff between diversity and optimality of solutions during the search process and is an efficient and effective tool for optimizing the multi-objective design of groundwater remediation systems under complicated hydrogeologic conditions.

  4. Hybrid evolutionary techniques in feed forward neural network with distributed error for classification of handwritten Hindi `SWARS'

    Science.gov (United States)

    Kumar, Somesh; Pratap Singh, Manu; Goel, Rajkumar; Lavania, Rajesh

    2013-12-01

    In this work, the performance of feedforward neural network with a descent gradient of distributed error and the genetic algorithm (GA) is evaluated for the recognition of handwritten 'SWARS' of Hindi curve script. The performance index for the feedforward multilayer neural networks is considered here with distributed instantaneous unknown error i.e. different error for different layers. The objective of the GA is to make the search process more efficient to determine the optimal weight vectors from the population. The GA is applied with the distributed error. The fitness function of the GA is considered as the mean of square distributed error that is different for each layer. Hence the convergence is obtained only when the minimum of different errors is determined. It has been analysed that the proposed method of a descent gradient of distributed error with the GA known as hybrid distributed evolutionary technique for the multilayer feed forward neural performs better in terms of accuracy, epochs and the number of optimal solutions for the given training and test pattern sets of the pattern recognition problem.

  5. Evolutionary dynamics of nitrogen fixation in the legume-rhizobia symbiosis.

    Science.gov (United States)

    Fujita, Hironori; Aoki, Seishiro; Kawaguchi, Masayoshi

    2014-01-01

    The stabilization of host-symbiont mutualism against the emergence of parasitic individuals is pivotal to the evolution of cooperation. One of the most famous symbioses occurs between legumes and their colonizing rhizobia, in which rhizobia extract nutrients (or benefits) from legume plants while supplying them with nitrogen resources produced by nitrogen fixation (or costs). Natural environments, however, are widely populated by ineffective rhizobia that extract benefits without paying costs and thus proliferate more efficiently than nitrogen-fixing cooperators. How and why this mutualism becomes stabilized and evolutionarily persists has been extensively discussed. To better understand the evolutionary dynamics of this symbiosis system, we construct a simple model based on the continuous snowdrift game with multiple interacting players. We investigate the model using adaptive dynamics and numerical simulations. We find that symbiotic evolution depends on the cost-benefit balance, and that cheaters widely emerge when the cost and benefit are similar in strength. In this scenario, the persistence of the symbiotic system is compatible with the presence of cheaters. This result suggests that the symbiotic relationship is robust to the emergence of cheaters, and may explain the prevalence of cheating rhizobia in nature. In addition, various stabilizing mechanisms, such as partner fidelity feedback, partner choice, and host sanction, can reinforce the symbiotic relationship by affecting the fitness of symbionts in various ways. This result suggests that the symbiotic relationship is cooperatively stabilized by various mechanisms. In addition, mixed nodule populations are thought to encourage cheater emergence, but our model predicts that, in certain situations, cheaters can disappear from such populations. These findings provide a theoretical basis of the evolutionary dynamics of legume-rhizobia symbioses, which is extendable to other single-host, multiple

  6. The puzzle of partial migration: Adaptive dynamics and evolutionary game theory perspectives.

    Science.gov (United States)

    De Leenheer, Patrick; Mohapatra, Anushaya; Ohms, Haley A; Lytle, David A; Cushing, J M

    2017-01-07

    We consider the phenomenon of partial migration which is exhibited by populations in which some individuals migrate between habitats during their lifetime, but others do not. First, using an adaptive dynamics approach, we show that partial migration can be explained on the basis of negative density dependence in the per capita fertilities alone, provided that this density dependence is attenuated for increasing abundances of the subtypes that make up the population. We present an exact formula for the optimal proportion of migrants which is expressed in terms of the vital rates of migrant and non-migrant subtypes only. We show that this allocation strategy is both an evolutionary stable strategy (ESS) as well as a convergence stable strategy (CSS). To establish the former, we generalize the classical notion of an ESS because it is based on invasion exponents obtained from linearization arguments, which fail to capture the stabilizing effects of the nonlinear density dependence. These results clarify precisely when the notion of a "weak ESS", as proposed in Lundberg (2013) for a related model, is a genuine ESS. Secondly, we use an evolutionary game theory approach, and confirm, once again, that partial migration can be attributed to negative density dependence alone. In this context, the result holds even when density dependence is not attenuated. In this case, the optimal allocation strategy towards migrants is the same as the ESS stemming from the analysis based on the adaptive dynamics. The key feature of the population models considered here is that they are monotone dynamical systems, which enables a rather comprehensive mathematical analysis.

  7. Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily

    Directory of Open Access Journals (Sweden)

    Bagnato S

    2014-04-01

    Full Text Available Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily. The aim of this paper is to evaluate the dynamics of Etna birch stands (Betula aetnensis Rafin following the cessation of silvicultural activities in the Etna Regional Park (Sicily. We investigated forest structure, natural regeneration, vegetation and deadwood in different forest types. Our findings highlighted three different dynamics for birch populations: stable birch stands in the high mountain area which might represent an edapho-climax forest; progressive dynamic birch stands in the intermediate mountain area, showing a gradual depletion of birch and a concomitant replacement with monospecific stands (calabrian pine, beech, oaks or mixed ones (with birch; pure birch stands (typical that tend to be regressive - especially under stressful conditions - and to be replaced by xerophilous grasslands. Following the cessation of coppicing and with stand ageing, the stumps transformation into more homogeneous stand structures have been increasing. Within the context of protected areas the restoration of coppice selection system (with appropriate adaptations could help to maintain the traditional forest landscape, acting as a silvicultural technique with low environmental and landscape impact.

  8. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.

    Directory of Open Access Journals (Sweden)

    C Brandon Ogbunugafor

    2016-01-01

    Full Text Available The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with

  9. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance.

    Science.gov (United States)

    Ogbunugafor, C Brandon; Wylie, C Scott; Diakite, Ibrahim; Weinreich, Daniel M; Hartl, Daniel L

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their

  10. Adaptive Landscape by Environment Interactions Dictate Evolutionary Dynamics in Models of Drug Resistance

    Science.gov (United States)

    Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L.

    2016-01-01

    The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with

  11. Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage.

    Science.gov (United States)

    Subramaniam, Saravanan; Mohapatra, Jajati K; Sharma, Gaurav K; Biswal, Jitendra K; Ranjan, Rajeev; Rout, Manoranjan; Das, Biswajit; Dash, Bana B; Sanyal, Aniket; Pattnaik, Bramhadev

    2015-08-05

    Foot-and-mouth disease (FMD) virus serotype O Ind2001 lineage within the Middle East-South Asia topotype is the major cause of recent FMD incidences in India. A sub-lineage of Ind2001 caused severe outbreaks in the southern region of the country during 2013 and also reported for the first time from Libya. In this study, we conducted a detailed evolutionary analysis of Ind2001 lineage. Phylogenetic analysis of Ind2001 lineage based on maximum likelihood method revealed two major splits and three sub-lineages. The mean nucleotide substitution rate for this lineage was calculated to be 6.338×10(-3)substitutions/site/year (s/s/y), which is similar to those of PanAsian sub-lineages. Evolutionary time scale analysis indicated that the Ind2001 lineage might have originated in 1989. The sub-lineage Ind2001d that caused 2013 outbreaks seems to be relatively more divergent genetically from other Ind2001 sub-lineages. Seven codons in the VP1 region of Ind2001 were found to be under positive selection. Four out of 24 recent Ind2001 strains tested in 2D-MNT had antigenic relationship value of <0.3 with the serotype O vaccine strain indicating intra-epidemic antigenic diversity. Amino acid substitutions found in these minor variants with reference to antigenic diversity have been discussed. The dominance of antigenically homologous strains indicates absence of vaccine immunity in the majority of the affected hosts. Taken together, the evolution of Ind2001 lineage deviates from the strict molecular clock and a typical lineage evolutionary dynamics characterized by periodic emergence and re-emergence of Ind2001 and PanAsia lineage have been observed in respect of serotype O.

  12. Nanoscopic dynamics in hybrid hydroxyapatite-CTAB composite

    Science.gov (United States)

    Dubey, P. S.; Sharma, V. K.; Mitra, S.; Verma, G.; Hassan, P. A.; Dutta, B.; Johnson, M.; Mukhopadhyay, R.

    2017-06-01

    Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. HAp nanoparticles were synthesized by the co-precipitation method using cetyltrimethylammonium bromide (CTAB) micelles as a template and are characterized using x-ray diffraction, electron microscopy, and thermal gravimetric measurements. Transmission electron microscope (TEM) demonstrates the formation of rod-shaped HAp. Dynamics of CTAB in HAp-CTAB composite as studied by using quasielastic neutron scattering (QENS) technique is reported here. HAp-CTAB composite provides an ideal system for studying the dynamics of CTAB micelles without any aqueous media. QENS data indicate that the observed dynamics are reminiscent of localized motions in ionic micellar systems, consisting of segmental and fast torsional motions. Segmental dynamics has been described with a model, in which hydrogen atoms in the alkyl chain undergoes localized translation diffusion and the CH3 unit associated with the head group undergo 3-fold jump rotation. Within this model, the hydrogen atoms in the alkyl chain undergo diffusion within spherical domains having different radii and diffusivities. A simple linear distribution of the radius and diffusivity has been assumed, in which the CH2 unit nearest to the head group has the least value and the ones furthest from the head group, that is, at the end of the alkyl chain has the largest value. The fast torsional motion is described by a 2-fold jump rotation model. Quantitative estimate of the different parameters characterizing various dynamical motions active within the time scale of the instrument is also presented. We have provided a detailed description of the observed dynamical features in hybrid HAp-CTAB composite, a potential candidate for biomedical applications.

  13. Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy.

    Science.gov (United States)

    Jones, Anita; Lowry, Kym; Aaskov, John; Holmes, Edward C; Kitchen, Andrew

    2010-01-01

    Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic diversity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic diversity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.

  14. Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura

    Directory of Open Access Journals (Sweden)

    Matos Margarida

    2009-06-01

    Full Text Available Abstract Here we present a correction to our article "Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura". We have recently detected an error concerning the application of the Ln RH formula – a test to detect positive selection – to our microsatellite data. Here we provide the corrected data and discuss its implications for our overall findings. The corrections presented here have produced some changes relative to our previous results, namely in a locus (dsub14 that presents indications of being affected by positive selection. In general, our populations present less consistent indications of positive selection for this particular locus in both periods studied – between generations 3 and 14 and between generation 14 and 40 of laboratory adaptation. Despite this, the main findings of our study regarding the possibility of positive selection acting on that particular microsatellite still hold. As previously concluded in our article, further studies should be performed on this specific microsatellite locus (and neighboring areas to elucidate in greater detail the evolutionary forces acting on this specific region of the O chromosome of Drosophila subobscura.

  15. Dynamic instability of cooperation due to diverse activity patterns in evolutionary social dilemmas

    Science.gov (United States)

    Xia, Cheng-Yi; Meloni, Sandro; Perc, Matjaž; Moreno, Yamir

    2015-03-01

    Individuals might abstain from participating in an instance of an evolutionary game for various reasons, ranging from lack of interest to risk aversion. In order to understand the consequences of such diverse activity patterns on the evolution of cooperation, we study a weak prisoner's dilemma where each player's participation is probabilistic rather than certain. Players that do not participate get a null payoff and are unable to replicate. We show that inactivity introduces cascading failures of cooperation, which are particularly severe on scale-free networks with frequently inactive hubs. The drops in the fraction of cooperators are sudden, while the spatiotemporal reorganization of compact cooperative clusters, and thus the recovery, takes time. Nevertheless, if the activity of players is directly proportional to their degree, or if the interaction network is not strongly heterogeneous, the overall evolution of cooperation is not impaired. This is because inactivity negatively affects the potency of low-degree defectors, who are hence unable to utilize on their inherent evolutionary advantage. Between cascading failures, the fraction of cooperators is therefore higher than usual, which lastly balances out the asymmetric dynamic instabilities that emerge due to intermittent blackouts of cooperative hubs.

  16. Evolutionary dynamics of a conserved sequence motif in the ribosomal genes of the ciliate Paramecium

    Directory of Open Access Journals (Sweden)

    Lynch Michael

    2010-05-01

    Full Text Available Abstract Background In protozoa, the identification of preserved motifs by comparative genomics is often impeded by difficulties to generate reliable alignments for non-coding sequences. Moreover, the evolutionary dynamics of regulatory elements in 3' untranslated regions (both in protozoa and metazoa remains a virtually unexplored issue. Results By screening Paramecium tetraurelia's 3' untranslated regions for 8-mers that were previously found to be preserved in mammalian 3' UTRs, we detect and characterize a motif that is distinctly conserved in the ribosomal genes of this ciliate. The motif appears to be conserved across Paramecium aurelia species but is absent from the ribosomal genes of four additional non-Paramecium species surveyed, including another ciliate, Tetrahymena thermophila. Motif-free ribosomal genes retain fewer paralogs in the genome and appear to be lost more rapidly relative to motif-containing genes. Features associated with the discovered preserved motif are consistent with this 8-mer playing a role in post-transcriptional regulation. Conclusions Our observations 1 shed light on the evolution of a putative regulatory motif across large phylogenetic distances; 2 are expected to facilitate the understanding of the modulation of ribosomal genes expression in Paramecium; and 3 reveal a largely unexplored--and presumably not restricted to Paramecium--association between the presence/absence of a DNA motif and the evolutionary fate of its host genes.

  17. Evolutionary dynamics of recent peste des petits ruminants virus epidemic in China during 2013-2014.

    Science.gov (United States)

    Bao, Jingyue; Wang, Qinghua; Li, Lin; Liu, Chunju; Zhang, Zhicheng; Li, Jinming; Wang, Shujuan; Wu, Xiaodong; Wang, Zhiliang

    2017-10-01

    Peste des petits ruminants virus (PPRV) causes a highly contagious disease, peste des petits ruminants (PPR), in sheep and goats which has been considered as a serious threat to the local economy in Africa and Asia. However, the in-depth evolutionary dynamics of PPRV during an epidemic is not well understood. We conducted phylogenetic analysis on genomic sequences of 25 PPRV strains from China 2013-2014 outbreaks. All these strains clustered into a novel clade in lineage 4. An evolutionary rate of 2.61 × 10(-6) nucleotide substitutions per site per day was estimated, dating the most recent common ancestor of PPRV China 2013-2014 strains to early August 2013. Transmission network analysis revealed that all the virus sequences could be grouped into five clusters of infection, suggesting long-distance animal transmission play an important role in the spread of PPRV in China. These results expanded our knowledge for PPRV evolution to achieve effective control measures. Copyright © 2017 Elsevier Inc. All rights reserved.

  18. Hybridization in East African swarm-raiding army ants

    DEFF Research Database (Denmark)

    Kronauer, Daniel Jc; Peters, Marcell K; Schöning, Caspar;

    2011-01-01

    Hybridization can have complex effects on evolutionary dynamics in ants because of the combination of haplodiploid sex-determination and eusociality. While hybrid non-reproductive workers have been found in a range of species, examples of gene-flow via hybrid queens and males are rare. We studied...

  19. Evolutionary genetic optimization of the injector beam dynamics for the ERL test facility at IHEP

    CERN Document Server

    Yi, Jiao

    2013-01-01

    The energy recovery linac test facility (ERL-TF), a compact ERL-FEL (free electron laser) two-purpose machine, was proposed at the Institute of High Energy Physics, Beijing. As one important component of the ERL-TF, the photo-injector started with a photocathode direct-current gun was designed and preliminarily optimized. In this paper an evolutionary genetic method, non-dominated sorting genetic algorithm II, is applied to optimize the injector beam dynamics, especially in the high-charge operation mode. Study shows that using an incident laser with rms transverse size of 1~1.2 mm, the normalized emittance of the electron beam can be kept below 1 mm.mrad at the end of the injector. This work, together with the previous optimization for the low-charge operation mode by using the iterative scan method, provides guidance and confidence for future constructing and commissioning of the ERL-TF injector.

  20. Evolutionary genetic optimization of the injector beam dynamics for the ERL test facility at IHEP

    Science.gov (United States)

    Jiao, Yi

    2014-08-01

    The energy recovery linac test facility (ERL-TF), a compact ERL-FEL (free electron laser) two-purpose machine, has been proposed at the Institute of High Energy Physics, Beijing. As one important component of the ERL-TF, the photo-injector was designed and preliminarily optimized. In this paper an evolutionary genetic method, non-dominated sorting genetic algorithm II, is applied to optimize the injector beam dynamics, especially in the high-charge operation mode. Study shows that using an incident laser with rms transverse size of 1-1.2 mm, the normalized emittance of the electron beam can be kept below 1 mm·mrad at the end of the injector. This work, together with the previous optimization of the low-charge operation mode by using the iterative scan method, provides guidance and confidence for future construction and commissioning of the ERL-TF injector.

  1. Co-Evolution of Opinion and Strategy in Persuasion Dynamics:. AN Evolutionary Game Theoretical Approach

    Science.gov (United States)

    Ding, Fei; Liu, Yun; Li, Yong

    In this paper, a new model of opinion formation within the framework of evolutionary game theory is presented. The model simulates strategic situations when people are in opinion discussion. Heterogeneous agents adjust their behaviors to the environment during discussions, and their interacting strategies evolve together with opinions. In the proposed game, we take into account payoff discount to join a discussion, and the situation that people might drop out of an unpromising game. Analytical and emulational results show that evolution of opinion and strategy always tend to converge, with utility threshold, memory length, and decision uncertainty parameters influencing the convergence time. The model displays different dynamical regimes when we set differently the rule when people are at a loss in strategy.

  2. Evolutionary decision-makings for the dynamic weapon-target assignment problem

    Institute of Scientific and Technical Information of China (English)

    CHEN Jie; XIN Bin; PENG ZhiHong; DOU LiHua; ZHANG Juan

    2009-01-01

    The dynamic weapon-target assignment (DWTA) problem is an important issue In the field of military command and control.An asset-based DWTA optimization model was proposed with four kinds of constraints considered,including capability constraints,strategy constraints,resource constraints and engagement feasibility constraints.A general "virtual"representation of decisions was presented to facilitate the generation of feasible decisions.The representation is in essence the permutation of all assignment pairs.A construction procedure converts the permutations into real feasible decisions.In order to solve this problem,three evolutionary decision-making algorithms,Including a genetic algorithm and two memeitc algorithms,were developed.Experimental results show that the memetic algorithm based on greedy local search can generate obviously better DWTA decisions,especially for large-scale problems,than the genetic algorithm and the memetic algorithm based on steepest local search.

  3. An Evolutionary Algorithm Approach to Link Prediction in Dynamic Social Networks

    CERN Document Server

    Bliss, Catherine A; Danforth, Christopher M; Dodds, Peter Sheridan

    2013-01-01

    Many real world, complex phenomena have underlying structures of evolving networks where nodes and links are added and removed over time. A central scientific challenge is the description and explanation of network dynamics, with a key test being the prediction of short and long term changes. For the problem of short-term link prediction, existing methods attempt to determine neighborhood metrics that correlate with the appearance of a link in the next observation period. Recent work has suggested that the incorporation of user-specific metadata and usage patterns can improve link prediction, however methodologies for doing so in a systematic way are largely unexplored in the literature. Here, we provide an approach to predicting future links by applying an evolutionary algorithm to weights which are used in a linear combination of sixteen neighborhood and node similarity indices. We examine Twitter reciprocal reply networks constructed at the time scale of weeks, both as a test of our general method and as a...

  4. Evolutionary history and dynamics of dog rabies virus in western and central Africa.

    Science.gov (United States)

    Talbi, Chiraz; Holmes, Edward C; de Benedictis, Paola; Faye, Ousmane; Nakouné, Emmanuel; Gamatié, Djibo; Diarra, Abass; Elmamy, Bezeid Ould; Sow, Adama; Adjogoua, Edgard Valery; Sangare, Oumou; Dundon, William G; Capua, Ilaria; Sall, Amadou A; Bourhy, Hervé

    2009-04-01

    The burden of rabies in Africa is estimated at 24,000 human deaths year(-1), almost all of which result from infection with dog rabies viruses (RABV). To investigate the evolutionary dynamics of RABV in western and central Africa, 92 isolates sampled from 27 African countries over 29 years were collected and sequenced. This revealed that RABV currently circulating in dogs in this region fell into a single lineage designated 'Africa 2'. A detailed analysis of the phylogeographical structure of this Africa 2 lineage revealed strong population subdivision at the country level, with only limited movement of virus among localities, including a possible east-to-west spread across Africa. In addition, Bayesian coalescent analysis suggested that the Africa 2 lineage was introduced into this region of Africa only recently (probably colonial influence and urbanization, and then spread relatively slowly, perhaps occupying the entire region in a 100 year period.

  5. Stochastic Win-Stay-Lose-Shift with dynamic aspirations in evolutionary social dilemmas

    CERN Document Server

    Amaral, Marco A; Perc, Matjaz; da Silva, Jafferson K L

    2016-01-01

    In times of plenty expectations rise, just as in times of crisis they fall. This can be mathematically described as a Win-Stay-Lose-Shift strategy with dynamic aspiration levels, where individuals aspire to be as wealthy as their average neighbor. Here we investigate this model in the realm of evolutionary social dilemmas on the square lattice and scale-free networks. By using the master equation and Monte Carlo simulations, we find that cooperators coexist with defectors in the whole phase diagram, even at high temptations to defect. We study the microscopic mechanism that is responsible for the striking persistence of cooperative behavior and find that cooperation spreads through second-order neighbors, rather than by means of network reciprocity that dominates in imitation-based models. For the square lattice the master equation can be solved analytically in the large temperature limit of the Fermi function, while for other cases the resulting differential equations must be solved numerically. Either way, ...

  6. Evolutionary dynamics and genetic diversity from three genes of Anguillid rhabdovirus

    DEFF Research Database (Denmark)

    Bellec, Laure; Cabon, Joelle; Bergmann, Sven

    2014-01-01

    Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially...... play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected...... from seven countries over 40 years using maximum-likelihood and Bayesian approaches. Phylogenetic trees from the three genes are congruent and allow two monophyletic groups, European and American, to be clearly distinguished. Results of nucleotide substitution rates per site per year indicate...

  7. Kinematic Constraints on Evolutionary Scenarios for Blue Compact Dwarf Galaxies I. Neutral Gas Dynamics

    CERN Document Server

    Van Zee, L; Skillman, E D; Zee, Liese van; Salzer, John J.; Skillman, Evan D.

    2001-01-01

    We present the results of high spatial resolution HI synthesis observations of six blue compact dwarf (BCD) galaxies. Optically, the selected galaxies have smooth, symmetric isophotes, and thus are the most likely of the BCD class to fade into an object morphologically similar to a dwarf elliptical when the current starburst ends. The neutral gas in all six galaxies appears to be rotationally supported, however, indicating that true morphological transformation from a BCD to a dE will require significant loss of angular momentum. Based on the observed neutral gas dynamics of these and other BCDs, it is unlikely that present-day BCDs will evolve directly into dwarf ellipticals after a starburst phase. We discuss alternative evolutionary scenarios for BCDs and place them within the larger context of galaxy formation and evolution models.

  8. Transmission Expansion Planning – A Multiyear Dynamic Approach Using a Discrete Evolutionary Particle Swarm Optimization Algorithm

    Directory of Open Access Journals (Sweden)

    Saraiva J. T.

    2012-10-01

    Full Text Available The basic objective of Transmission Expansion Planning (TEP is to schedule a number of transmission projects along an extended planning horizon minimizing the network construction and operational costs while satisfying the requirement of delivering power safely and reliably to load centres along the horizon. This principle is quite simple, but the complexity of the problem and the impact on society transforms TEP on a challenging issue. This paper describes a new approach to solve the dynamic TEP problem, based on an improved discrete integer version of the Evolutionary Particle Swarm Optimization (EPSO meta-heuristic algorithm. The paper includes sections describing in detail the EPSO enhanced approach, the mathematical formulation of the TEP problem, including the objective function and the constraints, and a section devoted to the application of the developed approach to this problem. Finally, the use of the developed approach is illustrated using a case study based on the IEEE 24 bus 38 branch test system.

  9. Hybridization in the Ensatina Ring Species, Strong selection against hybrids at a hybrid zone in the ensatina ring species complex and its evolutionary implications

    Energy Technology Data Exchange (ETDEWEB)

    Alexandrino, Joao; Baird, Stuart J.E.; Lawson, Lucinda; Macey, J. Robert; Moritz, Craig; Wake, David B.

    2005-04-22

    The analysis of interactions between lineages at varying levels of genetic divergence can provide insights into the process of speciation through the accumulation of incompatible mutations. Ring species, and especially the Ensatina eschscholtzii system exemplify this approach. The plethodontid salamanders Ensatina eschscholtzii xanthoptica and Ensatina eschscholtzii platensis hybridize in the Central Sierran foothills of California. We compared the genetic structure across two transects (southern and northern Calaveras Co.), one of which was re-sampled over 20 years, and examined diagnostic molecular markers (eight allozyme loci and mitochondrial DNA) and a diagnostic quantitative trait (color pattern). Key results across all studies were: (i) cline centers for all markers were coincident and the zones were narrow, with width estimates of 730m to 2000m; (ii) cline centers at the northern Calaveras transect were coincident between 1981 and 2001, demonstrating repeatability over 5 generations; (iii) there are very few if any putative F1's, but a relatively high number of backcrossed individuals (57-86 percent) in the central portion of transects; (iv) we found substantial linkage disequilibrium in all three studies and strong heterozygote deficit both in northern Calaveras, in 2001, and southern Calaveras. Both linkage disequilibrium and heterozygote deficit show maximum values near the center of the zones (R and Fis, approx. equal to 0.5). Using estimates of cline width and dispersal, we infer strong selection against hybrids (s* approx. equal to 46-75 percent). This is sufficient to promote accumulation of differences at loci that are neutral or under divergent selection, but would still allow for introgression of adaptive alleles. The evidence for strong, but incomplete isolation across this centrally located contact is consistent with theory suggesting a gradual increase in postzygotic incompatibility between allopatric populations subject to divergent

  10. Dynamic Hybrid Simulation of the Lunar Wake During ARTEMIS Crossing

    Science.gov (United States)

    Wiehle, S.; Plaschke, F.; Angelopoulos, V.; Auster, H.; Glassmeier, K.; Kriegel, H.; Motschmann, U. M.; Mueller, J.

    2010-12-01

    The interaction of the highly dynamic solar wind with the Moon is simulated with the A.I.K.E.F. (Adaptive Ion Kinetic Electron Fluid) code for the ARTEMIS P1 flyby on February 13, 2010. The A.I.K.E.F. hybrid plasma simulation code is the improved version of the Braunschweig code. It is able to automatically increase simulation grid resolution in areas of interest during runtime, which greatly increases resolution as well as performance. As the Moon has no intrinsic magnetic field and no ionosphere, the solar wind particles are absorbed at its surface, resulting in the formation of the lunar wake at the nightside. The solar wind magnetic field is basically convected through the Moon and the wake is slowly filled up with solar wind particles. However, this interaction is strongly influenced by the highly dynamic solar wind during the flyby. This is considered by a dynamic variation of the upstream conditions in the simulation using OMNI solar wind measurement data. By this method, a very good agreement between simulation and observations is achieved. The simulations show that the stationary structure of the lunar wake constitutes a tableau vivant in space representing the well-known Friedrichs diagram for MHD waves.

  11. Computational fluid dynamics challenges for hybrid air vehicle applications

    Science.gov (United States)

    Carrin, M.; Biava, M.; Steijl, R.; Barakos, G. N.; Stewart, D.

    2017-06-01

    This paper begins by comparing turbulence models for the prediction of hybrid air vehicle (HAV) flows. A 6 : 1 prolate spheroid is employed for validation of the computational fluid dynamics (CFD) method. An analysis of turbulent quantities is presented and the Shear Stress Transport (SST) k-ω model is compared against a k-ω Explicit Algebraic Stress model (EASM) within the unsteady Reynolds-Averaged Navier-Stokes (RANS) framework. Further comparisons involve Scale Adaptative Simulation models and a local transition transport model. The results show that the flow around the vehicle at low pitch angles is sensitive to transition effects. At high pitch angles, the vortices generated on the suction side provide substantial lift augmentation and are better resolved by EASMs. The validated CFD method is employed for the flow around a shape similar to the Airlander aircraft of Hybrid Air Vehicles Ltd. The sensitivity of the transition location to the Reynolds number is demonstrated and the role of each vehicle£s component is analyzed. It was found that the ¦ns contributed the most to increase the lift and drag.

  12. Variability and evolutionary implications of repetitive DNA dynamics in genome of Astyanax scabripinnis (Teleostei, Characidae)

    Science.gov (United States)

    Barbosa, Patrícia; Leal, Eliza Viola; da Silva, Maelin; de Almeida, Mara Cristina; Moreira-Filho, Orlando; Artoni, Roberto Ferreira

    2017-01-01

    Abstract DNA sequences of multiple copies help in understanding evolutionary mechanisms, genomic structures and karyotype differentiation. The current study investigates the organization and distribution of different repetitive DNA in the standard complement and B chromosomes in Astyanax scabripinnis (Jenyns, 1842) chromosomes from three allopatric populations in Campos do Jordão region, São Paulo State, Brazil. The location of microsatellite sequences showed different chromosome distribution between Lavrinha Farm Stream (LFS) and Lake of Pedalinho (LP) populations. However, the karyotype of these populations basically followed the pattern of dispersed distribution in the A complement, conspicuous in telomeric/interstitial regions and preferential accumulation in the B chromosome. The B chromosome showed heterogeneous location of microsatellite probes CA, CAC and GA. The H3 and H4 histone genes were isolated from the total genome of the species and then the chromosomal mapping was performed by fluorescence in situ hybridization (FISH). The FISH signals showed high similarity for the probes H3 and H4 mapping in genomes of the populations analyzed. The sequences (GATA)n revealed a sex-specific trend between the chromosomal location in males and females at (LFS) and (LP) populations. Although species that comprise the Astyanax scabripinnis complex do not have morphologically differentiated sex chromosomes, the preferential GATA location – sex-associated – may represent a sex chromosome in differentiation. PMID:28919955

  13. A hybrid algorithm for parallel molecular dynamics simulations

    CERN Document Server

    Mangiardi, Chris M

    2016-01-01

    This article describes an algorithm for hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-ranged forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with AVX and AVX-2 processors as well as Xeon-Phi co-processors.

  14. SMA Hybrid Composites for Dynamic Response Abatement Applications

    Science.gov (United States)

    Turner, Travis L.

    2000-01-01

    A recently developed constitutive model and a finite element formulation for predicting the thermomechanical response of Shape Memory Alloy (SMA) hybrid composite (SMAHC) structures is briefly described. Attention is focused on constrained recovery behavior in this study, but the constitutive formulation is also capable of modeling restrained or free recovery. Numerical results are shown for glass/epoxy panel specimens with embedded Nitinol actuators subjected to thermal and acoustic loads. Control of thermal buckling, random response, sonic fatigue, and transmission loss are demonstrated and compared to conventional approaches including addition of conventional composite layers and a constrained layer damping treatment. Embedded SMA actuators are shown to be significantly more effective in dynamic response abatement applications than the conventional approaches and are attractive for combination with other passive and/or active approaches.

  15. A dynamical system analysis of hybrid metric-Palatini cosmologies

    CERN Document Server

    Carloni, Sante; Lobo, Francisco S N

    2015-01-01

    The so called $f(X)$ hybrid metric-Palatini gravity presents a unique viable generalisation of the $f(R)$ theories within the metric-affine formalism. Here the cosmology of the $f(X)$ theories is studied using the dynamical system approach. The method consists of formulating the propagation equation in terms of suitable (expansion-normalised) variables as an autonomous system. The fixed points of the system then represent exact cosmological solutions described by power-law or de Sitter expansion. The formalism is applied to two classes of $f(X)$ models, revealing both standard cosmological fixed points and new accelerating solutions that can be attractors in the phase space. In addition, the fixed point with vanishing expansion rate are considered with special care in order to characterise the stability of Einstein static spaces and bouncing solutions.

  16. Optimal Control Policies of Pests for Hybrid Dynamical Systems

    Directory of Open Access Journals (Sweden)

    Baolin Kang

    2013-01-01

    Full Text Available We improve the traditional integrated pest management (IPM control strategies and formulate three specific management strategies, which can be described by hybrid dynamical systems. These strategies can not only effectively control pests but also reduce the abuse of pesticides and protect the natural enemies. The aim of this work is to study how the factors, such as natural enemies optimum choice in the two kinds of different pests, timings of natural enemy releases, dosages and timings of insecticide applications, and instantaneous killing rates of pesticides on both pests and natural enemies, can affect the success of IPM control programmes. The results indicate that the pests outbreak period or frequency largely depends on the optimal selective feeding of the natural enemy between one of the pests and the control tactics. Ultimately, we obtain the only pest needs to be controlled below a certain threshold while not supervising pest .

  17. A hybrid algorithm for parallel molecular dynamics simulations

    Science.gov (United States)

    Mangiardi, Chris M.; Meyer, R.

    2017-10-01

    This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.

  18. Tangled nature model of evolutionary dynamics reconsidered: Structural and dynamical effects of trait inheritance

    Science.gov (United States)

    Andersen, Christian Walther; Sibani, Paolo

    2016-05-01

    Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K . We first show that the interactions generated by our rule are nearly independent of K . Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time tw also survives at t >tw . Finally, survival probabilities of species are shown to decay as powers of the ratio t /tw , a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.

  19. Multivariate dynamic linear models for estimating the effect of experimental interventions in an evolutionary operations setup in dairy herds

    DEFF Research Database (Denmark)

    Stygar, Anna Helena; Krogh, Mogens Agerbo; Kristensen, Troels

    2017-01-01

    . The objective of this study was to construct a tool to assess the intervention effect on milk production in an evolutionary operations setup. The method used for this purpose was a dynamic linear model (DLM) with Kalman filtering. The DLM consisted of parameters describing milk yield in a herd, individual cows...

  20. Approaches to understanding the impact of life-history features on plant-pathogen co-evolutionary dynamics

    Science.gov (United States)

    Jeremy J. Burdon; Peter H. Thrall; Adnane Nemri

    2012-01-01

    Natural plant-pathogen associations are complex interactions in which the interplay of environment, host, and pathogen factors results in spatially heterogeneous ecological and epidemiological dynamics. The evolutionary patterns that result from the interaction of these factors are still relatively poorly understood. Recently, integration of the appropriate spatial and...

  1. Exploring the cation dynamics in lead-bromide hybrid perovskites

    Science.gov (United States)

    Motta, Carlo; El-Mellouhi, Fedwa; Sanvito, Stefano

    2016-06-01

    Density functional theory including a many-body treatment of dispersive forces is used to describe the interplay between structure and electronic properties of two prototypical Br-based hybrid perovskites, namely, CH3NH3PbBr3 and HC (NH2)2PbBr3 . We find that, like for some of their iodine-based counterparts, the molecules' orientation plays a crucial role in determining the shape of both the conduction and valence bands around the band edges. This is mostly evident in the case of CH3NH3PbBr3 , which is a direct band-gap semiconductor when the CH3NH3 group is oriented along the (111) direction but turns indirect when the orientation is (100). We have constructed a simple dipole model, with parameters all evaluated from ab initio calculations, to describe the molecules' depolarization dynamics. We find that, once the molecules are initially orientated along a given high-symmetry direction, their room-temperature depolarization depends on the specific material investigated. In particular we find that the ratio between the polarization decay constant of CH3NH3PbBr3 and that of HC (NH2)2PbBr3 is about 2 at room temperature. With these results at hand we suggest a simple luminescence decay experiment to prove our findings and establish a correlation between optical activity and the molecules' dynamics in these materials.

  2. Ancestor of the new archetypal biology: Goethe's dynamic typology as a model for contemporary evolutionary developmental biology.

    Science.gov (United States)

    Riegner, Mark F

    2013-12-01

    As understood historically, typological thinking has no place in evolutionary biology since its conceptual framework is viewed as incompatible with population thinking. In this article, I propose that what I describe as dynamic typological thinking has been confused with, and has been overshadowed by, a static form of typological thinking. This conflation results from an inability to grasp dynamic typological thinking due to the overlooked requirement to engage our cognitive activity in an unfamiliar way. Thus, analytical thinking alone is unsuited to comprehend the nature of dynamic typological thinking. Over 200 years ago, J. W. von Goethe, in his Metamorphosis of Plants (1790) and other writings, introduced a dynamic form of typological thinking that has been traditionally misunderstood and misrepresented. I describe in detail Goethe's phenomenological methodology and its contemporary value in understanding morphological patterns in living organisms. Furthermore, contrary to the implications of static typological thinking, dynamic typological thinking is perfectly compatible with evolutionary dynamics and, if rightly understood, can contribute significantly to the still emerging field of evolutionary developmental biology (evo-devo).

  3. Distribution and evolutionary dynamics of Stowaway Miniature Inverted repeat Transposable Elements (MITEs) in grasses.

    Science.gov (United States)

    Minaya, Miguel; Pimentel, Manuel; Mason-Gamer, Roberta; Catalan, Pilar

    2013-07-01

    The occurrence of Stowaway MITEs and their potential footprints in the grasses was assessed within an explicit phylogenetic framework. An organismal tree was used to analyze the distribution and evolutionary dynamics of these elements and their potential excision footprints in the fourth intron of the β-amylase gene and in other introns of several nuclear genes across the Poaceae. Megablast and discontiguous megablast searches in the Entrez nucleotide database were performed for the β-amylase, blz-1, dmc1, nuc, and xly genes MITEs. These elements and their potential footprints were distributed in introns and intergenic spacers of many other nuclear genes throughout the BEP lineages; however, they were absent in the studied PACCMAD lineages. A plausible underlying dynamic of successive acquisitions and deletions of β-amylase Stowaway MITEs in the temperate grasses could be explained by three alternative hypotheses: (i) a single early acquisition of a palindrome element, similar to Tc1-Mariner, in the fourth intron of the β-amylase gene in the ancestor of the Pooideae, followed by multiple independent losses, (ii) multiple independent acquisitions of MITEs in non-related pooid lineages or (iii) different waves of acquisition of MITEs, followed by multiple losses and horizontal transfers in the temperate grasses. This last hypothesis seems to fit best with the evidence found to date.

  4. Evolutionary dynamics of populations with conflicting interactions: Classification and analytical treatment considering asymmetry and power

    Science.gov (United States)

    Helbing, Dirk; Johansson, Anders

    2010-01-01

    Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination or cooperation of interacting entities will occur, be it spins, particles, bacteria, animals, or humans. Here, we analyze the case, where the entities are heterogeneous, particularly the case of two populations with conflicting interactions and two possible states. For such systems, explicit mathematical formulas will be determined for the stationary solutions and the associated eigenvalues, which determine their stability. In this way, four different types of system dynamics can be classified and the various kinds of phase transitions between them will be discussed. While these results are interesting from a physics point of view, they are also relevant for social, economic, and biological systems, as they allow one to understand conditions for (1) the breakdown of cooperation, (2) the coexistence of different behaviors (“subcultures”), (3) the evolution of commonly shared behaviors (“norms”), and (4) the occurrence of polarization or conflict. We point out that norms have a similar function in social systems that forces have in physics.

  5. Decomposition-Based Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Social Networks

    Directory of Open Access Journals (Sweden)

    Jingjing Ma

    2014-01-01

    Full Text Available Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

  6. Decomposition-based multiobjective evolutionary algorithm for community detection in dynamic social networks.

    Science.gov (United States)

    Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng

    2014-01-01

    Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.

  7. Spatiotemporal dynamics of condensins I and II: evolutionary insights from the primitive red alga Cyanidioschyzon merolae

    Science.gov (United States)

    Fujiwara, Takayuki; Tanaka, Kan; Kuroiwa, Tsuneyoshi; Hirano, Tatsuya

    2013-01-01

    Condensins are multisubunit complexes that play central roles in chromosome organization and segregation in eukaryotes. Many eukaryotic species have two different condensin complexes (condensins I and II), although some species, such as fungi, have condensin I only. Here we use the red alga Cyanidioschyzon merolae as a model organism because it represents the smallest and simplest organism that is predicted to possess both condensins I and II. We demonstrate that, despite the great evolutionary distance, spatiotemporal dynamics of condensins in C. merolae is strikingly similar to that observed in mammalian cells: condensin II is nuclear throughout the cell cycle, whereas condensin I appears on chromosomes only after the nuclear envelope partially dissolves at prometaphase. Unlike in mammalian cells, however, condensin II is confined to centromeres in metaphase, whereas condensin I distributes more broadly along arms. We firmly establish a targeted gene disruption technique in this organism and find, to our surprise, that condensin II is not essential for mitosis under laboratory growth conditions, although it plays a crucial role in facilitating sister centromere resolution in the presence of a microtubule drug. The results provide fundamental insights into the evolution of condensin-based chromosome architecture and dynamics. PMID:23783031

  8. A Comprehensive Study of Cyanobacterial Morphological and Ecological Evolutionary Dynamics through Deep Geologic Time

    Science.gov (United States)

    Harmon, Luke J.; Blank, Carrine E.

    2016-01-01

    Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record—phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth’s history have shaped—and been shaped by—evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and “Snowball Earth” glaciations and is associated with decrease in the evolutionary rates around 1.8–1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes–particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic

  9. Evolutionary dynamics of interlinked public goods traits: an experimental study of siderophore production in Pseudomonas aeruginosa.

    Science.gov (United States)

    Ross-Gillespie, A; Dumas, Z; Kümmerli, R

    2015-01-01

    Public goods cooperation is common in microbes, and there is much interest in understanding how such traits evolve. Research in recent years has identified several important factors that shape the evolutionary dynamics of such systems, yet few studies have investigated scenarios involving interactions between multiple public goods. Here, we offer general predictions about the evolutionary trajectories of two public goods traits having positive, negative or neutral regulatory influence on one another's expression, and we report on a test of some of our predictions in the context of Pseudomonas aeruginosa's production of two interlinked iron-scavenging siderophores. First, we confirmed that both pyoverdine and pyochelin siderophores do operate as public goods under appropriate environmental conditions. We then tracked their production in lines experimentally evolved under different iron-limitation regimes known to favour different siderophore expression profiles. Under strong iron limitation, where pyoverdine represses pyochelin, we saw a decline in pyoverdine and a concomitant increase in pyochelin - consistent with expansion of pyoverdine-defective cheats derepressed for pyochelin. Under moderate iron limitation, pyochelin declined - again consistent with an expected cheat invasion scenario - but there was no concomitant shift in pyoverdine because cross-suppression between the traits is unidirectional only. Alternating exposure to strong and moderate iron limitation caused qualitatively similar though lesser shifts compared to the constant-environment regimes. Our results confirm that the regulatory interconnections between public goods traits can significantly modulate the course of evolution, yet also suggest how we can start to predict the impacts such complexities will have on phenotypic divergence and community stability.

  10. Evolutionary Dynamics of Small RNAs in 27 Escherichia coli and Shigella Genomes

    Science.gov (United States)

    Skippington, Elizabeth; Ragan, Mark A.

    2012-01-01

    Small RNAs (sRNAs) are widespread in bacteria and play critical roles in regulating physiological processes. They are best characterized in Escherichia coli K-12 MG1655, where 83 sRNAs constitute nearly 2% of the gene complement. Most sRNAs act by base pairing with a target mRNA, modulating its translation and/or stability; many of these RNAs share only limited complementarity to their mRNA target, and require the chaperone Hfq to facilitate base pairing. Little is known about the evolutionary dynamics of bacterial sRNAs. Here, we apply phylogenetic and network analyses to investigate the evolutionary processes and principles that govern sRNA gene distribution in 27 E. coli and Shigella genomes. We identify core (encoded in all 27 genomes) and variable sRNAs; more than two-thirds of the E. coli K-12 MG1655 sRNAs are core, whereas the others show patterns of presence and absence that are principally due to genetic loss, not duplication or lateral genetic transfer. We present evidence that variable sRNAs are less tightly integrated into cellular genetic regulatory networks than are the core sRNAs, and that Hfq facilitates posttranscriptional cross talk between the E. coli–Shigella core and variable genomes. Finally, we present evidence that more than 80% of genes targeted by Hfq-associated core sRNAs have been transferred within the E. coli–Shigella clade, and that most of these genes have been transferred intact. These results suggest that Hfq and sRNAs help integrate laterally acquired genes into established regulatory networks. PMID:22223756

  11. Dynamic Power Management for Portable Hybrid Power-Supply Systems Utilizing Approximate Dynamic Programming

    Directory of Open Access Journals (Sweden)

    Jooyoung Park

    2015-05-01

    Full Text Available Recently, the optimization of power flows in portable hybrid power-supply systems (HPSSs has become an important issue with the advent of a variety of mobile systems and hybrid energy technologies. In this paper, a control strategy is considered for dynamically managing power flows in portable HPSSs employing batteries and supercapacitors. Our dynamic power management strategy utilizes the concept of approximate dynamic programming (ADP. ADP methods are important tools in the fields of stochastic control and machine learning, and the utilization of these tools for practical engineering problems is now an active and promising research field. We propose an ADP-based procedure based on optimization under constraints including the iterated Bellman inequalities, which can be solved by convex optimization carried out offline, to find the optimal power management rules for portable HPSSs. The effectiveness of the proposed procedure is tested through dynamic simulations for smartphone workload scenarios, and simulation results show that the proposed strategy can successfully cope with uncertain workload demands.

  12. Origin and evolutionary dynamics of Hepatitis B virus (HBV) genotype E in Madagascar.

    Science.gov (United States)

    Lo Presti, Alessandra; Andriamandimby, Soa Fy; Lai, Alessia; Angeletti, Silvia; Cella, Eleonora; Mottini, Giovanni; Guarino, Michele Pier Luca; Balotta, Claudia; Galli, Massimo; Heraud, Jean-Michel; Zehender, Gianguglielmo; Ciccozzi, Massimo

    2017-02-01

    Africa is one of the endemic regions of HBV infection. In particular, genotype E is highly endemic in most of sub-Saharan Africa such as West African countries where it represents more than 90% of total infections. Madagascar, which is classified as a high endemic area for HBV and where the most prevalent genotype is E, might play a relevant role in the dispersion of this genotype due to its crucial position in the Indian Ocean. The aim of this study was to investigate the origin, population dynamics, and circulation of HBV-E genotype in Madagascar through high-resolution phylogenetic and phylodynamic approaches. The phylogenetic tree indicated that Malagasy isolates were intermixed and closely related with sequences mostly from West African countries. The Bayesian tree highlighted three statistically supported clusters of Malagasy strains which dated back to the years 1981 (95% HPD: 1971-1992), 1986 (95% HPD: 1974-1996), and 1989 (95% HPD: 1974-2001). Population dynamics analysis showed an exponential increase in the number of HBV-E infections approximately from the year 1975 until 2000s. The migration analysis was also performed and a dynamic pattern of gene flow was identified. In conclusion, this study confirms previous observation of HBV-E circulation in Africa and expands these findings at Madagascar demonstrating its recent introduction, and highlighting the role of the African countries in the spread of HBV-E genotype. Further studies on molecular epidemiology of HBV genotype E are needed to clarify the evolutionary history of this genotype.

  13. Phylogenomic analysis reveals dynamic evolutionary history of the Drosophila heterochromatin protein 1 (HP1 gene family.

    Directory of Open Access Journals (Sweden)

    Mia T Levine

    Full Text Available Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.

  14. Divergent evolutionary and epidemiological dynamics of cassava mosaic geminiviruses in Madagascar.

    Science.gov (United States)

    De Bruyn, Alexandre; Harimalala, Mireille; Zinga, Innocent; Mabvakure, Batsirai M; Hoareau, Murielle; Ravigné, Virginie; Walters, Matthew; Reynaud, Bernard; Varsani, Arvind; Harkins, Gordon W; Martin, Darren P; Lett, Jean-Michel; Lefeuvre, Pierre

    2016-09-06

    Cassava mosaic disease (CMD) in Madagascar is caused by a complex of at least six African cassava mosaic geminivirus (CMG) species. This provides a rare opportunity for a comparative study of the evolutionary and epidemiological dynamics of distinct pathogenic crop-infecting viral species that coexist within the same environment. The genetic and spatial structure of CMG populations in Madagascar was studied and Bayesian phylogeographic modelling was applied to infer the origins of Madagascan CMG populations within the epidemiological context of related populations situated on mainland Africa and other south western Indian Ocean (SWIO) islands. The isolation and analysis of 279 DNA-A and 117 DNA-B sequences revealed the presence in Madagascar of four prevalent CMG species (South African cassava mosaic virus, SACMV; African cassava mosaic virus, ACMV; East African cassava mosaic Kenya virus, EACMKV; and East African cassava mosaic Cameroon virus, EACMCV), and of numerous CMG recombinants that have, to date, only ever been detected on this island. SACMV and ACMV, the two most prevalent viruses, displayed low degrees of genetic diversity and have most likely been introduced to the island only once. By contrast, EACMV-like CMG populations (consisting of East African cassava mosaic virus, EAMCKV, EACMCV and complex recombinants of these) were more diverse, more spatially structured, and displayed evidence of at least three independent introductions from mainland Africa. Although there were no statistically supported virus movement events between Madagascar and the other SWIO islands, at least one mainland African ACMV variant likely originated in Madagascar. Our study highlights both the complexity of CMD in Madagascar, and the distinct evolutionary and spatial dynamics of the different viral species that collectively are associated with this disease. Given that more distinct CMG species and recombinants have been found in Madagascar than any other similarly sized region

  15. Dynamic Modeling and Simulation on a Hybrid Power System for Electric Vehicle Applications

    Directory of Open Access Journals (Sweden)

    Hong-Wen He

    2010-11-01

    Full Text Available Hybrid power systems, formed by combining high-energy-density batteries and high-power-density ultracapacitors in appropriate ways, provide high-performance and high-efficiency power systems for electric vehicle applications. This paper first establishes dynamic models for the ultracapacitor, the battery and a passive hybrid power system, and then based on the dynamic models a comparative simulation between a battery only power system and the proposed hybrid power system was done under the UDDS (Urban Dynamometer Driving Schedule. The simulation results showed that the hybrid power system could greatly optimize and improve the efficiency of the batteries and their dynamic current was also decreased due to the participation of the ultracapacitors, which would have a good influence on batteries’ cycle life. Finally, the parameter matching for the passive hybrid power system was studied by simulation and comparisons.

  16. Biomass and nitrogen dynamics in an irrigated hybrid poplar plantation

    Energy Technology Data Exchange (ETDEWEB)

    McLaughlin, R.A.

    1985-01-01

    A 3-year study measured the effects of ground cover treatments and nitrogen fertilization on biomass and nitrogen dynamics in an irrigated hybrid poplar (Populus deltoides Bartr. x P. trichocarpa Torr. and Gray, clone NC-9922) plantation in northern Wisconsin. Annually fertilized (112 kg N/ha/yr) and unfertilized plots were either maintained weed-free (bare soil), allowed to revegetate with native weeds, or seeded to birdsfoot trefoil (Lotus corniculatus L.). Trees in bare soil plots responded to fertilization primarily in the third growing season, but total biomass of 3-year-old trees was not increased by annual fertilization. High nitrate-nitrogen concentrations in the soil solution suggested significant leaching in both unfertilized and fertilized bare soil plots in the first growing season, and in fertilized plots the second season. Nitrate-nitrogen concentrations declined sharply in fertilized bare soil plots during the third growing season. Cover crop biomass was greatest in the second year and declined thereafter due to declines in below-ground components. Fertilization increased tree growth in these plots, but cover crop treatments had no effect. Results of this study suggest that, under irrigated conditions, a cover crop can substantially reduce leaching losses of nutrients and serve as a slow-release pool of nitrogen after the trees achieve crown closure. Fertilization is not recommended in these plantations until the second growing season if a cover crop is present and the third growing season if complete weed control is practiced.

  17. Design of Hybrid Dynamic Balancer and Vibration Absorber

    Directory of Open Access Journals (Sweden)

    Y. R. Wang

    2014-01-01

    Full Text Available This study proposed a novel hybrid dynamic balancer and vibration absorber that is cheaper than active dampers and more effective than passive dampers. The proposed damping system does not need to be altered structurally to deal with different damping targets. Rather, the proposed vibration absorber is capable of self-adjustment to the optimal damping location in order to achieve balance and, thereby, optimize damping effects. The proposed device includes a groove under the damping target with inertial mass hung from a coil spring beneath. This allows the device to bounce vertically or rotate in order to reduce vibrations in the main body. The coil spring vibration absorber can also slide along the groove in order to adjust its location continuously until the vibrations in the system are minimized and the main body is balanced. Experiments verify the efficacy of the proposed device in improving damping performance beyond what has been achieved using conventional devices. We also provide an explanation of the theoretical underpinnings of the design as well as the implications of these findings with regard to future developments.

  18. Dynamics of asymmetrical hybridization in North American wood ferns: reconciling patterns of inheritance with gametophyte reproductive biology.

    Science.gov (United States)

    Testo, Weston L; Watkins, James E; Barrington, David S

    2015-04-01

    Hybridization is an important evolutionary force in plants, but the mechanisms underlying it have not been well studied for many groups. In particular, the drivers of non-random patterns of interspecific gene flow (asymmetrical hybridization) remain poorly understood, especially in the seed-free vascular plants. Here, we examine patterns of asymmetrical hybridization in two widespread fern hybrids from eastern North America and study the role of gametophyte ecology in the determination of hybridization bias. We characterized the maternal parentage of > 140 hybrid sporophytes by sequencing a c. 350-bp region of chloroplast DNA (cpDNA). To identify factors contributing to patterns of asymmetrical hybridization, we cultured gametophytes of the parental species and evaluated critical aspects of their reproductive biology. We found that asymmetrical hybridization was prevalent across the populations of both hybrids. Reproductive traits varied across species and suggest that selfing potential, antheridiogen responsiveness, sperm dispersal capacity and gamete size all contribute to the mediation of the direction of hybridization in this group. Our findings suggest that asymmetrical hybridization in ferns is driven by an array of reproductive traits. This study helps to sharpen and define a mechanistic understanding of patterns of hybridization in this group and demonstrates the importance of considering gametophyte biology when studying evolutionary processes in ferns.

  19. A Methodological Framework Based on the Dynamic-Evolutionary View of Heritage

    Directory of Open Access Journals (Sweden)

    Iva Mrak

    2013-09-01

    Full Text Available The paper describes the shifting perspective from the contemplative view to the dynamic-evolutionary view of heritage and the main characteristics of the resulting multi-criterial decision-aid tool for the evaluation of heritage. With the integration of conservation in planning processes and with opening of the procedures to public participation, there is a need for decision-aid tools that can help increase rationality and transparency in decision-making processes related to planning. By understanding the contemporary view of heritage and the landscape, it is possible to create tools capable of accounting for spatial complexity and the extant cultural, social, historic and economic relations. With this in mind, a specific tool was created that can be used for the analysis, diagnosis, evaluation and monitoring of spatial heritage (registered and under consideration for protection, identifying opportunities, defining strategies for heritage management processes, and in the creation and evaluation of development and management scenarios. The paper illustrates a shift in the consideration of heritage in spatial planning and presents an application of the developed model in a case study.

  20. Accurate discrimination of conserved coding and non-coding regions through multiple indicators of evolutionary dynamics

    Directory of Open Access Journals (Sweden)

    Pesole Graziano

    2009-09-01

    Full Text Available Abstract Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding. Results Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score. Conclusion We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.

  1. The effect of network structure on innovation initiation process: an evolutionary dynamics approach

    CERN Document Server

    Jafari, Afshin; Zolfagharzadeh, Mohammad Mahdi; Mohammadi, Mehdi

    2016-01-01

    In this paper we have proposed a basic agent-based model based on evolutionary dynamics for investigating innovation initiation process. In our model we suppose each agent will represent a firm which is interacting with other firms through a given network structure. We consider a two-hit process for presenting a potentially successful innovation in this model and therefore at each time step each firm can be in on of three different stages which are respectively, Ordinary, Innovative, and Successful. We design different experiments in order to investigate how different interaction networks may affect the process of presenting a successful innovation to the market. In this experiments, we use five different network structures, i.e. Erd\\H{o}s and R\\'enyi, Ring Lattice, Small World, Scale-Free and Distance-Based networks. According to the results of the simulations, for less frequent innovations like radical innovation, local structures are showing a better performance comparing to Scale-Free and Erd\\H{o}s and R\\...

  2. Evolutionary dynamics of clustered irregularly interspaced short palindromic repeat systems in the ocean metagenome.

    Science.gov (United States)

    Sorokin, Valery A; Gelfand, Mikhail S; Artamonova, Irena I

    2010-04-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, CRISPR-forming events and reconstructed the likely evolutionary history of cassettes that had common spacers. Metagenomic collections allow for relatively unbiased analysis of phage-host interactions and CRISPR evolution. The results of this study demonstrate that CRISPR cassettes retain the memory of the local virus population at a particular ocean location. CRISPR evolution may be described using a limited vocabulary of elementary events that have a natural biological interpretation.

  3. Evolutionary dynamics at high latitudes: speciation and extinction in polar marine faunas.

    Science.gov (United States)

    Clarke, Andrew; Crame, J Alistair

    2010-11-27

    Ecologists have long been fascinated by the flora and fauna of extreme environments. Physiological studies have revealed the extent to which lifestyle is constrained by low temperature but there is as yet no consensus on why the diversity of polar assemblages is so much lower than many tropical assemblages. The evolution of marine faunas at high latitudes has been influenced strongly by oceanic cooling during the Cenozoic and the associated onset of continental glaciations. Glaciation eradicated many shallow-water habitats, especially in the Southern Hemisphere, and the cooling has led to widespread extinction in some groups. While environmental conditions at glacial maxima would have been very different from those existing today, fossil evidence indicates that some lineages extend back well into the Cenozoic. Oscillations of the ice-sheet on Milankovitch frequencies will have periodically eradicated and exposed continental shelf habitat, and a full understanding of evolutionary dynamics at high latitude requires better knowledge of the links between the faunas of the shelf, slope and deep-sea. Molecular techniques to produce phylogenies, coupled with further palaeontological work to root these phylogenies in time, will be essential to further progress.

  4. A structured modeling approach for dynamic hybrid fuzzy-first principles models

    NARCIS (Netherlands)

    Lith, van Pascal F.; Betlem, Ben H.L.; Roffel, Brian

    2002-01-01

    Hybrid fuzzy-first principles models can be attractive if a complete physical model is difficult to derive. These hybrid models consist of a framework of dynamic mass and energy balances, supplemented with fuzzy submodels describing additional equations, such as mass transformation and transfer rate

  5. Fast electron dynamics in lower hybrid current drive experiment on HT-7 tokamak

    Institute of Scientific and Technical Information of China (English)

    Shi Yue-Jiang; Kuang Gang-Li; Li Jian-Gang; HT-7 Team; Wan Bao-Nian; Chen Zhong-Yong; Hu Li-Qun; Lin Shi-Yao; Ruan Huai-Lin; Qian Jin-Ping; Zhen Xiang-Jun; Ding Bo-Jiang

    2005-01-01

    The dynamic behaviour of fast electron in lower hybrid current drive (LHCD) experiments is a crucial issue in the sense of enhancing plasma performance. A new hard x-ray diagnostic system on HT-7 allows the investigation of the lower hybrid wave dynamics. The behaviour of fast electron is studied in several kinds of LHCD experiments, including long pulse discharges, high performance discharges and counter-LHCD experiments.

  6. Hybridization in East African swarm-raiding army ants

    DEFF Research Database (Denmark)

    Kronauer, Daniel Jc; Peters, Marcell K; Schöning, Caspar

    2011-01-01

    Hybridization can have complex effects on evolutionary dynamics in ants because of the combination of haplodiploid sex-determination and eusociality. While hybrid non-reproductive workers have been found in a range of species, examples of gene-flow via hybrid queens and males are rare. We studied...... hybridization in East African army ants (Dorylus subgenus Anomma) using morphology, mitochondrial DNA sequences, and nuclear microsatellites....

  7. Fitness, environmental changes and the growth of modularity- a quasispecies theory for the evolutionary dynamics of modularity

    Science.gov (United States)

    Niestemski, Liang; Park, Jeong-Man; Deem, Michael

    2015-03-01

    Although the modularity of a biological system is demonstrated and recognized, the evolution of the modularity is not well understood. We here present a quasispecies theory for the evolutionary dynamics of modularity. Complemented with numerical models, this analytical theory shows the calculation of the steady-state fitness in a randomly changing environment, the relationship between rate of environmental changes and rate of growth of modularity, as well as a principle of least action for the evolved modularity at steady state.

  8. Inductive reasoning and forecasting of population dynamics of Cylindrospermopsis raciborskii in three sub-tropical reservoirs by evolutionary computation.

    Science.gov (United States)

    Recknagel, Friedrich; Orr, Philip T; Cao, Hongqing

    2014-01-01

    Seven-day-ahead forecasting models of Cylindrospermopsis raciborskii in three warm-monomictic and mesotrophic reservoirs in south-east Queensland have been developed by means of water quality data from 1999 to 2010 and the hybrid evolutionary algorithm HEA. Resulting models using all measured variables as inputs as well as models using electronically measurable variables only as inputs forecasted accurately timing of overgrowth of C. raciborskii and matched well high and low magnitudes of observed bloom events with 0.45≤r(2)>0.61 and 0.4≤r(2)>0.57, respectively. The models also revealed relationships and thresholds triggering bloom events that provide valuable information on synergism between water quality conditions and population dynamics of C. raciborskii. Best performing models based on using all measured variables as inputs indicated electrical conductivity (EC) within the range of 206-280mSm(-1) as threshold above which fast growth and high abundances of C. raciborskii have been observed for the three lakes. Best models based on electronically measurable variables for the Lakes Wivenhoe and Somerset indicated a water temperature (WT) range of 25.5-32.7°C within which fast growth and high abundances of C. raciborskii can be expected. By contrast the model for Lake Samsonvale highlighted a turbidity (TURB) level of 4.8 NTU as indicator for mass developments of C. raciborskii. Experiments with online measured water quality data of the Lake Wivenhoe from 2007 to 2010 resulted in predictive models with 0.61≤r(2)>0.65 whereby again similar levels of EC and WT have been discovered as thresholds for outgrowth of C. raciborskii. The highest validity of r(2)=0.75 for an in situ data-based model has been achieved after considering time lags for EC by 7 days and dissolved oxygen by 1 day. These time lags have been discovered by a systematic screening of all possible combinations of time lags between 0 and 10 days for all electronically measurable variables. The so

  9. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

    Science.gov (United States)

    Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe

    2014-04-01

    Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially

  10. The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.

    Directory of Open Access Journals (Sweden)

    Bram Vrancken

    2014-04-01

    Full Text Available Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1 evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected

  11. Genetic structure in a dynamic baboon hybrid zone corroborates behavioural observations in a hybrid population

    NARCIS (Netherlands)

    Charpentier, M J E; Fontaine, M C; Cherel, E; Renoult, J P; Jenkins, T; Benoit, L; Barthès, N; Alberts, S C; Tung, J

    2012-01-01

    Behaviour and genetic structure are intimately related: mating patterns and patterns of movement between groups or populations influence the movement of genetic variation across the landscape and from one generation to the next. In hybrid zones, the behaviour of the hybridizing taxa can also impact

  12. Dynamic simulation and optimal control strategy for a parallel hybrid hydraulic excavator

    Institute of Scientific and Technical Information of China (English)

    Xiao LIN; Shuang-xia PAN; Dong-yun WANG

    2008-01-01

    The primary focus of this study is to investigate the control strategies of a hybrid system used in hydraulic excavators. First, the structure and evaluation target of hybrid hydraulic excavators are analyzed. Then the dynamic system model including batteries, motor and engine is built as the simulation environment to obtain control results. A so-called multi-work-point dynamic control strategy, which has both closed-loop speed PI (proportion integral) control and direct torque control, is proposed and studied in the simulation model. Simulation results indicate that the hybrid system with this strategy can meet the power demand and achieve better system stability and higher fuel efficiency.

  13. Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics

    Science.gov (United States)

    Ahsan, Syed Amir

    The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical

  14. Molecular characterization, genomic distribution and evolutionary dynamics of Short INterspersed Elements in the termite genome.

    Science.gov (United States)

    Luchetti, Andrea; Mantovani, Barbara

    2011-02-01

    Short INterspersed Elements (SINEs) in invertebrates, and especially in animal inbred genomes such that of termites, are poorly known; in this paper we characterize three new SINE families (Talub, Taluc and Talud) through the analyses of 341 sequences, either isolated from the Reticulitermes lucifugus genome or drawn from EST Genbank collection. We further add new data to the only isopteran element known so far, Talua. These SINEs are tRNA-derived elements, with an average length ranging from 258 to 372 bp. The tails are made up by poly(A) or microsatellite motifs. Their copy number varies from 7.9 × 10(3) to 10(5) copies, well within the range observed for other metazoan genomes. Species distribution, age and target site duplication analysis indicate Talud as the oldest, possibly inactive SINE originated before the onset of Isoptera (~150 Myr ago). Taluc underwent to substantial sequence changes throughout the evolution of termites and data suggest it was silenced and then re-activated in the R. lucifugus lineage. Moreover, Taluc shares a conserved sequence block with other unrelated SINEs, as observed for some vertebrate and cephalopod elements. The study of genomic environment showed that insertions are mainly surrounded by microsatellites and other SINEs, indicating a biased accumulation within non-coding regions. The evolutionary dynamics of Talu~ elements is explained through selective mechanisms acting in an inbred genome; in this respect, the study of termites' SINEs activity may provide an interesting framework to address the (co)evolution of mobile elements and the host genome.

  15. Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Jose Manuel C Tubio

    Full Text Available Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.

  16. Evolutionary Dynamics of the Cellulose Synthase Gene Superfamily in Grasses1[OPEN

    Science.gov (United States)

    Schwerdt, Julian G.; Wright, Frank; Oehme, Daniel; Wagner, John M.; Shirley, Neil J.; Burton, Rachel A.; Schreiber, Miriam; Zimmer, Jochen; Marshall, David F.; Waugh, Robbie; Fincher, Geoffrey B.

    2015-01-01

    Phylogenetic analyses of cellulose synthase (CesA) and cellulose synthase-like (Csl) families from the cellulose synthase gene superfamily were used to reconstruct their evolutionary origins and selection histories. Counterintuitively, genes encoding primary cell wall CesAs have undergone extensive expansion and diversification following an ancestral duplication from a secondary cell wall-associated CesA. Selection pressure across entire CesA and Csl clades appears to be low, but this conceals considerable variation within individual clades. Genes in the CslF clade are of particular interest because some mediate the synthesis of (1,3;1,4)-β-glucan, a polysaccharide characteristic of the evolutionarily successful grasses that is not widely distributed elsewhere in the plant kingdom. The phylogeny suggests that duplication of either CslF6 and/or CslF7 produced the ancestor of a highly conserved cluster of CslF genes that remain located in syntenic regions of all the grass genomes examined. A CslF6-specific insert encoding approximately 55 amino acid residues has subsequently been incorporated into the gene, or possibly lost from other CslFs, and the CslF7 clade has undergone a significant long-term shift in selection pressure. Homology modeling and molecular dynamics of the CslF6 protein were used to define the three-dimensional dispositions of individual amino acids that are subject to strong ongoing selection, together with the position of the conserved 55-amino acid insert that is known to influence the amounts and fine structures of (1,3;1,4)-β-glucans synthesized. These wall polysaccharides are attracting renewed interest because of their central roles as sources of dietary fiber in human health and for the generation of renewable liquid biofuels. PMID:25999407

  17. Geography and host species shape the evolutionary dynamics of U genogroup infectious hematopoietic necrosis virus

    Science.gov (United States)

    Black, Allison; Breyta, Rachel; Bedford, Trevor; Kurath, Gael

    2016-01-01

    Infectious hematopoietic necrosis virus (IHNV) is a negative-sense RNA virus that infects wild and cultured salmonids throughout the Pacific Coastal United States and Canada, from California to Alaska. Although infection of adult fish is usually asymptomatic, juvenile infections can result in high mortality events that impact salmon hatchery programs and commercial aquaculture. We used epidemiological case data and genetic sequence data from a 303 nt portion of the viral glycoprotein gene to study the evolutionary dynamics of U genogroup IHNV in the Pacific Northwestern United States from 1971 to 2013. We identified 114 unique genotypes among 1,219 U genogroup IHNV isolates representing 619 virus detection events. We found evidence for two previously unidentified, broad subgroups within the U genogroup, which we designated ‘UC’ and ‘UP’. Epidemiologic records indicated that UP viruses were detected more frequently in sockeye salmon (Oncorhynchus nerka) and in coastal waters of Washington and Oregon, whereas UC viruses were detected primarily in Chinook salmon (Oncorhynchus tshawytscha) and steelhead trout (Oncorhynchus mykiss) in the Columbia River Basin, which is a large, complex watershed extending throughout much of interior Washington, Oregon, and Idaho. These findings were supported by phylogenetic analysis and by FST. Ancestral state reconstruction indicated that early UC viruses in the Columbia River Basin initially infected sockeye salmon but then emerged via host shifts into Chinook salmon and steelhead trout sometime during the 1980s. We postulate that the development of these subgroups within U genogroup was driven by selection pressure for viral adaptation to Chinook salmon and steelhead trout within the Columbia River Basin.

  18. Reconstruction of the Evolutionary History of Saccharomyces cerevisiae x S. kudriavzevii Hybrids Based on Multilocus Sequence Analysis

    Science.gov (United States)

    Peris, David; Lopes, Christian A.; Arias, Armando; Barrio, Eladio

    2012-01-01

    In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages. PMID:23049811

  19. Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.

    Science.gov (United States)

    Peris, David; Lopes, Christian A; Arias, Armando; Barrio, Eladio

    2012-01-01

    In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages.

  20. Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis.

    Directory of Open Access Journals (Sweden)

    David Peris

    Full Text Available In recent years, interspecific hybridization and introgression are increasingly recognized as significant events in the evolution of Saccharomyces yeasts. These mechanisms have probably been involved in the origin of novel yeast genotypes and phenotypes, which in due course were to colonize and predominate in the new fermentative environments created by human manipulation. The particular conditions in which hybrids arose are still unknown, as well as the number of possible hybridization events that generated the whole set of natural hybrids described in the literature during recent years. In this study, we could infer at least six different hybridization events that originated a set of 26 S. cerevisiae x S. kudriavzevii hybrids isolated from both fermentative and non-fermentative environments. Different wine S. cerevisiae strains and European S. kudriavzevii strains were probably involved in the hybridization events according to gene sequence information, as well as from previous data on their genome composition and ploidy. Finally, we postulate that these hybrids may have originated after the introduction of vine growing and winemaking practices by the Romans to the present Northern vine-growing limits and spread during the expansion of improved viticulture and enology practices that occurred during the Late Middle Ages.

  1. Dynamic Modeling and Simulation of a Switched Reluctance Motor in a Series Hybrid Electric Vehicle

    Directory of Open Access Journals (Sweden)

    Siavash Sadeghi

    2010-04-01

    Full Text Available Dynamic behavior analysis of electric motors is required in order to accuratelyevaluate the performance, energy consumption and pollution level of hybrid electricvehicles. Simulation tools for hybrid electric vehicles are divided into steady state anddynamic models. Tools with steady-state models are useful for system-level analysiswhereas tools that utilize dynamic models give in-depth information about the behavior ofsublevel components. For the accurate prediction of hybrid electric vehicle performance,dynamic modeling of the motor and other components is necessary. Whereas the switchedreluctance machine is well suited for electric and hybrid electric vehicles, due to the simpleand rugged construction, low cost, and ability to operate over a wide speed range atconstant power, in this paper dynamic performance of the switched reluctance motor for eseries hybrid electric vehicles is investigated. For this purpose a switched reluctance motorwith its electrical drive is modeld and simulated first, and then the other components of aseries hybrid electric vehicle, such as battery, generator, internal combusion engine, andgearbox, are designed and linked with the electric motor. Finally a typical series hybridelectric vehicle is simulated for different drive cycles. The extensive simulation results showthe dynamic performance of SRM, battery, fuel consumption, and emissions.

  2. Modeling and Analysis of Hybrid Dynamic Systems Using Hybrid Petri Nets

    OpenAIRE

    GHOMRI Latefa; Alla, Hassane

    2008-01-01

    Some extensions of PNs permitting HDS modeling were presented here. The first models to be presented are continuous PNs. This model may be used for modeling either a continuous system or a discrete system. In this case, it is an approximation that is often satisfactory. Hybrid PNs combine in the same formalism a discrete PN and a continuous PN. Two hybrid PN models were considered in this chapter. The first, called the hybrid PN, has a deterministic behavior; this means that we can predict th...

  3. Evolutionary games and population dynamics: maintenance of cooperation in public goods games

    OpenAIRE

    Hauert, Christoph; Holmes, Miranda; Doebeli, Michael

    2006-01-01

    The emergence and abundance of cooperation in nature poses a tenacious and challenging puzzle to evolutionary biology. Cooperative behaviour seems to contradict Darwinian evolution because altruistic individuals increase the fitness of other members of the population at a cost to themselves. Thus, in the absence of supporting mechanisms, cooperation should decrease and vanish, as predicted by classical models for cooperation in evolutionary game theory, such as the Prisoner's Dilemma and publ...

  4. Development and Evaluation of a Hybrid Dynamical-Statistical Downscaling Method

    Science.gov (United States)

    Walton, Daniel Burton

    Regional climate change studies usually rely on downscaling of global climate model (GCM) output in order to resolve important fine-scale features and processes that govern local climate. Previous efforts have used one of two techniques: (1) dynamical downscaling, in which a regional climate model is forced at the boundaries by GCM output, or (2) statistical downscaling, which employs historical empirical relationships to go from coarse to fine resolution. Studies using these methods have been criticized because they either dynamical downscaled only a few GCMs, or used statistical downscaling on an ensemble of GCMs, but missed important dynamical effects in the climate change signal. This study describes the development and evaluation of a hybrid dynamical-statstical downscaling method that utilizes aspects of both dynamical and statistical downscaling to address these concerns. The first step of the hybrid method is to use dynamical downscaling to understand the most important physical processes that contribute to the climate change signal in the region of interest. Then a statistical model is built based on the patterns and relationships identified from dynamical downscaling. This statistical model can be used to downscale an entire ensemble of GCMs quickly and efficiently. The hybrid method is first applied to a domain covering Los Angeles Region to generate projections of temperature change between the 2041-2060 and 1981-2000 periods for 32 CMIP5 GCMs. The hybrid method is also applied to a larger region covering all of California and the adjacent ocean. The hybrid method works well in both areas, primarily because a single feature, the land-sea contrast in the warming, controls the overwhelming majority of the spatial detail. Finally, the dynamically downscaled temperature change patterns are compared to those produced by two commonly-used statistical methods, BCSD and BCCA. Results show that dynamical downscaling recovers important spatial features that the

  5. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014

    Science.gov (United States)

    Pang, Yong Kek; Chan, Kok Gan; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012–2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors—total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012–2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013–2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion

  6. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.

    Directory of Open Access Journals (Sweden)

    Xiang Yong Oong

    Full Text Available Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1% patients infected with at least one respiratory virus, 287 (14.3% and 183 (9.1% samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10. Phylogenetic reconstruction of haemagglutinin (HA gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%, Yamagata Clade 2 (48, 28.6% and Victoria Clade 1 (55, 32.7%. With neuraminidase (NA phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1 and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013, and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014. Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013, with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and

  7. Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.

    Science.gov (United States)

    Oong, Xiang Yong; Ng, Kim Tien; Lam, Tommy Tsan-Yuk; Pang, Yong Kek; Chan, Kok Gan; Hanafi, Nik Sherina; Kamarulzaman, Adeeba; Tee, Kok Keng

    2015-01-01

    Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respiratory virus, 287 (14.3%) and 183 (9.1%) samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10). Phylogenetic reconstruction of haemagglutinin (HA) gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%), Yamagata Clade 2 (48, 28.6%) and Victoria Clade 1 (55, 32.7%). With neuraminidase (NA) phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1) and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA) reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013), and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014). Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013), with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and sore

  8. Evolutionary macroecology

    Directory of Open Access Journals (Sweden)

    José Alexandre F. Diniz-Filho

    2013-10-01

    Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.

  9. A Dynamic Feature-Based Method for Hybrid Blurred/Multiple Object Detection in Manufacturing Processes

    Directory of Open Access Journals (Sweden)

    Tsun-Kuo Lin

    2016-01-01

    Full Text Available Vision-based inspection has been applied for quality control and product sorting in manufacturing processes. Blurred or multiple objects are common causes of poor performance in conventional vision-based inspection systems. Detecting hybrid blurred/multiple objects has long been a challenge in manufacturing. For example, single-feature-based algorithms might fail to exactly extract features when concurrently detecting hybrid blurred/multiple objects. Therefore, to resolve this problem, this study proposes a novel vision-based inspection algorithm that entails selecting a dynamic feature-based method on the basis of a multiclassifier of support vector machines (SVMs for inspecting hybrid blurred/multiple object images. The proposed algorithm dynamically selects suitable inspection schemes for classifying the hybrid images. The inspection schemes include discrete wavelet transform, spherical wavelet transform, moment invariants, and edge-feature-descriptor-based classification methods. The classification methods for single and multiple objects are adaptive region growing- (ARG- based and local adaptive region growing- (LARG- based learning approaches, respectively. The experimental results demonstrate that the proposed algorithm can dynamically select suitable inspection schemes by applying a selection algorithm, which uses SVMs for classifying hybrid blurred/multiple object samples. Moreover, the method applies suitable feature-based schemes on the basis of the classification results for employing the ARG/LARG-based method to inspect the hybrid objects. The method improves conventional methods for inspecting hybrid blurred/multiple objects and achieves high recognition rates for that in manufacturing processes.

  10. Hybrid molecular dynamics simulation for plasma induced damage analysis

    Science.gov (United States)

    Matsukuma, Masaaki

    2016-09-01

    In order to enable further device size reduction (also known as Moore's law) and improved power performance, the semiconductor industry is introducing new materials and device structures into the semiconductor fabrication process. Materials now include III-V compounds, germanium, cobalt, ruthenium, hafnium, and others. The device structure in both memory and logic has been evolving from planar to three dimensional (3D). One such device is the FinFET, where the transistor gate is a vertical fin made either of silicon, silicon-germanium or germanium. These changes have brought renewed interests in the structural damages caused by energetic ion bombardment of the fin sidewalls which are exposed to the ion flux from the plasma during the fin-strip off step. Better control of the physical damage of the 3D devices requires a better understanding of the damage formation mechanisms on such new materials and structures. In this study, the damage formation processes by ion bombardment have been simulated for Si and Ge substrate by Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid simulations and compared to the results from the classical molecular dynamics (MD) simulations. In our QM/MM simulations, the highly reactive region in which the structural damage is created is simulated with the Density Functional based Tight Binding (DFTB) method and the region remote from the primary region is simulated using classical MD with the Stillinger-Weber and Moliere potentials. The learn on the fly method is also used to reduce the computational load. Hence our QM/MM simulation is much faster than the full QC-MD simulations and the original QM/MM simulations. The amorphous layers profile simulated with QM/MM have obvious differences in their thickness for silicon and germanium substrate. The profile of damaged structure in the germanium substrate is characterized by a deeper tail then in silicon. These traits are also observed in the results from the mass selected ion beam

  11. ELECTRICAL AND DYNAMIC BRAKING OF THE HYBRID VEHICLE ON THE ROADS WITH LOW COUPLING COEFFICIENT

    Directory of Open Access Journals (Sweden)

    Sitovskyi, O.

    2013-06-01

    Full Text Available There were carried out theoretical researches of the processes of the electrical and dynamic braking of the vehicle with hybrid power-plant on the roads with low coupling coefficient, it was proved the probability of the wheels blocking appearing, during electrical and dynamic braking.

  12. Modelling and Simulation of System Dynamics of Hybrid-Driven Precision Press

    Institute of Scientific and Technical Information of China (English)

    LI Yonggang; ZHANG Ce; MENG Caifang; SONG Yimin

    2005-01-01

    Different from conventional mechanical systems with single degree of freedom (DOF), the main idea of the system of hybrid-driven precision press is to combine the motion of a constant speed motor with a servomotor via a two-DOF mechanism to provide flexible output. In order to make the feasibility clear, this paper studies theoretically the dynamic characteristics of this hybrid-driven mechanical system.Firstly,the dynamics model of the whole electromechanical system is set up by combining dynamic equations of DC motors with those of two-DOF nine-bar mechanism deduced by the Lagrange′s formula. Secondly through the numerical solution with the fourth Runge-Kutta, computer simulation about the dynamics is done, which shows that the designed and optimized hybrid-driven precision press is feasible in theory. These provide theoretical basis for later experimental research.

  13. Evolutionary dynamics of triosephosphate isomerase gene intron location pattern in Metazoa: A new perspective on intron evolution in animals.

    Science.gov (United States)

    Chen, Bing; Shao, Jingru; Zhuang, Huifu; Wen, Jianfan

    2017-02-20

    Intron evolution, including its dynamics in the evolutionary transitions and diversification of eukaryotes, remains elusive. Inadequate taxon sampling due to data shortage, unclear phylogenetic framework, and inappropriate outgroup application might be among the causes. Besides, the integrity of all the introns within a gene was often neglected previously. Taking advantage of the ancient conserved triosephosphate isomerase gene (tim), the relatively robust phylogeny of Metazoa, and choanoflagellates as outgroup, the evolutionary dynamics of tim intron location pattern (ILP) in Metazoa was investigated. From 133 representative species of ten phyla, 30 types of ILPs were identified. A most common one, which harbors the maximum six intron positions, is deduced to be the common ancestral tim ILP of Metazoa, which almost had formed in their protozoan ancestor and was surprisingly retained and passed down till to each ancestors of metazoan phyla. In the subsequent animal diversification, it underwent different evolutionary trajectories: within Deuterostomia, it was almost completely retained only with changes in a few species with relatively recently fast-evolving histories, while within the rapidly radiating Protostomia, besides few but remarkable retention, it usually displayed extensive intron losses and a few gains. Therefore, a common ancestral exon-intron arrangement pattern of an animal gene is definitely discovered; besides the 'intron-rich view' of early animal genes being confirmed, the novel insight that high exon-intron re-arrangements of genes seem to be associated with the relatively recently rapid evolution of lineages/species/genomes but have no correlation with the ancient major evolutionary transitions in animal evolution, is revealed. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Static and Dynamic Analyses of Long-Span Spatial Steel-Cable-Membrane Hybrid Structures

    Institute of Scientific and Technical Information of China (English)

    丁阳; 彭翼; 李忠献

    2003-01-01

    With the increment of the complexity of structural systems and the span of spatial structures, the interactions between parts of the structures, especially between some flexible substructures, become too complex to be analyzed clearly. In this paper, taking an actual gymnasium of a long-span spatial steel-cable-membrane hybrid structure as the calculation model, the static and dynamic analyses of the hybrid structures are performed by employing the global analysis of the whole hybrid structure and the substructural analysis of the truss arch substructure, the cable-membrane substructure, etc. In addition, the comparison of stresses and displacements of structural members in the global and substructural analyses is made. The numerical results show that serious errors exist in the substructural analysis of the hybrid structure, and the global analysis is necessary for the hybrid structure under the excitation of static loads and seismic loads.

  15. Dynamic Particle Weight Remapping in Hybrid PIC Hall-effect Thruster Simulation

    Science.gov (United States)

    2015-05-01

    International Electric Propulsion Conference and 6th Nano-satellite Symposium Hyogo-Kobe, Japan July 410, 2015 Robert Martin∗ ERC Incorporated, Huntsville...Algorithms, . 8Koo, J. and Martin, R., Pseudospectral model for hybrid PIC Hall -eect thruster simulation, 34th Int. Electric Propul- sion Conf...Paper 3. DATES COVERED (From - To) May 2015-July 2015 4. TITLE AND SUBTITLE Dynamic Particle Weight Remapping in Hybrid PIC Hall -effect Thruster

  16. Exciton dynamics and non-linearities in two-dimensional hybrid organic perovskites

    Science.gov (United States)

    Abdel-Baki, K.; Boitier, F.; Diab, H.; Lanty, G.; Jemli, K.; Lédée, F.; Garrot, D.; Deleporte, E.; Lauret, J. S.

    2016-02-01

    Due to their high potentiality for photovoltaic applications or coherent light sources, a renewed interest in hybrid organic perovskites has emerged for few years. When they are arranged in two dimensions, these materials can be considered as hybrid quantum wells. One consequence of the unique structure of 2D hybrid organic perovskites is a huge exciton binding energy that can be tailored through chemical engineering. We present experimental investigations of the exciton non-linearities by means of femtosecond pump-probe spectroscopy. The exciton dynamics is fitted with a bi-exponential decay with a free exciton life-time of ˜100 ps. Moreover, an ultrafast intraband relaxation (energy.

  17. Dynamic simulation of urban hybrid electric vehicles; Dynamische Simulation von Stadthybridfahrzeugen

    Energy Technology Data Exchange (ETDEWEB)

    Winke, Florian; Bargende, Michael [Stuttgart Univ. (Germany). Inst. fuer Verbrennungsmotoren und Kraftfahrwesen (IVK)

    2013-09-15

    As a result of the rising requirements on the development process of modern vehicles, simulation models for the prediction of fuel efficiency have become an irreplaceable tool in the automotive industry. Especially for the design of hybrid electric drivetrains, the increasingly short development cycles can only be met by the use of efficient simulation models. At the IVK of the University of Stuttgart, different approaches to simulating the longitudinal dynamics of hybrid electric vehicles were analysed and compared within the presented project. The focus of the investigations was on urban operation. The objective was to develop a hybrid vehicle concept that allows an equitable comparison with pure battery electric vehicles. (orig.)

  18. Plug-in hybrid electric vehicles in dynamical energy markets

    NARCIS (Netherlands)

    Kessels, J.T.B.A.; Bosch, P.P.J. van den

    2008-01-01

    The plug-in hybrid electric vehicle allows vehicle propulsion from multiple internal power sources. Electric energy from the grid can be utilized by means of the plug-in connection. An on-line energy management (EM) strategy is proposed to minimize the costs for taking energy from each power source.

  19. Plug-in hybrid electric vehicles in dynamical energy markets

    NARCIS (Netherlands)

    Kessels, J.T.B.A.; Bosch, P.P.J. van den

    2008-01-01

    The plug-in hybrid electric vehicle allows vehicle propulsion from multiple internal power sources. Electric energy from the grid can be utilized by means of the plug-in connection. An on-line energy management (EM) strategy is proposed to minimize the costs for taking energy from each power source.

  20. Hybrid proper orthogonal decomposition formulation for linear structural dynamics

    Science.gov (United States)

    Placzek, A.; Tran, D.-M.; Ohayon, R.

    2008-12-01

    Hybrid proper orthogonal decomposition (PODh) formulation is a POD-based reduced-order modeling method where the continuous equation of the physical system is projected on the POD modes obtained from a discrete model of the system. The aim of this paper is to evaluate the hybrid POD formulation and to compare it with other POD formulations on the simple case of a linear elastic rod subject to prescribed displacements in the perspective of building reduced-order models for coupled fluid-structure systems in the future. In the first part of the paper, the hybrid POD is compared to two other formulations for the response to an initial condition: an approach based on the discrete finite elements equation of the rod called the discrete POD (PODd), and an analytical approach using the exact solution of the problem and consequently called the analytical POD (PODa). This first step is useful to ensure that the PODh performs well with respect to the other formulations. The PODh is therefore used afterwards for the forced motion response where a displacement is imposed at the free end of the rod. The main contribution of this paper lies in the comparison of three techniques used to take into account the non-homogeneous Dirichlet boundary condition with the hybrid POD: the first method relies on control functions, the second on the penalty method and the third on Lagrange multipliers. Finally, the robustness of the hybrid POD is investigated on two examples involving firstly the introduction of structural damping and secondly a nonlinear force applied at the free end of the rod.

  1. On the Runtime of Randomized Local Search and Simple Evolutionary Algorithms for Dynamic Makespan Scheduling

    DEFF Research Database (Denmark)

    Neumann, Frank; Witt, Carsten

    2015-01-01

    combinatorial optimization problem, namely makespan scheduling. We study the model of a strong adversary which is allowed to change one job at regular intervals. Furthermore, we investigate the setting of random changes. Our results show that randomized local search and a simple evolutionary algorithm are very...

  2. Sectoral dynamics and technological convergence: an evolutionary analysis of eco-innovation in the automotive sector

    DEFF Research Database (Denmark)

    Faria, Lourenco; Andersen, Maj Munch

    2017-01-01

    We know from evolutionary theory that sectoral characteristics are important to innovation. This paper investigates if sectoral characteristics also are important to eco-innovation, a hitherto under-researched theme. We argue that research into possible sectoral patterns in eco-innovation is key ...... convergence of automakers’ strategies towards a diversified portfolio....

  3. DYNAMICS FOR VORTICES OF AN EVOLUTIONARY GINZBURG-LANDAU EQUATIONS IN 3 DIMENSIONS

    Institute of Scientific and Technical Information of China (English)

    刘祖汉

    2002-01-01

    This paper studies the asymptotic behavior of solutions to an evolutionary Ginzburg-Landau equation in 3 dimensions. It is shown that the motion of the Ginzburg-Landau vortex curves is the flow by its curvature. Away from the vortices, the author uses some measure theoretic arguments used by F. H. Lin in [16] to show the strong convergence of solutions.

  4. Measuring telomere length and telomere dynamics in evolutionary biology and ecology

    NARCIS (Netherlands)

    Nussey, Daniel H.; Baird, Duncan; Barrett, Emma; Boner, Winnie; Fairlie, Jennifer; Gemmell, Neil; Hartmann, Nils; Horn, Thorsten; Haussmann, Mark; Olsson, Mats; Turbill, Chris; Verhulst, Simon; Zahn, Sandrine; Monaghan, Pat

    2014-01-01

    Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, in

  5. Evolutionary Dynamics of rDNAs and U2 Small Nuclear DNAs in Triportheus (Characiformes, Triportheidae): High Variability and Particular Syntenic Organization.

    Science.gov (United States)

    Yano, Cassia Fernanda; Bertollo, Luiz Antonio Carlos; Rebordinos, Laureana; Merlo, Manuel Alejandro; Liehr, Thomas; Portela-Bens, Silvia; Cioffi, Marcelo de Bello

    2017-04-01

    Multigene families correspond to a group of genes tandemly repeated, showing enormous diversity in both number of units and genomic organization. In fishes, unlike rDNAs that have been well explored in cytogenetic studies, U2 small nuclear RNA (snRNA) genes are poorly investigated concerning their chromosomal localization. All Triportheus species (Characiformes, Triportheidae) studied so far carry a ZZ/ZW sex chromosomes system, where the W chromosome contains a huge 18S rDNA cistron. In some species the syntenic organization of rDNAs on autosomes was also verified. To explore this particular organization, we performed three-color-fluorescence in situ hybridization using 5S, 18S rDNA, and U2 snRNA genes as probes in eight Triportheus species. This work represents the first one analyzing the chromosomal distribution of U2 snRNA genes in genomes of Triportheidae. The variability in number of rDNA clusters, and the divergent syntenies for these three multigene families, put in evidence their evolutionary dynamism, revealing a much more complex organization of these genes than previously supposed for closely related species. Our study also provides additional data on the accumulation of repetitive sequences in the sex-specific chromosome. Besides, the chromosomal organization of U2 snDNAs among fish species is also reviewed.

  6. A system dynamics model based on evolutionary game theory for green supply chain management diffusion among Chinese manufacturers

    DEFF Research Database (Denmark)

    Tian, Yihui; Govindan, Kannan; Zhu, Qinghua

    2014-01-01

    In this study, a system dynamics (SD) model is developed to guide the subsidy policies to promote the diffusion of green supply chain management (GSCM) in China. The relationships of stakeholders such as government, enterprises and consumers are analyzed through evolutionary game theory. Finally......, the GSCM diffusion process is simulated by the model with a case study on Chinese automotive manufacturing industry. The results show that the subsidies for manufacturers are better than that for consumers to promote GSCM diffusion, and the environmental awareness is another influential key factor. © 2014...

  7. A Numerical Approach for Hybrid Simulation of Power System Dynamics Considering Extreme Icing Events

    DEFF Research Database (Denmark)

    Chen, Lizheng; Zhang, Hengxu; Wu, Qiuwei

    2017-01-01

    The global climate change leads to more extreme meteorological conditions such as icing weather, which have caused great losses to power systems. Comprehensive simulation tools are required to enhance the capability of power system risk assessment under extreme weather conditions. A hybrid...... numerical simulation scheme integrating icing weather events with power system dynamics is proposed to extend power system numerical simulation. A technique is developed to efficiently simulate the interaction of slow dynamics of weather events and fast dynamics of power systems. An extended package for PSS....../E enabling hybrid simulation of icing event and power system disturbance is developed, based on which a hybrid simulation platform is established. Numerical studies show that the functionality of power system simulation is greatly extended by taking into account the icing weather events....

  8. Dynamic Simulation of Carbonate Fuel Cell-Gas Turbine Hybrid Systems

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, R.A. (U. of California, Irvine, CA); Brouwer, J. (U. of California, Irvine, CA); Liese, E.A.; Gemmen, R.S.

    2006-04-01

    Hybrid fuel cell/gas turbine systems provide an efficient means of producing electricity from fossil fuels with ultra low emissions. However, there are many significant challenges involved in integrating the fuel cell with the gas turbine and other components of this type of system. The fuel cell and the gas turbine must maintain efficient operation and electricity production while protecting equipment during perturbations that may occur when the system is connected to the utility grid or in stand-alone mode. This paper presents recent dynamic simulation results from two laboratories focused on developing tools to aid in the design and dynamic analyses of hybrid fuel cell systems. The simulation results present the response of a carbonate fuel cell/gas turbine, or molten carbonate fuel cell/gas turbine, (MCFC/GT) hybrid system to a load demand perturbation. Initial results suggest that creative control strategies will be needed to ensure a flexible system with wide turndown and robust dynamic operation.

  9. A Distributed Cooperative Dynamic Task Planning Algorithm for Multiple Satellites Based on Multi-agent Hybrid Learning

    Institute of Scientific and Technical Information of China (English)

    WANG Chong; LI Jun; JING Ning; WANG Jun; CHEN Hao

    2011-01-01

    Traditionally,heuristic re-planning algorithms are used to tackle the problem of dynamic task planning for multiple satellites.However,the traditional heuristic strategies depend on the concrete tasks,which often affect the result's optimality.Noticing that the historical information of cooperative task planning will impact the latter planning results,we propose a hybrid learning algorithrn for dynamic multi-satellite task planning,which is based on the multi-agent reinforcement learning of policy iteration and the transfer learning.The reinforcement learning strategy of each satellite is described with neural networks.The policy neural network individuals with the best topological structure and weights are found by applying co-evolutionary search iteratively.To avoid the failure of the historical learning caused by the randomly occurring observation requests,a novel approach is proposed to balance the quality and efficiency of the task planning,which converts the historical leaming strategy to the current initial learning strategy by applying the transfer learning algorithm.The simulations and analysis show the feasibility and adaptability of the proposed approach especially for the situation with randomly occurring observation requests.

  10. Population Dynamics and the Optical Absorption in Hybrid Metal Nanoparticle - Semiconductor Quantum dot Nanosystem

    CERN Document Server

    Kim, Nam-Chol; Ko, Myong-Chol; So, Guang Hyok; Kim, Il-Guang

    2015-01-01

    We studied theoretically the population dynamics and the absorption spectrum of hybrid nanosystem consisted of a matal nanoparticle (MNP) and a semiconductor quantum dot(SQD). We investigated the exciton-plasmon coupling effects on the population dynamics and the absorption properties of the nanostructure. Our results show that the nonlinear optical response of the hybrid nanosystem can be greatly enhanced or depressed due to the exciton-plasmon couplings. The results obtained here may have the potential applications of nanoscale optical devices such as optical switches and quantum devices such as a single photon transistor.

  11. Dynamical control of quantum state transfer within hybrid open systems

    CERN Document Server

    Escher, B M; Clausen, J; Kurizki, G; Davidovich, L

    2010-01-01

    We analyze quantum state-transfer optimization within hybrid open systems, from a "noisy" (write-in) qubit to its "quiet" counterpart (storage qubit). Intriguing interplay is revealed between our ability to avoid bath-induced errors that profoundly depend on the bath-memory time and the limitations imposed by leakage out of the operational subspace. Counterintuitively, under no circumstances is the fastest transfer optimal (for a given transfer energy).

  12. Evolutionary dynamics of the LTR retrotransposons roo and rooA inferred from twelve complete Drosophila genomes

    Directory of Open Access Journals (Sweden)

    de la Chaux Nicole

    2009-08-01

    Full Text Available Abstract Background Roo is the most abundant retrotransposon in the fruit fly Drosophila melanogaster. Its evolutionary origins and dynamics are thus of special interest for understanding the evolutionary history of Drosophila genome organization. We here study the phylogenetic distribution and evolution of roo, and its highly diverged relative rooA in 12 completely sequenced genomes of the genus Drosophila. Results We identify a total of 164 roo copies, 57 of which were previously unidentified copies that occur in 9 of the 12 genomes. Additionally we find 66 rooA copies in four genomes and remnants of this element in two additional genomes. We further increased the number of elements by searching for individual roo/rooA sequence domains. Most of our roo and rooA elements have been recently inserted. Most elements within a genome are highly similar. A comparison of the phylogenetic tree of our roo and rooA elements shows that the split between roo and rooA took place early in Drosophila evolution. Furthermore there is one incongruency between the species tree and the phylogenetic tree of the roo element. This incongruency regards the placement of elements from D. mojavensis, which are more closely related to D. melanogaster than elements from D. willistoni. Conclusion Within genomes, the evolutionary dynamics of roo and rooA range from recent transpositional activity to slow decay and extinction. Among genomes, the balance of phylogenetic evidence, sequence divergence distribution, and the occurrence of solo-LTR elements suggests an origin of roo/rooA within the Drosophila clade. We discuss the possibility of a horizontal gene transfer of roo within this clade.

  13. Evolutionary dynamics of microsatellite distribution in plants: insight from the comparison of sequenced brassica, Arabidopsis and other angiosperm species.

    Directory of Open Access Journals (Sweden)

    Jiaqin Shi

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

  14. Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes

    Directory of Open Access Journals (Sweden)

    Podder Soumita

    2012-01-01

    Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.

  15. Dynamic selective environments and evolutionary traps in human-dominated landscapes.

    Science.gov (United States)

    Rodewald, Amanda D; Shustack, Daniel P; Jones, Todd M

    2011-09-01

    Human activities can alter selective environments in ways that can reduce the usefulness of certain ornamental traits as honest signals of individual quality and, in some cases, may create evolutionary traps, where rapid changes in selective environments result in maladaptive behavioral decisions. Using the sexually dichromatic, socially monogamous Northern Cardinal (Cardinalis cardinalis) as a model, we hypothesized that urbanization would erode the relationship between plumage coloration and reproductive success. Because the exotic Amur honeysuckle (Lonicera maackii) provides carotenoids, is a preferred habitat attribute, and increases vulnerability to nest predation, we predicted the presence of an evolutionary trap, whereby the brightest males would achieve the lowest reproductive success. Working at 14 forests in Ohio, USA, 2006-2008, we measured plumage color, monitored reproduction, and quantified habitat within territories. In rural landscapes, the brightest males bred earliest in the season and secured more preferred territories; however, annual reproduction declined with plumage brightness. Coloration of urban males was not associated with territory attributes or reproduction. Female redness across all landscapes was negatively related to reproduction. Poor reproductive performance of otherwise higher-quality males probably resulted from preferences for honeysuckle, which reduces annual reproduction when used as a nesting substrate early in the season. In this way, exotic shrubs prompted an evolutionary trap that was avoided in urban forests where anthropogenic resources disassociated male color and reproductive phenology and success. Our study illustrates how modified selective environments in human-dominated landscapes might shape microevolutionary processes in wild bird populations.

  16. Approximate dynamic programming recurrence relations for a hybrid optimal control problem

    Science.gov (United States)

    Lu, W.; Ferrari, S.; Fierro, R.; Wettergren, T. A.

    2012-06-01

    This paper presents a hybrid approximate dynamic programming (ADP) method for a hybrid dynamic system (HDS) optimal control problem, that occurs in many complex unmanned systems which are implemented via a hybrid architecture, regarding robot modes or the complex environment. The HDS considered in this paper is characterized by a well-known three-layer hybrid framework, which includes a discrete event controller layer, a discrete-continuous interface layer, and a continuous state layer. The hybrid optimal control problem (HOCP) is to nd the optimal discrete event decisions and the optimal continuous controls subject to a deterministic minimization of a scalar function regarding the system state and control over time. Due to the uncertainty of environment and complexity of the HOCP, the cost-to-go cannot be evaluated before the HDS explores the entire system state space; as a result, the optimal control, neither continuous nor discrete, is not available ahead of time. Therefore, ADP is adopted to learn the optimal control while the HDS is exploring the environment, because of the online advantage of ADP method. Furthermore, ADP can break the curses of dimensionality which other optimizing methods, such as dynamic programming (DP) and Markov decision process (MDP), are facing due to the high dimensions of HOCP.

  17. IMPLICIT REPRESENTATION FOR THE MODELLING OF HYBRID DYNAMIC SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Hybrid systems can be represented by a discrete event model interacting with a continuous model, and the interface by ideal switching components which modify the topology of a system at the switching time. This paper deals with the modelling of such systems using the bond graph approach. The paper shows the interest of the implicit representation: to derive a unique state equation with jumping parameters, to derive the implicit state equation with index of nilpotency one corresponding to each configuration, to analyze the properties of those models and to compute the discontinuity.

  18. Higher-order spin and charge dynamics in a quantum dot-lead hybrid system.

    Science.gov (United States)

    Otsuka, Tomohiro; Nakajima, Takashi; Delbecq, Matthieu R; Amaha, Shinichi; Yoneda, Jun; Takeda, Kenta; Allison, Giles; Stano, Peter; Noiri, Akito; Ito, Takumi; Loss, Daniel; Ludwig, Arne; Wieck, Andreas D; Tarucha, Seigo

    2017-09-22

    Understanding the dynamics of open quantum systems is important and challenging in basic physics and applications for quantum devices and quantum computing. Semiconductor quantum dots offer a good platform to explore the physics of open quantum systems because we can tune parameters including the coupling to the environment or leads. Here, we apply the fast single-shot measurement techniques from spin qubit experiments to explore the spin and charge dynamics due to tunnel coupling to a lead in a quantum dot-lead hybrid system. We experimentally observe both spin and charge time evolution via first- and second-order tunneling processes, and reveal the dynamics of the spin-flip through the intermediate state. These results enable and stimulate the exploration of spin dynamics in dot-lead hybrid systems, and may offer useful resources for spin manipulation and simulation of open quantum systems.

  19. Modelling Nonlinear Dynamic Textures using Hybrid DWT-DCT and Kernel PCA with GPU

    Science.gov (United States)

    Ghadekar, Premanand Pralhad; Chopade, Nilkanth Bhikaji

    2016-12-01

    Most of the real-world dynamic textures are nonlinear, non-stationary, and irregular. Nonlinear motion also has some repetition of motion, but it exhibits high variation, stochasticity, and randomness. Hybrid DWT-DCT and Kernel Principal Component Analysis (KPCA) with YCbCr/YIQ colour coding using the Dynamic Texture Unit (DTU) approach is proposed to model a nonlinear dynamic texture, which provides better results than state-of-art methods in terms of PSNR, compression ratio, model coefficients, and model size. Dynamic texture is decomposed into DTUs as they help to extract temporal self-similarity. Hybrid DWT-DCT is used to extract spatial redundancy. YCbCr/YIQ colour encoding is performed to capture chromatic correlation. KPCA is applied to capture nonlinear motion. Further, the proposed algorithm is implemented on Graphics Processing Unit (GPU), which comprise of hundreds of small processors to decrease time complexity and to achieve parallelism.

  20. Direct Measurement of Single-Molecule DNA Hybridization Dynamics with Single-Base Resolution.

    Science.gov (United States)

    He, Gen; Li, Jie; Ci, Haina; Qi, Chuanmin; Guo, Xuefeng

    2016-07-25

    Herein, we report label-free detection of single-molecule DNA hybridization dynamics with single-base resolution. By using an electronic circuit based on point-decorated silicon nanowires as electrical probes, we directly record the folding/unfolding process of individual hairpin DNAs with sufficiently high signal-to-noise ratio and bandwidth. These measurements reveal two-level current oscillations with strong temperature dependence, enabling us to determine the thermodynamic and kinetic properties of hairpin DNA hybridization. More importantly, successive, stepwise increases and decreases in device conductance at low temperature on a microsecond timescale are successfully observed, indicating a base-by-base unfolding/folding process. The process demonstrates a kinetic zipper model for DNA hybridization/dehybridization at the single base-pair level. This measurement capability promises a label-free single-molecule approach to probe biomolecular interactions with fast dynamics.

  1. Multiple steady states, limit cycles and chaotic attractors in evolutionary games with Logit Dynamics

    NARCIS (Netherlands)

    C.H. Hommes; M.I. Ochea

    2010-01-01

    This paper investigates, by means of simple, three and four strategy games, the occurrence of periodic and chaotic behaviour in a smooth version of the Best Response Dynamics, the Logit Dynamics. The main finding is that, unlike Replicator Dynamics, generic Hopf bifurcation and thus, stable limit cy

  2. Dynamics of CTAB in hybrid CTAB-hydroxyapatite system

    Science.gov (United States)

    Dubey, P.; Sharma, V. K.; Mitra, S.; Verma, G.; Hassan, P. A.; Johnson, M.; Mukhopadhyay, R.

    2016-05-01

    Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. Here we report dynamics of cetyltrimethylammonium bromide (CTAB) in HAp composite, prepared by co-precipitation method, as studied by quasielastic neutron scattering (QENS) technique. It is found that the observed dynamics involved two time scales associated with fast torsional motion and segmental motion of the CTAB monomers. In addition to segmental motion of the hydrogen atoms, few undergo torsional motion as well. Torsional dynamics was described by a 2-fold jump diffusion model. The segmental dynamics of CTAB has been described assumimg the hydrogen atoms undergoing diffusion inside a sphere of confined volume. While the diffusivity is found to increase with temperature, the spherical volumes within which the hydrogen atoms are undergoing diffusion remain almost unchanged.

  3. Reduction and identification for hybrid dynamical models of terrestrial locomotion

    Science.gov (United States)

    Burden, Samuel A.; Sastry, S. Shankar

    2013-06-01

    The study of terrestrial locomotion has compelling applications ranging from design of legged robots to development of novel prosthetic devices. From a first-principles perspective, the dynamics of legged locomotion seem overwhelmingly complex as nonlinear rigid body dynamics couple to a granular substrate through viscoelastic limbs. However, a surfeit of empirical data demonstrates that animals use a small fraction of their available degrees-of-freedom during locomotion on regular terrain, suggesting that a reduced-order model can accurately describe the dynamical variation observed during steady-state locomotion. Exploiting this emergent phenomena has the potential to dramatically simplify design and control of micro-scale legged robots. We propose a paradigm for studying dynamic terrestrial locomotion using empirically-validated reduced{order models.

  4. Dynamics of CTAB in hybrid CTAB-hydroxyapatite system

    Energy Technology Data Exchange (ETDEWEB)

    Dubey, P., E-mail: purushd@barc.gov.in; Sharma, V. K.; Mitra, S.; Mukhopadhyay, R. [Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai, 40085 (India); Verma, G.; Hassan, P. A. [Chemistry Division, Bhabha Atomic Research Centre, Mumbai, 40085 (India); Johnson, M. [Institut Laue-Langevin, BP 156, 6, rue Jules Horowitz, 38042 Grenoble Cedex 9 (France)

    2016-05-23

    Synthetic hydroxyapatite (HAp) is an important material in biomedical engineering due to its excellent biocompatibility and bioactivity. Here we report dynamics of cetyltrimethylammonium bromide (CTAB) in HAp composite, prepared by co-precipitation method, as studied by quasielastic neutron scattering (QENS) technique. It is found that the observed dynamics involved two time scales associated with fast torsional motion and segmental motion of the CTAB monomers. In addition to segmental motion of the hydrogen atoms, few undergo torsional motion as well. Torsional dynamics was described by a 2-fold jump diffusion model. The segmental dynamics of CTAB has been described assumimg the hydrogen atoms undergoing diffusion inside a sphere of confined volume. While the diffusivity is found to increase with temperature, the spherical volumes within which the hydrogen atoms are undergoing diffusion remain almost unchanged.

  5. Hybrid Monte Carlo algorithm for lattice QCD with two flavors of dynamical Ginsparg-Wilson quarks

    CERN Document Server

    Liu Chua

    1999-01-01

    We study aspects concerning numerical simulations of lattice QCD with two flavors of dynamical Ginsparg-Wilson quarks with degenerate masses. A hybrid Monte Carlo algorithm is described and a formula for the fermionic force is derived for two specific implementations. The implementation with the optimal rational approximation method is favored in both CPU time and memory consumption.

  6. Hybrid Monte Carlo algorithm for lattice QCD with two flavors of dynamical Ginsparg-Wilson quarks

    OpenAIRE

    Liu, Chuan

    1998-01-01

    We study aspects concerning numerical simulations of Lattice QCD with two flavors of dynamical Ginsparg-Wilson quarks with degenerate masses. A Hybrid Monte Carlo algorithm is described and the formula for the fermionic force is derived for two specific implementations. The implementation with optimal rational approximation method is favored both in CPU time and memory consumption.

  7. Modelling the Evolutionary Dynamics of Viruses within Their Hosts: A Case Study Using High-Throughput Sequencing

    Science.gov (United States)

    Senoussi, Rachid; Simon, Vincent; Moury, Benoît

    2012-01-01

    Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients βij exerted by variant j on variant i are equal to their fitness ratio, rj/ri. Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = −0.45%) and high (s = −13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F ST, were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts. PMID:22532800

  8. Distinguishing enzymes using metabolome data for the hybrid dynamic/static method

    Directory of Open Access Journals (Sweden)

    Nakayama Yoichi

    2007-05-01

    Full Text Available Abstract Background In the process of constructing a dynamic model of a metabolic pathway, a large number of parameters such as kinetic constants and initial metabolite concentrations are required. However, in many cases, experimental determination of these parameters is time-consuming. Therefore, for large-scale modelling, it is essential to develop a method that requires few experimental parameters. The hybrid dynamic/static (HDS method is a combination of the conventional kinetic representation and metabolic flux analysis (MFA. Since no kinetic information is required in the static module, which consists of MFA, the HDS method may dramatically reduce the number of required parameters. However, no adequate method for developing a hybrid model from experimental data has been proposed. Results In this study, we develop a method for constructing hybrid models based on metabolome data. The method discriminates enzymes into static modules and dynamic modules using metabolite concentration time series data. Enzyme reaction rate time series were estimated from the metabolite concentration time series data and used to distinguish enzymes optimally for the dynamic and static modules. The method was applied to build hybrid models of two microbial central-carbon metabolism systems using simulation results from their dynamic models. Conclusion A protocol to build a hybrid model using metabolome data and a minimal number of kinetic parameters has been developed. The proposed method was successfully applied to the strictly regulated central-carbon metabolism system, demonstrating the practical use of the HDS method, which is designed for computer modelling of metabolic systems.

  9. Translational systems biology using an agent-based approach for dynamic knowledge representation: An evolutionary paradigm for biomedical research.

    Science.gov (United States)

    An, Gary C

    2010-01-01

    The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.

  10. Evolutionary dynamics of the Pgk1 gene in the polyploid genus Kengyilia (Triticeae: Poaceae and its diploid relatives.

    Directory of Open Access Journals (Sweden)

    Xing Fan

    Full Text Available The level and pattern of nucleotide variation in duplicate gene provide important information on the evolutionary history of polyploids and divergent process between homoeologous loci within lineages. Kengyilia is a group of allohexaploid species with the StYP genomic constitutions in the wheat tribe. To investigate the evolutionary dynamics of the Pgk1 gene in Kengyilia and its diploid relatives, three copies of Pgk1 homoeologues were isolated from all sampled hexaploid Kengyilia species and analyzed with the Pgk1 sequences from 47 diploid taxa representing 18 basic genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1 Kengyilia species from the Central Asia and the Qinghai-Tibetan plateau have independent origins with geographically differentiated P genome donors and diverged levels of nucleotide diversity at Pgk1 locus; (2 a relatively long-time sweep event has allowed the Pgk1 gene within Agropyron to adapt to cold climate triggered by the recent uplifts of the Qinghai-Tibetan Plateau; (3 sweep event and population expansion might result in the difference in the d(N/d(S value of the Pgk1 gene in allopatric Agropyron populations, and this difference may be genetically transmitted to Kengyilia lineages via independent polyploidization events; (4 an 83 bp MITE element insertion has shaped the Pgk1 loci in the P genome lineage with different geographical regions; (5 the St and P genomes in Kengyilia were donated by Pseudoroegneria and Agropyron, respectively, and the Y genome is closely related to the Xp genome of Peridictyon sanctum. The interplay of evolutionary forces involving diverged natural selection, population expansion, and transposable events in geographically differentiated P genome donors could attribute to geographical differentiation of Kengyilia species via independent origins.

  11. Comparative Study of Lectin Domains in Model Species: New Insights into Evolutionary Dynamics

    Directory of Open Access Journals (Sweden)

    Sofie Van Holle

    2017-05-01

    Full Text Available Lectins are present throughout the plant kingdom and are reported to be involved in diverse biological processes. In this study, we provide a comparative analysis of the lectin families from model species in a phylogenetic framework. The analysis focuses on the different plant lectin domains identified in five representative core angiosperm genomes (Arabidopsis thaliana, Glycine max, Cucumis sativus, Oryza sativa ssp. japonica and Oryza sativa ssp. indica. The genomes were screened for genes encoding lectin domains using a combination of Basic Local Alignment Search Tool (BLAST, hidden Markov models, and InterProScan analysis. Additionally, phylogenetic relationships were investigated by constructing maximum likelihood phylogenetic trees. The results demonstrate that the majority of the lectin families are present in each of the species under study. Domain organization analysis showed that most identified proteins are multi-domain proteins, owing to the modular rearrangement of protein domains during evolution. Most of these multi-domain proteins are widespread, while others display a lineage-specific distribution. Furthermore, the phylogenetic analyses reveal that some lectin families evolved to be similar to the phylogeny of the plant species, while others share a closer evolutionary history based on the corresponding protein domain architecture. Our results yield insights into the evolutionary relationships and functional divergence of plant lectins.

  12. Dynamically configurable hybridization of plasmon modes in nanoring dimer arrays

    Science.gov (United States)

    Zhang, Lei; Dong, Zhaogang; Wang, Ying Min; Liu, Yan Jun; Zhang, Shuang; Yang, Joel Kwang Wei; Qiu, Cheng-Wei

    2015-07-01

    We present a novel strategy capable of dynamically configuring the plasmon-induced transparency (PIT) effect with a polarization-dependent controllability based on a nanoring dimer array. The controllable coupling strength between the superradiant and subradiant modes is due to the polarization-dependent field distributions. It is shown that this dynamically controlled PIT is realized with a modulation depth as high as 95%, and a linear dependence of the coupling strength on polarization angle is deduced using a coupled-oscillator model. We believe that our results will inspire further exciting achievements that utilize various polarization states of the electromagnetic wave and pave a way towards applications using PIT with dynamic controllability such as slow light, optical nonlinearities and chemical/bio-sensing.We present a novel strategy capable of dynamically configuring the plasmon-induced transparency (PIT) effect with a polarization-dependent controllability based on a nanoring dimer array. The controllable coupling strength between the superradiant and subradiant modes is due to the polarization-dependent field distributions. It is shown that this dynamically controlled PIT is realized with a modulation depth as high as 95%, and a linear dependence of the coupling strength on polarization angle is deduced using a coupled-oscillator model. We believe that our results will inspire further exciting achievements that utilize various polarization states of the electromagnetic wave and pave a way towards applications using PIT with dynamic controllability such as slow light, optical nonlinearities and chemical/bio-sensing. Electronic supplementary information (ESI) available: Method, mode supported by single nanoring, transmittance spectrum of single nanoring, comparison of transmittance spectra simulated under different illumination angles, diffraction coupling in the proposed nanoring dimer system, and the coupled Lorentz oscillator model and parameters

  13. Fuel cell-gas turbine hybrid system design part II: Dynamics and control

    Science.gov (United States)

    McLarty, Dustin; Brouwer, Jack; Samuelsen, Scott

    2014-05-01

    Fuel cell gas turbine hybrid systems have achieved ultra-high efficiency and ultra-low emissions at small scales, but have yet to demonstrate effective dynamic responsiveness or base-load cost savings. Fuel cell systems and hybrid prototypes have not utilized controls to address thermal cycling during load following operation, and have thus been relegated to the less valuable base-load and peak shaving power market. Additionally, pressurized hybrid topping cycles have exhibited increased stall/surge characteristics particularly during off-design operation. This paper evaluates additional control actuators with simple control methods capable of mitigating spatial temperature variation and stall/surge risk during load following operation of hybrid fuel cell systems. The novel use of detailed, spatially resolved, physical fuel cell and turbine models in an integrated system simulation enables the development and evaluation of these additional control methods. It is shown that the hybrid system can achieve greater dynamic response over a larger operating envelope than either individual sub-system; the fuel cell or gas turbine. Results indicate that a combined feed-forward, P-I and cascade control strategy is capable of handling moderate perturbations and achieving a 2:1 (MCFC) or 4:1 (SOFC) turndown ratio while retaining >65% fuel-to-electricity efficiency, while maintaining an acceptable stack temperature profile and stall/surge margin.

  14. New MPPT algorithm for PV applications based on hybrid dynamical approach

    KAUST Repository

    Elmetennani, S.

    2016-10-24

    This paper proposes a new Maximum Power Point Tracking (MPPT) algorithm for photovoltaic applications using the multicellular converter as a stage of power adaptation. The proposed MPPT technique has been designed using a hybrid dynamical approach to model the photovoltaic generator. The hybrid dynamical theory has been applied taking advantage of the particular topology of the multicellular converter. Then, a hybrid automata has been established to optimize the power production. The maximization of the produced solar energy is achieved by switching between the different operative modes of the hybrid automata, which is conditioned by some invariance and transition conditions. These conditions have been validated by simulation tests under different conditions of temperature and irradiance. Moreover, the performance of the proposed algorithm has been then evaluated by comparison with standard MPPT techniques numerically and by experimental tests under varying external working conditions. The results have shown the interesting features that the hybrid MPPT technique presents in terms of performance and simplicity for real time implementation.

  15. DiffAni: visualizing dynamic graphs with a hybrid of difference maps and animation.

    Science.gov (United States)

    Rufiange, Sébastien; McGuffin, Michael J

    2013-12-01

    Visualization of dynamically changing networks (graphs) is a significant challenge for researchers. Previous work has experimentally compared animation, small multiples, and other techniques, and found trade-offs between these. One potential way to avoid such trade-offs is to combine previous techniques in a hybrid visualization. We present two taxonomies of visualizations of dynamic graphs: one of non-hybrid techniques, and one of hybrid techniques. We also describe a prototype, called DiffAni, that allows a graph to be visualized as a sequence of three kinds of tiles: diff tiles that show difference maps over some time interval, animation tiles that show the evolution of the graph over some time interval, and small multiple tiles that show the graph state at an individual time slice. This sequence of tiles is ordered by time and covers all time slices in the data. An experimental evaluation of DiffAni shows that our hybrid approach has advantages over non-hybrid techniques in certain cases.

  16. Evolutionary dynamics of West Nile virus in the United States, 1999-2011: phylogeny, selection pressure and evolutionary time-scale analysis.

    Directory of Open Access Journals (Sweden)

    Germán Añez

    Full Text Available West Nile virus (WNV, an arbovirus maintained in a bird-mosquito enzootic cycle, can infect other vertebrates including humans. WNV was first reported in the US in 1999 where, to date, three genotypes belonging to WNV lineage I have been described (NY99, WN02, SW/WN03. We report here the WNV sequences obtained from two birds, one mosquito, and 29 selected human samples acquired during the US epidemics from 2006-2011 and our examination of the evolutionary dynamics in the open-reading frame of WNV isolates reported from 1999-2011. Maximum-likelihood and Bayesian methods were used to perform the phylogenetic analyses and selection pressure analyses were conducted with the HyPhy package. Phylogenetic analysis identified human WNV isolates within the main WNV genotypes that have circulated in the US. Within genotype SW/WN03, we have identified a cluster with strains derived from blood donors and birds from Idaho and North Dakota collected during 2006-2007, termed here MW/WN06. Using different codon-based and branch-site selection models, we detected a number of codons subjected to positive pressure in WNV genes. The mean nucleotide substitution rate for WNV isolates obtained from humans was calculated to be 5.06×10(-4 substitutions/site/year (s/s/y. The Bayesian skyline plot shows that after a period of high genetic variability following the introduction of WNV into the US, the WNV population appears to have reached genetic stability. The establishment of WNV in the US represents a unique opportunity to understand how an arbovirus adapts and evolves in a naïve environment. We describe a novel, well-supported cluster of WNV formed by strains collected from humans and birds from Idaho and North Dakota. Adequate genetic surveillance is essential to public health since new mutants could potentially affect viral pathogenesis, decrease performance of diagnostic assays, and negatively impact the efficacy of vaccines and the development of specific

  17. HybridArc: A novel radiation therapy technique combining optimized dynamic arcs and intensity modulation

    Energy Technology Data Exchange (ETDEWEB)

    Robar, James L., E-mail: james.robar@cdha.nshealth.ca [Department of Radiation Oncology, Dalhousie University, Halifax (Canada); Department of Physics and Atmospheric Science, Dalhousie University, Halifax (Canada); Thomas, Christopher [Department of Radiation Oncology, Dalhousie University, Halifax (Canada)

    2012-01-01

    This investigation focuses on possible dosimetric and efficiency advantages of HybridArc-a novel treatment planning approach combining optimized dynamic arcs with intensity-modulated radiation therapy (IMRT) beams. Application of this technique to two disparate sites, complex cranial tumors, and prostate was examined. HybridArc plans were compared with either dynamic conformal arc (DCA) or IMRT plans to determine whether HybridArc offers a synergy through combination of these 2 techniques. Plans were compared with regard to target volume dose conformity, target volume dose homogeneity, sparing of proximal organs at risk, normal tissue sparing, and monitor unit (MU) efficiency. For cranial cases, HybridArc produced significantly improved dose conformity compared with both DCA and IMRT but did not improve sparing of the brainstem or optic chiasm. For prostate cases, conformity was improved compared with DCA but not IMRT. Compared with IMRT, the dose homogeneity in the planning target volume was improved, and the maximum doses received by the bladder and rectum were reduced. Both arc-based techniques distribute peripheral dose over larger volumes of normal tissue compared with IMRT, whereas HybridArc involved slightly greater volumes of normal tissues compared with DCA. Compared with IMRT, cranial cases required 38% more MUs, whereas for prostate cases, MUs were reduced by 7%. For cranial cases, HybridArc improves dose conformity to the target. For prostate cases, dose conformity and homogeneity are improved compared with DCA and IMRT, respectively. Compared with IMRT, whether required MUs increase or decrease with HybridArc was site-dependent.

  18. Dynamic Modeling and Simulation of a Thermoelectric-Solar Hybrid Energy System Using an Inverse Dynamic Analysis Input Shaper

    Directory of Open Access Journals (Sweden)

    A. M. Yusop

    2014-01-01

    Full Text Available This study presents the behavioral model of thermal temperature and power generation of a thermoelectric-solar hybrid energy system exposed to dynamic transient sources. In the development of thermoelectric-solar hybrid energy system, studies have focused on the regulation of both systems separately. In practice, a separate control system affects hardware pricing. In this study, an inverse dynamic analysis shaping technique based on exponential function is applied to a solar array (SA to stabilize output voltage before this technique is combined with a thermoelectric module (TEM. This method can be used to estimate the maximum power point of the hybrid system by initially shaping the input voltage of SA. The behavior of the overall system can be estimated by controlling the behavior of SA, such that SA can follow the output voltage of TEM as the time constant of TEM is greater than that of SA. Moreover, by employing a continuous and differentiable function, the acquired output behavior of the hybrid system can be attained. Data showing the model is obtained from current experiments with predicted values of temperature, internal resistance, and current attributes of TEM. The simulation results show that the proposed input shaper can be used to trigger the output voltage of SA to follow the TEM behavior under transient conditions.

  19. Structural Dynamics of GaN Microcrystals in Evolutionary Selection Selective Area Growth probed by X-ray Microdiffraction

    Science.gov (United States)

    Kachkanov, V.; Leung, B.; Song, J.; Zhang, Y.; Tsai, M.-C.; Yuan, G.; Han, J.; O'Donnell, K. P.

    2014-01-01

    A method to grow high quality, single crystalline semiconductor material irrespective of the substrate would allow a cost-effective improvement to functionality and performance of optoelectronic devices. Recently, a novel type of substrate-insensitive growth process called Evolutionary Selection Selective Area Growth (ES-SAG) has been proposed. Here we report the use of X-ray microdiffraction to study the structural properties of GaN microcrystals grown by ES-SAG. Utilizing high resolution in both direct and reciprocal spaces, we have unraveled structural dynamics of GaN microcrystals in growth structures of different dimensions. It has been found that the geometric proportions of the growth constrictions play an important role: 2.6 μm and 4.5 μm wide growth tunnels favor the evolutionary selection mechanism, contrary to the case of 8.6 μm growth tunnels. It was also found that GaN microcrystal ensembles are dominated by slight tensile strain irrespective of growth tunnel shape. PMID:24722064

  20. Evolutionary dynamics of ecological niche in three Rhinogobio fishes from the upper Yangtze River inferred from morphological traits.

    Science.gov (United States)

    Wang, Meirong; Liu, Fei; Lin, Pengcheng; Yang, Shaorong; Liu, Huanzhang

    2015-02-01

    In the past decades, it has been debated whether ecological niche should be conserved among closely related species (phylogenetic niche conservatism, PNC) or largely divergent (traditional ecological niche theory and ecological speciation) and whether niche specialist and generalist might remain in equilibrium or niche generalist could not appear. In this study, we employed morphological traits to describe ecological niche and test whether different niche dimensions exhibit disparate evolutionary patterns. We conducted our analysis on three Rhinogobio fish species (R. typus,R. cylindricus, and R. ventralis) from the upper Yangtze River, China. Among the 32 measured morphological traits except body length, PCA extracted the first four principal components with their loading scores >1.000. To find the PNC among species, Mantel tests were conducted with the Euclidean distances calculated from the four principal components (representing different niche dimensions) against the pairwise distances calculated from mitochondrial cytochrome b sequence variations. The results showed that the second and the third niche dimension, both related to swimming ability and behavior, exhibited phylogenetic conservatism. Further comparison on niche breadth among these three species revealed that the fourth dimension of R. typus showed the greatest width, indicating that this dimension exhibited niche generalism. In conclusion, our results suggested that different niche dimensions could show different evolutionary dynamic patterns: they may exhibit PNC or not, and some dimensions may evolve generalism.

  1. Hybrid Dynamic Modeling and Control of Molten Carbonate Fuel Cell Stack Shutdown

    Institute of Scientific and Technical Information of China (English)

    LI Yong; CAO Guang-yi; ZHU Xin-jian

    2007-01-01

    A hybrid automaton modeling approach that incorporates state space partitioning, phase dynamic modeling and control law synthesis by control strategy is utilized to develop a hybrid automaton model of molten carbonate fuel cell (MCFC) stack shutdown. The shutdown operation is divided into several phases and their boundaries are decided according to a control strategy, which is a set of specifications about the dynamics of MCFC stack during shutdown. According to the control strategy, the specification of increasing stack temperature is satisfied in a phase that can be modeled accurately. The model for phase that has complex dynamic is approximated. The duration of this kind of phase is decreased to minimize the error caused by model approximation.

  2. Evolutionary history of Purple cone spruce (Picea purpurea) in the Qinghai-Tibet Plateau: homoploid hybrid origin and Pleistocene expansion.

    Science.gov (United States)

    Sun, Yongshuai; Abbott, Richard J; Li, Lili; Li, Long; Zou, Jiabin; Liu, Jianquan

    2014-02-01

    Hybridization and introgression can play an important role in speciation. Here, we examine their roles in the origin and evolution of Picea purpurea, a diploid spruce species occurring on the Qinghai-Tibet Plateau (QTP). Phylogenetic relationships and ecological differences between this species and its relatives, P. schrenkiana, P. likiangensis and P. wilsonii, are unclear. To clarify them, we surveyed sequence variation within and between them for 11 nuclear loci, three chloroplast (cp) and two mitochondrial (mt) DNA fragments, and examined their ecological requirements using ecological niche modelling. Initial analyses based on 11 nuclear loci rejected a close relationship between P. schrenkiana and P. purpurea. BP&P tests and ecological niche modelling indicated substantial divergence between the remaining three species and supported the species status of P. purpurea, which contained many private alleles as expected for a well-established species. Sequence variation for cpDNA and mtDNA suggested a close relationship between P. purpurea and P. wilsonii, while variation at the nuclear se1364 gene suggested P. purpurea was more closely related to P. likiangensis. Analyses of genetic divergence, Bayesian clustering and model comparison using approximate Bayesian computation (ABC) of nuclear (nr) DNA variation all supported the hypothesis that P. purpurea originated by homoploid hybrid speciation from P. wilsonii and P. likiangensis. The ABC analysis dated the origin of P. purpurea at the Pleistocene, and the estimated hybrid parameter indicated that 69% of its nuclear composition was contributed by P. likiangensis and 31% by P. wilsonii. Our results further suggested that during or immediately following its formation, P. purpurea was subject to organelle DNA introgression from P. wilsonii such that it came to possess both mtDNA and cpDNA of P. wilsonii. The estimated parameters indicated that following its origin, P. purpurea underwent an

  3. Evolutionary dynamics of rRNA gene clusters in cichlid fish

    Directory of Open Access Journals (Sweden)

    Nakajima Rafael T

    2012-10-01

    Full Text Available Abstract Background Among multigene families, ribosomal RNA (rRNA genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. Results The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. Conclusions The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a

  4. Evolutionary dynamics of rRNA gene clusters in cichlid fish

    Science.gov (United States)

    2012-01-01

    Background Among multigene families, ribosomal RNA (rRNA) genes are the most frequently studied and have been explored as cytogenetic markers to study the evolutionary history of karyotypes among animals and plants. In this report, we applied cytogenetic and genomic methods to investigate the organization of rRNA genes among cichlid fishes. Cichlids are a group of fishes that are of increasing scientific interest due to their rapid and convergent adaptive radiation, which has led to extensive ecological diversity. Results The present paper reports the cytogenetic mapping of the 5S rRNA genes from 18 South American, 22 African and one Asian species and the 18S rRNA genes from 3 African species. The data obtained were comparatively analyzed with previously published information related to the mapping of rRNA genes in cichlids. The number of 5S rRNA clusters per diploid genome ranged from 2 to 15, with the most common pattern being the presence of 2 chromosomes bearing a 5S rDNA cluster. Regarding 18S rDNA mapping, the number of sites ranged from 2 to 6, with the most common pattern being the presence of 2 sites per diploid genome. Furthermore, searching the Oreochromis niloticus genome database led to the identification of a total of 59 copies of 5S rRNA and 38 copies of 18S rRNA genes that were distributed in several genomic scaffolds. The rRNA genes were frequently flanked by transposable elements (TEs) and spread throughout the genome, complementing the FISH analysis that detect only clustered copies of rRNA genes. Conclusions The organization of rRNA gene clusters seems to reflect their intense and particular evolutionary pathway and not the evolutionary history of the associated taxa. The possible role of TEs as one source of rRNA gene movement, that could generates the spreading of ribosomal clusters/copies, is discussed. The present paper reinforces the notion that the integration of cytogenetic data and genomic analysis provides a more complete picture for

  5. Testability of evolutionary game dynamics models based on experimental economics data

    CERN Document Server

    Wang, Yijia; Wang, Zhijian

    2016-01-01

    In order to better understand the dynamic processes of a real game system, we need an appropriate dynamics model, so to evaluate the validity of a model is not a trivial task. Here, we demonstrate an approach, considering the dynamic patterns of angular momentum and speed as the measurement variables, for evaluating the validity of various dynamics models. Using the data in real time Rock-Paper-Scissors (RPS) games experiments, we obtain the experimental patterns, and then derive the related theoretical patterns from a series of typical dynamics models respectively. By testing the goodness-of-fit between the experimental and theoretical patterns, the validity of the models can be evaluated. One of the results is that, among all the non-parametric models tested, the best-known Replicator dynamics model performs almost worst, while the Projection dynamics model performs best. Besides providing new empirical patterns of social dynamics, we demonstrate that the approach can be an effective and rigorous method to ...

  6. An extension of the classification of evolutionary singular strategies in Adaptive Dynamics

    NARCIS (Netherlands)

    Boldin, Barbara; Diekmann, Odo

    2014-01-01

    The existing classification of evolutionarily singular strategies in Adaptive Dynamics (Geritz et al. in Evol Ecol 12:35–57, 1998; Metz et al. in Stochastic and spatial structures of dynamical systems, pp 183–231, 1996) assumes an invasion exponent that is differentiable twice as a function of both

  7. Analysis of Ant Colony Optimization and Population-Based Evolutionary Algorithms on Dynamic Problems

    DEFF Research Database (Denmark)

    Lissovoi, Andrei

    This thesis presents new running time analyses of nature-inspired algorithms on various dynamic problems. It aims to identify and analyse the features of algorithms and problem classes which allow efficient optimization to occur in the presence of dynamic behaviour. We consider the following...

  8. A Dynamic Multistage Hybrid Swarm Intelligence Optimization Algorithm for Function Optimization

    Directory of Open Access Journals (Sweden)

    Daqing Wu

    2012-01-01

    Full Text Available A novel dynamic multistage hybrid swarm intelligence optimization algorithm is introduced, which is abbreviated as DM-PSO-ABC. The DM-PSO-ABC combined the exploration capabilities of the dynamic multiswarm particle swarm optimizer (PSO and the stochastic exploitation of the cooperative artificial bee colony algorithm (CABC for solving the function optimization. In the proposed hybrid algorithm, the whole process is divided into three stages. In the first stage, a dynamic multiswarm PSO is constructed to maintain the population diversity. In the second stage, the parallel, positive feedback of CABC was implemented in each small swarm. In the third stage, we make use of the particle swarm optimization global model, which has a faster convergence speed to enhance the global convergence in solving the whole problem. To verify the effectiveness and efficiency of the proposed hybrid algorithm, various scale benchmark problems are tested to demonstrate the potential of the proposed multistage hybrid swarm intelligence optimization algorithm. The results show that DM-PSO-ABC is better in the search precision, and convergence property and has strong ability to escape from the local suboptima when compared with several other peer algorithms.

  9. Improved dynamic performance of hybrid PEM fuel cells and ultracapacitors for portable applications

    Energy Technology Data Exchange (ETDEWEB)

    Yalcinoz, T. [Department of Electrical and Computer Engineering, University of South Alabama, Mobile, AL 36688 (United States); Department of Electrical and Electronic Engineering, Nigde University, Nigde 51200 (Turkey); Alam, M.S. [Department of Electrical and Computer Engineering, University of South Alabama, Mobile, AL 36688 (United States)

    2008-04-15

    Transient power demand fluctuations and maintaining high energy density are important for many portable devices. Small fuel cells are potentially good candidates as alternative energy sources for portable applications. Hybrid power sources have some inherent properties which may be effectively utilized to improve the efficiency and dynamic response of the system. In this paper, an improved dynamic model considering the characteristics of the temperature and equivalent internal resistance is presented for proton exchange membrane (PEM) fuel cells. The dynamic behavior of a system with hybrid PEM fuel cells and an ultracapacitor bank is simulated. The hybrid PEM fuel cell/ultracapacitor bank system is used for powering a portable device (such as a laptop computer). The power requirement of a laptop computer varies significantly under different operation conditions. The analytical models of the hybrid system with PEM fuel cells and an ultracapacitor bank are designed and simulated by developing a detailed simulation software using Matlab, Simulink and SimPowerSystems Blockset for portable applications. (author)

  10. A HYBRID GRANULARITY PARALLEL ALGORITHM FOR PRECISE INTEGRATION OF STRUCTURAL DYNAMIC RESPONSES

    Institute of Scientific and Technical Information of China (English)

    Yuanyin Li; Xianlong Jin; Genguo Li

    2008-01-01

    Precise integration methods to solve structural dynamic responses and the corre-sponding time integration formula are composed of two parts: the multiplication of an exponential matrix with a vector and the integration term. The second term can be solved by the series solu-tion. Two hybrid granularity parallel algorithms are designed, that is, the exponential matrix and the first term are computed by the fine-grained parallel algorithm and the second term is com-puted by the coarse-grained parallel algorithm. Numerical examples show that these two hybrid granularity parallel algorithms obtain higher speedup and parallel efficiency than two existing parallel algorithms.

  11. Evolutionary analysis of the CACTA DNA-transposon Caspar across wheat species using sequence comparison and in situ hybridization.

    Science.gov (United States)

    Sergeeva, Ekaterina M; Salina, Elena A; Adonina, Irina G; Chalhoub, Boulos

    2010-07-01

    Mobile elements constitute a considerable part of the eukaryotic genome. This work is focused on the distribution and evolution of DNA-transposons in the genomes of diploid and allopolyploid Triticeae species and their role in the formation of functionally important chromosomal subtelomeric regions. The Caspar family is among the most abundant of CACTA DNA-transposons in Triticeae. To study the evolution of Caspar-like elements in Triticeae genomes, we analyzed their sequences and distribution in chromosomes by in situ hybridization. In total, 46 Caspar-like elements from the wheat and barley Caspar, Clifford, and Donald families were analyzed after being extracted from databases using the transposase consensus sequence. Sequence alignment and subsequent phylogenetic analyses revealed that the transposase DNA sequences formed three major distinct groups: (1) Clifford, (2) Caspar_Triticinae, and (3) Caspar_Hordeinae. Additionally, in situ hybridization demonstrated that Caspar_Triticinae transposons are predominantly compartmentalized in the subtelomeric chromosomal regions of wheat and its progenitors. Analysis of data suggested that compartmentalization in the subtelomeric chromosomal region was a characteristic feature of all the main groups of Caspar-like elements. Furthermore, a dot plot analysis of the terminal repeats demonstrated that the divergence of these repeats strictly correlated with the divergence of Caspar coding sequences. A clear distinction in the Caspar DNA sequences among the species Triticum/Aegilops (Caspar_Triticinae), Hordeum (Caspar_Hordeinae), and different distributions in individual hexaploid wheat genomes (A/B and D) suggest an independent proliferation of these elements in wheat (or its progenitors) and barley genomes. Thus, Caspar-like transposons can significantly contribute to the formation and differentiation of subtelomeric regions in Triticeae species.

  12. Between Pleasure and Contentment: Evolutionary Dynamics of Some Possible Parameters of Happiness.

    Science.gov (United States)

    Gao, Yue; Edelman, Shimon

    2016-01-01

    We offer and test a simple operationalization of hedonic and eudaimonic well-being ("happiness") as mediating variables that link outcomes to motivation. In six evolutionary agent-based simulation experiments, we compared the relative performance of agents endowed with different combinations of happiness-related traits (parameter values), under four types of environmental conditions. We found (i) that the effects of attaching more weight to longer-term than to momentary happiness and of extending the memory for past happiness are both stronger in an environment where food is scarce; (ii) that in such an environment "relative consumption," in which the agent's well-being is negatively affected by that of its neighbors, is more detrimental to survival when food is scarce; and (iii) that having a positive outlook, under which agents' longer-term happiness is increased by positive events more than it is decreased by negative ones, is generally advantageous.

  13. Dynamic instability of cooperation due to diverse activity patterns in evolutionary social dilemmas

    CERN Document Server

    Xia, Cheng-Yi; Perc, Matjaz; Moreno, Yamir

    2015-01-01

    Individuals might abstain from participating in an instance of an evolutionary game for various reasons, ranging from lack of interest to risk aversion. In order to understand the consequences of such diverse activity patterns on the evolution of cooperation, we study a weak prisoner's dilemma where each player's participation is probabilistic rather than certain. Players that do not participate get a null payoff and are unable to replicate. We show that inactivity introduces cascading failures of cooperation, which are particularly severe on scale-free networks with frequently inactive hubs. The drops in the fraction of cooperators are sudden, while the spatiotemporal reorganization of compact cooperative clusters, and thus the recovery, takes time. Nevertheless, if the activity of players is directly proportional to their degree, or if the interaction network is not strongly heterogeneous, the overall evolution of cooperation is not impaired. This is because inactivity negatively affects the potency of low-...

  14. Dynamic Hybrid Model for Short-Term Electricity Price Forecasting

    Directory of Open Access Journals (Sweden)

    Marin Cerjan

    2014-05-01

    Full Text Available Accurate forecasting tools are essential in the operation of electric power systems, especially in deregulated electricity markets. Electricity price forecasting is necessary for all market participants to optimize their portfolios. In this paper we propose a hybrid method approach for short-term hourly electricity price forecasting. The paper combines statistical techniques for pre-processing of data and a multi-layer (MLP neural network for forecasting electricity price and price spike detection. Based on statistical analysis, days are arranged into several categories. Similar days are examined by correlation significance of the historical data. Factors impacting the electricity price forecasting, including historical price factors, load factors and wind production factors are discussed. A price spike index (CWI is defined for spike detection and forecasting. Using proposed approach we created several forecasting models of diverse model complexity. The method is validated using the European Energy Exchange (EEX electricity price data records. Finally, results are discussed with respect to price volatility, with emphasis on the price forecasting accuracy.

  15. Hybrid bright-field and hologram imaging of cell dynamics

    Science.gov (United States)

    Byeon, Hyeokjun; Lee, Jaehyun; Doh, Junsang; Lee, Sang Joon

    2016-09-01

    Volumetric observation is essential for understanding the details of complex biological phenomena. In this study, a bright-field microscope, which provides information on a specific 2D plane, and a holographic microscope, which provides information spread over 3D volumes, are integrated to acquire two complementary images simultaneously. The developed system was successfully applied to capture distinct T-cell adhesion dynamics on inflamed endothelial layers, including capture, rolling, crawling, transendothelial migration, and subendothelial migration.

  16. Hybrid optimization of dynamic deployment for networked fire control system

    Institute of Scientific and Technical Information of China (English)

    Chen Chen; Jie Chen; Bin Xin

    2013-01-01

    With applying the information technology to the military field, the advantages and importance of the networked combat are more and more obvious. In order to make ful use of limited battle-field resources and maximal y destroy enemy targets from arbitrary angle in a limited time, the research on firepower nodes dynamic deployment becomes a key problem of command and control. Con-sidering a variety of tactical indexes and actual constraints in air defense, a mathematical model is formulated to minimize the ene-my target penetration probability. Based on characteristics of the mathematical model and demands of the deployment problems, an assistance-based algorithm is put forward which combines the ar-tificial potential field (APF) method with a memetic algorithm. The APF method is employed to solve the constraint handling prob-lem and generate feasible solutions. The constrained optimization problem transforms into an optimization problem of APF para-meters adjustment, and the dimension of the problem is reduced greatly. The dynamic deployment is accomplished by generation and refinement of feasible solutions. The simulation results show that the proposed algorithm is effective and feasible in dynamic situation.

  17. Dynamics of cancer progression and suppression: A novel evolutionary game theory based approach.

    Science.gov (United States)

    Banerjee, Jeet; Ranjan, Tanvi; Layek, Ritwik Kumar

    2015-01-01

    In this paper, a novel mathematical approach is proposed for the dynamics of progression and suppression of cancer. We define mutant cell density, ρ(μ) (μ × ρ), as a primary factor in cancer dynamics, and use logistic growth model and replicator equation for defining the dynamics of total cell density (ρ) and mutant fraction (μ), respectively. Furthermore, in the proposed model, we introduce an analytical expression for a control parameter D (drug), to suppress the proliferation of mutants with extra fitness level σ. Lastly, we present a comparison of the proposed model with some existing models of tumour growth.

  18. Bifurcation of resistive wall mode dynamics predicted by magnetohydrodynamic-kinetic hybrid theory

    Energy Technology Data Exchange (ETDEWEB)

    Yang, S. X.; Wang, Z. X., E-mail: zxwang@dlut.edu.cn [Key Laboratory of Materials Modification by Beams of the Ministry of Education, School of Physics and Optoelectronic Technology, Dalian University of Technology, Dalian 116024 (China); Wang, S.; Hao, G. Z., E-mail: haogz@swip.ac.cn; Song, X. M.; Wang, A. K. [Southwestern Institute of Physics, P.O.Box 432, Chengdu 610041 (China); Liu, Y. Q. [Culham Centre for Fusion Energy, Culham Science Centre, Abingdon OX14 3DB (United Kingdom); Southwestern Institute of Physics, P.O.Box 432, Chengdu 610041 (China)

    2015-09-15

    The magnetohydrodynamic-kinetic hybrid theory has been extensively and successfully applied for interpreting experimental observations of macroscopic, low frequency instabilities, such as the resistive wall mode, in fusion plasmas. In this work, it is discovered that an analytic version of the hybrid formulation predicts a bifurcation of the mode dynamics while varying certain physical parameters of the plasma, such as the thermal particle collisionality or the ratio of the thermal ion to electron temperatures. This bifurcation can robustly occur under reasonably large parameter spaces as well as with different assumptions, for instance, on the particle collision model. Qualitatively similar bifurcation features are also observed in full toroidal computations presented in this work, based on a non-perturbative hybrid formulation.

  19. Quantified Differential Dynamic Logic for Distributed Hybrid Systems

    Science.gov (United States)

    2010-05-01

    manual semantic reasoning. Other process- algebraic approaches, like χ [23], have been developed for modeling and sim- ulation. Verification is still...f(~s) using vectorial notation and we use ~s = ~t for element-wise equality. Formulas The formulas of QdL are defined as in first-order dynamic logic...like a Kleene algebra with tests [14]. QHPs are defined by the following grammar (α, β are QHPs, θ a term, i a variable of sort C, f is a function symbol

  20. A Paradoxical Consistency Between Dynamic and Conventional Derivatives on Hybrid Grids

    Institute of Scientific and Technical Information of China (English)

    Qin Sheng

    2008-01-01

    It has been evident that the theory and methods of dynamic derivatives are playing an increasingly important role in hybrid modeling and computations. Being constructed on various kinds of hybrid grids, that is, time scales, dynamic derivatives offer superior accuracy and flexibility in approximating mathematically important nat-ural processes with hard-to-predict singularities, such as the epidemic growth with un-predictable jump sizes and option market changes with high uncertainties, as com-pared with conventional derivatives. In this article, we shall review the novel new concepts, explore delicate relations between the most frequently used second-order dy-namic derivatives and conventional derivatives. We shall investigate necessary condi-tions for guaranteeing the consistency between the two derivatives. We will show that such a consistency may never exist in general. This implies that the dynamic derivatives provide entirely different new tools for sensitive modeling and approximations on hy-brid grids. Rigorous error analysis will be given via asymptotic expansions for further modeling and computational applications. Numerical experiments will also be given.

  1. A hybrid multi-objective evolutionary algorithm approach for handling sequence- and machine-dependent set-up times in unrelated parallel machine scheduling problem

    Indian Academy of Sciences (India)

    V K MANUPATI; G RAJYALAKSHMI; FELIX T S CHAN; J J THAKKAR

    2017-03-01

    This paper addresses a fuzzy mixed-integer non-linear programming (FMINLP) model by considering machine-dependent and job-sequence-dependent set-up times that minimize the total completion time,the number of tardy jobs, the total flow time and the machine load variation in the context of unrelated parallel machine scheduling (UPMS) problem. The above-mentioned multi-objectives were considered based on nonzero ready times, machine- and sequence-dependent set-up times and secondary resource constraints for jobs.The proposed approach considers unrelated parallel machines with inherent uncertainty in processing times and due dates. Since the problem is shown to be NP-hard in nature, it is a challenging task to find the optimal/nearoptimal solutions for conflicting objectives simultaneously in a reasonable time. Therefore, we introduced a new multi-objective-based evolutionary artificial immune non-dominated sorting genetic algorithm (AI-NSGA-II) to resolve the above-mentioned complex problem. The performance of the proposed multi-objective AI-NSGA-II algorithm has been compared to that of multi-objective particle swarm optimization (MOPSO) and conventionalnon-dominated sorting genetic algorithm (CNSGA-II), and it is found that the proposed multi-objective-based hybrid meta-heuristic produces high-quality solutions. Finally, the results obtained from benchmark instances and randomly generated instances as test problems evince the robust performance of the proposed multiobjective algorithm.

  2. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics.

    Science.gov (United States)

    Petsev, Nikolai D; Leal, L Gary; Shell, M Scott

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  3. Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Petsev, Nikolai D.; Leal, L. Gary; Shell, M. Scott [Department of Chemical Engineering, University of California at Santa Barbara, Santa Barbara, California 93106-5080 (United States)

    2015-01-28

    We present a new multiscale simulation methodology for coupling a region with atomistic detail simulated via molecular dynamics (MD) to a numerical solution of the fluctuating Navier-Stokes equations obtained from smoothed dissipative particle dynamics (SDPD). In this approach, chemical potential gradients emerge due to differences in resolution within the total system and are reduced by introducing a pairwise thermodynamic force inside the buffer region between the two domains where particles change from MD to SDPD types. When combined with a multi-resolution SDPD approach, such as the one proposed by Kulkarni et al. [J. Chem. Phys. 138, 234105 (2013)], this method makes it possible to systematically couple atomistic models to arbitrarily coarse continuum domains modeled as SDPD fluids with varying resolution. We test this technique by showing that it correctly reproduces thermodynamic properties across the entire simulation domain for a simple Lennard-Jones fluid. Furthermore, we demonstrate that this approach is also suitable for non-equilibrium problems by applying it to simulations of the start up of shear flow. The robustness of the method is illustrated with two different flow scenarios in which shear forces act in directions parallel and perpendicular to the interface separating the continuum and atomistic domains. In both cases, we obtain the correct transient velocity profile. We also perform a triple-scale shear flow simulation where we include two SDPD regions with different resolutions in addition to a MD domain, illustrating the feasibility of a three-scale coupling.

  4. A hybrid evolutionary algorithm for multi-objective anatomy-based dose optimization in high-dose-rate brachytherapy.

    Science.gov (United States)

    Lahanas, M; Baltas, D; Zamboglou, N

    2003-02-07

    Multiple objectives must be considered in anatomy-based dose optimization for high-dose-rate brachytherapy and a large number of parameters must be optimized to satisfy often competing objectives. For objectives expressed solely in terms of dose variances, deterministic gradient-based algorithms can be applied and a weighted sum approach is able to produce a representative set of non-dominated solutions. As the number of objectives increases, or non-convex objectives are used, local minima can be present and deterministic or stochastic algorithms such as simulated annealing either cannot be used or are not efficient. In this case we employ a modified hybrid version of the multi-objective optimization algorithm NSGA-II. This, in combination with the deterministic optimization algorithm, produces a representative sample of the Pareto set. This algorithm can be used with any kind of objectives, including non-convex, and does not require artificial importance factors. A representation of the trade-off surface can be obtained with more than 1000 non-dominated solutions in 2-5 min. An analysis of the solutions provides information on the possibilities available using these objectives. Simple decision making tools allow the selection of a solution that provides a best fit for the clinical goals. We show an example with a prostate implant and compare results obtained by variance and dose-volume histogram (DVH) based objectives.

  5. A hybrid evolutionary algorithm for multi-objective anatomy-based dose optimization in high-dose-rate brachytherapy

    Energy Technology Data Exchange (ETDEWEB)

    Lahanas, M [Department of Medical Physics and Engineering, Strahlenklinik, Klinikum Offenbach, 63069 Offenbach (Germany); Baltas, D [Department of Medical Physics and Engineering, Strahlenklinik, Klinikum Offenbach, 63069 Offenbach (Germany); Zamboglou, N [Department of Medical Physics and Engineering, Strahlenklinik, Klinikum Offenbach, 63069 Offenbach (Germany)

    2003-02-07

    Multiple objectives must be considered in anatomy-based dose optimization for high-dose-rate brachytherapy and a large number of parameters must be optimized to satisfy often competing objectives. For objectives expressed solely in terms of dose variances, deterministic gradient-based algorithms can be applied and a weighted sum approach is able to produce a representative set of non-dominated solutions. As the number of objectives increases, or non-convex objectives are used, local minima can be present and deterministic or stochastic algorithms such as simulated annealing either cannot be used or are not efficient. In this case we employ a modified hybrid version of the multi-objective optimization algorithm NSGA-II. This, in combination with the deterministic optimization algorithm, produces a representative sample of the Pareto set. This algorithm can be used with any kind of objectives, including non-convex, and does not require artificial importance factors. A representation of the trade-off surface can be obtained with more than 1000 non-dominated solutions in 2-5 min. An analysis of the solutions provides information on the possibilities available using these objectives. Simple decision making tools allow the selection of a solution that provides a best fit for the clinical goals. We show an example with a prostate implant and compare results obtained by variance and dose-volume histogram (DVH) based objectives.

  6. Evaluation of methods for extraction of the volitional EMG in dynamic hybrid muscle activation

    Directory of Open Access Journals (Sweden)

    Mizrahi Joseph

    2006-11-01

    Full Text Available Abstract Background Hybrid muscle activation is a modality used for muscle force enhancement, in which muscle contraction is generated from two different excitation sources: volitional and external, by means of electrical stimulation (ES. Under hybrid activation, the overall EMG signal is the combination of the volitional and ES-induced components. In this study, we developed a computational scheme to extract the volitional EMG envelope from the overall dynamic EMG signal, to serve as an input signal for control purposes, and for evaluation of muscle forces. Methods A "synthetic" database was created from in-vivo experiments on the Tibialis Anterior of the right foot to emulate hybrid EMG signals, including the volitional and induced components. The database was used to evaluate the results obtained from six signal processing schemes, including seven different modules for filtration, rectification and ES component removal. The schemes differed from each other by their module combinations, as follows: blocking window only, comb filter only, blocking window and comb filter, blocking window and peak envelope, comb filter and peak envelope and, finally, blocking window, comb filter and peak envelope. Results and conclusion The results showed that the scheme including all the modules led to an excellent approximation of the volitional EMG envelope, as extracted from the hybrid signal, and underlined the importance of the artifact blocking window module in the process. The results of this work have direct implications on the development of hybrid muscle activation rehabilitation systems for the enhancement of weakened muscles.

  7. Dynamic hybrid life cycle assessment of energy and carbon of multicrystalline silicon photovoltaic systems.

    Science.gov (United States)

    Zhai, Pei; Williams, Eric D

    2010-10-15

    This paper advances the life cycle assessment (LCA) of photovoltaic systems by expanding the boundary of the included processes using hybrid LCA and accounting for the technology-driven dynamics of embodied energy and carbon emissions. Hybrid LCA is an extended method that combines bottom-up process-sum and top-down economic input-output (EIO) methods. In 2007, the embodied energy was 4354 MJ/m(2) and the energy payback time (EPBT) was 2.2 years for a multicrystalline silicon PV system under 1700 kWh/m(2)/yr of solar radiation. These results are higher than those of process-sum LCA by approximately 60%, indicating that processes excluded in process-sum LCA, such as transportation, are significant. Even though PV is a low-carbon technology, the difference between hybrid and process-sum results for 10% penetration of PV in the U.S. electrical grid is 0.13% of total current grid emissions. Extending LCA from the process-sum to hybrid analysis makes a significant difference. Dynamics are characterized through a retrospective analysis and future outlook for PV manufacturing from 2001 to 2011. During this decade, the embodied carbon fell substantially, from 60 g CO(2)/kWh in 2001 to 21 g/kWh in 2011, indicating that technological progress is realizing reductions in embodied environmental impacts as well as lower module price.

  8. A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

    Directory of Open Access Journals (Sweden)

    Guoqin Mai

    2016-01-01

    Full Text Available Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.

  9. Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.

    Directory of Open Access Journals (Sweden)

    Vanessa Rodrigues Paixão-Côrtes

    Full Text Available Paired box (PAX genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.

  10. The dynamic evolutionary history of genome size in North American woodland salamanders.

    Science.gov (United States)

    Newman, Catherine E; Gregory, T Ryan; Austin, Christopher C

    2017-04-01

    The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

  11. Comparative evolutionary and developmental dynamics of the cotton (Gossypium hirsutum fiber transcriptome.

    Directory of Open Access Journals (Sweden)

    Mi-Jeong Yoo

    2014-01-01

    Full Text Available The single-celled cotton (Gossypium hirsutum fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ~5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution.

  12. Phylogenetic distribution and evolutionary dynamics of the sex determination genes doublesex and transformer in insects.

    Science.gov (United States)

    Geuverink, E; Beukeboom, L W

    2014-01-01

    Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects. © 2013 S. Karger AG, Basel.

  13. The architecture of river networks can drive the evolutionary dynamics of aquatic populations.

    Science.gov (United States)

    Thomaz, Andréa T; Christie, Mark R; Knowles, L Lacey

    2016-03-01

    It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures and downstream flow regimes affect the genetic structure of populations situated within river networks. Irrespective of the river length, our results illustrate that the extent of river branching, confluence position, and levels of asymmetric downstream migration dictate patterns of genetic variation in riverine populations. Comparisons between simple and highly branched rivers show a 20-fold increase in the overall genetic diversity and a sevenfold increase in the genetic differentiation between local populations. Given that most rivers have complex architectures, these results highlight the importance of incorporating riverscape information into evolutionary models of aquatic species and could help explain why riverine fishes represent a disproportionately large amount of global vertebrate diversity per unit of habitable area.

  14. Genetic variability and evolutionary dynamics of viruses of the family Closteroviridae

    Directory of Open Access Journals (Sweden)

    Luis eRubio

    2013-06-01

    Full Text Available RNA viruses have a great potential for genetic variation, rapid evolution and adaptation. Characterization of the genetic variation of viral populations provides relevant information on the processes involved in virus evolution and epidemiology and it is crucial for designing reliable diagnostic tools and developing efficient and durable disease control strategies. Here we performed an updated analysis of sequences available in Genbank and reviewed present knowledge on the genetic variability and evolutionary processes of viruses of the family Closteroviridae. Several factors have shaped the genetic structure and diversity of closteroviruses. I A strong negative selection seems to be responsible for the high genetic stability in space and time for some viruses. II Long distance migration, probably by human transport of infected propagative plant material, have caused that genetically similar virus isolates are found in distant geographical regions. III Recombination between divergent sequence variants have generated new genotypes and plays an important role for the evolution of some viruses of the family Closteroviridae. IV Interaction between virus strains or between different viruses in mixed infections may alter accumulation of certain strains. V Host change or virus transmission by insect vectors induced changes in the viral population structure due to positive selection of sequence variants with higher fitness for host-virus or vector-virus interaction (adaptation or by genetic drift due to random selection of sequence variants during the population bottleneck associated to the transmission process.

  15. 基于混合杂交与间歇变异的约束优化演化算法%A Constrained Evolutionary Algorithm Based on Hybrid Crossovers and Intermittent Mutation

    Institute of Scientific and Technical Information of China (English)

    周永华; 毛宗源

    2003-01-01

    In solving constrained optimization problems with genetic algorithms, more emphases are laid on handling constraints than increasing the search capability of algorithms, which often leed to unsatisfied results as reported inmost literatures. This paper proposes a new evolutionary algorithm for constrained optimization, emphasizing moreon increasing the search capability of the algorithm by means of hybrid crossovers and intermittent mutation while adopting a simple constraint handling technique called direct comparison. Numerical experiments and comparisons show the ettectiveness of the proposed algorithm.

  16. Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers.

    Science.gov (United States)

    Axelsen, Jacob Bock; Yaari, Rami; Grenfell, Bryan T; Stone, Lewi

    2014-07-01

    Human influenza occurs annually in most temperate climatic zones of the world, with epidemics peaking in the cold winter months. Considerable debate surrounds the relative role of epidemic dynamics, viral evolution, and climatic drivers in driving year-to-year variability of outbreaks. The ultimate test of understanding is prediction; however, existing influenza models rarely forecast beyond a single year at best. Here, we use a simple epidemiological model to reveal multiannual predictability based on high-quality influenza surveillance data for Israel; the model fit is corroborated by simple metapopulation comparisons within Israel. Successful forecasts are driven by temperature, humidity, antigenic drift, and immunity loss. Essentially, influenza dynamics are a balance between large perturbations following significant antigenic jumps, interspersed with nonlinear epidemic dynamics tuned by climatic forcing.

  17. Dynamical Mueller's Ratchet: Population Size Dependence of Evolutionary Paths in Bacteria

    Science.gov (United States)

    Lorenz, Dirk; Park, Jeong-Man; Deem, Michael; Michael Deem Team

    2011-03-01

    Experimental evolution has recently enabled the complete quantitative description of small-dimensional fitness landscapes. Quasispecies theory allows the mathematical modeling of evolution on such a landscape. Typically, analytic solutions for these models are only exactly solvable for the case of an infinite population. Here we use a functional integral representation of population dynamics and solve it using the Schwinger Boson method. This allows us to compute the first-order correction to the average fitness for finite populations. We will use these results to explain the experimental observations of dynamics of evolution in finite populations.

  18. Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection

    Science.gov (United States)

    Poulicard, Nils; Pacios, Luis Fernández; Gallois, Jean-Luc; Piñero, Daniel; García-Arenal, Fernando

    2016-01-01

    This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the

  19. Human Management of a Wild Plant Modulates the Evolutionary Dynamics of a Gene Determining Recessive Resistance to Virus Infection.

    Directory of Open Access Journals (Sweden)

    Nils Poulicard

    2016-08-01

    Full Text Available This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin. Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound

  20. Toward a Mechanics of Adaptive Behavior: Evolutionary Dynamics and Matching Theory Statics

    Science.gov (United States)

    McDowell, J. J.; Popa, Andrei

    2010-01-01

    One theory of behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of reinforcement. This computational theory implements Darwinian principles of selection, reproduction, and mutation, which operate on a population of potential behaviors by means of a genetic algorithm.…

  1. Mathematical Model and Its Hybrid Dynamic Mechanism in Intelligent Control of Ironmaking

    Institute of Scientific and Technical Information of China (English)

    LIU Xiang-guan; ZENG Jiu-sun; ZHAO Min

    2007-01-01

    A hybrid dynamic model was proposed, which considered both the hydrokinetic and the chaotic properties of the blast furnace ironmaking process; and great emphasis was put on its mechanism. The new model took the high complexity of the blast furnace as well as the effects of main parameters of the model into account, and the predicted results were in very good agreement with actual data.

  2. Modelling Beam Dynamics and RF Production in Two Beam Accelerators with a Hybrid Simulation Tool

    Science.gov (United States)

    Lidia, Steven

    2000-04-01

    A hybrid mapping and PIC code is described and applied to the study of transient-to-steady-state phenomena of beam dynamics and rf power production in relativistic-klystron two-beam accelerators. Beam and beamline parameters appropriate to a single device that produces 40-100 MW per meter over 10 meters with a 120 ns pulse length are described and used.

  3. Appendage modal coordinate truncation criteria in hybrid coordinate dynamic analysis. [for spacecraft attitude control

    Science.gov (United States)

    Likins, P.; Ohkami, Y.; Wong, C.

    1976-01-01

    The paper examines the validity of the assumption that certain appendage-distributed (modal) coordinates can be truncated from a system model without unacceptable degradation of fidelity in hybrid coordinate dynamic analysis for attitude control of spacecraft with flexible appendages. Alternative truncation criteria are proposed and their interrelationships defined. Particular attention is given to truncation criteria based on eigenvalues, eigenvectors, and controllability and observability. No definitive resolution of the problem is advanced, and exhaustive study is required to obtain ultimate truncation criteria.

  4. Numerical methodologies for investigation of moderate-velocity flow using a hybrid computational fluid dynamics - molecular dynamics simulation approach

    Energy Technology Data Exchange (ETDEWEB)

    Ko, Soon Heum [Linkoeping University, Linkoeping (Sweden); Kim, Na Yong; Nikitopoulos, Dimitris E.; Moldovan, Dorel [Louisiana State University, Baton Rouge (United States); Jha, Shantenu [Rutgers University, Piscataway (United States)

    2014-01-15

    Numerical approaches are presented to minimize the statistical errors inherently present due to finite sampling and the presence of thermal fluctuations in the molecular region of a hybrid computational fluid dynamics (CFD) - molecular dynamics (MD) flow solution. Near the fluid-solid interface the hybrid CFD-MD simulation approach provides a more accurate solution, especially in the presence of significant molecular-level phenomena, than the traditional continuum-based simulation techniques. It also involves less computational cost than the pure particle-based MD. Despite these advantages the hybrid CFD-MD methodology has been applied mostly in flow studies at high velocities, mainly because of the higher statistical errors associated with low velocities. As an alternative to the costly increase of the size of the MD region to decrease statistical errors, we investigate a few numerical approaches that reduce sampling noise of the solution at moderate-velocities. These methods are based on sampling of multiple simulation replicas and linear regression of multiple spatial/temporal samples. We discuss the advantages and disadvantages of each technique in the perspective of solution accuracy and computational cost.

  5. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Directory of Open Access Journals (Sweden)

    Ana Zafra Ruano

    2016-05-01

    Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

  6. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.

    Science.gov (United States)

    Zafra Ruano, Ana; Cilia, Elisa; Couceiro, José R; Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic; Luque, Irene; Lenaerts, Tom

    2016-05-01

    Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.

  7. Dynamic economic emission dispatch incorporating wind farms using modified co-evolutionary particle swarm optimization meta-heuristic algorithm

    Directory of Open Access Journals (Sweden)

    2015-03-01

    Full Text Available The dynamic economic load dispatch is one of the main problems of power systems generation and operation. The objective is to schedule power generation for units over a certain period of time, while satisfying operating constraints and load demand in each interval. Wind farms, as renewable energy resources are playing an increasing role in electricity generation. In this paper, a computational framework is presented to solve the dynamic economic emission dispatch problem with inclusion of wind farms considering their associated constraints. An optimization algorithm called modified co-evolutionary particle swarm optimization (MCPSO is proposed to solve the problem. In the proposed algorithm, two kinds of swarms evolve interactively where one of them is used to calculate the penalty factors (constraints handling and the other is used for searching good solutions (optimization process. In addition, some modifications such as using an inertia weight that decreases linearly during the simulation are made to improve the performance of the algorithm. Finally, the validity and superiority of the proposed method are demonstrated by simulation results on a modified IEEE benchmark system including six thermal units and two wind farms.

  8. Effects of behavioral response and vaccination policy on epidemic spreading - an approach based on evolutionary-game dynamics

    Science.gov (United States)

    Zhang, Hai-Feng; Wu, Zhi-Xi; Tang, Ming; Lai, Ying-Cheng

    2014-07-01

    How effective are governmental incentives to achieve widespread vaccination coverage so as to prevent epidemic outbreak? The answer largely depends on the complex interplay among the type of incentive, individual behavioral responses, and the intrinsic epidemic dynamics. By incorporating evolutionary games into epidemic dynamics, we investigate the effects of two types of incentives strategies: partial-subsidy policy in which certain fraction of the cost of vaccination is offset, and free-subsidy policy in which donees are randomly selected and vaccinated at no cost. Through mean-field analysis and computations, we find that, under the partial-subsidy policy, the vaccination coverage depends monotonically on the sensitivity of individuals to payoff difference, but the dependence is non-monotonous for the free-subsidy policy. Due to the role models of the donees for relatively irrational individuals and the unchanged strategies of the donees for rational individuals, the free-subsidy policy can in general lead to higher vaccination coverage. Our findings indicate that any disease-control policy should be exercised with extreme care: its success depends on the complex interplay among the intrinsic mathematical rules of epidemic spreading, governmental policies, and behavioral responses of individuals.

  9. Evolutionary constraints on visual cortex architecture from the dynamics of hallucinations.

    Science.gov (United States)

    Butler, Thomas Charles; Benayoun, Marc; Wallace, Edward; van Drongelen, Wim; Goldenfeld, Nigel; Cowan, Jack

    2012-01-10

    In the cat or primate primary visual cortex (V1), normal vision corresponds to a state where neural excitation patterns are driven by external visual stimuli. A spectacular failure mode of V1 occurs when such patterns are overwhelmed by spontaneously generated spatially self-organized patterns of neural excitation. These are experienced as geometric visual hallucinations. The problem of identifying the mechanisms by which V1 avoids this failure is made acute by recent advances in the statistical mechanics of pattern formation, which suggest that the hallucinatory state should be very robust. Here, we report how incorporating physiologically realistic long-range connections between inhibitory neurons changes the behavior of a model of V1. We find that the sparsity of long-range inhibition in V1 plays a previously unrecognized but key functional role in preserving the normal vision state. Surprisingly, it also contributes to the observed regularity of geometric visual hallucinations. Our results provide an explanation for the observed sparsity of long-range inhibition in V1--this generic architectural feature is an evolutionary adaptation that tunes V1 to the normal vision state. In addition, it has been shown that exactly the same long-range connections play a key role in the development of orientation preference maps. Thus V1's most striking long-range features--patchy excitatory connections and sparse inhibitory connections--are strongly constrained by two requirements: the need for the visual state to be robust and the developmental requirements of the orientational preference map.

  10. Genetic diversity of Chikungunya virus, India 2006-2010: evolutionary dynamics and serotype analyses.

    Science.gov (United States)

    Sumathy, K; Ella, Krishna M

    2012-03-01

    The genetic diversity of Chikungunya virus (CHIKV) causing recurring outbreaks in India since 2006 was studied. The 2006 epidemic was caused by a virus strain of the East, Central and South African (ECSA) genotype with 226A in the E1 glycoprotein. The variant strain with E1-A226V mutation caused outbreaks since 2007 in the state of Kerala where Aedes albopictus is the abundant mosquito vector. Molecular epidemiology data since 2007 is scarce from other regions of the country. RT-PCR, sequencing and phylogenetic analyses of CHIKV isolates from the 2009 to 2010 epidemics in the States of Tamil Nadu and Andhra Pradesh placed them in a separate clade within the ECSA lineage. The isolates of the study had 226A in the E1 glycoprotein. The isolates had a novel E1-K211E mutation that was under significant positive selection. E1-211E is highly conserved in the Asian genotype of the virus circulated by Aedes aegypti. Unique mutations in E2 glycoprotein were identified. The two sub-lineages of ECSA genotype circulating in India parallel the abundance of Ae. albopictus and Ae. aegypti. Novel mutations in the envelope glycoproteins suggest adaptive evolution of the virus to local vector abundance. Cross neutralization of the virus isolates from recurring Indian epidemics indicated that no distinct serotypes had evolved. The study has provided insights into the origin, distribution and evolutionary adaptation of the virus to local vector abundance in the region that has reportedly, the highest incidence of CHIKV infection in the world.

  11. Evolutionary dynamics of human Toll-like receptors and their different contributions to host defense.

    Directory of Open Access Journals (Sweden)

    Luis B Barreiro

    2009-07-01

    Full Text Available Infectious diseases have been paramount among the threats to health and survival throughout human evolutionary history. Natural selection is therefore expected to act strongly on host defense genes, particularly on innate immunity genes whose products mediate the direct interaction between the host and the microbial environment. In insects and mammals, the Toll-like receptors (TLRs appear to play a major role in initiating innate immune responses against microbes. In humans, however, it has been speculated that the set of TLRs could be redundant for protective immunity. We investigated how natural selection has acted upon human TLRs, as an approach to assess their level of biological redundancy. We sequenced the ten human TLRs in a panel of 158 individuals from various populations worldwide and found that the intracellular TLRs -- activated by nucleic acids and particularly specialized in viral recognition -- have evolved under strong purifying selection, indicating their essential non-redundant role in host survival. Conversely, the selective constraints on the TLRs expressed on the cell surface -- activated by compounds other than nucleic acids -- have been much more relaxed, with higher rates of damaging nonsynonymous and stop mutations tolerated, suggesting their higher redundancy. Finally, we tested whether TLRs have experienced spatially-varying selection in human populations and found that the region encompassing TLR10-TLR1-TLR6 has been the target of recent positive selection among non-Africans. Our findings indicate that the different TLRs differ in their immunological redundancy, reflecting their distinct contributions to host defense. The insights gained in this study foster new hypotheses to be tested in clinical and epidemiological genetics of infectious disease.

  12. The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

    Directory of Open Access Journals (Sweden)

    Agostinho Antunes

    2008-11-01

    Full Text Available The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA, paternal (Y-chromosome, and biparental nuclear (nDNA genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple, a lentivirus analogous to human immunodeficiency virus (HIV. In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST = 0.92; nDNA F(ST = 0.18, and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago, which expanded during the Late Pleistocene ( approximately 100,000 years ago into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years, another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

  13. The evolutionary dynamics of the lion Panthera leo revealed by host and viral population genomics.

    Science.gov (United States)

    Antunes, Agostinho; Troyer, Jennifer L; Roelke, Melody E; Pecon-Slattery, Jill; Packer, Craig; Winterbach, Christiaan; Winterbach, Hanlie; Hemson, Graham; Frank, Laurence; Stander, Philip; Siefert, Ludwig; Driciru, Margaret; Funston, Paul J; Alexander, Kathy A; Prager, Katherine C; Mills, Gus; Wildt, David; Bush, Mitch; O'Brien, Stephen J; Johnson, Warren E

    2008-11-01

    The lion Panthera leo is one of the world's most charismatic carnivores and is one of Africa's key predators. Here, we used a large dataset from 357 lions comprehending 1.13 megabases of sequence data and genotypes from 22 microsatellite loci to characterize its recent evolutionary history. Patterns of molecular genetic variation in multiple maternal (mtDNA), paternal (Y-chromosome), and biparental nuclear (nDNA) genetic markers were compared with patterns of sequence and subtype variation of the lion feline immunodeficiency virus (FIV(Ple)), a lentivirus analogous to human immunodeficiency virus (HIV). In spite of the ability of lions to disperse long distances, patterns of lion genetic diversity suggest substantial population subdivision (mtDNA Phi(ST) = 0.92; nDNA F(ST) = 0.18), and reduced gene flow, which, along with large differences in sero-prevalence of six distinct FIV(Ple) subtypes among lion populations, refute the hypothesis that African lions consist of a single panmictic population. Our results suggest that extant lion populations derive from several Pleistocene refugia in East and Southern Africa ( approximately 324,000-169,000 years ago), which expanded during the Late Pleistocene ( approximately 100,000 years ago) into Central and North Africa and into Asia. During the Pleistocene/Holocene transition ( approximately 14,000-7,000 years), another expansion occurred from southern refugia northwards towards East Africa, causing population interbreeding. In particular, lion and FIV(Ple) variation affirms that the large, well-studied lion population occupying the greater Serengeti Ecosystem is derived from three distinct populations that admixed recently.

  14. Dynamic nanocrystal response and high temperature growth of carbon nanotube-ferroelectric hybrid nanostructure

    Science.gov (United States)

    Kumar, Ashok; Scott, J. F.; Katiyar, R. S.

    2013-12-01

    A long standing problem related to the capping of carbon nanotubes (CNT) by inorganic materials at high temperature has been solved. In situ dynamic response of Pb(Zr0.52Ti0.48)O3 (PZT) nanocrystals attached to the wings of the outer surface of PZT/CNT hybrid-nanostructure has been demonstrated under a constant-energy high-resolution transmission electron microscopy (HRTEM) e-beam. PZT nanocrystals revealed that the crystal orientations, positions, faces, and hopping states change with time. HRTEM study has been performed to investigate the microstructure of hybrid nanostructures and nanosize polycrystal trapped across the wings. Raman spectroscopy was utilized to investigate the local structures, defects, crystal qualities and temperature dependent growth and degradation of hybrid nanostructures. Raman spectra indicate that MWCNT and PZT/MWCNT/n-Si possess good quality of CNT before and after PZT deposition until 650 °C. The monoclinic Cc/Cm phase of PZT which is optimum in piezoelectric properties was prominent in the hybrid structure and should be useful for device applications. An unusual hexagonal faceting oscillation of the nano-crystal perimeter on a 10-30 s period is also observed.A long standing problem related to the capping of carbon nanotubes (CNT) by inorganic materials at high temperature has been solved. In situ dynamic response of Pb(Zr0.52Ti0.48)O3 (PZT) nanocrystals attached to the wings of the outer surface of PZT/CNT hybrid-nanostructure has been demonstrated under a constant-energy high-resolution transmission electron microscopy (HRTEM) e-beam. PZT nanocrystals revealed that the crystal orientations, positions, faces, and hopping states change with time. HRTEM study has been performed to investigate the microstructure of hybrid nanostructures and nanosize polycrystal trapped across the wings. Raman spectroscopy was utilized to investigate the local structures, defects, crystal qualities and temperature dependent growth and degradation of

  15. Evolutionary genetics of human enterovirus 71: origin, population dynamics, natural selection, and seasonal periodicity of the VP1 gene.

    Science.gov (United States)

    Tee, Kok Keng; Lam, Tommy Tsan-Yuk; Chan, Yoke Fun; Bible, Jon M; Kamarulzaman, Adeeba; Tong, C Y William; Takebe, Yutaka; Pybus, Oliver G

    2010-04-01

    Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (n = 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.

  16. Robust transmission stabilization and dynamic switching in broadband hybrid waveguide systems with nonlinear gain and loss

    Science.gov (United States)

    Nguyen, Quan M.; Peleg, Avner; Tran, Thinh P.

    2015-01-01

    We develop a method for transmission stabilization and robust dynamic switching for colliding optical soliton sequences in broadband waveguide systems with nonlinear gain and loss. The method is based on employing hybrid waveguides, consisting of spans with linear gain and cubic loss, and spans with linear loss, cubic gain, and quintic loss. We show that the amplitude dynamics is described by a hybrid Lotka-Volterra (LV) model, and use the model to determine the physical parameter values required for enhanced transmission stabilization and switching. Numerical simulations with coupled nonlinear Schrödinger equations confirm the predictions of the LV model, and show complete suppression of radiative instability and pulse distortion. This enables stable transmission over distances larger by an order of magnitude compared with uniform waveguides with linear gain and cubic loss. Moreover, multiple on-off and off-on dynamic switching events are demonstrated over a wide range of soliton amplitudes, showing the superiority of hybrid waveguides compared with static switching in uniform waveguides.

  17. Hybrid internal model control and proportional control of chaotic dynamical systems

    Institute of Scientific and Technical Information of China (English)

    齐冬莲; 姚良宾

    2004-01-01

    A new chaos control method is proposed to take advantage of chaos or avoid it. The hybrid Internal Model Control and Proportional Control learning scheme are introduced. In order to gain the desired robust performance and ensure the system's stability, Adaptive Momentum Algorithms are also developed. Through properly designing the neural network plant model and neural network controller, the chaotic dynamical systems are controlled while the parameters of the BP neural network are modified. Taking the Lorenz chaotic system as example, the results show that chaotic dynamical systems can be stabilized at the desired orbits by this control strategy.

  18. Dynamical Coulomb blockade of the nonlocal conductance in normalmetal/superconductor hybrid structures

    Energy Technology Data Exchange (ETDEWEB)

    Kolenda, Stefan; Wolf, Michael J.; Beckmann, Detlef [Institut fuer Nanotechnologie, KIT, 76021 Karlsruhe (Germany)

    2013-07-01

    In normalmetal/superconductor hybrid structures nonlocal conductance is determined by crossed Andreev reflection (CAR) and elastic cotunneling (EC). This was investigated recently both experimentally and theoretically. Dynamical Coulomb blockade of EC and CAR was predicted theoretically. Here we report on experimental investigations of these effects. We found signatures of dynamical Coulomb blockade in local and nonlocal conductance in the normal state. In the superconducting state, we find s-shaped nonlocal differential conductance curves as a function of bias applied on both contacts. These curves were observed for bias voltages both below and above the gap. We compare our results to theory.

  19. Hybrid internal model control and proportional control of chaotic dynamical systems.

    Science.gov (United States)

    Qi, Dong-lian; Yao, Liang-bin

    2004-01-01

    A new chaos control method is proposed to take advantage of chaos or avoid it. The hybrid Internal Model Control and Proportional Control learning scheme are introduced. In order to gain the desired robust performance and ensure the system's stability, Adaptive Momentum Algorithms are also developed. Through properly designing the neural network plant model and neural network controller, the chaotic dynamical systems are controlled while the parameters of the BP neural network are modified. Taking the Lorenz chaotic system as example, the results show that chaotic dynamical systems can be stabilized at the desired orbits by this control strategy.

  20. Dynamic control of the location of nanoparticles in hybrid co-assemblies

    Science.gov (United States)

    Su, Zhilong; Li, Xiaokang; Jiang, Xuesong; Lin, Shaoliang; Yin, Jie

    2015-03-01

    We herein demonstrated an approach to control the spatial distribution of components in hybrid microspheres. Hybrid core-shell structured microspheres (CSMs) prepared through co-assembly were used as starting materials, which are comprised of anthracene-ended hyperbranched poly(ether amine) (AN-hPEA) in the shell and crystallized anthracene containing polyhedral oligomer silsesquioxane (AN-POSS). Upon thermal annealing at a temperature higher than the melting point of AN-POSS, the diffusion of AN-POSS from the core to the shell of CSM leads to a transition of morphology from the core-shell structure to core-transition-shell to the more stable homogeneous morphology, which has been revealed by experimental results of TEM and DSC. The mechanism for the morphology transition of CSM induced by the diffusion of AN-POSS was disclosed by a dissipative particle dynamics (DPD) simulation. A mathematical model for the diffusion of POSS in the hybrid microsphere is established according to Fick's law of diffusion and can be used to quantify its distribution in CSM. Thus, the spatial distribution of POSS in the microsphere can be controlled dynamically by tuning the temperature and time of thermal annealing.We herein demonstrated an approach to control the spatial distribution of components in hybrid microspheres. Hybrid core-shell structured microspheres (CSMs) prepared through co-assembly were used as starting materials, which are comprised of anthracene-ended hyperbranched poly(ether amine) (AN-hPEA) in the shell and crystallized anthracene containing polyhedral oligomer silsesquioxane (AN-POSS). Upon thermal annealing at a temperature higher than the melting point of AN-POSS, the diffusion of AN-POSS from the core to the shell of CSM leads to a transition of morphology from the core-shell structure to core-transition-shell to the more stable homogeneous morphology, which has been revealed by experimental results of TEM and DSC. The mechanism for the morphology transition

  1. Dynamic modelling of an adsorption storage tank using a hybrid approach combining computational fluid dynamics and process simulation

    Science.gov (United States)

    Mota, J.P.B.; Esteves, I.A.A.C.; Rostam-Abadi, M.

    2004-01-01

    A computational fluid dynamics (CFD) software package has been coupled with the dynamic process simulator of an adsorption storage tank for methane fuelled vehicles. The two solvers run as independent processes and handle non-overlapping portions of the computational domain. The codes exchange data on the boundary interface of the two domains to ensure continuity of the solution and of its gradient. A software interface was developed to dynamically suspend and activate each process as necessary, and be responsible for data exchange and process synchronization. This hybrid computational tool has been successfully employed to accurately simulate the discharge of a new tank design and evaluate its performance. The case study presented here shows that CFD and process simulation are highly complementary computational tools, and that there are clear benefits to be gained from a close integration of the two. ?? 2004 Elsevier Ltd. All rights reserved.

  2. Experiment investigation for dynamic behavior of hybrid fiber effects on reactive powder concrete

    Science.gov (United States)

    Wang, Liwen; Pang, Baojun; Yang, Zhenqi; Chi, Runqiang

    2010-03-01

    The influences of different hybrid fibers (steel fibers add polyvinyl-alcohol fibers) mixture rates for reactive power concrete's (RPC) dynamic mechanical behavior after high temperature burnt was investigated by the Split Hopkinson pressure bar (SHPB) device. A plumbic pulse shaper technique was applied in the experiment, PVDF stress gauge was used to monitor the stress uniformity state within the specimen. The strain rate was between 75~85s-1, base on the stressstrain curves and dynamic modes of concrete specimen, the hybrid fiber effect on the dynamic properties was determined. The results show, dynamic compression strength of specimens which mixed with steel fibers (1.0%,1.5%,2.0% vol. rate) and 0.1% PVA fibers is higher than normal reactive powder concrete (NRPC), but the toughness improves unconspicuous; while strength of the one which has both steel fiber (1.0%,1.5%,2.0% vol. rate) and 0.2%PVA fiber declines than NRPC but the toughness improves and the plastic behaviors strengthened, stress-strain curve has evident rising and plate portions. It can be deduced that the concrete with mixed two kinds of fibers has improved dynamic mechanical properties after high temperature burnt. By compounding previous literature results, the mechanism of the experimental results can be explained.

  3. Multi-objective evolutionary optimization of biological pest control with impulsive dynamics in soybean crops.

    Science.gov (United States)

    Cardoso, Rodrigo T N; da Cruz, André R; Wanner, Elizabeth F; Takahashi, Ricardo H C

    2009-08-01

    The biological pest control in agriculture, an environment-friendly practice, maintains the density of pests below an economic injury level by releasing a suitable quantity of their natural enemies. This work proposes a multi-objective numerical solution to biological pest control for soybean crops, considering both the cost of application of the control action and the cost of economic damages. The system model is nonlinear with impulsive control dynamics, in order to cope more effectively with the actual control action to be applied, which should be performed in a finite number of discrete time instants. The dynamic optimization problem is solved using the NSGA-II, a fast and trustworthy multi-objective genetic algorithm. The results suggest a dual pest control policy, in which the relative price of control action versus the associated additional harvest yield determines the usage of either a low control action strategy or a higher one.

  4. An Evolutionary Algorithm Approach to Link Prediction in Dynamic Social Networks

    OpenAIRE

    Bliss, Catherine A.; Frank, Morgan R.; Danforth, Christopher M.; Dodds, Peter Sheridan

    2013-01-01

    Many real world, complex phenomena have underlying structures of evolving networks where nodes and links are added and removed over time. A central scientific challenge is the description and explanation of network dynamics, with a key test being the prediction of short and long term changes. For the problem of short-term link prediction, existing methods attempt to determine neighborhood metrics that correlate with the appearance of a link in the next observation period. Recent work has sugg...

  5. From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors

    OpenAIRE

    Ana Zafra Ruano; Elisa Cilia; Couceiro, José R.; Javier Ruiz Sanz; Joost Schymkowitz; Frederic Rousseau; Irene Luque; Tom Lenaerts

    2016-01-01

    Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing...

  6. Co-Evolutionary Mechanisms of Emotional Bursts in Online Social Dynamics and Networks

    Directory of Open Access Journals (Sweden)

    Bosiljka Tadić

    2013-11-01

    Full Text Available Collective emotional behavior of users is frequently observed on various Web portals; however, its complexity and the role of emotions in the acting mechanisms are still not thoroughly understood. In this work, using the empirical data and agent-based modeling, a parallel analysis is performed of two archetypal systems—Blogs and Internet-Relayed-Chats—both of which maintain self-organized dynamics but not the same communication rules and time scales. The emphasis is on quantifying the collective emotions by means of fractal analysis of the underlying processes as well as topology of social networks, which arise and co-evolve in these stochastic processes. The results reveal that two distinct mechanisms, which are based on different use of emotions (an emotion is characterized by two components, arousal and valence, are intrinsically associated with two classes of emergent social graphs. Their hallmarks are the evolution of communities in accordance with the excess of the negative emotions on popular Blogs, on one side, and smooth spreading of the Bot’s emotional impact over the entire hierarchical network of chats, on the other. Another emphasis of this work is on the understanding of nonextensivity of the emotion dynamics; it was found that, in its own way, each mechanism leads to a reduced phase space of the emotion components when the collective dynamics takes place. That a non-additive entropy describes emotion dynamics, is further confirmed by computing the q-generalized Kolmogorov-Sinai entropy rate in the empirical data of chats as well as in the simulations of interacting emotional agents and Bots.

  7. Evolutionary dynamics of the most populated genotype on rugged fitness landscapes

    Science.gov (United States)

    Jain, Kavita

    2007-09-01

    We consider an asexual population evolving on rugged fitness landscapes which are defined on the multidimensional genotypic space and have many local optima. We track the most populated genotype as it changes when the population jumps from a fitness peak to a better one during the process of adaptation. This is done using the dynamics of the shell model which is a simplified version of the quasispecies model for infinite populations and standard Wright-Fisher dynamics for large finite populations. We show that the population fraction of a genotype obtained within the quasispecies model and the shell model match for fit genotypes and at short times, but the dynamics of the two models are identical for questions related to the most populated genotype. We calculate exactly several properties of the jumps in infinite populations, some of which were obtained numerically in previous works. We also present our preliminary simulation results for finite populations. In particular, we measure the jump distribution in time and find that it decays as t-2 as in the quasispecies problem.

  8. Magnitude judgments of loudness change for discrete, dynamic, and hybrid stimuli.

    Science.gov (United States)

    Pastore, Richard E; Flint, Jesse

    2011-04-01

    Recent investigations of loudness change within stimuli have identified differences as a function of direction of change and power range (e.g., Canévet, Acustica, 62, 2136-2142, 1986; Neuhoff, Nature, 395, 123-124, 1998), with claims of differences between dynamic and static stimuli. Experiment 1 provides the needed direct empirical evaluation of loudness change across static, dynamic, and hybrid stimuli. Consistent with recent findings for dynamic stimuli, quantitative and qualitative differences in pattern of loudness change were found as a function of power change direction. With identical patterns of loudness change, only quantitative differences were found across stimulus type. In Experiment 2, Points of Subjective loudness Equality (PSE) provided additional information about loudness judgments for the static and dynamic stimuli. Because the quantitative differences across stimulus type exceed the magnitude that could be expected based upon temporal integration by the auditory system, other factors need to be, and are, considered.

  9. Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.

    Science.gov (United States)

    Katz, Lee S; Petkau, Aaron; Beaulaurier, John; Tyler, Shaun; Antonova, Elena S; Turnsek, Maryann A; Guo, Yan; Wang, Susana; Paxinos, Ellen E; Orata, Fabini; Gladney, Lori M; Stroika, Steven; Folster, Jason P; Rowe, Lori; Freeman, Molly M; Knox, Natalie; Frace, Mike; Boncy, Jacques; Graham, Morag; Hammer, Brian K; Boucher, Yan; Bashir, Ali; Hanage, William P; Van Domselaar, Gary; Tarr, Cheryl L

    2013-07-02

    Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics. Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to

  10. The effect of mycorrhizal inoculation on hybrid poplar fine root dynamics in hydrocarbon contaminated soils

    Energy Technology Data Exchange (ETDEWEB)

    Gunderson, J.; Knight, J.D.; Van Rees, K.C.J. [Saskatchewan Univ., Saskatoon, SK (Canada). Dept. of Soil Science

    2006-07-01

    The biological remediation of contaminated soils using plants was discussed. Hybrid poplars are good candidates for phytoremediation because they root deeply, cycle large amounts of water and grow quickly. Their fine root system is pivotal in nutrient and water acquisition. Therefore, in order to maximize the phytoremediation potential, it is important to understand the response of the fine root system. In addition to degrading organic chemicals, ectomycorrhizal (ECM) fungi provide the host with greater access to nutrients. This study determined the relationship between residual soil hydrocarbons and soil properties at a field site. The effects of residual contamination on hybrid poplar fine root dynamics was also examined along with the effect of ectomycorrhizal colonization on hybrid poplar fine root dynamics when grown in diesel contaminated soil under controlled conditions. A minirhizotron camera inside a growth chamber captured images of mycorrhizal inoculation on hybrid poplar fine root production. Walker hybrid poplar seedlings were grown for 12 weeks in a control soil and also in a diesel contaminated soil. Seedlings were also grown in control and diesel contaminated, ectomycorrhizal inoculated soils. The inoculum was a mycorrhizal mix containing Pisolithus tinctorius and Rhizopogon spp. The images showed that colonization by ECM fungi increased hybrid poplar fine root production and aboveground biomass in a diesel contaminated soil compared to non-colonized trees in the same soil. Root:shoot ratios were much higher in the diesel contaminated/non-inoculated treatment than in either of the control soil treatments. Results of phytoremediation in diesel contaminated soil were better in the non-colonized treatment than in the colonized treatment. Both treatments removed more contaminants from the soil than the unplanted control. Much higher quantities of hydrocarbons were found sequestered in the roots from the inoculated treatment than from the non

  11. Extended inclusive fitness theory: synergy and assortment drives the evolutionary dynamics in biology and economics.

    Science.gov (United States)

    Jaffe, Klaus

    2016-01-01

    W.D. Hamilton's Inclusive Fitness Theory explains the conditions that favor the emergence and maintenance of social cooperation. Today we know that these include direct and indirect benefits an agent obtains by its actions, and through interactions with kin and with genetically unrelated individuals. That is, in addition to kin-selection, assortation or homophily, and social synergies drive the evolution of cooperation. An Extended Inclusive Fitness Theory (EIFT) synthesizes the natural selection forces acting on biological evolution and on human economic interactions by assuming that natural selection driven by inclusive fitness produces agents with utility functions that exploit assortation and synergistic opportunities. This formulation allows to estimate sustainable cost/benefit threshold ratios of cooperation among organisms and/or economic agents, using existent analytical tools, illuminating our understanding of the dynamic nature of society, the evolution of cooperation among kin and non-kin, inter-specific cooperation, co-evolution, symbioses, division of labor and social synergies. EIFT helps to promote an interdisciplinary cross fertilization of the understanding of synergy by, for example, allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics. Another example is a bio-economic understanding of the motivations of terrorists, which identifies different forms of terrorism.

  12. A hybrid approach using chaotic dynamics and global search algorithms for combinatorial optimization problems

    Science.gov (United States)

    Igeta, Hideki; Hasegawa, Mikio

    Chaotic dynamics have been effectively applied to improve various heuristic algorithms for combinatorial optimization problems in many studies. Currently, the most used chaotic optimization scheme is to drive heuristic solution search algorithms applicable to large-scale problems by chaotic neurodynamics including the tabu effect of the tabu search. Alternatively, meta-heuristic algorithms are used for combinatorial optimization by combining a neighboring solution search algorithm, such as tabu, gradient, or other search method, with a global search algorithm, such as genetic algorithms (GA), ant colony optimization (ACO), or others. In these hybrid approaches, the ACO has effectively optimized the solution of many benchmark problems in the quadratic assignment problem library. In this paper, we propose a novel hybrid method that combines the effective chaotic search algorithm that has better performance than the tabu search and global search algorithms such as ACO and GA. Our results show that the proposed chaotic hybrid algorithm has better performance than the conventional chaotic search and conventional hybrid algorithms. In addition, we show that chaotic search algorithm combined with ACO has better performance than when combined with GA.

  13. Dynamic Performance Comparison for MPPT-PV Systems using Hybrid Pspice/Matlab Simulation

    Science.gov (United States)

    Aouchiche, N.; Becherif, M.; HadjArab, A.; Aitcheikh, M. S.; Ramadan, H. S.; Cheknane, A.

    2016-10-01

    The power generated by solar photovoltaic (PV) module depends on the surrounding irradiance and temperature. This paper presents a hybrid Matlab™/Pspice™ simulation model of PV system, combined with Cadence software SLPS. The hybridization is performed in order to gain the advantages of both simulation tools such as accuracy and efficiency in both Pspice electronic circuit and Matlab™ mathematical modelling respectively. For this purpose, the PV panel and the boost converter are developed using Pspice™ and hybridized with the mathematical Matlab™ model of maximum power point method controller (MPPT) through SLPS. The main objective is verify the significance of using the proposed hybrid simulation techniques in comparing the different MPPT algorithms such as the perturbation and observation (P&O), incremental of conductance (Inc-Cond) and counter reaction voltage using pilot cell (Pilot-Cell). Various simulations are performed under different atmospheric conditions in order to evaluate the dynamic behaviour for the system under study in terms of stability, efficiency and rapidity.

  14. Dynamic nanocrystal response and high temperature growth of carbon nanotube-ferroelectric hybrid nanostructure.

    Science.gov (United States)

    Kumar, Ashok; Scott, J F; Katiyar, R S

    2014-01-21

    A long standing problem related to the capping of carbon nanotubes (CNT) by inorganic materials at high temperature has been solved. In situ dynamic response of Pb(Zr0.52Ti0.48)O3 (PZT) nanocrystals attached to the wings of the outer surface of PZT/CNT hybrid-nanostructure has been demonstrated under a constant-energy high-resolution transmission electron microscopy (HRTEM) e-beam. PZT nanocrystals revealed that the crystal orientations, positions, faces, and hopping states change with time. HRTEM study has been performed to investigate the microstructure of hybrid nanostructures and nanosize polycrystal trapped across the wings. Raman spectroscopy was utilized to investigate the local structures, defects, crystal qualities and temperature dependent growth and degradation of hybrid nanostructures. Raman spectra indicate that MWCNT and PZT/MWCNT/n-Si possess good quality of CNT before and after PZT deposition until 650 °C. The monoclinic Cc/Cm phase of PZT which is optimum in piezoelectric properties was prominent in the hybrid structure and should be useful for device applications. An unusual hexagonal faceting oscillation of the nano-crystal perimeter on a 10-30 s period is also observed.

  15. Dynamic modeling of hybrid energy storage systems coupled to photovoltaic generation in residential applications

    Science.gov (United States)

    Maclay, James D.; Brouwer, Jacob; Samuelsen, G. Scott

    A model of a photovoltaic (PV) powered residence in stand-alone configuration was developed and evaluated. The model assesses the sizing, capital costs, control strategies, and efficiencies of reversible fuel cells (RFC), batteries, and ultra-capacitors (UC) both individually, and in combination, as hybrid energy storage devices. The choice of control strategy for a hybrid energy storage system is found to have a significant impact on system efficiency, hydrogen production and component utilization. A hybrid energy storage system comprised of batteries and RFC has the advantage of reduced cost (compared to using a RFC as the sole energy storage device), high system efficiency and hydrogen energy production capacity. A control strategy that preferentially used the RFC before the battery in meeting load demand allows both grid independent operation and better RFC utilization compared to a system that preferentially used the battery before the RFC. Ultra-capacitors coupled with a RFC in a hybrid energy storage system contain insufficient energy density to meet dynamic power demands typical of residential applications.

  16. Exciton dynamics and non-linearities in two-dimensional hybrid organic perovskites

    Energy Technology Data Exchange (ETDEWEB)

    Abdel-Baki, K.; Boitier, F.; Diab, H.; Lanty, G.; Jemli, K.; Lédée, F.; Deleporte, E.; Lauret, J. S., E-mail: jean-sebastien.lauret@lac.u-psud.fr [Laboratoire Aimé Cotton, CNRS, Univ. Paris-Sud, ENS Cachan, Université Paris-Saclay, 91405 Orsay Cedex (France); Garrot, D. [GEMAC, CNRS, UVSQ, Université Paris-Saclay, 45 avenue des États Unis 78035 Versailles Cedex (France)

    2016-02-14

    Due to their high potentiality for photovoltaic applications or coherent light sources, a renewed interest in hybrid organic perovskites has emerged for few years. When they are arranged in two dimensions, these materials can be considered as hybrid quantum wells. One consequence of the unique structure of 2D hybrid organic perovskites is a huge exciton binding energy that can be tailored through chemical engineering. We present experimental investigations of the exciton non-linearities by means of femtosecond pump-probe spectroscopy. The exciton dynamics is fitted with a bi-exponential decay with a free exciton life-time of ∼100 ps. Moreover, an ultrafast intraband relaxation (<150 fs) is also reported. Finally, the transient modification of the excitonic line is analyzed through the moment analysis and described in terms of reduction of the oscillator strength and linewidth broadening. We show that excitonic non-linearities in 2D hybrid organic perovskites share some behaviours of inorganic semiconductors despite their high exciton binding energy.

  17. The Hybrid Dynamic Prototype Construction and Parameter Optimization with Genetic Algorithm for Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Chun-Liang Lu

    2015-10-01

    Full Text Available The optimized hybrid artificial intelligence model is a potential tool to deal with construction engineering and management problems. Support vector machine (SVM has achieved excellent performance in a wide variety of applications. Nevertheless, how to effectively reduce the training complexity for SVM is still a serious challenge. In this paper, a novel order-independent approach for instance selection, called the dynamic condensed nearest neighbor (DCNN rule, is proposed to adaptively construct prototypes in the training dataset and to reduce the redundant or noisy instances in a classification process for the SVM. Furthermore, a hybrid model based on the genetic algorithm (GA is proposed to simultaneously optimize the prototype construction and the SVM kernel parameters setting to enhance the classification accuracy. Several UCI benchmark datasets are considered to compare the proposed hybrid GA-DCNN-SVM approach with the previously published GA-based method. The experimental results illustrate that the proposed hybrid model outperforms the existing method and effectively improves the classification performance for the SVM.

  18. Fast and stable redox reactions of MnO₂/CNT hybrid electrodes for dynamically stretchable pseudocapacitors.

    Science.gov (United States)

    Gu, Taoli; Wei, Bingqing

    2015-07-21

    Pseudocapacitors, which are energy storage devices that take advantage of redox reactions to store electricity, have a different charge storage mechanism compared to lithium-ion batteries (LIBs) and electric double-layer capacitors (EDLCs), and they could realize further gains if they were used as stretchable power sources. The realization of dynamically stretchable pseudocapacitors and understanding of the underlying fundamentals of their mechanical-electrochemical relationship have become indispensable. We report herein the electrochemical performance of dynamically stretchable pseudocapacitors using buckled MnO2/CNT hybrid electrodes. The extremely small relaxation time constant of less than 0.15 s indicates a fast redox reaction at the MnO2/CNT hybrid electrodes, securing a stable electrochemical performance for the dynamically stretchable pseudocapacitors. This finding and the fundamental understanding gained from the pseudo-capacitive behavior coupled with mechanical deformation under a dynamic stretching mode would provide guidance to further improve their overall performance including a higher power density than LIBs, a higher energy density than EDLCs, and a long-life cycling stability. Most importantly, these results will potentially accelerate the applications of stretchable pseudocapacitors for flexible and biomedical electronics.

  19. Hybrid static/dynamic scheduling for already optimized dense matrix factorization

    CERN Document Server

    Donfack, Simplice; Gropp, William D; Kale, Vivek

    2011-01-01

    We present the use of a hybrid static/dynamic scheduling strategy of the task dependency graph for direct methods used in dense numerical linear algebra. This strategy provides a balance of data locality, load balance, and low dequeue overhead. We show that the usage of this scheduling in communication avoiding dense factorization leads to significant performance gains. On a 48 core AMD Opteron NUMA machine, our experiments show that we can achieve up to 64% improvement over a version of CALU that uses fully dynamic scheduling, and up to 30% improvement over the version of CALU that uses fully static scheduling. On a 16-core Intel Xeon machine, our hybrid static/dynamic scheduling approach is up to 8% faster than the version of CALU that uses a fully static scheduling or fully dynamic scheduling. Our algorithm leads to speedups over the corresponding routines for computing LU factorization in well known libraries. On the 48 core AMD NUMA machine, our best implementation is up to 110% faster than MKL, while on...

  20. Dynamic Modeling and Motion Simulation for A Winged Hybrid-Driven Underwater Glider

    Institute of Scientific and Technical Information of China (English)

    WANG Shu-xin; SUN Xiu-jun; WANG Yan-hui; WU Jian-guo; WANG Xiao-ming

    2011-01-01

    PETREL,a winged hybrid-driven underwater glider is a novel and practical marine survey platform which combines the features of legacy underwater glider and conventional AUV(autonomous underwater vehicle).It can be treated as a multi-rigid-body system with a floating base and a particular hydrodynamic profile.In this paper,theorems on linear and angular momentum are used to establish the dynamic equations of motion of each rigid body and the effect of translational and rotational motion of internal masses on the attitude control are taken into consideration.In addition,due to the unique external shape with fixed wings and deflectable rudders and the dual-drive operation in thrust and glide modes,the approaches of building dynamic model of conventional AUV and hydrodynamic model of submarine are introduced,and the tailored dynamic equations of the hybrid glider are formulated.Moreover,the behaviors of motion in glide and thrust operation are analyzed based on the simulation and the feasibility of the dynamic model is validated by data from lake field trials.

  1. State estimation of stochastic non-linear hybrid dynamic system using an interacting multiple model algorithm.

    Science.gov (United States)

    Elenchezhiyan, M; Prakash, J

    2015-09-01

    In this work, state estimation schemes for non-linear hybrid dynamic systems subjected to stochastic state disturbances and random errors in measurements using interacting multiple-model (IMM) algorithms are formulated. In order to compute both discrete modes and continuous state estimates of a hybrid dynamic system either an IMM extended Kalman filter (IMM-EKF) or an IMM based derivative-free Kalman filters is proposed in this study. The efficacy of the proposed IMM based state estimation schemes is demonstrated by conducting Monte-Carlo simulation studies on the two-tank hybrid system and switched non-isothermal continuous stirred tank reactor system. Extensive simulation studies reveal that the proposed IMM based state estimation schemes are able to generate fairly accurate continuous state estimates and discrete modes. In the presence and absence of sensor bias, the simulation studies reveal that the proposed IMM unscented Kalman filter (IMM-UKF) based simultaneous state and parameter estimation scheme outperforms multiple-model UKF (MM-UKF) based simultaneous state and parameter estimation scheme.

  2. A Novel Image Encryption Scheme Based on Multi-orbit Hybrid of Discrete Dynamical System

    Directory of Open Access Journals (Sweden)

    Ruisong Ye

    2014-10-01

    Full Text Available A multi-orbit hybrid image encryption scheme based on discrete chaotic dynamical systems is proposed. One generalized Arnold map is adopted to generate three orbits for three initial conditions. Another chaotic dynamical system, tent map, is applied to generate one pseudo-random sequence to determine the hybrid orbit points from which one of the three orbits of generalized Arnold map. The hybrid orbit sequence is then utilized to shuffle the pixels' positions of plain-image so as to get one permuted image. To enhance the encryption security, two rounds of pixel gray values' diffusion is employed as well. The proposed encryption scheme is simple and easy to manipulate. The security and performance of the proposed image encryption have been analyzed, including histograms, correlation coefficients, information entropy, key sensitivity analysis, key space analysis, differential analysis, etc. All the experimental results suggest that the proposed image encryption scheme is robust and secure and can be used for secure image and video communication applications.

  3. Optimizing performance of hybrid FSO/RF networks in realistic dynamic scenarios

    Science.gov (United States)

    Llorca, Jaime; Desai, Aniket; Baskaran, Eswaran; Milner, Stuart; Davis, Christopher

    2005-08-01

    Hybrid Free Space Optical (FSO) and Radio Frequency (RF) networks promise highly available wireless broadband connectivity and quality of service (QoS), particularly suitable for emerging network applications involving extremely high data rate transmissions such as high quality video-on-demand and real-time surveillance. FSO links are prone to atmospheric obscuration (fog, clouds, snow, etc) and are difficult to align over long distances due the use of narrow laser beams and the effect of atmospheric turbulence. These problems can be mitigated by using adjunct directional RF links, which provide backup connectivity. In this paper, methodologies for modeling and simulation of hybrid FSO/RF networks are described. Individual link propagation models are derived using scattering theory, as well as experimental measurements. MATLAB is used to generate realistic atmospheric obscuration scenarios, including moving cloud layers at different altitudes. These scenarios are then imported into a network simulator (OPNET) to emulate mobile hybrid FSO/RF networks. This framework allows accurate analysis of the effects of node mobility, atmospheric obscuration and traffic demands on network performance, and precise evaluation of topology reconfiguration algorithms as they react to dynamic changes in the network. Results show how topology reconfiguration algorithms, together with enhancements to TCP/IP protocols which reduce the network response time, enable the network to rapidly detect and act upon link state changes in highly dynamic environments, ensuring optimized network performance and availability.

  4. The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity.

    Directory of Open Access Journals (Sweden)

    Bruce R Levin

    Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR, together with associated genes (cas, form the CRISPR-cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host-phage interactions in a model CRISPR-cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs and CRISPR-escape mutant phage (CEMs obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10(-6, our population studies indicate that there is more to the dynamics of phage-host interactions and the establishment of a BIM-CEM arms race than predicted from existing assumptions about phage infection and CRISPR-cas immunity. Among the unanticipated observations are: (i the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two spacers, (ii the survival of sensitive bacteria despite the presence of high densities of phage, and (iii the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii and (iii can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these

  5. The evolutionary dynamics of variant antigen genes in Babesia reveal a history of genomic innovation underlying host-parasite interaction

    KAUST Repository

    Jackson, Andrew P.

    2014-05-05

    Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.

  6. Cancer systems biology in the genome sequencing era: part 2, evolutionary dynamics of tumor clonal networks and drug resistance.

    Science.gov (United States)

    Wang, Edwin; Zou, Jinfeng; Zaman, Naif; Beitel, Lenore K; Trifiro, Mark; Paliouras, Miltiadis

    2013-08-01

    A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor recurs. Genome sequencing and computational analysis allows to computational dissection of clones from tumors, while singe-cell genome sequencing including RNA-Seq allows profiling of these clones. This opens a new window for treating a tumor as a system in which clones are evolving. Future cancer systems biology studies should consider a tumor as an evolving system with multiple clones. Therefore, topics discussed in Part 2 of this review include evolutionary dynamics of clonal networks, early-warning signals (e.g., genome duplication events) for formation of fast-growing clones, dissecting tumor heterogeneity, and modeling of clone-clone-stroma interactions for drug resistance. The ultimate goal of the future systems biology analysis is to obtain a 'whole-system' understanding of a tumor and therefore provides a more efficient and personalized management strategies for cancer patients. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

  7. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms.

    Science.gov (United States)

    Fischer, Iris; Diévart, Anne; Droc, Gaetan; Dufayard, Jean-François; Chantret, Nathalie

    2016-03-01

    Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family. © 2016 American Society of Plant Biologists. All Rights Reserved.

  8. Evolutionary Dynamics of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) Subfamily in Angiosperms1[OPEN

    Science.gov (United States)

    Dufayard, Jean-François; Chantret, Nathalie

    2016-01-01

    Gene duplications are an important factor in plant evolution, and lineage-specific expanded (LSE) genes are of particular interest. Receptor-like kinases expanded massively in land plants, and leucine-rich repeat receptor-like kinases (LRR-RLK) constitute the largest receptor-like kinases family. Based on the phylogeny of 7,554 LRR-RLK genes from 31 fully sequenced flowering plant genomes, the complex evolutionary dynamics of this family was characterized in depth. We studied the involvement of selection during the expansion of this family among angiosperms. LRR-RLK subgroups harbor extremely contrasting rates of duplication, retention, or loss, and LSE copies are predominantly found in subgroups involved in environmental interactions. Expansion rates also differ significantly depending on the time when rounds of expansion or loss occurred on the angiosperm phylogenetic tree. Finally, using a dN/dS-based test in a phylogenetic framework, we searched for selection footprints on LSE and single-copy LRR-RLK genes. Selective constraint appeared to be globally relaxed at LSE genes, and codons under positive selection were detected in 50% of them. Moreover, the leucine-rich repeat domains, and specifically four amino acids in them, were found to be the main targets of positive selection. Here, we provide an extensive overview of the expansion and evolution of this very large gene family. PMID:26773008

  9. Host-Specific and Segment-Specific Evolutionary Dynamics of Avian and Human Influenza A Viruses: A Systematic Review.

    Science.gov (United States)

    Kim, Kiyeon; Omori, Ryosuke; Ueno, Keisuke; Iida, Sayaka; Ito, Kimihito

    2016-01-01

    Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.

  10. Hybrid Molecular and Spin Dynamics Simulations for Ensembles of Magnetic Nanoparticles for Magnetoresistive Systems.

    Science.gov (United States)

    Teich, Lisa; Schröder, Christian

    2015-11-13

    The development of magnetoresistive sensors based on magnetic nanoparticles which are immersed in conductive gel matrices requires detailed information about the corresponding magnetoresistive properties in order to obtain optimal sensor sensitivities. Here, crucial parameters are the particle concentration, the viscosity of the gel matrix and the particle structure. Experimentally, it is not possible to obtain detailed information about the magnetic microstructure, i.e., orientations of the magnetic moments of the particles that define the magnetoresistive properties, however, by using numerical simulations one can study the magnetic microstructure theoretically, although this requires performing classical spin dynamics and molecular dynamics simulations simultaneously. Here, we present such an approach which allows us to calculate the orientation and the trajectory of every single magnetic nanoparticle. This enables us to study not only the static magnetic microstructure, but also the dynamics of the structuring process in the gel matrix itself. With our hybrid approach, arbitrary sensor configurations can be investigated and their magnetoresistive properties can be optimized.

  11. Aeromechanical stability analysis of a multirotor vehicle with application to hybrid heavy lift helicopter dynamics

    Science.gov (United States)

    Venkatesan, C.; Friedmann, P. P.

    1984-01-01

    The Hybrid Heavy Lift Helicopter (HHLH) is a potential candidate vehicle aimed at providing heavy lift capability at low cost. This vehicle consists of a buoyant envelope attached to a supporting structure. Four rotor systems are also attached to the supporting structure. Nonlinear equations of motion capable of modeling the dynamics of this multi-rotor/support frame/vehicle system have been developed and used to study the fundamental aeromechanical stability characteristics of this class of vehicles. The mechanism of coupling between the blades, supporting structure and rigid body modes is identified and the effect of buoyancy ratio (buoyant lift/total weight) on the vehicle dynamics is studied. It is shown that dynamics effects have a major role in the design of such vehicles. The analytical model developed is also useful for studying the aeromechanical stability of single rotor and tandem rotor coupled rotor/fuselage systems.

  12. Aeromechanical stability analysis of a multirotor vehicle with application to hybrid heavy lift helicopter dynamics

    Science.gov (United States)

    Venkatesan, C.; Friedmann, P. P.

    1984-01-01

    The Hybrid Heavy Lift Helicopter (HHLH) is a potential candidate vehicle aimed at providing heavy lift capability at low cost. This vehicle consists of a buoyant envelope attached to a supporting structure. Four rotor systems are also attached to the supporting structure. Nonlinear equations of motion capable of modeling the dynamics of this multi-rotor/support frame/vehicle system have been developed and used to study the fundamental aeromechanical stability characteristics of this class of vehicles. The mechanism of coupling between the blades, supporting structure and rigid body modes is identified and the effect of buoyancy ratio (buoyant lift/total weight) on the vehicle dynamics is studied. It is shown that dynamics effects have a major role in the design of such vehicles. The analytical model developed is also useful for studying the aeromechanical stability of single rotor and tandem rotor coupled rotor/fuselage systems.

  13. A HYBRID SYSTEM FOR DYNAMIC ANALYSIS AND DESIGN OF COUPLED SHEAR WALLS

    Directory of Open Access Journals (Sweden)

    A BERRAIS

    2000-06-01

    Full Text Available Non-linear dynamic analysis techniques are rapidly being developed and have been recognized as indispensable tools. However, their use in the design office requires special experience. Consequently they are not generally accepted as analysis/design tools. Additionally, uncertainties are associated with the determination of the earthquake forces, the stiffness and strength of the structure; the selection of the mathematical models; and the form of the earthquake. In this paper a hybrid system for the non-linear dynamic analysis/design of coupled shear walls is briefly described. The system combines expert system technology with finite element method to carry out the dynamic analysis of coupled walls under earthquake forces. The system has been implemented using Quintec-Prolog, Quintec-Flex and FORTRAN 77, and runs on a SUN SPARC station under Unix system.

  14. A hybrid multiscale coarse-grained method for dynamics on complex networks

    CERN Document Server

    Shen, Chuansheng; Hou, Zhonghuai; Kurths, Jürgen

    2016-01-01

    Brute-force simulations for dynamics on very large networks are quite expensive. While phenomenological treatments may capture some macroscopic properties, they often ignore important microscopic details. Fortunately, one may be only interested in the property of local part and not in the whole network. Here, we propose a hybrid multiscale coarse-grained(HMCG) method which combines a fine Monte Carlo(MC) simulation on the part of nodes of interest with a more coarse Langevin dynamics on the rest part. We demonstrate the validity of our method by analyzing the equilibrium Ising model and the nonequilibrium susceptible-infected-susceptible model. It is found that HMCG not only works very well in reproducing the phase transitions and critical phenomena of the microscopic models, but also accelerates the evaluation of dynamics with significant computational savings compared to microscopic MC simulations directly for the whole networks. The proposed method is general and can be applied to a wide variety of network...

  15. Dynamical Safety Analysis of the SABR Fusion-Fission Hybrid Reactor

    Science.gov (United States)

    Sumner, Tyler; Stacey, Weston; Ghiaassian, Seyed

    2009-11-01

    A hybrid fusion-fission reactor for the transmutation of spent nuclear fuel is being developed at Georgia Tech. The Subcritical Advanced Burner Reactor (SABR) is a 3000 MWth sodium-cooled, metal TRU-Zr fueled fast reactor driven by a tokamak fusion neutron source based on ITER physics and technology. We are investigating the accident dynamics of SABR's coupled fission, fusion and heat removal systems to explore the safety characteristics of a hybrid reactor. Possible accident scenarios such as loss of coolant mass flow (LOFA), of power (LOPA) and of heat sink (LOHSA), as well as inadvertent reactivity insertions and fusion source excursion are being analyzed using the RELAP5-3D code, the ATHENA version of which includes liquid metal coolants.

  16. A hybrid analysis method for linear dynamic soil-structure interaction in time and frequency domain

    Institute of Scientific and Technical Information of China (English)

    丁海平; 廖振鹏

    2001-01-01

    A hybrid analysis method in time and frequency domains for linear soil-structure interaction is presented. First, the time domain solution of the system with Rayleigh damping excited by a short time impulse is obtained by the decoupling numerical simulation technique of near-field wave motion. Then, the corresponding frequency domain solution can be got by Fourier transform. According to the relationship between damping value and dynamic re-sponse of a system, the solution of the system with complex damping can be got by Taylor expansion. The hybrid method makes the best of decoupling and explicit algorithm in time domain, and increases the calculation efficien-cy for linear soil-structure interaction analysis.

  17. Dynamic Modeling and Control Strategy Optimization for a Hybrid Electric Tracked Vehicle

    Directory of Open Access Journals (Sweden)

    Hong Wang

    2015-01-01

    Full Text Available A new hybrid electric tracked bulldozer composed of an engine generator, two driving motors, and an ultracapacitor is put forward, which can provide high efficiencies and less fuel consumption comparing with traditional ones. This paper first presents the terramechanics of this hybrid electric tracked bulldozer. The driving dynamics for this tracked bulldozer is then analyzed. After that, based on analyzing the working characteristics of the engine, generator, and driving motors, the power train system model and control strategy optimization is established by using MATLAB/Simulink and OPTIMUS software. Simulation is performed under a representative working condition, and the results demonstrate that fuel economy of the HETV can be significantly improved.

  18. Control Systems for a Dynamic Multi-Physics Model of a Nuclear Hybrid Energy System

    Energy Technology Data Exchange (ETDEWEB)

    Greenwood, Michael Scott [ORNL; Fugate, David W [ORNL; Cetiner, Sacit M [ORNL

    2017-01-01

    A Nuclear Hybrid Energy System (NHES) uses a nuclear reactor as the basic power generation unit, and the power generated is used by multiple customers as either thermal power, electrical power, or both. The definition and architecture of a particular NHES can be adapted based on the needs and opportunities of different local markets. For example, locations in need of potable water may be best served by coupling a desalination plant to the NHES. Similarly, a location near oil refineries may have a need for emission-free hydrogen production. Using the flexible, multi-domain capabilities of Modelica, Argonne National Laboratory, Idaho National Laboratory, and Oak Ridge National Laboratory are investigating the dynamics (e.g., thermal hydraulics and electrical generation/consumption) and cost of a hybrid system. This paper examines the NHES work underway, emphasizing the control system developed for individual subsystems and the overall supervisory control system.

  19. Projected equations of motion approach to hybrid quantum/classical dynamics in dielectric-metal composites

    CERN Document Server

    McMillan, Ryan J; Grüning, Myrta

    2016-01-01

    We introduce a hybrid method for dielectric-metal composites that describes the dynamics of the metallic system classically whilst retaining a quantum description of the dielectric. The time-dependent dipole moment of the classical system is mimicked by the introduction of projected equations of motion (PEOM) and the coupling between the two systems is achieved through an effective dipole-dipole interaction. To benchmark this method, we model a test system (semiconducting quantum dot-metal nanoparticle hybrid). We begin by examining the energy absorption rate, showing agreement between the PEOM method and the analytical rotating wave approximation (RWA) solution. We then investigate population inversion and show that the PEOM method provides an accurate model for the interaction under ultrashort pulse excitation where the traditional RWA breaks down.

  20. Hybrid particle-field molecular dynamics simulations for dense polymer systems.

    Science.gov (United States)

    Milano, Giuseppe; Kawakatsu, Toshihiro

    2009-06-07

    We propose a theoretical scheme for a hybrid simulation technique where self-consistent field theory and molecular dynamics simulation are combined (MD-SCF). We describe the detail of the main implementation issues on the evaluation of a smooth three-dimensional spatial density distribution and its special gradient based on the positions of particles. The treatments of our multiscale model system on an atomic scale or on a specific coarse-grained scale are carefully discussed. We perform a series of test simulations on this hybrid model system and compare the structural correlations on the atomic scale with those of classical MD simulations. The results are very encouraging and open a way to an efficient strategy that possess the main advantages common to the SCF and the atomistic approaches, while avoiding the disadvantages of each of the treatments.