Co-evolutionary dynamics of the human-environment system in the Heihe River basin in the past 2000years.

PubMed

Lu, Zhixiang; Wei, Yongping; Feng, Qi; Xie, Jiali; Xiao, Honglang; Cheng, Guodong

2018-09-01

There is limited quantitative understanding of interactions between human and environmental systems over the millennial scale. We aim to reveal the co-evolutionary dynamics of the human-environment system in a river basin by simulating the water use and net primary production (NPP) allocation for human and environmental systems over the last 2000years in Heihe River basin (HRB) in northwest China. We partition the catchment total evapotranspiration (ET) into ET for human and environmental systems with a social-hydrological framework and estimate the NPP for human and environmental systems using the Box-Lieth model, then classify the co-evolutionary processes of the human-environment system into distinct phases using the rate of changes of NPP over time, and discover the trade-offs or synergies relationships between them based on the elasticity of change of the NPP for humans to the change of NPP for environment. The co-evolutionary dynamics of human-environment system in the HRB can be divided into four periods, including: Phase I (Han Dynasty-Yuan Dynasty): predevelopment characterized by nearly no trade-offs between human and environment; Phase II (Yuan Dynasty-RC): slow agricultural development: characterized by a small human win due to small trade-offs between human and environment; Phase III (RC-2000): rapid agricultural development: characterized by a large human win due to large trade-offs between human and environment, and Phase IV (2000-2010): a rebalance characterized by large human wins with a small-environment win due to synergies, although these occurred very occasionally. This study provides a quantitative approach to describe the co-evolution of the human-environment system from the perspective of trade-offs and synergies in the millennial scale for the first time. The relationships between humans and environment changed from trade-off to synergy with the implementation of the water reallocation scheme in 2000. These findings improve the understanding of how humans influence environmental systems and responses to environmental stresses. Copyright © 2018 Elsevier B.V. All rights reserved.

Ecological and Evolutionary Effects of Dispersal on Freshwater Zooplankton

ERIC Educational Resources Information Center

Allen, Michael R.

2009-01-01

A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate ecology with evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species…

Howling about Trophic Cascades

ERIC Educational Resources Information Center

Kowalewski, David

2012-01-01

Following evolutionary theory and an agriculture model, ecosystem research has stressed bottom-up dynamics, implying that top wild predators are epiphenomenal effects of more basic causes. As such, they are assumed expendable. A more modern co-evolutionary and wilderness approach--trophic cascades--instead suggests that top predators, whose…

Testing for coevolutionary diversification: linking pattern with process.

PubMed

Althoff, David M; Segraves, Kari A; Johnson, Marc T J

2014-02-01

Coevolutionary diversification is cited as a major mechanism driving the evolution of diversity, particularly in plants and insects. However, tests of coevolutionary diversification have focused on elucidating macroevolutionary patterns rather than the processes giving rise to such patterns. Hence, there is weak evidence that coevolution promotes diversification. This is in part due to a lack of understanding about the mechanisms by which coevolution can cause speciation and the difficulty of integrating results across micro- and macroevolutionary scales. In this review, we highlight potential mechanisms of coevolutionary diversification, outline approaches to examine this process across temporal scales, and propose a set of minimal requirements for demonstrating coevolutionary diversification. Our aim is to stimulate research that tests more rigorously for coevolutionary diversification. Copyright © 2013 Elsevier Ltd. All rights reserved.

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed

Foitzik, S; DeHeer, C J; Hunjan, D N; Herbers, J M

2001-06-07

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host.

Age structure and cooperation in coevolutionary games on dynamic network

NASA Astrophysics Data System (ADS)

Qin, Zilong; Hu, Zhenhua; Zhou, Xiaoping; Yi, Jingzhang

2015-04-01

Our proposed model imitates the growth of a population and describes the age structure and the level of cooperation in games on dynamic network with continuous changes of structure and topology. The removal of nodes and links caused by age-dependent attack, together with the nodes addition standing for the newborns of population, badly ruins Matthew effect in this coevolutionary process. Though the network is generated by growth and preferential attachment, it degenerates into random network and it is no longer heterogeneous. When the removal of nodes and links is equal to the addition of nodes and links, the size of dynamic network is maintained in steady-state, so is the low level of cooperation. Severe structure variation, homogeneous topology and continuous invasion of new defection jointly make dynamic network unsuitable for the survival of cooperator even when the probability with which the newborn players initially adopt the strategy cooperation is high, while things change slightly when the connections of newborn players are restricted. Fortunately, moderate interactions in a generation trigger an optimal recovering process to encourage cooperation. The model developed in this paper outlines an explanation of the cohesion changes in the development process of an organization. Some suggestions for cooperative behavior improvement are given in the end.

A Coevolutionary Arms Race: Understanding Plant-Herbivore Interactions

ERIC Educational Resources Information Center

Becklin, Katie M.

2008-01-01

Plants and insects share a long evolutionary history characterized by relationships that affect individual, population, and community dynamics. Plant-herbivore interactions are a prominent feature of this evolutionary history; it is by plant-herbivore interactions that energy is transferred from primary producers to the rest of the food web. Not…

Social transmission of a host defense against cuckoo parasitism.

PubMed

Davies, Nicholas B; Welbergen, Justin A

2009-06-05

Coevolutionary arms races between brood parasites and hosts involve genetic adaptations and counter-adaptations. However, hosts sometimes acquire defenses too rapidly to reflect genetic change. Our field experiments show that observation of cuckoo (Cuculus canorus) mobbing by neighbors on adjacent territories induced reed warblers (Acrocephalus scirpaceus) to increase the mobbing of cuckoos but not of parrots (a harmless control) on their own territory. In contrast, observation of neighbors mobbing parrots had no effect on reed warblers' responses to either cuckoos or parrots. These results indicate that social learning provides a mechanism by which hosts rapidly increase their nest defense against brood parasites. Such enemy-specific social transmission enables hosts to track fine-scale spatiotemporal variation in parasitism and may influence the coevolutionary trajectories and population dynamics of brood parasites and hosts.

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions

PubMed Central

Zu, Jian; Wang, Jinliang; Huang, Gang

2016-01-01

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey’s trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator’s trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions. PMID:27685540

Evolutionary Diversification of Prey and Predator Species Facilitated by Asymmetric Interactions.

PubMed

Zu, Jian; Wang, Jinliang; Huang, Gang

We investigate the influence of asymmetric interactions on coevolutionary dynamics of a predator-prey system by using the theory of adaptive dynamics. We assume that the defense ability of prey and the attack ability of predators all can adaptively evolve, either caused by phenotypic plasticity or by behavioral choice, but there are certain costs in terms of their growth rate or death rate. The coevolutionary model is constructed from a deterministic approximation of random mutation-selection process. To sum up, if prey's trade-off curve is globally weakly concave, then five outcomes of coevolution are demonstrated, which depend on the intensity and shape of asymmetric predator-prey interactions and predator's trade-off shape. Firstly, we find that if there is a weakly decelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species may occur, but after branching further coevolution may lead to extinction of the predator species with a larger trait value. However, if there is a weakly accelerating cost and a weakly accelerating benefit for predator species, then evolutionary branching in the predator species is also possible and after branching the dimorphic predator can evolutionarily stably coexist with a monomorphic prey species. Secondly, if the asymmetric interactions become a little strong, then prey and predators will evolve to an evolutionarily stable equilibrium, at which they can stably coexist on a long-term timescale of evolution. Thirdly, if there is a weakly accelerating cost and a relatively strongly accelerating benefit for prey species, then evolutionary branching in the prey species is possible and the finally coevolutionary outcome contains a dimorphic prey and a monomorphic predator species. Fourthly, if the asymmetric interactions become more stronger, then predator-prey coevolution may lead to cycles in both traits and equilibrium population densities. The Red Queen dynamic is a possible outcome under asymmetric predator-prey interactions.

Coevolution in host-parasite systems: behavioural strategies of slave-making ants and their hosts.

PubMed Central

Foitzik, S.; DeHeer, C. J.; Hunjan, D. N.; Herbers, J. M.

2001-01-01

Recently, avian brood parasites and their hosts have emerged as model systems for the study of host-parasite coevolution. However, empirical studies of the highly analogous social parasites, which use the workers of another eusocial species to raise their own young, have never explicitly examined the dynamics of these systems from a coevolutionary perspective. Here, we demonstrate interpopulational variation in behavioural interactions between a socially parasitic slave-maker ant and its host that is consistent with the expectations of host-parasite coevolution. Parasite pressure, as inferred by the size, abundance and raiding frequency of Protomognathus americanus colonies, was highest in a New York population of the host Leptothorax longispinosus and lowest in a West Virginia population. As host-parasite coevolutionary theory would predict, we found that the slave-makers and the hosts from New York were more effective at raiding and defending against raiders, respectively, than were conspecifics from the West Virginia population. Some of these variations in efficacy were brought about by apparently simple shifts in behaviour. These results demonstrate that defence mechanisms against social parasites can evolve, and they give the first indications of the existence of a coevolutionary arms race between a social parasite and its host. PMID:11375101

Coevolutionary dynamics of opinion propagation and social balance: The key role of small-worldness

NASA Astrophysics Data System (ADS)

Chen, Yan; Chen, Lixue; Sun, Xian; Zhang, Kai; Zhang, Jie; Li, Ping

2014-03-01

The propagation of various opinions in social networks, which influences human inter-relationships and even social structure, and hence is a most important part of social life. We have incorporated social balance into opinion propagation in social networks are influenced by social balance. The edges in networks can represent both friendly or hostile relations, and change with the opinions of individual nodes. We introduce a model to characterize the coevolutionary dynamics of these two dynamical processes on Watts-Strogatz (WS) small-world network. We employ two distinct evolution rules (i) opinion renewal; and (ii) relation adjustment. By changing the rewiring probability, and thus the small-worldness of the WS network, we found that the time for the system to reach balanced states depends critically on both the average path length and clustering coefficient of the network, which is different than other networked process like epidemic spreading. In particular, the system equilibrates most quickly when the underlying network demonstrates strong small-worldness, i.e., small average path lengths and large clustering coefficient. We also find that opinion clusters emerge in the process of the network approaching the global equilibrium, and a measure of global contrariety is proposed to quantify the balanced state of a social network.

Coevolutionary dynamics of rice blast resistance gene Pi-ta and Magnaporthe oryzae avirulence gene AVR-Pita 1

USDA-ARS?s Scientific Manuscript database

The Pi-ta gene in rice is effective in preventing infections by Magnaporthe oryzae strains that contain the corresponding avirulence gene, AVR-Pita1. Genome sequencing and mapping studies demonstrated that AVR-Pita1 is highly unstable, and diverse haplotypes of AVR-Pita1 have been identified from is...

Exploring Molecular Mechanisms of Paradoxical Activation in the BRAF Kinase Dimers: Atomistic Simulations of Conformational Dynamics and Modeling of Allosteric Communication Networks and Signaling Pathways

PubMed Central

Tse, Amanda; Verkhivker, Gennady M.

2016-01-01

The recent studies have revealed that most BRAF inhibitors can paradoxically induce kinase activation by promoting dimerization and enzyme transactivation. Despite rapidly growing number of structural and functional studies about the BRAF dimer complexes, the molecular basis of paradoxical activation phenomenon is poorly understood and remains largely hypothetical. In this work, we have explored the relationships between inhibitor binding, protein dynamics and allosteric signaling in the BRAF dimers using a network-centric approach. Using this theoretical framework, we have combined molecular dynamics simulations with coevolutionary analysis and modeling of the residue interaction networks to determine molecular determinants of paradoxical activation. We have investigated functional effects produced by paradox inducer inhibitors PLX4720, Dabrafenib, Vemurafenib and a paradox breaker inhibitor PLX7904. Functional dynamics and binding free energy analyses of the BRAF dimer complexes have suggested that negative cooperativity effect and dimer-promoting potential of the inhibitors could be important drivers of paradoxical activation. We have introduced a protein structure network model in which coevolutionary residue dependencies and dynamic maps of residue correlations are integrated in the construction and analysis of the residue interaction networks. The results have shown that coevolutionary residues in the BRAF structures could assemble into independent structural modules and form a global interaction network that may promote dimerization. We have also found that BRAF inhibitors could modulate centrality and communication propensities of global mediating centers in the residue interaction networks. By simulating allosteric communication pathways in the BRAF structures, we have determined that paradox inducer and breaker inhibitors may activate specific signaling routes that correlate with the extent of paradoxical activation. While paradox inducer inhibitors may facilitate a rapid and efficient communication via an optimal single pathway, the paradox breaker may induce a broader ensemble of suboptimal and less efficient communication routes. The central finding of our study is that paradox breaker PLX7904 could mimic structural, dynamic and network features of the inactive BRAF-WT monomer that may be required for evading paradoxical activation. The results of this study rationalize the existing structure-functional experiments by offering a network-centric rationale of the paradoxical activation phenomenon. We argue that BRAF inhibitors that amplify dynamic features of the inactive BRAF-WT monomer and intervene with the allosteric interaction networks may serve as effective paradox breakers in cellular environment. PMID:27861609

New frontiers in the study of human cultural and genetic evolution.

PubMed

Ross, Cody T; Richerson, Peter J

2014-12-01

In this review, we discuss the dynamic linkages between culture and the genetic evolution of the human species. We begin by briefly describing the framework of gene-culture coevolutionary (or dual-inheritance) models for human evolutionary change. Until recently, the literature on gene-culture coevolution was composed primarily of mathematical models and formalized theory describing the complex dynamics underlying human behavior, adaptation, and technological evolution, but had little empirical support concerning genetics. The rapid progress in the fields of molecular genetics and genomics, however, is now providing the kinds of data needed to produce rich empirical support for gene-culture coevolutionary models. We briefly outline how theoretical and methodological progress in genome sciences has provided ways for the strength of selection on genes to be evaluated, and then outline how evidence of selection on several key genes can be directly linked to human cultural practices. We then describe some exciting new directions in the empirical study of gene-culture coevolution, and conclude with a discussion of the role of gene-culture evolutionary models in the future integration of medical, biological, and social sciences. Copyright © 2014 Elsevier Ltd. All rights reserved.

Public goods games on adaptive coevolutionary networks

NASA Astrophysics Data System (ADS)

Pichler, Elgar; Shapiro, Avi M.

2017-07-01

Productive societies feature high levels of cooperation and strong connections between individuals. Public Goods Games (PGGs) are frequently used to study the development of social connections and cooperative behavior in model societies. In such games, contributions to the public good are made only by cooperators, while all players, including defectors, reap public goods benefits, which are shares of the contributions amplified by a synergy factor. Classic results of game theory show that mutual defection, as opposed to cooperation, is the Nash Equilibrium of PGGs in well-mixed populations, where each player interacts with all others. In this paper, we explore the coevolutionary dynamics of a low information public goods game on a complex network in which players adapt to their environment in order to increase individual payoffs relative to past payoffs parameterized by greediness. Players adapt by changing their strategies, either to cooperate or to defect, and by altering their social connections. We find that even if players do not know other players' strategies and connectivity, cooperation can arise and persist despite large short-term fluctuations.

Public goods games on adaptive coevolutionary networks.

PubMed

Pichler, Elgar; Shapiro, Avi M

2017-07-01

Productive societies feature high levels of cooperation and strong connections between individuals. Public Goods Games (PGGs) are frequently used to study the development of social connections and cooperative behavior in model societies. In such games, contributions to the public good are made only by cooperators, while all players, including defectors, reap public goods benefits, which are shares of the contributions amplified by a synergy factor. Classic results of game theory show that mutual defection, as opposed to cooperation, is the Nash Equilibrium of PGGs in well-mixed populations, where each player interacts with all others. In this paper, we explore the coevolutionary dynamics of a low information public goods game on a complex network in which players adapt to their environment in order to increase individual payoffs relative to past payoffs parameterized by greediness. Players adapt by changing their strategies, either to cooperate or to defect, and by altering their social connections. We find that even if players do not know other players' strategies and connectivity, cooperation can arise and persist despite large short-term fluctuations.

A Multipopulation Coevolutionary Strategy for Multiobjective Immune Algorithm

PubMed Central

Shi, Jiao; Gong, Maoguo; Ma, Wenping; Jiao, Licheng

2014-01-01

How to maintain the population diversity is an important issue in designing a multiobjective evolutionary algorithm. This paper presents an enhanced nondominated neighbor-based immune algorithm in which a multipopulation coevolutionary strategy is introduced for improving the population diversity. In the proposed algorithm, subpopulations evolve independently; thus the unique characteristics of each subpopulation can be effectively maintained, and the diversity of the entire population is effectively increased. Besides, the dynamic information of multiple subpopulations is obtained with the help of the designed cooperation operator which reflects a mutually beneficial relationship among subpopulations. Subpopulations gain the opportunity to exchange information, thereby expanding the search range of the entire population. Subpopulations make use of the reference experience from each other, thereby improving the efficiency of evolutionary search. Compared with several state-of-the-art multiobjective evolutionary algorithms on well-known and frequently used multiobjective and many-objective problems, the proposed algorithm achieves comparable results in terms of convergence, diversity metrics, and running time on most test problems. PMID:24672330

The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution.

PubMed

King, Kayla C; Auld, Stuart K J R; Wilson, Philip J; James, Janna; Little, Tom J

2013-02-01

Strong selection on parasites, as well as on hosts, is crucial for fueling coevolutionary dynamics. Selection will be especially strong if parasites that encounter resistant hosts are destroyed and diluted from the local environment. We tested whether spores of the bacterial parasite Pasteuria ramosa were passed through the gut (the route of infection) of their host, Daphnia magna, and whether passaged spores remained viable for a "second chance" at infecting a new host. In particular, we tested if this viability (estimated via infectivity) depended on host genotype, whether or not the genotype was susceptible, and on initial parasite dose. Our results show that Pasteuria spores generally remain viable after passage through both susceptible and resistant Daphnia. Furthermore, these spores remained infectious even after being frozen for several weeks. If parasites can get a second chance at infecting hosts in the wild, selection for infection success in the first instance will be reduced. This could also weaken reciprocal selection on hosts and slow the coevolutionary process.

Coevolutionary diversification creates nested-modular structure in phage–bacteria interaction networks

PubMed Central

Beckett, Stephen J.; Williams, Hywel T. P.

2013-01-01

Phage and their bacterial hosts are the most diverse and abundant biological entities in the oceans, where their interactions have a major impact on marine ecology and ecosystem function. The structure of interaction networks for natural phage–bacteria communities offers insight into their coevolutionary origin. At small phylogenetic scales, observed communities typically show a nested structure, in which both hosts and phages can be ranked by their range of resistance and infectivity, respectively. A qualitatively different multi-scale structure is seen at larger phylogenetic scales; a natural assemblage sampled from the Atlantic Ocean displays large-scale modularity and local nestedness within each module. Here, we show that such ‘nested-modular’ interaction networks can be produced by a simple model of host–phage coevolution in which infection depends on genetic matching. Negative frequency-dependent selection causes diversification of hosts (to escape phages) and phages (to track their evolving hosts). This creates a diverse community of bacteria and phage, maintained by kill-the-winner ecological dynamics. When the resulting communities are visualized as bipartite networks of who infects whom, they show the nested-modular structure characteristic of the Atlantic sample. The statistical significance and strength of this observation varies depending on whether the interaction networks take into account the density of the interacting strains, with implications for interpretation of interaction networks constructed by different methods. Our results suggest that the apparently complex community structures associated with marine bacteria and phage may arise from relatively simple coevolutionary origins. PMID:24516719

Quantitative genetic insights into the coevolutionary dynamics of male and female genitalia

PubMed Central

Evans, Jonathan P.; van Lieshout, Emile; Gasparini, Clelia

2013-01-01

The spectacular variability that typically characterizes male genital traits has largely been attributed to the role of sexual selection. Among the evolutionary mechanisms proposed to account for this diversity, two processes in particular have generated considerable interest. On the one hand, females may exploit postcopulatory mechanisms of selection to favour males with preferred genital traits (cryptic female choice; CFC), while on the other hand females may evolve structures or behaviours that mitigate the direct costs imposed by male genitalia (sexual conflict; SC). A critical but rarely explored assumption underlying both processes is that male and female reproductive traits coevolve, either via the classic Fisherian model of preference-trait coevolution (CFC) or through sexually antagonistic selection (SC). Here, we provide evidence for this prediction in the guppy (Poecilia reticulata), a polyandrous livebearing fish in which males transfer sperm internally to females via consensual and forced matings. Our results from a paternal half-sibling breeding design reveal substantial levels of additive genetic variation underlying male genital size and morphology—two traits known to predict mating success during non-consensual matings. Our subsequent finding that physically interacting female genital traits exhibit corresponding levels of genetic (co)variation reveals the potential intersexual coevolutionary dynamics of male and female genitalia, thereby fulfilling a fundamental assumption underlying CFC and SC theory. PMID:23720546

True Triaxial Experimental Study of Rockbursts Induced By Ramp and Cyclic Dynamic Disturbances

NASA Astrophysics Data System (ADS)

Su, Guoshao; Hu, Lihua; Feng, Xiating; Yan, Liubin; Zhang, Gangliang; Yan, Sizhou; Zhao, Bin; Yan, Zhaofu

2018-04-01

A modified rockburst testing system was utilized to reproduce rockbursts induced by ramp and cyclic dynamic disturbances with a low-intermediate strain rate of 2 × 10-3-5 × 10-3 s-1 in the laboratory. The experimental results show that both the ramp and cyclic dynamic disturbances play a significant role in inducing rockbursts. In the tests of rockbursts induced by a ramp dynamic disturbance, as the static stress before the dynamic disturbance increases, both the strength of specimens and the kinetic energy of the ejected fragments first increase and then decrease. In the tests of rockbursts induced by a cyclic dynamic disturbance, there exists a rockburst threshold of the static stress and the dynamic disturbance amplitude, and the kinetic energy of the ejected fragments first increases and then decreases as the cyclic dynamic disturbance frequency increases. The main differences between rockbursts induced by ramp dynamic disturbances and those induced by cyclic dynamic disturbances are as follows: the rockburst development process of the former is characterized by an impact failure feature, while that of the latter is characterized by a fatigue failure feature; the damage evolution curve of the specimen of the former has a leap-developing form with a significant catastrophic feature, while that of the latter has an inverted S-shape with a remarkable fatigue damage characteristic; the energy mechanism of the former involves the ramp dynamic disturbance giving extra elastic strain energy to rocks, while that of the latter involves the cyclic dynamic disturbance decreasing the ultimate energy storage capacity of rocks.

Understanding the Earth Systems: Expressions of Dynamic and Cyclic Thinking among University Students

ERIC Educational Resources Information Center

Batzri, Or; Ben Zvi Assaraf, Orit; Cohen, Carmit; Orion, Nir

2015-01-01

In this two-part study, we examine undergraduate university students' expression of two important system thinking characteristics--dynamic thinking and cyclic thinking--focusing particularly on students of geology. The study was conducted using an Earth systems questionnaire designed to elicit and reflect either dynamic or cyclic thinking. The…

Introducing TreeCollapse: a novel greedy algorithm to solve the cophylogeny reconstruction problem.

PubMed

Drinkwater, Benjamin; Charleston, Michael A

2014-01-01

Cophylogeny mapping is used to uncover deep coevolutionary associations between two or more phylogenetic histories at a macro coevolutionary scale. As cophylogeny mapping is NP-Hard, this technique relies heavily on heuristics to solve all but the most trivial cases. One notable approach utilises a metaheuristic to search only a subset of the exponential number of fixed node orderings possible for the phylogenetic histories in question. This is of particular interest as it is the only known heuristic that guarantees biologically feasible solutions. This has enabled research to focus on larger coevolutionary systems, such as coevolutionary associations between figs and their pollinator wasps, including over 200 taxa. Although able to converge on solutions for problem instances of this size, a reduction from the current cubic running time is required to handle larger systems, such as Wolbachia and their insect hosts. Rather than solving this underlying problem optimally this work presents a greedy algorithm called TreeCollapse, which uses common topological patterns to recover an approximation of the coevolutionary history where the internal node ordering is fixed. This approach offers a significant speed-up compared to previous methods, running in linear time. This algorithm has been applied to over 100 well-known coevolutionary systems converging on Pareto optimal solutions in over 68% of test cases, even where in some cases the Pareto optimal solution has not previously been recoverable. Further, while TreeCollapse applies a local search technique, it can guarantee solutions are biologically feasible, making this the fastest method that can provide such a guarantee. As a result, we argue that the newly proposed algorithm is a valuable addition to the field of coevolutionary research. Not only does it offer a significantly faster method to estimate the cost of cophylogeny mappings but by using this approach, in conjunction with existing heuristics, it can assist in recovering a larger subset of the Pareto front than has previously been possible.

Coevolutionary constraints in the sequence-space of macromolecular complexes reflect their self-assembly pathways.

PubMed

Mallik, Saurav; Kundu, Sudip

2017-07-01

Is the order in which biomolecular subunits self-assemble into functional macromolecular complexes imprinted in their sequence-space? Here, we demonstrate that the temporal order of macromolecular complex self-assembly can be efficiently captured using the landscape of residue-level coevolutionary constraints. This predictive power of coevolutionary constraints is irrespective of the structural, functional, and phylogenetic classification of the complex and of the stoichiometry and quaternary arrangement of the constituent monomers. Combining this result with a number of structural attributes estimated from the crystal structure data, we find indications that stronger coevolutionary constraints at interfaces formed early in the assembly hierarchy probably promotes coordinated fixation of mutations that leads to high-affinity binding with higher surface area, increased surface complementarity and elevated number of molecular contacts, compared to those that form late in the assembly. Proteins 2017; 85:1183-1189. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Coevolutionary network approach to cultural dynamics controlled by intolerance

NASA Astrophysics Data System (ADS)

Gracia-Lázaro, Carlos; Quijandría, Fernando; Hernández, Laura; Floría, Luis Mario; Moreno, Yamir

2011-12-01

Starting from Axelrod's model of cultural dissemination, we introduce a rewiring probability, enabling agents to cut the links with their unfriendly neighbors if their cultural similarity is below a tolerance parameter. For low values of tolerance, rewiring promotes the convergence to a frozen monocultural state. However, intermediate tolerance values prevent rewiring once the network is fragmented, resulting in a multicultural society even for values of initial cultural diversity in which the original Axelrod model reaches globalization.

The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution

PubMed Central

King, Kayla C; Auld, Stuart K J R; Wilson, Philip J; James, Janna; Little, Tom J

2013-01-01

Strong selection on parasites, as well as on hosts, is crucial for fueling coevolutionary dynamics. Selection will be especially strong if parasites that encounter resistant hosts are destroyed and diluted from the local environment. We tested whether spores of the bacterial parasite Pasteuria ramosa were passed through the gut (the route of infection) of their host, Daphnia magna, and whether passaged spores remained viable for a “second chance” at infecting a new host. In particular, we tested if this viability (estimated via infectivity) depended on host genotype, whether or not the genotype was susceptible, and on initial parasite dose. Our results show that Pasteuria spores generally remain viable after passage through both susceptible and resistant Daphnia. Furthermore, these spores remained infectious even after being frozen for several weeks. If parasites can get a second chance at infecting hosts in the wild, selection for infection success in the first instance will be reduced. This could also weaken reciprocal selection on hosts and slow the coevolutionary process. PMID:23467806

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees.

PubMed

Martínez-Aquino, Andrés

2016-08-01

Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host-parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a "compass" when "walking" through jungles of tangled phylogenetic trees.

Phylogenetic framework for coevolutionary studies: a compass for exploring jungles of tangled trees

PubMed Central

2016-01-01

Abstract Phylogenetics is used to detect past evolutionary events, from how species originated to how their ecological interactions with other species arose, which can mirror cophylogenetic patterns. Cophylogenetic reconstructions uncover past ecological relationships between taxa through inferred coevolutionary events on trees, for example, codivergence, duplication, host-switching, and loss. These events can be detected by cophylogenetic analyses based on nodes and the length and branching pattern of the phylogenetic trees of symbiotic associations, for example, host–parasite. In the past 2 decades, algorithms have been developed for cophylogetenic analyses and implemented in different software, for example, statistical congruence index and event-based methods. Based on the combination of these approaches, it is possible to integrate temporal information into cophylogenetical inference, such as estimates of lineage divergence times between 2 taxa, for example, hosts and parasites. Additionally, the advances in phylogenetic biogeography applying methods based on parametric process models and combined Bayesian approaches, can be useful for interpreting coevolutionary histories in a scenario of biogeographical area connectivity through time. This article briefly reviews the basics of parasitology and provides an overview of software packages in cophylogenetic methods. Thus, the objective here is to present a phylogenetic framework for coevolutionary studies, with special emphasis on groups of parasitic organisms. Researchers wishing to undertake phylogeny-based coevolutionary studies can use this review as a “compass” when “walking” through jungles of tangled phylogenetic trees. PMID:29491928

Dynamic strain aging in the high-temperature low-cycle fatigue of SA508 Cl. 3 forging steel

NASA Astrophysics Data System (ADS)

Lee, Byung Ho; Kim, In Sup

1995-10-01

The effect of dynamic strain aging on cyclic stress response and fatigue resistance of ASME SA508 Cl.3 forging steel for nuclear reactor pressure vessels has been evaluated in the temperature range of room temperature to 500°C. Total strain ranges and strain rates were varied from 0.7 to 2.0% and from 4 × 10 -4 to 1 × 10 -2 s -1, respectively. The cyclic stress response depended on the testing temperature, strain rate, and range. Generally, the initial cyclic hardening was immediately followed by cyclic softening at all strain rates. However, at 300°C, the operating temperature of nuclear reactor pressure vessels, the variation of cyclic stress amplitude showed the primary and secondary hardening stages dependent on the strain rate and strain range. Dynamic strain aging was manifested by enhanced cyclic hardening, distinguished secondary hardening, and negative strain rate sensitivity. A modified cell shutting model was described for the onset of the secondary hardening due to the dynamic strain aging and it was in good agreement with the experimental results. Fatigue life increased in strain rate at all testing temperatures. Specifically the fatigue life was longer at the dynamic strain aging temperature. Further, the dynamic strain aging was easy to initiate the crack, while crack propagation was retarded by crack branching and suppression of plastic zone, hence the dynamic strain aging caused the improvement of fatigue resistance.

The Role of Time-Scales in Socio-hydrology

NASA Astrophysics Data System (ADS)

Blöschl, Günter; Sivapalan, Murugesu

2016-04-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time scale interactions and the coevolution of humans and water. Water Resour. Res., 51, 6988-7022, doi:10.1002/2015WR017896.

Multiscale Modeling of Human-Water Interactions: The Role of Time-Scales

NASA Astrophysics Data System (ADS)

Bloeschl, G.; Sivapalan, M.

2015-12-01

Much of the interest in hydrological modeling in the past decades revolved around resolving spatial variability. With the rapid changes brought about by human impacts on the hydrologic cycle, there is now an increasing need to refocus on time dependency. We present a co-evolutionary view of hydrologic systems, in which every part of the system including human systems, co-evolve, albeit at different rates. The resulting coupled human-nature system is framed as a dynamical system, characterized by interactions of fast and slow time scales and feedbacks between environmental and social processes. This gives rise to emergent phenomena such as the levee effect, adaptation to change and system collapse due to resource depletion. Changing human values play a key role in the emergence of these phenomena and should therefore be considered as internal to the system in a dynamic way. The co-evolutionary approach differs from the traditional view of water resource systems analysis as it allows for path dependence, multiple equilibria, lock-in situations and emergent phenomena. The approach may assist strategic water management for long time scales through facilitating stakeholder participation, exploring the possibility space of alternative futures, and helping to synthesise the observed dynamics of different case studies. Future research opportunities include the study of how changes in human values are connected to human-water interactions, historical analyses of trajectories of system co-evolution in individual places and comparative analyses of contrasting human-water systems in different climate and socio-economic settings. Reference Sivapalan, M. and G. Blöschl (2015) Time Scale Interactions and the Co-evolution of Humans and Water. Water Resour. Res., 51, in press.

Testing co-evolutionary hypotheses over geological timescales: interactions between Mesozoic non-avian dinosaurs and cycads.

PubMed

Butler, Richard J; Barrett, Paul M; Kenrick, Paul; Penn, Malcolm G

2009-02-01

The significance of co-evolution over ecological timescales is well established, yet it remains unclear to what extent co-evolutionary processes contribute to driving large-scale evolutionary and ecological changes over geological timescales. Some of the most intriguing and pervasive long-term co-evolutionary hypotheses relate to proposed interactions between herbivorous non-avian dinosaurs and Mesozoic plants, including cycads. Dinosaurs have been proposed as key dispersers of cycad seeds during the Mesozoic, and temporal variation in cycad diversity and abundance has been linked to dinosaur faunal changes. Here we assess the evidence for proposed hypotheses of trophic and evolutionary interactions between these two groups using diversity analyses, a new database of Cretaceous dinosaur and plant co-occurrence data, and a geographical information system (GIS) as a visualisation tool. Phylogenetic evidence suggests that the origins of several key biological properties of cycads (e.g. toxins, bright-coloured seeds) likely predated the origin of dinosaurs. Direct evidence of dinosaur-cycad interactions is lacking, but evidence from extant ecosystems suggests that dinosaurs may plausibly have acted as seed dispersers for cycads, although it is likely that other vertebrate groups (e.g. birds, early mammals) also played a role. Although the Late Triassic radiations of dinosaurs and cycads appear to have been approximately contemporaneous, few significant changes in dinosaur faunas coincide with the late Early Cretaceous cycad decline. No significant spatiotemporal associations between particular dinosaur groups and cycads can be identified - GIS visualisation reveals disparities between the spatiotemporal distributions of some dinosaur groups (e.g. sauropodomorphs) and cycads that are inconsistent with co-evolutionary hypotheses. The available data provide no unequivocal support for any of the proposed co-evolutionary interactions between cycads and herbivorous dinosaurs - diffuse co-evolutionary scenarios that are proposed to operate over geological timescales are plausible, but such hypotheses need to be firmly grounded on direct evidence of interaction and may be difficult to support given the patchiness of the fossil record.

Dynamic Charge Storage in Ionic Liquids-Filled Nanopores: Insight from a Computational Cyclic Voltammetry Study.

PubMed

He, Yadong; Huang, Jingsong; Sumpter, Bobby G; Kornyshev, Alexei A; Qiao, Rui

2015-01-02

Understanding the dynamic charge storage in nanoporous electrodes with room-temperature ionic liquid electrolytes is essential for optimizing them to achieve supercapacitors with high energy and power densities. Herein, we report coarse-grained molecular dynamics simulations of the cyclic voltammetry of supercapacitors featuring subnanometer pores and model ionic liquids. We show that the cyclic charging and discharging of nanopores are governed by the interplay between the external field-driven ion transport and the sloshing dynamics of ions inside of the pore. The ion occupancy along the pore length depends strongly on the scan rate and varies cyclically during charging/discharging. Unlike that at equilibrium conditions or low scan rates, charge storage at high scan rates is dominated by counterions while the contribution by co-ions is marginal or negative. These observations help explain the perm-selective charge storage observed experimentally. We clarify the mechanisms underlying these dynamic phenomena and quantify their effects on the efficiency of the dynamic charge storage in nanopores.

Sustainable use of renewable resources in a stylized social-ecological network model under heterogeneous resource distribution

NASA Astrophysics Data System (ADS)

Barfuss, Wolfram; Donges, Jonathan F.; Wiedermann, Marc; Lucht, Wolfgang

2017-04-01

Human societies depend on the resources ecosystems provide. Particularly since the last century, human activities have transformed the relationship between nature and society at a global scale. We study this coevolutionary relationship by utilizing a stylized model of private resource use and social learning on an adaptive network. The latter process is based on two social key dynamics beyond economic paradigms: boundedly rational imitation of resource use strategies and homophily in the formation of social network ties. The private and logistically growing resources are harvested with either a sustainable (small) or non-sustainable (large) effort. We show that these social processes can have a profound influence on the environmental state, such as determining whether the private renewable resources collapse from overuse or not. Additionally, we demonstrate that heterogeneously distributed regional resource capacities shift the critical social parameters where this resource extraction system collapses. We make these points to argue that, in more advanced coevolutionary models of the planetary social-ecological system, such socio-cultural phenomena as well as regional resource heterogeneities should receive attention in addition to the processes represented in established Earth system and integrated assessment models.

Overcoming obstacles to interspecies hybridization of ash

Treesearch

Jennifer L. Koch; David W. Carey; Mary E. Mason; M. Nurul Islam-Faridi

2010-01-01

Tree species that share a long co-evolutionary history with insects and pathogens are likely to have developed mechanisms of resistance that allow them to coexist. When insects and pathogens are introduced to different parts of the world, high levels of susceptibility can be observed, presumably in part due to the lack of co-evolutionary history between the insect (or...

Population cycles: generalities, exceptions and remaining mysteries

PubMed Central

2018-01-01

Population cycles are one of nature's great mysteries. For almost a hundred years, innumerable studies have probed the causes of cyclic dynamics in snowshoe hares, voles and lemmings, forest Lepidoptera and grouse. Even though cyclic species have very different life histories, similarities in mechanisms related to their dynamics are apparent. In addition to high reproductive rates and density-related mortality from predators, pathogens or parasitoids, other characteristics include transgenerational reduced reproduction and dispersal with increasing-peak densities, and genetic similarity among populations. Experiments to stop cyclic dynamics and comparisons of cyclic and noncyclic populations provide some understanding but both reproduction and mortality must be considered. What determines variation in amplitude and periodicity of population outbreaks remains a mystery. PMID:29563267

Evolutionary dynamics of group interactions on structured populations: a review

PubMed Central

Perc, Matjaž; Gómez-Gardeñes, Jesús; Szolnoki, Attila; Floría, Luis M.; Moreno, Yamir

2013-01-01

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living 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 proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of 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. PMID:23303223

Co-evolutionary data mining for fuzzy rules: automatic fitness function creation phase space, and experiments

NASA Astrophysics Data System (ADS)

Smith, James F., III; Blank, Joseph A.

2003-03-01

An approach is being explored that involves embedding a fuzzy logic based resource manager in an electronic game environment. Game agents can function under their own autonomous logic or human control. This approach automates the data mining problem. The game automatically creates a cleansed database reflecting the domain expert's knowledge, it calls a data mining function, a genetic algorithm, for data mining of the data base as required and allows easy evaluation of the information extracted. The co-evolutionary fitness functions, chromosomes and stopping criteria for ending the game are discussed. Genetic algorithm and genetic program based data mining procedures are discussed that automatically discover new fuzzy rules and strategies. The strategy tree concept and its relationship to co-evolutionary data mining are examined as well as the associated phase space representation of fuzzy concepts. The overlap of fuzzy concepts in phase space reduces the effective strategies available to adversaries. Co-evolutionary data mining alters the geometric properties of the overlap region known as the admissible region of phase space significantly enhancing the performance of the resource manager. Procedures for validation of the information data mined are discussed and significant experimental results provided.

Population cycles: generalities, exceptions and remaining mysteries.

PubMed

Myers, Judith H

2018-03-28

Population cycles are one of nature's great mysteries. For almost a hundred years, innumerable studies have probed the causes of cyclic dynamics in snowshoe hares, voles and lemmings, forest Lepidoptera and grouse. Even though cyclic species have very different life histories, similarities in mechanisms related to their dynamics are apparent. In addition to high reproductive rates and density-related mortality from predators, pathogens or parasitoids, other characteristics include transgenerational reduced reproduction and dispersal with increasing-peak densities, and genetic similarity among populations. Experiments to stop cyclic dynamics and comparisons of cyclic and noncyclic populations provide some understanding but both reproduction and mortality must be considered. What determines variation in amplitude and periodicity of population outbreaks remains a mystery. © 2018 The Author(s).

The Role of Linkers in the Excited-State Dynamic Planarization Processes of Macrocyclic Oligothiophene 12-Mers.

PubMed

Kim, Woojae; Sung, Jooyoung; Park, Kyu Hyung; Shimizu, Hideyuki; Imamura, Mika; Han, Minwoo; Sim, Eunji; Iyoda, Masahiko; Kim, Dongho

2015-11-05

Linkers adjoining chromophores play an important role in modulating the structure of conjugated systems, which is bound up with their photophysical properties. However, to date, the focus of works dealing with linker effects was limited only to linear π-conjugated materials, and there have been no detailed studies on cyclic counterparts. Herein we report the linker effects on the dynamic planarization processes of π-conjugated macrocyclic oligothiophene 12-mers, where the different ratio between ethynylene and vinylene linkers was chosen to control the backbone rigidity. By analyzing transient fluorescence spectra, we demonstrate that the connecting linkers play a crucial role in the excited-state dynamics of cyclic conjugated systems. Faster dynamic planarization, longer exciton delocalization length, and higher degree of planarity were observed in vinylene inserted cyclic oligothiophenes. Molecular dynamics simulations and density functional theory calculations also stress the importance of the role of linkers in modulating the structure of cyclic oligothiophenes.

Dynamic augmentation restores anterior tibial translation in ACL suture repair: a biomechanical comparison of non-, static and dynamic augmentation techniques.

PubMed

Hoogeslag, Roy A G; Brouwer, Reinoud W; Huis In 't Veld, Rianne; Stephen, Joanna M; Amis, Andrew A

2018-02-03

There is a lack of objective evidence investigating how previous non-augmented ACL suture repair techniques and contemporary augmentation techniques in ACL suture repair restrain anterior tibial translation (ATT) across the arc of flexion, and after cyclic loading of the knee. The purpose of this work was to test the null hypotheses that there would be no statistically significant difference in ATT after non-, static- and dynamic-augmented ACL suture repair, and they will not restore ATT to normal values across the arc of flexion of the knee after cyclic loading. Eleven human cadaveric knees were mounted in a test rig, and knee kinematics from 0° to 90° of flexion were recorded by use of an optical tracking system. Measurements were recorded without load and with 89-N tibial anterior force. The knees were tested in the following states: ACL-intact, ACL-deficient, non-augmented suture repair, static tape augmentation and dynamic augmentation after 10 and 300 loading cycles. Only static tape augmentation and dynamic augmentation restored ATT to values similar to the ACL-intact state directly postoperation, and maintained this after cyclic loading. However, contrary to dynamic augmentation, the ATT after static tape augmentation failed to remain statistically less than for the ACL-deficient state after cyclic loading. Moreover, after cyclic loading, ATT was significantly less with dynamic augmentation when compared to static tape augmentation. In contrast to non-augmented ACL suture repair and static tape augmentation, only dynamic augmentation resulted in restoration of ATT values similar to the ACL-intact knee and decreased ATT values when compared to the ACL-deficient knee immediately post-operation and also after cyclic loading, across the arc of flexion, thus allowing the null hypotheses to be rejected. This may assist healing of the ruptured ACL. Therefore, this study would support further clinical evaluation of dynamic augmentation of ACL repair.

Coevolutionary dynamics of phenotypic diversity and contingent cooperation

PubMed Central

Wang, Long

2017-01-01

Phenotypic diversity is considered beneficial to the evolution of contingent cooperation, in which cooperators channel their help preferentially towards others of similar phenotypes. However, it remains largely unclear how phenotypic variation arises in the first place and thus leads to the construction of phenotypic complexity. Here we propose a mathematical model to study the coevolutionary dynamics of phenotypic diversity and contingent cooperation. Unlike previous models, our model does not assume any prescribed level of phenotypic diversity, but rather lets it be an evolvable trait. Each individual expresses one phenotype at a time and only the phenotypes expressed are visible to others. Moreover, individuals can differ in their potential of phenotypic variation, which is characterized by the number of distinct phenotypes they can randomly switch to. Each individual incurs a cost proportional to the number of potentially expressible phenotypes so as to retain phenotypic variation and expression. Our results show that phenotypic diversity coevolves with contingent cooperation under a wide range of conditions and that there exists an optimal level of phenotypic diversity best promoting contingent cooperation. It pays for contingent cooperators to elevate their potential of phenotypic variation, thereby increasing their opportunities of establishing cooperation via novel phenotypes, as these new phenotypes serve as secret tags that are difficult for defector to discover and chase after. We also find that evolved high levels of phenotypic diversity can occasionally collapse due to the invasion of defector mutants, suggesting that cooperation and phenotypic diversity can mutually reinforce each other. Thus, our results provide new insights into better understanding the coevolution of cooperation and phenotypic diversity. PMID:28141806

Phenotypic Mismatches Reveal Escape from Arms-Race Coevolution

PubMed Central

Hanifin, Charles T; Brodie, Edmund D; Brodie, Edmund D

2008-01-01

Because coevolution takes place across a broad scale of time and space, it is virtually impossible to understand its dynamics and trajectories by studying a single pair of interacting populations at one time. Comparing populations across a range of an interaction, especially for long-lived species, can provide insight into these features of coevolution by sampling across a diverse set of conditions and histories. We used measures of prey traits (tetrodotoxin toxicity in newts) and predator traits (tetrodotoxin resistance of snakes) to assess the degree of phenotypic mismatch across the range of their coevolutionary interaction. Geographic patterns of phenotypic exaggeration were similar in prey and predators, with most phenotypically elevated localities occurring along the central Oregon coast and central California. Contrary to expectations, however, these areas of elevated traits did not coincide with the most intense coevolutionary selection. Measures of functional trait mismatch revealed that over one-third of sampled localities were so mismatched that reciprocal selection could not occur given current trait distributions. Estimates of current locality-specific interaction selection gradients confirmed this interpretation. In every case of mismatch, predators were “ahead” of prey in the arms race; the converse escape of prey was never observed. The emergent pattern suggests a dynamic in which interacting species experience reciprocal selection that drives arms-race escalation of both prey and predator phenotypes at a subset of localities across the interaction. This coadaptation proceeds until the evolution of extreme phenotypes by predators, through genes of large effect, allows snakes to, at least temporarily, escape the arms race. PMID:18336073

A comparison of two reciprocating instruments using bending stress and cyclic fatigue tests.

PubMed

Scelza, Pantaleo; Harry, Davidowicz; Silva, Licinio Esmeraldo da; Barbosa, Igor Bastos; Scelza, Miriam Zaccaro

2015-01-01

The aim of this study was to comparatively evaluate the bending resistance at 45º, the static and dynamic cyclic fatigue life, and the fracture type of the WaveOne (Dentsply Maillefer, Ballaigues, Switzerland) 25-08 and Reciproc (VDW, Munich, Germany) 25-08 instruments. A total of 60 nickel-titanium (NiTi) instruments (30 Reciproc and 30 WaveOne) from three different lots, each of which was 25 mm in length, were tested. The bending resistance was evaluated through the results of a cantilever-bending test conducted using a universal testing machine. Static and dynamic cyclic fatigue testing was conducted using a custom-made device. For the static and dynamic tests, a cast Ni-Cr-Mo-Ti alloy metal block with an artificial canal measuring 1.77 mm in diameter and 20.00 mm in total length was used. A scanning electron microscope was used to determine the type of fracture. Statistical analyses were performed on the results. The WaveOne instrument was less flexible than the Reciproc (p < 0.05). The Reciproc instrument showed better resistance in the static and dynamic cyclic fatigue tests (p < 0.05). The transverse cross-section and geometry of the instruments were important factors in their resistance to bending and cyclic fracture. Both of the instruments showed ductile-type fracture characteristics. It can be concluded that the Reciproc 25-08 instrument was more resistant to static and dynamic cyclic fatigue than the WaveOne 25-08 instrument, while the WaveOne 25-08 instrument was less flexible. Bending and resistance to cyclic fracture were influenced by the instruments' geometries and transverse cross-sections. Both of the instruments showed ductile-type fracture characteristics.

Strategic variation in mobbing as a front line of defense against brood parasitism.

PubMed

Welbergen, Justin A; Davies, Nicholas B

2009-02-10

Coevolutionary arms races, where adaptations in one party select for counter-adaptations in another and vice versa, are fundamental to interactions between organisms and their predators, pathogens, and parasites [1]. Avian brood parasites and their hosts have emerged as model systems for studying such reciprocal coevolutionary processes [2, 3]. For example, hosts have evolved changes in egg appearance and rejection of foreign eggs in response to brood parasitism from cuckoos, and cuckoos have evolved host-egg mimicry as a counter-response [4-6]. However, the host's front line of defense is protecting the nest from being parasitized in the first place [7-10], yet little is known about the effectiveness of nest defense as an antiparasite adaptation, and its coevolutionary significance remains poorly understood [10]. Here we show first that mobbing of common cuckoos Cuculus canorus by reed warblers Acrocephalus scirpaceus is an effective defense against parasitism. Second, mobbing of cuckoos is a phenotypically plastic trait that is modified strategically according to local parasitism risk. This supports the view that hosts use a "defense in-depth strategy," with successive flexible lines of defense that coevolve with corresponding offensive lines of the parasite. This highlights the need for more holistic research into the coevolutionary consequences when multiple adaptations and counter-adaptations evolve in concert [11].

Brood-parasite interactions between great spotted cuckoos and magpies: a model system for studying coevolutionary relationships.

PubMed

Soler, Juan; Soler, Manuel

2000-11-01

Brood parasitism is one of the systems where coevolutionary processes have received the most research. Here, we review experiments that suggest a coevolutionary process between the great spotted cuckoo (Clamator glandarius) and its magpie (Pica pica) host. We focus on different stages of establishment of the relationship, from cuckoos selecting individual hosts and hosts defending their nests from adult cuckoos, to the ability of magpies to detect cuckoo eggs in their nests. Novel coevolutionary insights emerge from our synthesis of the literature, including how the evolution of "Mafia" behaviour in cuckoos does not necessarily inhibit the evolution of host recognition and rejection of cuckoo offspring, and how different populations of black-billed magpies in Europe have evolved specific host traits (e.g. nest and clutch size) as a result of interactions with the great spotted cuckoo. Finally, the results of the synthesis reveal the importance of using a meta-population approach when studying coevolution. This is especially relevant in those cases where gene flow among populations with different degrees of brood parasitism explains patterns of coexistence between defensive and non-defensive host phenotypes. We propose the use of a meta-population approach to distinguish between the "evolutionary equilibrium" hypothesis and the "evolutionary lag" hypothesis.

In Vivo Biochemistry: Single-Cell Dynamics of Cyclic Di-GMP in Escherichia coli in Response to Zinc Overload.

PubMed

Yeo, Jongchan; Dippel, Andrew B; Wang, Xin C; Hammond, Ming C

2018-01-09

Intracellular signaling enzymes drive critical changes in cellular physiology and gene expression, but their endogenous activities in vivo remain highly challenging to study in real time and for individual cells. Here we show that flow cytometry can be performed in complex media to monitor single-cell population distributions and dynamics of cyclic di-GMP signaling, which controls the bacterial colonization program. These in vivo biochemistry experiments are enabled by our second-generation RNA-based fluorescent (RBF) biosensors, which exhibit high fluorescence turn-on in response to cyclic di-GMP. Specifically, we demonstrate that intracellular levels of cyclic di-GMP in Escherichia coli are repressed with excess zinc, but not with other divalent metals. Furthermore, in both flow cytometry and fluorescence microscopy setups, we monitor the dynamic increase in cellular cyclic di-GMP levels upon zinc depletion and show that this response is due to de-repression of the endogenous diguanylate cyclase DgcZ. In the presence of zinc, cells exhibit enhanced cell motility and increased sensitivity to antibiotics due to inhibited biofilm formation. Taken together, these results showcase the application of RBF biosensors in visualizing single-cell dynamic changes in cyclic di-GMP signaling in direct response to environmental cues such as zinc and highlight our ability to assess whether observed phenotypes are related to specific signaling enzymes and pathways.

The genetic basis of a plant–insect coevolutionary key innovation

PubMed Central

Wheat, Christopher W.; Vogel, Heiko; Wittstock, Ute; Braby, Michael F.; Underwood, Dessie; Mitchell-Olds, Thomas

2007-01-01

Ehrlich and Raven formally introduced the concept of stepwise coevolution using butterfly and angiosperm interactions in an attempt to account for the impressive biological diversity of these groups. However, many biologists currently envision butterflies evolving 50 to 30 million years (Myr) after the major angiosperm radiation and thus reject coevolutionary origins of butterfly biodiversity. The unresolved central tenet of Ehrlich and Raven's theory is that evolution of plant chemical defenses is followed closely by biochemical adaptation in insect herbivores, and that newly evolved detoxification mechanisms result in adaptive radiation of herbivore lineages. Using one of their original butterfly-host plant systems, the Pieridae, we identify a pierid glucosinolate detoxification mechanism, nitrile-specifier protein (NSP), as a key innovation. Larval NSP activity matches the distribution of glucosinolate in their host plants. Moreover, by using five different temporal estimates, NSP seems to have evolved shortly after the evolution of the host plant group (Brassicales) (≈10 Myr). An adaptive radiation of these glucosinolate-feeding Pierinae followed, resulting in significantly elevated species numbers compared with related clades. Mechanistic understanding in its proper historical context documents more ancient and dynamic plant–insect interactions than previously envisioned. Moreover, these mechanistic insights provide the tools for detailed molecular studies of coevolution from both the plant and insect perspectives. PMID:18077380

Coevolution between invasive and native plants driven by chemical competition and soil biota.

PubMed

Lankau, Richard A

2012-07-10

Although reciprocal evolutionary responses between interacting species are a driving force behind the diversity of life, pairwise coevolution between plant competitors has received less attention than other species interactions and has been considered relatively less important in explaining ecological patterns. However, the success of species transported across biogeographic boundaries suggests a stronger role for evolutionary relationships in shaping plant interactions. Alliaria petiolata is a Eurasian species that has invaded North American forest understories, where it competes with native understory species in part by producing compounds that directly and indirectly slow the growth of competing species. Here I show that populations of A. petiolata from areas with a greater density of interspecific competitors invest more in a toxic allelochemical under common conditions. Furthermore, populations of a native competitor from areas with highly toxic invaders are more tolerant to competition from the invader, suggesting coevolutionary dynamics between the species. Field reciprocal transplants confirmed that native populations more tolerant to the invader had higher fitness when the invader was common, but these traits came at a cost when the invader was rare. Exotic species are often detrimentally dominant in their new range due to their evolutionary novelty; however, the development of new coevolutionary relationships may act to integrate exotic species into native communities.

Preliminary analysis of dynamic stall effects on a 91-meter wind turbine rotor

NASA Technical Reports Server (NTRS)

Wilson, Robert E.

1995-01-01

Analytical investigation of dynamic stall on HAWT (horizontal-axis wind turbines) rotor loads was conducted. Dynamic stall was modeled using the Gormont approach on the MOD-2 rotor, treating the blade as a rigid body teetering about a fixed axis. Blade flapwise bending moments at station 370 were determined with and without dynamic stall for spatial variations in local wind speed due to wind shear and yaw. The predicted mean flapwise bending moments were found to be in good agreement with test results. Results obtained with and without dynamic stall showed no significant difference for the mean flapwise bending moment. The cyclic bending moments calculated with and without dynamic stall effects were substantially the same. None of the calculated cyclic loads reached the level of the cyclic loads measured on the MOD-2 using the Boeing five-minute-average technique.

Predicting protein folding rate change upon point mutation using residue-level coevolutionary information.

PubMed

Mallik, Saurav; Das, Smita; Kundu, Sudip

2016-01-01

Change in folding kinetics of globular proteins upon point mutation is crucial to a wide spectrum of biological research, such as protein misfolding, toxicity, and aggregations. Here we seek to address whether residue-level coevolutionary information of globular proteins can be informative to folding rate changes upon point mutations. Generating residue-level coevolutionary networks of globular proteins, we analyze three parameters: relative coevolution order (rCEO), network density (ND), and characteristic path length (CPL). A point mutation is considered to be equivalent to a node deletion of this network and respective percentage changes in rCEO, ND, CPL are found linearly correlated (0.84, 0.73, and -0.61, respectively) with experimental folding rate changes. The three parameters predict the folding rate change upon a point mutation with 0.031, 0.045, and 0.059 standard errors, respectively. © 2015 Wiley Periodicals, Inc.

Newtonian dynamics in the plane corresponding to straight and cyclic motions on the hyperelliptic curve μ2=νn-1, n∈Z: Ergodicity, isochrony and fractals

NASA Astrophysics Data System (ADS)

Grinevich, P. G.; Santini, P. M.

2007-08-01

We study the complexification of the one-dimensional Newtonian particle in a monomial potential. We discuss two classes of motions on the associated Riemann surface: the rectilinear and the cyclic motions, corresponding to two different classes of real and autonomous Newtonian dynamics in the plane. The rectilinear motion has been studied in a number of papers, while the cyclic motion is much less understood. For small data, the cyclic time trajectories lead to isochronous dynamics. For bigger data the situation is quite complicated; computer experiments show that, for sufficiently small degree of the monomial, the motion is generically isochronous with integer period, which depends in a quite sensitive way on the initial data. If the degree of the monomial is sufficiently high, computer experiments show essentially chaotic behavior. We suggest a possible theoretical explanation of these different behaviors. We also introduce a two-parameter family of two-dimensional mappings, describing the motion of the center of the circle, as a convenient representation of the cyclic dynamics; we call such a mapping the center map. Computer experiments for the center map show a typical multifractal behavior with periodicity islands. Therefore the above complexification procedure generates dynamics amenable to analytic treatment and possessing a high degree of complexity.

Numerical Investigation of the Dynamic Properties of Intermittent Jointed Rock Models Subjected to Cyclic Uniaxial Compression

NASA Astrophysics Data System (ADS)

Liu, Yi; Dai, Feng; Zhao, Tao; Xu, Nu-wen

2017-01-01

Intermittent jointed rocks, which exist in a myriad of engineering projects, are extraordinarily susceptible to cyclic loadings. Understanding the dynamic fatigue properties of jointed rocks is necessary for evaluating the stability of rock engineering structures. This study numerically investigated the influences of cyclic loading conditions (i.e., frequency, maximum stress and amplitude) and joint geometric configurations (i.e., dip angle, persistency and interspace) on the dynamic fatigue mechanisms of jointed rock models. A reduction model of stiffness and strength was first proposed, and then, sixteen cyclic uniaxial loading tests with distinct loading parameters and joint geometries were simulated. Our results indicate that the reduction model can effectively reproduce the hysteresis loops and the accumulative plastic deformation of jointed rocks in the cyclic process. Both the loading parameters and the joint geometries significantly affect the dynamic properties, including the irreversible strain, damage evolution, dynamic residual strength and fatigue life. Three failure modes of jointed rocks, which are principally controlled by joint geometries, occur in the simulations: splitting failure through the entire rock sample, sliding failure along joint planes and mixed failure, which are principally controlled by joint geometries. Furthermore, the progressive failure processes of the jointed rock samples are numerically observed, and the different loading stages can be distinguished by the relationship between the number of broken bonds and the axial stress.

Competition-Colonization Trade-Offs, Competitive Uncertainty, and the Evolutionary Assembly of Species

PubMed Central

Pillai, Pradeep; Guichard, Frédéric

2012-01-01

We utilize a standard competition-colonization metapopulation model in order to study the evolutionary assembly of species. Based on earlier work showing how models assuming strict competitive hierarchies will likely lead to runaway evolution and self-extinction for all species, we adopt a continuous competition function that allows for levels of uncertainty in the outcome of competition. We then, by extending the standard patch-dynamic metapopulation model in order to include evolutionary dynamics, allow for the coevolution of species into stable communities composed of species with distinct limiting similarities. Runaway evolution towards stochastic extinction then becomes a limiting case controlled by the level of competitive uncertainty. We demonstrate how intermediate competitive uncertainty maximizes the equilibrium species richness as well as maximizes the adaptive radiation and self-assembly of species under adaptive dynamics with mutations of non-negligible size. By reconciling competition-colonization tradeoff theory with co-evolutionary dynamics, our results reveal the importance of intermediate levels of competitive uncertainty for the evolutionary assembly of species. PMID:22448253

The evolution of early cellular systems viewed through the lens of biological interactions.

PubMed

Poole, Anthony M; Lundin, Daniel; Rytkönen, Kalle T

2015-01-01

The minimal cell concept represents a pragmatic approach to the question of how few genes are required to run a cell. This is a helpful way to build a parts-list, and has been more successful than attempts to deduce a minimal gene set for life by inferring the gene repertoire of the last universal common ancestor, as few genes trace back to this hypothetical ancestral state. However, the study of minimal cellular systems is the study of biological outliers where, by practical necessity, coevolutionary interactions are minimized or ignored. In this paper, we consider the biological context from which minimal genomes have been removed. For instance, some of the most reduced genomes are from endosymbionts and are the result of coevolutionary interactions with a host; few such organisms are "free-living." As few, if any, biological systems exist in complete isolation, we expect that, as with modern life, early biological systems were part of an ecosystem, replete with organismal interactions. We favor refocusing discussions of the evolution of cellular systems on processes rather than gene counts. We therefore draw a distinction between a pragmatic minimal cell (an interesting engineering problem), a distributed genome (a system resulting from an evolutionary transition involving more than one cell) and the looser coevolutionary interactions that are ubiquitous in ecosystems. Finally, we consider the distributed genome and coevolutionary interactions between genomic entities in the context of early evolution.

Co-evolutionary interactions between host resistance and pathogen avirulence genes in rice-Magnaporthe oryzae pathosystem.

PubMed

Singh, Pankaj Kumar; Ray, Soham; Thakur, Shallu; Rathour, Rajeev; Sharma, Vinay; Sharma, Tilak Raj

2018-06-01

Rice and Magnaporthe oryzae constitutes an ideal pathosystem for studying host-pathogen interaction in cereals crops. There are two alternative hypotheses, viz. Arms race and Trench warfare, which explain the co-evolutionary dynamics of hosts and pathogens which are under continuous confrontation. Arms race proposes that both R- and Avr- genes of host and pathogen, respectively, undergo positive selection. Alternatively, trench warfare suggests that either R- or Avr- gene in the pathosystem is under balanced selection intending to stabilize the genetic advantage gained over the opposition. Here, we made an attempt to test the above-stated hypotheses in rice-M. oryzae pathosystem at loci of three R-Avr gene pairs, Piz-t-AvrPiz-t, Pi54-AvrPi54 and Pita-AvrPita using allele mining approach. Allele mining is an efficient way to capture allelic variants existing in the population and to study the selective forces imposed on the variants during evolution. Results of nucleotide diversity, neutrality statistics and phylogenetic analyses reveal that Piz-t, Pi54 and AvrPita are diversified and under positive selection at their corresponding loci, while their counterparts, AvrPiz-t, AvrPi54 and Pita are conserved and under balancing selection, in nature. These results imply that rice-M. oryzae populations are engaged in a trench warfare at least at the three R/Avr loci studied. It is a maiden attempt to study the co-evolution of three R-Avr gene pairs in this pathosystem. Knowledge gained from this study will help in understanding the evolutionary dynamics of host-pathogen interaction in a better way and will also aid in developing new durable blast resistant rice varieties in future. Copyright © 2018 Elsevier Inc. All rights reserved.

Dynamic Torsional and Cyclic Fracture Behavior of ProFile Rotary Instruments at Continuous or Reciprocating Rotation as Visualized with High-speed Digital Video Imaging.

PubMed

Tokita, Daisuke; Ebihara, Arata; Miyara, Kana; Okiji, Takashi

2017-08-01

This study examined the dynamic fracture behavior of nickel-titanium rotary instruments in torsional or cyclic loading at continuous or reciprocating rotation by means of high-speed digital video imaging. The ProFile instruments (size 30, 0.06 taper; Dentsply Maillefer, Ballaigues, Switzerland) were categorized into 4 groups (n = 7 in each group) as follows: torsional/continuous (TC), torsional/reciprocating (TR), cyclic/continuous (CC), and cyclic/reciprocating (CR). Torsional loading was performed by rotating the instruments by holding the tip with a vise. For cyclic loading, a custom-made device with a 38° curvature was used. Dynamic fracture behavior was observed with a high-speed camera. The time to fracture was recorded, and the fractured surface was examined with scanning electron microscopy. The TC group initially exhibited necking of the file followed by the development of an initial crack line. The TR group demonstrated opening and closing of a crack according to its rotation in the cutting and noncutting directions, respectively. The CC group separated without any detectable signs of deformation. In the CR group, initial crack formation was recognized in 5 of 7 samples. The reciprocating rotation exhibited a longer time to fracture in both torsional and cyclic fatigue testing (P < .05). The scanning electron microscopic images showed a severely deformed surface in the TR group. The dynamic fracture behavior of NiTi rotary instruments, as visualized with high-speed digital video imaging, varied between the different modes of rotation and different fatigue testing. Reciprocating rotation induced a slower crack propagation and conferred higher fatigue resistance than continuous rotation in both torsional and cyclic loads. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

MICROWAVE-ASSISTED PREPARATION OF CYCLIC UREAS FROM DIAMINES

EPA Science Inventory

Rajender S. Varma* and Yong-Jin Kim
Cyclic ureas are useful intermediates for a variety of pharmaceuticals and pesticides. One of the attractive approaches for the synthesis of cyclic ureas uses condensation of diamines with urea as a carbonyl source under dynamic evacuation. ...

Cyclicity of Suicides May Be Modulated by Internal or External - 11-Year Cycles: An Example of Suicide Rates in Finland

NASA Astrophysics Data System (ADS)

Dimitrov, B. D.; Atanassova, P. A.; Rachkova, M. I.

2009-12-01

Multicomponent cyclicity in monthly suicides (periods T = 18, 46 and 198 months) was found and close similarity with heliogeophysical activity (HGA) suggested by Dimitrov in 1999. The current report aimed at scrutinizing the results on suicide annual cyclicity (seasonality) in Slovenia as reported by Oravecz et al in 2007 as well as at analyzing suicide data from Finland in this regard. We postulated that: (i) trans-year (12-24 months) or far-trans-year long-term cycles of suicides might interfere with their seasonality; and (ii) associations to environmental factors with alike cyclicity (e.g. HGA, temperature) could exist. Annual suicide incidence from Oulu, Finland over years 1987-1999 was analyzed. Annual data on solar activity (sunspot index Rz or Wolf number), planetary geomagnetic activity (aa-index) and local daily mean temperatures were used. The exploration of underlying chronomes (time structures) was done by periodogram regression analysis with trigonometric approximation. We analyzed temporal dynamics, revealed cyclicity, decomposed and reconstructed significant cycles and correlated the time series data. Suicide seasonality in Slovenia during the years 1971-2002 (n=384 months, peak May-June) was considered and, although some discrepancies and methodological weaknesses were suspected, we further hypothesized about trans-year and/or longer (far-transyear) cyclic components. Suicide incidence data from Finland indicated that the 12.5-year cyclic component (or trend) was almost parallel (coherent) to the cyclic heliogeophysical parameters and similar to local decreasing temperature dynamics. Also, 8-year and 24.5-year cycles were revealed. A correlation between the 12.5-year suicide cycle and 11-year solar cycle was found (R=0.919, p=0.000009). Above findings on cyclicity and temporal correlations of suicides with cyclic environmental factors, even being still preliminary, might not only allow for further more specific analyses. They might also corroborate to improved forecasting and prevention and confer a better understanding of suicide dynamics and aetiology.

Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

PubMed

Burdon, J J; Thrall, P H; Ericson, L

2013-08-01

Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations. Copyright © 2013 Elsevier Ltd. All rights reserved.

Physical model of the immune response of bacteria against bacteriophage through the adaptive CRISPR-Cas immune system

NASA Astrophysics Data System (ADS)

Han, Pu; Niestemski, Liang Ren; Barrick, Jeffrey E.; Deem, Michael W.

2013-04-01

Bacteria and archaea have evolved an adaptive, heritable immune system that recognizes and protects against viruses or plasmids. This system, known as the CRISPR-Cas system, allows the host to recognize and incorporate short foreign DNA or RNA sequences, called ‘spacers’ into its CRISPR system. Spacers in the CRISPR system provide a record of the history of bacteria and phage coevolution. We use a physical model to study the dynamics of this coevolution as it evolves stochastically over time. We focus on the impact of mutation and recombination on bacteria and phage evolution and evasion. We discuss the effect of different spacer deletion mechanisms on the coevolutionary dynamics. We make predictions about bacteria and phage population growth, spacer diversity within the CRISPR locus, and spacer protection against the phage population.

Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles.

PubMed

Braga, Lucas P P; Alves, Rafael F; Dellias, Marina T F; Navarrete, Acacio A; Basso, Thiago O; Tsai, Siu M

2017-01-01

Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management to fertilization for plant biomass production, and it is known as fertirrigation. Here we evaluate public datasets of soil metagenomes mining for changes in antibiotic resistance genes (ARGs) of soils from sugarcane mesocosms repeatedly amended with vinasse. The metagenomes were annotated using the ResFam database. We found that the abundance of open read frames (ORFs) annotated as ARGs changed significantly across 43 different families ( p -value < 0.05). Co-occurrence network analysis revealed distinct patterns of interactions among ARGs, suggesting that nutrient amendment to soil microbial communities can impact on the coevolutionary dynamics of indigenous ARGs within soil resistome.

Hybrid Co-Evolutionary Motion Planning via Visibility-Based Repair

NASA Technical Reports Server (NTRS)

Dozier, Gerry; McCullough, Shaun; Brown, Edward, Jr.; Homaifar, Abdollah; Bikdash, Mar-wan

1997-01-01

This paper introduces a hybrid co-evolutionary system for global motion planning within unstructured environments. This system combines the concept of co-evolutionary search along with a concept that we refer to as the visibility-based repair to form a hybrid which quickly transforms infeasible motions into feasible ones. Also, this system makes use of a novel representation scheme for the obstacles within an environment. Our hybrid evolutionary system differs from other evolutionary motion planners in that (1) more emphasis is placed on repairing infeasible motions to develop feasible motions rather than using simulated evolution exclusively as a means of discovering feasible motions, (2) a continuous map of the environment is used rather than a discretized map, and (3) it develops global motion plans for multiple mobile destinations by co-evolving populations of sub-global motion plans. In this paper, we demonstrate the effectiveness of this system by using it to solve two challenging motion planning problems where multiple targets try to move away from a point robot.

Transitions from trees to cycles in adaptive flow networks

NASA Astrophysics Data System (ADS)

Martens, Erik A.; Klemm, Konstantin

2017-11-01

Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply. Theoretical and experimental studies have found that real-world transport networks exhibit both tree-like motifs and cycles. When the network is subject to load fluctuations, the presence of cyclic motifs may help to reduce flow fluctuations and, thus, render supply in the network more robust. While previous studies considered network topology via optimization principles, here, we take a dynamical systems approach and study a simple model of a flow network with dynamically adapting weights (conductances). We assume a spatially non-uniform distribution of rapidly fluctuating loads in the sinks and investigate what network configurations are dynamically stable. The network converges to a spatially non-uniform stable configuration composed of both cyclic and tree-like structures. Cyclic structures emerge locally in a transcritical bifurcation as the amplitude of the load fluctuations is increased. The resulting adaptive dynamics thus partitions the network into two distinct regions with cyclic and tree-like structures. The location of the boundary between these two regions is determined by the amplitude of the fluctuations. These findings may explain why natural transport networks display cyclic structures in the micro-vascular regions near terminal nodes, but tree-like features in the regions with larger veins.

On Fitts's and Hooke's laws: simple harmonic movement in upper-limb cyclical aiming.

PubMed

Guiard, Y

1993-03-01

Can discrete, single-shot movements and continuous, cyclical movements be reduced to a single concept? In the classical, computational approach to human motor behaviour, cyclical aimed movement has generally been considered to derive from discrete primitives through a concatenation mechanism. Much importance, accordingly, has been attached to discrete-movement paradigms and to techniques allowing the segmentation of continuous data. An alternative approach, suggested by the nonlinear dynamical systems theory, views discreteness as a limiting case of cyclicity. Although attempts have been made recently to account for discrete movements in dynamical terms, cyclical paradigms have been favoured. The concatenation interpretation of cyclical aimed movement is criticized on the ground that it implies a complete waste of mechanical energy once in every half-cycle. Some kinematic data from a one-dimensional reciprocal (i.e., cyclical) aiming experiment are reported, suggesting that human subjects do save muscular efforts from one movement to the next in upper-limb cyclical aiming. The experiment demonstrated convergence on simple harmonic motion as aiming tolerance was increased, an outcome interpreted with reference to Hooke's law, in terms of the muscles' capability of storing potential, elastic energy across movement reversals. Not only is the concatenation concept problematic for understanding cyclical aimed movements, but the very reality of discrete movements is questionable too. It is pointed out that discrete motor acts of real life are composed of complete cycles, rather than half-cycles.

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

PubMed Central

Rougon-Cardoso, Alejandra; Flores-Ponce, Mitzi; Ramos-Aboites, Hilda Eréndira; Martínez-Guerrero, Christian Eduardo; Hao, You-Jin; Cunha, Luis; Rodríguez-Martínez, Jonathan Alejandro; Ovando-Vázquez, Cesaré; Bermúdez-Barrientos, José Roberto; Abreu-Goodger, Cei; Chavarría-Hernández, Norberto; Simões, Nelson; Montiel, Rafael

2016-01-01

The entomopathogenic nematode Steinernema carpocapsae has been widely used for the biological control of insect pests. It shares a symbiotic relationship with the bacterium Xenorhabdus nematophila, and is emerging as a genetic model to study symbiosis and pathogenesis. We obtained a high-quality draft of the nematode’s genome comprising 84,613,633 bp in 347 scaffolds, with an N50 of 1.24 Mb. To improve annotation, we sequenced both short and long RNA and conducted shotgun proteomic analyses. S. carpocapsae shares orthologous genes with other parasitic nematodes that are absent in the free-living nematode C. elegans, it has ncRNA families that are enriched in parasites, and expresses proteins putatively associated with parasitism and pathogenesis, suggesting an active role for the nematode during the pathogenic process. Host and parasites might engage in a co-evolutionary arms-race dynamic with genes participating in their interaction showing signatures of positive selection. Our analyses indicate that the consequence of this arms race is better characterized by positive selection altering specific functions instead of just increasing the number of positively selected genes, adding a new perspective to these co-evolutionary theories. We identified a protein, ATAD-3, that suggests a relevant role for mitochondrial function in the evolution and mechanisms of nematode parasitism. PMID:27876851

Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens.

PubMed

Schulenburg, Hinrich; Ewbank, Jonathan J

2004-11-22

Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts.

Diversity and specificity in the interaction between Caenorhabditis elegans and the pathogen Serratia marcescens

PubMed Central

Schulenburg, Hinrich; Ewbank, Jonathan J

2004-01-01

Background Co-evolutionary arms races between parasites and hosts are considered to be of immense importance in the evolution of living organisms, potentially leading to highly dynamic life-history changes. The outcome of such arms races is in many cases thought to be determined by frequency dependent selection, which relies on genetic variation in host susceptibility and parasite virulence, and also genotype-specific interactions between host and parasite. Empirical evidence for these two prerequisites is scarce, however, especially for invertebrate hosts. We addressed this topic by analysing the interaction between natural isolates of the soil nematode Caenorhabditis elegans and the pathogenic soil bacterium Serratia marcescens. Results Our analysis reveals the presence of i) significant variation in host susceptibility, ii) significant variation in pathogen virulence, and iii) significant strain- and genotype-specific interactions between the two species. Conclusions The results obtained support the previous notion that highly specific interactions between parasites and animal hosts are generally widespread. At least for C. elegans, the high specificity is observed among isolates from the same population, such that it may provide a basis for and/or represent the outcome of co-evolutionary adaptations under natural conditions. Since both C. elegans and S. marcescens permit comprehensive molecular analyses, these two species provide a promising model system for inference of the molecular basis of such highly specific interactions, which are as yet unexplored in invertebrate hosts. PMID:15555070

Neural-Dynamic-Method-Based Dual-Arm CMG Scheme With Time-Varying Constraints Applied to Humanoid Robots.

PubMed

Zhang, Zhijun; Li, Zhijun; Zhang, Yunong; Luo, Yamei; Li, Yuanqing

2015-12-01

We propose a dual-arm cyclic-motion-generation (DACMG) scheme by a neural-dynamic method, which can remedy the joint-angle-drift phenomenon of a humanoid robot. In particular, according to a neural-dynamic design method, first, a cyclic-motion performance index is exploited and applied. This cyclic-motion performance index is then integrated into a quadratic programming (QP)-type scheme with time-varying constraints, called the time-varying-constrained DACMG (TVC-DACMG) scheme. The scheme includes the kinematic motion equations of two arms and the time-varying joint limits. The scheme can not only generate the cyclic motion of two arms for a humanoid robot but also control the arms to move to the desired position. In addition, the scheme considers the physical limit avoidance. To solve the QP problem, a recurrent neural network is presented and used to obtain the optimal solutions. Computer simulations and physical experiments demonstrate the effectiveness and the accuracy of such a TVC-DACMG scheme and the neural network solver.

The dynamics of charge transfer with and without a barrier: A very simplified model of cyclic voltammetry.

PubMed

Ouyang, Wenjun; Subotnik, Joseph E

2017-05-07

Using the Anderson-Holstein model, we investigate charge transfer dynamics between a molecule and a metal surface for two extreme cases. (i) With a large barrier, we show that the dynamics follow a single exponential decay as expected; (ii) without any barrier, we show that the dynamics are more complicated. On the one hand, if the metal-molecule coupling is small, single exponential dynamics persist. On the other hand, when the coupling between the metal and the molecule is large, the dynamics follow a biexponential decay. We analyze the dynamics using the Smoluchowski equation, develop a simple model, and explore the consequences of biexponential dynamics for a hypothetical cyclic voltammetry experiment.

Molecular Dynamics Simulations of a Cyclic DP-240 Amylose Fragment in a Periodic Cell: Glass Transition Temperature and Water Diffusion

USDA-ARS?s Scientific Manuscript database

Molecular dynamics simulations using AMB06C, an in-house carbohydrate force field, (NPT ensembles, 1atm) were carried out on a periodic cell that contained a cyclic-DP-240 amylose fragment and TIP3P water molecules. Molecular conformation and movement of the amylose fragment and water molecules at ...

Linking Individual and Collective Behavior in Adaptive Social Networks

NASA Astrophysics Data System (ADS)

Pinheiro, Flávio L.; Santos, Francisco C.; Pacheco, Jorge M.

2016-03-01

Adaptive social structures are known to promote the evolution of cooperation. However, up to now the characterization of the collective, population-wide dynamics resulting from the self-organization of individual strategies on a coevolving, adaptive network has remained unfeasible. Here we establish a (reversible) link between individual (micro)behavior and collective (macro)behavior for coevolutionary processes. We demonstrate that an adaptive network transforms a two-person social dilemma locally faced by individuals into a collective dynamics that resembles that associated with an N -person coordination game, whose characterization depends sensitively on the relative time scales between the entangled behavioral and network evolutions. In particular, we show that the faster the relative rate of adaptation of the network, the smaller the critical fraction of cooperators required for cooperation to prevail, thus establishing a direct link between network adaptation and the evolution of cooperation. The framework developed here is general and may be readily applied to other dynamical processes occurring on adaptive networks, notably, the spreading of contagious diseases or the diffusion of innovations.

Coevolution can reverse predator–prey cycles

PubMed Central

Cortez, Michael H.; Weitz, Joshua S.

2014-01-01

A hallmark of Lotka–Volterra models, and other ecological models of predator–prey interactions, is that in predator–prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator–prey coevolution can also drive population cycles where the opposite of canonical Lotka–Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage–cholera, mink–muskrat, and gyrfalcon–rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator–prey coevolution and reveal unique ways in which predator–prey coevolution can shape, and possibly reverse, community dynamics. PMID:24799689

Coevolution can reverse predator-prey cycles.

PubMed

Cortez, Michael H; Weitz, Joshua S

2014-05-20

A hallmark of Lotka-Volterra models, and other ecological models of predator-prey interactions, is that in predator-prey cycles, peaks in prey abundance precede peaks in predator abundance. Such models typically assume that species life history traits are fixed over ecologically relevant time scales. However, the coevolution of predator and prey traits has been shown to alter the community dynamics of natural systems, leading to novel dynamics including antiphase and cryptic cycles. Here, using an eco-coevolutionary model, we show that predator-prey coevolution can also drive population cycles where the opposite of canonical Lotka-Volterra oscillations occurs: predator peaks precede prey peaks. These reversed cycles arise when selection favors extreme phenotypes, predator offense is costly, and prey defense is effective against low-offense predators. We present multiple datasets from phage-cholera, mink-muskrat, and gyrfalcon-rock ptarmigan systems that exhibit reversed-peak ordering. Our results suggest that such cycles are a potential signature of predator-prey coevolution and reveal unique ways in which predator-prey coevolution can shape, and possibly reverse, community dynamics.

Network intrusion detection by the coevolutionary immune algorithm of artificial immune systems with clonal selection

NASA Astrophysics Data System (ADS)

Salamatova, T.; Zhukov, V.

2017-02-01

The paper presents the application of the artificial immune systems apparatus as a heuristic method of network intrusion detection for algorithmic provision of intrusion detection systems. The coevolutionary immune algorithm of artificial immune systems with clonal selection was elaborated. In testing different datasets the empirical results of evaluation of the algorithm effectiveness were achieved. To identify the degree of efficiency the algorithm was compared with analogs. The fundamental rules based of solutions generated by this algorithm are described in the article.

Sustainability and collapse in a coevolutionary model of local resource stocks and behavioral patterns on a social network

NASA Astrophysics Data System (ADS)

Wiedermann, Marc; Donges, Jonathan F.; Heitzig, Jobst; Kurths, Jürgen

2014-05-01

When investigating the causes and consequences of global change, the collective behavior of human beings is considered as having a considerable impact on natural systems. In our work, we propose a conceptual coevolutionary model simulating the dynamics of local renewable resources in interaction with simplistic societal agents exploiting those resources. The society is represented by a social network on which social traits may be transmitted between agents. These traits themselves induce a certain rate of exploitation of the resource, leading either to its depletion or sustainable existence. Traits are exchanged probabilistically according to their instantaneous individual payoff, and hence this process depends on the status of the natural resource. At the same time agents may adaptively restructure their set of acquaintances. Connections with agents having a different trait may be broken while new connections with agents of the same trait are established. We investigate which choices of social parameters, like the frequency of social interaction, rationality and rate of social network adaptation, cause the system to end in a sustainable state and, hence, what can be done to avoid a collapse of the entire system. The importance and influence of the social network structure is analyzed by the variation of link-densities in the underlying network topology and shows significant influence on the expected outcome of the model. For a static network with no adaptation we find a robust phase transition between the two different regimes, sustainable and non-sustainable, which co-exist in parameter space. High connectivity within the social network, e.g., high link-densities, in combination with a fast rate of social learning lead to a likely collapse of the entire co-evolutionary system, whereas slow learning and small network connectivity very likely result in the sustainable existence of the natural resources. Collapse may be avoided by an intelligent rewiring, e.g. adaptation, of the social network that may also lead to the isolation of misbehaving parts of the society. Our results may suggest that with the current trend to faster imitation and ever increasing global network connectivity, societies are becoming more vulnerable to environmental collapse if they remain myopic at the same time.

Dynamics of an experimental two bladed horizontal axis wind turbine with blade cyclic pitch variation

NASA Technical Reports Server (NTRS)

Hotenemser, K. H.; Swift, A. H. P.

1981-01-01

The turbine under study incorporates the combination of two features: the application of blade cyclic pitch variation; and the use of yaw angle control for rotor speed and torque regulation. Due to its emasculation by passive cyclic pitch variation the rotor can be rapidly yawed without encountering gyroscopic and aerodynamic hub moments and without noticeable out of plane excursions. The two bladed upwind rotor is vane stabilized and of very simple and rugged design. The principle was first checked out with a small scale wind tunnel model and then tested in the atmosphere with a 7.6 meter diameter experimental fully instrumented wind turbine driving a 3 phase alternator. The test results are summarized with respect to structural dynamics and yaw dynamics.

Emergence of evolutionary cycles in size-structured food webs.

PubMed

Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd

2016-11-07

The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed. Copyright © 2016 Elsevier Ltd. All rights reserved.

Comprehensive Forced Response Analysis of J2X Turbine Bladed-Discs with 360 Degree Variation in CFD Loading

NASA Technical Reports Server (NTRS)

Elrod, David; Christensen, Eric; Brown, Andrew

2011-01-01

The temporal frequency content of the dynamic pressure predicted by a 360 degree computational fluid dynamics (CFD) analysis of a turbine flow field provides indicators of forcing function excitation frequencies (e.g., multiples of blade pass frequency) for turbine components. For the Pratt and Whitney Rocketdyne J-2X engine turbopumps, Campbell diagrams generated using these forcing function frequencies and the results of NASTRAN modal analyses show a number of components with modes in the engine operating range. As a consequence, forced response and static analyses are required for the prediction of combined stress, high cycle fatigue safety factors (HCFSF). Cyclically symmetric structural models have been used to analyze turbine vane and blade rows, not only in modal analyses, but also in forced response and static analyses. Due to the tortuous flow pattern in the turbine, dynamic pressure loading is not cyclically symmetric. Furthermore, CFD analyses predict dynamic pressure waves caused by adjacent and non-adjacent blade/vane rows upstream and downstream of the row analyzed. A MATLAB script has been written to calculate displacements due to the complex cyclically asymmetric dynamic pressure components predicted by CFD analysis, for all grids in a blade/vane row, at a chosen turbopump running speed. The MATLAB displacements are then read into NASTRAN, and dynamic stresses are calculated, including an adjustment for possible mistuning. In a cyclically symmetric NASTRAN static analysis, static stresses due to centrifugal, thermal, and pressure loading at the mode running speed are calculated. MATLAB is used to generate the HCFSF at each grid in the blade/vane row. When compared to an approach assuming cyclic symmetry in the dynamic flow field, the current approach provides better assurance that the worst case safety factor has been identified. An extended example for a J-2X turbopump component is provided.

Statistical Laws Governing Fluctuations in Word Use from Word Birth to Word Death

PubMed Central

Petersen, Alexander M.; Tenenbaum, Joel; Havlin, Shlomo; Stanley, H. Eugene

2012-01-01

We analyze the dynamic properties of 107 words recorded in English, Spanish and Hebrew over the period 1800–2008 in order to gain insight into the coevolution of language and culture. We report language independent patterns useful as benchmarks for theoretical models of language evolution. A significantly decreasing (increasing) trend in the birth (death) rate of words indicates a recent shift in the selection laws governing word use. For new words, we observe a peak in the growth-rate fluctuations around 40 years after introduction, consistent with the typical entry time into standard dictionaries and the human generational timescale. Pronounced changes in the dynamics of language during periods of war shows that word correlations, occurring across time and between words, are largely influenced by coevolutionary social, technological, and political factors. We quantify cultural memory by analyzing the long-term correlations in the use of individual words using detrended fluctuation analysis. PMID:22423321

Statistical Laws Governing Fluctuations in Word Use from Word Birth to Word Death

NASA Astrophysics Data System (ADS)

Petersen, Alexander M.; Tenenbaum, Joel; Havlin, Shlomo; Stanley, H. Eugene

2012-03-01

We analyze the dynamic properties of 107 words recorded in English, Spanish and Hebrew over the period 1800-2008 in order to gain insight into the coevolution of language and culture. We report language independent patterns useful as benchmarks for theoretical models of language evolution. A significantly decreasing (increasing) trend in the birth (death) rate of words indicates a recent shift in the selection laws governing word use. For new words, we observe a peak in the growth-rate fluctuations around 40 years after introduction, consistent with the typical entry time into standard dictionaries and the human generational timescale. Pronounced changes in the dynamics of language during periods of war shows that word correlations, occurring across time and between words, are largely influenced by coevolutionary social, technological, and political factors. We quantify cultural memory by analyzing the long-term correlations in the use of individual words using detrended fluctuation analysis.

Novel insight into the origin of the growth dynamics of sauropod dinosaurs.

PubMed

Cerda, Ignacio Alejandro; Chinsamy, Anusuya; Pol, Diego; Apaldetti, Cecilia; Otero, Alejandro; Powell, Jaime Eduardo; Martínez, Ricardo Nestor

2017-01-01

Sauropod dinosaurs include the largest terrestrial animals and are considered to have uninterrupted rapid rates of growth, which differs from their more basal relatives, which have a slower cyclical growth. Here we examine the bone microstructure of several sauropodomorph dinosaurs, including basal taxa, as well as the more derived sauropods. Although our results agree that the plesiomorphic condition for Sauropodomorpha is cyclical growth dynamics, we found that the hypothesized dichotomy between the growth patterns of basal and more derived sauropodomorphs is not supported. Here, we show that sauropod-like growth dynamics of uninterrupted rapid growth also occurred in some basal sauropodomorphs, and that some basal sauropods retained the plesiomorphic cyclical growth patterns. Among the sauropodomorpha it appears that the basal taxa exploited different growth strategies, but the more derived Eusauropoda successfully utilized rapid, uninterrupted growth strategies.

Novel insight into the origin of the growth dynamics of sauropod dinosaurs

PubMed Central

Cerda, Ignacio Alejandro; Chinsamy, Anusuya; Pol, Diego; Apaldetti, Cecilia; Otero, Alejandro; Martínez, Ricardo Nestor

2017-01-01

Sauropod dinosaurs include the largest terrestrial animals and are considered to have uninterrupted rapid rates of growth, which differs from their more basal relatives, which have a slower cyclical growth. Here we examine the bone microstructure of several sauropodomorph dinosaurs, including basal taxa, as well as the more derived sauropods. Although our results agree that the plesiomorphic condition for Sauropodomorpha is cyclical growth dynamics, we found that the hypothesized dichotomy between the growth patterns of basal and more derived sauropodomorphs is not supported. Here, we show that sauropod-like growth dynamics of uninterrupted rapid growth also occurred in some basal sauropodomorphs, and that some basal sauropods retained the plesiomorphic cyclical growth patterns. Among the sauropodomorpha it appears that the basal taxa exploited different growth strategies, but the more derived Eusauropoda successfully utilized rapid, uninterrupted growth strategies. PMID:28654696

Extinction rates in tumour public goods games.

PubMed

Gerlee, Philip; Altrock, Philipp M

2017-09-01

Cancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumour cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here show that this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the time scales, in particular, in coevolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell-type-specific rates have to be accounted for explicitly. © 2017 The Authors.

Dynamic Microstructure Design Consortium

DTIC Science & Technology

2011-03-23

multiple realizations of polycrystalline microstructure. Cyclic microplasticity in favorably oriented martensite grains is the primary driver for the...can alter the residual stress distribution 13. The present work ex- plores how short-range microplastic deformation during cyclic loading promotes

On Budyko curve as a consequence of climate-soil-vegetation equilibrium hypothesis

NASA Astrophysics Data System (ADS)

Pande, S.

2012-04-01

A hypothesis that Budyko curve is a consequence of stable equilibriums of climate-soil-vegetation co-evolution is tested at biome scale. We assume that i) distribution of vegetation, soil and climate within a biome is a distribution of equilibriums of similar soil-vegetation dynamics and that this dynamics is different across different biomes and ii) soil and vegetation are in dynamic equilibrium with climate while in static equilibrium with each other. In order to test the hypothesis, a two stage regression is considered using MOPEX/Hydrologic Synthesis Project dataset for basins in eastern United States. In the first stage, multivariate regression (Seemingly Unrelated Regression) is performed for each biome with soil (estimated porosity and slope of soil water retention curve) and vegetation characteristics (5-week NDVI gradient) as dependent variables and aridity index, vegetation and soil characteristics as independent variables for respective dependent variables. The regression residuals of the first stage along with aridity index then serve as second stage independent variables while actual vaporization to precipitation ratio (vapor index) serving as dependent variable. Insignificance, if revealed, of a first stage parameter allows us to reject the role of corresponding soil or vegetation characteristics in the co-evolution hypothesis. Meanwhile the significance of second stage regression parameter corresponding to a first stage residual allow us to reject the hypothesis that Budyko curve is a locus "solely" of climate-soil-vegetation co-evolution equilibrium points. Results suggest lack of evidence for soil-vegetation co-evolution in Prairies and Mixed/SouthEast Forests (unlike in Deciduous Forests) though climate plays a dominant role in explaining within biome soil and vegetation characteristics across all the biomes. Preliminary results indicate absence of effects beyond climate-soil-vegetation co-evolution in explaining the ratio of annual total minimum monthly flows to precipitation in Deciduous Forests though other three biome types show presence of effects beyond co-evolutionary. Such an analysis can yield insights into the nature of hydrologic change when assessed along the Budyko curve as well as non co-evolutionary effects such as anthropogenic effects on basin scale annual water balances.

An evaluation of dynamic mutuality measurements and methods in cyclic time series

NASA Astrophysics Data System (ADS)

Xia, Xiaohua; Huang, Guitian; Duan, Na

2010-12-01

Several measurements and techniques have been developed to detect dynamic mutuality and synchronicity of time series in econometrics. This study aims to compare the performances of five methods, i.e., linear regression, dynamic correlation, Markov switching models, concordance index and recurrence quantification analysis, through numerical simulations. We evaluate the abilities of these methods to capture structure changing and cyclicity in time series and the findings of this paper would offer guidance to both academic and empirical researchers. Illustration examples are also provided to demonstrate the subtle differences of these techniques.

Cyclical Dynamics and Control of a Neuromechanical System

DTIC Science & Technology

2012-01-01

of the membrane potentials and synaptic conductances of neurons in the CPG model, or the lengths, velocities, and calcium concentrations in a muscle...empirical data. • We found that muscle is strongly self-stabilizing when activated cyclically, possibly because of the nonlinearity in how calcium binds and...only its natural calcium dynamics and length, velocity, and tension relationships, is strongly self-stabilizing. I plan to submit these results as an

Thermal Fatigue and Fracture Behavior of Ceramic Thermal Barrier Coatings

NASA Technical Reports Server (NTRS)

Zhu, Dong-Ming; Choi, Sung R.; Miller, Robert A.

2001-01-01

Thermal fatigue and fracture behavior of plasma-sprayed ceramic thermal barrier coatings has been investigated under high heat flux and thermal cyclic conditions. The coating crack propagation is studied under laser heat flux cyclic thermal loading, and is correlated with dynamic fatigue and strength test results. The coating stress response and inelasticity, fatigue and creep interactions, and interface damage mechanisms during dynamic thermal fatigue processes are emphasized.

Dark solitons, modulation instability and breathers in a chain of weakly nonlinear oscillators with cyclic symmetry

NASA Astrophysics Data System (ADS)

Fontanela, F.; Grolet, A.; Salles, L.; Chabchoub, A.; Hoffmann, N.

2018-01-01

In the aerospace industry the trend for light-weight structures and the resulting complex dynamic behaviours currently challenge vibration engineers. In many cases, these light-weight structures deviate from linear behaviour, and complex nonlinear phenomena can be expected. We consider a cyclically symmetric system of coupled weakly nonlinear undamped oscillators that could be considered a minimal model for different cyclic and symmetric aerospace structures experiencing large deformations. The focus is on localised vibrations that arise from wave envelope modulation of travelling waves. For the defocussing parameter range of the approximative nonlinear evolution equation, we show the possible existence of dark solitons and discuss their characteristics. For the focussing parameter range, we characterise modulation instability and illustrate corresponding nonlinear breather dynamics. Furthermore, we show that for stronger nonlinearity or randomness in initial conditions, transient breather-type dynamics and decay into bright solitons appear. The findings suggest that significant vibration localisation may arise due to mechanisms of nonlinear modulation dynamics.

Signatures of co-evolutionary host-pathogen interactions in the genome of the entomopathogenic nematode Steinernema carpocapsae.

PubMed

Flores-Ponce, Mitzi; Vallebueno-Estrada, Miguel; González-Orozco, Eduardo; Ramos-Aboites, Hilda E; García-Chávez, J Noé; Simões, Nelson; Montiel, Rafael

2017-04-26

The entomopathogenic nematode Steinernema carpocapsae has been used worldwide as a biocontrol agent for insect pests, making it an interesting model for understanding parasite-host interactions. Two models propose that these interactions are co-evolutionary processes in such a way that equilibrium is never reached. In one model, known as "arms race", new alleles in relevant genes are fixed in both host and pathogens by directional positive selection, producing recurrent and alternating selective sweeps. In the other model, known as"trench warfare", persistent dynamic fluctuations in allele frequencies are sustained by balancing selection. There are some examples of genes evolving according to both models, however, it is not clear to what extent these interactions might alter genome-level evolutionary patterns and intraspecific diversity. Here we investigate some of these aspects by studying genomic variation in S. carpocapsae and other pathogenic and free-living nematodes from phylogenetic clades IV and V. To look for signatures of an arms-race dynamic, we conducted massive scans to detect directional positive selection in interspecific data. In free-living nematodes, we detected a significantly higher proportion of genes with sites under positive selection than in parasitic nematodes. However, in these genes, we found more enriched Gene Ontology terms in parasites. To detect possible effects of dynamic polymorphisms interactions we looked for signatures of balancing selection in intraspecific genomic data. The observed distribution of Tajima's D values in S. carpocapsae was more skewed to positive values and significantly different from the observed distribution in the free-living Caenorhabditis briggsae. Also, the proportion of significant positive values of Tajima's D was elevated in genes that were differentially expressed after induction with insect tissues as compared to both non-differentially expressed genes and the global scan. Our study provides a first portrait of the effects that lifestyle might have in shaping the patterns of selection at the genomic level. An arms-race between hosts and pathogens seems to be affecting specific genetic functions but not necessarily increasing the number of positively selected genes. Trench warfare dynamics seem to be acting more generally in the genome, likely focusing on genes responding to the interaction, rather than targeting specific genetic functions.

Study of geometric phase using classical coupled oscillators

NASA Astrophysics Data System (ADS)

Bhattacharjee, Sharba; Dey, Biprateep; Mohapatra, Ashok K.

2018-05-01

We illustrate the geometric phase associated with the cyclic dynamics of a classical system of coupled oscillators. We use an analogy between a classical coupled oscillator and a two-state quantum mechanical system to represent the evolution of the oscillator on an equivalent Hilbert space, which may be represented as a trajectory on the surface of a sphere. The cyclic evolution of the system leads to a change in phase, which consists of a dynamic phase along with an additional phase shift dependent on the geometry of the evolution. A simple experiment suitable for advanced undergraduate students is designed to study the geometric phase incurred during cyclic evolution of a coupled oscillator.

Angular analysis of the cyclic impacting oscillations in a robotic grinding process

NASA Astrophysics Data System (ADS)

Rafieian, Farzad; Girardin, François; Liu, Zhaoheng; Thomas, Marc; Hazel, Bruce

2014-02-01

In a robotic machining process, a light-weight cutter or grinder is usually held by an articulated robot arm. Material removal is achieved by the rotating cutting tool while the robot end effector ensures that the tool follows a programmed trajectory in order to work on complex curved surfaces or to access hard-to-reach areas. One typical application of such process is maintenance and repair work on hydropower equipment. This paper presents an experimental study of the dynamic characteristics of material removal in robotic grinding, which is unlike conventional grinding due to the lower structural stiffness of the tool-holder robot. The objective of the study is to explore the cyclic nature of this mechanical operation to provide the basis for future development of better process control strategies. Grinding tasks that minimize the number of iterations to converge to the target surface can be better planned based on a good understanding and modeling of the cyclic material removal mechanism. A single degree of freedom dynamic analysis of the process suggests that material removal is performed through high-frequency impacts that mainly last for only a small fraction of the grinding disk rotation period. To detect these discrete cutting events in practice, a grinder is equipped with a rotary encoder. The encoder's signal is acquired through the angular sampling technique. A running cyclic synchronous average is applied to the speed signal to remove its non-cyclic events. The measured instantaneous rotational frequency clearly indicates the impacting nature of the process and captures the transient response excited by these cyclic impacts. The technique also locates the angular positions of cutting impacts in revolution cycles. It is thus possible to draw conclusions about the cyclic nature of dynamic changes in impact-cutting behavior when grinding with a flexible robot. The dynamics of the impacting regime and transient responses to impact-cutting excitations captured synchronously using the angular sampling technique provide feedback that can be used to regulate the material removal process. The experimental results also make it possible to correlate the energy required to remove a chip of metal through impacting with the measured drop in angular speed during grinding.

Endogenous technological and population change under increasing water scarcity

NASA Astrophysics Data System (ADS)

Pande, S.; Ertsen, M.; Sivapalan, M.

2014-08-01

Ancient civilizations may have dispersed or collapsed under extreme dry conditions. There are indications that the same may hold for modern societies. However, hydroclimatic change cannot be the sole predictor of the fate of contemporary societies in water-scarce regions. This paper focuses on technological change as a factor that may ameliorate the effects of increasing water scarcity and as such counter the effects of hydroclimatic changes. We study the role of technological change on the dynamics of coupled human-water systems, and model technological change as an endogenous process that depends on many factors intrinsic to coupled human-water dynamics. We do not treat technology as an exogenous random sequence of events, but assume that it results from societal actions. While the proposed model is a rather simple model of a coupled human-water system, it is shown to be capable of replicating patterns of technological, population, production and consumption per capita changes. The model demonstrates that technological change may indeed ameliorate the effects of increasing water scarcity, but typically it does so only to a certain extent. In general we find that endogenous technology change under increasing water scarcity helps to delay the peak of population size before it inevitably starts to decline. We also analyze the case when water remains constant over time and find that co-evolutionary trajectories can never grow at a constant rate; rather the rate itself grows with time. Thus our model does not predict a co-evolutionary trajectory of a socio-hydrological system where technological innovation harmoniously provides for a growing population. It allows either for an explosion or an eventual dispersal of population. The latter occurs only under increasing water scarcity. As a result, we draw the conclusion that declining consumption per capita despite technological advancement and increase in aggregate production may serve as a useful predictor of upcoming decline in contemporary societies in water-scarce basins.

Kinetic parameters and renal clearances of plasma adenosine 3′,5′-monophosphate and guanosine 3′,5′-monophosphate in man

PubMed Central

Broadus, Arthur E.; Kaminsky, Neil I.; Hardman, Joel G.; Sutherland, Earl W.; Liddle, Grant W.

1970-01-01

Kinetic parameters and the renal clearances of plasma adenosine 3′,5′-monophosphate (cyclic AMP) and guanosine 3′,5′-monophosphate (cyclic GMP) were evaluated in normal subjects using tritium-labeled cyclic nucleotides. Each tracer was administered both by single, rapid intravenous injection and by constant intravenous infusion, and the specific activities of the cyclic nucleotides in plasma and urine were determined. Both cyclic AMP and cyclic GMP were cleared from plasma by glomerular filtration. The kidney was found to add a variable quantity of endogenous cyclic AMP to the tubular urine, amounting to an average of approximately one-third of the total level of cyclic AMP excreted. Plasma was the source of virtually all of the cyclic GMP excreted. Plasma levels of the cyclic nucleotides appeared to be in dynamic steady state. The apparent volumes of distribution of both nucleotides exceeded extracellular fluid volume, averaging 27 and 38% of body weight for cyclic AMP and cyclic GMP, respectively. Plasma production rates ranged from 9 to 17 nmoles/min for cyclic AMP and from 7 to 13 nmoles/min for cyclic GMP. Plasma clearance rates averaged 668 ml/min for cyclic AMP and 855 ml/min for cyclic GMP. Approximately 85% of the elimination of the cyclic nucleotides from the circulation was due to extrarenal clearance. PMID:5480849

Coevolution of Cooperation and Partner Rewiring Range in Spatial Social Networks

NASA Astrophysics Data System (ADS)

Khoo, Tommy; Fu, Feng; Pauls, Scott

2016-11-01

In recent years, there has been growing interest in the study of coevolutionary games on networks. Despite much progress, little attention has been paid to spatially embedded networks, where the underlying geographic distance, rather than the graph distance, is an important and relevant aspect of the partner rewiring process. It thus remains largely unclear how individual partner rewiring range preference, local vs. global, emerges and affects cooperation. Here we explicitly address this issue using a coevolutionary model of cooperation and partner rewiring range preference in spatially embedded social networks. In contrast to local rewiring, global rewiring has no distance restriction but incurs a one-time cost upon establishing any long range link. We find that under a wide range of model parameters, global partner switching preference can coevolve with cooperation. Moreover, the resulting partner network is highly degree-heterogeneous with small average shortest path length while maintaining high clustering, thereby possessing small-world properties. We also discover an optimum availability of reputation information for the emergence of global cooperators, who form distant partnerships at a cost to themselves. From the coevolutionary perspective, our work may help explain the ubiquity of small-world topologies arising alongside cooperation in the real world.

Cyclic fatigue resistance of ProTaper Universal instruments when subjected to static and dynamic tests.

PubMed

Lopes, Hélio P; Britto, Izabelle M O; Elias, Carlos N; Machado de Oliveira, Julio C; Neves, Mônica A S; Moreira, Edson J L; Siqueira, José F

2010-09-01

This study evaluated the number of cycles to fracture of ProTaper Universal S2 instruments when subjected to static and dynamic cyclic fatigue tests. ProTaper Universal S2 instruments were used until fracture in an artificial curved canal under rotational speed of 300 rpm in either a static or a dynamic test model. Afterward, the length of the fractured segments was measured and fractured surfaces and helical shafts analyzed by scanning electron microscopy (SEM). The number of cycles to fracture was significantly increased when instruments were tested in the dynamic model (P<.001). Instrument separation occurred at the point of maximum flexure within the artificial canals, i.e., the midpoint of the curved canal segment. SEM analysis revealed that fractured surfaces exhibited characteristics of the ductile mode. Plastic deformation was not observed in the helical shaft of fractured instruments. The number of cycles to fracture ProTaper Universal S2 instruments significantly increased with the use of instruments in a dynamic cyclic fatigue test compared with a static model. These findings reinforce the need for performing continuous pecking motions during rotary instrumentation of curved root canals. Copyright (c) 2010 Mosby, Inc. All rights reserved.

Atomistic Structure and Dynamics of the Solvation Shell Formed by Organic Carbonates around Lithium Ions via Infrared Spectroscopies

NASA Astrophysics Data System (ADS)

Kuroda, Daniel; Fufler, Kristen

Lithium-ion batteries have become ubiquitous to the portable energy storage industry, but efficiency issues still remain. Currently, most technological and scientific efforts are focused on the electrodes with little attention on the electrolyte. For example, simple fundamental questions about the lithium ion solvation shell composition in commercially used electrolytes have not been answered. Using a combination of linear and non-linear IR spectroscopies and theoretical calculations, we have carried out a thorough investigation of the solvation structure and dynamics of the lithium ion in various linear and cyclic carbonates at common battery electrolyte concentrations. Our studies show that carbonates coordinate the lithium ion tetrahedrally. They also reveal that linear and cyclic carbonates have contrasting dynamics in which cyclic carbonates present the most ordered structure. Finally, our experiments demonstrate that simple structural modifications in the linear carbonates impact significantly the microscopic interactions of the system. The stark differences in the solvation structure and dynamics among different carbonates reveal previously unknown details about the molecular level picture of these systems.

Incest avoidance: oedipal and preoedipal, natural and cultural.

PubMed

Paul, Robert A

2010-12-01

Why do most people experience a subjective aversion to the idea of incestuous sexual relations? To help answer this question, recent strands of thinking in both cultural and evolutionary anthropology are considered together with psychoanalytic theories regarding incest avoidance. Coevolutionary theories that propose ways to think about genetic and cultural inheritance as partially independent of each other, evolutionary arguments about the reproductive advantages of incest avoidance, structuralist theory arguing for a kind of incest aversion unrelated to any possible Darwinian selective advantage, and other trends in biosocial research into the origins of the incest avoidance are considered. Finally, a synthesis is proposed that seeks to expand our understanding of the oedipal and preoedipal dynamics of the aversion as these are conceptualized in psychoanalytic theory.

The effect of cyclic feathering motions on dynamic rotor loads. [for helicopters

NASA Technical Reports Server (NTRS)

Harvey, K. W.

1974-01-01

The dynamic loads of a helicopter rotor in forward flight are influenced significantly by the geometric pitch angles between the structural axes of the hub and blade sections and the plane of rotation. The analytical study presented includes elastic coupling between inplane and out-of-plane deflections as a function of geometric pitch between the plane of rotation and the principal axes of inertia of each blade. The numerical evaluation is based on a transient analysis using lumped masses and elastic substructure techniques. A comparison of cases with and without cyclic feathering motion shows the effect on computed dynamic rotor loads.

Bistability and State Transition of a Delay Differential Equation Model of Neutrophil Dynamics

NASA Astrophysics Data System (ADS)

Ma, Suqi; Zhu, Kaiyi; Lei, Jinzhi

This paper studies the existence of bistable states and control strategies to induce state transitions of a delay differential equation model of neutrophil dynamics. We seek the conditions that a stable steady state and an oscillatory state coexist in the neutrophil dynamical system. Physiologically, stable steady state represents the healthy state, while oscillatory state is usually associated with diseases such as cyclical neutropenia. We study the control strategies to induce the transitions from the disease state to the healthy state by introducing temporal perturbations to system parameters. This study is valuable in designing clinical protocols for the treatment of cyclical neutropenia.

Development of new two-dimensional spectral/spatial code based on dynamic cyclic shift code for OCDMA system

NASA Astrophysics Data System (ADS)

Jellali, Nabiha; Najjar, Monia; Ferchichi, Moez; Rezig, Houria

2017-07-01

In this paper, a new two-dimensional spectral/spatial codes family, named two dimensional dynamic cyclic shift codes (2D-DCS) is introduced. The 2D-DCS codes are derived from the dynamic cyclic shift code for the spectral and spatial coding. The proposed system can fully eliminate the multiple access interference (MAI) by using the MAI cancellation property. The effect of shot noise, phase-induced intensity noise and thermal noise are used to analyze the code performance. In comparison with existing two dimensional (2D) codes, such as 2D perfect difference (2D-PD), 2D Extended Enhanced Double Weight (2D-Extended-EDW) and 2D hybrid (2D-FCC/MDW) codes, the numerical results show that our proposed codes have the best performance. By keeping the same code length and increasing the spatial code, the performance of our 2D-DCS system is enhanced: it provides higher data rates while using lower transmitted power and a smaller spectral width.

Towards a Molecular Movie: Real Time Observation of Hydrogen Bond Breaking by Transient 2D-IR Spectroscopy in a Cyclic Peptide

NASA Astrophysics Data System (ADS)

Kolano, Christoph; Helbing, Jan; Sander, Wolfram; Hamm, Peter

Transient two-dimensional infrared spectroscopy (T2D-IR) has been used to observe in real time the non-equilibrium structural dynamics of intramolecular hydrogen bond breaking in a small cyclic disulfide-bridged peptide.

Dynamic strain aging behavior of 10Cr steel under low cycle fatigue at 650°C

NASA Astrophysics Data System (ADS)

Mishnev, Roman; Dudova, Nadezhda; Kaibyshev, Rustam

2017-12-01

The low cycle fatigue behavior of a 10Cr-2W-0.7Mo-3Co-NbV steel with 80 ppm of B additions was studied at elevated temperatures of 600 and 650°C. The steel after normalizing and tempering at 770°C was tested under fully reversed tension-compression loading with the total strain amplitude controlled from ±0.2 to ±1.0% at temperatures of 600 and 650°C. It was revealed that the steel exhibits a positive temperature dependence of both the cyclic strain hardening exponent n' and the cyclic strength coefficient K ' during cyclic loading at 650°C. It was suggested that dynamic strain aging causes fatigue resistance degradation through facilitating microcrack initiation.

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

NASA Astrophysics Data System (ADS)

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-08-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

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

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure.

PubMed

Schleussner, Carl-Friedrich; Donges, Jonathan F; Engemann, Denis A; Levermann, Anders

2016-08-11

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking.

Tolerance-based punishment in continuous public goods game

NASA Astrophysics Data System (ADS)

Gao, Jia; Li, Zhi; Cong, Rui; Wang, Long

2012-08-01

Altruistic punishment for defectors is considered as a key motive for the explanation of cooperation. However, there is no clear border between the cooperative and defective behaviors in a continuous strategy game. We propose a model to study the effect of punishment on the evolution of cooperation in continuous public goods game, wherein individuals have the traits to punish the co-players based on social tolerance. We show that a reasonable punishment with a uniform tolerance can spur individuals to make more investments. Additionally, for a fixed punishment cost and a fixed fine, a moderate value of tolerance can result in the best promotion of cooperation. Furthermore, we investigate the coevolutionary dynamics of investment and tolerance. We find that the population splits into two branches: high-tolerance individuals who make high investments and low-tolerance individuals who make low investments. A dynamic equilibrium is achieved between these two types of individuals. Our work extends punishment to continuous cooperative behaviors and the results may enhance the understanding of altruistic punishment in the evolution of human cooperation.

Coevolutionary, coexisting learning and teaching agents model for prisoner’s dilemma games enhancing cooperation with assortative heterogeneous networks

NASA Astrophysics Data System (ADS)

Tanimoto, Jun

2013-07-01

Unlike other natural network systems, assortativity can be observed in most human social networks, although it has been reported that a social dilemma situation represented by the prisoner’s dilemma favors dissortativity to enhance cooperation. We established a new coevolutionary model for both agents’ strategy and network topology, where teaching and learning agents coexist. Remarkably, this model enables agents’ enhancing cooperation more than a learners-only model on a time-frozen scale-free network and produces an underlying assortative network with a fair degree of power-law distribution. The model may imply how and why assortative networks are adaptive in human society.

Governing Laws of Complex System Predictability under Co-evolving Uncertainty Sources: Theory and Nonlinear Geophysical Applications

NASA Astrophysics Data System (ADS)

Perdigão, R. A. P.

2017-12-01

Predictability assessments are traditionally made on a case-by-case basis, often by running the particular model of interest with randomly perturbed initial/boundary conditions and parameters, producing computationally expensive ensembles. These approaches provide a lumped statistical view of uncertainty evolution, without eliciting the fundamental processes and interactions at play in the uncertainty dynamics. In order to address these limitations, we introduce a systematic dynamical framework for predictability assessment and forecast, by analytically deriving governing equations of predictability in terms of the fundamental architecture of dynamical systems, independent of any particular problem under consideration. The framework further relates multiple uncertainty sources along with their coevolutionary interplay, enabling a comprehensive and explicit treatment of uncertainty dynamics along time, without requiring the actual model to be run. In doing so, computational resources are freed and a quick and effective a-priori systematic dynamic evaluation is made of predictability evolution and its challenges, including aspects in the model architecture and intervening variables that may require optimization ahead of initiating any model runs. It further brings out universal dynamic features in the error dynamics elusive to any case specific treatment, ultimately shedding fundamental light on the challenging issue of predictability. The formulated approach, framed with broad mathematical physics generality in mind, is then implemented in dynamic models of nonlinear geophysical systems with various degrees of complexity, in order to evaluate their limitations and provide informed assistance on how to optimize their design and improve their predictability in fundamental dynamical terms.

Cyber Security Research Frameworks For Coevolutionary Network Defense

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

Rush, George D.; Tauritz, Daniel Remy

Several architectures have been created for developing and testing systems used in network security, but most are meant to provide a platform for running cyber security experiments as opposed to automating experiment processes. In the first paper, we propose a framework termed Distributed Cyber Security Automation Framework for Experiments (DCAFE) that enables experiment automation and control in a distributed environment. Predictive analysis of adversaries is another thorny issue in cyber security. Game theory can be used to mathematically analyze adversary models, but its scalability limitations restrict its use. Computational game theory allows us to scale classical game theory to larger,more » more complex systems. In the second paper, we propose a framework termed Coevolutionary Agent-based Network Defense Lightweight Event System (CANDLES) that can coevolve attacker and defender agent strategies and capabilities and evaluate potential solutions with a custom network defense simulation. The third paper is a continuation of the CANDLES project in which we rewrote key parts of the framework. Attackers and defenders have been redesigned to evolve pure strategy, and a new network security simulation is devised which specifies network architecture and adds a temporal aspect. We also add a hill climber algorithm to evaluate the search space and justify the use of a coevolutionary algorithm.« less

Success of cuckoo catfish brood parasitism reflects coevolutionary history and individual experience of their cichlid hosts

PubMed Central

Polačik, Matej; Smith, Carl; Honza, Marcel; Reichard, Martin

2018-01-01

Obligate brood parasites manipulate other species into raising their offspring. Avian and insect brood parasitic systems demonstrate how interacting species engage in reciprocal coevolutionary arms races through behavioral and morphological adaptations and counteradaptations. Mouthbrooding cichlid fishes are renowned for their remarkable evolutionary radiations and complex behaviors. In Lake Tanganyika, mouthbrooding cichlids are exploited by the only obligate nonavian vertebrate brood parasite, the cuckoo catfish Synodontis multipunctatus. We show that coevolutionary history and individual learning both have a major impact on the success of cuckoo catfish parasitism between coevolved sympatric and evolutionarily naïve allopatric cichlid species. The rate of cuckoo catfish parasitism in coevolved Tanganyikan hosts was 3 to 11 times lower than in evolutionarily naïve cichlids. Moreover, using experimental infections, we demonstrate that parasite egg rejection in sympatric hosts was much higher, leading to seven times greater parasite survival in evolutionarily naïve than sympatric hosts. However, a high rejection frequency of parasitic catfish eggs by coevolved sympatric hosts came at a cost of increased rejection of their own eggs. A significant cost of catfish parasitism was universal, except for coevolved sympatric cichlid species with previous experience of catfish parasitism, demonstrating that learning and individual experience both contribute to a successful host response. PMID:29732407

Archaeogenomic insights into the adaptation of plants to the human environment: pushing plant-hominin co-evolution back to the Pliocene.

PubMed

Allaby, Robin G; Kistler, Logan; Gutaker, Rafal M; Ware, Roselyn; Kitchen, James L; Smith, Oliver; Clarke, Andrew C

2015-02-01

The colonization of the human environment by plants, and the consequent evolution of domesticated forms is increasingly being viewed as a co-evolutionary plant-human process that occurred over a long time period, with evidence for the co-evolutionary relationship between plants and humans reaching ever deeper into the hominin past. This developing view is characterized by a change in emphasis on the drivers of evolution in the case of plants. Rather than individual species being passive recipients of artificial selection pressures and ultimately becoming domesticates, entire plant communities adapted to the human environment. This evolutionary scenario leads to systems level genetic expectations from models that can be explored through ancient DNA and Next Generation Sequencing approaches. Emerging evidence suggests that domesticated genomes fit well with these expectations, with periods of stable complex evolution characterized by large amounts of change associated with relatively small selective value, punctuated by periods in which changes in one-half of the plant-hominin relationship cause rapid, low-complexity adaptation in the other. A corollary of a single plant-hominin co-evolutionary process is that clues about the initiation of the domestication process may well lie deep within the hominin lineage. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Assembly constraints drive co-evolution among ribosomal constituents.

PubMed

Mallik, Saurav; Akashi, Hiroshi; Kundu, Sudip

2015-06-23

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

Migratory behavior of birds affects their coevolutionary relationship with blood parasites.

PubMed

Jenkins, Tania; Thomas, Gavin H; Hellgren, Olof; Owens, Ian P F

2012-03-01

Host traits, such as migratory behavior, could facilitate the dispersal of disease-causing parasites, potentially leading to the transfer of infections both across geographic areas and between host species. There is, however, little quantitative information on whether variation in such host attributes does indeed affect the evolutionary outcome of host-parasite associations. Here, we employ Leucocytozoon blood parasites of birds, a group of parasites closely related to avian malaria, to study host-parasite coevolution in relation to host behavior using a phylogenetic comparative approach. We reconstruct the molecular phylogenies of both the hosts and parasites and use cophylogenetic tools to assess whether each host-parasite association contributes significantly to the overall congruence between the two phylogenies. We find evidence for a significant fit between host and parasite phylogenies in this system, but show that this is due only to associations between nonmigrant parasites and their hosts. We also show that migrant bird species harbor a greater genetic diversity of parasites compared with nonmigrant species. Taken together, these results suggest that the migratory habits of birds could influence their coevolutionary relationship with their parasites, and that consideration of host traits is important in predicting the outcome of coevolutionary interactions. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.

Dynamic characteristics and simplified numerical methods of an all-vertical-piled wharf in offshore deep water

NASA Astrophysics Data System (ADS)

Zhang, Hua-qing; Sun, Xi-ping; Wang, Yuan-zhan; Yin, Ji-long; Wang, Chao-yang

2015-10-01

There has been a growing trend in the development of offshore deep-water ports in China. For such deep sea projects, all-vertical-piled wharves are suitable structures and generally located in open waters, greatly affected by wave action. Currently, no systematic studies or simplified numerical methods are available for deriving the dynamic characteristics and dynamic responses of all-vertical-piled wharves under wave cyclic loads. In this article, we compare the dynamic characteristics of an all-vertical-piled wharf with those of a traditional inshore high-piled wharf through numerical analysis; our research reveals that the vibration period of an all-vertical-piled wharf under cyclic loading is longer than that of an inshore high-piled wharf and is much closer to the period of the loading wave. Therefore, dynamic calculation and analysis should be conducted when designing and calculating the characteristics of an all-vertical-piled wharf. We establish a dynamic finite element model to examine the dynamic response of an all-vertical-piled wharf under wave cyclic loads and compare the results with those under wave equivalent static load; the comparison indicates that dynamic amplification of the structure is evident when the wave dynamic load effect is taken into account. Furthermore, a simplified dynamic numerical method for calculating the dynamic response of an all-vertical-piled wharf is established based on the P-Y curve. Compared with finite element analysis, the simplified method is more convenient to use and applicable to large structural deformation while considering the soil non-linearity. We confirmed that the simplified method has acceptable accuracy and can be used in engineering applications.

Contrasting Patterns in Mammal–Bacteria Coevolution: Bartonella and Leptospira in Bats and Rodents

PubMed Central

Lei, Bonnie R.; Olival, Kevin J.

2014-01-01

Background Emerging bacterial zoonoses in bats and rodents remain relatively understudied. We conduct the first comparative host–pathogen coevolutionary analyses of bacterial pathogens in these hosts, using Bartonella spp. and Leptospira spp. as a model. Methodology/Principal Findings We used published genetic data for 51 Bartonella genotypes from 24 bat species, 129 Bartonella from 38 rodents, and 26 Leptospira from 20 bats. We generated maximum likelihood and Bayesian phylogenies for hosts and bacteria, and tested for coevoutionary congruence using programs ParaFit, PACO, and Jane. Bartonella spp. and their bat hosts had a significant coevolutionary fit (ParaFitGlobal = 1.9703, P≤0.001; m2 global value = 7.3320, P≤0.0001). Bartonella spp. and rodent hosts also indicated strong overall patterns of cospeciation (ParaFitGlobal = 102.4409, P≤0.001; m2 global value = 86.532, P≤0.0001). In contrast, we were unable to reject independence of speciation events in Leptospira and bats (ParaFitGlobal = 0.0042, P = 0.84; m2 global value = 4.6310, P = 0.5629). Separate analyses of New World and Old World data subsets yielded results congruent with analysis from entire datasets. We also conducted event-based cophylogeny analyses to reconstruct likely evolutionary histories for each group of pathogens and hosts. Leptospira and bats had the greatest number of host switches per parasite (0.731), while Bartonella and rodents had the fewest (0.264). Conclusions/Significance In both bat and rodent hosts, Bartonella exhibits significant coevolution with minimal host switching, while Leptospira in bats lacks evolutionary congruence with its host and has high number of host switches. Reasons underlying these variable coevolutionary patterns in host range are likely due to differences in disease-specific transmission and host ecology. Understanding the coevolutionary patterns and frequency of host-switching events between bacterial pathogens and their hosts will allow better prediction of spillover between mammal reservoirs, and ultimately to humans. PMID:24651646

Proceedings of the Third International Symposium on Ground Freezing Held at Hanover, New Hampshire on 22-24 June 1982.

DTIC Science & Technology

1982-01-01

The cyclicly changing axial stresses a . and a are leading to the dynamic stress path which loads the frozen soil [MN/m’) samples. It is obvious that...Fig. 5 are related to a sinoidal dynamic axial loading . Figure a sample temperature of T = -10*C, in 4 shows schematically a triaxial test re- Fig. 6...Czajkowski (1978), Behaviour of Fro-ry phase was not reached. zen Clay under Cyclic Axial Loading , Journal of the Geotechnical Engineer- ing Division

Cyclic dynamics in a simple vertebrate predator-prey community.

PubMed

Gilg, Olivier; Hanski, Ilkka; Sittler, Benoît

2003-10-31

The collared lemming in the high-Arctic tundra in Greenland is preyed upon by four species of predators that show marked differences in the numbers of lemmings each consumes and in the dependence of their dynamics on lemming density. A predator prey model based on the field-estimated predator responses robustly predicts 4-year periodicity in lemming dynamics, in agreement with long-term empirical data. There is no indication in the field that food or space limits lemming population growth, nor is there need in the model to consider those factors. The cyclic dynamics are driven by a 1-year delay in the numerical response of the stoat and stabilized by strongly density-dependent predation by the arctic fox, the snowy owl, and the long-tailed skua.

Precisely cyclic sand: self-organization of periodically sheared frictional grains.

PubMed

Royer, John R; Chaikin, Paul M

2015-01-06

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain-friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many-degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic.

Precisely cyclic sand: Self-organization of periodically sheared frictional grains

PubMed Central

Royer, John R.; Chaikin, Paul M.

2015-01-01

The disordered static structure and chaotic dynamics of frictional granular matter has occupied scientists for centuries, yet there are few organizational principles or guiding rules for this highly hysteretic, dissipative material. We show that cyclic shear of a granular material leads to dynamic self-organization into several phases with different spatial and temporal order. Using numerical simulations, we present a phase diagram in strain–friction space that shows chaotic dispersion, crystal formation, vortex patterns, and most unusually a disordered phase in which each particle precisely retraces its unique path. However, the system is not reversible. Rather, the trajectory of each particle, and the entire frictional, many–degrees-of-freedom system, organizes itself into a limit cycle absorbing state. Of particular note is that fact that the cyclic states are spatially disordered, whereas the ordered states are chaotic. PMID:25538298

Using dynamic mode decomposition to extract cyclic behavior in the stock market

NASA Astrophysics Data System (ADS)

Hua, Jia-Chen; Roy, Sukesh; McCauley, Joseph L.; Gunaratne, Gemunu H.

2016-04-01

The presence of cyclic expansions and contractions in the economy has been known for over a century. The work reported here searches for similar cyclic behavior in stock valuations. The variations are subtle and can only be extracted through analysis of price variations of a large number of stocks. Koopman mode analysis is a natural approach to establish such collective oscillatory behavior. The difficulty is that even non-cyclic and stochastic constituents of a finite data set may be interpreted as a sum of periodic motions. However, deconvolution of these irregular dynamical facets may be expected to be non-robust, i.e., to depend on specific data set. We propose an approach to differentiate robust and non-robust features in a time series; it is based on identifying robust features with reproducible Koopman modes, i.e., those that persist between distinct sub-groupings of the data. Our analysis of stock data discovered four reproducible modes, one of which has period close to the number of trading days/year. To the best of our knowledge these cycles were not reported previously. It is particularly interesting that the cyclic behaviors persisted through the great recession even though phase relationships between stocks within the modes evolved in the intervening period.

A norm knockout method on indirect reciprocity to reveal indispensable norms

PubMed Central

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-01-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out. PMID:28276485

A norm knockout method on indirect reciprocity to reveal indispensable norms

NASA Astrophysics Data System (ADS)

Yamamoto, Hitoshi; Okada, Isamu; Uchida, Satoshi; Sasaki, Tatsuya

2017-03-01

Although various norms for reciprocity-based cooperation have been suggested that are evolutionarily stable against invasion from free riders, the process of alternation of norms and the role of diversified norms remain unclear in the evolution of cooperation. We clarify the co-evolutionary dynamics of norms and cooperation in indirect reciprocity and also identify the indispensable norms for the evolution of cooperation. Inspired by the gene knockout method, a genetic engineering technique, we developed the norm knockout method and clarified the norms necessary for the establishment of cooperation. The results of numerical investigations revealed that the majority of norms gradually transitioned to tolerant norms after defectors are eliminated by strict norms. Furthermore, no cooperation emerges when specific norms that are intolerant to defectors are knocked out.

Cyclic sedimentation pattern in Lake Veetka, southeast Estonia: a case study

NASA Astrophysics Data System (ADS)

Saarse, Leili

2015-03-01

A sediment core from Lake Veetka, southeast Estonia, 1077 cm in length and covering 10,500 calibrated years, was examined using loss-on-ignition, grain-size distribution and AMS 14C dating to reconstruct depositional dynamics. The studied core, recovered from the northern part of the lake, shows a cyclic pattern of organic and mineral matter concentration with cycle durations of 100-400 years. Cyclicity is displayed better in sediments laid down between 9,200 and 5,600 cal BP. Within two time windows (5,600-5,100 cal BP and from 1,200 cal BP to the present), sediment composition changed drastically on account of a high and fluctuating mineral matter content, obviously driven by different factors. Little Ice Age cooling is characterised by the highest proportion of mineral matter, and the Medieval Warm Period is typified by high organic matter content. The cyclic change of organic and mineral matter has been related to climate dynamics, most likely an alternation of wet and dry conditions, changes in the water level of the lake and differences in bioproduction

On Design Mining: Coevolution and Surrogate Models.

PubMed

Preen, Richard J; Bull, Larry

2017-01-01

Design mining is the use of computational intelligence techniques to iteratively search and model the attribute space of physical objects evaluated directly through rapid prototyping to meet given objectives. It enables the exploitation of novel materials and processes without formal models or complex simulation. In this article, we focus upon the coevolutionary nature of the design process when it is decomposed into concurrent sub-design-threads due to the overall complexity of the task. Using an abstract, tunable model of coevolution, we consider strategies to sample subthread designs for whole-system testing and how best to construct and use surrogate models within the coevolutionary scenario. Drawing on our findings, we then describe the effective design of an array of six heterogeneous vertical-axis wind turbines.

Tracing Water Vapor and Ice During Dust Growth

NASA Astrophysics Data System (ADS)

Krijt, Sebastiaan; Ciesla, Fred J.; Bergin, Edwin A.

2016-12-01

The processes that govern the evolution of dust and water (in the form of vapor or ice) in protoplanetary disks are intimately connected. We have developed a model that simulates dust coagulation, dust dynamics (settling, turbulent mixing), vapor diffusion, and condensation/sublimation of volatiles onto grains in a vertical column of a protoplanetary disk. We employ the model to study how dust growth and dynamics influence the vertical distribution of water vapor and water ice in the region just outside the radial snowline. Our main finding is that coagulation (boosted by the enhanced stickiness of icy grains) and the ensuing vertical settling of solids results in water vapor being depleted, but not totally removed, from the region above the snowline on a timescale commensurate with the vertical turbulent mixing timescale. Depending on the strength of the turbulence and the temperature, the depletion can reach factors of up to ˜50 in the disk atmosphere. In our isothermal column, this vapor depletion results in the vertical snowline moving closer to the midplane (by up to 2 gas scale heights) and the gas-phase {{C}}/{{O}} ratio above the vertical snowline increasing. Our findings illustrate the importance of dynamical effects and the need for understanding coevolutionary dynamics of gas and solids in planet-forming environments.

A simple electrostatic switch important in the activation of type I protein kinase A by cyclic AMP.

PubMed

Vigil, Dominico; Lin, Jung-Hsin; Sotriffer, Christoph A; Pennypacker, Juniper K; McCammon, J Andrew; Taylor, Susan S

2006-01-01

Cyclic AMP activates protein kinase A by binding to an inhibitory regulatory (R) subunit and releasing inhibition of the catalytic (C) subunit. Even though crystal structures of regulatory and catalytic subunits have been solved, the precise molecular mechanism by which cyclic AMP activates the kinase remains unknown. The dynamic properties of the cAMP binding domain in the absence of cAMP or C-subunit are also unknown. Here we report molecular-dynamics simulations and mutational studies of the RIalpha R-subunit that identify the C-helix as a highly dynamic switch which relays cAMP binding to the helical C-subunit binding regions. Furthermore, we identify an important salt bridge which links cAMP binding directly to the C-helix that is necessary for normal activation. Additional mutations show that a hydrophobic "hinge" region is not as critical for the cross-talk in PKA as it is in the homologous EPAC protein, illustrating how cAMP can control diverse functions using the evolutionarily conserved cAMP-binding domains.

Integrating molecular dynamics and co-evolutionary analysis for reliable target prediction and deregulation of the allosteric inhibition of aspartokinase for amino acid production.

PubMed

Chen, Zhen; Rappert, Sugima; Sun, Jibin; Zeng, An-Ping

2011-07-20

Deregulation of allosteric inhibition of enzymes is a challenge for strain engineering and has been achieved so far primarily by random mutation and trial-and-error. In this work, we used aspartokinase, an important allosteric enzyme for industrial amino acids production, to demonstrate a predictive approach that combines protein dynamics and evolution for a rational reengineering of enzyme allostery. Molecular dynamic simulation of aspartokinase III (AK3) from Escherichia coli and statistical coupling analysis of protein sequences of the aspartokinase family allowed to identify a cluster of residues which are correlated during protein motion and coupled during the evolution. This cluster of residues forms an interconnected network mediating the allosteric regulation, including most of the previously reported positions mutated in feedback insensitive AK3 mutants. Beyond these mutation positions, we have successfully constructed another twelve targeted mutations of AK3 desensitized toward lysine inhibition. Six threonine-insensitive mutants of aspartokinase I-homoserine dehydrogenase I (AK1-HD1) were also created based on the predictions. The proposed approach can be widely applied for the deregulation of other allosteric enzymes. Copyright © 2011 Elsevier B.V. All rights reserved.

The Dynamics of Coalition Formation on Complex Networks

NASA Astrophysics Data System (ADS)

Auer, S.; Heitzig, J.; Kornek, U.; Schöll, E.; Kurths, J.

2015-08-01

Complex networks describe the structure of many socio-economic systems. However, in studies of decision-making processes the evolution of the underlying social relations are disregarded. In this report, we aim to understand the formation of self-organizing domains of cooperation (“coalitions”) on an acquaintance network. We include both the network’s influence on the formation of coalitions and vice versa how the network adapts to the current coalition structure, thus forming a social feedback loop. We increase complexity from simple opinion adaptation processes studied in earlier research to more complex decision-making determined by costs and benefits, and from bilateral to multilateral cooperation. We show how phase transitions emerge from such coevolutionary dynamics, which can be interpreted as processes of great transformations. If the network adaptation rate is high, the social dynamics prevent the formation of a grand coalition and therefore full cooperation. We find some empirical support for our main results: Our model develops a bimodal coalition size distribution over time similar to those found in social structures. Our detection and distinguishing of phase transitions may be exemplary for other models of socio-economic systems with low agent numbers and therefore strong finite-size effects.

Floquet stability analysis of the longitudinal dynamics of two hovering model insects

PubMed Central

Wu, Jiang Hao; Sun, Mao

2012-01-01

Because of the periodically varying aerodynamic and inertial forces of the flapping wings, a hovering or constant-speed flying insect is a cyclically forcing system, and, generally, the flight is not in a fixed-point equilibrium, but in a cyclic-motion equilibrium. Current stability theory of insect flight is based on the averaged model and treats the flight as a fixed-point equilibrium. In the present study, we treated the flight as a cyclic-motion equilibrium and used the Floquet theory to analyse the longitudinal stability of insect flight. Two hovering model insects were considered—a dronefly and a hawkmoth. The former had relatively high wingbeat frequency and small wing-mass to body-mass ratio, and hence very small amplitude of body oscillation; while the latter had relatively low wingbeat frequency and large wing-mass to body-mass ratio, and hence relatively large amplitude of body oscillation. For comparison, analysis using the averaged-model theory (fixed-point stability analysis) was also made. Results of both the cyclic-motion stability analysis and the fixed-point stability analysis were tested by numerical simulation using complete equations of motion coupled with the Navier–Stokes equations. The Floquet theory (cyclic-motion stability analysis) agreed well with the simulation for both the model dronefly and the model hawkmoth; but the averaged-model theory gave good results only for the dronefly. Thus, for an insect with relatively large body oscillation at wingbeat frequency, cyclic-motion stability analysis is required, and for their control analysis, the existing well-developed control theories for systems of fixed-point equilibrium are no longer applicable and new methods that take the cyclic variation of the flight dynamics into account are needed. PMID:22491980

Global attractors and extinction dynamics of cyclically competing species.

PubMed

Rulands, Steffen; Zielinski, Alejandro; Frey, Erwin

2013-05-01

Transitions to absorbing states are of fundamental importance in nonequilibrium physics as well as ecology. In ecology, absorbing states correspond to the extinction of species. We here study the spatial population dynamics of three cyclically interacting species. The interaction scheme comprises both direct competition between species as in the cyclic Lotka-Volterra model, and separated selection and reproduction processes as in the May-Leonard model. We show that the dynamic processes leading to the transient maintenance of biodiversity are closely linked to attractors of the nonlinear dynamics for the overall species' concentrations. The characteristics of these global attractors change qualitatively at certain threshold values of the mobility and depend on the relative strength of the different types of competition between species. They give information about the scaling of extinction times with the system size and thereby the stability of biodiversity. We define an effective free energy as the negative logarithm of the probability to find the system in a specific global state before reaching one of the absorbing states. The global attractors then correspond to minima of this effective energy landscape and determine the most probable values for the species' global concentrations. As in equilibrium thermodynamics, qualitative changes in the effective free energy landscape indicate and characterize the underlying nonequilibrium phase transitions. We provide the complete phase diagrams for the population dynamics and give a comprehensive analysis of the spatio-temporal dynamics and routes to extinction in the respective phases.

Disulfide exchange in hydrogen-bonded cyclic assemblies: stereochemical self-selection by double dynamic chemistry.

PubMed

ten Cate, A Tessa; Dankers, Patricia Y W; Sijbesma, Rint P; Meijer, E W

2005-07-22

Stereoselective cyclization of cystine-based bifunctional 2-ureido-4[1H]-pyrimidinone derivatives in CDCl(3) solutions was demonstrated by (1)H NMR spectroscopy. Thiolate-catalyzed disulfide exchange in solution led to the equilibration of different diastereomers of 1. At low concentrations, where formation of cyclic assemblies is the dominant mode of association, the molecules act as their own template. At these concentrations the meso diastereomer is formed preferentially, indicating a higher stability of its cyclic assemblies under the applied conditions, in comparison to the other diastereomers.

Sensitivity of polycrystal plasticity to slip system kinematic hardening laws for Al 7075-T6

DOE PAGES

Hennessey, Conor; Castelluccio, Gustavo M.; McDowell, David L.

2017-02-01

The prediction of formation and early growth of microstructurally small fatigue cracks requires use of constitutive models that accurately estimate local states of stress, strain, and cyclic plastic strain. However, few research efforts have attempted to systematically consider the sensitivity of overall cyclic stress-strain hysteresis and higher order mean stress relaxation and plastic strain ratcheting responses introduced by the slip system back-stress formulation in crystal plasticity, even for face centered cubic (FCC) crystal systems. This paper explores the performance of two slip system level kinematic hardening models using a finite element crystal plasticity implementation as a User Material Subroutine (UMAT)more » within ABAQUS, with fully implicit numerical integration. The two kinematic hardening formulations aim to reproduce the cyclic deformation of polycrystalline Al 7075-T6 in terms of both macroscopic cyclic stress-strain hysteresis loop shape, as well as ratcheting and mean stress relaxation under strain- or stress-controlled loading with mean strain or stress, respectively. The first formulation is an Armstrong-Frederick type hardening-dynamic recovery law for evolution of the back stress. This approach is capable of reproducing observed deformation under completely reversed uniaxial loading conditions, but overpredicts the rate of cyclic ratcheting and associated mean stress relaxation. The second formulation corresponds to a multiple back stress Ohno-Wang type hardening law with nonlinear dynamic recovery. The adoption of this back stress evolution law greatly improves the capability to model experimental results for polycrystalline specimens subjected to cycling with mean stress or strain. As a result, the relation of such nonlinear dynamic recovery effects are related to slip system interactions with dislocation substructures.« less

Sensitivity of polycrystal plasticity to slip system kinematic hardening laws for Al 7075-T6

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

Hennessey, Conor; Castelluccio, Gustavo M.; McDowell, David L.

The prediction of formation and early growth of microstructurally small fatigue cracks requires use of constitutive models that accurately estimate local states of stress, strain, and cyclic plastic strain. However, few research efforts have attempted to systematically consider the sensitivity of overall cyclic stress-strain hysteresis and higher order mean stress relaxation and plastic strain ratcheting responses introduced by the slip system back-stress formulation in crystal plasticity, even for face centered cubic (FCC) crystal systems. This paper explores the performance of two slip system level kinematic hardening models using a finite element crystal plasticity implementation as a User Material Subroutine (UMAT)more » within ABAQUS, with fully implicit numerical integration. The two kinematic hardening formulations aim to reproduce the cyclic deformation of polycrystalline Al 7075-T6 in terms of both macroscopic cyclic stress-strain hysteresis loop shape, as well as ratcheting and mean stress relaxation under strain- or stress-controlled loading with mean strain or stress, respectively. The first formulation is an Armstrong-Frederick type hardening-dynamic recovery law for evolution of the back stress. This approach is capable of reproducing observed deformation under completely reversed uniaxial loading conditions, but overpredicts the rate of cyclic ratcheting and associated mean stress relaxation. The second formulation corresponds to a multiple back stress Ohno-Wang type hardening law with nonlinear dynamic recovery. The adoption of this back stress evolution law greatly improves the capability to model experimental results for polycrystalline specimens subjected to cycling with mean stress or strain. As a result, the relation of such nonlinear dynamic recovery effects are related to slip system interactions with dislocation substructures.« less

Long-term shifts in the cyclicity of outbreaks of a forest-defoliating insect

Treesearch

Andrew J. ​Allstadt; Kyle J. Haynes; Andrew M. Liebhold; Derek M. Johnson

2013-01-01

Recent collapses of population cycles in several species highlight the mutable nature of population behavior as well as the potential role of human-induced environmental change in causing population dynamics to shift. We investigate changes in the cyclicity of gypsy moth (Lymantria dispar) outbreaks by applying wavelet analysis to an 86-year time...

Multilevel Modeling of Two Cyclical Processes: Extending Differential Structural Equation Modeling to Nonlinear Coupled Systems

ERIC Educational Resources Information Center

Butner, Jonathan; Amazeen, Polemnia G.; Mulvey, Genna M.

2005-01-01

The authors present a dynamical multilevel model that captures changes over time in the bidirectional, potentially asymmetric influence of 2 cyclical processes. S. M. Boker and J. Graham's (1998) differential structural equation modeling approach was expanded to the case of a nonlinear coupled oscillator that is common in bimanual coordination…

Experimentally observed evolution between dynamic patterns and intrinsic localized modes in a driven nonlinear electrical cyclic lattice

NASA Astrophysics Data System (ADS)

Shige, S.; Miyasaka, K.; Shi, W.; Soga, Y.; Sato, M.; Sievers, A. J.

2018-02-01

Locked intrinsic localized modes (ILMs) and large amplitude lattice spatial modes (LSMs) have been experimentally measured for a driven 1-D nonlinear cyclic electric transmission line, where the nonlinear element is a saturable capacitor. Depending on the number of cells and electrical lattice damping an LSM of fixed shape can be tuned across the modal spectrum. Interestingly, by tuning the driver frequency away from this spectrum the LSM can be continuously converted into ILMs and vice versa. The differences in pattern formation between simulations and experimental findings are due to a low concentration of impurities. Through this novel nonlinear excitation and switching channel in cyclic lattices either energy balanced or unbalanced LSMs and ILMs may occur. Because of the general nature of these dynamical results for nonintegrable lattices applications are to be expected. The ultimate stability of driven aero machinery containing nonlinear periodic structures may be one example.

Wave kinetics of random fibre lasers

PubMed Central

Churkin, D V.; Kolokolov, I V.; Podivilov, E V.; Vatnik, I D.; Nikulin, M A.; Vergeles, S S.; Terekhov, I S.; Lebedev, V V.; Falkovich, G.; Babin, S A.; Turitsyn, S K.

2015-01-01

Traditional wave kinetics describes the slow evolution of systems with many degrees of freedom to equilibrium via numerous weak non-linear interactions and fails for very important class of dissipative (active) optical systems with cyclic gain and losses, such as lasers with non-linear intracavity dynamics. Here we introduce a conceptually new class of cyclic wave systems, characterized by non-uniform double-scale dynamics with strong periodic changes of the energy spectrum and slow evolution from cycle to cycle to a statistically steady state. Taking a practically important example—random fibre laser—we show that a model describing such a system is close to integrable non-linear Schrödinger equation and needs a new formalism of wave kinetics, developed here. We derive a non-linear kinetic theory of the laser spectrum, generalizing the seminal linear model of Schawlow and Townes. Experimental results agree with our theory. The work has implications for describing kinetics of cyclical systems beyond photonics. PMID:25645177

Female Genitalia Concealment Promotes Intimate Male Courtship in a Water Strider

PubMed Central

Han, Chang S.; Jablonski, Piotr G.

2009-01-01

Violent coercive mating initiation is typical for animals with sexual conflict over mating. In these species, the coevolutionary arms-race between female defenses against coercive mating and male counter-adaptations for increased mating success leads to coevolutionary chases of male and female traits that influence the mating. It has been controversial whether one of the sexes can evolve traits that allow them to “win” this arms race. Here, we use morphological analysis (traditional and scanning electron micrographs), laboratory experiments and comparative methods to show how females of a species characterized by typical coercive mating initiation appear to “win” a particular stage of the sexual conflict by evolving morphology to hide their genitalia from direct, forceful access by males. In an apparent response to the female morphological adaptation, males of this species added to their typically violent coercive mounting of the female new post-mounting, pre-copulatory courtship signals produced by tapping the water's surface with the mid-legs. These courtship signals are intimate in the sense that they are aimed at the female, on whom the male is already mounted. Females respond to the signals by exposing their hidden genitalia for copulatory intromission. Our results indicate that the apparent victory of coevolutionary arms race by one sex in terms of morphology may trigger evolution of a behavioral phenotype in the opposite sex. PMID:19516886

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen.

PubMed

Frantzeskakis, Lamprinos; Kracher, Barbara; Kusch, Stefan; Yoshikawa-Maekawa, Makoto; Bauer, Saskia; Pedersen, Carsten; Spanu, Pietro D; Maekawa, Takaki; Schulze-Lefert, Paul; Panstruga, Ralph

2018-05-22

Powdery mildews are biotrophic pathogenic fungi infecting a number of economically important plants. The grass powdery mildew, Blumeria graminis, has become a model organism to study host specialization of obligate biotrophic fungal pathogens. We resolved the large-scale genomic architecture of B. graminis forma specialis hordei (Bgh) to explore the potential influence of its genome organization on the co-evolutionary process with its host plant, barley (Hordeum vulgare). The near-chromosome level assemblies of the Bgh reference isolate DH14 and one of the most diversified isolates, RACE1, enabled a comparative analysis of these haploid genomes, which are highly enriched with transposable elements (TEs). We found largely retained genome synteny and gene repertoires, yet detected copy number variation (CNV) of secretion signal peptide-containing protein-coding genes (SPs) and locally disrupted synteny blocks. Genes coding for sequence-related SPs are often locally clustered, but neither the SPs nor the TEs reside preferentially in genomic regions with unique features. Extended comparative analysis with different host-specific B. graminis formae speciales revealed the existence of a core suite of SPs, but also isolate-specific SP sets as well as congruence of SP CNV and phylogenetic relationship. We further detected evidence for a recent, lineage-specific expansion of TEs in the Bgh genome. The characteristics of the Bgh genome (largely retained synteny, CNV of SP genes, recently proliferated TEs and a lack of significant compartmentalization) are consistent with a "one-speed" genome that differs in its architecture and (co-)evolutionary pattern from the "two-speed" genomes reported for several other filamentous phytopathogens.

Nonlinear Synergistic Emergence and Predictability in Complex Systems: Theory and Hydro-Climatic Applications

NASA Astrophysics Data System (ADS)

Perdigão, Rui A. P.; Hall, Julia; Pires, Carlos A. L.; Blöschl, Günter

2017-04-01

Classical and stochastic dynamical system theories assume structural coherence and dynamic recurrence with invariants of motion that are not necessarily so. These are grounded on the unproven assumption of universality in the dynamic laws derived from statistical kinematic evaluation of non-representative empirical records. As a consequence, the associated formulations revolve around a restrictive set of configurations and intermittencies e.g. in an ergodic setting, beyond which any predictability is essentially elusive. Moreover, dynamical systems are fundamentally framed around dynamic codependence among intervening processes, i.e. entail essentially redundant interactions such as couplings and feedbacks. That precludes synergistic cooperation among processes that, whilst independent from each other, jointly produce emerging dynamic behaviour not present in any of the intervening parties. In order to overcome these fundamental limitations, we introduce a broad class of non-recursive dynamical systems that formulate dynamic emergence of unprecedented states in a fundamental synergistic manner, with fundamental principles in mind. The overall theory enables innovations to be predicted from the internal system dynamics before any a priori information is provided about the associated dynamical properties. The theory is then illustrated to anticipate, from non-emergent records, the spatiotemporal emergence of multiscale hyper chaotic regimes, critical transitions and structural coevolutionary changes in synthetic and real-world complex systems. Example applications are provided within the hydro-climatic context, formulating and dynamically forecasting evolving hydro-climatic distributions, including the emergence of extreme precipitation and flooding in a structurally changing hydro-climate system. Validation is then conducted with a posteriori verification of the simulated dynamics against observational records. Agreement between simulations and observations is confirmed with robust nonlinear information diagnostics.

Dynamic Increase in Corticomuscular Coherence during Bilateral, Cyclical Ankle Movements

PubMed Central

Yoshida, Takashi; Masani, Kei; Zabjek, Karl; Chen, Robert; Popovic, Milos R.

2017-01-01

In humans, the midline primary motor cortex is active during walking. However, the exact role of such cortical participation is unknown. To delineate the role of the primary motor cortex in walking, we examined whether the primary motor cortex would activate leg muscles during movements that retained specific requirements of walking (i.e., locomotive actions). We recorded electroencephalographic and electromyographic signals from 15 healthy, young men while they sat and performed bilateral, cyclical ankle movements. During dorsiflexion, near-20-Hz coherence increased cyclically between the midline primary motor cortex and the co-contracting antagonistic pair (i.e., tibialis anterior and medial gastrocnemius muscles) in both legs. Thus, we have shown that dynamic increase in corticomuscular coherence, which has been observed during walking, also occurs during simple bilateral cyclical movements of the feet. A possible mechanism for such coherence is corticomuscular communication, in which the primary motor cortex participates in the control of movement. Furthermore, because our experimental task isolated certain locomotive actions, the observed coherence suggests that the human primary motor cortex may participate in these actions (i.e., maintaining a specified movement frequency, bilaterally coordinating the feet, and stabilizing the posture of the feet). Additional studies are needed to identify the exact cortical and subcortical interactions that cause corticomuscular coherence and to further delineate the functional role of the primary motor cortex during bilateral cyclical movements such as walking. PMID:28420971

Comparing a Coevolutionary Genetic Algorithm for Multiobjective Optimization

NASA Technical Reports Server (NTRS)

Lohn, Jason D.; Kraus, William F.; Haith, Gary L.; Clancy, Daniel (Technical Monitor)

2002-01-01

We present results from a study comparing a recently developed coevolutionary genetic algorithm (CGA) against a set of evolutionary algorithms using a suite of multiobjective optimization benchmarks. The CGA embodies competitive coevolution and employs a simple, straightforward target population representation and fitness calculation based on developmental theory of learning. Because of these properties, setting up the additional population is trivial making implementation no more difficult than using a standard GA. Empirical results using a suite of two-objective test functions indicate that this CGA performs well at finding solutions on convex, nonconvex, discrete, and deceptive Pareto-optimal fronts, while giving respectable results on a nonuniform optimization. On a multimodal Pareto front, the CGA finds a solution that dominates solutions produced by eight other algorithms, yet the CGA has poor coverage across the Pareto front.

Experimental evaluation of cyclic fatigue resistance of four different nickel-titanium instruments after immersion in sodium hypochlorite and/or sterilization

PubMed Central

BULEM, Üreyen Kaya; KECECI, Ayse Diljin; GULDAS, Hilmi Egemen

2013-01-01

NiTi instruments have a high risk of separation due to torsional or flexural fatigue (cyclic fatigue). Chemomechanical preparation, cleaning procedures, chemical disinfection and sterilization cause the corrosion of endodontic instruments that may weaken the fracture resistance of the instruments. Objective To assess the effects of NaOCl immersion and autoclave sterilization on the cyclic fatigue resistance of ProFile, FlexMaster, Mtwo and TwistedFiles NiTi instruments (tip size 25, 0.06 taper, n=160). Material and Methods The instruments (n=10 for each subgroup) were dynamically immersed in NaOCl; immersed in NaOCl and sterilized in one autoclave cycle; 5 cycles immersed in NaOCl and sterilized in autoclave and not immersed in NaOCl and not sterilized (control group). Dynamic cyclic fatigue resistance was tested. The number of cycles to failure (NCF) were statistically analyzed (P<0.05). Results Kruskall-Wallis test indicated significant differences among the tested instruments in terms of NCF (P=0.000). The mean NCF of Mtwo (556.75) was higher than that of the Twisted File, Flexmaster and ProFile, 483.1, 376.12, 365.25, respectively. NaOCl immersion and autoclave sterilization have no effect on the NCF values of the tested instruments (P>.05). Conclusions Cyclic fatigue resistance of the tested NiTi instruments cannot be adversely affected by NaOCl immersion and autoclave sterilization. Production process (TwistedFiles) or design (Twisted Files, FlexMaster, Mtwo and ProFile) of the instruments can influence their cyclic fatigue resistance. PMID:24473715

Biologically relevant conformational features of linear and cyclic proteolipid protein (PLP) peptide analogues obtained by high-resolution nuclear magnetic resonance and molecular dynamics

NASA Astrophysics Data System (ADS)

Kordopati, Golfo G.; Tzoupis, Haralambos; Troganis, Anastassios N.; Tsivgoulis, Gerasimos M.; Golic Grdadolnik, Simona; Simal, Carmen; Tselios, Theodore V.

2017-09-01

Proteolipid protein (PLP) is one of the main proteins of myelin sheath that are destroyed during the progress of multiple sclerosis (MS). The immunodominant PLP139-151 epitope is known to induce experimental autoimmune encephalomyelitis (EAE, animal model of MS), wherein residues 144 and 147 are recognized by T cell receptor (TCR) during the formation of trimolecular complex with peptide-antigen and major histocompability complex. The conformational behavior of linear and cyclic peptide analogues of PLP, namely PLP139-151 and cyclic (139-151) (L144, R147) PLP139-151, have been studied in solution by means of nuclear magnetic resonance (NMR) methods in combination with unrestrained molecular dynamics simulations. The results indicate that the side chains of mutated amino acids in the cyclic analogue have different spatial orientation compared with the corresponding side chains of the linear analogue, which can lead to reduced affinity to TCR. NMR experiments combined with theoretical calculations pave the way for the design and synthesis of potent restricted peptides of immunodominant PLP139-151 epitope as well as non peptide mimetics that rises as an ultimate goal.

Dynamic strain aging in stress controlled creep-fatigue tests of 316L stainless steel under different loading conditions

NASA Astrophysics Data System (ADS)

Jiang, Huifeng; Chen, Xuedong; Fan, Zhichao; Dong, Jie; Jiang, Heng; Lu, Shouxiang

2009-08-01

Stress controlled fatigue-creep tests were carried out for 316L stainless steel under different loading conditions, i.e. different loading levels at the fixed temperature (loading condition 1, LC1) and different temperatures at the fixed loading level (loading condition 2, LC2). Cyclic deformation behaviors were investigated with respect to the evolutions of strain amplitude and mean strain. Abrupt mean strain jumps were found during cyclic deformation, which was in response to the dynamic strain aging effect. Moreover, as to LC1, when the minimum stress is negative at 550 °C, abrupt mean strain jumps occur at the early stage of cyclic deformation and there are many jumps during the whole process. While the minimum stress is positive, mean strain only jumps once at the end of deformation. Similar results were also found in LC2, when the loading level is fixed at -100 to 385 MPa, at higher temperatures (560, 575 °C), abrupt mean strain jumps occur at the early stage of cyclic deformation and there are many jumps during the whole process. While at lower temperature (540 °C), mean strain only jumps once at the end of deformation.

Chronic radiation exposure modifies temporal dynamics of cytogenetic but not reproductive indicators in Scots pine populations.

PubMed

Geras'kin, Stanislav; Oudalova, Alla; Kuzmenkov, Alexey; Vasiliyev, Denis

2018-04-18

Over a period of 13 years (2003-2015), reproductive and cytogenetic effects are investigated in Scots pine populations growing in the Bryansk region of Russia radioactively contaminated as a result of the Chernobyl accident. In reference populations, the frequencies of cytogenetic abnormalities are shown to change with time in a cyclic manner. In chronically exposed populations, the cyclic patterns in temporal dynamics of cytogenetic abnormalities appear to be disturbed. In addition, a tendency to decrease in the frequencies of cytogenetic abnormalities with time as well as an increase in their variability with dose rate is revealed. In contrast, no significant impact of chronic radiation exposure on the time dynamics of reproductive indexes is detected. Finally, long-term observations on chronically exposed Scots pine populations revealed qualitative differences in the temporal dynamics of reproductive and cytogenetic indicators. Copyright © 2018 Elsevier Ltd. All rights reserved.

Co-evolution of payoff strategy and interaction strategy in prisoner's dilemma game

NASA Astrophysics Data System (ADS)

Zhang, Kangjie; Cheng, Hongyan

2016-11-01

Co-evolutionary dynamical models, providing a realistic paradigm for investigating complex system, have been extensively studied. In this paper, the co-evolution of payoff strategy and interaction strategy is studied. Starting with an initial Gaussian distribution of payoff strategy r with the mean u and the variance q, we focus on the final distribution of the payoff strategy. We find that final distribution of the payoff strategy may display different structures depending on parameters. In the ranges u < - 1 and u > 3, the distribution displays a single-peak structure which is symmetric about r = u. The distribution manifests itself as a double-peak structure in the range - 1 < u < 3 although a fake three-peak structure shows up in range 1 < u < 2. The explanations on the formation of different types of payoff strategy distributions are presented.

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

DOE PAGES

Roux, Simon; Hawley, Alyse K.; Torres Beltran, Monica; ...

2014-08-29

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186more » microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs.« less

Clustered marginalization of minorities during social transitions induced by co-evolution of behaviour and network structure

PubMed Central

Schleussner, Carl-Friedrich; Donges, Jonathan F.; Engemann, Denis A.; Levermann, Anders

2016-01-01

Large-scale transitions in societies are associated with both individual behavioural change and restructuring of the social network. These two factors have often been considered independently, yet recent advances in social network research challenge this view. Here we show that common features of societal marginalization and clustering emerge naturally during transitions in a co-evolutionary adaptive network model. This is achieved by explicitly considering the interplay between individual interaction and a dynamic network structure in behavioural selection. We exemplify this mechanism by simulating how smoking behaviour and the network structure get reconfigured by changing social norms. Our results are consistent with empirical findings: The prevalence of smoking was reduced, remaining smokers were preferentially connected among each other and formed increasingly marginalized clusters. We propose that self-amplifying feedbacks between individual behaviour and dynamic restructuring of the network are main drivers of the transition. This generative mechanism for co-evolution of individual behaviour and social network structure may apply to a wide range of examples beyond smoking. PMID:27510641

Accelerated testing of composites

NASA Technical Reports Server (NTRS)

Papazian, H. A.

1983-01-01

It is shown that the Zhurkov method for testing the strength of solids can be applied to dynamic tension and to cyclic loading and provides a viable approach to accelerated testing of composites. Data from the literature are used to demonstrate a straightforward application of the method to dynamic tension of glass fiber and cyclic loading for glass/polymer, metal matrix, and graphite/epoxy composites. Zhurkov's equation can be used at relatively high loads to obtain failure times at any temperature of interest. By taking a few data points at one or two other temperatures the spectrum of failure times can be expanded to temperatures not easily accessible.

The diastolic function to cyclic variation of myocardial ultrasonic backscatter relation: the influence of parameterized diastolic filling (PDF) formalism determined chamber properties.

PubMed

Lloyd, Christopher W; Shmuylovich, Leonid; Holland, Mark R; Miller, James G; Kovács, Sándor J

2011-08-01

Myocardial tissue characterization represents an extension of currently available echocardiographic imaging. The systematic variation of backscattered energy during the cardiac cycle (the "cyclic variation" of backscatter) has been employed to characterize cardiac function in a wide range of investigations. However, the mechanisms responsible for observed cyclic variation remain incompletely understood. As a step toward determining the features of cardiac structure and function that are responsible for the observed cyclic variation, the present study makes use of a kinematic approach of diastolic function quantitation to identify diastolic function determinants that influence the magnitude and timing of cyclic variation. Echocardiographic measurements of 32 subjects provided data for determination of the cyclic variation of backscatter to diastolic function relation characterized in terms of E-wave determined, kinematic model-based parameters of chamber stiffness, viscosity/relaxation and load. The normalized time delay of cyclic variation appears to be related to the relative viscoelasticity of the chamber and predictive of the kinematic filling dynamics as determined using the parameterized diastolic filling formalism (with r-values ranging from .44 to .59). The magnitude of cyclic variation does not appear to be strongly related to the kinematic parameters. Copyright © 2011 World Federation for Ultrasound in Medicine & Biology. Published by Elsevier Inc. All rights reserved.

Fatigue behaviour of core-spun yarns containing filament by means of cyclic dynamic loading

NASA Astrophysics Data System (ADS)

Esin, S.; Osman, B.

2017-10-01

The behaviour of yarns under dynamic loading is important that leads to understand the growth characteristics which is exposed to repetitive loadings during usage of fabric made from these yarns. Fabric growth is undesirable property that originated from low resilience characteristics of fabric. In this study, the effects of the filament fineness and yarn linear density on fatigue behaviour of rigid-core spun yarns were determined. Cotton covered yarns containing different filament fineness of polyester (PET) draw textured yarns (DTY) (100d/36f, 100d/96f, 100d/144f, 100d/192f and 100d/333f) and yarn linear densities (37 tex, 30 tex, 25 tex and 21 tex) were manufactured by using a modified ring spinning system at the same spinning parameters. Repetitive loads were applied for 25 cycles at levels between 0.1 and 3 N. Dynamic modulus and dynamic strain of yarn samples were analyzed statistically. Results showed that filament fineness and yarn linear density have significance effect on dynamic modulus and dynamic strain after cyclic loading.

The butterfly plant arms-race escalated by gene and genome duplications

PubMed Central

Edger, Patrick P.; Heidel-Fischer, Hanna M.; Bekaert, Michaël; Rota, Jadranka; Glöckner, Gernot; Platts, Adrian E.; Heckel, David G.; Der, Joshua P.; Wafula, Eric K.; Tang, Michelle; Hofberger, Johannes A.; Smithson, Ann; Hall, Jocelyn C.; Blanchette, Matthieu; Bureau, Thomas E.; Wright, Stephen I.; dePamphilis, Claude W.; Eric Schranz, M.; Barker, Michael S.; Conant, Gavin C.; Wahlberg, Niklas; Vogel, Heiko; Pires, J. Chris; Wheat, Christopher W.

2015-01-01

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits. PMID:26100883

The butterfly plant arms-race escalated by gene and genome duplications.

PubMed

Edger, Patrick P; Heidel-Fischer, Hanna M; Bekaert, Michaël; Rota, Jadranka; Glöckner, Gernot; Platts, Adrian E; Heckel, David G; Der, Joshua P; Wafula, Eric K; Tang, Michelle; Hofberger, Johannes A; Smithson, Ann; Hall, Jocelyn C; Blanchette, Matthieu; Bureau, Thomas E; Wright, Stephen I; dePamphilis, Claude W; Eric Schranz, M; Barker, Michael S; Conant, Gavin C; Wahlberg, Niklas; Vogel, Heiko; Pires, J Chris; Wheat, Christopher W

2015-07-07

Coevolutionary interactions are thought to have spurred the evolution of key innovations and driven the diversification of much of life on Earth. However, the genetic and evolutionary basis of the innovations that facilitate such interactions remains poorly understood. We examined the coevolutionary interactions between plants (Brassicales) and butterflies (Pieridae), and uncovered evidence for an escalating evolutionary arms-race. Although gradual changes in trait complexity appear to have been facilitated by allelic turnover, key innovations are associated with gene and genome duplications. Furthermore, we show that the origins of both chemical defenses and of molecular counter adaptations were associated with shifts in diversification rates during the arms-race. These findings provide an important connection between the origins of biodiversity, coevolution, and the role of gene and genome duplications as a substrate for novel traits.

Cyclic stretch-induced stress fiber dynamics - Dependence on strain rate, Rho-kinase and MLCK

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

Lee, Chin-Fu; Haase, Candice; Deguchi, Shinji

2010-10-22

Research highlights: {yields} Cyclic stretch induces stress fiber disassembly, reassembly and fusion perpendicular to the direction of stretch. {yields} Stress fiber disassembly and reorientation were not induced at low stretch frequency. {yields} Stretch caused actin fiber formation parallel to stretch in distinct locations in cells treated with Rho-kinase and MLCK inhibitors. -- Abstract: Stress fiber realignment is an important adaptive response to cyclic stretch for nonmuscle cells, but the mechanism by which such reorganization occurs is not known. By analyzing stress fiber dynamics using live cell microscopy, we revealed that stress fiber reorientation perpendicular to the direction of cyclic uniaxialmore » stretching at 1 Hz did not involve disassembly of the stress fiber distal ends located at focal adhesion sites. Instead, these distal ends were often used to assemble new stress fibers oriented progressively further away from the direction of stretch. Stress fiber disassembly and reorientation were not induced when the frequency of stretch was decreased to 0.01 Hz, however. Treatment with the Rho-kinase inhibitor (Y27632) reduced stress fibers to thin fibers located in the cell periphery which bundled together to form thick fibers oriented parallel to the direction of stretching at 1 Hz. In contrast, these thin fibers remained diffuse in cells subjected to stretch at 0.01 Hz. Cyclic stretch at 1 Hz also induced actin fiber formation parallel to the direction of stretch in cells treated with the myosin light chain kinase (MLCK) inhibitor ML-7, but these fibers were located centrally rather than peripherally. These results shed new light on the mechanism by which stress fibers reorient in response to cyclic stretch in different regions of the actin cytoskeleton.« less

Using 1H and 13C NMR chemical shifts to determine cyclic peptide conformations: a combined molecular dynamics and quantum mechanics approach.

PubMed

Nguyen, Q Nhu N; Schwochert, Joshua; Tantillo, Dean J; Lokey, R Scott

2018-05-10

Solving conformations of cyclic peptides can provide insight into structure-activity and structure-property relationships, which can help in the design of compounds with improved bioactivity and/or ADME characteristics. The most common approaches for determining the structures of cyclic peptides are based on NMR-derived distance restraints obtained from NOESY or ROESY cross-peak intensities, and 3J-based dihedral restraints using the Karplus relationship. Unfortunately, these observables are often too weak, sparse, or degenerate to provide unequivocal, high-confidence solution structures, prompting us to investigate an alternative approach that relies only on 1H and 13C chemical shifts as experimental observables. This method, which we call conformational analysis from NMR and density-functional prediction of low-energy ensembles (CANDLE), uses molecular dynamics (MD) simulations to generate conformer families and density functional theory (DFT) calculations to predict their 1H and 13C chemical shifts. Iterative conformer searches and DFT energy calculations on a cyclic peptide-peptoid hybrid yielded Boltzmann ensembles whose predicted chemical shifts matched the experimental values better than any single conformer. For these compounds, CANDLE outperformed the classic NOE- and 3J-coupling-based approach by disambiguating similar β-turn types and also enabled the structural elucidation of the minor conformer. Through the use of chemical shifts, in conjunction with DFT and MD calculations, CANDLE can help illuminate conformational ensembles of cyclic peptides in solution.

Dynamical analysis of an n‑H‑T cosmological quintessence real gas model with a general equation of state

NASA Astrophysics Data System (ADS)

Ivanov, Rossen I.; Prodanov, Emil M.

2018-01-01

The cosmological dynamics of a quintessence model based on real gas with general equation of state is presented within the framework of a three-dimensional dynamical system describing the time evolution of the number density, the Hubble parameter and the temperature. Two global first integrals are found and examples for gas with virial expansion and van der Waals gas are presented. The van der Waals system is completely integrable. In addition to the unbounded trajectories, stemming from the presence of the conserved quantities, stable periodic solutions (closed orbits) also exist under certain conditions and these represent models of a cyclic Universe. The cyclic solutions exhibit regions characterized by inflation and deflation, while the open trajectories are characterized by inflation in a “fly-by” near an unstable critical point.

MULTISCALE MODEL OF CRISPR-INDUCED COEVOLUTIONARY DYNAMICS: DIVERSIFICATION AT THE INTERFACE OF LAMARCK AND DARWIN

PubMed Central

Childs, Lauren M; Held, Nicole L; Young, Mark J; Whitaker, Rachel J; Weitz, Joshua S

2012-01-01

The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active. PMID:22759281

A model for the multiplex dynamics of two-mode and one-mode networks, with an application to employment preference, friendship, and advice

PubMed Central

Snijders, Tom A.B.; Lomi, Alessandro; Torló, Vanina Jasmine

2012-01-01

We propose a new stochastic actor-oriented model for the co-evolution of two-mode and one-mode networks. The model posits that activities of a set of actors, represented in the two-mode network, co-evolve with exchanges and interactions between the actors, as represented in the one-mode network. The model assumes that the actors, not the activities, have agency. The empirical value of the model is demonstrated by examining how employment preferences co-evolve with friendship and advice relations in a group of seventy-five MBA students. The analysis shows that activity in the two-mode network, as expressed by number of employment preferences, is related to activity in the friendship network, as expressed by outdegrees. Further, advice ties between students lead to agreement with respect to employment preferences. In addition, considering the multiplexity of advice and friendship ties yields a better understanding of the dynamics of the advice relation: tendencies to reciprocation and homophily in advice relations are mediated to an important extent by friendship relations. The discussion pays attention to the implications of this study in the broader context of current efforts to model the co-evolutionary dynamics of social networks and individual behavior. PMID:23690653

Influence of Secondary Cyclic Hardening on the Low Cycle Fatigue Behavior of Nitrogen Alloyed 316LN Stainless Steel

NASA Astrophysics Data System (ADS)

Prasad Reddy, G. V.; Sandhya, R.; Mathew, M. D.; Sankaran, S.

2013-12-01

In this article, the occurrence of secondary cyclic hardening (SCH) and its effect on high-temperature cyclic deformation and fatigue life of 316LN Stainless steel are presented. SCH is found to result from planar slip mode of deformation and enhance the degree of hardening over and above that resulted from dynamic strain aging. The occurrence of SCH is strongly governed by the applied strain amplitude, test temperature, and the nitrogen content in the 316LN SS. Under certain test conditions, SCH is noticed to decrease the low cycle fatigue life with the increasing nitrogen content.

Role of Dynamics in the Autoinhibition and Activation of the Hyperpolarization-activated Cyclic Nucleotide-modulated (HCN) Ion Channels*♦

PubMed Central

VanSchouwen, Bryan; Akimoto, Madoka; Sayadi, Maryam; Fogolari, Federico; Melacini, Giuseppe

2015-01-01

The hyperpolarization-activated cyclic nucleotide-modulated (HCN) ion channels control rhythmicity in neurons and cardiomyocytes. Cyclic AMP allosterically modulates HCN through the cAMP-dependent formation of a tetrameric gating ring spanning the intracellular region (IR) of HCN, to which cAMP binds. Although the apo versus holo conformational changes of the cAMP-binding domain (CBD) have been previously mapped, only limited information is currently available on the HCN IR dynamics, which have been hypothesized to play a critical role in the cAMP-dependent gating of HCN. Here, using molecular dynamics simulations validated and complemented by experimental NMR and CD data, we comparatively analyze HCN IR dynamics in the four states of the thermodynamic cycle arising from the coupling between cAMP binding and tetramerization equilibria. This extensive set of molecular dynamics trajectories captures the active-to-inactive transition that had remained elusive for other CBDs, and it provides unprecedented insight on the role of IR dynamics in HCN autoinhibition and its release by cAMP. Specifically, the IR tetramerization domain becomes more flexible in the monomeric states, removing steric clashes that the apo-CDB structure would otherwise impose. Furthermore, the simulations reveal that the active/inactive structural transition for the apo-monomeric CBD occurs through a manifold of pathways that are more divergent than previously anticipated. Upon cAMP binding, these pathways become disallowed, pre-confining the CBD conformational ensemble to a tetramer-compatible state. This conformational confinement primes the IR for tetramerization and thus provides a model of how cAMP controls HCN channel gating. PMID:25944904

A Critical Assessment of Cyclic Softening and Hardening Behavior in a Near- α Titanium Alloy During Thermomechanical Fatigue

NASA Astrophysics Data System (ADS)

Prasad, Kartik; Sarkar, Rajdeep; Rao, K. Bhanu Sankara; Sundararaman, M.

2016-10-01

Thermomechanical fatigue behavior of Ti-alloy Timetal 834 has been studied at two temperature intervals viz. 573 K to 723 K (300 °C to 450 °C) and 723 K to 873 K (450 °C to 600 °C) under mechanical strain-controlled cycling. Among the temperatures studied, the alloy exhibited initial cyclic softening followed by cyclic hardening at 723 K (450 °C) in the temperature interval of 573 K to 723 K (300 °C to 450 °C). However, continuous cyclic hardening was observed at 723 K (450 °C) in 723 K to 873 K (450 °C to 600 °C). At 573 K (300 °C) and 873 K (600 °C), cyclic softening was observed in the cyclic stress response curves in both the temperature intervals. The dislocation substructure was observed to be planar in both the modes of TMF loading. Based on TEM microstructures and few unconventional fatigue tests, the observed cyclic hardening is attributed to dynamic strain aging. The reduced fatigue life at 723 K to 873 K (450 °C to 600 °C) under OP-TMF loading was attributed to the combined effect of cyclic hardening (leading to early strain localization and crack initiation), oxidation, and development of tensile mean stresses.

Mosquito biology. Evolution of sexual traits influencing vectorial capacity in anopheline mosquitoes.

PubMed

Mitchell, Sara N; Kakani, Evdoxia G; South, Adam; Howell, Paul I; Waterhouse, Robert M; Catteruccia, Flaminia

2015-02-27

The availability of genome sequences from 16 anopheline species provides unprecedented opportunities to study the evolution of reproductive traits relevant for malaria transmission. In Anopheles gambiae, a likely candidate for sexual selection is male 20-hydroxyecdysone (20E). Sexual transfer of this steroid hormone as part of a mating plug dramatically changes female physiological processes intimately tied to vectorial capacity. By combining phenotypic studies with ancestral state reconstructions and phylogenetic analyses, we show that mating plug transfer and male 20E synthesis are both derived characters that have coevolved in anophelines, driving the adaptation of a female 20E-interacting protein that promotes oogenesis via mechanisms also favoring Plasmodium survival. Our data reveal coevolutionary dynamics of reproductive traits between the sexes likely to have shaped the ability of anophelines to transmit malaria. Copyright © 2015, American Association for the Advancement of Science.

Integrated multi-omic analyses in Biomphalaria-Schistosoma dialogue reveal the immunobiological significance of FREP-SmPoMuc interaction.

PubMed

Portet, Anaïs; Pinaud, Silvain; Tetreau, Guillaume; Galinier, Richard; Cosseau, Céline; Duval, David; Grunau, Christoph; Mitta, Guillaume; Gourbal, Benjamin

2017-10-01

The fresh water snail Biomphalaria glabrata is one of the vectors of the trematode pathogen Schistosoma mansoni, which is one of the agents responsible of human schistosomiasis. In this host-parasite interaction, co-evolutionary dynamic results into an infectivity mosaic known as compatibility polymorphism. Integrative approaches including large scale molecular approaches have been conducted in recent years to improve our understanding of the mechanisms underlying compatibility. This review presents the combination of integrated Multi-Omic approaches leading to the discovery of two repertoires of polymorphic and/or diversified interacting molecules: the parasite antigens S. mansoni polymorphic mucins (SmPoMucs) and the B. glabrata immune receptors fibrinogen-related proteins (FREPs). We argue that their interactions may be major components for defining the compatible/incompatible status of a specific snail/schistosome combination. Copyright © 2017 Elsevier Ltd. All rights reserved.

Playing on a pathogen's weakness: using evolution to guide sustainable plant disease control strategies.

PubMed

Zhan, Jiasui; Thrall, Peter H; Papaïx, Julien; Xie, Lianhui; Burdon, Jeremy J

2015-01-01

Wild plants and their associated pathogens are involved in ongoing interactions over millennia that have been modified by coevolutionary processes to limit the spatial extent and temporal duration of disease epidemics. These interactions are disrupted by modern agricultural practices and social activities, such as intensified monoculture using superior varieties and international trading of agricultural commodities. These activities, when supplemented with high resource inputs and the broad application of agrochemicals, create conditions uniquely conducive to widespread plant disease epidemics and rapid pathogen evolution. To be effective and durable, sustainable disease management requires a significant shift in emphasis to overtly include ecoevolutionary principles in the design of adaptive management programs aimed at minimizing the evolutionary potential of plant pathogens by reducing their genetic variation, stabilizing their evolutionary dynamics, and preventing dissemination of pathogen variants carrying new infectivity or resistance to agrochemicals.

The evolutionary and ecological consequences of animal social networks: emerging issues.

PubMed

Kurvers, Ralf H J M; Krause, Jens; Croft, Darren P; Wilson, Alexander D M; Wolf, Max

2014-06-01

The first generation of research on animal social networks was primarily aimed at introducing the concept of social networks to the fields of animal behaviour and behavioural ecology. More recently, a diverse body of evidence has shown that social fine structure matters on a broader scale than initially expected, affecting many key ecological and evolutionary processes. Here, we review this development. We discuss the effects of social network structure on evolutionary dynamics (genetic drift, fixation probabilities, and frequency-dependent selection) and social evolution (cooperation and between-individual behavioural differences). We discuss how social network structure can affect important coevolutionary processes (host-pathogen interactions and mutualisms) and population stability. We also discuss the potentially important, but poorly studied, role of social network structure on dispersal and invasion. Throughout, we highlight important areas for future research. Copyright © 2014 Elsevier Ltd. All rights reserved.

The Evolutionary Ecology of Plant Disease: A Phylogenetic Perspective.

PubMed

Gilbert, Gregory S; Parker, Ingrid M

2016-08-04

An explicit phylogenetic perspective provides useful tools for phytopathology and plant disease ecology because the traits of both plants and microbes are shaped by their evolutionary histories. We present brief primers on phylogenetic signal and the analytical tools of phylogenetic ecology. We review the literature and find abundant evidence of phylogenetic signal in pathogens and plants for most traits involved in disease interactions. Plant nonhost resistance mechanisms and pathogen housekeeping functions are conserved at deeper phylogenetic levels, whereas molecular traits associated with rapid coevolutionary dynamics are more labile at branch tips. Horizontal gene transfer disrupts the phylogenetic signal for some microbial traits. Emergent traits, such as host range and disease severity, show clear phylogenetic signals. Therefore pathogen spread and disease impact are influenced by the phylogenetic structure of host assemblages. Phylogenetically rare species escape disease pressure. Phylogenetic tools could be used to develop predictive tools for phytosanitary risk analysis and reduce disease pressure in multispecies cropping systems.

The Evolution of Sexually Antagonistic Phenotypes

PubMed Central

Perry, Jennifer C.; Rowe, Locke

2015-01-01

Sexual conflict occurs whenever there is sexually antagonistic selection on shared traits. When shared traits result from interactions (e.g., mating rate) and have a different genetic basis in each sex (i.e., interlocus conflict), then sex-specific traits that shift the value of these interaction traits toward the sex-specific optimum will be favored. Male traits can be favored that increase the fitness of their male bearers, but decrease the fitness of interacting females. Likewise, female traits that reduce the costs of interacting with harmful males may simultaneously impose costs on males. If the evolution of these antagonistic traits changes the nature of selection acting on the opposite sex, interesting coevolutionary dynamics will result. Here we examine three current issues in the study of sexually antagonistic interactions: the female side of sexual conflict, the ecological context of sexual conflict, and the strength of evidence for sexually antagonistic coevolution. PMID:26032715

Cloning of the unculturable parasite Pasteuria ramosa and its Daphnia host reveals extreme genotype-genotype interactions.

PubMed

Luijckx, Pepijn; Ben-Ami, Frida; Mouton, Laurence; Du Pasquier, Louis; Ebert, Dieter

2011-02-01

The degree of specificity in host-parasite interactions has important implications for ecology and evolution. Unfortunately, specificity can be difficult to determine when parasites cannot be cultured. In such cases, studies often use isolates of unknown genetic composition, which may lead to an underestimation of specificity. We obtained the first clones of the unculturable bacterium Pasteuria ramosa, a parasite of Daphnia magna. Clonal genotypes of the parasite exhibited much more specific interactions with host genotypes than previous studies using isolates. Clones of P. ramosa infected fewer D. magna genotypes than isolates and host clones were either fully susceptible or fully resistant to the parasite. Our finding enhances our understanding of the evolution of virulence and coevolutionary dynamics in this system. We recommend caution when using P. ramosa isolates as the presence of multiple genotypes may influence the outcome and interpretation of some experiments. © 2010 Blackwell Publishing Ltd/CNRS.

A sensitivity study of fast outlet glaciers to short timescale cyclical perturbations

NASA Astrophysics Data System (ADS)

Aykutlug, E.; Dupont, T. K.

2015-01-01

The dynamic response of outlet glaciers on short (annual to decadal) timescales is affected by various external forcings, such as basal or oceanic conditions. Understanding the sensitivity of the dynamic response to such forcings can help assess more accurate ice volume projections. In this work, we investigate the spatiotemporal sensitivity of outlet glaciers to fast cyclical forcings using a one-dimensional depth and width-averaged heuristic model. Our results indicate that even on such short timescales, nonlinearities in ice dynamics may lead to an asymmetric response, despite the forcing functions being symmetric around each reference value. Results also show that such short-timescale effects become more pronounced as glaciers become closer to flotation. While being qualitatively similar for both downsloping and upsloping bed geometries, the results indicate higher sensitivity for upsloping ("West Antarctica-like") beds. The range in asymmetric response for different configurations motivate parameterizing or including short-timescale effects in models while investigating the dynamic behavior of outlet glaciers.

The Effect of Dynamic Recrystallization on Monotonic and Cyclic Behaviour of Al-Cu-Mg Alloy.

PubMed

Tomczyk, Adam; Seweryn, Andrzej; Grądzka-Dahlke, Małgorzata

2018-05-23

The paper presents an investigation that was conducted to determine the possibility of the occurrence of the process of dynamic recrystallization in 2024 alloy during monotonic tensile and creep tests at the elevated temperatures of 100 °C, 200 °C, and 300 °C. As-extruded material was subjected to creep process with constant force at elevated temperatures, until two varying degrees of deformation were reached. After cooling at ambient temperature, the pre-deformed material was subjected to monotonic and fatigue tests as well as metallographic analysis. The process of dynamic recrystallization was determined in monotonic tests to occur at low strain rate (0.0015/s) only at the temperature of 300 °C. However, in the creep tests, this process occurred with varying efficiency, both during creep at 200 °C and 300 °C. Dynamic recrystallization was indicated to have a significant influence on the monotonic and cyclic properties of the material.

Memory-Based Multiagent Coevolution Modeling for Robust Moving Object Tracking

PubMed Central

Wang, Yanjiang; Qi, Yujuan; Li, Yongping

2013-01-01

The three-stage human brain memory model is incorporated into a multiagent coevolutionary process for finding the best match of the appearance of an object, and a memory-based multiagent coevolution algorithm for robust tracking the moving objects is presented in this paper. Each agent can remember, retrieve, or forget the appearance of the object through its own memory system by its own experience. A number of such memory-based agents are randomly distributed nearby the located object region and then mapped onto a 2D lattice-like environment for predicting the new location of the object by their coevolutionary behaviors, such as competition, recombination, and migration. Experimental results show that the proposed method can deal with large appearance changes and heavy occlusions when tracking a moving object. It can locate the correct object after the appearance changed or the occlusion recovered and outperforms the traditional particle filter-based tracking methods. PMID:23843739

Memory-based multiagent coevolution modeling for robust moving object tracking.

PubMed

Wang, Yanjiang; Qi, Yujuan; Li, Yongping

2013-01-01

The three-stage human brain memory model is incorporated into a multiagent coevolutionary process for finding the best match of the appearance of an object, and a memory-based multiagent coevolution algorithm for robust tracking the moving objects is presented in this paper. Each agent can remember, retrieve, or forget the appearance of the object through its own memory system by its own experience. A number of such memory-based agents are randomly distributed nearby the located object region and then mapped onto a 2D lattice-like environment for predicting the new location of the object by their coevolutionary behaviors, such as competition, recombination, and migration. Experimental results show that the proposed method can deal with large appearance changes and heavy occlusions when tracking a moving object. It can locate the correct object after the appearance changed or the occlusion recovered and outperforms the traditional particle filter-based tracking methods.

A quantitative trait locus for recognition of foreign eggs in the host of a brood parasite.

PubMed

Martín-Gálvez, D; Soler, J J; Martínez, J G; Krupa, A P; Richard, M; Soler, M; Møller, A P; Burke, T

2006-03-01

Avian brood parasites reduce the reproductive output of their hosts and thereby select for defence mechanisms such as ejection of parasitic eggs. Such defence mechanisms simultaneously select for counter-defences in brood parasites, causing a coevolutionary arms race. Although coevolutionary models assume that defences and counter-defences are genetically influenced, this has never been demonstrated for brood parasites. Here, we give strong evidence for genetic differences between ejector and nonejectors, which could allow the study of such host defence at the genetic level, as well as studies of maintenance of genetic variation in defences. Briefly, we found that magpies, that are the main host of the great spotted cuckoo in Europe, have alleles of one microsatellite locus (Ase64) that segregate between accepters and rejecters of experimental parasitic eggs. Furthermore, differences in ejection rate among host populations exploited by the brood parasite covaried significantly with the genetic distance for this locus.

Co-evolution for Problem Simplification

NASA Technical Reports Server (NTRS)

Haith, Gary L.; Lohn, Jason D.; Cplombano, Silvano P.; Stassinopoulos, Dimitris

1999-01-01

This paper explores a co-evolutionary approach applicable to difficult problems with limited failure/success performance feedback. Like familiar "predator-prey" frameworks this algorithm evolves two populations of individuals - the solutions (predators) and the problems (prey). The approach extends previous work by rewarding only the problems that match their difficulty to the level of solut,ion competence. In complex problem domains with limited feedback, this "tractability constraint" helps provide an adaptive fitness gradient that, effectively differentiates the candidate solutions. The algorithm generates selective pressure toward the evolution of increasingly competent solutions by rewarding solution generality and uniqueness and problem tractability and difficulty. Relative (inverse-fitness) and absolute (static objective function) approaches to evaluating problem difficulty are explored and discussed. On a simple control task, this co-evolutionary algorithm was found to have significant advantages over a genetic algorithm with either a static fitness function or a fitness function that changes on a hand-tuned schedule.

Integrating instance selection, instance weighting, and feature weighting for nearest neighbor classifiers by coevolutionary algorithms.

PubMed

Derrac, Joaquín; Triguero, Isaac; Garcia, Salvador; Herrera, Francisco

2012-10-01

Cooperative coevolution is a successful trend of evolutionary computation which allows us to define partitions of the domain of a given problem, or to integrate several related techniques into one, by the use of evolutionary algorithms. It is possible to apply it to the development of advanced classification methods, which integrate several machine learning techniques into a single proposal. A novel approach integrating instance selection, instance weighting, and feature weighting into the framework of a coevolutionary model is presented in this paper. We compare it with a wide range of evolutionary and nonevolutionary related methods, in order to show the benefits of the employment of coevolution to apply the techniques considered simultaneously. The results obtained, contrasted through nonparametric statistical tests, show that our proposal outperforms other methods in the comparison, thus becoming a suitable tool in the task of enhancing the nearest neighbor classifier.

Cuckoos, cowbirds and hosts: adaptations, trade-offs and constraints.

PubMed

Krüger, Oliver

2007-10-29

The interactions between brood parasitic birds and their host species provide one of the best model systems for coevolution. Despite being intensively studied, the parasite-host system provides ample opportunities to test new predictions from both coevolutionary theory as well as life-history theory in general. I identify four main areas that might be especially fruitful: cuckoo female gentes as alternative reproductive strategies, non-random and nonlinear risks of brood parasitism for host individuals, host parental quality and targeted brood parasitism, and differences and similarities between predation risk and parasitism risk. Rather than being a rare and intriguing system to study coevolutionary processes, I believe that avian brood parasites and their hosts are much more important as extreme cases in the evolution of life-history strategies. They provide unique examples of trade-offs and situations where constraints are either completely removed or particularly severe.

Environmental feedback drives cooperation in spatial social dilemmas

NASA Astrophysics Data System (ADS)

Szolnoki, Attila; Chen, Xiaojie

2017-12-01

Exploiting others is beneficial individually but it could also be detrimental globally. The reverse is also true: a higher cooperation level may change the environment in a way that is beneficial for all competitors. To explore the possible consequence of this feedback we consider a coevolutionary model where the local cooperation level determines the payoff values of the applied prisoner's dilemma game. We observe that the coevolutionary rule provides a significantly higher cooperation level comparing to the traditional setup independently of the topology of the applied interaction graph. Interestingly, this cooperation supporting mechanism offers lonely defectors a high surviving chance for a long period hence the relaxation to the final cooperating state happens logarithmically slow. As a consequence, the extension of the traditional evolutionary game by considering interactions with the environment provides a good opportunity for cooperators, but their reward may arrive with some delay.

Electromechanical fatigue in IPMC under dynamic energy harvesting conditions

NASA Astrophysics Data System (ADS)

Krishnaswamy, Arvind; Roy Mahapatra, D.

2011-04-01

Ionic polymer-metal composites (IPMCs) are an interesting subset of smart, multi-functional materials that have shown promises in energy conversion technologies. Being electromechanically coupled, IPMCs can function as dynamic actuators and sensors, transducers for energy conversion and harvesting, as well as artificial muscles for medical and industrial applications. Like all natural materials, even IPMCs undergo fatigue under dynamic load conditions. Here, we investigate the electromechanical fatigue induced in the IPMCs due to the application of cyclic mechanical bending deformation under hydrodynamic energy harvesting condition. Considering the viscoelastic nature of the IPMC, we employ an analytical approach to modeling electromechanical fatigue primarily under the cyclic stresses induced in the membrane. The polymer-metal composite undergoes cyclic softening throughout the fatigue life without attaining a saturated state of charge migration. However, it results in (1) degradation of electromechanical performance; (2) nucleation and growth of microscopic cracks in the metal electrodes; (3) delamination of metal electrodes at the polymer-electrode interface. To understand these processes, we employ a phenomenological approach based on experimentally measured relaxation properties of the IPMC membrane. Electromechanical performance improves significantly with self-healing like properties for a certain range of relaxation time. This is due to reorientation of the backbone polymer chains which eventually leads to a regenerative process with increased charge transport.

Slow crack growth versus creep cavity coalescence: Competing failure mechanisms during high-temperature deformation of advanced ceramics

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

Jenkins, M.G.; Kohles, S.S.; Stevens, T.L.

1996-12-31

Duality of failure mechanisms (slow crack growth from pre-existing defects versus cumulative creep damage) is examined in a silicon nitride advanced ceramic recently tested at elevated-temperatures. Static (constant stress over time), dynamic (monotonically-increasing stress over time), and cyclic (fluctuating stress over time) fatigue behaviors were evaluated in tension in ambient air at temperatures of 1150, 1260, and 1370{degrees}C for a hot-isostatically pressed monolithic {beta}-silicon nitride. At 1150{degrees}C, all three types of fatigue results showed the similar failure mechanism of slow crack growth (SCG). At 1260 and 1370{degrees}C the failure mechanism was more complex. Failure under static fatigue was dominated bymore » the accumulation of creep damage via diffusion-controlled cavities. In dynamic fatigue, failure occurred by SCG at high stress rates (>10{sup {minus}2}MPa/s) and by creep damage at low stress rates ({le}10{sup {minus}2} MPa/s). For cyclic fatigue, such rate effects influenced the stress rupture results in which times to failure were greater for dynamic and cyclic fatigue than for static fatigue. Elucidation of failure mechanisms is necessary for accurate prediction of long-term survivability and reliability of structural ceramics.« less

Effects of resource quality on the population dynamics of the Indian meal moth Plodia interpunctella and its granulovirus.

PubMed

McVean, Ross I; Sait, Steve M; Thompson, David J; Begon, Mike

2002-03-01

Although the Plodia interpunctella-granulovirus system is one of the most studied models for insect-pathogen interactions, there are relatively few precise data on the dynamics of the virus in coexisting populations of these two organisms. Previous work has suggested that resource quality, in terms of the diet supplied to P. interpunctella, has a strong effect on the population dynamics of host and pathogen. Here we investigate the impact of resource-dependent host patterns of abundance on pathogen dynamics and prevalence. In the laboratory, three populations of P. interpunctella feeding on a good quality food and infected with a granulovirus were compared with three populations also infected with a granulovirus but feeding on poor quality food. Populations feeding on good quality food produced larger adult moths, and had greater numbers of adult moths, healthy larvae, and virus-infected larvae. A higher proportion of larvae in these good quality populations were infected with virus, and adult moths exhibited cyclic fluctuations in abundance, unlike those on poor quality food. This cyclic behaviour was shown to be associated with cycles in the age structure of the larval population. Previous theoretical work suggests that these cycles may result from asymmetric competition between young and old larvae. Cyclic fluctuations in the proportion of infected larvae, that occurred on good, but not on poor quality food, were also shown to be related to cycles in the age structure of the larval population.

Coevolutionary arms race versus host defense chase in a tropical herbivore-plant system.

PubMed

Endara, María-José; Coley, Phyllis D; Ghabash, Gabrielle; Nicholls, James A; Dexter, Kyle G; Donoso, David A; Stone, Graham N; Pennington, R Toby; Kursar, Thomas A

2017-09-05

Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus Inga and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between Inga species was correlated with similarity in defenses. There was no correlation with phylogeny, a result consistent with our observations that the expression of defenses in Inga is independent of phylogeny. Furthermore, host defensive traits explained 40% of herbivore community similarity. Analyses at finer taxonomic scales showed that different lepidopteran clades select hosts based on different defenses, suggesting taxon-specific histories of herbivore-host plant interactions. Finally, we compared the phylogeny and defenses of Inga to phylogenies for the major lepidopteran clades. We found that closely related herbivores fed on Inga with similar defenses rather than on closely related plants. Together, these results suggest that plant defenses might be more evolutionarily labile than the herbivore traits related to host association. Hence, there is an apparent asymmetry in the evolutionary interactions between Inga and its herbivores. Although plants may evolve under selection by herbivores, we hypothesize that herbivores may not show coevolutionary adaptations, but instead "chase" hosts based on the herbivore's own traits at the time that they encounter a new host, a pattern more consistent with resource tracking than with the arms race model of coevolution.

Coevolutionary arms race versus host defense chase in a tropical herbivore–plant system

PubMed Central

Coley, Phyllis D.; Ghabash, Gabrielle; Nicholls, James A.; Donoso, David A.; Stone, Graham N.; Pennington, R. Toby; Kursar, Thomas A.

2017-01-01

Coevolutionary models suggest that herbivores drive diversification and community composition in plants. For herbivores, many questions remain regarding how plant defenses shape host choice and community structure. We addressed these questions using the tree genus Inga and its lepidopteran herbivores in the Amazon. We constructed phylogenies for both plants and insects and quantified host associations and plant defenses. We found that similarity in herbivore assemblages between Inga species was correlated with similarity in defenses. There was no correlation with phylogeny, a result consistent with our observations that the expression of defenses in Inga is independent of phylogeny. Furthermore, host defensive traits explained 40% of herbivore community similarity. Analyses at finer taxonomic scales showed that different lepidopteran clades select hosts based on different defenses, suggesting taxon-specific histories of herbivore–host plant interactions. Finally, we compared the phylogeny and defenses of Inga to phylogenies for the major lepidopteran clades. We found that closely related herbivores fed on Inga with similar defenses rather than on closely related plants. Together, these results suggest that plant defenses might be more evolutionarily labile than the herbivore traits related to host association. Hence, there is an apparent asymmetry in the evolutionary interactions between Inga and its herbivores. Although plants may evolve under selection by herbivores, we hypothesize that herbivores may not show coevolutionary adaptations, but instead “chase” hosts based on the herbivore’s own traits at the time that they encounter a new host, a pattern more consistent with resource tracking than with the arms race model of coevolution. PMID:28827317

Mechanical annealing under low-amplitude cyclic loading in micropillars

NASA Astrophysics Data System (ADS)

Cui, Yi-nan; Liu, Zhan-li; Wang, Zhang-jie; Zhuang, Zhuo

2016-04-01

Mechanical annealing has been demonstrated to be an effective method for decreasing the overall dislocation density in submicron single crystal. However, simultaneously significant shape change always unexpectedly happens under extremely high monotonic loading to drive the pre-existing dislocations out of the free surfaces. In the present work, through in situ TEM experiments it is found that cyclic loading with low stress amplitude can drive most dislocations out of the submicron sample with virtually little change of the shape. The underlying dislocation mechanism is revealed by carrying out discrete dislocation dynamic (DDD) simulations. The simulation results indicate that the dislocation density decreases within cycles, while the accumulated plastic strain is small. By comparing the evolution of dislocation junction under monotonic, cyclic and relaxation deformation, the cumulative irreversible slip is found to be the key factor of promoting junction destruction and dislocation annihilation at free surface under low-amplitude cyclic loading condition. By introducing this mechanics into dislocation density evolution equations, the critical conditions for mechanical annealing under cyclic and monotonic loadings are discussed. Low-amplitude cyclic loading which strengthens the single crystal without seriously disturbing the structure has the potential applications in the manufacture of defect-free nano-devices.

Beta1 integrin inhibits apoptosis induced by cyclic stretch in annulus fibrosus cells via ERK1/2 MAPK pathway.

PubMed

Zhang, Kai; Ding, Wei; Sun, Wei; Sun, Xiao-jiang; Xie, You-zhuan; Zhao, Chang-qing; Zhao, Jie

2016-01-01

Low back pain is associated with intervertebral disc degeneration (IVDD) due to cellular loss through apoptosis. Mechanical factors play an important role in maintaining the survival of the annulus fibrosus (AF) cells and the deposition of extracellular matrix. However, the mechanisms that excessive mechanical forces lead to AF cell apoptosis are not clear. The present study was to look for how AF cells sense mechanical changes. In vivo experiments, the involvement of mechanoreceptors in apoptosis was examined by RT-PCR and/or immunoblotting in the lumbar spine of rats subjected to unbalanced dynamic and static forces. In vitro experiments, we investigated apoptotic signaling pathways in untransfected and transfected AF cells with the lentivirus vector for rat β1 integrin overexpression after cyclic stretch. Apoptosis in AF cells was assessed using flow cytometry, Hoechst 33258 nuclear staining. Western blotting was used to analyze expression of β1 integrin and caspase-3 and ERK1/2 MAPK signaling molecules. In the rat IVDD model, unbalanced dynamic and static forces induced apoptosis of disc cells, which corresponded to decreased expression of β1 integrin. Cyclic stretch-induced apoptosis in rat AF cells correlated with the activation of caspase-3 and with decreased levels of β1 integrin and the phosphorylation levels of ERK1/2 activation level. However, the overexpression of β1 integrin in AF cells ameliorated cyclic stretch-induced apoptosis and decreased caspase-3 activation. Furthermore, ERK1/2-specific inhibitor promotes apoptosis in vector β1-infected AF cells. These results suggest that the disruption of β1 integrin signaling may underlie disc cell apoptosis induced by mechanical stress. Further work is necessary to fully elucidate the pathophysiological mechanisms that underlie IVDD caused by unbalanced dynamic and static forces.

Unintentional force changes in cyclical tasks performed by an abundant system: Empirical observations and a dynamical model.

PubMed

Reschechtko, Sasha; Hasanbarani, Fariba; Akulin, Vladimir M; Latash, Mark L

2017-05-14

The study explored unintentional force changes elicited by removing visual feedback during cyclical, two-finger isometric force production tasks. Subjects performed two types of tasks at 1Hz, paced by an auditory metronome. One - Force task - required cyclical changes in total force while maintaining the sharing, defined as relative contribution of a finger to total force. The other task - Share task - required cyclical changes in sharing while keeping total force unchanged. Each trial started under full visual feedback on both force and sharing; subsequently, feedback on the variable that was instructed to stay constant was frozen, and finally feedback on the other variable was also removed. In both tasks, turning off visual feedback on total force elicited a drop in the mid-point of the force cycle and an increase in the peak-to-peak force amplitude. Turning off visual feedback on sharing led to a drift of mean share toward 50:50 across both tasks. Without visual feedback there was consistent deviation of the two force time series from the in-phase pattern (typical of the Force task) and from the out-of-phase pattern (typical of the Share task). This finding is in contrast to most earlier studies that demonstrated only two stable patterns, in-phase and out-of-phase. We interpret the results as consequences of drifts of parameters in a dynamical system leading in particular to drifts in the referent finger coordinates toward their actual coordinates. The relative phase desynchronization is caused by the right-left differences in the hypothesized drift processes, consistent with the dynamic dominance hypothesis. Copyright © 2017 IBRO. Published by Elsevier Ltd. All rights reserved.

Unintentional force changes in cyclical tasks performed by an abundant system: Empirical observations and a dynamical model

PubMed Central

Reschechtko, Sasha; Hasanbarani, Fariba; Akulin, Vladimir M.; Latash, Mark L.

2017-01-01

The study explored unintentional force changes elicited by removing visual feedback during cyclical, two-finger isometric force production tasks. Subjects performed two types of tasks at 1 Hz, paced by an auditory metronome. One – Force task – required cyclical changes in total force while maintaining the sharing, defined as relative contribution of a finger to total force. The other task – Share task – required cyclical changes in sharing while keeping total force unchanged. Each trial started under full visual feedback on both force and sharing; subsequently, feedback on the variable that was instructed to stay constant was frozen, and finally feedback on the other variable was also removed. In both tasks, turning off visual feedback on total force elicited a drop in the mid-point of the force cycle and an increase in the peak-to-peak force amplitude. Turning off visual feedback on sharing led to a drift of mean share toward 50:50 across both tasks. Without visual feedback there was consistent deviation of the two force time series from the in-phase pattern (typical of the Force task) and from the out-of-phase pattern (typical of the Share task). This finding is in contrast to most earlier studies that demonstrated only two stable patterns, in-phase and out-of-phase. We interpret the results as consequences of drifts of parameters in a dynamical system leading in particular to drifts in the referent finger coordinates toward their actual coordinates. The relative phase desynchronization is caused by the right-left differences in the hypothesized drift processes, consistent with the dynamic dominance hypothesis. PMID:28344070

Crystal structures of RIalpha subunit of cyclic adenosine 5'-monophosphate (cAMP)-dependent protein kinase complexed with (Rp)-adenosine 3',5'-cyclic monophosphothioate and (Sp)-adenosine 3',5'-cyclic monophosphothioate, the phosphothioate analogues of cAMP.

PubMed

Wu, Jian; Jones, John M; Nguyen-Huu, Xuong; Ten Eyck, Lynn F; Taylor, Susan S

2004-06-01

Cyclic adenosine 5'-monophosphate (cAMP) is an ancient signaling molecule, and in vertebrates, a primary target for cAMP is cAMP-dependent protein kinase (PKA). (R(p))-adenosine 3',5'-cyclic monophosphothioate ((R(p))-cAMPS) and its analogues are the only known competitive inhibitors and antagonists for cAMP activation of PKA, while (S(p))-adenosine 3',5'-cyclic monophosphothioate ((S(p))-cAMPS) functions as an agonist. The crystal structures of a Delta(1-91) deletion mutant of the RIalpha regulatory subunit of PKA bound to (R(p))-cAMPS and (S(p))-cAMPS were determined at 2.4 and 2.3 A resolution, respectively. While the structures are similar to each other and to the crystal structure of RIalpha bound to cAMP, differences in the dynamical properties of the protein when (R(p))-cAMPS is bound are apparent. The structures highlight the critical importance of the exocyclic oxygen's interaction with the invariant arginine in the phosphate binding cassette (PBC) and the importance of this interaction for the dynamical properties of the interactions that radiate out from the PBC. The conformations of the phosphate binding cassettes containing two invariant arginine residues (Arg209 on domain A, and Arg333 on domain B) are somewhat different due to the sulfur interacting with this arginine. Furthermore, the B-site ligand together with the entire domain B show significant differences in their overall dynamic properties in the crystal structure of Delta(1-91) RIalpha complexed with (R(p))-cAMPS phosphothioate analogue ((R(p))-RIalpha) compared to the cAMP- and (S(p))-cAMPS-bound type I and II regulatory subunits, based on the temperature factors. In all structures, two structural solvent molecules exist within the A-site ligand binding pocket; both mediate water-bridged interactions between the ligand and the protein. No structured waters are in the B-site pocket. Owing to the higher resolution data, the N-terminal segment (109-117) of the RIalpha subunit can also be traced. This strand forms an intermolecular antiparallel beta-sheet with the same strand in an adjacent molecule and implies that the RIalpha subunit can form a weak homodimer even in the absence of its dimerization domain.

Current observations with a decaying cosmological constant allow for chaotic cyclic cosmology

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

Ellis, George F.R.; Platts, Emma; Weltman, Amanda

2016-04-01

We use the phase plane analysis technique of Madsen and Ellis [1] to consider a universe with a true cosmological constant as well as a cosmological 'constant' that is decaying. Time symmetric dynamics for the inflationary era allows eternally bouncing models to occur. Allowing for scalar field dynamic evolution, we find that if dark energy decays in the future, chaotic cyclic universes exist provided the spatial curvature is positive. This is particularly interesting in light of current observations which do not yet rule out either closed universes or possible evolution of the cosmological constant. We present only a proof ofmore » principle, with no definite claim on the physical mechanism required for the present dark energy to decay.« less

Mate Limitation in Fungal Plant Parasites Can Lead to Cyclic Epidemics in Perennial Host Populations.

PubMed

Ravigné, Virginie; Lemesle, Valérie; Walter, Alicia; Mailleret, Ludovic; Hamelin, Frédéric M

2017-03-01

Fungal plant parasites represent a growing concern for biodiversity and food security. Most ascomycete species are capable of producing different types of infectious spores both asexually and sexually. Yet the contributions of both types of spores to epidemiological dynamics have still to been fully researched. Here we studied the effect of mate limitation in parasites which perform both sexual and asexual reproduction in the same host. Since mate limitation implies positive density dependence at low population density, we modeled the dynamics of such species with both density-dependent (sexual) and density-independent (asexual) transmission rates. A first simple SIR model incorporating these two types of transmission from the infected compartment, suggested that combining sexual and asexual spore production can generate persistently cyclic epidemics in a significant part of the parameter space. It was then confirmed that cyclic persistence could occur in realistic situations by parameterizing a more detailed model fitting the biology of the Black Sigatoka disease of banana, for which literature data are available. We discuss the implications of these results for research on and management of Sigatoka diseases of banana.

Runaway cultural niche construction

PubMed Central

Rendell, Luke; Fogarty, Laurel; Laland, Kevin N.

2011-01-01

Cultural niche construction is a uniquely potent source of selection on human populations, and a major cause of recent human evolution. Previous theoretical analyses have not, however, explored the local effects of cultural niche construction. Here, we use spatially explicit coevolutionary models to investigate how cultural processes could drive selection on human genes by modifying local resources. We show that cultural learning, expressed in local niche construction, can trigger a process with dynamics that resemble runaway sexual selection. Under a broad range of conditions, cultural niche-constructing practices generate selection for gene-based traits and hitchhike to fixation through the build up of statistical associations between practice and trait. This process can occur even when the cultural practice is costly, or is subject to counteracting transmission biases, or the genetic trait is selected against. Under some conditions a secondary hitchhiking occurs, through which genetic variants that enhance the capability for cultural learning are also favoured by similar dynamics. We suggest that runaway cultural niche construction could have played an important role in human evolution, helping to explain why humans are simultaneously the species with the largest relative brain size, the most potent capacity for niche construction and the greatest reliance on culture. PMID:21320897

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease

PubMed Central

Hoberg, Eric P.; Brooks, Daniel R.

2015-01-01

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host–parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)—phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference—provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. PMID:25688014

Ecology and evolution of viruses infecting uncultivated SUP05 bacteria as revealed by single-cell- and meta-genomics

PubMed Central

Roux, Simon; Hawley, Alyse K; Torres Beltran, Monica; Scofield, Melanie; Schwientek, Patrick; Stepanauskas, Ramunas; Woyke, Tanja; Hallam, Steven J; Sullivan, Matthew B

2014-01-01

Viruses modulate microbial communities and alter ecosystem functions. However, due to cultivation bottlenecks, specific virus–host interaction dynamics remain cryptic. In this study, we examined 127 single-cell amplified genomes (SAGs) from uncultivated SUP05 bacteria isolated from a model marine oxygen minimum zone (OMZ) to identify 69 viral contigs representing five new genera within dsDNA Caudovirales and ssDNA Microviridae. Infection frequencies suggest that ∼1/3 of SUP05 bacteria is viral-infected, with higher infection frequency where oxygen-deficiency was most severe. Observed Microviridae clonality suggests recovery of bloom-terminating viruses, while systematic co-infection between dsDNA and ssDNA viruses posits previously unrecognized cooperation modes. Analyses of 186 microbial and viral metagenomes revealed that SUP05 viruses persisted for years, but remained endemic to the OMZ. Finally, identification of virus-encoded dissimilatory sulfite reductase suggests SUP05 viruses reprogram their host's energy metabolism. Together, these results demonstrate closely coupled SUP05 virus–host co-evolutionary dynamics with the potential to modulate biogeochemical cycling in climate-critical and expanding OMZs. DOI: http://dx.doi.org/10.7554/eLife.03125.001 PMID:25171894

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

PubMed

Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

2017-03-01

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

Effect of cyclic loading and retightening on reverse torque value in external and internal implants.

PubMed

Cho, Woong-Rae; Huh, Yoon-Hyuk; Park, Chan-Jin; Cho, Lee-Ra

2015-08-01

The aim of this study was to evaluate the effect of cyclic loading and screw retightening on reverse torque value (RTV) in external and internal type implants. Cement-retained abutments were connected with 30 Ncm torque to external and internal type implants. Experimental groups were classified according to implant connection type and retightening/loading protocol. In groups with no retightening, RTV was evaluated after cyclic loading for 100,000 cycles. In groups with retightening, RTV was measured after 3, 10, 100 cycles as well as every 20,000 cycles until 100,000 cycles of loading. Every group showed decreased RTV after cyclic loading. Before and after cyclic loading, external type implants had significantly higher RTVs than internal type implants. In external type implants, retightening did not affect the decrease in RTV. In contrast, retightening 5 times and retightening after 10 cycles of dynamic loading was effective for maintaining RTV in internal type implants. Retightening of screws is more effective in internal type implants than external type implants. Retightening of screws is recommended in the early stage of functional loading.

A micro-mechanical model to determine changes of collagen fibrils under cyclic loading

NASA Astrophysics Data System (ADS)

Chen, Michelle L.; Susilo, Monica E.; Ruberti, Jeffrey A.; Nguyen, Thao D.

Dynamic mechanical loading induces growth and remodeling in biological tissues. It can alter the degradation rate and intrinsic mechanical properties of collagen through cellular activity. Experiments showed that repeated cyclic loading of a dense collagen fibril substrate increased collagen stiffness and strength, lengthened the substrate, but did not significantly change the fibril areal fraction or fibril anisotropy (Susilo, et al. ``Collagen Network Hardening Following Cyclic Tensile Loading'', Interface Focus, submitted). We developed a model for the collagen fibril substrate (Tonge, et al. ``A micromechanical modeling study of the mechanical stabilization of enzymatic degradation of collagen tissues'', Biophys J, in press.) to probe whether changes in the fibril morphology and mechanical properties can explain the tissue-level properties observed during cyclic loading. The fibrils were modeled as a continuous distribution of wavy elastica, based on experimental measurements of fibril density and collagen anisotropy, and can experience damage after a critical stress threshold. Other mechanical properties in the model were fit to the stress response measured before and after the extended cyclic loading to determine changes in the strength and stiffness of collagen fibrils.

Effect of nitrogen on high temperature low cycle fatigue behaviors in type 316L stainless steel

NASA Astrophysics Data System (ADS)

Kim, Dae Whan; Ryu, Woo-Seog; Hong, Jun Hwa; Choi, Si-Kyung

1998-04-01

Strain-controlled low cycle fatigue (LCF) tests were conducted in the temperature range of RT-600°C and air atmosphere to investigate the nitrogen effect on LCF behavior of type 316L stainless steels with different nitrogen contents (0.04-0.15%). The waveform of LCF was a symmetrical triangle with a strain amplitude of ±0.5% and a constant strain rate of 2×10 -3/s was employed for most tests. Cyclic stress response of the alloys exhibited a gradual cyclic softening at RT, but a cyclic hardening at an early stage of fatigue life at 300-600°C. The hardening at high temperature was attributed to dynamic strain aging (DSA). Nitrogen addition decreased hardening magnitude (maximum cyclic stress — first cyclic stress) because nitrogen retarded DSA for these conditions. The dislocation structures were changed from cell to planar structure with increasing temperature and nitrogen addition by DSA and short range order (SRO). Fatigue life was a maximum at 0.1% nitrogen content, which was attributed to the balance between DSA and SRO.

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe

PubMed Central

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R.; Niu, Gang; Chen, Xiaoyuan

2012-01-01

Purpose: The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/64Cu dual-labeled cyclic RGD peptide. Methods: The integrin αvβ3 binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. Results: The dual-labeled probe 64Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). Conclusion: The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models. PMID:22916074

Dynamic PET and Optical Imaging and Compartment Modeling using a Dual-labeled Cyclic RGD Peptide Probe.

PubMed

Zhu, Lei; Guo, Ning; Li, Quanzheng; Ma, Ying; Jacboson, Orit; Lee, Seulki; Choi, Hak Soo; Mansfield, James R; Niu, Gang; Chen, Xiaoyuan

2012-01-01

The aim of this study is to determine if dynamic optical imaging could provide comparable kinetic parameters to that of dynamic PET imaging by a near-infrared dye/(64)Cu dual-labeled cyclic RGD peptide. The integrin α(v)β(3) binding RGD peptide was conjugated with a macrocyclic chelator 1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid (DOTA) for copper labeling and PET imaging and a near-infrared dye ZW-1 for optical imaging. The in vitro biological activity of RGD-C(DOTA)-ZW-1 was characterized by cell staining and receptor binding assay. Sixty-min dynamic PET and optical imaging were acquired on a MDA-MB-435 tumor model. Singular value decomposition (SVD) method was applied to compute the dynamic optical signal from the two-dimensional optical projection images. Compartment models were used to quantitatively analyze and compare the dynamic optical and PET data. The dual-labeled probe (64)Cu-RGD-C(DOTA)-ZW-1 showed integrin specific binding in vitro and in vivo. The binding potential (Bp) derived from dynamic optical imaging (1.762 ± 0.020) is comparable to that from dynamic PET (1.752 ± 0.026). The signal un-mixing process using SVD improved the accuracy of kinetic modeling of 2D dynamic optical data. Our results demonstrate that 2D dynamic optical imaging with SVD analysis could achieve comparable quantitative results as dynamic PET imaging in preclinical xenograft models.

Comparison of mechanical compressive properties of commercial and autologous fibrin glues for tissue engineering applications.

PubMed

Cravens, Matthew G; Behn, Anthony W; Dragoo, Jason L

2017-11-01

Fibrin glues are widely used in orthopedic surgery as adhesives and hemostatic agents. We evaluated the compressive properties of selected fibrin glues in order to identify which are appropriate for tissue regeneration applications subject to compression. Uniaxial unconfined compression tests were performed on fibrin gels prepared from commercial and autologous products: (1) Evicel (Ethicon), (2) Tisseel (Baxter), (3) Angel (Arthrex), and (4) ProPlaz (Biorich). Cyclic loads were applied from 0 to 30% strain for 100cycles at 0.5Hz. Following cyclic testing, specimens were subjected to ramp displacement of 1% strain per second to 80% strain. Throughout cyclic loading, Evicel and Tisseel deformed (shortened) less than Angel at all but one time point, and deformed less than ProPlaz at cycles 10 and 20. The dynamic moduli, peak stress, and strain energy were significantly greater in Tisseel than all other groups. Evicel displayed significantly greater dynamic moduli, peak stress, and strain energy than Angel and ProPlaz. Following cyclic testing, Tisseel and Evicel were significantly less deformed than Angel. No specimens exhibited gross failure during ramp loading to 80% strain. Ramp loading trends mirrored those of cyclic loading. The tested commercial glues were significantly more resistant to compression than the autologous products. The compressive properties of Tisseel were approximately twice those of Evicel. All preparations displayed moduli multiple orders of magnitude less than that of native articular cartilage. We conclude that in knee surgeries requiring fibrin glue to undergo compression of daily activity, commercial products are preferable to autologous preparations from platelet-poor plasma, though both will deform significantly. Copyright © 2017 Elsevier Ltd. All rights reserved.

Influence of different manufacturing methods on the cyclic fatigue of rotary nickel-titanium endodontic instruments.

PubMed

Rodrigues, Renata C V; Lopes, Hélio P; Elias, Carlos N; Amaral, Georgiana; Vieira, Victor T L; De Martin, Alexandre S

2011-11-01

The aim of this study was to evaluate, by static and dynamic cyclic fatigue tests, the number of cycles to fracture (NCF) 2 types of rotary NiTi instruments: Twisted File (SybronEndo, Orange, CA), which is manufactured by a proprietary twisting process, and RaCe files (FKG Dentaire, La Chaux-de-Fonds, Switzerland), which are manufactured by grinding. Twenty Twisted Files (TFs) and 20 RaCe files #25/.006 taper instruments were allowed to rotate freely in an artificial curved canal at 310 rpm in a static or a dynamic model until fracture occurred. Measurements of the fractured fragments showed that fracture occurred at the point of maximum flexure in the midpoint of the curved segment. The NCF was significantly lower for RaCe instruments compared with TFs. The NCF was also lower for instruments subjected to the static test compared with the dynamic model in both groups. Scanning electron microscopic analysis revealed ductile morphologic characteristics on the fractured surfaces of all instruments and no plastic deformation in their helical shafts. Rotary NiTi endodontic instruments manufactured by twisting present greater resistance to cyclic fatigue compared with instruments manufactured by grinding. The fracture mode observed in all instruments was of the ductile type. Copyright © 2011 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

The Second International Piping Integrity Research Group (IPIRG-2) program. Final report, October 1991--April 1996

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

Hopper, A.; Wilowski, G.; Scott, P.

1997-03-01

The IPIRG-2 program was an international group program managed by the US NRC and funded by organizations from 15 nations. The emphasis of the IPIRG-2 program was the development of data to verify fracture analyses for cracked pipes and fittings subjected to dynamic/cyclic load histories typical of seismic events. The scope included: (1) the study of more complex dynamic/cyclic load histories, i.e., multi-frequency, variable amplitude, simulated seismic excitations, than those considered in the IPIRG-1 program, (2) crack sizes more typical of those considered in Leak-Before-Break (LBB) and in-service flaw evaluations, (3) through-wall-cracked pipe experiments which can be used to validatemore » LBB-type fracture analyses, (4) cracks in and around pipe fittings, such as elbows, and (5) laboratory specimen and separate effect pipe experiments to provide better insight into the effects of dynamic and cyclic load histories. Also undertaken were an uncertainty analysis to identify the issues most important for LBB or in-service flaw evaluations, updating computer codes and databases, the development and conduct of a series of round-robin analyses, and analyst`s group meetings to provide a forum for nuclear piping experts from around the world to exchange information on the subject of pipe fracture technology. 17 refs., 104 figs., 41 tabs.« less

Cyclic Game Dynamics Driven by Iterated Reasoning

PubMed Central

Frey, Seth; Goldstone, Robert L.

2013-01-01

Recent theories from complexity science argue that complex dynamics are ubiquitous in social and economic systems. These claims emerge from the analysis of individually simple agents whose collective behavior is surprisingly complicated. However, economists have argued that iterated reasoning–what you think I think you think–will suppress complex dynamics by stabilizing or accelerating convergence to Nash equilibrium. We report stable and efficient periodic behavior in human groups playing the Mod Game, a multi-player game similar to Rock-Paper-Scissors. The game rewards subjects for thinking exactly one step ahead of others in their group. Groups that play this game exhibit cycles that are inconsistent with any fixed-point solution concept. These cycles are driven by a “hopping” behavior that is consistent with other accounts of iterated reasoning: agents are constrained to about two steps of iterated reasoning and learn an additional one-half step with each session. If higher-order reasoning can be complicit in complex emergent dynamics, then cyclic and chaotic patterns may be endogenous features of real-world social and economic systems. PMID:23441191

Theoretical design of the cyclic lipopeptide nanotube as a molecular channel in the lipid bilayer, molecular dynamics and quantum mechanics approach.

PubMed

Khavani, Mohammad; Izadyar, Mohammad; Housaindokht, Mohammad Reza

2015-10-14

In this article, cyclic peptides (CP) with lipid substituents were theoretically designed. The dynamical behavior of the CP dimers and the cyclic peptide nanotube (CPNT) without lipid substituents in the solution (water and chloroform) during the 50 ns molecular dynamic (MD) simulations has been investigated. As a result, the CP dimers and CPNT in a non-polar solvent are more stable than in a polar solvent and CPNT is a good container for non-polar small molecules such as chloroform. The effect of the lipid substituents on the CP dimers and CPNT has been investigated in the next stage of our studies. Accordingly, these substituents increase the stability of the CP dimers and CPNT, significantly, in polar solvents. MM-PBSA and MM-GBSA calculations confirm that substitution has an important effect on the stability of the CP dimers and CPNT. Finally, the dynamical behavior of CPNT with lipid substituents in a fully hydrated DMPC bilayer shows the high ability of this structure for molecule transmission across the lipid membrane. This structure is stable enough to be used as a molecular channel. DFT calculations on the CP dimers in the gas phase, water and chloroform, indicate that H-bond formation is the driving force for dimerization. CP dimers are more stable in the gas phase in comparison to in solution. HOMO-LUMO orbital analysis indicates that the interaction of the CP units in the dimer structures is due to the molecular orbital interactions between the NH and CO groups.

[A microstructural approach to fatigue crack processes in poly crystalline BCC materials]. Progress report

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

Gerberich, W.W.

1992-12-31

Objective was to study fatigue where a combination of low temperature and cyclic loading produced cyclic cleavage in bcc Fe-base systems. Both dislocation dynamics and quasi-statics of crack growth were probed. This document reviews progress over the past 6 years: hydrogen embrittlement and cleavage, computations (stress near crack tip), dislocation emission from grain boundaries, fracture process zones, and understanding brittle fracture at the atomistic/dislocation scales and at the microscopic/macroscopic scale.

The detailed 3D multi-loop aggregate/rosette chromatin architecture and functional dynamic organization of the human and mouse genomes.

PubMed

Knoch, Tobias A; Wachsmuth, Malte; Kepper, Nick; Lesnussa, Michael; Abuseiris, Anis; Ali Imam, A M; Kolovos, Petros; Zuin, Jessica; Kockx, Christel E M; Brouwer, Rutger W W; van de Werken, Harmen J G; van IJcken, Wilfred F J; Wendt, Kerstin S; Grosveld, Frank G

2016-01-01

The dynamic three-dimensional chromatin architecture of genomes and its co-evolutionary connection to its function-the storage, expression, and replication of genetic information-is still one of the central issues in biology. Here, we describe the much debated 3D architecture of the human and mouse genomes from the nucleosomal to the megabase pair level by a novel approach combining selective high-throughput high-resolution chromosomal interaction capture ( T2C ), polymer simulations, and scaling analysis of the 3D architecture and the DNA sequence. The genome is compacted into a chromatin quasi-fibre with ~5 ± 1 nucleosomes/11 nm, folded into stable ~30-100 kbp loops forming stable loop aggregates/rosettes connected by similar sized linkers. Minor but significant variations in the architecture are seen between cell types and functional states. The architecture and the DNA sequence show very similar fine-structured multi-scaling behaviour confirming their co-evolution and the above. This architecture, its dynamics, and accessibility, balance stability and flexibility ensuring genome integrity and variation enabling gene expression/regulation by self-organization of (in)active units already in proximity. Our results agree with the heuristics of the field and allow "architectural sequencing" at a genome mechanics level to understand the inseparable systems genomic properties.

Micromechanics of soil responses in cyclic simple shear tests

NASA Astrophysics Data System (ADS)

Cui, Liang; Bhattacharya, Subhamoy; Nikitas, George

2017-06-01

Offshore wind turbine (OWT) foundations are subjected to a combination of cyclic and dynamic loading arising from wind, wave, rotor and blade shadowing. Under cyclic loading, most soils change their characteristics including stiffness, which may cause the system natural frequency to approach the loading frequency and lead to unplanned resonance and system damage or even collapse. To investigate such changes and the underlying micromechanics, a series of cyclic simple shear tests were performed on the RedHill 110 sand with different shear strain amplitudes, vertical stresses and initial relative densities of soil. The test results showed that: (a) Vertical accumulated strain is proportional to the shear strain amplitude but inversely proportional to relative density of soil; (b) Shear modulus increases rapidly in the initial loading cycles and then the rate of increase diminishes and the shear modulus remains below an asymptote; (c) Shear modulus increases with increasing vertical stress and relative density, but decreasing with increasing strain amplitude. Coupled DEM simulations were performed using PFC2D to analyse the micromechanics underlying the cyclic behaviour of soils. Micromechanical parameters (e.g. fabric tensor, coordination number) were examined to explore the reasons for the various cyclic responses to different shear strain amplitudes or vertical stresses. Both coordination number and magnitude of fabric anisotropy contribute to the increasing shear modulus.

Detection of significant protein coevolution.

PubMed

Ochoa, David; Juan, David; Valencia, Alfonso; Pazos, Florencio

2015-07-01

The evolution of proteins cannot be fully understood without taking into account the coevolutionary linkages entangling them. From a practical point of view, coevolution between protein families has been used as a way of detecting protein interactions and functional relationships from genomic information. The most common approach to inferring protein coevolution involves the quantification of phylogenetic tree similarity using a family of methodologies termed mirrortree. In spite of their success, a fundamental problem of these approaches is the lack of an adequate statistical framework to assess the significance of a given coevolutionary score (tree similarity). As a consequence, a number of ad hoc filters and arbitrary thresholds are required in an attempt to obtain a final set of confident coevolutionary signals. In this work, we developed a method for associating confidence estimators (P values) to the tree-similarity scores, using a null model specifically designed for the tree comparison problem. We show how this approach largely improves the quality and coverage (number of pairs that can be evaluated) of the detected coevolution in all the stages of the mirrortree workflow, independently of the starting genomic information. This not only leads to a better understanding of protein coevolution and its biological implications, but also to obtain a highly reliable and comprehensive network of predicted interactions, as well as information on the substructure of macromolecular complexes using only genomic information. The software and datasets used in this work are freely available at: http://csbg.cnb.csic.es/pMT/. pazos@cnb.csic.es Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

New World feline APOBEC3 potently controls inter-genus lentiviral transmission.

PubMed

Konno, Yoriyuki; Nagaoka, Shumpei; Kimura, Izumi; Yamamoto, Keisuke; Kagawa, Yumiko; Kumata, Ryuichi; Aso, Hirofumi; Ueda, Mahoko Takahashi; Nakagawa, So; Kobayashi, Tomoko; Koyanagi, Yoshio; Sato, Kei

2018-04-10

The apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) gene family appears only in mammalian genomes. Some A3 proteins can be incorporated into progeny virions and inhibit lentiviral replication. In turn, the lentiviral viral infectivity factor (Vif) counteracts the A3-mediated antiviral effect by degrading A3 proteins. Recent investigations have suggested that lentiviral vif genes evolved to combat mammalian APOBEC3 proteins, and have further proposed that the Vif-A3 interaction may help determine the co-evolutionary history of cross-species lentiviral transmission in mammals. Here we address the co-evolutionary relationship between two New World felids, the puma (Puma concolor) and the bobcat (Lynx rufus), and their lentiviruses, which are designated puma lentiviruses (PLVs). We demonstrate that PLV-A Vif counteracts the antiviral action of APOBEC3Z3 (A3Z3) of both puma and bobcat, whereas PLV-B Vif counteracts only puma A3Z3. The species specificity of PLV-B Vif is irrespective of the phylogenic relationships of feline species in the genera Puma, Lynx and Acinonyx. We reveal that the amino acid at position 178 in the puma and bobcat A3Z3 is exposed on the protein surface and determines the sensitivity to PLV-B Vif-mediated degradation. Moreover, although both the puma and bobcat A3Z3 genes are polymorphic, their sensitivity/resistance to PLV Vif-mediated degradation is conserved. To the best of our knowledge, this is the first study suggesting that the host A3 protein potently controls inter-genus lentiviral transmission. Our findings provide the first evidence suggesting that the co-evolutionary arms race between lentiviruses and mammals has occurred in the New World.

Evolutionary behaviour, trade-offs and cyclic and chaotic population dynamics.

PubMed

Hoyle, Andy; Bowers, Roger G; White, Andy

2011-05-01

Many studies of the evolution of life-history traits assume that the underlying population dynamical attractor is stable point equilibrium. However, evolutionary outcomes can change significantly in different circumstances. We present an analysis based on adaptive dynamics of a discrete-time demographic model involving a trade-off whose shape is also an important determinant of evolutionary behaviour. We derive an explicit expression for the fitness in the cyclic region and consequently present an adaptive dynamic analysis which is algebraic. We do this fully in the region of 2-cycles and (using a symbolic package) almost fully for 4-cycles. Simulations illustrate and verify our results. With equilibrium population dynamics, trade-offs with accelerating costs produce a continuously stable strategy (CSS) whereas trade-offs with decelerating costs produce a non-ES repellor. The transition to 2-cycles produces a discontinuous change: the appearance of an intermediate region in which branching points occur. The size of this region decreases as we move through the region of 2-cycles. There is a further discontinuous fall in the size of the branching region during the transition to 4-cycles. We extend our results numerically and with simulations to higher-period cycles and chaos. Simulations show that chaotic population dynamics can evolve from equilibrium and vice-versa.

Endogenously determined cycles: empirical evidence from livestock industries.

PubMed

McCullough, Michael P; Huffaker, Ray; Marsh, Thomas L

2012-04-01

This paper applies the techniques of phase space reconstruction and recurrence quantification analysis to investigate U.S. livestock cycles in relation to recent literature on the business cycle. Results are presented for pork and cattle cycles, providing empirical evidence that the cycles themselves have slowly diminished. By comparing the evolution of production processes for the two livestock cycles we argue that the major cause for this moderation is largely endogenous. The analysis suggests that previous theoretical models relying solely on exogenous shocks to create cyclical patterns do not fully capture changes in system dynamics. Specifically, the biological constraint in livestock dynamics has become less significant while technology and information are relatively more significant. Concurrently, vertical integration of the supply chain may have improved inventory management, all resulting in a small, less deterministic, cyclical effect.

Dynamic generation of light states with discrete symmetries

NASA Astrophysics Data System (ADS)

Cordero, S.; Nahmad-Achar, E.; Castaños, O.; López-Peña, R.

2018-01-01

A dynamic procedure is established within the generalized Tavis-Cummings model to generate light states with discrete point symmetries, given by the cyclic group Cn. We consider arbitrary dipolar coupling strengths of the atoms with a one-mode electromagnetic field in a cavity. The method uses mainly the matter-field entanglement properties of the system, which can be extended to any number of three-level atoms. An initial state constituted by the superposition of two states with definite total excitation numbers, |ψ〉 M1,and |ψ〉 M 2, is considered. It can be generated by the proper selection of the time of flight of an atom passing through the cavity. We demonstrate that the resulting Husimi function of the light is invariant under cyclic point transformations of order n =| M1-M2| .

Gene-Culture Coevolutionary Games

ERIC Educational Resources Information Center

Blute, Marion

2006-01-01

Gene-culture interactions have largely been modelled employing population genetic-type models. Moreover, in the most notable application to date, the "interactive" modes have been one way rather than bidirectional. This paper suggests using game theoretic, fully interactive models. Employing the logic utilized in population ecology for coevolution…

Sexual selection modulates genetic conflicts and patterns of genomic imprinting

PubMed Central

Faria, Gonçalo S.; Varela, Susana A. M.; Gardner, Andy

2017-01-01

Recent years have seen a surge of interest in linking the theories of kin selection and sexual selection. In particular, there is a growing appreciation that kin selection, arising through demographic factors such as sex‐biased dispersal, may modulate sexual conflicts, including in the context of male–female arms races characterized by coevolutionary cycles. However, evolutionary conflicts of interest need not only occur between individuals, but may also occur within individuals, and sex‐specific demography is known to foment such intragenomic conflict in relation to social behavior. Whether and how this logic holds in the context of sexual conflict—and, in particular, in relation to coevolutionary cycles—remains obscure. We develop a kin‐selection model to investigate the interests of different genes involved in sexual and intragenomic conflict, and we show that consideration of these conflicting interests yields novel predictions concerning parent‐of‐origin specific patterns of gene expression and the detrimental effects of different classes of mutation and epimutation at loci underpinning sexually selected phenotypes. PMID:27991659

The phylogenetic structure of plant-pollinator networks increases with habitat size and isolation.

PubMed

Aizen, Marcelo A; Gleiser, Gabriela; Sabatino, Malena; Gilarranz, Luis J; Bascompte, Jordi; Verdú, Miguel

2016-01-01

Similarity among species in traits related to ecological interactions is frequently associated with common ancestry. Thus, closely related species usually interact with ecologically similar partners, which can be reinforced by diverse co-evolutionary processes. The effect of habitat fragmentation on the phylogenetic signal in interspecific interactions and correspondence between plant and animal phylogenies is, however, unknown. Here, we address to what extent phylogenetic signal and co-phylogenetic congruence of plant-animal interactions depend on habitat size and isolation by analysing the phylogenetic structure of 12 pollination webs from isolated Pampean hills. Phylogenetic signal in interspecific interactions differed among webs, being stronger for flower-visiting insects than plants. Phylogenetic signal and overall co-phylogenetic congruence increased independently with hill size and isolation. We propose that habitat fragmentation would erode the phylogenetic structure of interaction webs. A decrease in phylogenetic signal and co-phylogenetic correspondence in plant-pollinator interactions could be associated with less reliable mutualism and erratic co-evolutionary change. © 2015 John Wiley & Sons Ltd/CNRS.

Female burying beetles benefit from male desertion: sexual conflict and counter-adaptation over parental investment.

PubMed

Boncoraglio, Giuseppe; Kilner, Rebecca M

2012-01-01

Sexual conflict drives the coevolution of sexually antagonistic traits, such that an adaptation in one sex selects an opposing coevolutionary response from the other. Although many adaptations and counteradaptations have been identified in sexual conflict over mating interactions, few are known for sexual conflict over parental investment. Here we investigate a possible coevolutionary sequence triggered by mate desertion in the burying beetle Nicrophorus vespilloides, where males commonly leave before their offspring reach independence. Rather than suffer fitness costs as a consequence, our data suggest that females rely on the male's absence to recoup some of the costs of larval care, presumably because they are then free to feed themselves on the carcass employed for breeding. Consequently, forcing males to stay until the larvae disperse reduces components of female fitness to a greater extent than caring for young singlehandedly. Therefore we suggest that females may have co-evolved to anticipate desertion by their partners so that they now benefit from the male's absence.

Female Burying Beetles Benefit from Male Desertion: Sexual Conflict and Counter-Adaptation over Parental Investment

PubMed Central

Boncoraglio, Giuseppe; Kilner, Rebecca M.

2012-01-01

Sexual conflict drives the coevolution of sexually antagonistic traits, such that an adaptation in one sex selects an opposing coevolutionary response from the other. Although many adaptations and counteradaptations have been identified in sexual conflict over mating interactions, few are known for sexual conflict over parental investment. Here we investigate a possible coevolutionary sequence triggered by mate desertion in the burying beetle Nicrophorus vespilloides, where males commonly leave before their offspring reach independence. Rather than suffer fitness costs as a consequence, our data suggest that females rely on the male's absence to recoup some of the costs of larval care, presumably because they are then free to feed themselves on the carcass employed for breeding. Consequently, forcing males to stay until the larvae disperse reduces components of female fitness to a greater extent than caring for young singlehandedly. Therefore we suggest that females may have co-evolved to anticipate desertion by their partners so that they now benefit from the male's absence. PMID:22355390

Na+/K+-ATPase resistance and cardenolide sequestration: basal adaptations to host plant toxins in the milkweed bugs (Hemiptera: Lygaeidae: Lygaeinae)

PubMed Central

Bramer, Christiane; Dobler, Susanne; Deckert, Jürgen; Stemmer, Michael; Petschenka, Georg

2015-01-01

Despite sequestration of toxins being a common coevolutionary response to plant defence in phytophagous insects, the macroevolution of the traits involved is largely unaddressed. Using a phylogenetic approach comprising species from four continents, we analysed the ability to sequester toxic cardenolides in the hemipteran subfamily Lygaeinae, which is widely associated with cardenolide-producing Apocynaceae. In addition, we analysed cardenolide resistance of their Na+/K+-ATPases, the molecular target of cardenolides. Our data indicate that cardenolide sequestration and cardenolide-resistant Na+/K+-ATPase are basal adaptations in the Lygaeinae. In two species that shifted to non-apocynaceous hosts, the ability to sequester was secondarily reduced, yet Na+/K+-ATPase resistance was maintained. We suggest that both traits evolved together and represent major coevolutionary adaptations responsible for the evolutionary success of lygaeine bugs. Moreover, specialization on cardenolides was not an evolutionary dead end, but enabled this insect lineage to host shift to cardenolide-producing plants from distantly related families. PMID:25808891

Mathematical model and metaheuristics for simultaneous balancing and sequencing of a robotic mixed-model assembly line

NASA Astrophysics Data System (ADS)

Li, Zixiang; Janardhanan, Mukund Nilakantan; Tang, Qiuhua; Nielsen, Peter

2018-05-01

This article presents the first method to simultaneously balance and sequence robotic mixed-model assembly lines (RMALB/S), which involves three sub-problems: task assignment, model sequencing and robot allocation. A new mixed-integer programming model is developed to minimize makespan and, using CPLEX solver, small-size problems are solved for optimality. Two metaheuristics, the restarted simulated annealing algorithm and co-evolutionary algorithm, are developed and improved to address this NP-hard problem. The restarted simulated annealing method replaces the current temperature with a new temperature to restart the search process. The co-evolutionary method uses a restart mechanism to generate a new population by modifying several vectors simultaneously. The proposed algorithms are tested on a set of benchmark problems and compared with five other high-performing metaheuristics. The proposed algorithms outperform their original editions and the benchmarked methods. The proposed algorithms are able to solve the balancing and sequencing problem of a robotic mixed-model assembly line effectively and efficiently.

An analysis of parameter sensitivities of preference-inspired co-evolutionary algorithms

NASA Astrophysics Data System (ADS)

Wang, Rui; Mansor, Maszatul M.; Purshouse, Robin C.; Fleming, Peter J.

2015-10-01

Many-objective optimisation problems remain challenging for many state-of-the-art multi-objective evolutionary algorithms. Preference-inspired co-evolutionary algorithms (PICEAs) which co-evolve the usual population of candidate solutions with a family of decision-maker preferences during the search have been demonstrated to be effective on such problems. However, it is unknown whether PICEAs are robust with respect to the parameter settings. This study aims to address this question. First, a global sensitivity analysis method - the Sobol' variance decomposition method - is employed to determine the relative importance of the parameters controlling the performance of PICEAs. Experimental results show that the performance of PICEAs is controlled for the most part by the number of function evaluations. Next, we investigate the effect of key parameters identified from the Sobol' test and the genetic operators employed in PICEAs. Experimental results show improved performance of the PICEAs as more preferences are co-evolved. Additionally, some suggestions for genetic operator settings are provided for non-expert users.

Recurrence quantification analysis to characterize cyclical components of environmental elemental exposures during fetal and postnatal development

PubMed Central

Austin, Christine; Gennings, Chris; Tammimies, Kristiina; Bölte, Sven; Arora, Manish

2017-01-01

Environmental exposures to essential and toxic elements may alter health trajectories, depending on the timing, intensity, and mixture of exposures. In epidemiologic studies, these factors are typically analyzed as a function of elemental concentrations in biological matrices measured at one or more points in time. Such an approach, however, fails to account for the temporal cyclicity in the metabolism of environmental chemicals, which if perturbed may lead to adverse health outcomes. Here, we conceptualize and apply a non-linear method–recurrence quantification analysis (RQA)–to quantify cyclical components of prenatal and early postnatal exposure profiles for elements essential to normal development, including Zn, Mn, Mg, and Ca, and elements associated with deleterious health effects or narrow tolerance ranges, including Pb, As, and Cr. We found robust evidence of cyclical patterns in the metabolic profiles of nutrient elements, which we validated against randomized twin-surrogate time-series, and further found that nutrient dynamical properties differ from those of Cr, As, and Pb. Furthermore, we extended this approach to provide a novel method of quantifying dynamic interactions between two environmental exposures. To achieve this, we used cross-recurrence quantification analysis (CRQA), and found that elemental nutrient-nutrient interactions differed from those involving toxicants. These rhythmic regulatory interactions, which we characterize in two geographically distinct cohorts, have not previously been uncovered using traditional regression-based approaches, and may provide a critical unit of analysis for environmental and dietary exposures in epidemiological studies. PMID:29112980

Emergence of unusual coexistence states in cyclic game systems.

PubMed

Park, Junpyo; Do, Younghae; Jang, Bongsoo; Lai, Ying-Cheng

2017-08-07

Evolutionary games of cyclic competitions have been extensively studied to gain insights into one of the most fundamental phenomena in nature: biodiversity that seems to be excluded by the principle of natural selection. The Rock-Paper-Scissors (RPS) game of three species and its extensions [e.g., the Rock-Paper-Scissors-Lizard-Spock (RPSLS) game] are paradigmatic models in this field. In all previous studies, the intrinsic symmetry associated with cyclic competitions imposes a limitation on the resulting coexistence states, leading to only selective types of such states. We investigate the effect of nonuniform intraspecific competitions on coexistence and find that a wider spectrum of coexistence states can emerge and persist. This surprising finding is substantiated using three classes of cyclic game models through stability analysis, Monte Carlo simulations and continuous spatiotemporal dynamical evolution from partial differential equations. Our finding indicates that intraspecific competitions or alternative symmetry-breaking mechanisms can promote biodiversity to a broader extent than previously thought.

Can human mesenchymal stem cells survive on a NiTi implant material subjected to cyclic loading?

PubMed

Habijan, T; Glogowski, T; Kühn, S; Pohl, M; Wittsiepe, J; Greulich, C; Eggeler, G; Schildhauer, T A; Köller, M

2011-06-01

Nickel-titanium shape memory alloys (NiTi-SMAs) exhibit mechanical and chemical properties which make them attractive candidate materials for various types of biomedical applications. However, the high nickel content of NiTi-SMAs may result in adverse tissue reactions, especially when they are considered for load-bearing implants. It is generally assumed that a protective titanium oxide layer separates the metallic alloy from its environment and that this explains the good biocompatibility of NiTi. Cyclic loading may result in failure of the protective oxide layer. The scientific objective of this work was to find out whether cyclic dynamic strain, in a range relevant for orthopedic implants, diminishes the biocompatibility of NiTi-SMAs. In order to analyze the biocompatibility of NiTi-SMA surfaces subjected to cyclic loading, NiTi-SMA tensile specimens were preloaded with mesenchymal stem cells, transferred to a sterile cell culture system and fixed to the pull rods of a tensile testing machine. Eighty-six thousand and four hundred strain cycles at 2% pseudoelastic strain were performed for a period of 24 h or 7 days. Cytokines (IL-6, IL-8 and VEGF) and nickel ion release were determined within the cell culture medium. Adherent cells on the tensile specimens were stained with calcein-AM and propidium iodide to determine cell viability. Dynamic loading of the tensile specimens did not influence the viability of adherent human mesenchymal stem cells (hMSCs) after 24 h or 7 days compared with the non-strained control. Dynamic cycles of loading and unloading did not affect nickel ion release from the tensile specimens. The release of IL-6 from hMSCs cultured under dynamic conditions was significantly higher after mechanical load (873 pg ml(-1)) compared with static conditions (323 pg ml(-1)). The present work demonstrates that a new type of mechanical in vitro cell culture experiment can provide information which previously could only be obtained in large animal experiments. Copyright © 2011 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Counterintuitive effects of large-scale predator removal on a midlatitude rodent community

Treesearch

John L Maron; Dean E. Pearson; Robert J. Fletcher

2010-01-01

Historically, small mammals have been focal organisms for studying predator-prey dynamics, principally because of interest in explaining the drivers of the cyclical dynamics exhibited by northern vole, lemming, and hare populations. However, many small-mammal species occur at relatively low and fairly stable densities at temperate latitudes, and our understanding of...

Effect of climate fluctuation on long-term vegetation dynamics in Carolina bay wetlands

Treesearch

Chrissa Stroh; Diane De Steven; Glenn Guntenspergen

2008-01-01

Carolina bays and similar depression wetlands of the U. S. Southeastern Coastal Plain have hydrologic regimes that are driven primarily by rainfall. Therefore, climate fluctuations such as drought cycles have the potential to shape long-term vegetation dynamics. Models suggest two potential long-term responses to hydrologic fluctuations, either cyclic change...

Fatigue crack propagation behavior of ultrahigh molecular weight polyethylene.

PubMed

Connelly, G M; Rimnac, C M; Wright, T M; Hertzberg, R W; Manson, J A

1984-01-01

The relative fatigue crack propagation resistance of plain and carbon fiber-reinforced ultrahigh molecular weight polyethylene (UHMWPE) was determined from cyclic loading tests performed on compact tension specimens machined from the tibial components of total knee prostheses. Both materials were characterized by dynamic mechanical spectroscopy, X-ray diffraction, and differential scanning calorimetry. The cyclic tests used loading in laboratory air at 5 Hz using a sinusoidal wave form. Dynamic mechanical spectroscopy showed that the reinforced UHMWPE had a higher elastic storage modulus than the plain UHMWPE, whereas X-ray diffraction and differential scanning calorimetry showed that the percent crystallinity and degree of order in the crystalline regions were similar for the two materials. Fatigue crack propagation in both materials proved to be very sensitive to small changes in the applied cyclic stress intensity range. A 10% increase in stress intensity resulted in approximately an order of magnitude increase in fatigue crack growth rate. The fatigue crack propagation resistance of the reinforced UHMWPE was found to be significantly worse than that of the plain UHMWPE. This result was attributed to poor bonding between the carbon fibers and the UHMWPE matrix and the ductile nature of the matrix itself.

Revisiting the formation of cyclic clusters in liquid ethanol

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

Balanay, Mannix P.; Fan, Haiyan, E-mail: haiyan.fan@nu.edu.kz; Kim, Dong Hee

2016-04-21

The liquid phase of ethanol in pure and in non-polar solvents was studied at room temperature using Fourier transform infrared (FT-IR) and {sup 1}H nuclear magnetic resonance (NMR) spectroscopies together with theoretical approach. The FT-IR spectra for pure ethanol and solution in cyclohexane at different dilution stages are consistent with {sup 1}H NMR results. The results from both methods were best explained by the results of the density functional theory based on a multimeric model. It is suggested that cyclic trimers and tetramers are dominated in the solution of cyclohexane/hexane with the concentration greater than 0.5M at room temperature. Inmore » liquid ethanol, while the primary components at room temperature are cyclic trimers and tetramers, there is a certain amount (∼14%) of open hydroxide group representing the existence of chain like structures in the equilibria. The cyclic cluster model in the liquid and concentrated solution phase (>0.5M) can be used to explain the anomalously lower freezing point of ethanol (159 K) than that of water (273 K) at ambient conditions. In addition, {sup 1}H NMR at various dilution stages reveals the dynamics for the formation of cyclic clusters.« less

Effect of cyclic loading and retightening on reverse torque value in external and internal implants

PubMed Central

Cho, Woong-Rae; Huh, Yoon-Hyuk; Park, Chan-Jin

2015-01-01

PURPOSE The aim of this study was to evaluate the effect of cyclic loading and screw retightening on reverse torque value (RTV) in external and internal type implants. MATERIALS AND METHODS Cement-retained abutments were connected with 30 Ncm torque to external and internal type implants. Experimental groups were classified according to implant connection type and retightening/loading protocol. In groups with no retightening, RTV was evaluated after cyclic loading for 100,000 cycles. In groups with retightening, RTV was measured after 3, 10, 100 cycles as well as every 20,000 cycles until 100,000 cycles of loading. RESULTS Every group showed decreased RTV after cyclic loading. Before and after cyclic loading, external type implants had significantly higher RTVs than internal type implants. In external type implants, retightening did not affect the decrease in RTV. In contrast, retightening 5 times and retightening after 10 cycles of dynamic loading was effective for maintaining RTV in internal type implants. CONCLUSION Retightening of screws is more effective in internal type implants than external type implants. Retightening of screws is recommended in the early stage of functional loading. PMID:26330975

Behavior of nonplastic silty soils under cyclic loading.

PubMed

Ural, Nazile; Gunduz, Zeki

2014-01-01

The engineering behavior of nonplastic silts is more difficult to characterize than is the behavior of clay or sand. Especially, behavior of silty soils is important in view of the seismicity of several regions of alluvial deposits in the world, such as the United States, China, and Turkey. In several hazards substantial ground deformation, reduced bearing capacity, and liquefaction of silty soils have been attributed to excess pore pressure generation during dynamic loading. In this paper, an experimental study of the pore water pressure generation of silty soils was conducted by cyclic triaxial tests on samples of reconstituted soils by the slurry deposition method. In all tests silty samples which have different clay percentages were studied under different cyclic stress ratios. The results have showed that in soils having clay content equal to and less than 10%, the excess pore pressure ratio buildup was quicker with an increase in different cyclic stress ratios. When fine and clay content increases, excess pore water pressure decreases constant cyclic stress ratio in nonplastic silty soils. In addition, the applicability of the used criteria for the assessment of liquefaction susceptibility of fine grained soils is examined using laboratory test results.

Behavior of Nonplastic Silty Soils under Cyclic Loading

PubMed Central

Ural, Nazile; Gunduz, Zeki

2014-01-01

The engineering behavior of nonplastic silts is more difficult to characterize than is the behavior of clay or sand. Especially, behavior of silty soils is important in view of the seismicity of several regions of alluvial deposits in the world, such as the United States, China, and Turkey. In several hazards substantial ground deformation, reduced bearing capacity, and liquefaction of silty soils have been attributed to excess pore pressure generation during dynamic loading. In this paper, an experimental study of the pore water pressure generation of silty soils was conducted by cyclic triaxial tests on samples of reconstituted soils by the slurry deposition method. In all tests silty samples which have different clay percentages were studied under different cyclic stress ratios. The results have showed that in soils having clay content equal to and less than 10%, the excess pore pressure ratio buildup was quicker with an increase in different cyclic stress ratios. When fine and clay content increases, excess pore water pressure decreases constant cyclic stress ratio in nonplastic silty soils. In addition, the applicability of the used criteria for the assessment of liquefaction susceptibility of fine grained soils is examined using laboratory test results. PMID:24672343

Resurgence of oscillation in coupled oscillators under delayed cyclic interaction

NASA Astrophysics Data System (ADS)

Bera, Bidesh K.; Majhi, Soumen; Ghosh, Dibakar

2017-07-01

This paper investigates the emergence of amplitude death and revival of oscillations from the suppression states in a system of coupled dynamical units interacting through delayed cyclic mode. In order to resurrect the oscillation from amplitude death state, we introduce asymmetry and feedback parameter in the cyclic coupling forms as a result of which the death region shrinks due to higher asymmetry and lower feedback parameter values for coupled oscillatory systems. Some analytical conditions are derived for amplitude death and revival of oscillations in two coupled limit cycle oscillators and corresponding numerical simulations confirm the obtained theoretical results. We also report that the death state and revival of oscillations from quenched state are possible in the network of identical coupled oscillators. The proposed mechanism has also been examined using chaotic Lorenz oscillator.

Helminth Community Dynamics in Populations of Blue-Winged Teal (Anas discors) Using Two Distinct Migratory Corridors.

PubMed

Garvon, Jason M; Fedynich, Alan M; Peterson, Markus J; Pence, Danny B

2011-01-01

The influence of spatially distinct host subpopulations on helminth community structure and pattern was examined in a migratory avian host species. Forty helminth species represented by 24,082 individuals were collected from 184 blue-winged teal (Anas discors; BWT) from 2 primary migratory corridors in Florida (eastern migratory corridor; EMC) and Louisiana and Texas (western migratory corridor; WMC). Mean species richness was greater in BWT from the WMC (x̅±SE = 10.2 ± 0.3 species) than the EMC (8.6 ± 0.2). The helminth community from the WMC had higher abundances of 6 common/intermediate species. Corridor helminth communities were similar in species composition but less similar when incorporating abundances of those species. Overlapping distributions of phylogenetically related host species that share generalist helminth species across ecologically similar habitats seem to mitigate the isolating mechanisms that are necessary for the distinct coevolutionary pathways to develop between adjacent corridors.

Three is much more than two in coarsening dynamics of cyclic competitions

NASA Astrophysics Data System (ADS)

Mitarai, Namiko; Gunnarson, Ivar; Pedersen, Buster Niels; Rosiek, Christian Anker; Sneppen, Kim

2016-04-01

The classical game of rock-paper-scissors has inspired experiments and spatial model systems that address the robustness of biological diversity. In particular, the game nicely illustrates that cyclic interactions allow multiple strategies to coexist for long-time intervals. When formulated in terms of a one-dimensional cellular automata, the spatial distribution of strategies exhibits coarsening with algebraically growing domain size over time, while the two-dimensional version allows domains to break and thereby opens the possibility for long-time coexistence. We consider a quasi-one-dimensional implementation of the cyclic competition, and study the long-term dynamics as a function of rare invasions between parallel linear ecosystems. We find that increasing the complexity from two to three parallel subsystems allows a transition from complete coarsening to an active steady state where the domain size stays finite. We further find that this transition happens irrespective of whether the update is done in parallel for all sites simultaneously or done randomly in sequential order. In both cases, the active state is characterized by localized bursts of dislocations, followed by longer periods of coarsening. In the case of the parallel dynamics, we find that there is another phase transition between the active steady state and the coarsening state within the three-line system when the invasion rate between the subsystems is varied. We identify the critical parameter for this transition and show that the density of active boundaries has critical exponents that are consistent with the directed percolation universality class. On the other hand, numerical simulations with the random sequential dynamics suggest that the system may exhibit an active steady state as long as the invasion rate is finite.

Synthesis and conformational analysis by 1H NMR and restrained molecular dynamics simulations of the cyclic decapeptide [Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly

NASA Astrophysics Data System (ADS)

Buono, Ronald A.; Kucharczyk, Nathalie; Neuenschwander, Magrit; Kemmink, Johan; Hwang, Lih-Yueh; Fauchère, Jean-Luc; Venanzi, Carol A.

1996-06-01

The design of enzyme mimics with therapeutic and industrial applications has interested both experimental and computational chemists for several decades. Recent advances in the computational methodology of restrained molecular dynamics, used in conjunction with data obtained from two-dimensional 1H NMR spectroscopy, make it a promising method to study peptide and protein structure and function. Several issues, however, need to be addressed in order to assess the validity of this method for its explanatory and predictive value. Among the issues addressed in this study are: the accuracy and generizability of the GROMOS peptide molecular mechanics force field; the effect of inclusion of solvent on the simulations; and the effect of different types of restraining algorithms on the computational results. The decapeptide Ser-Tyr-Ser-Met-Glu-His-Phe-Arg-Trp-Gly, which corresponds to the sequence of ACTH1-10, has been synthesized, cyclized, and studied by two-dimensional 1H NMR spectroscopy. Restrained molecular dynamics (RMD) and time-averaged restrained molecular dynamics (TARMD) simulations were carried out on four different distance-geometry starting structures in order to determine and contrast the behavior of cyclic ACTH1-10 in vacuum and in solution. For the RMD simulations, the structures did not fit the NOE data well, even at high values of the restraining potential. The TARMD simulation method, however, was able to give structures that fit the NOE data at high values of the restraining potential. In both cases, inclusion of explicit solvent molecules in the simulation had little effect on the quality of the fit, although it was found to dampen the motion of the cyclic peptide. For both simulation techniques, the number and size of the NOE violations increased as the restraining potential approached zero. This is due, presumably, to inadequacies in the force field. Additional TARMD vacuum-phase simulations, run with a larger memory length or with a larger sampling size (16 additional distance-geometry structures), yielded no significantly different results. The computed data were then analyzed to help explain the sparse NOE data and poor chymotryptic activity of the cyclic peptide. Cyclic ACTH1-10, which contains the functional moieties of the catalytic triad of chymotrypsin, was evaluated as a potential mimic of chymotrypsin by measurement of the rate of hydrolysis of esters of L-and d-phenylalanine. The poor rate of hydrolysis is attributed to the flexibility of the decapeptide, the motion of the side chains, which result in the absence of long-range NOEs, the small size of the macrocycle relative to that of the substrate, and the inappropriate orientation of the Gly, His, and Ser residues. The results demonstrate the utility of this method in computer-aided molecular design of cyclic peptides and suggest structural modifications for future work based on a larger and more rigid peptide framework.

Scaling analysis of heart beat fluctuations data and its relationship with cyclic alternating pattern data during sleep

NASA Astrophysics Data System (ADS)

de León-Lomelí, R.; Murguía, J. S.; Chouvarda, I.; Méndez, M. O.; González-Galván, E.; Alba, A.

2016-01-01

During sleep there exists a nonlinear dynamic phenomenon, which is called cyclic alternating pattern. This phenomenon is generated in the brain and is composed of a series of events of short duration known as A-phases. It has been shown that A-phases can be found in other physiological systems such as the cardiovascular. However, there is no evidence that shows the temporal influence of the A-phases with the cardiovascular system. For this purpose, we consider the scaling method known as detrended fluctuation analysis (DFA). The analysis was carried out in well sleepers and insomnia people, and the numerical results show an increment in the scaling parameter for the insomnia subjects compared with the normal ones. In addition, the results of the heart dynamics suggests a persistent behavior toward the 1/f-noise.

Macromolecular 'size' and 'hardness' drives structure in solvent-swollen blends of linear, cyclic, and star polymers.

PubMed

Gartner, Thomas E; Jayaraman, Arthi

2018-01-17

In this paper, we apply molecular simulation and liquid state theory to uncover the structure and thermodynamics of homopolymer blends of the same chemistry and varying chain architecture in the presence of explicit solvent species. We use hybrid Monte Carlo (MC)/molecular dynamics (MD) simulations in the Gibbs ensemble to study the swelling of ∼12 000 g mol -1 linear, cyclic, and 4-arm star polystyrene chains in toluene. Our simulations show that the macroscopic swelling response is indistinguishable between the various architectures and matches published experimental data for the solvent annealing of linear polystyrene by toluene vapor. We then use standard MD simulations in the NPT ensemble along with polymer reference interaction site model (PRISM) theory to calculate effective polymer-solvent and polymer-polymer Flory-Huggins interaction parameters (χ eff ) in these systems. As seen in the macroscopic swelling results, there are no significant differences in the polymer-solvent and polymer-polymer χ eff between the various architectures. Despite similar macroscopic swelling and effective interaction parameters between various architectures, the pair correlation function between chain centers-of-mass indicates stronger correlations between cyclic or star chains in the linear-cyclic blends and linear-star blends, compared to linear chain-linear chain correlations. Furthermore, we note striking similarities in the chain-level correlations and the radius of gyration of cyclic and 4-arm star architectures of identical molecular weight. Our results indicate that the cyclic and star chains are 'smaller' and 'harder' than their linear counterparts, and through comparison with MD simulations of blends of soft spheres with varying hardness and size we suggest that these macromolecular characteristics are the source of the stronger cyclic-cyclic and star-star correlations.

Host responses to historical climate change shape parasite communities in North America’s intermountain west

USDA-ARS?s Scientific Manuscript database

Host-parasite co-speciation, in which parasite divergence occurs in response to host divergence, is commonly proposed as a driver of parasite diversification, yet few empirical examples of strict co-speciation exist. Host-parasite co-evolutionary histories commonly reflect complex mosaics of co-spe...

Reduction in fecundity and shifts in cellular processes by a native virus on an invasive insect

USDA-ARS?s Scientific Manuscript database

Pathogens and their vectors have co-evolutionary histories that are intricately intertwined with their ecologies, environments and genetic interactions. The majority of non-persistently transmitted plant viruses are transmitted by aphid species. One important aphid vector in soybean-growing regions ...

Toward a Pedagogy of Ecological Responsibility: Learning to Reinhabit the Earth.

ERIC Educational Resources Information Center

Mische, Patricia M.

1992-01-01

Environmental damage harms the rights of future generations. Peace and disarmament are environmental issues necessitating rethinking of national security. Coevolutionary ethics involve balancing the individual with the common good and establishing equilibrium among the biosphere, technosphere, sociosphere, and the sphere of mind and spirit. (SK)

Predictions of Control Inputs, Periodic Responses and Damping Levels of an Isolated Experimental Rotor in Trimmed Flight

NASA Technical Reports Server (NTRS)

Gaonkar, G. H.; Subramanian, S.

1996-01-01

Since the early 1990s the Aeroflightdynamics Directorate at the Ames Research Center has been conducting tests on isolated hingeless rotors in hover and forward flight. The primary objective is to generate a database on aeroelastic stability in trimmed flight for torsionally soft rotors at realistic tip speeds. The rotor test model has four soft inplane blades of NACA 0012 airfoil section with low torsional stiffness. The collective pitch and shaft tilt are set prior to each test run, and then the rotor is trimmed in the following sense: the longitudinal and lateral cyclic pitch controls are adjusted through a swashplate to minimize the 1/rev flapping moment at the 12 percent radial station. In hover, the database comprises lag regressive-mode damping with pitch variations. In forward flight the database comprises cyclic pitch controls, root flap moment and lag regressive-mode damping with advance ratio, shaft angle and pitch variations. This report presents the predictions and their correlation with the database. A modal analysis is used, in which nonrotating modes in flap bending, lag bending and torsion are computed from the measured blade mass and stiffness distributions. The airfoil aerodynamics is represented by the ONERA dynamic stall models of lift, drag and pitching moment, and the wake dynamics is represented by a state-space wake model. The trim analysis of finding, the cyclic controls and the corresponding, periodic responses is based on periodic shooting with damped Newton iteration; the Floquet transition matrix (FTM) comes out as a byproduct. The stabillty analysis of finding the frequencies and damping levels is based on the eigenvalue-eigenvector analysis of the FTM. All the structural and aerodynamic states are included from modeling to trim analysis. A major finding is that dynamic wake dramatically improves the correlation for the lateral cyclic pitch control. Overall, the correlation is fairly good.

The role of colonization in the dynamics of patchy populations of a cyclic vole species.

PubMed

Glorvigen, Petter; Gundersen, Gry; Andreassen, Harry P; Ims, Rolf A

2013-09-01

The crash phase of vole populations with cyclic dynamics regularly leads to vast areas of uninhabited habitats. Yet although the capacity for cyclic voles to re-colonize such empty space is likely to be large and predicted to have become evolved as a distinct life history trait, the processes of colonization and its effect on the spatio-temporal dynamics have been little studied. Here we report from an experiment with root voles (Microtus oeconomus) specifically targeted at quantifying the process of colonization of empty patches from distant source patches and its resultant effect on local vole deme size variation in a patchy landscape. Three experimental factors: habitat quality, predation risk and inter-patch distance were employed among 24 habitat patches in a 100 × 300-m experimental area. The first-born cohort in the spring efficiently colonized almost all empty patches irrespective of the degree of patch isolation and predation risk, but this was dependent on habitat quality. Just after the initial colonization wave the deme sizes in patches of the same quality were underdispersed relative to Poisson variance, indicating regulated (density-dependent) settlement. Towards the end of the breeding season local demographic processes acted to smooth out the initial post-colonization differences among source and colonization patches, and among patches of initially different quality. However, at this time demographic stochasticity had also given rise to a large (overdispersed) variation in deme sizes that may have contributed to an overshadowing of the effect of other factors. The results of this experiment confirmed our expectation that the space-filling capacity of voles is large. The costs associated with transience appeared to be so low, at least at the spatial scale considered in this experiment, that such costs are not likely to substantially constrain habitat selection and colonization in the increase phase of cyclic patchy populations.

Response of an arctic predator guild to collapsing lemming cycles

PubMed Central

Schmidt, Niels M.; Ims, Rolf A.; Høye, Toke T.; Gilg, Olivier; Hansen, Lars H.; Hansen, Jannik; Lund, Magnus; Fuglei, Eva; Forchhammer, Mads C.; Sittler, Benoit

2012-01-01

Alpine and arctic lemming populations appear to be highly sensitive to climate change, and when faced with warmer and shorter winters, their well-known high-amplitude population cycles may collapse. Being keystone species in tundra ecosystems, changed lemming dynamics may convey significant knock-on effects on trophically linked species. Here, we analyse long-term (1988–2010), community-wide monitoring data from two sites in high-arctic Greenland and document how a collapse in collared lemming cyclicity affects the population dynamics of the predator guild. Dramatic changes were observed in two highly specialized lemming predators: snowy owl and stoat. Following the lemming cycle collapse, snowy owl fledgling production declined by 98 per cent, and there was indication of a severe population decline of stoats at one site. The less specialized long-tailed skua and the generalist arctic fox were more loosely coupled to the lemming dynamics. Still, the lemming collapse had noticeable effects on their reproductive performance. Predator responses differed somewhat between sites in all species and could arise from site-specific differences in lemming dynamics, intra-guild interactions or subsidies from other resources. Nevertheless, population extinctions and community restructuring of this arctic endemic predator guild are likely if the lemming dynamics are maintained at the current non-cyclic, low-density state. PMID:22977153

Response of an arctic predator guild to collapsing lemming cycles.

PubMed

Schmidt, Niels M; Ims, Rolf A; Høye, Toke T; Gilg, Olivier; Hansen, Lars H; Hansen, Jannik; Lund, Magnus; Fuglei, Eva; Forchhammer, Mads C; Sittler, Benoit

2012-11-07

Alpine and arctic lemming populations appear to be highly sensitive to climate change, and when faced with warmer and shorter winters, their well-known high-amplitude population cycles may collapse. Being keystone species in tundra ecosystems, changed lemming dynamics may convey significant knock-on effects on trophically linked species. Here, we analyse long-term (1988-2010), community-wide monitoring data from two sites in high-arctic Greenland and document how a collapse in collared lemming cyclicity affects the population dynamics of the predator guild. Dramatic changes were observed in two highly specialized lemming predators: snowy owl and stoat. Following the lemming cycle collapse, snowy owl fledgling production declined by 98 per cent, and there was indication of a severe population decline of stoats at one site. The less specialized long-tailed skua and the generalist arctic fox were more loosely coupled to the lemming dynamics. Still, the lemming collapse had noticeable effects on their reproductive performance. Predator responses differed somewhat between sites in all species and could arise from site-specific differences in lemming dynamics, intra-guild interactions or subsidies from other resources. Nevertheless, population extinctions and community restructuring of this arctic endemic predator guild are likely if the lemming dynamics are maintained at the current non-cyclic, low-density state.

Host social organization and mating system shape parasite transmission opportunities in three European bat species.

PubMed

van Schaik, J; Kerth, G

2017-02-01

For non-mobile parasites living on social hosts, infection dynamics are strongly influenced by host life history and social system. We explore the impact of host social systems on parasite population dynamics by comparing the infection intensity and transmission opportunities of three mite species of the genus Spinturnix across their three European bat hosts (Myotis daubentonii, Myotis myotis, Myotis nattereri) during the bats' autumn mating season. Mites mainly reproduce in host maternity colonies in summer, but as these colonies are closed, opportunities for inter-colony transmission are limited to host interactions during the autumn mating season. The three investigated hosts differ considerably in their social system, most notably in maternity colony size, mating system, and degree of male summer aggregation. We observed marked differences in parasite infection during the autumn mating period between the species, closely mirroring the predictions made based on the social systems of the hosts. Increased host aggregation sizes in summer yielded higher overall parasite prevalence and intensity, both in male and female hosts. Moreover, parasite levels in male hosts differentially increased throughout the autumn mating season in concordance with the degree of contact with female hosts afforded by the different mating systems of the hosts. Critically, the observed host-specific differences have important consequences for parasite population structure and will thus affect the coevolutionary dynamics between the interacting species. Therefore, in order to accurately characterize host-parasite dynamics in hosts with complex social systems, a holistic approach that investigates parasite infection and transmission across all periods is warranted.

Genetic consequences of forest population dynamics influenced by historic climatic variability in the western USA

Treesearch

Robert D. Westfall; Constance I. Millar

2004-01-01

We review recent advances in climate science that show cyclic climatic variation over multiple time scales and give examples of the impacts of this variation on plant populations in the western USA. The paleohistorical reconstructions we review and others indicate that plant specles track these cycles in individualistically complex ways. These dynamic histories suggest...

Relation between heart beat fluctuations and cyclic alternating pattern during sleep in insomnia patients.

PubMed

de Leon-Lomeli, R; Murguia, J S; Chouvarda, I; Mendez, M O; Gonzalez-Galvan, E; Alba, A; Milioli, G; Grassi, A; Terzano, M G; Parrino, L

2014-01-01

Insomnia is a condition that affects the nervous and muscular system. Thirty percent of the population between 18 and 60 years suffers from insomnia. The effects of this disorder involve problems such as poor school or job performance and traffic accidents. In addition, patients with insomnia present changes in the cardiac function during sleep. Furthermore, the structure of electroencephalographic A-phases, which builds up the Cyclic Alternating Pattern during sleep, is related to the insomnia events. Therefore, the relationship between these brain activations (A-phases) and the autonomic nervous system would be of interest, revealing the interplay of central and autonomic activity during insomnia. With this goal, a study of the relationship between A-phases and heart rate fluctuations is presented. Polysomnography recording of five healthy subjects, five sleep misperception patients and five patients with psychophysiological insomnia were used in the study. Detrended Fluctuation Analysis (DFA) was used in order to evaluate the heart rate dynamics and this was correlated with the number of A-phases. The results suggest that pathological patients present changes in the dynamics of the heart rate. This is reflected in the modification of A-phases dynamics, which seems to modify of heart rate dynamics.

Human Adaptive Behavior in Common Pool Resource Systems

PubMed Central

Brandt, Gunnar; Merico, Agostino; Vollan, Björn; Schlüter, Achim

2012-01-01

Overexploitation of common-pool resources, resulting from uncooperative harvest behavior, is a major problem in many social-ecological systems. Feedbacks between user behavior and resource productivity induce non-linear dynamics in the harvest and the resource stock that complicate the understanding and the prediction of the co-evolutionary system. With an adaptive model constrained by data from a behavioral economic experiment, we show that users’ expectations of future pay-offs vary as a result of the previous harvest experience, the time-horizon, and the ability to communicate. In our model, harvest behavior is a trait that adjusts to continuously changing potential returns according to a trade-off between the users’ current harvest and the discounted future productivity of the resource. Given a maximum discount factor, which quantifies the users’ perception of future pay-offs, the temporal dynamics of harvest behavior and ecological resource can be predicted. Our results reveal a non-linear relation between the previous harvest and current discount rates, which is most sensitive around a reference harvest level. While higher than expected returns resulting from cooperative harvesting in the past increase the importance of future resource productivity and foster sustainability, harvests below the reference level lead to a downward spiral of increasing overexploitation and disappointing returns. PMID:23285180

Evolution in action: climate change, biodiversity dynamics and emerging infectious disease.

PubMed

Hoberg, Eric P; Brooks, Daniel R

2015-04-05

Climatological variation and ecological perturbation have been pervasive drivers of faunal assembly, structure and diversification for parasites and pathogens through recurrent events of geographical and host colonization at varying spatial and temporal scales of Earth history. Episodic shifts in climate and environmental settings, in conjunction with ecological mechanisms and host switching, are often critical determinants of parasite diversification, a view counter to more than a century of coevolutionary thinking about the nature of complex host-parasite assemblages. Parasites are resource specialists with restricted host ranges, yet shifts onto relatively unrelated hosts are common during phylogenetic diversification of parasite lineages and directly observable in real time. The emerging Stockholm Paradigm resolves this paradox: Ecological Fitting (EF)--phenotypic flexibility and phylogenetic conservatism in traits related to resource use, most notably host preference--provides many opportunities for rapid host switching in changing environments, without the evolution of novel host-utilization capabilities. Host shifts via EF fuel the expansion phase of the Oscillation Hypothesis of host range and speciation and, more generally, the generation of novel combinations of interacting species within the Geographic Mosaic Theory of Coevolution. In synergy, an environmental dynamic of Taxon Pulses establishes an episodic context for host and geographical colonization. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Living on the Edge: Parasite Prevalence Changes Dramatically across a Range Edge in an Invasive Gecko.

PubMed

Coates, Andrew; Barnett, Louise K; Hoskin, Conrad; Phillips, Ben L

2017-02-01

Species interactions can determine range limits, and parasitism is the most intimate of such interactions. Intriguingly, the very conditions on range edges likely change host-parasite dynamics in nontrivial ways. Range edges are often associated with clines in host density and with environmental transitions, both of which may affect parasite transmission. On advancing range edges, founder events and fitness/dispersal costs of parasitism may also cause parasites to be lost on range edges. Here we examine the prevalence of three species of parasite across the range edge of an invasive gecko, Hemidactylus frenatus, in northeastern Australia. The gecko's range edge spans the urban-woodland interface at the edge of urban areas. Across this edge, gecko abundance shows a steep decline, being lower in the woodland. Two parasite species (a mite and a pentastome) are coevolved with H. frenatus, and these species become less prevalent as the geckos become less abundant. A third species of parasite (another pentastome) is native to Australia and has no coevolutionary history with H. frenatus. This species became more prevalent as the geckos become less abundant. These dramatic shifts in parasitism (occurring over 3.5 km) confirm that host-parasite dynamics can vary substantially across the range edge of this gecko host.

The Granuloma in Tuberculosis: Dynamics of a Host–Pathogen Collusion

PubMed Central

Ehlers, Stefan; Schaible, Ulrich E.

2012-01-01

A granuloma is defined as an inflammatory mononuclear cell infiltrate that, while capable of limiting growth of Mycobacterium tuberculosis, also provides a survival niche from which the bacteria may disseminate. The tuberculosis lesion is highly dynamic and shaped by both, immune response elements and the pathogen. In the granuloma, M. tuberculosis switches to a non-replicating but energy-generating life style whose detailed molecular characterization can identify novel targets for chemotherapy. To secure transmission to a new host, M. tuberculosis has evolved to drive T cell immunity to the point that necrotizing granulomas leak into bronchial cavities to facilitate expectoration of bacilli. From an evolutionary perspective it is therefore questionable whether vaccination and immunity enhancing strategies that merely mimic the natural immune response directed against M. tuberculosis infection can overcome pulmonary tuberculosis in the adult population. Juxtaposition of molecular pathology and immunology with microbial physiology and the use of novel imaging approaches afford an integrative view of the granuloma’s contribution to the life cycle of M. tuberculosis. This review revisits the different input of innate and adaptive immunity in granuloma biogenesis, with a focus on the co-evolutionary forces that redirect immune responses also to the benefit of the pathogen, i.e., its survival, propagation, and transmission. PMID:23308075

[Gypsy moth Lymantria dispar L. in the South Urals: Patterns in population dynamics and modelling].

PubMed

Soukhovolsky, V G; Ponomarev, V I; Sokolov, G I; Tarasova, O V; Krasnoperova, P A

2015-01-01

The analysis is conducted on population dynamics of gypsy moth from different habitats of the South Urals. The pattern of cyclic changes in population density is examined, the assessment of temporal conjugation in time series of gypsy moth population dynamics from separate habitats of the South Urals is carried out, the relationships between population density and weather conditions are studied. Based on the results obtained, a statistical model of gypsy moth population dynamics in the South Urals is designed, and estimations are given of regulatory and modifying factors effects on the population dynamics.

Assessment of the role of cross section on fatigue resistance of rotary files when used in reciprocation.

PubMed

Sekar, Vadhana; Kumar, Ranjith; Nandini, Suresh; Ballal, Suma; Velmurugan, Natanasabapathy

2016-01-01

The purpose of this study was to assess the role of cross section on cyclic fatigue resistance of One Shape, Revo-S SU, and Mtwo rotary files in continuous rotation and reciprocating motion in dynamic testing model. A total of 90 new rotary One Shape, Revo-S SU, and Mtwo files (ISO size 25, taper 0.06, length 25 mm) were subjected to continuous rotation or reciprocating motion. A cyclic fatigue testing device was fabricated with 60° angle of curvature and 5 mm radius. The dynamic testing of these files was performed using an electric motor which permitted the reproduction of pecking motion. All instruments were rotated or reciprocated until fracture occurred. The time taken for each instrument to fracture was recorded. All the fractured files were analyzed under a scanning electron microscope (SEM) to detect the mode of fracture. Statistical analysis was performed using one-way ANOVA, followed by Tukey's honestly significant difference post hoc test. The time taken for instruments in reciprocating motion to fail under cyclic loading was significantly longer when compared with groups in continuous rotary motion. There was a statistically significant difference between Mtwo rotary and the other two groups in both continuous and reciprocating motion. One Shape rotary files recorded significantly longer duration to fracture resistance when compared with Revo-S SU files in both continuous and reciprocating motion. SEM observations showed that the instruments of all groups had undergone a ductile mode of fracture. Reciprocating motion improved the cyclic fatigue resistance of all tested groups.

Assessment of the role of cross section on fatigue resistance of rotary files when used in reciprocation

PubMed Central

Sekar, Vadhana; Kumar, Ranjith; Nandini, Suresh; Ballal, Suma; Velmurugan, Natanasabapathy

2016-01-01

Objective: The purpose of this study was to assess the role of cross section on cyclic fatigue resistance of One Shape, Revo-S SU, and Mtwo rotary files in continuous rotation and reciprocating motion in dynamic testing model. Materials and Methods: A total of 90 new rotary One Shape, Revo-S SU, and Mtwo files (ISO size 25, taper 0.06, length 25 mm) were subjected to continuous rotation or reciprocating motion. A cyclic fatigue testing device was fabricated with 60° angle of curvature and 5 mm radius. The dynamic testing of these files was performed using an electric motor which permitted the reproduction of pecking motion. All instruments were rotated or reciprocated until fracture occurred. The time taken for each instrument to fracture was recorded. All the fractured files were analyzed under a scanning electron microscope (SEM) to detect the mode of fracture. Statistical analysis was performed using one-way ANOVA, followed by Tukey's honestly significant difference post hoc test. Results: The time taken for instruments in reciprocating motion to fail under cyclic loading was significantly longer when compared with groups in continuous rotary motion. There was a statistically significant difference between Mtwo rotary and the other two groups in both continuous and reciprocating motion. One Shape rotary files recorded significantly longer duration to fracture resistance when compared with Revo-S SU files in both continuous and reciprocating motion. SEM observations showed that the instruments of all groups had undergone a ductile mode of fracture. Conclusion: Reciprocating motion improved the cyclic fatigue resistance of all tested groups. PMID:28042272

Tension degradation of anterior cruciate ligament grafts with dynamic flexion-extension loading: a biomechanical model in porcine knees.

PubMed

Dargel, Jens; Koebke, Jürgen; Brüggemann, Gert-Peter; Pennig, Dietmar; Schmidt-Wiethoff, Rüdiger

2009-10-01

This study investigates the influence of various femoral anterior cruciate ligament graft fixation methods on the amount of tension degradation and the initial fixation strength after cyclic flexion-extension loading in a porcine knee model. One hundred twenty porcine digital extensor tendons, used as 4-stranded free tendon grafts, were fixated within porcine femoral bone tunnels by use of extracortical button, cross-pin, or interference screw fixation. One hundred twenty porcine patellar tendon-bone grafts were fixated by use of cross-pin, interference screw, or press-fit fixation. Each femur-graft complex was submitted to cyclic flexion-extension loading for 1,000 cycles throughout different loading ranges, and the total loss of tension was determined. After cyclic testing, the grafts were loaded to failure, and the data were compared with a pullout series without cyclic loading. Tension degradation after 1,000 cycles of flexion-extension loading averaged 62.6% +/- 10.0% in free tendon grafts and 48.9% +/- 13.35% in patellar tendon-bone grafts. There was no influence of the loading range on the total amount of tension degradation. The total amount of tension degradation was the highest with interference screw fixation of free tendon and patellar tendon-bone grafts. Despite excessive loss of tension, the initial fixation strength of the femur-graft complex was not reduced. The method of femoral graft fixation significantly influenced tension degradation during dynamic flexion-extension loading. Femoral graft fixation methods that secure the graft close to the tunnel entrance and that displace the graft substance from the center of the bone tunnel show the largest amount of tension degradation during cyclic flexion-extension loading. The graft substance, not the fixation site, was the weakest link of the graft complex within this investigation. We believe that the graft fixation method should be considered when aiming to improve the precision of femoral graft placement in anterior cruciate ligament reconstruction.

Themes from variation: probing the commonalities of symbiotic associations.

PubMed

Saffo, Mary Beth

2002-04-01

Research on symbiosis (including antagonistic and mutualistic associations) wrestles, directly or indirectly, with the paradox: why are symbiotic associations so prevalent in the biosphere in the face of ubiquitous immune or antibiotic defenses among organisms? The symposium "Living Together: the Dynamics of Symbiotic Interactions" considered several questions: 1. How do symbiotic species partners come together? Do symbioses share similar patterns of signal recognition and response? 2. What roles do nutrients and metabolites play in symbiotic interactions, and how are metabolic exchanges affected by environmental changes? 3. In what ways do the dynamics of multispecies symbioses differ from two-species associations? 4. How do antagonistic (parasitic, pathogenic) symbioses differ from mutualistic ones? In what ways do changes in the biotic and physical environment affect the evolutionary balance of symbiotic associations? 5. What are the coevolutionary patterns of symbiotic associations? 6. Which research techniques, and strategies of experimental design, might be useful across a broad range of symbiotic associations?Two themes emerged from the symposium. First, all the participants have incorporated multiple techniques and perspectives into their work, approaches which facilitate the understanding of symbiotic dynamics at several levels of biological organization. Secondly, many of the papers addressed genetic and environmental variation in symbiotic interactions. Such approaches are useful tools for analysis of the mechanics of interspecies interactions and for characterization of the most important factors which influence them. They provide us with the tools to evaluate symbioses in a world of complexity, variation and change.

A novel dimerization interface of cyclic nucleotide binding domain, which is disrupted in presence of cAMP: implications for CNG channels gating.

PubMed

Gushchin, Ivan Y; Gordeliy, Valentin I; Grudinin, Sergei

2012-09-01

Cyclic nucleotide binding domain (CNBD) is a ubiquitous domain of effector proteins involved in signalling cascades of prokaryota and eukaryota. CNBD activation by cyclic nucleotide monophosphate (cNMP) is studied well in the case of several proteins. However, this knowledge is hardly applicable to cNMP-modulated cation channels. Despite the availability of CNBD crystal structures of bacterial cyclic nucleotide-gated (CNG) and mammalian hyperpolarization-activated cyclic nucleotide-modulated (HCN) channels in presence and absence of the cNMP, the full understanding of CNBD conformational changes during activation is lacking. Here, we describe a novel CNBD dimerization interface found in crystal structures of bacterial CNG channel MlotiK1 and mammalian cAMP-activated guanine nucleotide-exchange factor Epac2. Molecular dynamics simulations show that the found interface is stable on the studied timescale of 100 ns, in contrast to the dimerization interface, reported previously. Comparisons with cN-bound structures of CNBD show that the dimerization is incompatible with cAMP binding. Thus, the cAMP-dependent monomerization of CNBD may be an alternative mechanism of the cAMP sensing. Based on these findings, we propose a model of the bacterial CNG channel modulation by cAMP.

Dynamic actuation of a novel laser-processed NiTi linear actuator

NASA Astrophysics Data System (ADS)

Pequegnat, A.; Daly, M.; Wang, J.; Zhou, Y.; Khan, M. I.

2012-09-01

A novel laser processing technique, capable of locally modifying the shape memory effect, was applied to enhance the functionality of a NiTi linear actuator. By altering local transformation temperatures, an additional memory was imparted into a monolithic NiTi wire to enable dynamic actuation via controlled resistive heating. Characterizations of the actuator load, displacement and cyclic properties were conducted using a custom-built spring-biased test set-up. Monotonic tensile testing was also implemented to characterize the deformation behaviour of the martensite phase. Observed differences in the deformation behaviour of laser-processed material were found to affect the magnitude of the active strain. Furthermore, residual strain during cyclic actuation testing was found to stabilize after 150 cycles while the recoverable strain remained constant. This laser-processed actuator will allow for the realization of new applications and improved control methods for shape memory alloys.

Comparison of cyclic fatigue and torsional resistance in reciprocating single-file systems and continuous rotary instrumentation systems.

PubMed

da Frota, Matheus F; Espir, Camila G; Berbert, Fábio L C V; Marques, André A F; Sponchiado-Junior, Emílio C; Tanomaru-Filho, Mario; Garcia, Lucas F R; Bonetti-Filho, Idomeo

2014-12-01

As compared with continuous rotary systems, reciprocating motion is believed to increase the fatigue resistance of NiTi instruments. We compared the cyclic fatigue and torsional resistance of reciprocating single-file systems and continuous rotary instrumentation systems in simulated root canals. Eighty instruments from the ProTaper Universal, WaveOne, MTwo, and Reciproc systems (n = 20) were submitted to dynamic bending testing in stainless-steel simulated curved canals. Axial displacement of the simulated canals was performed with half of the instruments (n = 10), with back-and-forth movements in a range of 1.5 mm. Time until fracture was recorded, and the number of cycles until instrument fracture was calculated. Cyclic fatigue resistance was greater for reciprocating systems than for rotary systems (P < 0.05). Instruments from the Reciproc and WaveOne systems significantly differed only when axial displacement occurred (P < 0.05). Instruments of the ProTaper Universal and MTwo systems did not significantly differ (P > 0.05). Cyclic fatigue and torsional resistance were greater for reciprocating systems than for continuous rotary systems, irrespective of axial displacement.

3D DDD modelling of dislocation-precipitate interaction in a nickel-based single crystal superalloy under cyclic deformation

NASA Astrophysics Data System (ADS)

Lin, Bing; Huang, Minsheng; Zhao, Liguo; Roy, Anish; Silberschmidt, Vadim; Barnard, Nick; Whittaker, Mark; McColvin, Gordon

2018-06-01

Strain-controlled cyclic deformation of a nickel-based single crystal superalloy has been modelled using three-dimensional (3D) discrete dislocation dynamics (DDD) for both [0 0 1] and [1 1 1] orientations. The work focused on the interaction between dislocations and precipitates during cyclic plastic deformation at elevated temperature, which has not been well studied yet. A representative volume element with cubic γ‧-precipitates was chosen to represent the material, with enforced periodical boundary conditions. In particular, cutting of superdislocations into precipitates was simulated by a back-force method. The global cyclic stress-strain responses were captured well by the DDD model when compared to experimental data, particularly the effects of crystallographic orientation. Dislocation evolution showed that considerably high density of dislocations was produced for [1 1 1] orientation when compared to [0 0 1] orientation. Cutting of dislocations into the precipitates had a significant effect on the plastic deformation, leading to material softening. Contour plots of in-plane shear strain proved the development of heterogeneous strain field, resulting in the formation of shear-band embryos.

Restructuring of Educational Systems in the Digital Age from a Co-Evolutionary Perspective

ERIC Educational Resources Information Center

Davis, N.; Eickelmann, B.; Zaka, P.

2013-01-01

There have been repeated calls for restructuring of schooling to take advantage of information and communication technologies (ICT). This article recognizes an increasing range of radical restructuring resulting from the co-evolution of education and digital technologies in school systems and related activity in the global ecosystem. Research of…

A survey of the foliar and soil arthropod communities in sunflower (Helianthus annuus) fields in central and eastern South Dakota

USDA-ARS?s Scientific Manuscript database

The long coevolutionary history between sunflowers (Helianthus annuus, Asterales: Asteraceae) and arthropods in the Northern Great Plains has resulted in a commonly grown oilseed crop that harbors a large diversity of insects. A bioenventory of foliar and subterranean arthropods was performed in 22 ...

Sexual selection modulates genetic conflicts and patterns of genomic imprinting.

PubMed

Faria, Gonçalo S; Varela, Susana A M; Gardner, Andy

2017-03-01

Recent years have seen a surge of interest in linking the theories of kin selection and sexual selection. In particular, there is a growing appreciation that kin selection, arising through demographic factors such as sex-biased dispersal, may modulate sexual conflicts, including in the context of male-female arms races characterized by coevolutionary cycles. However, evolutionary conflicts of interest need not only occur between individuals, but may also occur within individuals, and sex-specific demography is known to foment such intragenomic conflict in relation to social behavior. Whether and how this logic holds in the context of sexual conflict-and, in particular, in relation to coevolutionary cycles-remains obscure. We develop a kin-selection model to investigate the interests of different genes involved in sexual and intragenomic conflict, and we show that consideration of these conflicting interests yields novel predictions concerning parent-of-origin specific patterns of gene expression and the detrimental effects of different classes of mutation and epimutation at loci underpinning sexually selected phenotypes. © 2016 The Author(s). Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

Reciprocal selection causes a coevolutionary arms race between crossbills and lodgepole pine.

PubMed

Benkman, Craig W; Parchman, Thomas L; Favis, Amanda; Siepielski, Adam M

2003-08-01

Few studies have shown both reciprocal selection and reciprocal adaptations for a coevolving system in the wild. The goal of our study was to determine whether the patterns of selection on Rocky Mountain lodgepole pine (Pinus contorta spp. latifolia) and red crossbills (Loxia curvirostra complex) were concordant with earlier published evidence of reciprocal adaptations in lodgepole pine and crossbills on isolated mountain ranges in the absence of red squirrels (Tamiasciurus hudsonicus). We found that selection (directional) by crossbills on lodgepole pine where Tamiasciurus are absent was divergent from the selection (directional) exerted by Tamiasciurus on lodgepole pine. This resulted in divergent selection between areas with and without Tamiasciurus that was congruent with the geographic patterns of cone variation. In the South Hills, Idaho, where Tamiasciurus are absent and red crossbills are thought to be coevolving with lodgepole pine, crossbills experienced stabilizing selection on bill size, with cone structure as the agent of selection. These results show that crossbills and lodgepole pine exhibit reciprocal adaptations in response to reciprocal selection, and they provide insight into the traits mediating and responding to selection in a coevolutionary arms race.

Escalation of a coevolutionary arms race through host rejection of brood parasitic young.

PubMed

Langmore, Naomi E; Hunt, Sarah; Kilner, Rebecca M

2003-03-13

Cuckoo nestlings that evict all other young from the nest soon after hatching impose a high reproductive cost on their hosts. In defence, hosts have coevolved strategies to prevent brood parasitism. Puzzlingly, they do not extend beyond the egg stage. Thus, hosts adept at recognizing foreign eggs remain vulnerable to exploitation by cuckoo nestlings. Here we show that the breach of host egg defences by cuckoos creates a new stage in the coevolutionary cycle. We found that defences used during the egg-laying period by host superb fairy-wrens (Malurus cyaneus) are easily evaded by the Horsfield's bronze-cuckoo (Chrysococcyx basalis), a specialist fairy-wren brood parasite. However, although hosts never deserted their own broods, they later abandoned 40% of nests containing a lone Horsfield's bronze-cuckoo nestling, and 100% of nests with a lone shining bronze-cuckoo nestling (Chrysococcyx lucidus), an occasional fairy-wren brood parasite. Our experiments demonstrate that host discrimination against evictor-cuckoo nestlings is possible, and suggest that it has selected for the evolution of nestling mimicry in bronze-cuckoos.

A further analysis of the role of heterogeneity in coevolutionary spatial games

NASA Astrophysics Data System (ADS)

Cardinot, Marcos; Griffith, Josephine; O'Riordan, Colm

2018-03-01

Heterogeneity has been studied as one of the most common explanations of the puzzle of cooperation in social dilemmas. A large number of papers have been published discussing the effects of increasing heterogeneity in structured populations of agents, where it has been established that heterogeneity may favour cooperative behaviour if it supports agents to locally coordinate their strategies. In this paper, assuming an existing model of a heterogeneous weighted network, we aim to further this analysis by exploring the relationship (if any) between heterogeneity and cooperation. We adopt a weighted network which is fully populated by agents playing both the Prisoner's Dilemma or the Optional Prisoner's Dilemma games with coevolutionary rules, i.e., not only the strategies but also the link weights evolve over time. Surprisingly, results show that the heterogeneity of link weights (states) on their own does not always promote cooperation; rather cooperation is actually favoured by the increase in the number of overlapping states and not by the heterogeneity itself. We believe that these results can guide further research towards a more accurate analysis of the role of heterogeneity in social dilemmas.

Coevolutionary Free Lunches

NASA Technical Reports Server (NTRS)

Wolpert, David H.; Macready, William G.

2005-01-01

Recent work on the foundations of optimization has begun to uncover its underlying rich structure. In particular, the "No Free Lunch" (NFL) theorems [WM97] state that any two algorithms are equivalent when their performance is averaged across all possible problems. This highlights the need for exploiting problem-specific knowledge to achieve better than random performance. In this paper we present a general framework covering most search scenarios. In addition to the optimization scenarios addressed in the NFL results, this framework covers multi-armed bandit problems and evolution of multiple co-evolving agents. As a particular instance of the latter, it covers "self-play" problems. In these problems the agents work together to produce a champion, who then engages one or more antagonists in a subsequent multi-player game In contrast to the traditional optimization case where the NFL results hold, we show that in self-play there are free lunches: in coevolution some algorithms have better performance than other algorithms, averaged across all possible problems. However in the typical coevolutionary scenarios encountered in biology, where there is no champion, NFL still holds.

Analyzing the dynamics of cell cycle processes from fixed samples through ergodic principles

PubMed Central

Wheeler, Richard John

2015-01-01

Tools to analyze cyclical cellular processes, particularly the cell cycle, are of broad value for cell biology. Cell cycle synchronization and live-cell time-lapse observation are widely used to analyze these processes but are not available for many systems. Simple mathematical methods built on the ergodic principle are a well-established, widely applicable, and powerful alternative analysis approach, although they are less widely used. These methods extract data about the dynamics of a cyclical process from a single time-point “snapshot” of a population of cells progressing through the cycle asynchronously. Here, I demonstrate application of these simple mathematical methods to analysis of basic cyclical processes—cycles including a division event, cell populations undergoing unicellular aging, and cell cycles with multiple fission (schizogony)—as well as recent advances that allow detailed mapping of the cell cycle from continuously changing properties of the cell such as size and DNA content. This includes examples using existing data from mammalian, yeast, and unicellular eukaryotic parasite cell biology. Through the ongoing advances in high-throughput cell analysis by light microscopy, electron microscopy, and flow cytometry, these mathematical methods are becoming ever more important and are a powerful complementary method to traditional synchronization and time-lapse cell cycle analysis methods. PMID:26543196

Structure of 1-alkyl-1-methylpyrrolidinium bis(trifluoromethylsulfonyl)amide ionic liquids with linear, branched, and cyclic alkyl groups.

PubMed

Kashyap, Hemant K; Santos, Cherry S; Murthy, N Sanjeeva; Hettige, Jeevapani J; Kerr, Kijana; Ramati, Sharon; Gwon, JinHee; Gohdo, Masao; Lall-Ramnarine, Sharon I; Wishart, James F; Margulis, Claudio J; Castner, Edward W

2013-12-12

X-ray scattering and molecular dynamics simulations have been carried out to investigate structural differences and similarities in the condensed phase between pyrrolidinium-based ionic liquids paired with the bis(trifluoromethylsulfonyl)amide (NTf2(-)) anion where the cationic tail is linear, branched, or cyclic. This is important in light of the charge and polarity type alternations that have recently been shown to be present in the case of liquids with cations of moderately long linear tails. For this study, we have chosen to use the 1-alkyl-1-methylpyrrolidinium, Pyrr(1,n(+)) with n = 5 or 7, as systems with linear tails, 1-(2-ethylhexyl)-1-methylpyrrolidinium, Pyrr(1,EtHx(+)), as a system with a branched tail, and 1-(cyclohexylmethyl)-1-methylpyrrolidinium, Pyrr(1,ChxMe(+)), as a system with a cyclic tail. We put these results into context by comparing these data with recently published results for the Pyrr(1,n(+))/NTf2(-) ionic liquids with n = 4, 6, 8, and 10.1,2 General methods for interpreting the structure function S(q) in terms of q-dependent natural partitionings are described. This allows for an in-depth analysis of the scattering data based on molecular dynamics (MD) trajectories that highlight the effect of modifying the cationic tail.

The development and validation of a numerical integration method for non-linear viscoelastic modeling

PubMed Central

Ramo, Nicole L.; Puttlitz, Christian M.

2018-01-01

Compelling evidence that many biological soft tissues display both strain- and time-dependent behavior has led to the development of fully non-linear viscoelastic modeling techniques to represent the tissue’s mechanical response under dynamic conditions. Since the current stress state of a viscoelastic material is dependent on all previous loading events, numerical analyses are complicated by the requirement of computing and storing the stress at each step throughout the load history. This requirement quickly becomes computationally expensive, and in some cases intractable, for finite element models. Therefore, we have developed a strain-dependent numerical integration approach for capturing non-linear viscoelasticity that enables calculation of the current stress from a strain-dependent history state variable stored from the preceding time step only, which improves both fitting efficiency and computational tractability. This methodology was validated based on its ability to recover non-linear viscoelastic coefficients from simulated stress-relaxation (six strain levels) and dynamic cyclic (three frequencies) experimental stress-strain data. The model successfully fit each data set with average errors in recovered coefficients of 0.3% for stress-relaxation fits and 0.1% for cyclic. The results support the use of the presented methodology to develop linear or non-linear viscoelastic models from stress-relaxation or cyclic experimental data of biological soft tissues. PMID:29293558

How does selfing affect the dynamics of selfish transposable elements?

PubMed

Boutin, Thibaud S; Le Rouzic, Arnaud; Capy, Pierre

2012-03-07

Many theoretical models predicting the dynamics of transposable elements (TEs) in genomes, populations, and species have already been proposed. However, most of them only focus on populations of sexual diploid individuals, and TE dynamics in populations partly composed by autogamous individuals remains poorly investigated. To estimate the impact of selfing on TE dynamics, the short- and long-term evolution of TEs was simulated in outcrossing populations with various proportions of selfing individuals. Selfing has a deep impact on TE dynamics: the higher the selfing rate, the lower the probability of invasion. Already known non-equilibrium dynamics (complete loss, domestication, cyclical invasion of TEs) can all be described whatever the mating system. However, their pattern and their respective frequencies greatly depend on the selfing rate. For instance, in cyclical dynamics resulting from interactions between autonomous and non-autonomous copies, cycles are faster when the selfing rate increases. Interestingly, an abrupt change in the mating system from sexuality to complete asexuality leads to the loss of all the elements over a few hundred generations. In general, for intermediate selfing rates, the transposition activity remains maintained. Our theoretical results evidence that a clear and systematic contrast in TE content according to the mating system is expected, with a smooth transition for intermediate selfing rates. Several parameters impact the TE copy number, and all dynamics described in allogamous populations can be also observed in partly autogamous species. This study thus provides new insights to understand the complex signal from empirical comparison of closely related species with different mating systems.

Assessment of surface relief and short cracks under cyclic creep in a type 316LN austenitic stainless steel

NASA Astrophysics Data System (ADS)

Sarkar, Aritra; Nagesha, A.; Parameswaran, P.; Sandhya, R.; Laha, K.

2015-12-01

Formation of surface relief and short cracks under cyclic creep (stress-controlled fatigue) in type 316LN stainless steel was studied at temperatures ranging from ambient to 923 K using scanning electron microscopy technique. The surface topography and crack distribution behaviour under cyclic creep were found to be strong functions of testing temperature due to the difference in strain accumulation. At 823 K, surface relief mainly consisted of fine slip markings due to negligible accumulation of strain as a consequence of dynamic strain ageing (DSA) which led to an increase in the cyclic life. Persistent slip markings (PSM) with distinct extrusions containing minute cracks were seen to prevail in the temperature range 873-923 K, indicating a higher slip activity causing higher strain accumulation in the absence of DSA. Besides, a large number of secondary cracks (both transgranular and intergranular) which were partially accentuated by severe oxidation, were observed. Extensive cavitation-induced grain boundary cracking took place at 923 K, which coalesced with PSM-induced transgranular cracks resulting in failure dominated by creep that in turn led to a drastic reduction in cyclic life. Investigations on the influence of stress rate were also carried out which underlined the presence of DSA at 823 K. At 923 K, lowering the stress rate caused further strengthening of the contribution from creep damage marked by a shift in the damage mechanism from cyclic slip to diffusion.

The Wacker oxidation of allyl alcohol along cyclic-intermediate routes: An ab initio molecular dynamics investigation

NASA Astrophysics Data System (ADS)

Imandi, Venkataramana; Nair, Nisanth N.

2016-09-01

The absence of isotope scrambling observed by Henry and coworkers in the Wacker oxidation of deuterated allylic alcohol was used by them as support for the inner-sphere mechanism hydroxypalladation mechanism. One of the assumptions used to interpret their experimental data was that allyl alcohol oxidation takes place through non-cyclic intermediate routes as in the case of ethene. Here we verify this assumption through ab initio metadynamics simulations of the Wacker oxidation of allyl alcohol in explicit solvent. Importance of our results in interpreting the isotope scrambling experiments is discussed.

Effect of ion-beam treatment on structure and fracture resistance of 12Cr1MoV steel under static, cyclic and dynamic loading

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

Panin, S. V., E-mail: svp@ispms.tsc.ru; Vlasov, I. V., E-mail: good0@yandex.ru; Sergeev, V. P., E-mail: retc@ispms.tsc.ru

2015-10-27

Features of the structure and properties modification of 12Cr1MoV steel subjected to irradiation by zirconium ion beam have been investigated with the use of optical and electron microscopy as well as microhardness measurement. It has been shown that upon treatment the structure modification occurred across the entire cross-section of specimens with the thickness of 1 mm. Changes in the mechanical properties of these specimens under static, cyclic and impact loading are interpreted in terms of identified structure changes.

The Crystal Structures of Apo and cAMP-Bound GlxR from Corynebacterium glutamicum Reveal Structural and Dynamic Changes upon cAMP Binding in CRP/FNR Family Transcription Factors

PubMed Central

Townsend, Philip D.; Jungwirth, Britta; Pojer, Florence; Bußmann, Michael; Money, Victoria A.; Cole, Stewart T.; Pühler, Alfred; Tauch, Andreas; Bott, Michael; Cann, Martin J.; Pohl, Ehmke

2014-01-01

The cyclic AMP-dependent transcriptional regulator GlxR from Corynebacterium glutamicum is a member of the super-family of CRP/FNR (cyclic AMP receptor protein/fumarate and nitrate reduction regulator) transcriptional regulators that play central roles in bacterial metabolic regulatory networks. In C. glutamicum, which is widely used for the industrial production of amino acids and serves as a non-pathogenic model organism for members of the Corynebacteriales including Mycobacterium tuberculosis, the GlxR homodimer controls the transcription of a large number of genes involved in carbon metabolism. GlxR therefore represents a key target for understanding the regulation and coordination of C. glutamicum metabolism. Here we investigate cylic AMP and DNA binding of GlxR from C. glutamicum and describe the crystal structures of apo GlxR determined at a resolution of 2.5 Å, and two crystal forms of holo GlxR at resolutions of 2.38 and 1.82 Å, respectively. The detailed structural analysis and comparison of GlxR with CRP reveals that the protein undergoes a distinctive conformational change upon cyclic AMP binding leading to a dimer structure more compatible to DNA-binding. As the two binding sites in the GlxR homodimer are structurally identical dynamic changes upon binding of the first ligand are responsible for the allosteric behavior. The results presented here show how dynamic and structural changes in GlxR lead to optimization of orientation and distance of its two DNA-binding helices for optimal DNA recognition. PMID:25469635

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

PubMed

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

2013-01-01

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

Complex coevolutionary history of symbiotic Bacteroidales bacteria of various protists in the gut of termites

PubMed Central

Noda, Satoko; Hongoh, Yuichi; Sato, Tomoyuki; Ohkuma, Moriya

2009-01-01

Background The microbial community in the gut of termites is responsible for the efficient decomposition of recalcitrant lignocellulose. Prominent features of this community are its complexity and the associations of prokaryotes with the cells of cellulolytic flagellated protists. Bacteria in the order Bacteroidales are involved in associations with a wide variety of gut protist species as either intracellular endosymbionts or surface-attached ectosymbionts. In particular, ectosymbionts exhibit distinct morphological patterns of the associations. Therefore, these Bacteroidales symbionts provide an opportunity to investigate not only the coevolutionary relationships with the host protists and their morphological evolution but also how symbiotic associations between prokaryotes and eukaryotes occur and evolve within a complex symbiotic community. Results Molecular phylogeny of 31 taxa of Bacteroidales symbionts from 17 protist genera in 10 families was examined based on 16S rRNA gene sequences. Their localization, morphology, and specificity were also examined by fluorescent in situ hybridizations. Although a monophyletic grouping of the ectosymbionts occurred in three related protist families, the symbionts of different protist genera were usually dispersed among several phylogenetic clusters unique to termite-gut bacteria. Similar morphologies of the associations occurred in multiple lineages of the symbionts. Nevertheless, the symbionts of congeneric protist species were closely related to one another, and in most cases, each host species harbored a unique Bacteroidales species. The endosymbionts were distantly related to the ectosymbionts examined so far. Conclusion The coevolutionary history of gut protists and their associated Bacteroidales symbionts is complex. We suggest multiple independent acquisitions of the Bacteroidales symbionts by different protist genera from a pool of diverse bacteria in the gut community. In this sense, the gut could serve as a reservoir of diverse bacteria for associations with the protist cells. The similar morphologies are considered a result of evolutionary convergence. Despite the complicated evolutionary history, the host-symbiont relationships are mutually specific, suggesting their cospeciations at the protist genus level with only occasional replacements. PMID:19586555

Type III Effector Diversification via Both Pathoadaptation and Horizontal Transfer in Response to a Coevolutionary Arms Race

PubMed Central

Ma, Wenbo; Dong, Frederick F. T; Stavrinides, John; Guttman, David S

2006-01-01

The concept of the coevolutionary arms race holds a central position in our understanding of pathogen–host interactions. Here we identify the molecular mechanisms and follow the stepwise progression of an arms race in a natural system. We show how the evolution and function of the HopZ family of type III secreted effector proteins carried by the plant pathogen Pseudomonas syringae are influenced by a coevolutionary arms race between pathogen and host. We surveyed 96 isolates of P. syringae and identified three homologs (HopZ1, HopZ2, and HopZ3) distributed among ∼45% of the strains. All alleles were sequenced and their expression was confirmed. Evolutionary analyses determined that the diverse HopZ1 homologs are ancestral to P. syringae, and have diverged via pathoadaptive mutational changes into three functional and two degenerate forms, while HopZ2 and HopZ3 have been brought into P. syringae via horizontal transfer from other ecologically similar bacteria. A PAML selection analysis revealed that the C terminus of HopZ1 is under strong positive selection. Despite the extensive genetic variation observed in this family, all three homologs have cysteine–protease activity, although their substrate specificity may vary. The introduction of the ancestral hopZ1 allele into strains harboring alternate alleles results in a resistance protein-mediated defense response in their respective hosts, which is not observed with the endogenous allele. These data indicate that the P. syringae HopZ family has undergone allelic diversification via both pathoadaptive mutational changes and horizontal transfer in response to selection imposed by the host defense system. This genetic diversity permits the pathogen to avoid host defenses while still maintaining a virulence-associated protease, thereby allowing it to thrive on its current host, while simultaneously impacting its host range. PMID:17194219

From engineering hydrology to Earth system science: milestones in the transformation of hydrologic science

NASA Astrophysics Data System (ADS)

Sivapalan, Murugesu

2018-03-01

Hydrology has undergone almost transformative changes over the past 50 years. Huge strides have been made in the transition from early empirical approaches to rigorous approaches based on the fluid mechanics of water movement on and below the land surface. However, progress has been hampered by problems posed by the presence of heterogeneity, including subsurface heterogeneity present at all scales. The inability to measure or map the heterogeneity everywhere prevented the development of balance equations and associated closure relations at the scales of interest, and has led to the virtual impasse we are presently in, in terms of development of physically based models needed for hydrologic predictions. An alternative to the mapping of heterogeneity everywhere is a new Earth system science view, which sees the heterogeneity as the end result of co-evolutionary hydrological, geomorphological, ecological, and pedological processes, each operating at a different rate, which help to shape the landscapes that we find in nature, including the heterogeneity that we do not readily see. The expectation is that instead of specifying exact details of the heterogeneity in our models, we can replace it (without loss of information) with the ecosystem function that they perform. Guided by this new Earth system science perspective, development of hydrologic science is now addressing new questions using novel holistic co-evolutionary approaches as opposed to the physical, fluid mechanics based reductionist approaches that we inherited from the recent past. In the emergent Anthropocene, the co-evolutionary view has expanded further to involve interactions and feedbacks with human-social processes as well. In this paper, I present my own perspective of key milestones in the transformation of hydrologic science from engineering hydrology to Earth system science, drawn from the work of several students and colleagues of mine, and discuss their implication for hydrologic observations, theory development, and predictions.

Diversity patterns amongst herbivorous dinosaurs and plants during the Cretaceous: implications for hypotheses of dinosaur/angiosperm co-evolution.

PubMed

Butler, R J; Barrett, P M; Kenrick, P; Penn, M G

2009-03-01

Palaeobiologists frequently attempt to identify examples of co-evolutionary interactions over extended geological timescales. These hypotheses are often intuitively appealing, as co-evolution is so prevalent in extant ecosystems, and are easy to formulate; however, they are much more difficult to test than their modern analogues. Among the more intriguing deep time co-evolutionary scenarios are those that relate changes in Cretaceous dinosaur faunas to the primary radiation of flowering plants. Demonstration of temporal congruence between the diversifications of co-evolving groups is necessary to establish whether co-evolution could have occurred in such cases, but is insufficient to prove whether it actually did take place. Diversity patterns do, however, provide a means for falsifying such hypotheses. We have compiled a new database of Cretaceous dinosaur and plant distributions from information in the primary literature. This is used as the basis for plotting taxonomic diversity and occurrence curves for herbivorous dinosaurs (Sauropodomorpha, Stegosauria, Ankylosauria, Ornithopoda, Ceratopsia, Pachycephalosauria and herbivorous theropods) and major groups of plants (angiosperms, Bennettitales, cycads, cycadophytes, conifers, Filicales and Ginkgoales) that co-occur in dinosaur-bearing formations. Pairwise statistical comparisons were made between various floral and faunal groups to test for any significant similarities in the shapes of their diversity curves through time. We show that, with one possible exception, diversity patterns for major groups of herbivorous dinosaurs are not positively correlated with angiosperm diversity. In other words, at the level of major clades, there is no support for any diffuse co-evolutionary relationship between herbivorous dinosaurs and flowering plants. The diversification of Late Cretaceous pachycephalosaurs (excluding the problematic taxon Stenopelix) shows a positive correlation, but this might be spuriously related to poor sampling in the Turonian-Santonian interval. Stegosauria shows a significant negative correlation with flowering plants and a significant positive correlation with the nonflowering cycadophytes (cycads, Bennettitales). This interesting pattern is worthy of further investigation, and it reflects the decline of both stegosaurs and cycadophytes during the Early Cretaceous.

The Conundrum of Modern Art : Prestige-Driven Coevolutionary Aesthetics Trumps Evolutionary Aesthetics among Art Experts.

PubMed

Verpooten, Jan; Dewitte, Siegfried

2017-03-01

Two major mechanisms of aesthetic evolution have been suggested. One focuses on naturally selected preferences (Evolutionary Aesthetics), while the other describes a process of evaluative coevolution whereby preferences coevolve with signals. Signaling theory suggests that expertise moderates these mechanisms. In this article we set out to verify this hypothesis in the domain of art and use it to elucidate Western modern art's deviation from naturally selected preferences. We argue that this deviation is consistent with a Coevolutionary Aesthetics mechanism driven by prestige-biased social learning among art experts. In order to test this hypothesis, we conducted two studies in which we assessed the effects on lay and expert appreciation of both the biological relevance of the given artwork's depicted content, viz., facial beauty, and the prestige specific to the artwork's associated context (MoMA). We found that laypeople appreciate artworks based on their depictions of facial beauty, mediated by aesthetic pleasure, which is consistent with previous studies. In contrast, experts appreciate the artworks based on the prestige of the associated context, mediated by admiration for the artist. Moreover, experts appreciate artworks depicting neutral faces to a greater degree than artworks depicting attractive faces. These findings thus corroborate our contention that expertise moderates the Evolutionary and Coevolutionary Aesthetics mechanisms in the art domain. Furthermore, our findings provide initial support for our proposal that prestige-driven coevolution with expert evaluations plays a decisive role in modern art's deviation from naturally selected preferences. After discussing the limitations of our research as well as the relation that our results bear on cultural evolution theory, we provide a number of suggestions for further research into the potential functions of expert appreciation that deviates from naturally selected preferences, on the one hand, and expertise as a moderator of these mechanisms in other cultural domains, on the other.

Accelerated Dynamic Corrosion Test Method Development

DTIC Science & Technology

test method has poor correlation to outdoor exposures, particularly for non-chromate primers. As a result, more realistic cyclic environmental...exposures have been developed to more closely resemble actual atmospheric corrosion damage. Several existing tests correlate well with the outdoor performance

Exploring the efficacy of cyclic vs static aspiration in a cerebral thrombectomy model: an initial proof of concept study.

PubMed

Simon, Scott; Grey, Casey Paul; Massenzo, Trisha; Simpson, David G; Longest, P Worth

2014-11-01

Current technology for endovascular thrombectomy in ischemic stroke utilizes static loading and is successful in approximately 85% of cases. Existing technology uses either static suction (applied via a continuous pump or syringe) or flow arrest with a proximal balloon. In this paper we evaluate the potential of cyclic loading in aspiration thrombectomy. In order to evaluate the efficacy of cyclic aspiration, a model was created using a Penumbra aspiration system, three-way valve and Penumbra 5Max catheter. Synthetic clots were aspirated at different frequencies and using different aspiration mediums. Success or failure of clot removal and time were recorded. All statistical analyses were based on either a one-way or two-way analysis of variance, Holm-Sidak pairwise multiple comparison procedure (α=0.05). Cyclic aspiration outperformed static aspiration in overall clot removal and removal speed (p<0.001). Within cyclic aspiration, Max Hz frequencies (∼6.3 Hz) cleared clots faster than 1 Hz (p<0.001) and 2 Hz (p=0.024). Loading cycle dynamics (specific pressure waveforms) affected speed and overall clearance (p<0.001). Water as the aspiration medium was more effective at clearing clots than air (p=0.019). Cyclic aspiration significantly outperformed static aspiration in speed and overall clearance of synthetic clots in our experimental model. Within cyclic aspiration, efficacy is improved by increasing cycle frequency, utilizing specific pressure cycle waveforms and using water rather than air as the aspiration medium. These findings provide a starting point for altering existing thrombectomy technology or perhaps the development of new technologies with higher recanalization rates. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions.

PubMed

Duneau, David; Luijckx, Pepijn; Ben-Ami, Frida; Laforsch, Christian; Ebert, Dieter

2011-02-22

Infection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them. Using the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes. Our results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary cycles. We discuss how different steps can explain different aspects of the coevolutionary dynamics of the system: the properties of the attachment step, explaining the rapid evolution of infectivity and the properties of later parasite proliferation explaining the evolution of virulence. Our study underlines the importance of resolving the infection process in order to better understand host-parasite interactions.

Carbon nanorings with inserted acenes: Breaking symmetry in excited state dynamics

DOE PAGES

Franklin-Mergarejo, R.; Alvarez, D. Ondarse; Tretiak, S.; ...

2016-08-10

Conjugated cycloparaphenylene rings have unique electronic properties being the smallest segments of carbon nanotubes. Their conjugated backbones support delocalized electronic excitations, which dynamics is strongly influenced by cyclic geometry. Here we present a comparative theoretical study of the electronic and vibrational energy relaxation and redistribution in photoexcited cycloparaphenylene carbon nanorings with inserted naphthalene, anthracene, and tetracene units using non-adiabatic excited-state molecular dynamics simulations. Calculated excited state structures reflect modifications of optical selection rules and appearance of low-energy electronic states localized on the acenes due to gradual departure from a perfect circular symmetry. After photoexcitation, an ultrafast electronic energy relaxation tomore » the lowest excited state is observed on the time scale of hundreds of femtoseconds in all molecules studied. Concomitantly, the efficiency of the exciton trapping in the acene raises when moving from naphthalene to anthracene and to tetracene, being negligible in naphthalene, and ~60% and 70% in anthracene and tetracene within the first 500 fs after photoexcitation. Observed photoinduced dynamics is further analyzed in details using induced molecular distortions, delocatization properties of participating electronic states and non-adiabatic coupling strengths. Lastly, our results provide a number of insights into design of cyclic molecular systems for electronic and light-harvesting applications.« less

Autogenic dynamics of debris-flow fans

NASA Astrophysics Data System (ADS)

van den Berg, Wilco; de Haas, Tjalling; Braat, Lisanne; Kleinhans, Maarten

2015-04-01

Alluvial fans develop their semi-conical shape by cyclic avulsion of their geomorphologically active sector from a fixed fan apex. These cyclic avulsions have been attributed to both allogenic and autogenic forcings and processes. Autogenic dynamics have been extensively studied on fluvial fans through physical scale experiments, and are governed by cyclic alternations of aggradation by unconfined sheet flow, fanhead incision leading to channelized flow, channel backfilling and avulsion. On debris-flow fans, however, autogenic dynamics have not yet been directly observed. We experimentally created debris-flow fans under constant extrinsic forcings, and show that autogenic dynamics are a fundamental intrinsic process on debris-flow fans. We found that autogenic cycles on debris-flow fans are driven by sequences of backfilling, avulsion and channelization, similar to the cycles on fluvial fans. However, the processes that govern these sequences are unique for debris-flow fans, and differ fundamentally from the processes that govern autogenic dynamics on fluvial fans. We experimentally observed that backfilling commenced after the debris flows reached their maximum possible extent. The next debris flows then progressively became shorter, driven by feedbacks on fan morphology and flow-dynamics. The progressively decreasing debris-flow length caused in-channel sedimentation, which led to increasing channel overflow and wider debris flows. This reduced the impulse of the liquefied flow body to the flow front, which then further reduced flow velocity and runout length, and induced further in-channel sedimentation. This commenced a positive feedback wherein debris flows became increasingly short and wide, until the channel was completely filled and the apex cross-profile was plano-convex. At this point, there was no preferential transport direction by channelization, and the debris flows progressively avulsed towards the steepest, preferential, flow path. Simultaneously, the debris flows started to channelize, forced by increasingly effective concentration of the flow impulse to the flow front, which caused more effective lateral levee formation and an increasingly well-defined channel. This process continued until the debris flows reached their maximum possible extent and the cycle was reverted. Channelization occurred in the absence of erosion, in contrast with fluvial fans. Backfilling and channelization cycles were gradual and symmetric, requiring multiple debris flows to be completed. These results add debris-flow fans to the spectrum of fan-shaped aqueous systems that are affected by autogenic dynamics, now ranging from low-gradient rivers systems to steep-gradient mass-flow fans.

The interplay between seasonality and density: consequences for female breeding decisions in a small cyclic herbivore

PubMed Central

2014-01-01

Background Cyclic rodent population dynamics are subjected to both intrinsic regulatory processes such as density-dependence and extrinsic environmental forcing. Among extrinsic factors, seasonal environmental variation is understood to facilitate cycles. In rodents, these processes have been studied mostly independently and their relative importance for population dynamics is poorly known. Results We performed a detailed analysis of common vole (Microtus arvalis) reproduction in a cyclic population using a spatially extensive data set over 17 years in central-western France. Environmental seasonality was the main source of explained variation in common vole reproduction. Additionally, inter-annual variation in the environment explained a smaller part of the variance in reproduction in spring and summer than in winter, whereas the effect of density was only found in autumn and winter. In particular, we detected a strong impact of plant productivity on fecundity during the breeding season, with low vegetation productivity being able to bring vole reproduction nearly to a halt. In contrast, vole reproduction during autumn and winter was mainly shaped by intrinsic factors, with only the longer and heavier females being able to reproduce. The effect of population density on reproduction was negative, mediated by direct negative effects on the proportion of breeders in autumn and winter during outbreak years and by a delayed negative effect on litter size the following year. Conclusions During the main breeding season, variability of female vole reproduction is predominantly shaped by food resources, suggesting that only highly productive environment may induce vole outbreaks. During fall and winter, variability of female vole reproduction is mainly controlled by intrinsic factors, with high population density suppressing reproduction. This suggests, in this cyclic population, that negative direct density dependence on reproduction could explain winter declines after outbreaks. PMID:24886481

The interplay between seasonality and density: consequences for female breeding decisions in a small cyclic herbivore.

PubMed

Pinot, Adrien; Gauffre, Bertrand; Bretagnolle, Vincent

2014-05-28

Cyclic rodent population dynamics are subjected to both intrinsic regulatory processes such as density-dependence and extrinsic environmental forcing. Among extrinsic factors, seasonal environmental variation is understood to facilitate cycles. In rodents, these processes have been studied mostly independently and their relative importance for population dynamics is poorly known. We performed a detailed analysis of common vole (Microtus arvalis) reproduction in a cyclic population using a spatially extensive data set over 17 years in central-western France. Environmental seasonality was the main source of explained variation in common vole reproduction. Additionally, inter-annual variation in the environment explained a smaller part of the variance in reproduction in spring and summer than in winter, whereas the effect of density was only found in autumn and winter. In particular, we detected a strong impact of plant productivity on fecundity during the breeding season, with low vegetation productivity being able to bring vole reproduction nearly to a halt. In contrast, vole reproduction during autumn and winter was mainly shaped by intrinsic factors, with only the longer and heavier females being able to reproduce. The effect of population density on reproduction was negative, mediated by direct negative effects on the proportion of breeders in autumn and winter during outbreak years and by a delayed negative effect on litter size the following year. During the main breeding season, variability of female vole reproduction is predominantly shaped by food resources, suggesting that only highly productive environment may induce vole outbreaks. During fall and winter, variability of female vole reproduction is mainly controlled by intrinsic factors, with high population density suppressing reproduction. This suggests, in this cyclic population, that negative direct density dependence on reproduction could explain winter declines after outbreaks.

Persistent explosive activity at Stromboli investigated with OP-FTIR and SO2 cameras

NASA Astrophysics Data System (ADS)

Burton, M. R.; La Spina, A.; Sawyer, G. M.; Harris, A. J.

2012-12-01

Stromboli volcano in Italy exhibits what is perhaps one of the most well-known examples of cyclic activity, in the form of its regular explosions, which send a few m3 of material 100-200 m into the air every 10-20 minutes. Recent developments in measurements of volatile release from Stromboli using a series of novel approaches have allowed this cyclic behaviour to be examined in detail. In particular, the use of an automated OP-FTIR has revealed unprecedented detail in the dynamics of degassing from individual craters at the summit of Stromboli. Furthermore, the variations in composition of explosive degassing from Stromboli demonstrate a deep source ~2 km for the gas slugs which produce explosions at this volcano, in contrast to the commonly-held view that gas coalescence at shallow depth is responsible for the behaviour. The SO2 camera has revealed fascinating new details on the dynamics of degassing at Stromboli, and has allowed direct quantification of the amount of gas released during explosions and through quiescent degassing. The remarkable observation that 99% of degassing takes place quiescently, and that the explosions, whilst apparently more significant, are in fact a secondary process compared with the mass and energy involved in background, quiet processes. The new insight that the explosions are actually only a relatively minor aspect of the activity (in terms of mass and energy) actually makes the regularity of the cyclic explosive activity still more remarkable. In this paper we present a detailed overview of the state of the art of our understanding of cyclic explosive activity at Stromboli volcano from the perspective of recent advances in geochemical monitoring of the gas emissions. We also report initial results from a multidisciplinary campaign on Stromboli which utilised both OP-FTIR and SO2 camera techniques.

Motional timescale predictions by molecular dynamics simulations: case study using proline and hydroxyproline sidechain dynamics.

PubMed

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-02-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use (13) C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Copyright © 2013 Wiley Periodicals, Inc.

A Simulation of Coevolution Using Playing Cards

ERIC Educational Resources Information Center

Tatina, Robert

2007-01-01

In this article, the author describes a simulation of a coevolutionary "arms race" and introduce a way of teaching it that lets students use the theory of natural selection to explain the outcomes of the simulation. The simulation uses the numerical cards from an UNO[R] playing card deck to represent the speeds of individuals in populations of…

Seed dispersal in limber and southwestern white pine: Comparing core and peripheral populations

Treesearch

Diana F. Tomback; Sheridan Samano; Elizabeth L. Pruett; Anna W. Schoettle

2011-01-01

According to the geographic mosaic theory of coevolution (Thompson 2005), the potential for coevolutionary relationships between interacting species varies with the presence of other species within a community. This implies that the strength of coevolution between two species may vary geographically. In this study, we ask whether there is a shift in vertebrate seed...

The use and application of phylogeography for invertebrate conservation research and planning

Treesearch

Ryan C. Garrick; Chester J. Sands; Paul Sunnucks

2006-01-01

To conserve evolutionary processes within taxa as well as local co-evolutionary associations among taxa, habitat reservation and production forestry management needs to take account of natural genetic-geographic patterns. While vertebrates tend to have at least moderate dispersal and gene flow on a landscape-scale, there are good reasons to expect many small,...

Three Groups of Transposable Elements with Contrasting Copy Number Dynamics and Host Responses in the Maize (Zea mays ssp. mays) Genome

PubMed Central

Diez, Concepcion M.; Meca, Esteban; Tenaillon, Maud I.; Gaut, Brandon S.

2014-01-01

Most angiosperm nuclear DNA is repetitive and derived from silenced transposable elements (TEs). TE silencing requires substantial resources from the plant host, including the production of small interfering RNAs (siRNAs). Thus, the interaction between TEs and siRNAs is a critical aspect of both the function and the evolution of plant genomes. Yet the co-evolutionary dynamics between these two entities remain poorly characterized. Here we studied the organization of TEs within the maize (Zea mays ssp mays) genome, documenting that TEs fall within three groups based on the class and copy numbers. These groups included DNA elements, low copy RNA elements and higher copy RNA elements. The three groups varied statistically in characteristics that included length, location, age, siRNA expression and 24∶22 nucleotide (nt) siRNA targeting ratios. In addition, the low copy retroelements encompassed a set of TEs that had previously been shown to decrease expression within a 24 nt siRNA biogenesis mutant (mop1). To investigate the evolutionary dynamics of the three groups, we estimated their abundance in two landraces, one with a genome similar in size to that of the maize reference and the other with a 30% larger genome. For all three accessions, we assessed TE abundance as well as 22 nt and 24 nt siRNA content within leaves. The high copy number retroelements are under targeted similarly by siRNAs among accessions, appear to be born of a rapid bust of activity, and may be currently transpositionally dead or limited. In contrast, the lower copy number group of retrolements are targeted more dynamically and have had a long and ongoing history of transposition in the maize genome. PMID:24743518

On Reciprocal Causation in the Evolutionary Process.

PubMed

Svensson, Erik I

2018-01-01

Recent calls for a revision of standard evolutionary theory (SET) are based partly on arguments about the reciprocal causation. Reciprocal causation means that cause-effect relationships are bi-directional, as a cause could later become an effect and vice versa. Such dynamic cause-effect relationships raise questions about the distinction between proximate and ultimate causes, as originally formulated by Ernst Mayr. They have also motivated some biologists and philosophers to argue for an Extended Evolutionary Synthesis (EES). The EES will supposedly expand the scope of the Modern Synthesis (MS) and SET, which has been characterized as gene-centred, relying primarily on natural selection and largely neglecting reciprocal causation. Here, I critically examine these claims, with a special focus on the last conjecture. I conclude that reciprocal causation has long been recognized as important by naturalists, ecologists and evolutionary biologists working in the in the MS tradition, although it it could be explored even further. Numerous empirical examples of reciprocal causation in the form of positive and negative feedback are now well known from both natural and laboratory systems. Reciprocal causation have also been explicitly incorporated in mathematical models of coevolutionary arms races, frequency-dependent selection, eco-evolutionary dynamics and sexual selection. Such dynamic feedback were already recognized by Richard Levins and Richard Lewontin in their bok The Dialectical Biologist . Reciprocal causation and dynamic feedback might also be one of the few contributions of dialectical thinking and Marxist philosophy in evolutionary theory. I discuss some promising empirical and analytical tools to study reciprocal causation and the implications for the EES. Finally, I briefly discuss how quantitative genetics can be adapated to studies of reciprocal causation, constructive inheritance and phenotypic plasticity and suggest that the flexibility of this approach might have been underestimated by critics of contemporary evolutionary biology.

The escalatory Red Queen: Population extinction and replacement following arms race dynamics in poplar rust.

PubMed

Persoons, Antoine; Hayden, Katherine J; Fabre, Bénédicte; Frey, Pascal; De Mita, Stéphane; Tellier, Aurélien; Halkett, Fabien

2017-04-01

Host-parasite systems provide convincing examples of Red Queen co-evolutionary dynamics. Yet, a key process underscored in Van Valen's theory - that arms race dynamics can result in extinction - has never been documented. One reason for this may be that most sampling designs lack the breadth needed to illuminate the rapid pace of adaptation by pathogen populations. In this study, we used a 25-year temporal sampling to decipher the demographic history of a plant pathogen: the poplar rust fungus, Melampsora larici-populina. A major adaptive event occurred in 1994 with the breakdown of R7 resistance carried by several poplar cultivars widely planted in Western Europe since 1982. The corresponding virulence rapidly spread in M. larici-populina populations and nearly reached fixation in northern France, even on susceptible hosts. Using both temporal records of virulence profiles and temporal population genetic data, our analyses revealed that (i) R7 resistance breakdown resulted in the emergence of a unique and homogeneous genetic group, the so-called cultivated population, which predominated in northern France for about 20 years, (ii) selection for Vir7 individuals brought with it multiple other virulence types via hitchhiking, resulting in an overall increase in the population-wide number of virulence types and (iii) - above all - the emergence of the cultivated population superseded the initial population which predominated at the same place before R7 resistance breakdown. Our temporal analysis illustrates how antagonistic co-evolution can lead to population extinction and replacement, hence providing direct evidence for the escalation process which is at the core of Red Queen dynamics. © 2016 John Wiley & Sons Ltd.

Distinct Thermophysical and Interfacial Properties Associated with Low Molecular Weight Cyclic Polystyrene in Bulk and Confined States: Tg and Fragility

NASA Astrophysics Data System (ADS)

Zhang, Lanhe; Elupula, Ravinder; Grayson, Scott; Torkelson, John

Cyclic or ring polymers represent an exciting class of topologically distinctive polymers. The influence of ``end-to-end'' tethering and the unusual conformational properties associated with cyclic topologies have led to polymer dynamics significantly different from the linear counterpart. Bulk cyclic polystyrene (c-PS) exhibits very weak Tg- and fragility-molecular weight (MW) dependences compared to linear PS. In stark contrast to the substantial Tg-confinement effects in linear PS, a nearly completely suppressed confinement effect is discovered in low MW c-PS. The cyclic topology strongly restricts polymer-substrate interactions. Therefore, the near elimination of the Tg-confinement effect in c-PS originates mainly from a very weak perturbation to Tg near the free surface. Upon nanoscale confinement, linear PS films have been shown to have significantly reduced fragility compared to bulk. Despite having similar bulk fragility as high MW linear PS, low MW c-PS films show major suppression in fragility reduction with decreasing thickness. Due to a lack of chain ends, properties associated with the ring structure are not prone to be perturbed by either MW reduction or confinement. This result indicates a strong correlation between the susceptibility of fragility perturbation and the susceptibility of Tg perturbation, caused by chain topology and/or by confinement. This work was supported by The Dow Chemical Company, a McCormick School of Engineering Fellowship, and the NSF.

Finite element analysis of the cyclic indentation of bilayer enamel

NASA Astrophysics Data System (ADS)

Jia, Yunfei; Xuan, Fu-zhen; Chen, Xiaoping; Yang, Fuqian

2014-04-01

Tooth enamel is often subjected to repeated contact and often experiences contact deformation in daily life. The mechanical strength of the enamel determines the biofunctionality of the tooth. Considering the variation of the rod arrangement in outer and inner enamel, we approximate enamel as a bilayer structure and perform finite element analysis of the cyclic indentation of the bilayer structure, to mimic the repeated contact of enamel during mastication. The dynamic deformation behaviour of both the inner enamel and the bilayer enamel is examined. The material parameters of the inner and outer enamel used in the analysis are obtained by fitting the finite element results with the experimental nanoindentation results. The penetration depth per cycle at the quasi-steady state is used to describe the depth propagation speed, which exhibits a two-stage power-law dependence on the maximum indentation load and the amplitude of the cyclic load, respectively. The continuous penetration of the indenter reflects the propagation of the plastic zone during cyclic indentation, which is related to the energy dissipation. The outer enamel serves as a protective layer due to its great resistance to contact deformation in comparison to the inner enamel. The larger equivalent plastic strain and lower stresses in the inner enamel during cyclic indentation, as calculated from the finite element analysis, indicate better crack/fracture resistance of the inner enamel.

Cyclic occurrence of fire and its role in carbon dynamics along an edaphic moisture gradient in longleaf pine ecosystems.

PubMed

Whelan, Andrew; Mitchell, Robert; Staudhammer, Christina; Starr, Gregory

2013-01-01

Fire regulates the structure and function of savanna ecosystems, yet we lack understanding of how cyclic fire affects savanna carbon dynamics. Furthermore, it is largely unknown how predicted changes in climate may impact the interaction between fire and carbon cycling in these ecosystems. This study utilizes a novel combination of prescribed fire, eddy covariance (EC) and statistical techniques to investigate carbon dynamics in frequently burned longleaf pine savannas along a gradient of soil moisture availability (mesic, intermediate and xeric). This research approach allowed us to investigate the complex interactions between carbon exchange and cyclic fire along the ecological amplitude of longleaf pine. Over three years of EC measurement of net ecosystem exchange (NEE) show that the mesic site was a net carbon sink (NEE = -2.48 tonnes C ha(-1)), while intermediate and xeric sites were net carbon sources (NEE = 1.57 and 1.46 tonnes C ha(-1), respectively), but when carbon losses due to fuel consumption were taken into account, all three sites were carbon sources (10.78, 7.95 and 9.69 tonnes C ha(-1) at the mesic, intermediate and xeric sites, respectively). Nonetheless, rates of NEE returned to pre-fire levels 1-2 months following fire. Consumption of leaf area by prescribed fire was associated with reduction in NEE post-fire, and the system quickly recovered its carbon uptake capacity 30-60 days post fire. While losses due to fire affected carbon balances on short time scales (instantaneous to a few months), drought conditions over the final two years of the study were a more important driver of net carbon loss on yearly to multi-year time scales. However, longer-term observations over greater environmental variability and additional fire cycles would help to more precisely examine interactions between fire and climate and make future predictions about carbon dynamics in these systems.

Cyclic Occurrence of Fire and Its Role in Carbon Dynamics along an Edaphic Moisture Gradient in Longleaf Pine Ecosystems

PubMed Central

Whelan, Andrew; Mitchell, Robert; Staudhammer, Christina; Starr, Gregory

2013-01-01

Fire regulates the structure and function of savanna ecosystems, yet we lack understanding of how cyclic fire affects savanna carbon dynamics. Furthermore, it is largely unknown how predicted changes in climate may impact the interaction between fire and carbon cycling in these ecosystems. This study utilizes a novel combination of prescribed fire, eddy covariance (EC) and statistical techniques to investigate carbon dynamics in frequently burned longleaf pine savannas along a gradient of soil moisture availability (mesic, intermediate and xeric). This research approach allowed us to investigate the complex interactions between carbon exchange and cyclic fire along the ecological amplitude of longleaf pine. Over three years of EC measurement of net ecosystem exchange (NEE) show that the mesic site was a net carbon sink (NEE = −2.48 tonnes C ha−1), while intermediate and xeric sites were net carbon sources (NEE = 1.57 and 1.46 tonnes C ha−1, respectively), but when carbon losses due to fuel consumption were taken into account, all three sites were carbon sources (10.78, 7.95 and 9.69 tonnes C ha−1 at the mesic, intermediate and xeric sites, respectively). Nonetheless, rates of NEE returned to pre-fire levels 1–2 months following fire. Consumption of leaf area by prescribed fire was associated with reduction in NEE post-fire, and the system quickly recovered its carbon uptake capacity 30–60 days post fire. While losses due to fire affected carbon balances on short time scales (instantaneous to a few months), drought conditions over the final two years of the study were a more important driver of net carbon loss on yearly to multi-year time scales. However, longer-term observations over greater environmental variability and additional fire cycles would help to more precisely examine interactions between fire and climate and make future predictions about carbon dynamics in these systems. PMID:23335986

Analytical and experimental evaluation of an aluminum bridge deck panel. Part 1, Service load performance.

DOT National Transportation Integrated Search

1999-01-01

Deck deterioration is responsible for the majority of deficient bridge ratings in the United States (Sotiropoulos & GangaRao, 1993). Subject to dynamic loading, cyclic loading, and occasional overloading, bridge decks are the most severely stressed e...

Mean field dynamics of the coexistence phase in generalized cyclic competitions

NASA Astrophysics Data System (ADS)

Mowlaei, Shahir; Roman, Ahmed; Pleimling, Michel

2014-03-01

Multispecies Lotka-Volterra models have been a rich source of inspiration in multidisciplinary areas of research due to their inherent nonlinearity which yields intriguing and complex behavior for a large class of competition schemes. Of particular interest here is a subclass of these models where competition is realized in a cyclic manner through a variety of reactions. The goal is to predict and quantify emerging two-dimensional patterns in the coexistence regime. The focus will further be on a set of models that can be analyzed without using the cumbersome machinery of slow-manifolds. This work is supported by the US National Science Foundation through grant DMR-1205309.

Characterizing the Collagen Fiber Orientation in Pericardial Leaflets Under Mechanical Loading Conditions

PubMed Central

Alavi, S. Hamed; Ruiz, Victor; Krasieva, Tatiana; Botvinick, Elliot L.; Kheradvar, Arash

2014-01-01

When implanted inside the body, bioprosthetic heart valve leaflets experience a variety of cyclic mechanical stresses such as shear stress due to blood flow when the valve is open, flexural stress due to cyclic opening and closure of the valve, and tensile stress when the valve is closed. These types of stress lead to a variety of failure modes. In either a natural valve leaflet or a processed pericardial tissue leaflet, collagen fibers reinforce the tissue and provide structural integrity such that the very thin leaflet can stand enormous loads related to cyclic pressure changes. The mechanical response of the leaflet tissue greatly depends on collagen fiber concentration, characteristics, and orientation. Thus, understating the microstructure of pericardial tissue and its response to dynamic loading is crucial for the development of more durable heart valve, and computational models to predict heart valves’ behavior. In this work, we have characterized the 3D collagen fiber arrangement of bovine pericardial tissue leaflets in response to a variety of different loading conditions under Second-Harmonic Generation Microscopy. This real-time visualization method assists in better understanding of the effect of cyclic load on collagen fiber orientation in time and space. PMID:23180029

Non-geometric fluxes, quasi-Hopf twist deformations, and nonassociative quantum mechanics

NASA Astrophysics Data System (ADS)

Mylonas, Dionysios; Schupp, Peter; Szabo, Richard J.

2014-12-01

We analyse the symmetries underlying nonassociative deformations of geometry in non-geometric R-flux compactifications which arise via T-duality from closed strings with constant geometric fluxes. Starting from the non-abelian Lie algebra of translations and Bopp shifts in phase space, together with a suitable cochain twist, we construct the quasi-Hopf algebra of symmetries that deforms the algebra of functions and the exterior differential calculus in the phase space description of nonassociative R-space. In this setting, nonassociativity is characterised by the associator 3-cocycle which controls non-coassociativity of the quasi-Hopf algebra. We use abelian 2-cocycle twists to construct maps between the dynamical nonassociative star product and a family of associative star products parametrized by constant momentum surfaces in phase space. We define a suitable integration on these nonassociative spaces and find that the usual cyclicity of associative noncommutative deformations is replaced by weaker notions of 2-cyclicity and 3-cyclicity. Using this star product quantization on phase space together with 3-cyclicity, we formulate a consistent version of nonassociative quantum mechanics, in which we calculate the expectation values of area and volume operators, and find coarse-graining of the string background due to the R-flux.

Combined nuclear magnetic resonance spectroscopy and molecular dynamics study of growth hormone releasing hexapeptide GHRP-6 and a cyclic analogue.

PubMed

Fernández-Oliva, Miguel; Santana, Héctor; Suardíaz, Reynier; Gavín, José A; Pérez, Carlos S

2012-05-01

The Growth Hormone Releasing Hexapeptide, GHRP-6 was the first of a family of synthetic peptides that enhance the release of the Growth Hormone by the pituitary gland in a dose-dependent manner. Since its discovery, it has been used as a benchmark and starting point in numerous researches aiming to obtain new drugs. Complete resonance assignment of GHRP-6 NMR spectra in both open and cyclic forms are reported, showing some differences to random coil chemical shifts. Connectivities observed in the ROESY spectra indicate spatial proximity between the aromatic residues side-chains in both molecules, as well as between residues DPhe5 and Lys6 sidechains. An ensemble of 10 structures was generated for each one of the molecules, showing RMSD values indicative of nonrandom structures. Molecular Dynamics simulations, both with and without explicit solvent, were carried out for GHRP-6 and its cyclic analogue. Conformational analysis performed on the trajectories showed a nonrandom structure with a well preserved backbone. The presence of geometrical patterns resembling those typical of π-π interactions in both peptides, suggest that this kind of interactions may be relevant for the biological activity of GHRP-6. Same conclusion can be drawn from the spatial proximity of residues DPhe5 and Lys6 sidechains. Copyright © 2012 John Wiley & Sons, Ltd.

Cyclic fatigue of endodontic nickel titanium rotary instruments: static and dynamic tests.

PubMed

Li, Uei-Ming; Lee, Bor-Shiunn; Shih, Chin-Tsai; Lan, Wan-Hong; Lin, Chun-Pin

2002-06-01

Endodontic instruments upon rotation are subjected to both tensile and compressive stress in curved canals. This stress is localized at the point of curvature. The purpose of this study was to evaluate the cyclic fatigue of 0.04 ProFile nickel titanium rotary instruments operating at different rotational speeds and varied distances of pecking motion in metal blocks that simulated curved canals. A total of 150 ProFile instruments were made to rotate freely in sloped metal blocks at speeds of 200, 300, or 400 rpm by a contra-angle handpiece mounted on an Instron machine. The electric motor and Instron machine were activated until the instruments were broken in two different modes, static and dynamic pecking-motion. The fractured surfaces of separated instruments were examined under a scanning electron microscope. All data obtained were analyzed by a stepwise multiple regression method using a 95% confidence interval. The results demonstrated that the time to failure significantly decreased as the angles of curvature or the rotational speeds increased. However, as pecking distances increased, the time to failure increased. This is because a longer pecking distance gives the instrument a longer time interval before it once again passes through the highest stress area. Microscopic evaluation indicated that ductile fracture was the major cyclic failure mode. To prevent breakage of a NiTi rotary instrument, appropriate rotational speeds and continuous pecking motion in the root canals are recommended.

Dynamic mechanical properties of hydroxyapatite-reinforced and porous starch-based degradable biomaterials.

PubMed

Mano, J F; Vaz, C M; Mendes, S C; Reis, R L; Cunha, A M

1999-12-01

It has been shown that blends of starch with a poly(ethylene-vinyl-alcohol) copolymer, EVOH, designated as SEVA-C, present an interesting combination of mechanical, degradation and biocompatible properties, specially when filled with hydroxyapatite (HA). Consequently, they may find a range of applications in the biomaterials field. This work evaluated the influence of HA fillers and of blowing agents (used to produce porous architectures) over the viscoelastic properties of SEVA-C polymers, as seen by dynamic mechanical analysis (DMA), in order to speculate on their performances when withstanding cyclic loading in the body. The composite materials presented a promising performance under dynamic mechanical solicitation conditions. Two relaxations were found being attributed to the starch and EVOH phases. The EVOH relaxation process may be very useful in vivo improving the implants performance under cyclic loading. DMA results also showed that it is possible to produce SEVA-C compact surface/porous core architectures with a mechanical performance similar to that of SEVA-C dense materials. This may allow for the use of these materials as bone replacements or scaffolds that must withstand loads when implanted. Copyright 1999 Kluwer Academic Publishers

Cyclic and Linear Monoterpenes in Phospholipid Membranes: Phase Behavior, Bilayer Structure, and Molecular Dynamics.

PubMed

Pham, Quoc Dat; Topgaard, Daniel; Sparr, Emma

2015-10-13

Monoterpenes are abundant in essential oils extracted from plants. These relatively small and hydrophobic molecules have shown important biological functions, including antimicrobial activity and membrane penetration enhancement. The interaction between the monoterpenes and lipid bilayers is considered important to the understanding of the biological functions of monoterpenes. In this study, we investigated the effect of cyclic and linear monoterpenes on the structure and dynamics of lipids in model membranes. We have studied the ternary system 1,2-dimyristoyl-sn-glycero-3-phosphocholine-monoterpene-water as a model with a focus on dehydrated conditions. By combining complementary techniques, including differential scanning calorimetry, solid-state nuclear magnetic resonance, and small- and wide-angle X-ray scattering, bilayer structure, phase transitions, and lipid molecular dynamics were investigated at different water contents. Monoterpenes cause pronounced melting point depression and phase segregation in lipid bilayers, and the extent of these effects depends on the hydration conditions. The addition of a small amount of thymol to the fluid bilayer (volume fraction of 0.03 in the bilayer) leads to an increased order in the acyl chain close to the bilayer interface. The findings are discussed in relation to biological systems and lipid formulations.

The effects of dynamic compressive loading on biodegradable implants of 50-50% polylactic Acid-polyglycolic Acid.

PubMed

Thompson, D E; Agrawal, C M; Athanasiou, K

1996-01-01

Biodegradable implants that release growth factors or other bioactive agents in a controlled manner are investigated to enhance the repair of musculoskeletal tissues. In this study, the in vitro release characteristics and mechanical properties of a 50:50 polylactic acid/polyglycolic acid two phase implant were examined over a 6-week period under no-load conditions or under a cyclic compressive load, such as that experienced when walking slowly during rehabilitation. The results demonstrated that a cyclic compressive load significantly slows the decrease of molecular chain size during the first week, significantly increases protein release for the first 2-3 weeks, and significantly stiffens the implant for the first 3 weeks. It was also shown that protein release is initially high and steadily decreases with time until the molecular weight declines to about 20% of its original value (approximately 4 weeks). Once this threshold is reached, increased protein release, surface deformation, and mass loss occurs. This study also showed that dynamic loading and the environment in which an implant is placed affect its biodegradation. Therefore, it may be essential that in vitro degradation studies of these or similar implants include a dynamic functional environment.

An amphibian chemical defense phenotype is inducible across life history stages.

PubMed

Bucciarelli, Gary M; Shaffer, H Bradley; Green, David B; Kats, Lee B

2017-08-15

Inducible phenotypic responses to environmental variation are ubiquitous across the tree of life, but it remains an open question whether amphibian chemical defense phenotypes are inducible. Tetrodotoxin (TTX) is a key chemical defense trait in North American and Eurasian newts (Salamandridae). We tested if TTX can be induced by exposing populations of adult and larval California newts (Taricha torosa) to sustained stressful conditions while longitudinally quantifying TTX concentrations. Adult newts rapidly increased chemical defenses in response to simulated predator attacks and consistently maintained elevated TTX concentrations relative to wild, non-captive individuals. We also found that laboratory-reared larvae maintained chemical defenses nearly three-fold greater than those of siblings reared in streams. Collectively, our results indicate that amphibian chemical defenses are not fixed. Instead, toxins are maintained at a baseline concentration that can quickly be increased in response to perceived risk with substantial increases to toxicity. Therefore, it is crucial that inducible variation be accounted for when considering ecological dynamics of chemically defended animals and coevolutionary predator-prey and mimic-model relationships.

Linking environmental risk assessment and communication: An experiment in co-evolving scientific and social knowledge

USGS Publications Warehouse

Graffy, E.A.; Booth, N.L.

2008-01-01

Dissemination of information to decision-makers and enhanced methods of public participation are often put forward as antidotes to a perceived disconnect between risk assessment and risk communication in the public domain. However, mechanisms that support both the provision of routine, timely and relevant technical knowledge to the public and meaningful opportunities for public participation in the evaluation and management of risk are few. We argue for the need to re-conceptualise the institutional context in which risk research and communication occur as one in which scientific knowledge and public understanding are co-evolutionary instead of independent or sequential. Here, we report on an experiment to promote coevolution of environmental risk assessment and risk communication through the instrumental use of a web-based platform that dynamically links expert and public discourses through common information sources, linked scenario evaluations, and opportunities for iterative dialogue. On the basis of technical feasibility, research value and public communication capacity, we conclude that there is potential for further refinement of the methodologies presented here. Copyright ?? 2008 Inderscience Enterprises Ltd.

Human sexual conflict from molecules to culture.

PubMed

Gorelik, Gregory; Shackelford, Todd K

2011-12-15

Coevolutionary arms races between males and females have equipped both sexes with mutually manipulative and defensive adaptations. These adaptations function to benefit individual reproductive interests at the cost of the reproductive interests of opposite-sex mates, and arise from evolutionary dynamics such as parental investment (unequal reproductive costs between the sexes) and sexual selection (unequal access to opposite-sex mates). Individuals use these adaptations to hijack others' reproductive systems, psychological states, and behaviors--essentially using other individuals as extended phenotypes of themselves. Such extended phenotypic manipulation of sexual rivals and opposite-sex mates is enacted by humans with the aid of hormones, pheromones, neurotransmitters, emotions, language, mind-altering substances, social institutions, technologies, and ideologies. Furthermore, sexual conflict may be experienced at an individual level when maternal genes and paternal genes are in conflict within an organism. Sexual conflict may be physically and emotionally destructive, but may also be exciting and constructive for relationships. By extending the biological concept of sexual conflict into social and cultural domains, scholars may successfully bridge many of the interdisciplinary gaps that separate the sciences from the humanities.

Evolutionary dynamics of interactions between plants and their enemies: comparison of herbivorous insects and pathogens.

PubMed

Wininger, Kerry; Rank, Nathan

2017-11-01

Plants colonized land over 400 million years ago. Shortly thereafter, organisms began to consume terrestrial plant tissue as a nutritional resource. Most plant enemies are plant pathogens or herbivores, and they impose natural selection for plants to evolve defenses. These traits generate selection pressures on enemies. Coevolution between terrestrial plants and their enemies is an important element of the evolutionary history of both groups. However, coevolutionary studies of plant-pathogen interactions have tended to focus on different research topics than plant-herbivore interactions. Specifically, studies of plant-pathogen interactions often adopt a "gene-for-gene" conceptual framework. In contrast, studies of plants and herbivores often investigate escalation or elaboration of plant defense and herbivore adaptations to overcome it. The main exceptions to the general pattern are studies that focus on small, sessile herbivores that share many features with plant pathogens, studies that incorporate both herbivores and pathogens into a single investigation, and studies that test aspects of Thompson's geographic mosaic theory for coevolution. We discuss the implications of these findings for future research. © 2017 New York Academy of Sciences.

The coevolution of partner switching and strategy updating in non-excludable public goods game

NASA Astrophysics Data System (ADS)

Li, Yixiao; Shen, Bin

2013-10-01

Spatial public goods game is a popular metaphor to model the dilemma of collective cooperation on graphs, yet the non-excludable property of public goods has seldom been considered in previous models. Based upon a coevolutionary model where agents play public goods games and adjust their partnerships, the present model incorporates the non-excludable property of public goods: agents are able to adjust their participation in the games hosted by others, whereas they cannot exclude others from their own games. In the coevolution, a directed and dynamical network which represents partnerships among autonomous agents is evolved. We find that non-excludable property counteracts the positive effect of partner switching, i.e., the equilibrium level of cooperation is lower than that in the situation of excludable public goods game. Therefore, we study the effect of individual punishment that cooperative agents pay a personal cost to decrease benefits of those defective neighbors who participate in their hosted games. It is found that the cooperation level in the whole population is heightened in the presence of such a costly behavior.

Dynamic Aftershock Triggering Correlated with Cyclic Loading in the Slip Direction

NASA Astrophysics Data System (ADS)

Hardebeck, J.

2014-12-01

Dynamic stress changes have been shown to contribute to aftershock triggering, but the physical triggering mechanisms are not fully understood. Some proposed mechanisms are based on dynamic stress loading of the target fault in a direction that encourages earthquake slip (e.g. dynamic Coulomb stress triggering), while other mechanisms are based on fault weakening due to shaking. If dynamic stress loading in the fault slip direction plays a role in aftershock triggering, we would expect to see a relationship between the dynamic stress orientations and the aftershock focal mechanisms. Alternatively, if dynamic stress change triggering functions only through a fault weakening mechanism that is independent of the slip direction of the target fault, no such relationship is expected. I study aftershock sequences of 4 M≥6.7 mainshocks in southern California, and find a small but significant relationship between modeled dynamic stress direction and aftershock focal mechanisms. The mainshock dynamic stress changes have two observed impacts: changing the focal mechanisms in a given location to favor those aligned with the dynamic stress change, and changing the spatial distribution of seismicity to favor locations where the dynamic stress change aligns with the background stress. The aftershock focal mechanisms are significantly more aligned with the dynamic stress changes than the preshock mechanisms for only the first 0.5-1 year following most mainshocks, although for at least 10 years following Hector Mine. Dynamic stress effects on focal mechanisms are best observed at long periods (30-60 sec). Dynamic stress effects are only observed when using metrics based on repeated stress cycling in the same direction, for example considering the dominant stress orientation over the full time series, and not for the peak dynamic stress. These results imply that dynamic aftershock triggering operates at least in part through cyclic loading in the direction of fault slip, although non-directional fault weakening may be important as well. This suggests that the orientation of the dynamic stresses, as well as their amplitude, should be considered in the development of physics-based aftershock forecasting models.

Dynamic digestive physiology of a female reproductive organ in a polyandrous butterfly

PubMed Central

Plakke, Melissa S.; Deutsch, Aaron B.; Meslin, Camille; Clark, Nathan L.; Morehouse, Nathan I.

2015-01-01

ABSTRACT Reproductive traits experience high levels of selection because of their direct ties to fitness, often resulting in rapid adaptive evolution. Much of the work in this area has focused on male reproductive traits. However, a more comprehensive understanding of female reproductive adaptations and their relationship to male characters is crucial to uncover the relative roles of sexual cooperation and conflict in driving co-evolutionary dynamics between the sexes. We focus on the physiology of a complex female reproductive adaptation in butterflies and moths: a stomach-like organ in the female reproductive tract called the bursa copulatrix that digests the male ejaculate (spermatophore). Little is known about how the bursa digests the spermatophore. We characterized bursa proteolytic capacity in relation to female state in the polyandrous butterfly Pieris rapae. We found that the virgin bursa exhibits extremely high levels of proteolytic activity. Furthermore, in virgin females, bursal proteolytic capacity increases with time since eclosion and ambient temperature, but is not sensitive to the pre-mating social environment. Post copulation, bursal proteolytic activity decreases rapidly before rebounding toward the end of a mating cycle, suggesting active female regulation of proteolysis and/or potential quenching of proteolysis by male ejaculate constituents. Using transcriptomic and proteomic approaches, we report identities for nine proteases actively transcribed by bursal tissue and/or expressed in the bursal lumen that may contribute to observed bursal proteolysis. We discuss how these dynamic physiological characteristics may function as female adaptations resulting from sexual conflict over female remating rate in this polyandrous butterfly. PMID:25994634

Sarcoporia polyspora (Basidiomycota, Polyporales): a rare wood-decay fungus newly recorded from South America

Treesearch

Daiana Bortoluzzi Baldoni; Beatriz Ortiz-Santana; Gilberto Coelho; Zaida I. Antoniolli; Rodrigo J.S. Jacques

2014-01-01

Brown-rot fungi degrade almost exclusively wood cellulosic materials participating in the, carbon cycle and soil formation of many forest regions, these are especially important on boreal and cultivated coniferous forests. These fungi and forests may have a common co-evolutionary history. Studying wood-inhabiting fungi in cultivated pine forests in Southern Brazil, we...

Event Processing and Variable Part of Sample Period Determining in Combined Systems Using GA

NASA Astrophysics Data System (ADS)

Strémy, Maximilián; Závacký, Pavol; Jedlička, Martin

2011-01-01

This article deals with combined dynamic systems and usage of modern techniques in dealing with these systems, focusing particularly on sampling period design, cyclic processing tasks and related processing algorithms in the combined event management systems using genetic algorithms.

Building toy models of proteins using coevolutionary information

NASA Astrophysics Data System (ADS)

Cheng, Ryan; Raghunathan, Mohit; Onuchic, Jose

2015-03-01

Recent developments in global statistical methodologies have advanced the analysis of large collections of protein sequences for coevolutionary information. Coevolution between amino acids in a protein arises from compensatory mutations that are needed to maintain the stability or function of a protein over the course of evolution. This gives rise to quantifiable correlations between amino acid positions within the multiple sequence alignment of a protein family. Here, we use Direct Coupling Analysis (DCA) to infer a Potts model Hamiltonian governing the correlated mutations in a protein family to obtain the sequence-dependent interaction energies of a toy protein model. We demonstrate that this methodology predicts residue-residue interaction energies that are consistent with experimental mutational changes in protein stabilities as well as other computational methodologies. Furthermore, we demonstrate with several examples that DCA could be used to construct a structure-based model that quantitatively agrees with experimental data on folding mechanisms. This work serves as a potential framework for generating models of proteins that are enriched by evolutionary data that can potentially be used to engineer key functional motions and interactions in protein systems. This research has been supported by the NSF INSPIRE award MCB-1241332 and by the CTBP sponsored by the NSF (Grant PHY-1427654).

A coevolutionary arms race causes ecological speciation in crossbills.

PubMed

Smith, Julie W; Benkman, Craig W

2007-04-01

We examined three ecological factors potentially causing premating reproductive isolation to determine whether divergent selection as a result of coevolution between South Hills crossbills (Loxia curvirostra complex) and Rocky Mountain lodgepole pine (Pinus contorta latifolia) promotes ecological speciation. One factor was habitat isolation arising because of enhanced seed defenses of lodgepole pine in the South Hills. This caused the crossbill call types (morphologically and vocally differentiated forms) adapted to alternative resources to be rare. Another occurred when crossbills of other call types moved into the South Hills late in the breeding season and feeding conditions were deteriorating so that relatively few non-South Hills crossbills bred ("immigrant infecundity"). Finally, among those crossbills that bred, pairing was strongly assortative by call type (behavioral isolation). Total reproductive isolation between South Hills crossbills and the two other crossbills most common in the South Hills (call types 2 and 5) summed to .9975 and .9998, respectively, on a scale of 0 (no reproductive isolation) to 1 (complete reproductive isolation). These extremely high levels of reproductive isolation indicate that the divergent selection resulting from the coevolutionary arms race between crossbills and lodgepole pine is causing the South Hills crossbill to speciate.

Do arms races punctuate evolutionary stasis? Unified insights from phylogeny, phylogeography and microevolutionary processes.

PubMed

Toju, Hirokazu; Sota, Teiji

2009-09-01

One of the major controversies in evolutionary biology concerns the processes underlying macroevolutionary patterns in which prolonged stasis is disrupted by rapid, short-term evolution that leads species to new adaptive zones. Recent advances in the understanding of contemporary evolution have suggested that such rapid evolution can occur in the wild as a result of environmental changes. Here, we examined a novel hypothesis that evolutionary stasis is punctuated by co-evolutionary arms races, which continuously alter adaptive peaks and landscapes. Based on the phylogeny of long-mouthed weevils in the genus Curculio, likelihood ratio tests showed that the macroevolutionary pattern of the weevils coincides with the punctuational evolution model. A coalescent analysis of a species, Curculio camelliae, the mouthpart of which has diverged considerably among populations because of an arms race with its host plant, further suggested that major evolutionary shifts had occurred within 7000 generations. Through a microevolutionary analysis of the species, we also found that natural selection acting through co-evolutionary interactions is potentially strong enough to drive rapid evolutionary shifts between adaptive zones. Overall, we posit that co-evolution is an important factor driving the history of organismal evolution.

A slowly evolving host moves first in symbiotic interactions

NASA Astrophysics Data System (ADS)

Damore, James; Gore, Jeff

2011-03-01

Symbiotic relationships, both parasitic and mutualistic, are ubiquitous in nature. Understanding how these symbioses evolve, from bacteria and their phages to humans and our gut microflora, is crucial in understanding how life operates. Often, symbioses consist of a slowly evolving host species with each host only interacting with its own sub-population of symbionts. The Red Queen hypothesis describes coevolutionary relationships as constant arms races with each species rushing to evolve an advantage over the other, suggesting that faster evolution is favored. Here, we use a simple game theoretic model of host- symbiont coevolution that includes population structure to show that if the symbionts evolve much faster than the host, the equilibrium distribution is the same as it would be if it were a sequential game where the host moves first against its symbionts. For the slowly evolving host, this will prove to be advantageous in mutualisms and a handicap in antagonisms. The model allows for symbiont adaptation to its host, a result that is robust to changes in the parameters and generalizes to continuous and multiplayer games. Our findings provide insight into a wide range of symbiotic phenomena and help to unify the field of coevolutionary theory.

Epidemiological, evolutionary and co-evolutionary implications of context-dependent parasitism

PubMed Central

Vale, Pedro F.; Wilson, Alastair J.; Best, Alex; Boots, Mike; Little, Tom J.

2013-01-01

Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster growing parasites do not appear to cause more damage and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa we show how easily an interaction can shift from a severe interaction, i.e. when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modelling pathogen evolution and disease spread under different levels of infection severity, and find that environmental shifts that promote tolerance ultimately result in populations harbouring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus our results suggest two mechanisms that could underlie co-evolutionary hot- and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection. PMID:21460572

Epidemiological, evolutionary, and coevolutionary implications of context-dependent parasitism.

PubMed

Vale, Pedro F; Wilson, Alastair J; Best, Alex; Boots, Mike; Little, Tom J

2011-04-01

Abstract Victims of infection are expected to suffer increasingly as parasite population growth increases. Yet, under some conditions, faster-growing parasites do not appear to cause more damage, and infections can be quite tolerable. We studied these conditions by assessing how the relationship between parasite population growth and host health is sensitive to environmental variation. In experimental infections of the crustacean Daphnia magna and its bacterial parasite Pasteuria ramosa, we show how easily an interaction can shift from a severe interaction, that is, when host fitness declines substantially with each unit of parasite growth, to a tolerable relationship by changing only simple environmental variables: temperature and food availability. We explored the evolutionary and epidemiological implications of such a shift by modeling pathogen evolution and disease spread under different levels of infection severity and found that environmental shifts that promote tolerance ultimately result in populations harboring more parasitized individuals. We also find that the opportunity for selection, as indicated by the variance around traits, varied considerably with the environmental treatment. Thus, our results suggest two mechanisms that could underlie coevolutionary hotspots and coldspots: spatial variation in tolerance and spatial variation in the opportunity for selection.

Non-singular and cyclic universe from the modified GUP

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

Salah, Maha; Hammad, Fayçal; Faizal, Mir

In this paper, we investigate the effects of a new version of the generalized uncertainty principle (modified GUP) on the dynamics of the Universe. As the modified GUP will modify the relation between the entropy and area of the apparent horizon, it will also deform the Friedmann equations within Jacobson's approach. We explicitly find these deformed Friedmann equations governing the modified GUP-corrected dynamics of such a Universe. It is shown that the modified GUP-deformed Jacobson's approach implies an upper bound for the density of such a Universe. The Big Bang singularity can therefore also be avoided using the modified GUP-correctionsmore » to horizons' thermodynamics. In fact, we are able to analyze the pre Big Bang state of the Universe. Furthermore, the equations imply that the expansion of the Universe will come to a halt and then will immediately be followed by a contracting phase. When the equations are extrapolated beyond the maximum rate of contraction, a cyclic Universe scenario emerges.« less

Ultrafast Relaxation Dynamics of Photoexcited Zinc-Porphyrin: Electronic-Vibrational Coupling

DOE PAGES

Abraham, Baxter; Nieto-Pescador, Jesus; Gundlach, Lars

2016-08-02

Cyclic tetrapyrroles are the active core of compounds with crucial roles in living systems, such as hemoglobin and chlorophyll, and in technology as photocatalysts and light absorbers for solar energy conversion. Zinc-tetraphenylporphyrin (Zn-TPP) is a prototypical cyclic tetrapyrrole that has been intensely studied in past decades. Because of its importance for photochemical processes the optical properties are of particular interest, and, accordingly, numerous studies have focused on light absorption and excited-state dynamics of Zn-TPP. Relaxation after photoexcitation in the Soret band involves internal conversion that is preceded by an ultrafast process. This relaxation process has been observed by several groups.more » Until now, it has not been established if it involves a higher lying ”dark” state or vibrational relaxation in the excited S 2 state. Here we combine high time resolution electronic and vibrational spectroscopy to show that this process constitutes vibrational relaxation in the anharmonic 2 potential.« less

Ultrafast Relaxation Dynamics of Photoexcited Zinc-Porphyrin: Electronic-Vibrational Coupling

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

Abraham, Baxter; Nieto-Pescador, Jesus; Gundlach, Lars

Cyclic tetrapyrroles are the active core of compounds with crucial roles in living systems, such as hemoglobin and chlorophyll, and in technology as photocatalysts and light absorbers for solar energy conversion. Zinc-tetraphenylporphyrin (Zn-TPP) is a prototypical cyclic tetrapyrrole that has been intensely studied in past decades. Because of its importance for photochemical processes the optical properties are of particular interest, and, accordingly, numerous studies have focused on light absorption and excited-state dynamics of Zn-TPP. Relaxation after photoexcitation in the Soret band involves internal conversion that is preceded by an ultrafast process. This relaxation process has been observed by several groups.more » Until now, it has not been established if it involves a higher lying ”dark” state or vibrational relaxation in the excited S 2 state. Here we combine high time resolution electronic and vibrational spectroscopy to show that this process constitutes vibrational relaxation in the anharmonic 2 potential.« less

Allothermal steam gasification of biomass in cyclic multi-compartment bubbling fluidized-bed gasifier/combustor - new reactor concept.

PubMed

Iliuta, Ion; Leclerc, Arnaud; Larachi, Faïçal

2010-05-01

A new reactor concept of allothermal cyclic multi-compartment fluidized bed steam biomass gasification is proposed and analyzed numerically. The concept combines space and time delocalization to approach an ideal allothermal gasifier. Thermochemical conversion of biomass in periodic time and space sequences of steam biomass gasification and char/biomass combustion is simulated in which the exothermic combustion compartments provide heat into an array of interspersed endothermic steam gasification compartments. This should enhance unit heat integration and thermal efficiency and procure N(2)-free biosyngas with recourse neither to oxygen addition in steam gasification nor contact between flue and syngas. The dynamic, one-dimensional, multi-component, non-isothermal model developed for this concept accounts for detailed solid and gas flow dynamics whereupon gasification/combustion reaction kinetics, thermal effects and freeboard-zone reactions were tied. Simulations suggest that allothermal operation could be achieved with switch periods in the range of a minute supporting practical feasibility for portable small-scale gasification units. Copyright 2009 Elsevier Ltd. All rights reserved.

Spatial games with cyclic interactions: the response of empty sites

NASA Astrophysics Data System (ADS)

Brown, Bart; Pleimling, Michel

2015-03-01

Predator-prey models of the May-Leonard family employ empty sites in a spatial setting as an intermediate step in the reproduction process. This requirement makes the number and arrangement of empty sites important to the formation of space-time patterns. We study the density of empty sites in a stochastic predator-prey model in which the species compete in a cyclic way in two dimensions. In some cases systems of this type quickly form domains of neutral species after which all predation, and therefore, reproduction occur near the interface of competing domains. Using Monte Carlo simulations we investigate the relationship of this density of empty sites to the time-dependent domain length. We further explore the dynamics by introducing perturbations to the interaction rates of the system after which we measure the perturbed density, i.e. the response of empty sites, as the system relaxes. A dynamical scaling behavior is observed in the response of empty sites. This work is supported by the US National Science Foundation through Grant DMR-1205309.

500-year climate cycles stacking of recent centennial warming documented in an East Asian pollen record

PubMed Central

Xu, Deke; Lu, Houyuan; Chu, Guoqiang; Wu, Naiqin; Shen, Caiming; Wang, Can; Mao, Limi

2014-01-01

Here we presented a high-resolution 5350-year pollen record from a maar annually laminated lake in East Asia (EA). Pollen record reflected the dynamics of vertical vegetation zones and temperature change. Spectral analysis on pollen percentages/concentrations of Pinus and Quercus, and a temperature proxy, revealed ~500-year quasi-periodic cold-warm fluctuations during the past 5350 years. This ~500-year cyclic climate change occurred in EA during the mid-late Holocene and even the last 150 years dominated by anthropogenic forcing. It was almost in phase with a ~500-year periodic change in solar activity and Greenland temperature change, suggesting that ~500-year small variations in solar output played a prominent role in the mid-late Holocene climate dynamics in EA, linked to high latitude climate system. Its last warm phase might terminate in the next several decades to enter another ~250-year cool phase, and thus this future centennial cyclic temperature minimum could partially slow down man-made global warming. PMID:24402348

Insight of Transmembrane Processes of Self-Assembling Nanotubes Based on a Cyclic Peptide Using Coarse Grained Molecular Dynamics Simulation.

PubMed

Fu, Yankai; Yan, Tingxuan; Xu, Xia

2017-09-28

Transmembrane self-assembling cyclic peptide (SCP) nanotubes are promising candidates for delivering specific molecules through cell membranes. The detailed mechanisms behind the transmembrane processes, as well as stabilization factors of transmembrane structures, are difficult to elucidate through experiments. In this study, the effects of peptide sequence and oligomeric state on the transmembrane capabilities of SCP nanotubes and the perturbation of embedded SCP nanotubes acting on the membrane were investigated based on coarse grained molecular dynamics simulation. The simulation results reveal that hydrophilic SCP oligomers result in the elevation of the energy barrier while the oligomerization of hydrophobic SCPs causes the reduction of the energy barrier, further leading to membrane insertion. Once SCP nanotubes are embedded, membrane properties such as density, thickness, ordering state and lateral mobility are adjusted along the radial direction. This study provides insight into the transmembrane strategy of SCP nanotubes and sheds light on designing novel transport systems.

Non-singular and cyclic universe from the modified GUP

NASA Astrophysics Data System (ADS)

Salah, Maha; Hammad, Fayçal; Faizal, Mir; Farag Ali, Ahmed

2017-02-01

In this paper, we investigate the effects of a new version of the generalized uncertainty principle (modified GUP) on the dynamics of the Universe. As the modified GUP will modify the relation between the entropy and area of the apparent horizon, it will also deform the Friedmann equations within Jacobson's approach. We explicitly find these deformed Friedmann equations governing the modified GUP-corrected dynamics of such a Universe. It is shown that the modified GUP-deformed Jacobson's approach implies an upper bound for the density of such a Universe. The Big Bang singularity can therefore also be avoided using the modified GUP-corrections to horizons' thermodynamics. In fact, we are able to analyze the pre Big Bang state of the Universe. Furthermore, the equations imply that the expansion of the Universe will come to a halt and then will immediately be followed by a contracting phase. When the equations are extrapolated beyond the maximum rate of contraction, a cyclic Universe scenario emerges.

Motional timescale predictions by molecular dynamics simulations: Case study using proline and hydroxyproline sidechain dynamics

PubMed Central

Aliev, Abil E; Kulke, Martin; Khaneja, Harmeet S; Chudasama, Vijay; Sheppard, Tom D; Lanigan, Rachel M

2014-01-01

We propose a new approach for force field optimizations which aims at reproducing dynamics characteristics using biomolecular MD simulations, in addition to improved prediction of motionally averaged structural properties available from experiment. As the source of experimental data for dynamics fittings, we use 13C NMR spin-lattice relaxation times T1 of backbone and sidechain carbons, which allow to determine correlation times of both overall molecular and intramolecular motions. For structural fittings, we use motionally averaged experimental values of NMR J couplings. The proline residue and its derivative 4-hydroxyproline with relatively simple cyclic structure and sidechain dynamics were chosen for the assessment of the new approach in this work. Initially, grid search and simplexed MD simulations identified large number of parameter sets which fit equally well experimental J couplings. Using the Arrhenius-type relationship between the force constant and the correlation time, the available MD data for a series of parameter sets were analyzed to predict the value of the force constant that best reproduces experimental timescale of the sidechain dynamics. Verification of the new force-field (termed as AMBER99SB-ILDNP) against NMR J couplings and correlation times showed consistent and significant improvements compared to the original force field in reproducing both structural and dynamics properties. The results suggest that matching experimental timescales of motions together with motionally averaged characteristics is the valid approach for force field parameter optimization. Such a comprehensive approach is not restricted to cyclic residues and can be extended to other amino acid residues, as well as to the backbone. Proteins 2014; 82:195–215. © 2013 Wiley Periodicals, Inc. PMID:23818175

Cuckoos versus hosts in insects and birds: adaptations, counter-adaptations and outcomes.

PubMed

Kilner, Rebecca M; Langmore, Naomi E

2011-11-01

Avian parents and social insect colonies are victimized by interspecific brood parasites-cheats that procure costly care for their dependent offspring by leaving them in another species' nursery. Birds and insects defend themselves from attack by brood parasites; their defences in turn select counter-strategies in the parasite, thus setting in motion antagonistic co-evolution between the two parties. Despite their considerable taxonomic disparity, here we show striking parallels in the way that co-evolution between brood parasites and their hosts proceeds in insects and birds. First, we identify five types of co-evolutionary arms race from the empirical literature, which are common to both systems. These are: (a) directional co-evolution of weaponry and armoury; (b) furtiveness in the parasite countered by strategies in the host to expose the parasite; (c) specialist parasites mimicking hosts who escape by diversifying their genetic signatures; (d) generalist parasites mimicking hosts who escape by favouring signatures that force specialization in the parasite; and (e) parasites using crypsis to evade recognition by hosts who then simplify their signatures to make the parasite more detectable. Arms races a and c are well characterized in the theoretical literature on co-evolution, but the other types have received little or no formal theoretical attention. Empirical work suggests that hosts are doomed to lose arms races b and e to the parasite, in the sense that parasites typically evade host defences and successfully parasitize the nest. Nevertheless hosts may win when the co-evolutionary trajectory follows arms race a, c or d. Next, we show that there are four common outcomes of the co-evolutionary arms race for hosts. These are: (1) successful resistance; (2) the evolution of defence portfolios (or multiple lines of resistance); (3) acceptance of the parasite; and (4) tolerance of the parasite. The particular outcome is not determined by the type of preceding arms race but depends more on whether hosts or parasites control the co-evolutionary trajectory: tolerance is an outcome that parasites inflict on hosts, whereas the other three outcomes are more dependent on properties intrinsic to the host species. Finally, our review highlights considerable interspecific variation in the complexity and depth of host defence portfolios. Whether this variation is adaptive or merely reflects evolutionary lag is unclear. We propose an adaptive explanation, which centres on the relative strength of two opposing processes: strategy-facilitation, in which one line of host defence promotes the evolution of another form of resistance, and strategy-blocking, in which one line of defence may relax selection on another so completely that it causes it to decay. We suggest that when strategy-facilitation outweighs strategy-blocking, hosts will possess complex defence portfolios and we identify selective conditions in which this is likely to be the case. © 2011 The Authors. Biological Reviews © 2011 Cambridge Philosophical Society.

Fetal programming: prenatal testosterone treatment leads to follicular persistence/luteal defects; partial restoration of ovarian function by cyclic progesterone treatment.

PubMed

Manikkam, Mohan; Steckler, Teresa L; Welch, Kathleen B; Inskeep, E Keith; Padmanabhan, Vasantha

2006-04-01

Prenatal testosterone (T) excess during midgestation leads to estrous cycle defects and polycystic ovaries in sheep. We hypothesized that follicular persistence causes polycystic ovaries and that cyclic progesterone (P) treatment would overcome follicular persistence and restore cyclicity. Twice-weekly blood samples for P measurements were taken from control (C; n = 16) and prenatally T-treated (T60; n = 14; 100 mg T, im, twice weekly from d 30-90 of gestation) Suffolk sheep starting before the onset of puberty and continuing through the second breeding season. A subset of C and T60 sheep were treated cyclically with a modified controlled internal drug-releasing device for 13-14 d every 17 d during the first anestrus (CP, 7; TP, 6). Transrectal ovarian ultrasonography was performed for 8 d in the first and 21 d in the second breeding season. Prenatal T excess reduced the number, but increased the duration of progestogenic cycles, reduced the proportion of ewes with normal cycles, increased the proportion of ewes with subluteal cycles, decreased the proportion of ewes with ovulatory cycles, induced the occurrence of persistent follicles, and reduced the number of corpora lutea in those that cycled. Cyclic P treatment in anestrus, which produced one third the P concentration seen during luteal phase of cycle, did not reduce the number of persistent follicles, but increased the number of progestogenic cycles while reducing their duration. These findings suggested that follicular persistence might contribute to the polycystic ovarian morphology. Cyclic P treatment was able to only partially restore follicular dynamics, but this may be related to the low replacement concentrations of P achieved.

Cyclic fatigue resistance of R-Pilot, WaveOne Gold Glider, and ProGlider glide path instruments.

PubMed

Keskin, Cangül; İnan, Uğur; Demiral, Murat; Keleş, Ali

2018-02-17

The aim of the present study was to compare the cyclic fatigue resistance of R-Pilot (VDW; Munich, Germany) with ProGlider (Denstply Sirona; Ballaigues, Switzerland) and WaveOne Gold Glider (Denstply Sirona; Ballaigues, Switzerland) glide path instruments. R-Pilot, ProGlider, and WaveOne Gold Glider instruments were collected (n = 15) and tested in a dynamic cyclic fatigue test device, which has an artificial canal with 60° angle of curvature and a 5-mm radius of curvature. All instruments were operated until fracture occurred, and both time to fracture (TF) and the lengths of the fractured fragments were recorded. Mean and standard deviations of TF and fragment length were calculated for each reciprocating system. TF data and fractured fragment length data were subjected to one-way ANOVA and post-hoc Tukey tests (P < 0.05). Also a Weibull analysis was performed on TF data. The cyclic fatigue resistance values of the WaveOne Gold Glider and R-Pilot were significantly higher than those of the ProGlider (P < 0.05), with no significant difference between them (P > 0.05). Weibull analysis revealed that WaveOne Gold Glider showed the highest predicted TF value for 99% survival rate, which was followed by R-Pilot and ProGlider. Regarding the length of the fractured tips, there were no significant differences among the instruments (P > 0.05). The reciprocating WaveOne Gold Glider and R-Pilot instruments had significantly higher cyclic fatigue resistance than rotary ProGlider instruments. This study reported that novel reciprocating glide path instruments exhibited higher cyclic fatigue resistance than rotating glide path instrument.

SYNERGISTIC EFFECTS of CYCLIC TENSION and TRANSFORMING GROWTH FACTOR-β1 on the AORTIC VALVE MYOFIBROBLAST

PubMed Central

Merryman, W. David; Lukoff, Howard D.; Long, Rebecca A.; Engelmayr, George C.; Hopkins, Richard A.; Sacks, Michael S.

2007-01-01

Background Phenotypically, the aortic valve interstitial cell (AVIC) is a dynamic myofibroblast, appearing contractile and activated in times of development, disease, and remodeling. The precise mechanism of phenotypic modulation is unclear, but it is speculated that both biomechanical and biochemical factors are influential. Therefore, we hypothesized that isolated and combined treatments of cyclic tension and TGF-β1 would alter the phenotype and subsequent collagen biosynthesis of AVICs in situ. Methods and Results Porcine aortic valve leaflets received 7 and 14 day treatments of 15% cyclic stretch (Tension), 0.5 ng/ml TGF-β1 (TGF), 15% cyclic stretch and 0.5 ng/ml TGF-β1 (Tension+TGF), or neither mechanical nor cytokine stimuli (Null). Tissues were homogenized and assayed for AVIC phenotype (smooth muscle α-actin (SMA)) and collagen biosynthesis (via heat shock protein 47 (Hsp47) which was further verified with type I collagen C-terminal propeptide (CICP)). At both 7 and 14 days, SMA, Hsp47, and CICP quantities were significantly greater (p<0.001) in the Tension+TGF group compared to all other groups. Additionally, Tension alone appeared to maintain SMA and Hsp47 levels that were measured at day 0, while TGF alone elicited an increase in SMA and Hsp47 compared to day 0 levels. Null treatment revealed diminished proteins at both time points. Conclusions Elevated TGF-β1 levels, in the presence of cyclic mechanical tension, resulted in synergistic increases in the contractile and biosynthetic proteins in AVICs. Since cyclic mechanical stimuli can never be relieved in vivo, the presence of TGF-β1 (possibly from infiltrating macrophages) may result in overly biosynthetic AVICs, leading to altered ECM architecture, compromised valve function, and ultimately degenerative valvular disease. PMID:17868877

An integrative relational point of view.

PubMed

Wachtel, Paul L

2014-09-01

This article, part of a special section on the Relational Foundations of Psychotherapy, describes a particular relational approach called cyclical psychodynamics. Cyclical psychodynamics is rooted both in the relational perspective in psychoanalysis and in an integrative melding of psychodynamic, cognitive-behavioral, systemic, and experiential points of view. Central to its theoretical structure is a focus on the vicious and virtuous circles that perpetuate (or contribute to changing) personality patterns that may have originated in childhood but that persist because they often generate the very feedback from others that is necessary to keep them going. As a consequence of this latter focus, the relational foundation of cyclical psychodynamic therapy addresses in equal and dynamically reciprocal fashion both the therapeutic relationship in the consulting room and the key relationships outside the consulting room that play an essential role in the maintenance or change of the problematic patterns the person has come to therapy to work on. PsycINFO Database Record (c) 2014 APA, all rights reserved.

Implementation of DSC model and application for analysis of field pile tests under cyclic loading

NASA Astrophysics Data System (ADS)

Shao, Changming; Desai, Chandra S.

2000-05-01

The disturbed state concept (DSC) model, and a new and simplified procedure for unloading and reloading behavior are implemented in a nonlinear finite element procedure for dynamic analysis for coupled response of saturated porous materials. The DSC model is used to characterize the cyclic behavior of saturated clays and clay-steel interfaces. In the DSC, the relative intact (RI) behavior is characterized by using the hierarchical single surface (HISS) plasticity model; and the fully adjusted (FA) behavior is modeled by using the critical state concept. The DSC model is validated with respect to laboratory triaxial tests for clay and shear tests for clay-steel interfaces. The computer procedure is used to predict field behavior of an instrumented pile subjected to cyclic loading. The predictions provide very good correlation with the field data. They also yield improved results compared to those from a HISS model with anisotropic hardening, partly because the DSC model allows for degradation or softening and interface response.

Formation mechanism of glyoxal-DNA adduct, a DNA cross-link precursor.

PubMed

Vilanova, B; Fernández, D; Casasnovas, R; Pomar, A M; Alvarez-Idaboy, J R; Hernández-Haro, N; Grand, A; Adrover, M; Donoso, J; Frau, J; Muñoz, F; Ortega-Castro, J

2017-05-01

DNA nucleobases undergo non-enzymatic glycation to nucleobase adducts which can play important roles in vivo. In this work, we conducted a comprehensive experimental and theoretical kinetic study of the mechanisms of formation of glyoxal-guanine adducts over a wide pH range in order to elucidate the molecular basis for the glycation process. Also, we performed molecular dynamics simulations to investigate how open or cyclic glyoxal-guanine adducts can cause structural changes in an oligonucleotide model. A thermodynamic study of other glycating agents including methylglyoxal, acrolein, crotonaldehyde, 4-hydroxynonenal and 3-deoxyglucosone revealed that, at neutral pH, cyclic adducts were more stable than open adducts; at basic pH, however, the open adducts of 3-deoxyglucosone, methylglyoxal and glyoxal were more stable than their cyclic counterparts. This result can be ascribed to the ability of the adducts to cross-link DNA. The new insights may contribute to improve our understanding of the connection between glycation and DNA cross-linking. Copyright © 2017 Elsevier B.V. All rights reserved.

Formation Of Nano Layered Lamellar Structure In a Processed γ-TiAl Based Alloy

NASA Astrophysics Data System (ADS)

Heshmati-Manesh, S.; Shakoorian, H.; Armaki, H. Ghassemi; Ahmadabadi, M. Nili

2009-06-01

In this research, microstructures of an intermetallic alloy based on γ-TiAl has been investigated by optical and transmission electron microscopy. Samples of Ti-47Al-2Cr alloy were subjected to either a cyclic heat treatment or thermomechanical treatment with the aim of microstructural refinement. In both cases it was found that very fine lamellar structure with an interlamellar spacing in the nano scale is formed. Upon cyclic heat treatment, nano layers of α2 and γ ordered intermetallic phases were either formed during rapid cooling cycle in competition with massive structure formation, or formed as secondary lamellar structure during final stages of cyclic heat treatment. Also, TEM observations in hot forged specimens with initial lamellar structure revealed that micro twins form during the deformation within lamellar structure with twinning plates parallel to lamellar interfaces. Concurrent dynamic recrystallisation results in a nano layered structure with an interlamellar spacing of less than 100 nm.

Dynamic room temperature precipitation during cyclic deformation of an Al-Zn-Mg-Cu alloy

NASA Astrophysics Data System (ADS)

Hutchinson, C. R.; de Geuser, F.; Deschamps, A.

The effect of pre-straining on a precipitation heat treatment is a well-chartered area and is relevant to a number of Al alloy manufacturing processes. When straining and precipitation occur concurrently, the situation is less clear. This may arise during creep, fatigue or elevated temperature forming operations. Straining introduces dislocations and strain-induced vacancies that may enhance nucleation and growth processes but the dislocations may also shear and/or cause precipitate dissolution. This study reports a systematic characterization of precipitation during room temperature cyclic deformation of the AA7050 (Al-Zn-Mg-Cu) alloy. The mechanical response is monitored using plastic strain controlled cyclic deformation tests and the precipitation state is characterized using small angle x-ray scattering. It is shown that the precipitate volume fraction increases with the number of deformation cycles and is well correlated with the hardening increment observed but the mean precipitate radii remains relatively constant during cycling at 4-5A.

Deformation Behavior of Recycled Concrete Aggregate during Cyclic and Dynamic Loading Laboratory Tests

PubMed Central

Sas, Wojciech; Głuchowski, Andrzej; Gabryś, Katarzyna; Soból, Emil; Szymański, Alojzy

2016-01-01

Recycled concrete aggregate (RCA) is a relatively new construction material, whose applications can replace natural aggregates. To do so, extensive studies on its mechanical behavior and deformation characteristics are still necessary. RCA is currently used as a subbase material in the construction of roads, which are subject to high settlements due to traffic loading. The deformation characteristics of RCA must, therefore, be established to find the possible fatigue and damage behavior for this new material. In this article, a series of triaxial cyclic loading and resonant column tests is used to characterize fatigue in RCA as a function of applied deviator stress after long-term cyclic loading. A description of the shakedown phenomenon occurring in the RCA and calculations of its resilient modulus (Mr) as a function of fatigue are also presented. Test result analysis with the stress-life method on the Wohler S-N diagram shows the RCA behavior in accordance with the Basquin law. PMID:28773905

Development of structural correlations and synchronization from adaptive rewiring in networks of Kuramoto oscillators

NASA Astrophysics Data System (ADS)

Papadopoulos, Lia; Kim, Jason Z.; Kurths, Jürgen; Bassett, Danielle S.

2017-07-01

Synchronization of non-identical oscillators coupled through complex networks is an important example of collective behavior, and it is interesting to ask how the structural organization of network interactions influences this process. Several studies have explored and uncovered optimal topologies for synchronization by making purposeful alterations to a network. On the other hand, the connectivity patterns of many natural systems are often not static, but are rather modulated over time according to their dynamics. However, this co-evolution and the extent to which the dynamics of the individual units can shape the organization of the network itself are less well understood. Here, we study initially randomly connected but locally adaptive networks of Kuramoto oscillators. In particular, the system employs a co-evolutionary rewiring strategy that depends only on the instantaneous, pairwise phase differences of neighboring oscillators, and that conserves the total number of edges, allowing the effects of local reorganization to be isolated. We find that a simple rule—which preserves connections between more out-of-phase oscillators while rewiring connections between more in-phase oscillators—can cause initially disordered networks to organize into more structured topologies that support enhanced synchronization dynamics. We examine how this process unfolds over time, finding a dependence on the intrinsic frequencies of the oscillators, the global coupling, and the network density, in terms of how the adaptive mechanism reorganizes the network and influences the dynamics. Importantly, for large enough coupling and after sufficient adaptation, the resulting networks exhibit interesting characteristics, including degree-frequency and frequency-neighbor frequency correlations. These properties have previously been associated with optimal synchronization or explosive transitions in which the networks were constructed using global information. On the contrary, by considering a time-dependent interplay between structure and dynamics, this work offers a mechanism through which emergent phenomena and organization can arise in complex systems utilizing local rules.

The impact of resource dependence of the mechanisms of life on the spatial population dynamics of an in silico microbial community

NASA Astrophysics Data System (ADS)

Daly, Aisling J.; Baetens, Jan M.; De Baets, Bernard

2016-12-01

Biodiversity has a critical impact on ecosystem functionality and stability, and thus the current biodiversity crisis has motivated many studies of the mechanisms that sustain biodiversity, a notable example being non-transitive or cyclic competition. We therefore extend existing microscopic models of communities with cyclic competition by incorporating resource dependence in demographic processes, characteristics of natural systems often oversimplified or overlooked by modellers. The spatially explicit nature of our individual-based model of three interacting species results in the formation of stable spatial structures, which have significant effects on community functioning, in agreement with experimental observations of pattern formation in microbial communities.

Spatial patterns and biodiversity in off-lattice simulations of a cyclic three-species Lotka-Volterra model

NASA Astrophysics Data System (ADS)

Avelino, P. P.; Bazeia, D.; Losano, L.; Menezes, J.; de Oliveira, B. F.

2018-02-01

Stochastic simulations of cyclic three-species spatial predator-prey models are usually performed in square lattices with nearest-neighbour interactions starting from random initial conditions. In this letter we describe the results of off-lattice Lotka-Volterra stochastic simulations, showing that the emergence of spiral patterns does occur for sufficiently high values of the (conserved) total density of individuals. We also investigate the dynamics in our simulations, finding an empirical relation characterizing the dependence of the characteristic peak frequency and amplitude on the total density. Finally, we study the impact of the total density on the extinction probability, showing how a low population density may jeopardize biodiversity.

Interspecific comparison of constitutive ash phloem phenolic chemistry reveals compounds unique to Manchurian ash, a species resistant to emerald ash borer

Treesearch

Justin G.A. Whitehill; Stephen O. Opiyo; Jennifer L. Koch; Daniel A. Herms; Donald F. Cipollini; Pierluigi Bonello

2012-01-01

The emerald ash borer (Agrilus planipennis, EAB) is an invasive wood-borer indigenous to Asia and is responsible for widespread ash (Fraxinus spp.) mortality in the U.S. and Canada. Resistance and susceptibility to EAB varies among Fraxinus spp., which is a result of their co-evolutionary history with the pest....

Investigation of the Reliability of Bridge Elements Reinforced with Basalt Plastic Fibers

NASA Astrophysics Data System (ADS)

Koval', T. I.

2017-09-01

The poorly studied problem on the reliability and durability of basalt-fiber-reinforced concrete bridge elements is considered. A method of laboratory research into the work of specimens of the concrete under a manyfold cyclic dynamic load is proposed. The first results of such experiments are presented.

Climate variability drives population cycling and synchrony

Treesearch

Lars Y. Pomara; Benjamin Zuckerberg

2017-01-01

Aim There is mounting concern that climate change will lead to the collapse of cyclic population dynamics, yet the influence of climate variability on population cycling remains poorly understood. We hypothesized that variability in survival and fecundity, driven by climate variability at different points in the life cycle, scales up from...

Transient Dynamic Response and Failure of Composite Structure Under Cyclic Loading with Fluid Structure Interaction

DTIC Science & Technology

2014-09-01

TERMS fluid structure interaction, composite structures shipbuilding, fatigue loading 15. NUMBER OF PAGES 85 16. PRICE CODE 17. SECURITY...under the three point bending test. All the composites exhibit an initial nonlinear and inelastic deformation trend and end with a catastrophic abrupt

A natural example of fluid-mediated brittle-ductile cyclicity in quartz veins from Olkiluoto Island, SW Finland

NASA Astrophysics Data System (ADS)

Marchesini, Barbara; Garofalo, Paolo S.; Viola, Giulio; Mattila, Jussi; Menegon, Luca

2017-04-01

Brittle faults are well known as preferential conduits for localised fluid flow in crystalline rocks. Their study can thus reveal fundamental details of the physical-chemical properties of the flowing fluid phase and of the mutual feedbacks between mechanical properties of faults and fluids. Crustal deformation at the brittle-ductile transition may occur by a combination of competing brittle fracturing and viscous flow processes, with short-lived variations in fluid pressure as a viable mechanism to produce this cyclicity switch. Therefore, a detailed study of the fluid phases potentially present in faults can help to better constrain the dynamic evolution of crustal strength within the seismogenic zone, as a function of varying fluid phase characteristics. With the aim to 1) better understand the complexity of brittle-ductile cyclicity under upper to mid-crustal conditions and 2) define the physical and chemical features of the involved fluid phase, we present the preliminary results of a recently launched (micro)structural and geochemical project. We study deformed quartz veins associated with brittle-ductile deformation zones on Olkiluoto Island, chosen as the site for the Finnish deep repository for spent nuclear fuel excavated in the Paleoproterozoic crust of southwestern Finland. The presented results stem from the study of brittle fault zone BFZ300, which is a mixed brittle and ductile deformation zone characterized by complex kinematics and associated with multiple generations of quartz veins, and which serves as a pertinent example of the mechanisms of fluid flow-deformation feedbacks during brittle-ductile cyclicity in nature. A kinematic and dynamic mesostructural study is being integrated with the detailed analysis of petrographic thin sections from the fault core and its immediate surroundings with the aim to reconstruct the mechanical deformation history along the entire deformation zone. Based on the observed microstructures, it was possible to recognize three distinct episodes of ductile deformation alternating with at least three brittle episodes. Preliminary fluid inclusion data show that, during crystallization and brittle-viscous deformation, quartz crystals hosted homogeneous and heterogeneous (boiling) aqueous fluids with a large salinity (11.7-0 wt% NaCleq) and Thtot (410-200 °C) range. Boiling occurred at 200-260 °C. Variations of fluid temperature and density (hence, viscosity) may thus have induced localized cyclic switches between brittle and ductile deformation in quartz, with implications on the bulk regional crustal strength. Preliminary EBSD analysis also supports the hypothesis of cyclic switches between brittle and viscous deformation.

Rational Design of Cyclic Antimicrobial Peptides Based on BPC194 and BPC198.

PubMed

Cirac, Anna D; Torné, Maria; Badosa, Esther; Montesinos, Emilio; Salvador, Pedro; Feliu, Lidia; Planas, Marta

2017-06-24

A strategy for the design of antimicrobial cyclic peptides derived from the lead compounds c(KKLKKFKKLQ) ( BPC194 ) and c(KLKKKFKKLQ) ( BPC198 ) is reported. First, the secondary β-structure of BPC194 and BPC198 was analyzed by carrying out molecular dynamics (MD) simulations. Then, based on the sequence pattern and the β-structure of BPC194 or BPC198 , fifteen analogues were designed and synthesized on solid-phase. The best peptides ( BPC490 , BPC918, and BPC924 ) showed minimum inhibitory concentration (MIC) values <6.2 μM against Pseudomonas syringae pv. syringae and Xanthomonas axonopodis pv. vesicatoria , and an MIC value of 12.5 to 25 μM against Erwinia amylovora , being as active as BPC194 and BPC198 . Interestingly, these three analogues followed the structural pattern defined from the MD simulations of the parent peptides. Thus, BPC490 maintained the parallel alignment of the hydrophilic pairs K¹-K⁸, K²-K⁷, and K⁴-K⁵, whereas BPC918 and BPC924 included the two hydrophilic interactions K³-Q 10 and K⁵-K⁸. In short, MD simulations have proved to be very useful for ascertaining the structural features of cyclic peptides that are crucial for their biological activity. Such approaches could be further employed for the development of new antibacterial cyclic peptides.

Evolution of specialization under non-equilibrium population dynamics.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2013-03-21

We analyze the evolution of specialization in resource utilization in a mechanistically underpinned discrete-time model using the adaptive dynamics approach. We assume two nutritionally equivalent resources that in the absence of consumers grow sigmoidally towards a resource-specific carrying capacity. The consumers use resources according to the law of mass-action with rates involving trade-off. The resulting discrete-time model for the consumer population has over-compensatory dynamics. We illuminate the way non-equilibrium population dynamics affect the evolutionary dynamics of the resource consumption rates, and show that evolution to the trimorphic coexistence of a generalist and two specialists is possible due to asynchronous non-equilibrium population dynamics of the specialists. In addition, various forms of cyclic evolutionary dynamics are possible. Furthermore, evolutionary suicide may occur even without Allee effects and demographic stochasticity. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantum optimal control of isomerization dynamics of a one-dimensional reaction-path model dominated by a competing dissociation channel

NASA Astrophysics Data System (ADS)

Kurosaki, Yuzuru; Artamonov, Maxim; Ho, Tak-San; Rabitz, Herschel

2009-07-01

Quantum wave packet optimal control simulations with intense laser pulses have been carried out for studying molecular isomerization dynamics of a one-dimensional (1D) reaction-path model involving a dominant competing dissociation channel. The 1D intrinsic reaction coordinate model mimics the ozone open→cyclic ring isomerization along the minimum energy path that successively connects the ozone cyclic ring minimum, the transition state (TS), the open (global) minimum, and the dissociative O2+O asymptote on the O3 ground-state A1' potential energy surface. Energetically, the cyclic ring isomer, the TS barrier, and the O2+O dissociation channel lie at ˜0.05, ˜0.086, and ˜0.037 hartree above the open isomer, respectively. The molecular orientation of the modeled ozone is held constant with respect to the laser-field polarization and several optimal fields are found that all produce nearly perfect isomerization. The optimal control fields are characterized by distinctive high temporal peaks as well as low frequency components, thereby enabling abrupt transfer of the time-dependent wave packet over the TS from the open minimum to the targeted ring minimum. The quick transition of the ozone wave packet avoids detrimental leakage into the competing O2+O channel. It is possible to obtain weaker optimal laser fields, resulting in slower transfer of the wave packets over the TS, when a reduced level of isomerization is satisfactory.

A simple, physiologically-based model of sea turtle remigration intervals and nesting population dynamics: Effects of temperature.

PubMed

Neeman, Noga; Spotila, James R; O'Connor, Michael P

2015-09-07

Variation in the yearly number of sea turtles nesting at rookeries can interfere with population estimates and obscure real population dynamics. Previous theoretical models suggested that this variation in nesting numbers may be driven by changes in resources at the foraging grounds. We developed a physiologically-based model that uses temperatures at foraging sites to predict foraging conditions, resource accumulation, remigration probabilities, and, ultimately, nesting numbers for a stable population of sea turtles. We used this model to explore several scenarios of temperature variation at the foraging grounds, including one-year perturbations and cyclical temperature oscillations. We found that thermally driven resource variation can indeed synchronize nesting in groups of turtles, creating cohorts, but that these cohorts tend to break down over 5-10 years unless regenerated by environmental conditions. Cohorts were broken down faster at lower temperatures. One-year perturbations of low temperature had a synchronizing effect on nesting the following year, while high temperature perturbations tended to delay nesting in a less synchronized way. Cyclical temperatures lead to cyclical responses both in nesting numbers and remigration intervals, with the amplitude and lag of the response depending on the duration of the cycle. Overall, model behavior is consistent with observations at nesting beaches. Future work should focus on refining the model to fit particular nesting populations and testing further whether or not it may be used to predict observed nesting numbers and remigration intervals. Copyright © 2015 Elsevier Ltd. All rights reserved.

Cyclic AMP is a key regulator of M1 to M2a phenotypic conversion of microglia in the presence of Th2 cytokines.

PubMed

Ghosh, Mousumi; Xu, Yong; Pearse, Damien D

2016-01-13

Microglia and macrophages play a central role in neuroinflammation. Pro-inflammatory cytokines trigger their conversion to a classically activated (M1) phenotype, sustaining inflammation and producing a cytotoxic environment. Conversely, anti-inflammatory cytokines polarize the cells towards an alternatively activated (M2), tissue reparative phenotype. Elucidation of the signal transduction pathways involved in M1 to M2 phenotypic conversion may provide insight into how the innate immune response can be harnessed during distinct phases of disease or injury to mediate neuroprotection and neurorepair. Microglial cells (cell line and primary) were subjected to combined cyclic adenosine monophosphate (cyclic AMP) and IL-4, or either alone, in the presence of pro-inflammatory mediators, lipopolysaccharide (LPS), or tumor necrosis factor-α (TNF-α). Their effects on the expression of characteristic markers for M1 and M2 microglia were assessed. Similarly, the M1 and M2 phenotypes of microglia and macrophages within the lesion site were then evaluated following a contusive spinal cord injury (SCI) to the thoracic (T8) spinal cord of rats and mice when the agents were administered systemically. It was demonstrated that cyclic AMP functions synergistically with IL-4 to promote M1 to M2 conversion of microglia in culture. The combination of cyclic AMP and IL-4, but neither alone, induced an Arg-1(+)/iNOS(-)cell phenotype with concomitant expression of other M2-specific markers including TG2 and RELM-α. M2-converted microglia showed ameliorated production of pro-inflammatory cytokines (TNF-α and IP-10) and reactive oxygen species, with no alteration in phagocytic properties. M2a conversion required protein kinase A (PKA), but not the exchange protein directly activated by cyclic AMP (EPAC). Systemic delivery of cyclic AMP and IL-4 after experimental SCI also promoted a significant M1 to M2a phenotypic change in microglia and macrophage population dynamics in the lesion. Using primary microglia, microglial cell lines, and experimental models of CNS injury, we demonstrate that cyclic AMP levels are a critical determinant in M1-M2 polarization. High levels of cyclic AMP promoted an Arg-1(+) M2a phenotype when microglia were activated with pro-inflammatory stimuli and Th2 cytokines. Th2 cytokines or cyclic AMP independently did not promote these changes. Phenotypic conversion of microglia provides a powerful new therapeutic approach for altering the balance of cytotoxic to reparative microglia in a diversity of neurological diseases and injury.

Numerical Modeling of Earthquake-Induced Landslide Using an Improved Discontinuous Deformation Analysis Considering Dynamic Friction Degradation of Joints

NASA Astrophysics Data System (ADS)

Huang, Da; Song, Yixiang; Cen, Duofeng; Fu, Guoyang

2016-12-01

Discontinuous deformation analysis (DDA) as an efficient technique has been extensively applied in the dynamic simulation of discontinuous rock mass. In the original DDA (ODDA), the Mohr-Coulomb failure criterion is employed as the judgment principle of failure between contact blocks, and the friction coefficient is assumed to be constant in the whole calculation process. However, it has been confirmed by a host of shear tests that the dynamic friction of rock joints degrades. Therefore, the friction coefficient should be gradually reduced during the numerical simulation of an earthquake-induced rockslide. In this paper, based on the experimental results of cyclic shear tests on limestone joints, exponential regression formulas are fitted for dynamic friction degradation, which is a function of the relative velocity, the amplitude of cyclic shear displacement and the number of its cycles between blocks with an edge-to-edge contact. Then, an improved DDA (IDDA) is developed by implementing the fitting regression formulas and a modified removing technique of joint cohesion, in which the cohesion is removed once the `sliding' or `open' state between blocks appears for the first time, into the ODDA. The IDDA is first validated by comparing with the theoretical solutions of the kinematic behaviors of a sliding block on an inclined plane under dynamic loading. Then, the program is applied to model the Donghekou landslide triggered by the 2008 Wenchuan earthquake in China. The simulation results demonstrate that the dynamic friction degradation of joints has great influences on the runout and velocity of sliding mass. Moreover, the friction coefficient possesses higher impact than the cohesion of joints on the kinematic behaviors of the sliding mass.

Free energy landscape remodeling of the cardiac pacemaker channel explains the molecular basis of familial sinus bradycardia

PubMed Central

Boulton, Stephen; Akimoto, Madoka; Akbarizadeh, Sam; Melacini, Giuseppe

2017-01-01

The hyperpolarization-activated and cyclic nucleotide-modulated ion channel (HCN) drives the pacemaker activity in the heart, and its malfunction can result in heart disorders. One such disorder, familial sinus bradycardia, is caused by the S672R mutation in HCN, whose electrophysiological phenotypes include a negative shift in the channel activation voltage and an accelerated HCN deactivation. The outcomes of these changes are abnormally low resting heart rates. However, the molecular mechanism underlying these electrophysiological changes is currently not fully understood. Crystallographic investigations indicate that the S672R mutation causes limited changes in the structure of the HCN intracellular gating tetramer, but its effects on protein dynamics are unknown. Here, we utilize comparative S672R versus WT NMR analyses to show that the S672R mutation results in extensive perturbations of the dynamics in both apo- and holo-forms of the HCN4 isoform, reflecting how S672R remodels the free energy landscape for the modulation of HCN4 by cAMP, i.e. the primary cyclic nucleotide modulator of HCN channels. We show that the S672R mutation results in a constitutive shift of the dynamic auto-inhibitory equilibrium toward inactive states of HCN4 and broadens the free-energy well of the apo-form, enhancing the millisecond to microsecond dynamics of the holo-form at sites critical for gating cAMP binding. These S672R-induced variations in dynamics provide a molecular basis for the electrophysiological phenotypes of this mutation and demonstrate that the pathogenic effects of the S672R mutation can be rationalized primarily in terms of modulations of protein dynamics. PMID:28174302

Temporal dynamics of Puumala hantavirus infection in cyclic populations of bank voles.

PubMed

Voutilainen, Liina; Kallio, Eva R; Niemimaa, Jukka; Vapalahti, Olli; Henttonen, Heikki

2016-02-18

Understanding the dynamics of zoonotic pathogens in their reservoir host populations is a prerequisite for predicting and preventing human disease epidemics. The human infection risk of Puumala hantavirus (PUUV) is highest in northern Europe, where populations of the rodent host (bank vole, Myodes glareolus) undergo cyclic fluctuations. We conducted a 7-year capture-mark-recapture study to monitor seasonal and multiannual patterns of the PUUV infection rate in bank vole populations exhibiting a 3-year density cycle. Infected bank voles were most abundant in mid-winter months during years of increasing or peak host density. Prevalence of PUUV infection in bank voles exhibited a regular, seasonal pattern reflecting the annual population turnover and accumulation of infections within each year cohort. In autumn, the PUUV transmission rate tracked increasing host abundance, suggesting a density-dependent transmission. However, prevalence of PUUV infection was similar during the increase and peak years of the density cycle despite a twofold difference in host density. This may result from the high proportion of individuals carrying maternal antibodies constraining transmission during the cycle peak years. Our exceptionally intensive and long-term dataset provides a solid basis on which to develop models to predict the dynamic public health threat posed by PUUV in northern Europe.

Experimental investigation on the effects of non-cyclical frequency and amplitude variation on dynamic stall

NASA Astrophysics Data System (ADS)

Heintz, Kyle C.

An experimental study of a cambered airfoil undergoing non-cyclical, transient pitch trajectories and the resulting effects on the dynamic stall phenomenon is presented. Surface pressure measurements and airfoil incidence angle are acquired simultaneously to resolve instantaneous aerodynamic load coefficients at Mach numbers ranging from 0.2 to 0.4. Derived from these coefficients are various formulations of the aerodynamic damping factor, referred to copiously throughout. Using a two-motor mechanism, each providing independent frequency and amplitude input to the airfoil, unique pitch motions can be implemented by actively controlling the phase between inputs. This work primarily focuses on three pitch motion schemas, the first of which is a "chirp" style trajectory featuring concurrent exponential frequency growth and amplitude decay. Second, these parameters are tested separately to determine their individual contributions. Lastly, a novel dual harmonic pitch motion is devised which rapidly traverses dynamic stall regimes on an inter-cycle basis by modulating the static-stall penetration angle. Throughout all results presented, there is evidence that for consecutive pitch-cycles, the process of dynamic stall is affected when prior oscillations prior have undergone deeper stall-penetration angles. In other words when stall-penetration is descending, retreating from a regime of light or deep stall, statistics of load coefficients, such as damping coefficient, maximum lift, minimum quarter-chord moment, and their phase relationships, do not match the values seen when stall-penetration was growing. The outcomes herein suggest that the airfoil retains some memory of previous flow separation which has the potential to change the influence of the dynamic stall vortex.

Comment on "Asymmetric coevolutionary networks facilitate biodiversity maintenance"

USGS Publications Warehouse

Holland, J. Nathaniel; Okuyama, Toshinori; DeAngelis, Donald L.

2006-01-01

Bascompte et al. (Reports, 21 April 2006, p. 431) used network asymmetries to explain mathematical conditions necessary for stability in historic models of mutualism. The Lotka-Volterra equations they used artificially created conditions in which some factor, such as asymmetric interaction strengths, is necessary for community coexistence. We show that a more realistic model incorporating nonlinear functional responses requires no such condition and is consistent with their data.

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

PubMed Central

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-01

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology. PMID:18199838

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks.

PubMed

Juan, David; Pazos, Florencio; Valencia, Alfonso

2008-01-22

Interacting or functionally related protein families tend to have similar phylogenetic trees. Based on this observation, techniques have been developed to predict interaction partners. The observed degree of similarity between the phylogenetic trees of two proteins is the result of many different factors besides the actual interaction or functional relationship between them. Such factors influence the performance of interaction predictions. One aspect that can influence this similarity is related to the fact that a given protein interacts with many others, and hence it must adapt to all of them. Accordingly, the interaction or coadaptation signal within its tree is a composite of the influence of all of the interactors. Here, we introduce a new estimator of coevolution to overcome this and other problems. Instead of relying on the individual value of tree similarity between two proteins, we use the whole network of similarities between all of the pairs of proteins within a genome to reassess the similarity of that pair, thereby taking into account its coevolutionary context. We show that this approach offers a substantial improvement in interaction prediction performance, providing a degree of accuracy/coverage comparable with, or in some cases better than, that of experimental techniques. Moreover, important information on the structure, function, and evolution of macromolecular complexes can be inferred with this methodology.

Coevolution of Cyanogenic Bamboos and Bamboo Lemurs on Madagascar

PubMed Central

Ballhorn, Daniel J.; Rakotoarivelo, Fanny Patrika; Kautz, Stefanie

2016-01-01

Feeding strategies of specialist herbivores often originate from the coevolutionary arms race of plant defenses and counter-adaptations of herbivores. The interaction between bamboo lemurs and cyanogenic bamboos on Madagascar represents a unique system to study diffuse coevolutionary processes between mammalian herbivores and plant defenses. Bamboo lemurs have different degrees of dietary specialization while bamboos show different levels of chemical defense. In this study, we found variation in cyanogenic potential (HCNp) and nutritive characteristics among five sympatric bamboo species in the Ranomafana area, southeastern Madagascar. The HCNp ranged from 209±72 μmol cyanide*g-1 dwt in Cathariostachys madagascariensis to no cyanide in Bambusa madagascariensis. Among three sympatric bamboo lemur species, the greater bamboo lemur (Prolemur simus) has the narrowest food range as it almost exclusively feeds on the highly cyanogenic C. madagascariensis. Our data suggest that high HCNp is the derived state in bamboos. The ancestral state of lemurs is most likely "generalist" while the ancestral state of bamboo lemurs was determined as equivocal. Nevertheless, as recent bamboo lemurs comprise several "facultative specialists" and only one "obligate specialist" adaptive radiation due to increased flexibility is likely. We propose that escaping a strict food plant specialization enabled facultative specialist bamboo lemurs to inhabit diverse geographical areas. PMID:27532127

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy.

PubMed

Verin, Mélissa; Tellier, Aurélien

2018-04-20

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts' genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy. © 2018 The Author(s). Evolution © 2018 The Society for the Study of Evolution.

Evolution of spatially structured host-parasite interactions.

PubMed

Lion, S; Gandon, S

2015-01-01

Spatial structure has dramatic effects on the demography and the evolution of species. A large variety of theoretical models have attempted to understand how local dispersal may shape the coevolution of interacting species such as host-parasite interactions. The lack of a unifying framework is a serious impediment for anyone willing to understand current theory. Here, we review previous theoretical studies in the light of a single epidemiological model that allows us to explore the effects of both host and parasite migration rates on the evolution and coevolution of various life-history traits. We discuss the impact of local dispersal on parasite virulence, various host defence strategies and local adaptation. Our analysis shows that evolutionary and coevolutionary outcomes crucially depend on the details of the host-parasite life cycle and on which life-history trait is involved in the interaction. We also discuss experimental studies that support the effects of spatial structure on the evolution of host-parasite interactions. This review highlights major similarities between some theoretical results, but it also reveals an important gap between evolutionary and coevolutionary models. We discuss possible ways to bridge this gap within a more unified framework that would reconcile spatial epidemiology, evolution and coevolution. © 2014 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

Within-population covariation between sexual reproduction and susceptibility to local parasites.

PubMed

Gibson, Amanda K; Xu, Julie Y; Lively, Curtis M

2016-09-01

Evolutionary biology has yet to reconcile the ubiquity of sex with its costs relative to asexual reproduction. Here, we test the hypothesis that coevolving parasites maintain sex in their hosts. Specifically, we examined the distributions of sexual reproduction and susceptibility to local parasites within a single population of freshwater snails (Potamopyrgus antipodarum). Susceptibility to local trematode parasites (Microphallus sp.) is a relative measure of the strength of coevolutionary selection in this system. Thus, if coevolving parasites maintain sex, sexual snails should be common where susceptibility is high. We tested this prediction in a mixed population of sexual and asexual snails by measuring the susceptibility of snails from multiple sites in a lake. Consistent with the prediction, the frequency of sexual snails was tightly and positively correlated with susceptibility to local parasites. Strikingly, in just two years, asexual females increased in frequency at sites where susceptibility declined. We also found that the frequency of sexual females covaries more strongly with susceptibility than with the prevalence of Microphallus infection in the field. In linking susceptibility to the frequency of sexual hosts, our results directly implicate spatial variation in coevolutionary selection in driving the geographic mosaic of sex. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Evolving learning rules and emergence of cooperation in spatial prisoner's dilemma.

PubMed

Moyano, Luis G; Sánchez, Angel

2009-07-07

In the evolutionary Prisoner's dilemma (PD) game, agents play with each other and update their strategies in every generation according to some microscopic dynamical rule. In its spatial version, agents do not play with every other but, instead, interact only with their neighbours, thus mimicking the existing of a social or contact network that defines who interacts with whom. In this work, we explore evolutionary, spatial PD systems consisting of two types of agents, each with a certain update (reproduction, learning) rule. We investigate two different scenarios: in the first case, update rules remain fixed for the entire evolution of the system; in the second case, agents update both strategy and update rule in every generation. We show that in a well-mixed population the evolutionary outcome is always full defection. We subsequently focus on two-strategy competition with nearest-neighbour interactions on the contact network and synchronised update of strategies. Our results show that, for an important range of the parameters of the game, the final state of the system is largely different from that arising from the usual setup of a single, fixed dynamical rule. Furthermore, the results are also very different if update rules are fixed or evolve with the strategies. In these respect, we have studied representative update rules, finding that some of them may become extinct while others prevail. We describe the new and rich variety of final outcomes that arise from this co-evolutionary dynamics. We include examples of other neighbourhoods and asynchronous updating that confirm the robustness of our conclusions. Our results pave the way to an evolutionary rationale for modelling social interactions through game theory with a preferred set of update rules.

Unintended consequence of managing the coupled humans and water: the irrigation efficiency paradox

NASA Astrophysics Data System (ADS)

Liu, Y.

2015-12-01

Water shortage most severely restricts the socio-economic development of many arid and semi-arid regions in the world, for which water-saving technology is believed to be an effective solution. However, as a realworld case, the total water consumption of Xinjiang Uygur Autonomous Region of China continued to increase as irrigation efficiency dramatically improved through the application of water-saving technology in the study period 1998-2010. This phenomenon, known as the irrigation efficiency paradox or Jevons paradox, is interpreted as an economic rebound effect. In this study, we explore the dynamic feedbacks between humans and water in this paradox through a socio-hydrological perspective. We analyze the co-evolutionary trajectory of coupled human-water dynamics from 1950 to 2010 to provide it a general context. A conceptual socio-hydrological model based on five key elements, namely, irrigation land, water-saving technology, water consumption, societal sensitivity to water scarcity, and the policy mix, is constructed. The policy mix to be adopted is determined by a social decision-making process mainly based on the societal sensitivity, which reflects the societal preference on two sorts of policies: (i) irrigation land control and (ii) water-saving technology promotion. Modeling results verify the hypothesized mechanism by successfully reproducing the observed dynamics including the emergence of the efficiency paradox. Our analysis indicates that the implementation of more adaptive rules may even eliminate the paradox. The effects of different initial policy mixes are also explored, and the results show that land control policies should be given equal priority when dealing with water scarcity. These findings point to a double-helix-type co-evolution of humans and water.

Invited Review: A review of deterministic effects in cyclic variability of internal combustion engines

DOE PAGES

Finney, Charles E.; Kaul, Brian C.; Daw, C. Stuart; ...

2015-02-18

Here we review developments in the understanding of cycle to cycle variability in internal combustion engines, with a focus on spark-ignited and premixed combustion conditions. Much of the research on cyclic variability has focused on stochastic aspects, that is, features that can be modeled as inherently random with no short term predictability. In some cases, models of this type appear to work very well at describing experimental observations, but the lack of predictability limits control options. Also, even when the statistical properties of the stochastic variations are known, it can be very difficult to discern their underlying physical causes andmore » thus mitigate them. Some recent studies have demonstrated that under some conditions, cyclic combustion variations can have a relatively high degree of low dimensional deterministic structure, which implies some degree of predictability and potential for real time control. These deterministic effects are typically more pronounced near critical stability limits (e.g. near tipping points associated with ignition or flame propagation) such during highly dilute fueling or near the onset of homogeneous charge compression ignition. We review recent progress in experimental and analytical characterization of cyclic variability where low dimensional, deterministic effects have been observed. We describe some theories about the sources of these dynamical features and discuss prospects for interactive control and improved engine designs. In conclusion, taken as a whole, the research summarized here implies that the deterministic component of cyclic variability will become a pivotal issue (and potential opportunity) as engine manufacturers strive to meet aggressive emissions and fuel economy regulations in the coming decades.« less

A comparative study of gold UCLA-type and CAD/CAM titanium implant abutments

PubMed Central

Park, Ji-Man; Lee, Jai-Bong; Heo, Seong-Joo

2014-01-01

PURPOSE The aim of this study was to evaluate the interface accuracy of computer-assisted designed and manufactured (CAD/CAM) titanium abutments and implant fixture compared to gold-cast UCLA abutments. MATERIALS AND METHODS An external connection implant system (Mark III, n=10) and an internal connection implant system (Replace Select, n=10) were used, 5 of each group were connected to milled titanium abutment and the rest were connected to the gold-cast UCLA abutments. The implant fixture and abutment were tightened to torque of 35 Ncm using a digital torque gauge, and initial detorque values were measured 10 minutes after tightening. To mimic the mastication, a cyclic loading was applied at 14 Hz for one million cycles, with the stress amplitude range being within 0 N to 100 N. After the cyclic loading, detorque values were measured again. The fixture-abutment gaps were measured under a microscope and recorded with an accuracy of ±0.1 µm at 50 points. RESULTS Initial detorque values of milled abutment were significantly higher than those of cast abutment (P<.05). Detorque values after one million dynamic cyclic loadings were not significantly different (P>.05). After cyclic loading, detorque values of cast abutment increased, but those of milled abutment decreased (P<.05). There was no significant difference of gap dimension between the milled abutment group and the cast abutment group after cyclic loading. CONCLUSION In conclusion, CAD/CAM milled titanium abutment can be fabricated with sufficient accuracy to permit screw joint stability between abutment and fixture comparable to that of the traditional gold cast UCLA abutment. PMID:24605206

Dynamic landscape of the local translation at activated synapses.

PubMed

Khlebodarova, T M; Kogai, V V; Trifonova, E A; Likhoshvai, V A

2018-01-01

The mammalian target of rapamycin (mTOR) signaling pathway is the central regulator of cap-dependent translation at the synapse. Disturbances in mTOR pathway have been associated with several neurological diseases, such as autism and epilepsy. RNA-binding protein FMRP, a negative regulator of translation initiation, is one of the key components of the local translation system. Activation and inactivation of FMRP occurs via phosphorylation by S6 kinase and dephosphorylation by PP2A phosphatase, respectively. S6 kinase and PP2A phosphatase are activated in response to mGluR receptor stimulation through different signaling pathways and at different rates. The dynamic aspects of this system are poorly understood. We developed a mathematical model of FMRP-dependent regulation of postsynaptic density (PSD) protein synthesis in response to mGluR receptor stimulation and conducted in silico experiments to study the regulatory circuit functioning. The modeling results revealed the possibility of generating oscillatory (cyclic and quasi-cyclic), chaotic and even hyperchaotic dynamics of postsynaptic protein synthesis as well as the presence of multiple attractors in a wide range of parameters of the local translation system. The results suggest that autistic disorders associated with mTOR pathway hyperactivation may be due to impaired proteome stability associated with the formation of complex dynamic regimes of PSD protein synthesis in response to stimulation of mGluR receptors on the postsynaptic membrane of excitatory synapses on pyramidal hippocampal cells.

The sleep-wake-cycle: basic mechanisms.

PubMed

Jones, B E

1989-11-01

The physiologic characteristics of the sleep-wake states have been well defined and some of the chemical and neuron systems that participate in the cyclic generation and maintenance of these states have been identified. The actual dynamic process by which these systems interact to generate the basic sleep-wake cycle, however, remains a mystery.

Asymmetrical Cortical Processing of Radial Expansioncontraction in Infants and Adults

ERIC Educational Resources Information Center

Shirai, Nobu; Birtles, Deirdre; Wattam-Bell, John; Yamaguchi, Masami K.; Kanazawa, So; Atkinson, Janette; Braddick, Oliver

2009-01-01

We report asymmetrical cortical responses (steady-state visual evoked potentials) to radial expansion and contraction in human infants and adults. Forty-four infants (22 3-month-olds and 22 4-month-olds) and nine adults viewed dynamic dot patterns which cyclically (2.1 Hz) alternate between radial expansion (or contraction) and random directional…

Cyclical Dynamics in Idiosyncratic Labor Market Risk.

ERIC Educational Resources Information Center

Storesletten, Kjetil; Telmer, Chris I.; Yaron, Amir

2004-01-01

Is individual labor income more risky in recessions? This is a difficult question to answer because existing panel data sets are so short. To address this problem, we develop a generalized method of moments estimator that conditions on the macroeeonomic history that each member of the panel has experienced. Variation in the cross-sectional…

The effects of spatial dynamics on a wormhole throat

NASA Astrophysics Data System (ADS)

Alias, Anuar; Wan Abdullah, Wan Ahmad Tajuddin

2018-02-01

Previous studies on dynamic wormholes were focused on the dynamics of the wormhole itself, be it either rotating or evolutionary in character and also in various frameworks from classical to braneworld cosmological models. In this work, we modeled a dynamic factor that represents the spatial dynamics in terms of spacetime expansion and contraction surrounding the wormhole itself. Using an RS2-based braneworld cosmological model, we modified the spacetime metric of Wong and subsequently employed the method of Bronnikov, where it is observed that a traversable wormhole is easier to exist in an expanding brane universe, however it is difficult to exist in a contracting brane universe due to stress-energy tensors requirement. This model of spatial dynamic factor affecting the wormhole throat can also be applied on the cyclic or the bounce universe model.

Big-bounce cosmology from quantum gravity: The case of a cyclical Bianchi I universe

NASA Astrophysics Data System (ADS)

Moriconi, Riccardo; Montani, Giovanni; Capozziello, Salvatore

2016-07-01

We analyze the classical and quantum dynamics of a Bianchi I model in the presence of a small negative cosmological constant characterizing its evolution in term of the dust-time dualism. We demonstrate that in a canonical metric approach, the cosmological singularity is removed in correspondence to a positive defined value of the dust energy density. Furthermore, the quantum big bounce is connected to the Universe's turning point via a well-defined semiclassical limit. Then we can reliably infer that the proposed scenario is compatible with a cyclical universe picture. We also show how, when the contribution of the dust energy density is sufficiently high, the proposed scenario can be extended to the Bianchi IX cosmology and therefore how it can be regarded as a paradigm for the generic cosmological model. Finally, we investigate the origin of the observed cutoff on the cosmological dynamics, demonstrating how the big-bounce evolution can be mimicked by the same semiclassical scenario, where the negative cosmological constant is replaced via a polymer discretization of the Universe's volume. A direct proportionality law between these two parameters is then established.

Sensor selection cost optimisation for tracking structurally cyclic systems: a P-order solution

NASA Astrophysics Data System (ADS)

Doostmohammadian, M.; Zarrabi, H.; Rabiee, H. R.

2017-08-01

Measurements and sensing implementations impose certain cost in sensor networks. The sensor selection cost optimisation is the problem of minimising the sensing cost of monitoring a physical (or cyber-physical) system. Consider a given set of sensors tracking states of a dynamical system for estimation purposes. For each sensor assume different costs to measure different (realisable) states. The idea is to assign sensors to measure states such that the global cost is minimised. The number and selection of sensor measurements need to ensure the observability to track the dynamic state of the system with bounded estimation error. The main question we address is how to select the state measurements to minimise the cost while satisfying the observability conditions. Relaxing the observability condition for structurally cyclic systems, the main contribution is to propose a graph theoretic approach to solve the problem in polynomial time. Note that polynomial time algorithms are suitable for large-scale systems as their running time is upper-bounded by a polynomial expression in the size of input for the algorithm. We frame the problem as a linear sum assignment with solution complexity of ?.

Resolving the infection process reveals striking differences in the contribution of environment, genetics and phylogeny to host-parasite interactions

PubMed Central

2011-01-01

Background Infection processes consist of a sequence of steps, each critical for the interaction between host and parasite. Studies of host-parasite interactions rarely take into account the fact that different steps might be influenced by different factors and might, therefore, make different contributions to shaping coevolution. We designed a new method using the Daphnia magna - Pasteuria ramosa system, one of the rare examples where coevolution has been documented, in order to resolve the steps of the infection and analyse the factors that influence each of them. Results Using the transparent Daphnia hosts and fluorescently-labelled spores of the bacterium P. ramosa, we identified a sequence of infection steps: encounter between parasite and host; activation of parasite dormant spores; attachment of spores to the host; and parasite proliferation inside the host. The chances of encounter had been shown to depend on host genotype and environment. We tested the role of genetic and environmental factors in the newly described activation and attachment steps. Hosts of different genotypes, gender and species were all able to activate endospores of all parasite clones tested in different environments; suggesting that the activation cue is phylogenetically conserved. We next established that parasite attachment occurs onto the host oesophagus independently of host species, gender and environmental conditions. In contrast to spore activation, attachment depended strongly on the combination of host and parasite genotypes. Conclusions Our results show that different steps are influenced by different factors. Host-type-independent spore activation suggests that this step can be ruled out as a major factor in Daphnia-Pasteuria coevolution. On the other hand, we show that the attachment step is crucial for the pronounced genetic specificities of this system. We suggest that this one step can explain host population structure and could be a key force behind coevolutionary cycles. We discuss how different steps can explain different aspects of the coevolutionary dynamics of the system: the properties of the attachment step, explaining the rapid evolution of infectivity and the properties of later parasite proliferation explaining the evolution of virulence. Our study underlines the importance of resolving the infection process in order to better understand host-parasite interactions. PMID:21342515

Thermo-Mechanical Analyses of Dynamically Loaded Rubber Cylinders

NASA Technical Reports Server (NTRS)

Johnson, Arthur R.; Chen, Tzi-Kang

2002-01-01

Thick rubber components are employed by the Army to carry large loads. In tanks, rubber covers road wheels and track systems to protect roadways. It is difficult for design engineers to simulate the details of the hysteretic heating for large strain viscoelastic deformations. In this study, an approximation to the viscoelastic energy dissipated per unit time is investigated for use in estimating mechanically induced viscoelastic heating. Coupled thermo-mechanical simulations of large cyclic deformations of rubber cylinders are presented. The cylinders are first compressed axially and then cyclically loaded about the compressed state. Details of the algorithm and some computational issues are discussed. The coupled analyses are conducted for tall and short rubber cylinders both with and without imbedded metal disks.

Effect of vortex generators on the power conversion performance and structural dynamic loads of the Mod-2 wind turbine

NASA Technical Reports Server (NTRS)

Sullivan, T. L.

1984-01-01

Applying vortex generators from 20 to 100 percent span of the Mod-2 rotor resulted in a projected increase in annual energy capture of 20 percent and reduced the wind speed at which rated power is reached by nearly 3 m/sec. Application of vortex generators from 20 to 70 percent span, the fixed portion of the Mod-2 rotor, resulted in a projected increase in annual energy capture of about half this. This improved performance came at the cost of a small increase in cyclic blade loads in below rated power conditions. Cyclic blade loads were found to correlate well with the change in wind speed during one rotor revolution.

Metabolic principles of river basin organization.

PubMed

Rodriguez-Iturbe, Ignacio; Caylor, Kelly K; Rinaldo, Andrea

2011-07-19

The metabolism of a river basin is defined as the set of processes through which the basin maintains its structure and responds to its environment. Green (or biotic) metabolism is measured via transpiration and blue (or abiotic) metabolism through runoff. A principle of equal metabolic rate per unit area throughout the basin structure is developed and tested in a river basin characterized by large heterogeneities in precipitation, vegetation, soil, and geomorphology. This principle is suggested to have profound implications for the spatial organization of river basin hydrologic dynamics, including the minimization of energy expenditure known to control the scale-invariant characteristics of river networks over several orders of magnitude. Empirically derived, remarkably constant rates of average transpiration per unit area through the basin structure lead to a power law for the probability distribution of transpiration from a randomly chosen subbasin. The average runoff per unit area, evaluated for subbasins of a wide range of topological magnitudes, is also shown to be remarkably constant independently of size. A similar result is found for the rainfall after accounting for canopy interception. Allometric scaling of metabolic rates with size, variously addressed in the biological literature and network theory under the label of Kleiber's law, is similarly derived. The empirical evidence suggests that river basin metabolic activity is linked with the spatial organization that takes place around the drainage network and therefore with the mechanisms responsible for the fractal geometry of the network, suggesting a new coevolutionary framework for biological, geomorphological, and hydrologic dynamics.

Phylogenetic escalation and decline of plant defense strategies

PubMed Central

Agrawal, Anurag A.; Fishbein, Mark

2008-01-01

As the basal resource in most food webs, plants have evolved myriad strategies to battle consumption by herbivores. Over the past 50 years, plant defense theories have been formulated to explain the remarkable variation in abundance, distribution, and diversity of secondary chemistry and other defensive traits. For example, classic theories of enemy-driven evolutionary dynamics have hypothesized that defensive traits escalate through the diversification process. Despite the fact that macroevolutionary patterns are an explicit part of defense theories, phylogenetic analyses have not been previously attempted to disentangle specific predictions concerning (i) investment in resistance traits, (ii) recovery after damage, and (iii) plant growth rate. We constructed a molecular phylogeny of 38 species of milkweed and tested four major predictions of defense theory using maximum-likelihood methods. We did not find support for the growth-rate hypothesis. Our key finding was a pattern of phyletic decline in the three most potent resistance traits (cardenolides, latex, and trichomes) and an escalation of regrowth ability. Our neontological approach complements more common paleontological approaches to discover directional trends in the evolution of life and points to the importance of natural enemies in the macroevolution of species. The finding of macroevolutionary escalating regowth ability and declining resistance provides a window into the ongoing coevolutionary dynamics between plants and herbivores and suggests a revision of classic plant defense theory. Where plants are primarily consumed by specialist herbivores, regrowth (or tolerance) may be favored over resistance traits during the diversification process. PMID:18645183

Relevance of aerodynamic modelling for load reduction control strategies of two-bladed wind turbines

NASA Astrophysics Data System (ADS)

Luhmann, B.; Cheng, P. W.

2014-06-01

A new load reduction concept is being developed for the two-bladed prototype of the Skywind 3.5MW wind turbine. Due to transport and installation advantages both offshore and in complex terrain two-bladed turbine designs are potentially more cost-effective than comparable three-bladed configurations. A disadvantage of two-bladed wind turbines is the increased fatigue loading, which is a result of asymmetrically distributed rotor forces. The innovative load reduction concept of the Skywind prototype consists of a combination of cyclic pitch control and tumbling rotor kinematics to mitigate periodic structural loading. Aerodynamic design tools must be able to model correctly the advanced dynamics of the rotor. In this paper the impact of the aerodynamic modelling approach is investigated for critical operational modes of a two-bladed wind turbine. Using a lifting line free wake vortex code (FVM) the physical limitations of the classical blade element momentum theory (BEM) can be evaluated. During regular operation vertical shear and yawed inflow are the main contributors to periodic blade load asymmetry. It is shown that the near wake interaction of the blades under such conditions is not fully captured by the correction models of BEM approach. The differing prediction of local induction causes a high fatigue load uncertainty especially for two-bladed turbines. The implementation of both cyclic pitch control and a tumbling rotor can mitigate the fatigue loading by increasing the aerodynamic and structural damping. The influence of the time and space variant vorticity distribution in the near wake is evaluated in detail for different cyclic pitch control functions and tumble dynamics respectively. It is demonstrated that dynamic inflow as well as wake blade interaction have a significant impact on the calculated blade forces and need to be accounted for by the aerodynamic modelling approach. Aeroelastic simulations are carried out using the high fidelity multi body simulation software SIMPACK. The aerodynamic loads are calculated using ECN's AeroModule and NREL's BEM code Aerodynl3.

Thermodynamics of the general diffusion process: Equilibrium supercurrent and nonequilibrium driven circulation with dissipation

NASA Astrophysics Data System (ADS)

Qian, H.

2015-07-01

Unbalanced probability circulation, which yields cyclic motions in phase space, is the defining characteristics of a stationary diffusion process without detailed balance. In over-damped soft matter systems, such behavior is a hallmark of the presence of a sustained external driving force accompanied with dissipations. In an under-damped and strongly correlated system, however, cyclic motions are often the consequences of a conservative dynamics. In the present paper, we give a novel interpretation of a class of diffusion processes with stationary circulation in terms of a Maxwell-Boltzmann equilibrium in which cyclic motions are on the level set of stationary probability density function thus non-dissipative, e.g., a supercurrent. This implies an orthogonality between stationary circulation J ss ( x) and the gradient of stationary probability density f ss ( x) > 0. A sufficient and necessary condition for the orthogonality is a decomposition of the drift b( x) = j( x) + D( x)∇φ( x) where ∇ṡ j( x) = 0 and j( x) ṡ∇φ( x) = 0. Stationary processes with such Maxwell-Boltzmann equilibrium has an underlying conservative dynamics , and a first integral ϕ( x) ≡ -ln f ss (x) = const, akin to a Hamiltonian system. At all time, an instantaneous free energy balance equation exists for a given diffusion system; and an extended energy conservation law among an entire family of diffusion processes with different parameter α can be established via a Helmholtz theorem. For the general diffusion process without the orthogonality, a nonequilibrium cycle emerges, which consists of external driven φ-ascending steps and spontaneous φ-descending movements, alternated with iso-φ motions. The theory presented here provides a rich mathematical narrative for complex mesoscopic dynamics, with contradistinction to an earlier one [H. Qian et al., J. Stat. Phys. 107, 1129 (2002)]. This article is supplemented with comments by H. Ouerdane and a final reply by the author.

Biaxially mechanical tuning of 2-D reversible and irreversible surface topologies through simultaneous and sequential wrinkling.

PubMed

Yin, Jie; Yagüe, Jose Luis; Boyce, Mary C; Gleason, Karen K

2014-02-26

Controlled buckling is a facile means of structuring surfaces. The resulting ordered wrinkling topologies provide surface properties and features desired for multifunctional applications. Here, we study the biaxially dynamic tuning of two-dimensional wrinkled micropatterns under cyclic mechanical stretching/releasing/restretching simultaneously or sequentially. A biaxially prestretched PDMS substrate is coated with a stiff polymer deposited by initiated chemical vapor deposition (iCVD). Applying a mechanical release/restretch cycle in two directions loaded simultaneously or sequentially to the wrinkled system results in a variety of dynamic and tunable wrinkled geometries, the evolution of which is investigated using in situ optical profilometry, numerical simulations, and theoretical modeling. Results show that restretching ordered herringbone micropatterns, created through sequential release of biaxial prestrain, leads to reversible and repeatable surface topography. The initial flat surface and the same wrinkled herringbone pattern are obtained alternatively after cyclic release/restretch processes, owing to the highly ordered structure leaving no avenue for trapping irregular topological regions during cycling as further evidenced by the uniformity of strains distributions and negligible residual strain. Conversely, restretching disordered labyrinth micropatterns created through simultaneous release shows an irreversible surface topology whether after sequential or simultaneous restretching due to creation of irregular surface topologies with regions of highly concentrated strain upon formation of the labyrinth which then lead to residual strains and trapped topologies upon cycling; furthermore, these trapped topologies depend upon the subsequent strain histories as well as the cycle. The disordered labyrinth pattern varies after each cyclic release/restretch process, presenting residual shallow patterns instead of achieving a flat state. The ability to dynamically tune the highly ordered herringbone patterning through mechanical stretching or other actuation makes these wrinkles excellent candidates for tunable multifunctional surfaces properties such as reflectivity, friction, anisotropic liquid flow or boundary layer control.

An efficient approach to the analysis of rail surface irregularities accounting for dynamic train-track interaction and inelastic deformations

NASA Astrophysics Data System (ADS)

Andersson, Robin; Torstensson, Peter T.; Kabo, Elena; Larsson, Fredrik

2015-11-01

A two-dimensional computational model for assessment of rolling contact fatigue induced by discrete rail surface irregularities, especially in the context of so-called squats, is presented. Dynamic excitation in a wide frequency range is considered in computationally efficient time-domain simulations of high-frequency dynamic vehicle-track interaction accounting for transient non-Hertzian wheel-rail contact. Results from dynamic simulations are mapped onto a finite element model to resolve the cyclic, elastoplastic stress response in the rail. Ratcheting under multiple wheel passages is quantified. In addition, low cycle fatigue impact is quantified using the Jiang-Sehitoglu fatigue parameter. The functionality of the model is demonstrated by numerical examples.

Influence of electron radiation and temperature on the cyclic, matrix dominated response of graphite-epoxy

NASA Technical Reports Server (NTRS)

Reed, Susan M.; Herakovich, Carl T.; Sykes, George F., Jr.

1987-01-01

The effects of electron radiation and elevated temperature on the matrix-dominated cyclic response of standard T300/934 and a chemically modified T300/934 graphite-epoxy are characterized. Both materials were subjected to 1.0 x 10 to the 10th rads of 1.0 MeV electron irradiation, under vacuum, to simulate 30 years in geosynchronous orbit. Cyclic tests were performed at room temperature and elevated temperature (121 C) on 4-ply unidirectional laminates to characterize the effects associated with irradiation and elevated temperature. Both materials exhibited energy dissipation in their response at elevated temperature. The irradiated modified material also exhibited energy dissipation at room temperature. The combination of elevated temperature and irradiation resulted in the most severe effects in the form of lower proportional limits, and greater energy dissipation. Dynamic-mechanical analysis demonstrated that the glass transition temperature, T(g), of the standard material was lowered 39 C by irradiation, wereas the T(g) of the modified material was lowered 28 C by irradiation. Thermomechanical analysis showed the occurrence of volatile products generated upon heating of the irradiated materials.

Cyclic Solvent Vapor Annealing for Rapid, Robust Vertical Orientation of Features in BCP Thin Films

NASA Astrophysics Data System (ADS)

Paradiso, Sean; Delaney, Kris; Fredrickson, Glenn

2015-03-01

Methods for reliably controlling block copolymer self assembly have seen much attention over the past decade as new applications for nanostructured thin films emerge in the fields of nanopatterning and lithography. While solvent assisted annealing techniques are established as flexible and simple methods for achieving long range order, solvent annealing alone exhibits a very weak thermodynamic driving force for vertically orienting domains with respect to the free surface. To address the desire for oriented features, we have investigated a cyclic solvent vapor annealing (CSVA) approach that combines the mobility benefits of solvent annealing with selective stress experienced by structures oriented parallel to the free surface as the film is repeatedly swollen with solvent and dried. Using dynamical self-consistent field theory (DSCFT) calculations, we establish the conditions under which the method significantly outperforms both static and cyclic thermal annealing and implicate the orientation selection as a consequence of the swelling/deswelling process. Our results suggest that CSVA may prove to be a potent method for the rapid formation of highly ordered, vertically oriented features in block copolymer thin films.

Cyclic multiverses

NASA Astrophysics Data System (ADS)

Marosek, Konrad; Dąbrowski, Mariusz P.; Balcerzak, Adam

2016-09-01

Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (`non-singular' bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (`singular' bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two `parallel' universes with their physical evolution [physical coupling constants c(t) and G(t)] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion - the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans-Dicke theory where varying G(t) is replaced by the dynamical Brans-Dicke field φ(t) though these theories are slightly different.

A new method for assessing relative dynamic motion of vertebral bodies during cyclic loading in vitro.

PubMed

Dean, J C; Wilcox, C H; Daniels, A U; Goodwin, R R; Van Wagoner, E; Dunn, H K

1991-01-01

A new experimental technique for measuring generalized three-dimensional motion of vertebral bodies during cyclic loading in vitro is presented. The system consists of an orthogonal array of three lasers mounted rigidly to one vertebra, and a set of three mutually orthogonal charge-coupled devices mounted rigidly to an adjacent vertebra. Each laser strikes a corresponding charge-coupled device screen. The mathematical model of the system is reduced to a linear set of equations with consequent matrix algebra allowing fast real-time data reduction during cyclic movements of the spine. The range and accuracy of the system is well suited for studying thoracolumbar motion segments. Distinct advantages of the system include miniaturization of the components, the elimination of the need for mechanical linkages between the bodies, and a high degree of accuracy which is not dependent on viewing volume as found in photogrammetric systems. More generally, the spectrum of potential applications of systems of this type to the real-time measurement of the relative motion of two bodies is extremely broad.

Maternal androgens in avian brood parasites and their hosts: responses to parasitism and competition?

USGS Publications Warehouse

Hahn, Caldwell; Wingfield, John C.; Fox, David M.; Walker, Brian G.; Thomley, Jill E

2017-01-01

In the coevolutionary dynamic of avian brood parasites and their hosts, maternal (or transgenerational) effects have rarely been investigated. We examined the potential role of elevated yolk testosterone in eggs of the principal brood parasite in North America, the brown-headed cowbird, and three of its frequent host species. Elevated maternal androgens in eggs are a common maternal effect observed in many avian species when breeding conditions are unfavorable. These steroids accelerate embryo development, shorten incubation period, increase nestling growth rate, and enhance begging vigor, all traits that can increase the survival of offspring. We hypothesized that elevated maternal androgens in host eggs are a defense against brood parasitism. Our second hypothesis was that elevated maternal androgens in cowbird eggs are a defense against intra-specific competition. For host species, we found that elevated yolk testosterone was correlated with parasitized nests of small species, those whose nest success is most reduced by cowbird parasitism. For cowbirds, we found that elevated yolk testosterone was correlated with eggs in multiply-parasitized nests, which indicate intra-specific competition for nests due to high cowbird density. We propose experimental work to further examine the use of maternal effects by cowbirds and their hosts.

OPTIMIZING THROUGH CO-EVOLUTIONARY AVALANCHES

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

S. BOETTCHER; A. PERCUS

2000-08-01

We explore a new general-purpose heuristic for finding high-quality solutions to hard optimization problems. The method, called extremal optimization, is inspired by ''self-organized critically,'' a concept introduced to describe emergent complexity in many physical systems. In contrast to Genetic Algorithms which operate on an entire ''gene-pool'' of possible solutions, extremal optimization successively replaces extremely undesirable elements of a sub-optimal solution with new, random ones. Large fluctuations, called ''avalanches,'' ensue that efficiently explore many local optima. Drawing upon models used to simulate far-from-equilibrium dynamics, extremal optimization complements approximation methods inspired by equilibrium statistical physics, such as simulated annealing. With only onemore » adjustable parameter, its performance has proved competitive with more elaborate methods, especially near phase transitions. Those phase transitions are found in the parameter space of most optimization problems, and have recently been conjectured to be the origin of some of the hardest instances in computational complexity. We will demonstrate how extremal optimization can be implemented for a variety of combinatorial optimization problems. We believe that extremal optimization will be a useful tool in the investigation of phase transitions in combinatorial optimization problems, hence valuable in elucidating the origin of computational complexity.« less

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time.

PubMed

Koskella, Britt; Parr, Nicole

2015-08-19

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host-parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics.

The evolution of bacterial resistance against bacteriophages in the horse chestnut phyllosphere is general across both space and time

PubMed Central

Koskella, Britt; Parr, Nicole

2015-01-01

Insight to the spatial and temporal scales of coevolution is key to predicting the outcome of host–parasite interactions and spread of disease. For bacteria infecting long-lived hosts, selection to overcome host defences is just one factor shaping the course of evolution; populations will also be competing with other microbial species and will themselves be facing infection by bacteriophage viruses. Here, we examine the temporal and spatial patterns of bacterial adaptation against natural phage populations from within leaves of horse chestnut trees. Using a time-shift experiment with both sympatric and allopatric phages from either contemporary or earlier points in the season, we demonstrate that bacterial resistance is higher against phages from the past, regardless of spatial sympatry or how much earlier in the season phages were collected. Similarly, we show that future bacterial hosts are more resistant to both sympatric and allopatric phages than contemporary bacterial hosts. Together, our results suggest the evolution of relatively general bacterial resistance against phages in nature and are contrasting to previously observed patterns of phage adaptation to bacteria from the same tree hosts over the same time frame, indicating a potential asymmetry in coevolutionary dynamics. PMID:26150663

Evolutionary pattern in the OXT-OXTR system in primates: coevolution and positive selection footprints.

PubMed

Vargas-Pinilla, Pedro; Paixão-Côrtes, Vanessa Rodrigues; Paré, Pamela; Tovo-Rodrigues, Luciana; Vieira, Carlos Meton de Alencar Gadelha; Xavier, Agatha; Comas, David; Pissinatti, Alcides; Sinigaglia, Marialva; Rigo, Maurício Menegatti; Vieira, Gustavo Fioravanti; Lucion, Aldo B; Salzano, Francisco Mauro; Bortolini, Maria Cátira

2015-01-06

Oxytocin is a nonapeptide involved in a wide range of physiologic and behavioral functions. Until recently, it was believed that an unmodified oxytocin sequence was present in all placental mammals. This study analyzed oxytocin (OXT) in 29 primate species and the oxytocin receptor (OXTR) in 21 of these species. We report here three novel OXT forms in the New World monkeys, as well as a more extensive distribution of a previously described variant (Leu8Pro). In structural terms, these OXTs share the same three low-energy conformations in solution during molecular dynamic simulations, with subtle differences in their side chains. A consistent signal of positive selection was detected in the Cebidae family, and OXT position 8 showed a statistically significant (P = 0.013) correlation with litter size. Several OXTR changes were identified, some of them promoting gain or loss of putative phosphorylation sites, with possible consequences for receptor internalization and desensitization. OXTR amino acid sites are under positive selection, and intramolecular and intermolecular coevolutionary processes with OXT were also detected. We suggest that some New World monkey OXT-OXTR forms can be correlated to male parental care through the increase of cross-reactivity with its correlated vasopressin system.

Evolution of learning strategies in temporally and spatially variable environments: A review of theory

PubMed Central

Aoki, Kenichi; Feldman, Marcus W.

2013-01-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change – coevolutionary, two-timescale, and information decay – are compared and shown to sometimes yield contradictory results. The so-called Rogers’ paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers’ paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. PMID:24211681

Evolution of learning strategies in temporally and spatially variable environments: a review of theory.

PubMed

Aoki, Kenichi; Feldman, Marcus W

2014-02-01

The theoretical literature from 1985 to the present on the evolution of learning strategies in variable environments is reviewed, with the focus on deterministic dynamical models that are amenable to local stability analysis, and on deterministic models yielding evolutionarily stable strategies. Individual learning, unbiased and biased social learning, mixed learning, and learning schedules are considered. A rapidly changing environment or frequent migration in a spatially heterogeneous environment favors individual learning over unbiased social learning. However, results are not so straightforward in the context of learning schedules or when biases in social learning are introduced. The three major methods of modeling temporal environmental change--coevolutionary, two-timescale, and information decay--are compared and shown to sometimes yield contradictory results. The so-called Rogers' paradox is inherent in the two-timescale method as originally applied to the evolution of pure strategies, but is often eliminated when the other methods are used. Moreover, Rogers' paradox is not observed for the mixed learning strategies and learning schedules that we review. We believe that further theoretical work is necessary on learning schedules and biased social learning, based on models that are logically consistent and empirically pertinent. Copyright © 2013 Elsevier Inc. All rights reserved.

Analyzing the dynamics of cell cycle processes from fixed samples through ergodic principles.

PubMed

Wheeler, Richard John

2015-11-05

Tools to analyze cyclical cellular processes, particularly the cell cycle, are of broad value for cell biology. Cell cycle synchronization and live-cell time-lapse observation are widely used to analyze these processes but are not available for many systems. Simple mathematical methods built on the ergodic principle are a well-established, widely applicable, and powerful alternative analysis approach, although they are less widely used. These methods extract data about the dynamics of a cyclical process from a single time-point "snapshot" of a population of cells progressing through the cycle asynchronously. Here, I demonstrate application of these simple mathematical methods to analysis of basic cyclical processes--cycles including a division event, cell populations undergoing unicellular aging, and cell cycles with multiple fission (schizogony)--as well as recent advances that allow detailed mapping of the cell cycle from continuously changing properties of the cell such as size and DNA content. This includes examples using existing data from mammalian, yeast, and unicellular eukaryotic parasite cell biology. Through the ongoing advances in high-throughput cell analysis by light microscopy, electron microscopy, and flow cytometry, these mathematical methods are becoming ever more important and are a powerful complementary method to traditional synchronization and time-lapse cell cycle analysis methods. © 2015 Wheeler. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

Quantification of cancellous bone-compaction due to DHS Blade insertion and influence upon cut-out resistance.

PubMed

Windolf, Markus; Muths, Raphael; Braunstein, Volker; Gueorguiev, Boyko; Hänni, Markus; Schwieger, Karsten

2009-01-01

Compaction of cancellous bone is believed to prevent cut-out. This in vitro study quantified the compaction in the femoral head due to insertion of a dynamic hip screw-blade with and without predrilling and investigated the resulting implant anchorage under cyclic loading. Eight pairs of human cadaveric femoral heads were instrumented with a dynamic hip screw-blade made of Polyetheretherketon. Pairwise instrumentation was performed either with or without predrilling the specimens. CT scanning was performed before and after implantation, to measure bone-compaction. Subsequently the implant was removed and a third scan was performed to analyze the relaxation of the bone structure. Commercial implants were reinserted and the specimens were cyclically loaded until onset of cut-out occurred. The bone-implant interface was monitored by means of fluoroscopic imaging throughout the experiment. Paired t-tests were performed to identify differences regarding compaction, relaxation and cycles to failure. Bone density in the surrounding of the implant increased about 30% for the non-predrilled and 20% for the predrilled group when inserting the implant. After implant removal the predrilled specimens fully relaxed; the non-predrilled group showed about 10% plastic deformation. No differences were found regarding cycles to failure (P=0.32). Significant bone-compaction due to blade insertion was verified. Even though compaction was lower when predrilling the specimens, mainly elastic deformation was present, which is believed to primarily enhance the implant anchorage. Cyclic loading tests confirmed this thesis. The importance of the implantation technique with regard to predrilling is therefore decreased.

Changes in fibroblast mechanostat set point and mechanosensitivity: an adaptive response to mechanical stress in floppy eyelid syndrome.

PubMed

Ezra, Daniel G; Ellis, James S; Beaconsfield, Michèle; Collin, Richard; Bailly, Maryse

2010-08-01

Floppy eyelid syndrome (FES) is an acquired hyperelasticity disorder affecting the upper eyelid. The tarsal plate becomes hyperelastic with a loss of intrinsic rigidity. As a result, the eyelid is subjected to cyclic mechanical stress. This condition was used as a model to investigate changes in dynamic fibroblast contractility in the context of chronic cyclic mechanical stress. Contractile efficiency was investigated in a free-floating, three-dimensional collagen matrix model. Intrinsic cellular force measurements and responses to changes in gel tension were explored using a tensioning culture force monitor (t-CFM). Gene expression differences between cell lines exhibiting differences in contractile phenotype were explored with a genome level microarray platform and RT-PCR. FES tarsal plate fibroblasts (TFs) showed an increased contractile efficiency compared with the control, and t-CFM measurements confirmed a higher intrinsic cellular force at plateau levels. Cyclic stretch/relaxation experiments determined that TFs in FES maintained a functional tensional homeostasis response but with an altered sensitivity, operating around a higher mechanostat set point. Gene expression array and RT-PCR analysis identified V-CAM1 and PPP1R3C as being upregulated in FES TFs. These changes may represent an adaptive response that allows tensional homeostasis to be maintained at the high levels of tissue stress experienced in FES. Gene expression studies point to a role for V-CAM1 and PPP1R3C in mediating changes in the dynamic range of mechanosensitivity of TFs. This work identifies FES as a useful model for the study of adaptive physiological responses to mechanical stress.

Discrete dynamical laser equation for the critical onset of bistability, entanglement and disappearance

NASA Astrophysics Data System (ADS)

Abdul, M.; Farooq, U.; Akbar, Jehan; Saif, F.

2018-06-01

We transform the semi-classical laser equation for single mode homogeneously broadened lasers to a one-dimensional nonlinear map by using the discrete dynamical approach. The obtained mapping, referred to as laser logistic mapping (LLM), characteristically exhibits convergent, cyclic and chaotic behavior depending on the control parameter. Thus, the so obtained LLM explains stable, bistable, multi-stable, and chaotic solutions for output field intensity. The onset of bistability takes place at a critical value of the effective gain coefficient. The obtained analytical results are confirmed through numerical calculations.

Pathogen evolution across the agro-ecological interface: implications for disease management.

PubMed

Burdon, Jeremy J; Thrall, Peter H

2008-02-01

Infectious disease is a major causal factor in the demography of human, plant and animal populations. While it is generally accepted in medical, veterinary and agricultural contexts that variation in host resistance and pathogen virulence and aggressiveness is of central importance to understanding patterns of infection, there has been remarkably little effort to directly investigate causal links between population genetic structure and disease dynamics, and even less work on factors influencing host-pathogen coevolution. The lack of empirical evidence is particularly surprising, given the potential for such variation to not only affect disease dynamics and prevalence, but also when or where new diseases or pathotypes emerge. Increasingly, this lack of knowledge has led to calls for an integrated approach to disease management, incorporating both ecological and evolutionary processes. Here, we argue that plant pathogens occurring in agro-ecosystems represent one clear example where the application of evolutionary principles to disease management would be of great benefit, as well as providing model systems for advancing our ability to generalize about the long-term coevolutionary dynamics of host-pathogen systems. We suggest that this is particularly the case given that agro-ecological host-pathogen interactions represent a diversity of situations ranging from those that only involve agricultural crops through to those that also include weedy crop relatives or even unrelated native plant communities. We begin by examining some of the criteria that are important in determining involvement in agricultural pathogen evolution by noncrop plants. Throughout we use empirical examples to illustrate the fact that different processes may dominate in different systems, and suggest that consideration of life history and spatial structure are central to understanding dynamics and direction of the interaction. We then discuss the implications that such interactions have for disease management in agro-ecosystems and how we can influence those outcomes. Finally, we identify several major gaps where future research could increase our ability to utilize evolutionary principles in managing disease in agro-ecosystems.

Effects of cyclic flexure on endothelial permeability and apoptosis in arterial segments perfused ex vivo.

PubMed

Van Epps, J Scott; Chew, Douglas W; Vorp, David A

2009-10-01

Certain arteries (e.g., coronary, femoral, etc.) are exposed to cyclic flexure due to their tethering to surrounding tissue beds. It is believed that such stimuli result in a spatially variable biomechanical stress distribution, which has been implicated as a key modulator of remodeling associated with atherosclerotic lesion localization. In this study we utilized a combined ex vivo experimental/computational methodology to address the hypothesis that local variations in shear and mural stress associated with cyclic flexure influence the distribution of early markers of atherogenesis. Bilateral porcine femoral arteries were surgically harvested and perfused ex vivo under pulsatile arterial conditions. One of the paired vessels was exposed to cyclic flexure (0-0.7 cm(-1)) at 1 Hz for 12 h. During the last hour, the perfusate was supplemented with Evan's blue dye-labeled albumin. A custom tissue processing protocol was used to determine the spatial distribution of endothelial permeability, apoptosis, and proliferation. Finite element and computational fluid dynamics techniques were used to determine the mural and shear stress distributions, respectively, for each perfused segment. Biological data obtained experimentally and mechanical stress data estimated computationally were combined in an experiment-specific manner using multiple linear regression analyses. Arterial segments exposed to cyclic flexure had significant increases in intimal and medial apoptosis (3.42+/-1.02 fold, p=0.029) with concomitant increases in permeability (1.14+/-0.04 fold, p=0.026). Regression analyses revealed specific mural stress measures including circumferential stress at systole, and longitudinal pulse stress were quantitatively correlated with the distribution of permeability and apoptosis. The results demonstrated that local variation in mechanical stress in arterial segments subjected to cyclic flexure indeed influence the extent and spatial distribution of the early atherogenic markers. In addition, the importance of including mural stresses in the investigation of vascular mechanopathobiology was highlighted. Specific example results were used to describe a potential mechanism by which systemic risk factors can lead to a heterogeneous disease.

Real-time monitoring of electrically evoked catecholamine signals in the songbird striatum using in vivo fast-scan cyclic voltammetry.

PubMed

Smith, Amanda R; Garris, Paul A; Casto, Joseph M

2015-01-01

Fast-scan cyclic voltammetry is a powerful technique for monitoring rapid changes in extracellular neurotransmitter levels in the brain. In vivo fast-scan cyclic voltammetry has been used extensively in mammalian models to characterize dopamine signals in both anesthetized and awake preparations, but has yet to be applied to a non-mammalian vertebrate. The goal of this study was to establish in vivo fast-scan cyclic voltammetry in a songbird, the European starling, to facilitate real-time measurements of extracellular catecholamine levels in the avian striatum. In urethane-anesthetized starlings, changes in catecholamine levels were evoked by electrical stimulation of the ventral tegmental area and measured at carbon-fiber microelectrodes positioned in the medial and lateral striata. Catecholamines were elicited by different stimulations, including trains related to phasic dopamine signaling in the rat, and were analyzed to quantify presynaptic mechanisms governing exocytotic release and neuronal uptake. Evoked extracellular catecholamine dynamics, maximal amplitude of the evoked catecholamine signal, and parameters for catecholamine release and uptake did not differ between striatal regions and were similar to those determined for dopamine in the rat dorsomedial striatum under similar conditions. Chemical identification of measured catecholamine by its voltammogram was consistent with the presence of both dopamine and norepinephrine in striatal tissue content. However, the high ratio of dopamine to norepinephrine in tissue content and the greater sensitivity of the carbon-fiber microelectrode to dopamine compared to norepinephrine favored the measurement of dopamine. Thus, converging evidence suggests that dopamine was the predominate analyte of the electrically evoked catecholamine signal measured in the striatum by fast-scan cyclic voltammetry. Overall, comparisons between the characteristics of these evoked signals suggested a similar presynaptic regulation of dopamine in the starling and rat striatum. Fast-scan cyclic voltammetry thus has the potential to be an invaluable tool for investigating the neural underpinnings of behavior in birds. Copyright © 2015 Elsevier B.V. All rights reserved.

Real-time monitoring of electrically evoked catecholamine signals in the songbird striatum using in vivo fast-scan cyclic voltammetry

PubMed Central

Smith, Amanda R.; Garris, Paul A.; Casto, Joseph M.

2015-01-01

Fast-scan cyclic voltammetry is a powerful technique for monitoring rapid changes in extracellular neurotransmitter levels in the brain. In vivo fast-scan cyclic voltammetry has been used extensively in mammalian models to characterize dopamine signals in both anesthetized and awake preparations, but has yet to be applied to a non-mammalian vertebrate. The goal of this study was to establish in vivo fast-scan cyclic voltammetry in a songbird, the European starling, to facilitate real-time measurements of extracellular catecholamine levels in the avian striatum. In urethane-anesthetized starlings, changes in catecholamine levels were evoked by electrical stimulation of the ventral tegmental area and measured at carbon-fiber microelectrodes positioned in the medial and lateral striata. Catecholamines were elicited by different stimulations, including trains related to phasic dopamine signaling in the rat, and were analyzed to quantify presynaptic mechanisms governing exocytotic release and neuronal uptake. Evoked extracellular catecholamine dynamics, maximal amplitude of the evoked catecholamine signal, and parameters for catecholamine release and uptake did not differ between striatal regions and were similar to those determined for dopamine in the rat dorsomedial striatum under similar conditions. Chemical identification of measured catecholamine by its voltammogram was consistent with the presence of both dopamine and norepinephrine in striatal tissue content. However, the high ratio of dopamine to norepinephrine in tissue content and the greater sensitivity of the carbon-fiber microelectrode to dopamine compared to norepinephrine favored the measurement of dopamine. Thus, converging evidence suggests that dopamine was the predominate analyte of the electrically evoked catecholamine signal measured in the striatum by fast-scan cyclic voltammetry. Overall, comparisons between the characteristics of these evoked signals suggested a similar presynaptic regulation of dopamine in the starling and rat striatum. Fast-scan cyclic voltammetry thus has the potential to be an invaluable tool for investigating the neural underpinnings of behavior in birds. PMID:25900708

Metapopulation dynamics and the evolution of dispersal

NASA Astrophysics Data System (ADS)

Parvinen, Kalle

A metapopulation consists of local populations living in habitat patches. In this chapter metapopulation dynamics and the evolution of dispersal is studied in two metapopulation models defined in discrete time. In the first model there are finitely many patches, and in the other one there are infinitely many patches, which allows to incorporate catastrophes into the model. In the first model, cyclic local population dynamics can be either synchronized or not, and increasing dispersal both synchronizes and stabilizes metapopulation dynamics. On the other hand, the type of dynamics has a strong effect on the evolution of dispersal. In case of non-synchronized metapopulation dynamics, dispersal is much more beneficial than in the case of synchronized metapopulation dynamics. Local dynamics has a substantial effect also on the possibility of evolutionary branching in both models. Furthermore, with an Allee effect in the local dynamics of the second model, even evolutionary suicide can occur. It is an evolutionary process in which a viable population adapts in such a way that it can no longer persist.

Inelastic Deformation of Metals and Structures under Dynamic and Quasi-Static Cyclic Loading.

DTIC Science & Technology

1983-05-01

the above inequa - lities is denoted by *. Note that ratchetting limits p corresponding to perfect plasticity material (Figo4b) can be generated from the...due to the employment of the kinematic hardening rule. In the intermediate regime R1 +R2, the behaviour changes from R1 to R2 when sufficient hardening

Walking dynamics of the passive compass-gait model under OGY-based control: Emergence of bifurcations and chaos

NASA Astrophysics Data System (ADS)

Gritli, Hassène; Belghith, Safya

2017-06-01

An analysis of the passive dynamic walking of a compass-gait biped model under the OGY-based control approach using the impulsive hybrid nonlinear dynamics is presented in this paper. We describe our strategy for the development of a simplified analytical expression of a controlled hybrid Poincaré map and then for the design of a state-feedback control. Our control methodology is based mainly on the linearization of the impulsive hybrid nonlinear dynamics around a desired nominal one-periodic hybrid limit cycle. Our analysis of the controlled walking dynamics is achieved by means of bifurcation diagrams. Some interesting nonlinear phenomena are displayed, such as the period-doubling bifurcation, the cyclic-fold bifurcation, the period remerging, the period bubbling and chaos. A comparison between the raised phenomena in the impulsive hybrid nonlinear dynamics and the hybrid Poincaré map under control was also presented.

The crack effect on instability in a machine tool spindle with gas bearings

NASA Astrophysics Data System (ADS)

Huang, Bo-Wun

2005-09-01

Gas-bearing spindles are required for increased spindle speed in precise machining. Due to manufacturing flaws or cyclic loading, cracks frequently appear in a rotating spindle systems. Cracks markedly affect the dynamic characteristics of rotating machinery. Hence, in this study, high-speed spindles with gas bearings and the crack effect on the instability dynamics are considered. Most investigations on dynamic characteristics of the spindle system were confined to ball-bearing-type spindles. This work examines the dynamic instability in a cracked rotating spindle system with gas bearings. A round Euler-Bernoulli beam is used to approximate the spindle. The Hamilton principle is applied to derive the equation of motion for the spindle system. The effects of crack depth, rotation speed and provided air pressure on the dynamic instability of a rotating spindle system are studied

Space Shuttle Main Engine structural analysis and data reduction/evaluation. Volume 7: High pressure fuel turbo-pump third stage impeller analysis

NASA Technical Reports Server (NTRS)

Pool, Kirby V.

1989-01-01

This volume summarizes the analysis used to assess the structural life of the Space Shuttle Main Engine (SSME) High Pressure Fuel Turbo-Pump (HPFTP) Third Stage Impeller. This analysis was performed in three phases, all using the DIAL finite element code. The first phase was a static stress analysis to determine the mean (non-varying) stress and static margin of safety for the part. The loads involved were steady state pressure and centrifugal force due to spinning. The second phase of the analysis was a modal survey to determine the vibrational modes and natural frequencies of the impeller. The third phase was a dynamic response analysis to determine the alternating component of the stress due to time varying pressure impulses at the outlet (diffuser) side of the impeller. The results of the three phases of the analysis show that the Third Stage Impeller operates very near the upper limits of its capability at full power level (FPL) loading. The static loading alone creates stresses in some areas of the shroud which exceed the yield point of the material. Additional cyclic loading due to the dynamic force could lead to a significant reduction in the life of this part. The cyclic stresses determined in the dynamic response phase of this study are based on an assumption regarding the magnitude of the forcing function.

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance.

PubMed

Glasl, Bettina; Herndl, Gerhard J; Frade, Pedro R

2016-09-01

Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics.

Probing the interaction between cHAVc3 peptide and the EC1 domain of E-cadherin using NMR and molecular dynamics simulations.

PubMed

Alaofi, Ahmed; Farokhi, Elinaz; Prasasty, Vivitri D; Anbanandam, Asokan; Kuczera, Krzysztof; Siahaan, Teruna J

2017-01-01

The goal of this work is to probe the interaction between cyclic cHAVc3 peptide and the EC1 domain of human E-cadherin protein. Cyclic cHAVc3 peptide (cyclo(1,6)Ac-CSHAVC-NH 2 ) binds to the EC1 domain as shown by chemical shift perturbations in the 2D 1 H,- 15 N-HSQC NMR spectrum. The molecular dynamics (MD) simulations of the EC1 domain showed folding of the C-terminal tail region into the main head region of the EC1 domain. For cHAVc3 peptide, replica exchange molecular dynamics (REMD) simulations generated five structural clusters of cHAVc3 peptide. Representative structures of cHAVc3 and the EC1 structure from MD simulations were used in molecular docking experiments with NMR constraints to determine the binding site of the peptide on EC1. The results suggest that cHAVc3 binds to EC1 around residues Y36, S37, I38, I53, F77, S78, H79, and I94. The dissociation constants (K d values) of cHAVc3 peptide to EC1 were estimated using the NMR chemical shifts data and the estimated K d s are in the range of .5 × 10 -5 -7.0 × 10 -5  M.

The microbiome of coral surface mucus has a key role in mediating holobiont health and survival upon disturbance

PubMed Central

Glasl, Bettina; Herndl, Gerhard J; Frade, Pedro R

2016-01-01

Microbes are well-recognized members of the coral holobiont. However, little is known about the short-term dynamics of mucus-associated microbial communities under natural conditions and after disturbances, and how these dynamics relate to the host's health. Here we examined the natural variability of prokaryotic communities (based on 16S ribosomal RNA gene amplicon sequencing) associating with the surface mucus layer (SML) of Porites astreoides, a species exhibiting cyclical mucus aging and shedding. Shifts in the prokaryotic community composition during mucus aging led to the prevalence of opportunistic and potentially pathogenic bacteria (Verrucomicrobiaceae and Vibrionaceae) in aged mucus and to a twofold increase in prokaryotic abundance. After the release of aged mucus sheets, the community reverted to its original state, dominated by Endozoicimonaceae and Oxalobacteraceae. Furthermore, we followed the fate of the coral holobiont upon depletion of its natural mucus microbiome through antibiotics treatment. After re-introduction to the reef, healthy-looking microbe-depleted corals started exhibiting clear signs of bleaching and necrosis. Recovery versus mortality of the P. astreoides holobiont was related to the degree of change in abundance distribution of the mucus microbiome. We conclude that the natural prokaryotic community inhabiting the coral SML contributes to coral health and that cyclical mucus shedding has a key role in coral microbiome dynamics. PMID:26953605

Enzyme-modified carbon-fiber microelectrode for the quantification of dynamic fluctuations of nonelectroactive analytes using fast-scan cyclic voltammetry.

PubMed

Lugo-Morales, Leyda Z; Loziuk, Philip L; Corder, Amanda K; Toups, J Vincent; Roberts, James G; McCaffrey, Katherine A; Sombers, Leslie A

2013-09-17

Neurotransmission occurs on a millisecond time scale, but conventional methods for monitoring nonelectroactive neurochemicals are limited by slow sampling rates. Despite a significant global market, a sensor capable of measuring the dynamics of rapidly fluctuating, nonelectroactive molecules at a single recording site with high sensitivity, electrochemical selectivity, and a subsecond response time is still lacking. To address this need, we have enabled the real-time detection of dynamic glucose fluctuations in live brain tissue using background-subtracted, fast-scan cyclic voltammetry. The novel microbiosensor consists of a simple carbon fiber surface modified with an electrodeposited chitosan hydrogel encapsulating glucose oxidase. The selectivity afforded by voltammetry enables quantitative and qualitative measurements of enzymatically generated H2O2 without the need for additional strategies to eliminate interfering agents. The microbiosensors possess a sensitivity and limit of detection for glucose of 19.4 ± 0.2 nA mM(-1) and 13.1 ± 0.7 μM, respectively. They are stable, even under deviations from physiological normoxic conditions, and show minimal interference from endogenous electroactive substances. Using this approach, we have quantitatively and selectively monitored pharmacologically evoked glucose fluctuations with unprecedented chemical and spatial resolution. Furthermore, this novel biosensing strategy is widely applicable to the immobilization of any H2O2 producing enzyme, enabling rapid monitoring of many nonelectroactive enzyme substrates.

Neural network controller development and implementation for spark ignition engines with high EGR levels.

PubMed

Vance, Jonathan Blake; Singh, Atmika; Kaul, Brian C; Jagannathan, Sarangapani; Drallmeier, James A

2007-07-01

Past research has shown substantial reductions in the oxides of nitrogen (NOx) concentrations by using 10%-25% exhaust gas recirculation (EGR) in spark ignition (SI) engines (see Dudek and Sain, 1989). However, under high EGR levels, the engine exhibits strong cyclic dispersion in heat release which may lead to instability and unsatisfactory performance preventing commercial engines to operate with high EGR levels. A neural network (NN)-based output feedback controller is developed to reduce cyclic variation in the heat release under high levels of EGR even when the engine dynamics are unknown by using fuel as the control input. A separate control loop was designed for controlling EGR levels. The stability analysis of the closed-loop system is given and the boundedness of the control input is demonstrated by relaxing separation principle, persistency of excitation condition, certainty equivalence principle, and linear in the unknown parameter assumptions. Online training is used for the adaptive NN and no offline training phase is needed. This online learning feature and model-free approach is used to demonstrate the applicability of the controller on a different engine with minimal effort. Simulation results demonstrate that the cyclic dispersion is reduced significantly using the proposed controller when implemented on an engine model that has been validated experimentally. For a single cylinder research engine fitted with a modern four-valve head (Ricardo engine), experimental results at 15% EGR indicate that cyclic dispersion was reduced 33% by the controller, an improvement of fuel efficiency by 2%, and a 90% drop in NOx from stoichiometric operation without EGR was observed. Moreover, unburned hydrocarbons (uHC) drop by 6% due to NN control as compared to the uncontrolled scenario due to the drop in cyclic dispersion. Similar performance was observed with the controller on a different engine.

Cyclic Mechanical Loading Is Essential for Rac1-Mediated Elongation and Remodeling of the Embryonic Mitral Valve.

PubMed

Gould, Russell A; Yalcin, Huseyin C; MacKay, Joanna L; Sauls, Kimberly; Norris, Russell; Kumar, Sanjay; Butcher, Jonathan T

2016-01-11

During valvulogenesis, globular endocardial cushions elongate and remodel into highly organized thin fibrous leaflets. Proper regulation of this dynamic process is essential to maintain unidirectional blood flow as the embryonic heart matures. In this study, we tested how mechanosensitive small GTPases, RhoA and Rac1, coordinate atrioventricular valve (AV) differentiation and morphogenesis. RhoA activity and its regulated GTPase-activating protein FilGAP are elevated during early cushion formation but decreased considerably during valve remodeling. In contrast, Rac1 activity was nearly absent in the early cushions but increased substantially as the valve matured. Using gain- and loss-of-function assays, we determined that the RhoA pathway was essential for the contractile myofibroblastic phenotype present in early cushion formation but was surprisingly insufficient to drive matrix compaction during valve maturation. The Rac1 pathway was necessary to induce matrix compaction in vitro through increased cell adhesion, elongation, and stress fiber alignment. Facilitating this process, we found that acute cyclic stretch was a potent activator of RhoA and subsequently downregulated Rac1 activity via FilGAP. On the other hand, chronic cyclic stretch reduced active RhoA and downstream FilGAP, which enabled Rac1 activation. Finally, we used partial atrial ligation experiments to confirm in vivo that altered cyclic mechanical loading augmented or restricted cushion elongation and thinning, directly through potentiation of active Rac1 and active RhoA, respectively. Together, these results demonstrate that cyclic mechanical signaling coordinates the RhoA to Rac1 signaling transition essential for proper embryonic mitral valve remodeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cyclic fatigue of three types of rotary nickel-titanium files in a dynamic model.

PubMed

Yao, James H; Schwartz, Scott A; Beeson, Thomas J

2006-01-01

The cyclic fatigue resistance of three types of nickel-titanium rotary files was compared in a model using reciprocating axial movement. The influence of file size and taper was also investigated and fracture patterns were examined under SEM. The 10 experimental groups consisted of ProFiles, K3s, and RaCe files, size 25 in .04 and .06 tapers, as well as ProFiles and K3s, size 40 in .04 and .06 tapers. Each file was rotated freely at 300 rpm inside a stainless steel tube with a 60 degree and 5 mm radius of curvature. A continuous 3 mm oscillating axial motion was applied at 1 cycle per second by attaching an electric dental handpiece to the most inferior load cell of an Instron machine using a custom-made jig. The number of rotations to failure was determined and analyzed using analysis of variance and Tukey's post hoc tests. Overall, K3 25/.04 files were significantly more resistant to cyclic fatigue compared to any other group in this study. In the 25/.04 category, K3s were significantly more resistant to failure than ProFiles and RaCe files. Also in the same category, ProFiles significantly outlasted RaCe files. In the 25/.06 group, K3s and ProFiles were significantly more resistant to failure than RaCe files, but K3s were not significantly different than ProFiles. In the 40/.04 and 40/.06 groups, K3s were significantly more resistant to cyclic fatigue than ProFiles. SEM observations demonstrated mostly a ductile mode of fracture. The results suggest that different cross-sectional designs, diameters, and tapers all contribute to a nickel-titanium instrument's vulnerability to cyclic failure.

Towards a better understanding of the respective effects of milk yield and body condition dynamics on reproduction in Holstein dairy cows.

PubMed

Cutullic, E; Delaby, L; Gallard, Y; Disenhaus, C

2012-03-01

The overall reproductive performance has decreased over the last decades, involving changes in cyclicity, oestrous behaviour and fertility. High milk yield (MY), low body condition score (BCS) and large body condition (BC) loss have been identified as risk factors. However, these effects are often confounded, as high MY and body lipid reserve mobilization are correlated. The aim of this study was to evaluate the respective effects of MY and BC on post-partum ovarian cyclicity, oestrus and fertility of Holstein cows. This study provides novel information, as MY and BC change were uncoupled in the overall dataset that included 98 lactations and milk progesterone profiles. Cows were assigned to two feeding-level groups: high feed, which achieved high MY and moderate BC loss throughout lactation (8410 kg, -1.17 unit from calving to nadir BCS), and low feed, which limited MY and triggered a large BC loss (5719 kg, -1.54 unit). MY and BC had different effects at different stages of the reproductive process. Cyclicity as well as non-fertilization and early embryo mortality were mainly driven by body lipid reserves, whereas oestrous behaviour and late embryo mortality were related to MY. The results point to possible uncoupling between cyclicity, oestrus and early and late embryo survival allowing compensation along the reproductive process and leading to similar final reproductive performance. In compact calving systems, which require high pregnancy rates within a short period, higher MY strategies appear unsuitable even where BCS is maintained, owing to depressed oestrous behaviour and probably increased late embryo mortality, which delays rebreeding. Similarly, strategies that compromise cyclicity and fertility by excessively low BCS are unsuitable.

Experimental and Numerical Studies on Development of Fracture Process Zone (FPZ) in Rocks under Cyclic and Static Loadings

NASA Astrophysics Data System (ADS)

Ghamgosar, M.; Erarslan, N.

2016-03-01

The development of fracture process zones (FPZ) in the Cracked Chevron Notched Brazilian Disc (CCNBD) monsonite and Brisbane tuff specimens was investigated to evaluate the mechanical behaviour of brittle rocks under static and various cyclic loadings. An FPZ is a region that involves different types of damage around the pre-existing and/or stress-induced crack tips in engineering materials. This highly damaged area includes micro- and meso-cracks, which emerge prior to the main fracture growth or extension and ultimately coalescence to macrofractures, leading to the failure. The experiments and numerical simulations were designed for this study to investigate the following features of FPZ in rocks: (1) ligament connections and (2) microcracking and its coalescence in FPZ. A Computed Tomography (CT) scan technique was also used to investigate the FPZ behaviour in selected rock specimens. The CT scan results showed that the fracturing velocity is entirely dependent on the appropriate amount of fracture energy absorbed in rock specimens due to the change of frequency and amplitudes of the dynamic loading. Extended Finite Element Method (XFEM) was used to compute the displacements, tensile stress distribution and plastic energy dissipation around the propagating crack tip in FPZ. One of the most important observations, the shape of FPZ and its extension around the crack tip, was made using numerical and experimental results, which supported the CT scan results. When the static rupture and the cyclic rupture were compared, the main differences are twofold: (1) the number of fragments produced is much greater under cyclic loading than under static loading, and (2) intergranular cracks are formed due to particle breakage under cyclic loading compared with smooth and bright cracks along cleavage planes under static loading.

Translocation Thermodynamics of Linear and Cyclic Nonaarginine into Model DPPC Bilayer via Coarse-Grained Molecular Dynamics Simulation: Implications of Pore Formation and Nonadditivity

PubMed Central

2015-01-01

Structural mechanisms and underlying thermodynamic determinants of efficient internalization of charged cationic peptides (cell-penetrating peptides, CPPs) such as TAT, polyarginine, and their variants, into cells, cellular constructs, and model membrane/lipid bilayers (large and giant unilamellar or multilamelar vesicles) continue to garner significant attention. Two widely held views on the translocation mechanism center on endocytotic and nonendocytotic (diffusive) processes. Espousing the view of a purely diffusive internalization process (supported by recent experimental evidence, [Säälik, P.; et al. J. Controlled Release2011, 153, 117–125]), we consider the underlying free energetics of the translocation of a nonaarginine peptide (Arg9) into a model DPPC bilayer. In the case of the Arg9 cationic peptide, recent experiments indicate a higher internalization efficiency of the cyclic structure (cyclic Arg9) relative to the linear conformer. Furthermore, recent all-atom resolution molecular dynamics simulations of cyclic Arg9 [Huang, K.; et al. Biophys. J., 2013, 104, 412–420] suggested a critical stabilizing role of water- and lipid-constituted pores that form within the bilayer as the charged Arg9 translocates deep into the bilayer center. Herein, we use umbrella sampling molecular dynamics simulations with coarse-grained Martini lipids, polarizable coarse-grained water, and peptide to explore the dependence of translocation free energetics on peptide structure and conformation via calculation of potentials of mean force along preselected reaction paths allowing and preventing membrane deformations that lead to pore formation. Within the context of the coarse-grained force fields we employ, we observe significant barriers for Arg9 translocation from bulk aqueous solution to bilayer center. Moreover, we do not find free-energy minima in the headgroup–water interfacial region, as observed in simulations using all-atom force fields. The pore-forming paths systematically predict lower free-energy barriers (ca. 90 kJ/mol lower) than the non pore-forming paths, again consistent with all-atom force field simulations. The current force field suggests no preference for the more compact or covalently cyclic structures upon entering the bilayer. Decomposition of the PMF into the system’s components indicates that the dominant stabilizing contribution along the pore-forming path originates from the membrane as both layers of it deformed due to the formation of pore. Furthermore, our analysis revealed that although there is significant entropic stabilization arising from the enhanced configurational entropy exposing more states as the peptide moves through the bilayer, the enthalpic loss (as predicted by the interactions of this coarse-grained model) far outweighs any former stabilization, thus leading to significant barrier to translocation. Finally, we observe reduction in the translocation free-energy barrier for a second Arg9 entering the bilayer in the presence of an initial peptide restrained at the center, again, in qualitative agreement with all-atom force fields. PMID:24506488

Life extending control: An interdisciplinary engineering thrust

NASA Technical Reports Server (NTRS)

Lorenzo, Carl F.; Merrill, Walter C.

1991-01-01

The concept of Life Extending Control (LEC) is introduced. Possible extensions to the cyclic damage prediction approach are presented based on the identification of a model from elementary forms. Several candidate elementary forms are presented. These extensions will result in a continuous or differential form of the damage prediction model. Two possible approaches to the LEC based on the existing cyclic damage prediction method, the measured variables LEC and the estimated variables LEC, are defined. Here, damage estimates or measurements would be used directly in the LEC. A simple hydraulic actuator driven position control system example is used to illustrate the main ideas behind LEC. Results from a simple hydraulic actuator example demonstrate that overall system performance (dynamic plus life) can be maximized by accounting for component damage in the control design.

Development of a new connection for precast concrete walls subjected to cyclic loading

NASA Astrophysics Data System (ADS)

Vaghei, Ramin; Hejazi, Farzad; Taheri, Hafez; Jaafar, Mohd Saleh; Aziz, Farah Nora Aznieta Abdul

2017-01-01

The Industrialized Building System (IBS) was recently introduced to minimize the time and cost of project construction. Accordingly, ensuring the integration of the connection of precast components in IBS structures is an important factor that ensures stability of buildings subjected to dynamic loads from earthquakes, vehicles, and machineries. However, structural engineers still lack knowledge on the proper connection and detailed joints of IBS structure construction. Therefore, this study proposes a special precast concrete wall-to-wall connection system for dynamic loads that resists multidirectional imposed loads and reduces vibration effects (PI2014701723). This system is designed to connect two adjacent precast wall panels by using two steel U-shaped channels (i.e., male and female joints). During casting, each joint is adapted for incorporation into a respective wall panel after considering the following conditions: one side of the steel channel opens into the thickness face of the panel; a U-shaped rubber is implemented between the two channels to dissipate the vibration effect; and bolts and nuts are used to create an extension between the two U-shaped male and female steel channels. The developed finite element model of the precast wall is subjected to cyclic loads to evaluate the performance of the proposed connection during an imposed dynamic load. Connection performance is then compared with conventional connections based on the energy dissipation, stress, deformation, and concrete damage in the plastic range. The proposed precast connection is capable of exceeding the energy absorption of precast walls subjected to dynamic load, thereby improving its resistance behavior in all principal directions.

Modeling of abnormal mechanical properties of nickel-based single crystal superalloy by three-dimensional discrete dislocation dynamics

NASA Astrophysics Data System (ADS)

Yang, Hui; Li, Zhenhuan; Huang, Minsheng

2014-12-01

Unlike common single crystals, the nickel-based single crystal superalloy shows surprisingly anomalous flow strength (i.e. with the increase of temperature, the yield strength first increases to a peak value and then decreases) and tension-compression (TC) asymmetry. A comprehensive three-dimensional discrete dislocation dynamics (3D-DDD) procedure was developed to model these abnormal mechanical properties. For this purpose, a series of complicated dynamic evolution details of Kear-Wilsdorf (KW) locks, which are closely related to the flow strength anomaly and TC asymmetry, were incorporated into this 3D-DDD framework. Moreover, the activation of the cubic slip system, which is the origin of the decrease in yield strength with increasing temperature at relatively high temperatures, was especially taken into account by introducing a competition criterion between the unlocking of the KW locks and the activation of the cubic slip system. To test our framework, a series of 3D-DDD simulations were performed on a representative volume cell model with a cuboidal Ni3Al precipitate phase embedded in a nickel matrix. Results show that the present 3D-DDD procedure can successfully capture the dynamic evolution of KW locks, the flow strength anomaly and TC asymmetry. Then, the underlying dislocation mechanisms leading to these abnormal mechanical responses were investigated and discussed in detail. Finally, a cyclic deformation of the nickel-based single crystal superalloy was modeled by using the present DDD model, with a special focus on the influence of KW locks on the Bauschinger effect and cyclic softening.

Analysis of Handling Qualities Design Criteria for Active Inceptor Force-Feel Characteristics

NASA Technical Reports Server (NTRS)

Malpica, Carlos A.; Lusardi, Jeff A.

2013-01-01

The force-feel system characteristics of the cyclic inceptors of most helicopters are set based on the characteristics of the mechanical components in the control system (mass, springs, friction dampers, etc.). For these helicopters, the force-feel characteristics typically remain constant over the entire flight envelope, with perhaps a trim release to minimize control forces while maneuvering. With the advent of fly-by-wire control systems and active inceptors in helicopters, the force-feel characteristics are now determined by the closed-loop response of the active inceptor itself as defined by the inertia, force/displacement gradient, damping, breakout force and detent shape configuration parameters in the inceptor control laws. These systems give the flexibility to dynamically prescribe different feel characteristics for different control modes or flight conditions, and the ability to provide tactile cueing to the pilot through the actively controlled side-stick or center-stick cyclic inceptor. For rotorcraft, a few studies have been conducted to assess the effects of cyclic force-feel characteristics on handling qualities in flight. An early study provided valuable insight into the static force-deflection characteristics (force gradient) and the number of axes controlled by the side-stick controller for the U.S. Army's Advanced Digital/Optical Control System (ADOCS) demonstrator aircraft [1]. The first of a series of studies providing insight on the inceptor dynamic force-feel characteristics was conducted on the NASA/Army CH-47B variable-stability helicopter [2]. This work led to a proposed requirement that set boundaries based on the cyclic natural frequency and inertia, with the stipulation of a lower damping ratio limit of 0.3 [3]. A second study was conducted by the Canadian Institute for Aerospace Research using their variable-stability Bell 205A helicopter [4]. This research suggested boundaries for stick dynamics based on natural frequency and damping ratio. While these two studies produced boundaries for acceptable/unacceptable stick dynamics for rotorcraft, they were not able to provide guidance on how variations of the stick dynamics in the acceptable region impact handling qualities. More recently, a ground based simulation study [5] suggested little benefit was to be obtained from variations of the damping ratio for a side-stick controller exhibiting high natural frequencies (greater than 17 rad/s) and damping ratios (greater than 2.0). A flight test campaign was conducted concurrently on the RASCAL JUH-60A in-flight simulator and the ACT/FHS EC-135 in flight simulator [6]. Upon detailed analysis of the pilot evaluations the study identified a clear preference for a high damping ratio and natural frequency of the center stick inceptors. Side stick controllers were found to be less sensitive to the damping. While these studies have compiled a substantial amount of data, in the form of qualitative and quantitative pilot opinion, a fundamental analysis of the effect of the inceptor force-feel system on flight control is found to be lacking. The study of Ref. [6] specifically concluded that a systematic analysis was necessary, since discrepancies with the assigned handling qualities showed that proposed analytical design metrics, or criteria, were not suitable. The overall goal of the present study is to develop a clearer fundamental understanding of the underlying mechanisms associated with the inceptor dynamics that govern the handling qualities using a manageable analytical methodology.

Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study.

PubMed

Kanti Si, Mrinal; Sen, Anik; Ganguly, Bishwajit

2017-05-10

G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves. In this study, linear and cyclic protonated diamines showed remarkable binding affinity for G-tetrads using hydrogen bonding interactions. The DFT M06-2X/6-31G(d)//B3LYP/6-31+G(d) level of theory showed that the cyclic ee-1,2-CHDA (equatorial-equatorial form of 1,2-disubstituted cyclohexadiamine di-cation) binds to the G-tetrads very strongly (∼70.0 kcal mol -1 ), with a much higher binding energy than the linear protonated diamines. The binding affinity of ligands for G-tetrads with counterions has also been examined. The binding preference of these small ligands for G-tetrads is higher than for DNA-duplex. The binding affinity of an intercalated acridine-based ligand (BRACO-19) for G-quadruplexes has been examined and the binding energy is relatively lower than that for the 1,2 disubstituted cyclohexadiamine di-cation with G-tetrads. The atoms-in-molecules (AIM) analysis reveals that the hydrogen bonding interactions between the organic systems with G-tetrads are primarily electrostatic in nature. The molecular dynamics simulations performed using a classical force field (GROMACS) also supported the phosphate backbone sites of G-quadruplex-DNA to bind to these diamines. To mimic the structural pattern of BRACO-19, the designed inhibitor N,2-bis-2(3,4-aminocyclohexyl) acetamide (9) examined possesses two 1,2-CHDA moieties linked through an acetamide group. The molecular dynamics results showed that the designed molecule 9 can efficiently bind to the base-pairs and the phosphate backbone of G quadruplex-DNA using H-bonding interactions. The binding affinity calculated for the intercalated acridine-based drug (BRACO-19) with G-quadruplexes is weaker compared to ee-1,2-CHDA. These ligands deliver a different binding motif (hydrogen bonding) compared to the reported G-quadruplex binders of π-delocalized systems and will kindle interest in examining such scaffolds to stabilize DNA.

Conservation of coevolving protein interfaces bridges prokaryote–eukaryote homologies in the twilight zone

PubMed Central

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-01-01

Protein–protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein–protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein–protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein–protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach. PMID:27965389

Conservation of coevolving protein interfaces bridges prokaryote-eukaryote homologies in the twilight zone.

PubMed

Rodriguez-Rivas, Juan; Marsili, Simone; Juan, David; Valencia, Alfonso

2016-12-27

Protein-protein interactions are fundamental for the proper functioning of the cell. As a result, protein interaction surfaces are subject to strong evolutionary constraints. Recent developments have shown that residue coevolution provides accurate predictions of heterodimeric protein interfaces from sequence information. So far these approaches have been limited to the analysis of families of prokaryotic complexes for which large multiple sequence alignments of homologous sequences can be compiled. We explore the hypothesis that coevolution points to structurally conserved contacts at protein-protein interfaces, which can be reliably projected to homologous complexes with distantly related sequences. We introduce a domain-centered protocol to study the interplay between residue coevolution and structural conservation of protein-protein interfaces. We show that sequence-based coevolutionary analysis systematically identifies residue contacts at prokaryotic interfaces that are structurally conserved at the interface of their eukaryotic counterparts. In turn, this allows the prediction of conserved contacts at eukaryotic protein-protein interfaces with high confidence using solely mutational patterns extracted from prokaryotic genomes. Even in the context of high divergence in sequence (the twilight zone), where standard homology modeling of protein complexes is unreliable, our approach provides sequence-based accurate information about specific details of protein interactions at the residue level. Selected examples of the application of prokaryotic coevolutionary analysis to the prediction of eukaryotic interfaces further illustrate the potential of this approach.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes.

PubMed

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-08-07

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary 'arms race' between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres.

Culture-gene coevolution of individualism-collectivism and the serotonin transporter gene.

PubMed

Chiao, Joan Y; Blizinsky, Katherine D

2010-02-22

Culture-gene coevolutionary theory posits that cultural values have evolved, are adaptive and influence the social and physical environments under which genetic selection operates. Here, we examined the association between cultural values of individualism-collectivism and allelic frequency of the serotonin transporter functional polymorphism (5-HTTLPR) as well as the role this culture-gene association may play in explaining global variability in prevalence of pathogens and affective disorders. We found evidence that collectivistic cultures were significantly more likely to comprise individuals carrying the short (S) allele of the 5-HTTLPR across 29 nations. Results further show that historical pathogen prevalence predicts cultural variability in individualism-collectivism owing to genetic selection of the S allele. Additionally, cultural values and frequency of S allele carriers negatively predict global prevalence of anxiety and mood disorder. Finally, mediation analyses further indicate that increased frequency of S allele carriers predicted decreased anxiety and mood disorder prevalence owing to increased collectivistic cultural values. Taken together, our findings suggest culture-gene coevolution between allelic frequency of 5-HTTLPR and cultural values of individualism-collectivism and support the notion that cultural values buffer genetically susceptible populations from increased prevalence of affective disorders. Implications of the current findings for understanding culture-gene coevolution of human brain and behaviour as well as how this coevolutionary process may contribute to global variation in pathogen prevalence and epidemiology of affective disorders, such as anxiety and depression, are discussed.

Co-evolution in a landrace meta-population: two closely related pathogens interacting with the same host can lead to different adaptive outcomes

PubMed Central

Rau, Domenico; Rodriguez, Monica; Leonarda Murgia, Maria; Balmas, Virgilio; Bitocchi, Elena; Bellucci, Elisa; Nanni, Laura; Attene, Giovanna; Papa, Roberto

2015-01-01

We examined the local adaptation patterns in a system comprising several interconnected heterogeneous plant populations from which populations of two phylogenetically closely related pathogens were also sampled. The host is Hordeum vulgare (cultivated barley); the pathogens are Pyrenophora teres f. teres (net form) and Pyrenophora teres f. maculata (spot form), the causal agents of barley net blotch. We integrated two approaches, the comparison between the population structures of the host and the pathogens, and a cross-inoculation test. We demonstrated that two closely related pathogens with very similar niche specialisation and life-styles can give rise to different co-evolutionary outcomes on the same host. Indeed, we detected local adaptation for the net form of the pathogen but not for the spot form. We also provided evidence that an a-priori well-known resistance quantitative-trait-locus on barley chromosome 6H is involved in the co-evolutionary ‘arms race’ between the plant and the net-form pathogen. Moreover, data suggested latitudinal clines of host resistance and that different ecological conditions can result in differential selective pressures at different sites. Our data are of interest for on-farm conservation of plant genetic resources, as also in establishing efficient breeding programs and strategies for deployment of resistance genes of P. teres. PMID:26248796

Evolution of tolerance by magpies to brood parasitism by great spotted cuckoos.

PubMed

Soler, J J; Martín-Gálvez, D; Martínez, J G; Soler, M; Canestrari, D; Abad-Gómez, J M; Møller, A P

2011-07-07

Hosts may use two different strategies to ameliorate negative effects of a given parasite burden: resistance or tolerance. Although both resistance and tolerance of parasitism should evolve as a consequence of selection pressures owing to parasitism, the study of evolutionary patterns of tolerance has traditionally been neglected by animal biologists. Here, we explore geographical covariation between tolerance of magpies (Pica pica) and brood parasitism by the great spotted cuckoo (Clamator glandarius) in nine different sympatric populations. We estimated tolerance as the slope of the regression of number of magpie fledglings (i.e. host fitness) on number of cuckoo eggs laid in non-depredated nests (which broadly equals parasite burden). We also estimated prevalence of parasitism and level of host resistance (i.e. rejection rates of mimetic model eggs) in these nine populations. In accordance with the hypothetical role of tolerance in the coevolutionary process between magpies and cuckoos we found geographical variation in tolerance estimates that positively covaried with prevalence of parasitism. Levels of resistance and tolerance were not associated, possibly suggesting the lack of a trade-off between the two kinds of defences against great spotted cuckoo parasitism for magpies. We discuss the results in the framework of a mosaic of coevolutionary interactions along the geographical distribution of magpies and great spotted cuckoos for which we found evidence that tolerance plays a major role.

Spatial relationships in a dendritic network: the herpetofaunal metacommunity of the Mattole River catchment of northwest California.

Treesearch

Hartwell Welsh; Garth Hodgson

2010-01-01

We investigated the aquatic and riparian herpetofauna in a 789 km² river catchment in northwest California to examine competing theories of biotic community structuring in catchment stream networks. Research in fluvial geomorphology has resulted in multi-scale models of dynamic processes that cyclically create, maintain, and destroy environments in stream...

Molecular Engineering for Mechanically Resilient and Stretchable Electronic Polymers and Composites

DTIC Science & Technology

2016-06-08

conjugated polymers and composites by analysis of the structural determinants of the mechanical properties. We developed coarse-grained molecular...dynamics simulations that predicted the mechanical properties of conjugated polymers and polymer -fullerene composites. We elucidated the mechanical...We also determined the effect of cyclic stretching on the microstructure and mechanical properties of conjugated polymers . We used many of

Life-stage differences in spatial genetic structure in an irruptive forest insect: implications for dispersal and spatial synchrony

Treesearch

Patrick M.A. James; Barry Cooke; Bryan M.T. Brunet; Lisa M. Lumley; Felix A.H. Sperling; Marie-Josee Fortin; Vanessa S. Quinn; Brian R. Sturtevant

2015-01-01

Dispersal determines the flux of individuals, energy and information and is therefore a key determinant of ecological and evolutionary dynamics. Yet, it remains difficult to quantify its importance relative to other factors. This is particularly true in cyclic populations in which demography, drift and dispersal contribute to spatio-temporal variability in genetic...

Molecular Transport in Ionic Polymer Membranes Under an Applied Voltage

DTIC Science & Technology

2013-11-22

in Porous Carbon Electrodes in Supercapacitors Using in Situ Infrared Spectroelectrochemistry, Journal of the American Chemical Society (08 2013...3. Ion Dynamics in Porous Carbon Electrodes in Supercapacitors Using in situ Infrared Spectroelectrochemistry Electrochemical double layer...capacitors (EDLC), or supercapacitors , rely on electrosorption of ions by porous carbon electrodes and offer a higher power and a longer cyclic

Mesoscopic interactions and species coexistence in evolutionary game dynamics of cyclic competitions.

PubMed

Cheng, Hongyan; Yao, Nan; Huang, Zi-Gang; Park, Junpyo; Do, Younghae; Lai, Ying-Cheng

2014-12-15

Evolutionary dynamical models for cyclic competitions of three species (e.g., rock, paper, and scissors, or RPS) provide a paradigm, at the microscopic level of individual interactions, to address many issues in coexistence and biodiversity. Real ecosystems often involve competitions among more than three species. By extending the RPS game model to five (rock-paper-scissors-lizard-Spock, or RPSLS) mobile species, we uncover a fundamental type of mesoscopic interactions among subgroups of species. In particular, competitions at the microscopic level lead to the emergence of various local groups in different regions of the space, each involving three species. It is the interactions among the groups that fundamentally determine how many species can coexist. In fact, as the mobility is increased from zero, two transitions can occur: one from a five- to a three-species coexistence state and another from the latter to a uniform, single-species state. We develop a mean-field theory to show that, in order to understand the first transition, group interactions at the mesoscopic scale must be taken into account. Our findings suggest, more broadly, the importance of mesoscopic interactions in coexistence of great many species.

Comprehensive Forced Response Analysis of J2X Turbine Bladed-Discs with 36- Degree Variation in CFD Loading

NASA Technical Reports Server (NTRS)

Elrod, David; Christensen, Eric; Brown, Andrew

2011-01-01

At NASA/MSFC, Structural Dynamics personnel continue to perform advanced analysis for the turbomachinery in the J2X Rocket Engine, which is under consideration for the new Space Launch System. One of the most challenging analyses in the program is predicting turbine blade structural capability. Resonance was predicted by modal analysis, so comprehensive forced response analyses using high fidelity cyclic symmetric finite element models were initiated as required. Analysis methodologies up to this point have assumed the flow field could be fully described by a sector, so the loading on every blade would be identical as it travelled through it. However, in the J2X the CFD flow field varied over the 360 deg of a revolution because of the flow speeds and tortuous axial path. MSFC therefore developed a complex procedure using Nastran Dmap's and Matlab scripts to apply this circumferentially varying loading onto the cyclically symmetric structural models to produce accurate dynamic stresses for every blade on the disk. This procedure is coupled with static, spin, and thermal loading to produce high cycle fatigue safety factors resulting in much more accurate analytical assessments of the blades.

Direct observation of ring-opening dynamics in strong-field ionized selenophene using femtosecond inner-shell absorption spectroscopy

DOE PAGES

Lackner, Florian; Chatterley, Adam S.; Pemmaraju, C. D.; ...

2016-12-21

Femtosecond extreme ultraviolet transient absorption spectroscopy is used to explore strong-field ionization induced dynamics in selenophene (C 4H 4Se). The dynamics are monitored in real-time from the viewpoint of the Se atom by recording the temporal evolution of element-specific spectral features near the Se 3d inner-shell absorption edge (~58 eV). The interpretation of the experimental results is supported by first-principles time-dependent density functional theory calculations. The experiments simultaneously capture the instantaneous population of stable molecular ions, the emergence and decay of excited cation states, and the appearance of atomic fragments. The experiments reveal, in particular, insight into the strong-field inducedmore » ring-opening dynamics in the selenophene cation, which are traced by the emergence of non-cyclic molecules as well as the liberation of Se + ions within an overall time scale of approximately 170 fs. In this study, we propose that both products may be associated with dynamics on the same electronic surfaces but with different degrees of vibrational excitation. The time-dependent inner-shell absorption features provide direct evidence for a complex relaxation mechanism that may be approximated by a two-step model, whereby the initially prepared, excited cyclic cation decays within τ 1 = 80 ± 30 fs into a transient molecular species, which then gives rise to the emergence of bare Se + and ring-open cations within an additional τ 2 = 80 ± 30 fs. The combined experimental and theoretical results suggest a close relationship between σ* excited cation states and the observed ring-opening reactions. In conclusion, the findings demonstrate that the combination of femtosecond time-resolved core-level spectroscopy with ab initio estimates of spectroscopic signatures provide new insights into complex, ultrafast photochemical reactions such as ring-opening dynamics in organic molecules in real-time and with simultaneous sensitivity for electronic and structural rearrangements.« less

Characterizing dynamic amplitude of low-frequency fluctuation and its relationship with dynamic functional connectivity: An application to schizophrenia.

PubMed

Fu, Zening; Tu, Yiheng; Di, Xin; Du, Yuhui; Pearlson, G D; Turner, J A; Biswal, Bharat B; Zhang, Zhiguo; Calhoun, V D

2017-09-20

The human brain is a highly dynamic system with non-stationary neural activity and rapidly-changing neural interaction. Resting-state dynamic functional connectivity (dFC) has been widely studied during recent years, and the emerging aberrant dFC patterns have been identified as important features of many mental disorders such as schizophrenia (SZ). However, only focusing on the time-varying patterns in FC is not enough, since the local neural activity itself (in contrast to the inter-connectivity) is also found to be highly fluctuating from research using high-temporal-resolution imaging techniques. Exploring the time-varying patterns in brain activity and their relationships with time-varying brain connectivity is important for advancing our understanding of the co-evolutionary property of brain network and the underlying mechanism of brain dynamics. In this study, we introduced a framework for characterizing time-varying brain activity and exploring its associations with time-varying brain connectivity, and applied this framework to a resting-state fMRI dataset including 151 SZ patients and 163 age- and gender matched healthy controls (HCs). In this framework, 48 brain regions were first identified as intrinsic connectivity networks (ICNs) using group independent component analysis (GICA). A sliding window approach was then adopted for the estimation of dynamic amplitude of low-frequency fluctuation (dALFF) and dFC, which were used to measure time-varying brain activity and time-varying brain connectivity respectively. The dALFF was further clustered into six reoccurring states by the k-means clustering method and the group difference in occurrences of dALFF states was explored. Lastly, correlation coefficients between dALFF and dFC were calculated and the group difference in these dALFF-dFC correlations was explored. Our results suggested that 1) ALFF of brain regions was highly fluctuating during the resting-state and such dynamic patterns are altered in SZ, 2) dALFF and dFC were correlated in time and their correlations are altered in SZ. The overall results support and expand prior work on abnormalities of brain activity, static FC (sFC) and dFC in SZ, and provide new evidence on aberrant time-varying brain activity and its associations with brain connectivity in SZ, which might underscore the disrupted brain cognitive functions in this mental disorder. Copyright © 2017 Elsevier Inc. All rights reserved.

Quantum optimal control pathways of ozone isomerization dynamics subject to competing dissociation: A two-state one-dimensional model

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

Kurosaki, Yuzuru, E-mail: kurosaki.yuzuru@jaea.go.jp; Ho, Tak-San, E-mail: tsho@Princeton.EDU; Rabitz, Herschel, E-mail: hrabitz@Princeton.EDU

We construct a two-state one-dimensional reaction-path model for ozone open → cyclic isomerization dynamics. The model is based on the intrinsic reaction coordinate connecting the cyclic and open isomers with the O{sub 2} + O asymptote on the ground-state {sup 1}A{sup ′} potential energy surface obtained with the high-level ab initio method. Using this two-state model time-dependent wave packet optimal control simulations are carried out. Two possible pathways are identified along with their respective band-limited optimal control fields; for pathway 1 the wave packet initially associated with the open isomer is first pumped into a shallow well on the excitedmore » electronic state potential curve and then driven back to the ground electronic state to form the cyclic isomer, whereas for pathway 2 the corresponding wave packet is excited directly to the primary well of the excited state potential curve. The simulations reveal that the optimal field for pathway 1 produces a final yield of nearly 100% with substantially smaller intensity than that obtained in a previous study [Y. Kurosaki, M. Artamonov, T.-S. Ho, and H. Rabitz, J. Chem. Phys. 131, 044306 (2009)] using a single-state one-dimensional model. Pathway 2, due to its strong coupling to the dissociation channel, is less effective than pathway 1. The simulations also show that nonlinear field effects due to molecular polarizability and hyperpolarizability are small for pathway 1 but could become significant for pathway 2 because much higher field intensity is involved in the latter. The results suggest that a practical control may be feasible with the aid of a few lowly excited electronic states for ozone isomerization.« less

The influence of topographic and dynamic cyclic variables on the distribution of small cetaceans in a shallow coastal system.

PubMed

de Boer, Marijke N; Simmonds, Mark P; Reijnders, Peter J H; Aarts, Geert

2014-01-01

The influence of topographic and temporal variables on cetacean distribution at a fine-scale is still poorly understood. To study the spatial and temporal distribution of harbour porpoise Phocoena phocoena and the poorly known Risso's dolphin Grampus griseus we carried out land-based observations from Bardsey Island (Wales, UK) in summer (2001-2007). Using Kernel analysis and Generalized Additive Models it was shown that porpoises and Risso's appeared to be linked to topographic and dynamic cyclic variables with both species using different core areas (dolphins to the West and porpoises to the East off Bardsey). Depth, slope and aspect and a low variation in current speed (for Risso's) were important in explaining the patchy distributions for both species. The prime temporal conditions in these shallow coastal systems were related to the tidal cycle (Low Water Slack and the flood phase), lunar cycle (a few days following the neap tidal phase), diel cycle (afternoons) and seasonal cycle (peaking in August) but differed between species on a temporary but predictable basis. The measure of tidal stratification was shown to be important. Coastal waters generally show a stronger stratification particularly during neap tides upon which the phytoplankton biomass at the surface rises reaching its maximum about 2-3 days after neap tide. It appeared that porpoises occurred in those areas where stratification is maximised and Risso's preferred more mixed waters. This fine-scale study provided a temporal insight into spatial distribution of two species that single studies conducted over broader scales (tens or hundreds of kilometers) do not achieve. Understanding which topographic and cyclic variables drive the patchy distribution of porpoises and Risso's in a Headland/Island system may form the initial basis for identifying potentially critical habitats for these species.

Dynamic effect of the tibialis posterior muscle on the arch of the foot during cyclic axial loading.

PubMed

Kamiya, Tomoaki; Uchiyama, Eiichi; Watanabe, Kota; Suzuki, Daisuke; Fujimiya, Mineko; Yamashita, Toshihiko

2012-11-01

The most common cause of acquired flatfoot deformity is tibialis posterior tendon dysfunction. The present study compared the change in medial longitudinal arch height during cyclic axial loading with and without activated tibialis posterior tendon force. Fourteen normal, fresh frozen cadaveric legs were used. A total of 10,000 cyclic axial loadings of 500 N were applied to the longitudinal axis of the tibia. The 32-N tibialis posterior tendon forces were applied to the specimens of the active group (n=7). Specimens of another group (non-active group, n=7) were investigated without the tibialis posterior tendon force. The bony arch index was calculated from the displacement of the navicular height. The mean initial bony arch indexes with maximal weightbearing were 0.239 (SD 0.009) in active group and 0.239 (SD 0.014) in non-active group. After 7000 cycles, the bony arch indexes with maximal weightbearing were significantly greater in the active group (mean 0.214, SD 0.013) than in the non-active group (mean 0.199, SD 0.013). The mean bony arch indexes with maximal weightbearing after 10,000 cycles were 0.212 (SD 0.011) in the active group and 0.196 (SD 0.015) in the non-active group. The passive supportive structures were inadequate, and the tibialis posterior muscle was essential to maintain the medial longitudinal arch of the foot in the dynamic weightbearing condition. The findings underscore that physical therapy and arch supportive equipments are important to prevent flatfoot deformity in the condition of weakness or dysfunction of the tibialis posterior muscle. Copyright © 2012 Elsevier Ltd. All rights reserved.

Validation of the Dynamic Recrystallization (DRX) Mechanism for Whisker and Hillock Growth on Sn Thin Films

NASA Astrophysics Data System (ADS)

Vianco, P. T.; Neilsen, M. K.; Rejent, J. A.; Grant, R. P.

2015-10-01

A study was performed to validate a first-principles model for whisker and hillock formation based on the cyclic dynamic recrystallization (DRX) mechanism in conjunction with long-range diffusion. The test specimens were evaporated Sn films on Si having thicknesses of 0.25 μm, 0.50 μm, 1.0 μm, 2.0 μm, and 4.9 μm. Air annealing was performed at 35°C, 60°C, 100°C, 120°C, or 150°C over a time duration of 9 days. The stresses, anelastic strains, and strain rates in the Sn films were predicted by a computational model based upon the constitutive properties of 95.5Sn-3.9Ag-0.6Cu (wt.%) as a surrogate for pure Sn. The cyclic DRX mechanism and, in particular, whether long whiskers or hillocks were formed, was validated by comparing the empirical data against the three hierarchal requirements: (1) DRX to occur at all: ɛc = A D o m Z n , (2) DRX to be cyclic: D o < 2 D r, and (3) Grain boundary pinning (thin films): h versus d. Continuous DRX took place in the 2.0- μm and 4.9- μm films that resulted in short stubby whiskers. Depleted zones, which resulted solely from a tensile stress-driven diffusion mechanism, confirmed the pervasiveness of long-range diffusion so that it did not control whisker or hillock formation other than a small loss of activity by reduced thermal activation at lower temperatures. A first-principles DRX model paves the way to develop like mitigation strategies against long whisker growth.

Locking design affects the jamming of screws in locking plates.

PubMed

Sandriesser, Sabrina; Rupp, Markus; Greinwald, Markus; Heiss, Christian; Augat, Peter; Alt, Volker

2018-06-01

The seizing of locking screws is a frequently encountered clinical problem during implant removal of locking compression plates (LCP) after completion of fracture healing. The aim of this study was to investigate the effect of two different locking mechanisms on the seizing of locking screws. Specifically, the removal torques before and after cyclic dynamic loading were assessed for screws inserted at the manufacturer-recommended torque or at an increased insertion torque. The seizing of 3.5-mm angular stable screws was assessed as a function of insertion torque for two different locking mechanisms (Thread & Conus and Thread Only). Locking screws (n=10 for each configuration) were inserted either according to the manufacturer-recommended torque or at an increased torque of 150% to simulate an over-insertion of the screw. Half of the screws were removed directly after insertion and the remaining half was removed after a dynamic load protocol of 100,000 cycles. The removal torques of locking screws exceeded the insertion torques for all tested conditions confirming the adequacy of the test setup in mimicking screw seizing in locked plating. Screw seizing was more pronounced for Thread Only design (+37%) compared to Thread & Conus design (+14%; P<0.0001). Cyclic loading of the locking construct consistently resulted in an increased seizing of the locking screws (P<0.0001). Clinical observations from patients treated with the Thread & Conus locking design confirm the biomechanical findings of reduction in seizing effect by using a Thread & Conus design. In conclusion, both over-tightening and cyclic loading are potential causes for screw seizing in locking plate implants. Both effects were found to be less pronounced in the Thread & Conus design as compared to the traditional Thread Only design. © 2018 Elsevier Ltd. All rights reserved.

Spiraling patterns in evolutionary models inspired by bacterial games with cyclic dominance

NASA Astrophysics Data System (ADS)

Mobilia, Mauro

2015-03-01

Understanding the mechanisms allowing the maintenance of biodiversity is a central issue in biology. Evolutionary game theory, where the success of one species depends on what the others are doing, provides a promising framework to investigate this complex problem. Experiments on microbial populations have shown that cyclic local interactions promote species coexistence. In this context, rock-paper-scissors games - in which rock crushes scissors, scissors cut paper, and paper wraps rock - are often used to model the dynamics of populations in cyclic competition. After a brief survey of some inspiring experiments, I will discuss the subtle interplay between individuals' mobility and their local interactions in two-dimensional rock-paper-scissors systems. This leads to the loss of biodiversity above a certain mobility threshold, and to the formation of spiraling patterns below the critical mobility rate. I will then study a generic rock-paper-scissors metapopulation model formulated on a two-dimensional grid of patches. When these have a large carrying capacity, the model's dynamics is faithfully described in terms of the system's complex Ginzburg-Landau equation properly derived from a multiscale expansion. The properties of the ensuing complex Ginzburg-Landau equation are exploited to derive the system's phase diagram and to characterize the spatio-temporal properties of the spiraling patterns in each phase. This enables us to analyze the spiral waves stability, how these are influenced by linear and nonlinear diffusion, and to discuss phenomena such as far-field breakup. Presentation mainy based on joint work with B. Szczesny and A. M. Rucklidge. Fruitful earlier collaborations with E. Frey, Q. He, T. Reichenbach, and U. C. Täuber are also acknowledged. Work supported by the UK EPSRC (Grant No. EP/P505593/1).

Validation of the dynamic recrystallization (DRX) mechanism for whisker and hillock growth on thin films

DOE PAGES

Vianco, Paul T.; Neilsen, Michael K.; Rejent, Jerome A.; ...

2015-05-01

Our study was performed to validate a first-principles model for whisker and hillock formation based on the cyclic dynamic recrystallization (DRX) mechanism in conjunction with long-range diffusion. The test specimens were evaporated Sn films on Si having thicknesses of 0.25 μm, 0.50 μm, 1.0 μm, 2.0 μm, and 4.9 μm. Air annealing was performed at 35°C, 60°C, 100°C, 120°C, or 150°C over a time duration of 9 days. The stresses, anelastic strains, and strain rates in the Sn films were predicted by a computational model based upon the constitutive properties of 95.5Sn-3.9Ag-0.6Cu (wt.%) as a surrogate for pure Sn. Themore » cyclic DRX mechanism and, in particular, whether long whiskers or hillocks were formed, was validated by comparing the empirical data against the three hierarchal requirements: (1) DRX to occur at all: εc = A D o m Z n , (2) DRX to be cyclic: D o < 2D r, and (3) Grain boundary pinning (thin films): h versus d. Continuous DRX took place in the 2.0-μm and 4.9-μm films that resulted in short stubby whiskers. Depleted zones, which resulted solely from a tensile stress-driven diffusion mechanism, confirmed the pervasiveness of long-range diffusion so that it did not control whisker or hillock formation other than a small loss of activity by reduced thermal activation at lower temperatures. Furthermore, a first-principles DRX model paves the way to develop like mitigation strategies against long whisker growth.« less

Sun's influence on climate: Explored with SDO

NASA Astrophysics Data System (ADS)

Lundstedt, H.

2010-09-01

Stunning images and movies recorded of the Sun, with Solar Dynamics Observatory (SDO), makes one wonder: How would this change our view on the Sun-Earth climate coupling? SDO shows a much more variable Sun, on all spatial and temporal scales. Detailed pictures of solar storms are foreseen to improve our understanding of the direct Sun-Earth coupling. Dynamo models, described by dynamical systems using input from helioseismic observations, are foreseen to improve our knowledge of the the Sun's cyclic influence on climate. Both the direct-, and the cycle-influence will be discussed in view of the new SDO observations.

Intermittent crack growth in fatigue

NASA Astrophysics Data System (ADS)

Kokkoniemi, R.; Miksic, A.; Ovaska, M.; Laurson, L.; Alava, M. J.

2017-07-01

Fatigue occurs under cyclic loading at stresses below a material’s static strength limit. We consider fatigue crack growth as a stochastic process and perform crack growth experiments in a metal (copper). We follow optically cracks propagating from initial edge notches. The main interest is in the dynamics of the crack growth—the Paris’ law and the initiation phase prior to that—and especially the intermittency this is discovered to display. How the sampling of the crack advancement, performed at regular intervals, influences such measurement results is analysed by the analogy of planar crack dynamics in slow, driven growth.

Metabolic analyzer. [for measuring metabolic rate and breathing dynamics of human beings

NASA Technical Reports Server (NTRS)

Rummel, J. A.; Perry, C. L. (Inventor)

1974-01-01

An apparatus is described for the measurement of metabolic rate and breathing dynamics in which inhaled and exhaled breath are sensed by sealed, piston-displacement type spirometers. These spirometers electrically measure the volume of inhaled and exhaled breath. A mass spectrometer analyzes simultaneously for oxygen, carbon dioxide, nitrogen and water vapor. Computation circuits are responsive to the outputs of the spirometers, mass spectrometer, temperature, pressure and timing signals and compute oxygen consumption, carbon dioxide production, minute volume and respiratory exchange ratio. A selective indicator provides for read-out of these data at predetermined cyclic intervals.

Effect of water temperature on cyclic fatigue properties of glass-fiber-reinforced hybrid composite resin and its fracture pattern after flexural testing.

PubMed

Kuroda, Soichi; Shinya, Akikazu; Vallittu, Pekka K; Nakasone, Yuji; Shinya, Akiyoshi

2013-02-01

To evaluate in vitro the influence of dynamic loading applied to a glass-fiber-reinforced hybrid composite resin on its flexural strength in a moist, simulated oral environment. Three-point flexural strength specimens were subjected to cyclic loading in water at 37°C and 55°C to investigate the influence of immersion temperature on impact fatigue properties. Specimens were subjected to cyclic impact loading at 1 Hz for up to 5 × 105 cycles to obtain the number of cycles to failure, the number of unbroken specimens after 5 × 105 cycles, and the residual flexural strength of unbroken specimens. Maximum loads of 100, 200, and 300 N were chosen for both the non-reinforced and the glass-fiber reinforced hybrid composite resins. The mean residual flexural strength for 100 N impact loading at temperatures of 37°C and 55°C was 634 and 636 MPa, respectively. All specimens fractured at fewer than 5 × 105 cycles for loads of 200 and 300 N. Reduced numbers of cycles to fracture and lower fatigue values were observed as both the maximum load and immersion temperature increased.

A Deep Machine Learning Method for Classifying Cyclic Time Series of Biological Signals Using Time-Growing Neural Network.

PubMed

Gharehbaghi, Arash; Linden, Maria

2017-10-12

This paper presents a novel method for learning the cyclic contents of stochastic time series: the deep time-growing neural network (DTGNN). The DTGNN combines supervised and unsupervised methods in different levels of learning for an enhanced performance. It is employed by a multiscale learning structure to classify cyclic time series (CTS), in which the dynamic contents of the time series are preserved in an efficient manner. This paper suggests a systematic procedure for finding the design parameter of the classification method for a one-versus-multiple class application. A novel validation method is also suggested for evaluating the structural risk, both in a quantitative and a qualitative manner. The effect of the DTGNN on the performance of the classifier is statistically validated through the repeated random subsampling using different sets of CTS, from different medical applications. The validation involves four medical databases, comprised of 108 recordings of the electroencephalogram signal, 90 recordings of the electromyogram signal, 130 recordings of the heart sound signal, and 50 recordings of the respiratory sound signal. Results of the statistical validations show that the DTGNN significantly improves the performance of the classification and also exhibits an optimal structural risk.

The effects of dynamic loading on the intervertebral disc.

PubMed

Chan, Samantha C W; Ferguson, Stephen J; Gantenbein-Ritter, Benjamin

2011-11-01

Loading is important to maintain the balance of matrix turnover in the intervertebral disc (IVD). Daily cyclic diurnal assists in the transport of large soluble factors across the IVD and its surrounding circulation and applies direct and indirect stimulus to disc cells. Acute mechanical injury and accumulated overloading, however, could induce disc degeneration. Recently, there is more information available on how cyclic loading, especially axial compression and hydrostatic pressure, affects IVD cell biology. This review summarises recent studies on the response of the IVD and stem cells to applied cyclic compression and hydrostatic pressure. These studies investigate the possible role of loading in the initiation and progression of disc degeneration as well as quantifying a physiological loading condition for the study of disc degeneration biological therapy. Subsequently, a possible physiological/beneficial loading range is proposed. This physiological/beneficial loading could provide insight into how to design loading regimes in specific system for the testing of various biological therapies such as cell therapy, chemical therapy or tissue engineering constructs to achieve a better final outcome. In addition, the parameter space of 'physiological' loading may also be an important factor for the differentiation of stem cells towards most ideally 'discogenic' cells for tissue engineering purpose.

Structure of the cyclic peptide [W8S]contryphan Vn: effect of the tryptophan/serine substitution on trans-cis proline isomerization.

PubMed

Nepravishta, Ridvan; Mandaliti, Walter; Melino, Sonia; Eliseo, Tommaso; Paci, Maurizio

2014-12-01

The structural characterization of [W8S]contryphan Vn, an analogue of Contryphan Vn with tryptophan 8 substituted with a serine residue (W8S), was performed by NMR spectroscopy, molecular dynamics simulations and fluorescence spectroscopy. Contryphan Vn, a bioactive cyclic peptide from the venom of the cone snail Conus ventricosus, contains an S-S bridge between two cysteines and a D-tryptophan. Like other Contryphans, [W8S]contryphan Vn has proline 7 isomerized trans, while the proline 4 has nearly equivalent populations of cis and trans configurations. The thermodynamic and kinetic parameters of the trans-cis isomerization of proline 4 were measured. The isomers of [W8S]contryphan Vn with proline 4 in cis and trans show structural differences. The absence of the salt bridge between the same Asp2 and Lys6, present in Contryphan Vn, may be attributed to the lack of the hydrophobic side chain of Trp8 where it likely protects the electrostatic interactions. These results may contribute to identifying, in these cyclic peptides, the structural determinants of the mechanism of proline trans-cis isomerization, this being also an important step in protein folding.

Frequency-dependent selection can lead to evolution of high mutation rates.

PubMed

Rosenbloom, Daniel I S; Allen, Benjamin

2014-05-01

Theoretical and experimental studies have shown that high mutation rates can be advantageous, especially in novel or fluctuating environments. Here we examine how frequency-dependent competition may lead to fluctuations in trait frequencies that exert upward selective pressure on mutation rates. We use a mathematical model to show that cyclical trait dynamics generated by "rock-paper-scissors" competition can cause the mutation rate in a population to converge to a high evolutionarily stable mutation rate, reflecting a trade-off between generating novelty and reproducing past success. Introducing recombination lowers the evolutionarily stable mutation rate but allows stable coexistence between mutation rates above and below the evolutionarily stable rate. Even considering strong mutational load and ignoring the costs of faithful replication, evolution favors positive mutation rates if the selective advantage of prevailing in competition exceeds the ratio of recombining to nonrecombining offspring. We discuss a number of genomic mechanisms that may meet our theoretical requirements for the adaptive evolution of mutation. Overall, our results suggest that local mutation rates may be higher on genes influencing cyclical competition and that global mutation rates in asexual species may be higher in populations subject to strong cyclical competition.

The evolution of social learning rules: payoff-biased and frequency-dependent biased transmission.

PubMed

Kendal, Jeremy; Giraldeau, Luc-Alain; Laland, Kevin

2009-09-21

Humans and other animals do not use social learning indiscriminately, rather, natural selection has favoured the evolution of social learning rules that make selective use of social learning to acquire relevant information in a changing environment. We present a gene-culture coevolutionary analysis of a small selection of such rules (unbiased social learning, payoff-biased social learning and frequency-dependent biased social learning, including conformism and anti-conformism) in a population of asocial learners where the environment is subject to a constant probability of change to a novel state. We define conditions under which each rule evolves to a genetically polymorphic equilibrium. We find that payoff-biased social learning may evolve under high levels of environmental variation if the fitness benefit associated with the acquired behaviour is either high or low but not of intermediate value. In contrast, both conformist and anti-conformist biases can become fixed when environment variation is low, whereupon the mean fitness in the population is higher than for a population of asocial learners. Our examination of the population dynamics reveals stable limit cycles under conformist and anti-conformist biases and some highly complex dynamics including chaos. Anti-conformists can out-compete conformists when conditions favour a low equilibrium frequency of the learned behaviour. We conclude that evolution, punctuated by the repeated successful invasion of different social learning rules, should continuously favour a reduction in the equilibrium frequency of asocial learning, and propose that, among competing social learning rules, the dominant rule will be the one that can persist with the lowest frequency of asocial learning.

Evolutionary origins of a novel host plant detoxification gene in butterflies.

PubMed

Fischer, Hanna M; Wheat, Christopher W; Heckel, David G; Vogel, Heiko

2008-05-01

Chemical interactions between plants and their insect herbivores provide an excellent opportunity to study the evolution of species interactions on a molecular level. Here, we investigate the molecular evolutionary events that gave rise to a novel detoxifying enzyme (nitrile-specifier protein [NSP]) in the butterfly family Pieridae, previously identified as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries, and screening databases we found NSP to be a member of an insect-specific gene family, which we characterized and named the NSP-like gene family. Members consist of variable tandem repeats, are gut expressed, and are found across Insecta evolving in a dynamic, ongoing birth-death process. In the Lepidoptera, multiple copies of single-domain major allergen genes are present and originate via tandem duplications. Multiple domain genes are found solely within the brassicaceous-feeding Pieridae butterflies, one of them being NSP and another called major allergen (MA). Analyses suggest that NSP and its paralog MA have a unique single-domain evolutionary origin, being formed by intragenic domain duplication followed by tandem whole-gene duplication. Duplicates subsequently experienced a period of relaxed constraint followed by an increase in constraint, perhaps after neofunctionalization. NSP and its ortholog MA are still experiencing high rates of change, reflecting a dynamic evolution consistent with the known role of NSP in plant-insect interactions. Our results provide direct evidence to the hypothesis that gene duplication is one of the driving forces for speciation and adaptation, showing that both within- and whole-gene tandem duplications are a powerful force underlying evolutionary adaptation.

Modelling human decision-making in coupled human and natural systems

NASA Astrophysics Data System (ADS)

Feola, G.

2012-12-01

A solid understanding of human decision-making is essential to analyze the complexity of coupled human and natural systems (CHANS) and inform policies to promote resilience in the face of environmental change. Human decisions drive and/or mediate the interactions and feedbacks, and contribute to the heterogeneity and non-linearity that characterize CHANS. However, human decision-making is usually over-simplistically modeled, whereby human agents are represented deterministically either as dumb or clairvoyant decision-makers. Decision-making models fall short in the integration of both environmental and human behavioral drivers, and concerning the latter, tend to focus on only one category, e.g. economic, cultural, or psychological. Furthermore, these models render a linear decision-making process and therefore fail to account for the recursive co-evolutionary dynamics in CHANS. As a result, these models constitute only a weak basis for policy-making. There is therefore scope and an urgent need for better approaches to human decision-making, to produce the knowledge that can inform vulnerability reduction policies in the face of environmental change. This presentation synthesizes the current state-of-the-art of modelling human decision-making in CHANS, with particular reference to agricultural systems, and delineates how the above mentioned shortcomings can be overcome. Through examples from research on pesticide use and adaptation to climate change, both based on the integrative agent-centered framework (Feola and Binder, 2010), the approach for an improved understanding of human agents in CHANS are illustrated. This entails: integrative approach, focus on behavioral dynamics more than states, feedbacks between individual and system levels, and openness to heterogeneity.

Asymmetrical, inversely graded, upstream-migrating cyclic steps in marine settings: Late Miocene-early Pliocene Fish Creek-Vallecito Basin, southern California

NASA Astrophysics Data System (ADS)

Gong, Chenglin; Chen, Liuqin; West, Logan

2017-10-01

Cyclic steps are ubiquitous in modern sedimentary environments, yet their recognition remains sparse in the rock record. Here, we interpret three sets of undulating backsets (1 to 3) recognized in the late Miocene-early Pliocene Latrania Formation in the Anza-Borrego Desert, the Fish Creek-Vallecito Basin, southern California, USA as the first cm- to dm-scale outcrop record of cyclic steps, based on asymmetrical cross-sections, upstream migration, and inversely graded laminae. Upstream migration and asymmetrical cross-sections of backsets and concomitant backset laminae are attributed to supercritical-to-subcritical flow transitions through weak hydraulic jumps, which are composed of: (i) thin (tens of centimetres) and slower (reported as flow velocities (Ū) of 0.45 to 1.45 m s- 1, with mean value of Ū = 0.89 m s- 1) subcritical (represented by internal Froude numbers (Fr) of 0.67 to 0.99, with mean value of Fr = 0.84) turbidity currents on the stoss sides, and (ii) thin (tens of centimetres) and faster (reported as Ū of 0.99 to 4.03 m s- 1, with mean value of Ū = 2.24 m s- 1) supercritical (represented by Fr of 1.84 to 3.07, with mean value of Fr = 2.42) turbidity flows on the lee sides. The inversely graded laminae in the troughs of backsets are 2 to 5 cm thick, and consist of two discrete divisions: (i) 1 to 2 cm thick, lower finer-grained divisions made up of parallel laminated siltstones, overlain by very fine- to fine-grained sandstones, and (ii) 2 to 3 cm thick, upper divisions composed of medium- to coarse-grained sandstones, with sporadic occurrence of subrounded pebbles. These inversely graded laminae are related to stratified, collisional and/or frictional traction carpets under conditions of high fall-out rates. Due to the poor preservation potential of cyclic steps, the rock record of cyclic steps is generally considered to be rare. The present outcrop-based study presents a detailed analysis of sedimentary facies, growth patterns, and flow dynamics of marine cyclic steps, thereby contributing to better understand architectural styles and lithological properties of cyclic steps in the geological record.

A cyclic universe approach to fine tuning

DOE PAGES

Alexander, Stephon; Cormack, Sam; Gleiser, Marcelo

2016-04-05

We present a closed bouncing universe model where the value of coupling constants is set by the dynamics of a ghost-like dilatonic scalar field. We show that adding a periodic potential for the scalar field leads to a cyclic Friedmann universe where the values of the couplings vary randomly from one cycle to the next. While the shuffling of values for the couplings happens during the bounce, within each cycle their time-dependence remains safely within present observational bounds for physically-motivated values of the model parameters. Our model presents an alternative to solutions of the fine tuning problem based on stringmore » landscape scenarios. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP(3).« less

A cyclic universe approach to fine tuning

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

Alexander, Stephon; Cormack, Sam; Gleiser, Marcelo

We present a closed bouncing universe model where the value of coupling constants is set by the dynamics of a ghost-like dilatonic scalar field. We show that adding a periodic potential for the scalar field leads to a cyclic Friedmann universe where the values of the couplings vary randomly from one cycle to the next. While the shuffling of values for the couplings happens during the bounce, within each cycle their time-dependence remains safely within present observational bounds for physically-motivated values of the model parameters. Our model presents an alternative to solutions of the fine tuning problem based on stringmore » landscape scenarios. (C) 2016 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). Funded by SCOAP(3).« less

Investigation of Mechanical Damping Characteristic in Short Fiberglass Reinforced Polycarbonate Composites

NASA Astrophysics Data System (ADS)

Cho, Myoung-Rae; Kim, Hyung-Ick; Jang, Jae-Soon; Suhr, Jonghwan; Prate, Devin R.; Chun, David

2013-06-01

The focus of this study is to experimentally investigate the effect of debonding stress, the interface between the fibers and the polymer matrix, on the damping properties of the short fiberglass reinforced polymer composites. In this study, short fiberglass reinforced polycarbonate composite materials were fabricated and characterized for their tensile properties by varying the fiberglass loading fraction. The debonding stress was evaluated by coupling the acoustic emission technique with the tensile testing. After the determination of the debonding stress was completed, dynamic cyclic testing was performed in order to investigate the effect of debonding on the damping properties of the polymer composites. It was experimentally observed in this study that the debonding can facilitate the stick-slip friction under cyclic loadings, which then gives rise to better damping performance in the fiberglass composites.

Dynamic oxidation behavior at 1000 and 1100 C of four nickel-base cast alloys, NASA-TRW VIA, B-1900, 713C, and 738X

NASA Technical Reports Server (NTRS)

Sanders, W. A.

1974-01-01

The superalloys NASA-TRW VIA, B-1900, 713C, and 738X were tested cyclically and isothermally for resistance to oxidation in high velocity gas streams for 100 hours at specimen temperatures of 1000 C and 1100 C. Alloys VIA and B-1900, which were the most oxidation resistant, displayed slight and very similar weight changes and metal losses. Alloy 713C also sustained only slight metal losses, but it exhibited some tendency to spall. Alloy 738X was found to be the most susceptible to cyclic oxidation; this resulted in heavy spalling, which in turn caused high weight losses and high metal losses. Oxidation test results are related to the amounts of chromium aluminum, and the refractory metals in the alloys investigated.

Noise induced aperiodic rotations of particles trapped by a non-conservative force

NASA Astrophysics Data System (ADS)

Ortega-Piwonka, Ignacio; Angstmann, Christopher N.; Henry, Bruce I.; Reece, Peter J.

2018-04-01

We describe a mechanism whereby random noise can play a constructive role in the manifestation of a pattern, aperiodic rotations, that would otherwise be damped by internal dynamics. The mechanism is described physically in a theoretical model of overdamped particle motion in two dimensions with symmetric damping and a non-conservative force field driven by noise. Cyclic motion only occurs as a result of stochastic noise in this system. However, the persistence of the cyclic motion is quantified by parameters associated with the non-conservative forcing. Unlike stochastic resonance or coherence resonance, where noise can play a constructive role in amplifying a signal that is otherwise below the threshold for detection, in the mechanism considered here, the signal that is detected does not exist without the noise. Moreover, the system described here is a linear system.

Thermoviscoplastic model with application to copper

NASA Technical Reports Server (NTRS)

Freed, Alan D.

1988-01-01

A viscoplastic model is developed which is applicable to anisothermal, cyclic, and multiaxial loading conditions. Three internal state variables are used in the model; one to account for kinematic effects, and the other two to account for isotropic effects. One of the isotropic variables is a measure of yield strength, while the other is a measure of limit strength. Each internal state variable evolves through a process of competition between strain hardening and recovery. There is no explicit coupling between dynamic and thermal recovery in any evolutionary equation, which is a useful simplification in the development of the model. The thermodynamic condition of intrinsic dissipation constrains the thermal recovery function of the model. Application of the model is made to copper, and cyclic experiments under isothermal, thermomechanical, and nonproportional loading conditions are considered. Correlations and predictions of the model are representative of observed material behavior.

The Geometric Phase of Stock Trading.

PubMed

Altafini, Claudio

2016-01-01

Geometric phases describe how in a continuous-time dynamical system the displacement of a variable (called phase variable) can be related to other variables (shape variables) undergoing a cyclic motion, according to an area rule. The aim of this paper is to show that geometric phases can exist also for discrete-time systems, and even when the cycles in shape space have zero area. A context in which this principle can be applied is stock trading. A zero-area cycle in shape space represents the type of trading operations normally carried out by high-frequency traders (entering and exiting a position on a fast time-scale), while the phase variable represents the cash balance of a trader. Under the assumption that trading impacts stock prices, even zero-area cyclic trading operations can induce geometric phases, i.e., profits or losses, without affecting the stock quote.

A simplified rotor system mathematical model for piloted flight dynamics simulation

NASA Technical Reports Server (NTRS)

Chen, R. T. N.

1979-01-01

The model was developed for real-time pilot-in-the-loop investigation of helicopter flying qualities. The mathematical model included the tip-path plane dynamics and several primary rotor design parameters, such as flapping hinge restraint, flapping hinge offset, blade Lock number, and pitch-flap coupling. The model was used in several exploratory studies of the flying qualities of helicopters with a variety of rotor systems. The basic assumptions used and the major steps involved in the development of the set of equations listed are described. The equations consisted of the tip-path plane dynamic equation, the equations for the main rotor forces and moments, and the equation for control phasing required to achieve decoupling in pitch and roll due to cyclic inputs.

Effects of predation efficiencies on the dynamics of a tritrophic food chain.

PubMed

Cassinari, Maria Paola; Groppi, Maria; Tebaldi, Claudio

2007-07-01

In this paper the dynamics of a tritrophic food chain (resource, consumer, top predator) is investigated, with particular attention not only to equilibrium states but also to cyclic behaviours that the system may exhibit. The analysis is performed in terms of two bifurcation parameters, denoted by p and q, which measure the efficiencies of the interaction processes. The persistence of the system is discussed, characterizing in the (p; q) plane the regions of existence and stability of biologically significant steady states and those of existence of limit cycles. The bifurcations occurring are discussed, and their implications with reference to biological control problems are considered. Examples of the rich dynamics exhibited by the model, including a chaotic regime, are described.

Decision making on fitness landscapes

NASA Astrophysics Data System (ADS)

Arthur, R.; Sibani, P.

2017-04-01

We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. We develop a model very similar to the Tangled Nature Model of Christensen et al. that we call the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures.

Tangled nature: a model of evolutionary ecology.

PubMed

Christensen, Kim; di Collobiano, Simone A; Hall, Matt; Jensen, Henrik J

2002-05-07

We discuss a simple model of co-evolution. In order to emphasize the effect of interaction between individuals, the entire population is subjected to the same physical environment. Species are emergent structures and extinction, origination and diversity are entirely a consequence of co-evolutionary interaction between individuals. For comparison, we consider both asexual and sexually reproducing populations. In either case, the system evolves through periods of hectic reorganization separated by periods of coherent stable coexistence. Copyright 2002 Elsevier Science Ltd. All rights reserved.

Basins of coexistence and extinction in spatially extended ecosystems of cyclically competing species.

PubMed

Ni, Xuan; Yang, Rui; Wang, Wen-Xu; Lai, Ying-Cheng; Grebogi, Celso

2010-12-01

Microscopic models based on evolutionary games on spatially extended scales have recently been developed to address the fundamental issue of species coexistence. In this pursuit almost all existing works focus on the relevant dynamical behaviors originated from a single but physically reasonable initial condition. To gain comprehensive and global insights into the dynamics of coexistence, here we explore the basins of coexistence and extinction and investigate how they evolve as a basic parameter of the system is varied. Our model is cyclic competitions among three species as described by the classical rock-paper-scissors game, and we consider both discrete lattice and continuous space, incorporating species mobility and intraspecific competitions. Our results reveal that, for all cases considered, a basin of coexistence always emerges and persists in a substantial part of the parameter space, indicating that coexistence is a robust phenomenon. Factors such as intraspecific competition can, in fact, promote coexistence by facilitating the emergence of the coexistence basin. In addition, we find that the extinction basins can exhibit quite complex structures in terms of the convergence time toward the final state for different initial conditions. We have also developed models based on partial differential equations, which yield basin structures that are in good agreement with those from microscopic stochastic simulations. To understand the origin and emergence of the observed complicated basin structures is challenging at the present due to the extremely high dimensional nature of the underlying dynamical system. © 2010 American Institute of Physics.

Dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes.

PubMed

Li, Rui; Fan, Jianfen; Li, Hui; Yan, Xiliang; Yu, Yi

2015-07-07

Classical molecular dynamics simulations have been performed to investigate the dynamic behaviors and transport properties of ethanol molecules in transmembrane cyclic peptide nanotubes (CPNTs) with various radii, i.e., 8×(WL¯)n=3,4,5/POPE. The results show that ethanol molecules spontaneously fill the octa- and deca-CPNTs, but not the hexa-CPNT. In the octa-CPNT, ethanol molecules are trapped at individual gaps with their carbon skeletons perpendicular to the tube axis and hydroxyl groups towards the tube wall, forming a broken single-file chain. As the channel radius increases, ethanol molecules inside the deca-CPNT tend to form a tubular layer and the hydroxyl groups mainly stretch towards the tube axis. Computations of diffusion coefficients indicate that ethanol molecules in the octa-CPNT nearly lost their diffusion abilities, while those in the deca-CPNT diffuse as 4.5 times as in a (8, 8) carbon nanotube with a similar tube diameter. The osmotic and diffusion permeabilities (pf and pd, respectively) of the octa- and deca-CPNTs transporting ethanol were deduced for the first time. The distributions of the gauche and trans conformers of ethanol molecules in two CPNTs are quite similar, both with approximately 57% gauche conformers. The non-bonded interactions of channel ethanol with a CPNT wall and surrounding ethanol were explored. The potential of mean force elucidates the mechanism underlying the transporting characteristics of channel ethanol in a transmembrane CPNT.

High-Speed Optical Wide-Area Data-Communication Network

NASA Technical Reports Server (NTRS)

Monacos, Steve P.

1994-01-01

Proposed fiber-optic wide-area network (WAN) for digital communication balances input and output flows of data with its internal capacity by routing traffic via dynamically interconnected routing planes. Data transmitted optically through network by wavelength-division multiplexing in synchronous or asynchronous packets. WAN implemented with currently available technology. Network is multiple-ring cyclic shuffle exchange network ensuring traffic reaches its destination with minimum number of hops.

Cyclic variation of ultrasonic backscattering from porcine whole blood under pulsatile flow

NASA Astrophysics Data System (ADS)

Lin, Yu-Hong

1997-10-01

The cyclic variation of ultrasonic backscattering from blood under pulsatile flow is believed to be related to the change of aggregation state of red cells and is only observed in whole blood. This study was to investigate the phenomenon by an invasive approach which was performed by inserting a 10 MHz catheter mounted transducer into a vessel. For ultrasonic measurement from blood, the most fundamental scheme is the hematocrit dependence. The backscatter maximum location was changed as the blood was stirred or stationary, as well as under steady laminar or turbulent flows. The same trend was also observed under pulsatile flow with 10% to 50% hematocrits in this study, as the backscattering to hematocrit curves were plotted at different times during a flow cycle. When the cyclic variation at 20 beats per minute (BPM) was interpreted in time domain, the enhanced aggregation at the beginning of shearing was observed. At 20 BPM with 40% hematocrit, the amplitude of cyclic variation was reduced when the shear rate was increased and the threshold of 150 s-1 was estimated. The results showed that there was no cyclic variation at 60 BPM. The backscattering was also plotted against the mean flow velocity, which demonstrated the hysteresis loops. The ultrasonic measurements showed that the relationship between the forward and backward paths of the loops were altered as beat rate, hematocrit, and shear rate were varied. Since the pulsatile flow was very complicated, a computational fluid dynamics package, FIDAPTM, was used to compute the shear rate based on the Power Law Model for non-Newtonian fluid viscosity. The non- Newtonian index and consistency in the model were computed from the viscosity to shear rate curves at 10% to 50% hematocrits measured by a cone-plate viscometer. For in vivo measurements, small pigs were used as models. Ultrasonic backscattering measurements were performed in the arteries and veins. The effect of stenosis was also investigated at the site below the renal branch in the artery. The results show that the cyclic variation from whole blood was mediated by the shear rate, hematocrit, beat rate, and fibrinogen concentration.

Blob-Spring Model for the Dynamics of Ring Polymer in Obstacle Environment

NASA Astrophysics Data System (ADS)

Lele, Ashish K.; Iyer, Balaji V. S.; Juvekar, Vinay A.

2008-07-01

The dynamical behavior of cyclic macromolecules in a fixed obstacle (FO) environment is very different than the behavior of linear chains in the same topological environment; while the latter relax by a snake-like reptational motion from their chain ends the former can relax only by contour length fluctuations since they are endless. Duke, Obukhov and Rubinstein proposed a scaling model (the DOR model) to interpret the dynamical scaling exponents shown by Monte Carlo simulations of rings in a FO environment. We present a model (blob-spring model) to describe the dynamics of flexible and non-concatenated ring polymer in FO environment based on a theoretical formulation developed for the dynamics of an unentangled fractal polymer. We argue that the perpetual evolution of ring perimeter by the motion of contour segments results in an extra frictional load. Our model predicts self-similar dynamics with scaling exponents for the molecular weight dependence of diffusion coefficient and relaxation times that are in agreement with the scaling model proposed by Obukhov et al.

The common redstart as a suitable model to study cuckoo-host coevolution in a unique ecological context.

PubMed

Samaš, Peter; Rutila, Jarkko; Grim, Tomáš

2016-11-25

Co-evolutionary arms-races result in spatio-temporally dynamic relationships between interacting species, e.g., brood parasites and their avian hosts. However, majority of avian co-evolutionary studies are limited to "snap-shots" of a single breeding season in an open-nesting host. In a long-term study (11 breeding seasons), we explored a unique system between the brood parasitic common cuckoo (Cuculus canorus) and its host, the common redstart (Phoenicurus phoenicurus) which is exceptional among all cuckoo hosts due to being a cavity nester. Conditions in cavities are different from open nests, e.g., lower risks of predation, more favourable microclimate, increased risks of unsuccessful eviction of host offspring by the cuckoo nestling. Different conditions in cavities thus can be expected to shape parasite-host coevolution differently from what is typically studied in open nesting hosts. In our highly parasitised nest-box population (32.5%, n = 569 nests) only 35.7% of cuckoo eggs were laid into the nest cup and incubated by redstarts. Host nests shifted availability to later into the breeding season from 2006 to 2016 and cuckoos followed this trend by also shifting their timing of parasitism. Although previous studies revealed that redstarts selectively eject experimental non-mimetic eggs (desertion was not a specific response to foreign eggs), the hosts never ejected naturally-laid cuckoo eggs or cuckoo eggs cross-fostered into naturally non-parasitised nests. We solve the long-standing debate about the origin of cuckoo eggs found on the nest rim: we gained the first direct video-recording evidence that eggs found on the nest rim were mislaid by parasites and not ejected by hosts. Naturally-parasitised nests were deserted more often (18.6%) than control non-parasitized nests (5.6%) or nests artificially parasitised by us (1.4%). This suggests that the sight of the laying cuckoo female is the primary cue that triggers egg rejection (by desertion) in this host. Review of data from this and other study sites (10 populations, n = 853 experiments) demonstrates high variability in rejection rates and shows that populations facing higher parasitism rates reject parasitic eggs with higher frequencies. Surprisingly, cuckoo chicks either growing solitarily or with redstart chicks did not differ in their fledging success. We suggest that the redstart is an ideal model system to study the flexibility and limits of brood parasite-host co-evolution in an extreme ecological setting.

Coevolution study of mitochondria respiratory chain proteins: toward the understanding of protein--protein interaction.

PubMed

Yang, Ming; Ge, Yan; Wu, Jiayan; Xiao, Jingfa; Yu, Jun

2011-05-20

Coevolution can be seen as the interdependency between evolutionary histories. In the context of protein evolution, functional correlation proteins are ever-present coordinated evolutionary characters without disruption of organismal integrity. As to complex system, there are two forms of protein--protein interactions in vivo, which refer to inter-complex interaction and intra-complex interaction. In this paper, we studied the difference of coevolution characters between inter-complex interaction and intra-complex interaction using "Mirror tree" method on the respiratory chain (RC) proteins. We divided the correlation coefficients of every pairwise RC proteins into two groups corresponding to the binary protein--protein interaction in intra-complex and the binary protein--protein interaction in inter-complex, respectively. A dramatical discrepancy is detected between the coevolution characters of the two sets of protein interactions (Wilcoxon test, p-value = 4.4 × 10(-6)). Our finding reveals some critical information on coevolutionary study and assists the mechanical investigation of protein--protein interaction. Furthermore, the results also provide some unique clue for supramolecular organization of protein complexes in the mitochondrial inner membrane. More detailed binding sites map and genome information of nuclear encoded RC proteins will be extraordinary valuable for the further mitochondria dynamics study. Copyright © 2011. Published by Elsevier Ltd.

Avian vision and the evolution of egg color mimicry in the common cuckoo.

PubMed

Stoddard, Mary Caswell; Stevens, Martin

2011-07-01

Coevolutionary arms races are a potent force in evolution, and brood parasite-host dynamics provide classical examples. Different host-races of the common cuckoo, Cuculus canorus, lay eggs in the nests of other species, leaving all parental care to hosts. Cuckoo eggs often (but not always) appear to match remarkably the color and pattern of host eggs, thus reducing detection by hosts. However, most studies of egg mimicry focus on human assessments or reflectance spectra, which fail to account for avian vision. Here, we use discrimination and tetrachromatic color space modeling of bird vision to quantify egg background and spot color mimicry in the common cuckoo and 11 of its principal hosts, and we relate this to egg rejection by different hosts. Egg background color and luminance are strongly mimicked by most cuckoo host-races, and mimicry is better when hosts show strong rejection. We introduce a novel measure of color mimicry-"color overlap"-and show that cuckoo and host background colors increasingly overlap in avian color space as hosts exhibit stronger rejection. Finally, cuckoos with better background color mimicry also have better pattern mimicry. Our findings reveal new information about egg mimicry that would be impossible to derive by the human eye. © 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.