Toward a method for tracking virus evolutionary trajectory applied to the pandemic H1N1 2009 influenza virus.

PubMed

Squires, R Burke; Pickett, Brett E; Das, Sajal; Scheuermann, Richard H

2014-12-01

In 2009 a novel pandemic H1N1 influenza virus (H1N1pdm09) emerged as the first official influenza pandemic of the 21st century. Early genomic sequence analysis pointed to the swine origin of the virus. Here we report a novel computational approach to determine the evolutionary trajectory of viral sequences that uses data-driven estimations of nucleotide substitution rates to track the gradual accumulation of observed sequence alterations over time. Phylogenetic analysis and multiple sequence alignments show that sequences belonging to the resulting evolutionary trajectory of the H1N1pdm09 lineage exhibit a gradual accumulation of sequence variations and tight temporal correlations in the topological structure of the phylogenetic trees. These results suggest that our evolutionary trajectory analysis (ETA) can more effectively pinpoint the evolutionary history of viruses, including the host and geographical location traversed by each segment, when compared against either BLAST or traditional phylogenetic analysis alone. Copyright © 2014 Elsevier B.V. All rights reserved.

Treatment resistance in urothelial carcinoma: an evolutionary perspective.

PubMed

Vlachostergios, Panagiotis J; Faltas, Bishoy M

2018-05-02

The emergence of treatment-resistant clones is a critical barrier to cure in patients with urothelial carcinoma. Setting the stage for the evolution of resistance, urothelial carcinoma is characterized by extensive mutational heterogeneity, which is detectable even in patients with early stage disease. Chemotherapy and immunotherapy both act as selective pressures that shape the evolutionary trajectory of urothelial carcinoma throughout the course of the disease. A detailed understanding of the dynamics of evolutionary drivers is required for the rational development of curative therapies. Herein, we describe the molecular basis of the clonal evolution of urothelial carcinomas and the use of genomic approaches to predict treatment responses. We discuss various mechanisms of resistance to chemotherapy with a focus on the mutagenic effects of the DNA dC->dU-editing enzymes APOBEC3 family of proteins. We also review the evolutionary mechanisms underlying resistance to immunotherapy, such as the loss of clonal tumour neoantigens. By dissecting treatment resistance through an evolutionary lens, the field will advance towards true precision medicine for urothelial carcinoma.

Rapid Preliminary Design of Interplanetary Trajectories Using the Evolutionary Mission Trajectory Generator

NASA Technical Reports Server (NTRS)

Englander, Jacob

2016-01-01

This set of tutorial slides is an introduction to the Evolutionary Mission Trajectory Generator (EMTG), NASA Goddard Space Flight Center's autonomous tool for preliminary design of interplanetary missions. This slide set covers the basics of creating and post-processing simple interplanetary missions in EMTG using both high-thrust chemical and low-thrust electric propulsion along with a variety of operational constraints.

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana

PubMed Central

Fournier-Level, Alexandre; Perry, Emily O.; Wang, Jonathan A.; Braun, Peter T.; Migneault, Andrew; Cooper, Martha D.; Metcalf, C. Jessica E.; Schmitt, Johanna

2016-01-01

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico “resurrection experiments” showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation. PMID:27140640

Predicting the evolutionary dynamics of seasonal adaptation to novel climates in Arabidopsis thaliana.

PubMed

Fournier-Level, Alexandre; Perry, Emily O; Wang, Jonathan A; Braun, Peter T; Migneault, Andrew; Cooper, Martha D; Metcalf, C Jessica E; Schmitt, Johanna

2016-05-17

Predicting whether and how populations will adapt to rapid climate change is a critical goal for evolutionary biology. To examine the genetic basis of fitness and predict adaptive evolution in novel climates with seasonal variation, we grew a diverse panel of the annual plant Arabidopsis thaliana (multiparent advanced generation intercross lines) in controlled conditions simulating four climates: a present-day reference climate, an increased-temperature climate, a winter-warming only climate, and a poleward-migration climate with increased photoperiod amplitude. In each climate, four successive seasonal cohorts experienced dynamic daily temperature and photoperiod variation over a year. We measured 12 traits and developed a genomic prediction model for fitness evolution in each seasonal environment. This model was used to simulate evolutionary trajectories of the base population over 50 y in each climate, as well as 100-y scenarios of gradual climate change following adaptation to a reference climate. Patterns of plastic and evolutionary fitness response varied across seasons and climates. The increased-temperature climate promoted genetic divergence of subpopulations across seasons, whereas in the winter-warming and poleward-migration climates, seasonal genetic differentiation was reduced. In silico "resurrection experiments" showed limited evolutionary rescue compared with the plastic response of fitness to seasonal climate change. The genetic basis of adaptation and, consequently, the dynamics of evolutionary change differed qualitatively among scenarios. Populations with fewer founding genotypes and populations with genetic diversity reduced by prior selection adapted less well to novel conditions, demonstrating that adaptation to rapid climate change requires the maintenance of sufficient standing variation.

Diminishing-returns epistasis decreases adaptability along an evolutionary trajectory.

PubMed

Wünsche, Andrea; Dinh, Duy M; Satterwhite, Rebecca S; Arenas, Carolina Diaz; Stoebel, Daniel M; Cooper, Tim F

2017-03-01

Populations evolving in constant environments exhibit declining adaptability. Understanding the basis of this pattern could reveal underlying processes determining the repeatability of evolutionary outcomes. In principle, declining adaptability can be due to a decrease in the effect size of beneficial mutations, a decrease in the rate at which they occur, or some combination of both. By evolving Escherichia coli populations started from different steps along a single evolutionary trajectory, we show that declining adaptability is best explained by a decrease in the size of available beneficial mutations. This pattern reflected the dominant influence of negative genetic interactions that caused new beneficial mutations to confer smaller benefits in fitter genotypes. Genome sequencing revealed that starting genotypes that were more similar to one another did not exhibit greater similarity in terms of new beneficial mutations, supporting the view that epistasis acts globally, having a greater influence on the effect than on the identity of available mutations along an adaptive trajectory. Our findings provide support for a general mechanism that leads to predictable phenotypic evolutionary trajectories.

The Evolution of Different Forms of Sociality: Behavioral Mechanisms and Eco-Evolutionary Feedback

PubMed Central

van der Post, Daniel J.; Verbrugge, Rineke; Hemelrijk, Charlotte K.

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from “leader-follower” societies to “fission-fusion” societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality. PMID:25629313

The evolution of different forms of sociality: behavioral mechanisms and eco-evolutionary feedback.

PubMed

van der Post, Daniel J; Verbrugge, Rineke; Hemelrijk, Charlotte K

2015-01-01

Different forms of sociality have evolved via unique evolutionary trajectories. However, it remains unknown to what extent trajectories of social evolution depend on the specific characteristics of different species. Our approach to studying such trajectories is to use evolutionary case-studies, so that we can investigate how grouping co-evolves with a multitude of individual characteristics. Here we focus on anti-predator vigilance and foraging. We use an individual-based model, where behavioral mechanisms are specified, and costs and benefits are not predefined. We show that evolutionary changes in grouping alter selection pressures on vigilance, and vice versa. This eco-evolutionary feedback generates an evolutionary progression from "leader-follower" societies to "fission-fusion" societies, where cooperative vigilance in groups is maintained via a balance between within- and between-group selection. Group-level selection is generated from an assortment that arises spontaneously when vigilant and non-vigilant foragers have different grouping tendencies. The evolutionary maintenance of small groups, and cooperative vigilance in those groups, is therefore achieved simultaneously. The evolutionary phases, and the transitions between them, depend strongly on behavioral mechanisms. Thus, integrating behavioral mechanisms and eco-evolutionary feedback is critical for understanding what kinds of intermediate stages are involved during the evolution of particular forms of sociality.

Dynamical trade-offs arise from antagonistic coevolution and decrease intraspecific diversity.

PubMed

Huang, Weini; Traulsen, Arne; Werner, Benjamin; Hiltunen, Teppo; Becks, Lutz

2017-12-12

Trade-offs play an important role in evolution. Without trade-offs, evolution would maximize fitness of all traits leading to a "master of all traits". The shape of trade-offs has been shown to determine evolutionary trajectories and is often assumed to be static and independent of the actual evolutionary process. Here we propose that coevolution leads to a dynamical trade-off. We test this hypothesis in a microbial predator-prey system and show that the bacterial growth-defense trade-off changes from concave to convex, i.e., defense is effective and cheap initially, but gets costly when predators coevolve. We further explore the impact of such dynamical trade-offs by a novel mathematical model incorporating de novo mutations for both species. Predator and prey populations diversify rapidly leading to higher prey diversity when the trade-off is concave (cheap). Coevolution results in more convex (costly) trade-offs and lower prey diversity compared to the scenario where only the prey evolves.

An Automatic Medium to High Fidelity Low-Thrust Global Trajectory Toolchain; EMTG-GMAT

NASA Technical Reports Server (NTRS)

Beeson, Ryne T.; Englander, Jacob A.; Hughes, Steven P.; Schadegg, Maximillian

2015-01-01

Solving the global optimization, low-thrust, multiple-flyby interplanetary trajectory problem with high-fidelity dynamical models requires an unreasonable amount of computational resources. A better approach, and one that is demonstrated in this paper, is a multi-step process whereby the solution of the aforementioned problem is solved at a lower-fidelity and this solution is used as an initial guess for a higher-fidelity solver. The framework presented in this work uses two tools developed by NASA Goddard Space Flight Center: the Evolutionary Mission Trajectory Generator (EMTG) and the General Mission Analysis Tool (GMAT). EMTG is a medium to medium-high fidelity low-thrust interplanetary global optimization solver, which now has the capability to automatically generate GMAT script files for seeding a high-fidelity solution using GMAT's local optimization capabilities. A discussion of the dynamical models as well as thruster and power modeling for both EMTG and GMAT are given in this paper. Current capabilities are demonstrated with examples that highlight the toolchains ability to efficiently solve the difficult low-thrust global optimization problem with little human intervention.

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

PubMed

Ispolatov, Iaroslav; Madhok, Vaibhav; Doebeli, Michael

2016-02-07

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

Niche construction through phenological plasticity: life history dynamics and ecological consequences.

PubMed

Donohue, Kathleen

2005-04-01

The ability of an organism to alter the environment that it experiences has been termed 'niche construction'. Plants have several ways whereby they can determine the environment to which they are exposed at different life stages. This paper discusses three of these: plasticity in dispersal, flowering timing and germination timing. It reviews pathways through which niche construction alters evolutionary and ecological trajectories by altering the selective environment to which organisms are exposed, the phenotypic expression of plastic characters, and the expression of genetic variation. It provides examples whereby niche construction creates positive or negative feedbacks between phenotypes and environments, which in turn cause novel evolutionary constraints and novel life-history expression. Copyright New Phytologist (2005).

An obligate brood parasite trapped in the intraspecific arms race of its hosts.

PubMed

Lyon, Bruce E; Eadie, John McA

2004-11-18

Reciprocal selection pressures often lead to close and adaptive matching of traits in coevolved species. A failure of one species to match the evolutionary trajectories of another is often attributed to evolutionary lags or to differing selection pressures across a geographic mosaic. Here we show that mismatches in adaptation of interacting species--an obligate brood parasitic duck and each of its two main hosts--are best explained by the evolutionary dynamics within the host species. Rejection of the brood parasite's eggs was common by both hosts, despite a lack of detectable cost of parasitism to the hosts. Egg rejection markedly reduced parasite fitness, but egg mimicry experiments revealed no phenotypic natural selection for more mimetic parasitic eggs. These paradoxical results were resolved by the discovery of intraspecific brood parasitism and conspecific egg rejection within the hosts themselves. The apparent arms race between species seems instead to be an incidental by-product of within-species conflict, with little recourse for evolutionary response by the parasite.

De Novo Evolutionary Emergence of a Symmetrical Protein Is Shaped by Folding Constraints

PubMed Central

Smock, Robert G.; Yadid, Itamar; Dym, Orly; Clarke, Jane; Tawfik, Dan S.

2016-01-01

Summary Molecular evolution has focused on the divergence of molecular functions, yet we know little about how structurally distinct protein folds emerge de novo. We characterized the evolutionary trajectories and selection forces underlying emergence of β-propeller proteins, a globular and symmetric fold group with diverse functions. The identification of short propeller-like motifs (<50 amino acids) in natural genomes indicated that they expanded via tandem duplications to form extant propellers. We phylogenetically reconstructed 47-residue ancestral motifs that form five-bladed lectin propellers via oligomeric assembly. We demonstrate a functional trajectory of tandem duplications of these motifs leading to monomeric lectins. Foldability, i.e., higher efficiency of folding, was the main parameter leading to improved functionality along the entire evolutionary trajectory. However, folding constraints changed along the trajectory: initially, conflicts between monomer folding and oligomer assembly dominated, whereas subsequently, upon tandem duplication, tradeoffs between monomer stability and foldability took precedence. PMID:26806127

Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper

PubMed Central

Yin, Wei; Wang, Zong-ji; Li, Qi-ye; Lian, Jin-ming; Zhou, Yang; Lu, Bing-zheng; Jin, Li-jun; Qiu, Peng-xin; Zhang, Pei; Zhu, Wen-bo; Wen, Bo; Huang, Yi-jun; Lin, Zhi-long; Qiu, Bi-tao; Su, Xing-wen; Yang, Huan-ming; Zhang, Guo-jie; Yan, Guang-mei; Zhou, Qi

2016-01-01

Snakes have numerous features distinctive from other tetrapods and a rich history of genome evolution that is still obscure. Here, we report the high-quality genome of the five-pacer viper, Deinagkistrodon acutus, and comparative analyses with other representative snake and lizard genomes. We map the evolutionary trajectories of transposable elements (TEs), developmental genes and sex chromosomes onto the snake phylogeny. TEs exhibit dynamic lineage-specific expansion, and many viper TEs show brain-specific gene expression along with their nearby genes. We detect signatures of adaptive evolution in olfactory, venom and thermal-sensing genes and also functional degeneration of genes associated with vision and hearing. Lineage-specific relaxation of functional constraints on respective Hox and Tbx limb-patterning genes supports fossil evidence for a successive loss of forelimbs then hindlimbs during snake evolution. Finally, we infer that the ZW sex chromosome pair had undergone at least three recombination suppression events in the ancestor of advanced snakes. These results altogether forge a framework for our deep understanding into snakes' history of molecular evolution. PMID:27708285

Chaos and the (un)predictability of evolution in a changing environment

PubMed Central

Rego-Costa, Artur; Débarre, Florence; Chevin, Luis-Miguel

2018-01-01

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution, by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability. PMID:29235104

Evolution of resource cycling in ecosystems and individuals.

PubMed

Crombach, Anton; Hogeweg, Paulien

2009-06-01

Resource cycling is a defining process in the maintenance of the biosphere. Microbial communities, ranging from simple to highly diverse, play a crucial role in this process. Yet the evolutionary adaptation and speciation of micro-organisms have rarely been studied in the context of resource cycling. In this study, our basic questions are how does a community evolve its resource usage and how are resource cycles partitioned? We design a computational model in which a population of individuals evolves to take up nutrients and excrete waste. The waste of one individual is another's resource. Given a fixed amount of resources, this leads to resource cycles. We find that the shortest cycle dominates the ecological dynamics, and over evolutionary time its length is minimized. Initially a single lineage processes a long cycle of resources, later crossfeeding lineages arise. The evolutionary dynamics that follow are determined by the strength of indirect selection for resource cycling. We study indirect selection by changing the spatial setting and the strength of direct selection. If individuals are fixed at lattice sites or direct selection is low, indirect selection result in lineages that structure their local environment, leading to 'smart' individuals and stable patterns of resource dynamics. The individuals are good at cycling resources themselves and do this with a short cycle. On the other hand, if individuals randomly change position each time step, or direct selection is high, individuals are more prone to crossfeeding: an ecosystem based solution with turbulent resource dynamics, and individuals that are less capable of cycling resources themselves. In a baseline model of ecosystem evolution we demonstrate different eco-evolutionary trajectories of resource cycling. By varying the strength of indirect selection through the spatial setting and direct selection, the integration of information by the evolutionary process leads to qualitatively different results from individual smartness to cooperative community structures.

A rich diversity of opercle bone shape among teleost fishes

PubMed Central

Small, Clayton M.; Knope, Matthew L.

2017-01-01

The opercle is a prominent craniofacial bone supporting the gill cover in all bony fish and has been the subject of morphological, developmental, and genetic investigation. We surveyed the shapes of this bone among 110 families spanning the teleost tree and examined its pattern of occupancy in a principal component-based morphospace. Contrasting with expectations from the literature that suggest the local morphospace would be only sparsely occupied, we find primarily dense, broad filling of the morphological landscape, indicating rich diversity. Phylomorphospace plots suggest that dynamic evolution underlies the observed spatial patterning. Evolutionary transits through the morphospaces are sometimes long, and occur in a variety of directions. The trajectories seem to represent both evolutionary divergences and convergences, the latter supported by convevol analysis. We suggest that that this pattern of occupancy reflects the various adaptations of different groups of fishes, seemingly paralleling their diverse marine and freshwater ecologies and life histories. Opercle shape evolution within the acanthomorphs, spiny ray-finned fishes, appears to have been especially dynamic. PMID:29281662

Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles.

PubMed

Orozco-terWengel, Pablo; Kapun, Martin; Nolte, Viola; Kofler, Robert; Flatt, Thomas; Schlötterer, Christian

2012-10-01

The genomic basis of adaptation to novel environments is a fundamental problem in evolutionary biology that has gained additional importance in the light of the recent global change discussion. Here, we combined laboratory natural selection (experimental evolution) in Drosophila melanogaster with genome-wide next generation sequencing of DNA pools (Pool-Seq) to identify alleles that are favourable in a novel laboratory environment and traced their trajectories during the adaptive process. Already after 15 generations, we identified a pronounced genomic response to selection, with almost 5000 single nucleotide polymorphisms (SNP; genome-wide false discovery rates < 0.005%) deviating from neutral expectation. Importantly, the evolutionary trajectories of the selected alleles were heterogeneous, with the alleles falling into two distinct classes: (i) alleles that continuously rise in frequency; and (ii) alleles that at first increase rapidly but whose frequencies then reach a plateau. Our data thus suggest that the genomic response to selection can involve a large number of selected SNPs that show unexpectedly complex evolutionary trajectories, possibly due to nonadditive effects. © 2012 Blackwell Publishing Ltd.

The Frequency of Fitness Peak Shifts Is Increased at Expanding Range Margins Due to Mutation Surfing

PubMed Central

Burton, Olivia J.; Travis, Justin M. J.

2008-01-01

Dynamic species' ranges, those that are either invasive or shifting in response to environmental change, are the focus of much recent interest in ecology, evolution, and genetics. Understanding how range expansions can shape evolutionary trajectories requires the consideration of nonneutral variability and genetic architecture, yet the majority of empirical and theoretical work to date has explored patterns of neutral variability. Here we use forward computer simulations of population growth, dispersal, and mutation to explore how range-shifting dynamics can influence evolution on rugged fitness landscapes. We employ a two-locus model, incorporating sign epistasis, and find that there is an increased likelihood of fitness peak shifts during a period of range expansion. Maladapted valley genotypes can accumulate at an expanding range front through a phenomenon called mutation surfing, which increases the likelihood that a mutation leading to a higher peak will occur. Our results indicate that most peak shifts occur close to the expanding front. We also demonstrate that periods of range shifting are especially important for peak shifting in species with narrow geographic distributions. Our results imply that trajectories on rugged fitness landscapes can be modified substantially when ranges are dynamic. PMID:18505864

The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection.

PubMed

Payen, Celia; Di Rienzi, Sara C; Ong, Giang T; Pogachar, Jamie L; Sanchez, Joseph C; Sunshine, Anna B; Raghuraman, M K; Brewer, Bonita J; Dunham, Maitreya J

2014-03-20

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another.

The Dynamics of Diverse Segmental Amplifications in Populations of Saccharomyces cerevisiae Adapting to Strong Selection

PubMed Central

Payen, Celia; Di Rienzi, Sara C.; Ong, Giang T.; Pogachar, Jamie L.; Sanchez, Joseph C.; Sunshine, Anna B.; Raghuraman, M. K.; Brewer, Bonita J.; Dunham, Maitreya J.

2014-01-01

Population adaptation to strong selection can occur through the sequential or parallel accumulation of competing beneficial mutations. The dynamics, diversity, and rate of fixation of beneficial mutations within and between populations are still poorly understood. To study how the mutational landscape varies across populations during adaptation, we performed experimental evolution on seven parallel populations of Saccharomyces cerevisiae continuously cultured in limiting sulfate medium. By combining quantitative polymerase chain reaction, array comparative genomic hybridization, restriction digestion and contour-clamped homogeneous electric field gel electrophoresis, and whole-genome sequencing, we followed the trajectory of evolution to determine the identity and fate of beneficial mutations. During a period of 200 generations, the yeast populations displayed parallel evolutionary dynamics that were driven by the coexistence of independent beneficial mutations. Selective amplifications rapidly evolved under this selection pressure, in particular common inverted amplifications containing the sulfate transporter gene SUL1. Compared with single clones, detailed analysis of the populations uncovers a greater complexity whereby multiple subpopulations arise and compete despite a strong selection. The most common evolutionary adaptation to strong selection in these populations grown in sulfate limitation is determined by clonal interference, with adaptive variants both persisting and replacing one another. PMID:24368781

Chaos and the (un)predictability of evolution in a changing environment.

PubMed

Rego-Costa, Artur; Débarre, Florence; Chevin, Luis-Miguel

2018-02-01

Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolution, the loss of diversity and the role of trade-offs.

PubMed

Best, Alex; Bowers, Roger; White, Andy

2015-06-01

We investigate how the loss of previously evolved diversity in host resistance to disease is dependent on the complexity of the underlying evolutionary trade-off. Working within the adaptive dynamics framework, using graphical tools (pairwise invasion plots, PIPs; trait evolution plots, TEPs) and algebraic analysis we consider polynomial trade-offs of increasing degree. Our focus is on the evolutionary trajectory of the dimorphic population after it has been attracted to an evolutionary branching point. We show that for sufficiently complex trade-offs (here, polynomials of degree three or higher) the resulting invasion boundaries can form closed 'oval' areas of invadability and strategy coexistence. If no attracting singular strategies exist within this region, then the population is destined to evolve outside of the region of coexistence, resulting in the loss of one strain. In particular, the loss of diversity in this model always occurs in such a way that the remaining strain is not attracted back to the branching point but to an extreme of the trade-off, meaning the diversity is lost forever. We also show similar results for a non-polynomial but complex trade-off, and for a different eco-evolutionary model. Our work further highlights the importance of trade-offs to evolutionary behaviour. Copyright © 2015 Elsevier Inc. All rights reserved.

The role of protein dynamics in the evolution of new enzyme function.

PubMed

Campbell, Eleanor; Kaltenbach, Miriam; Correy, Galen J; Carr, Paul D; Porebski, Benjamin T; Livingstone, Emma K; Afriat-Jurnou, Livnat; Buckle, Ashley M; Weik, Martin; Hollfelder, Florian; Tokuriki, Nobuhiko; Jackson, Colin J

2016-11-01

Enzymes must be ordered to allow the stabilization of transition states by their active sites, yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic cycles. The biophysical principles that determine how specific protein dynamics evolve and how remote mutations affect catalytic activity are poorly understood. Here we examine a 'molecular fossil record' that was recently obtained during the laboratory evolution of a phosphotriesterase from Pseudomonas diminuta to an arylesterase. Analysis of the structures and dynamics of nine protein variants along this trajectory, and three rationally designed variants, reveals cycles of structural destabilization and repair, evolutionary pressure to 'freeze out' unproductive motions and sampling of distinct conformations with specific catalytic properties in bi-functional intermediates. This work establishes that changes to the conformational landscapes of proteins are an essential aspect of molecular evolution and that change in function can be achieved through enrichment of preexisting conformational sub-states.

Patterns of cranial ontogeny in lacertid lizards: morphological and allometric disparity.

PubMed

Urošević, A; Ljubisavljević, K; Ivanović, A

2013-02-01

We explored the ontogenetic dynamics of the morphological and allometric disparity in the cranium shapes of twelve lacertid lizard species. The analysed species (Darevskia praticola, Dinarolacerta mosorensis, Iberolacerta horvathi, Lacerta agilis, L. trilineata, L. viridis, Podarcis erhardii, P. melisellensis, P. muralis, P. sicula, P. taurica and Zootoca vivipara) can be classified into different ecomorphs: terrestrial lizards that inhabit vegetated habitats (habitats with lush or sparse vegetation), saxicolous and shrub-climbing lizards. We observed that there was an overall increase in the morphological disparity (MD) during the ontogeny of the lacertid lizards. The ventral cranium, which is involved in the mechanics of jaw movement and feeding, showed higher levels of MD, an ontogenetic shift in the morphospace planes and more variable allometric patterns than more conserved dorsal crania. With respect to ecology, the allometric trajectories of the shrub-climbing species tended to cluster together, whereas the allometric trajectories of the saxicolous species were highly dispersed. Our results indicate that the ontogenetic patterns of morphological and allometric disparity in the lacertid lizards are modified by ecology and functional constraints and that the identical mechanisms that lead to intraspecific morphological variation also produce morphological divergence at higher taxonomic levels. © 2012 The Authors. Journal of Evolutionary Biology © 2012 European Society For Evolutionary Biology.

Epigenetic battle of the sexes. Comment on: ;Epigenetic game theory: How to compute the epigenetic control of maternal-to-zygotic transition; by Qian Wang et al.

NASA Astrophysics Data System (ADS)

Wu, Song

2017-03-01

Qian Wang et al. present an interesting framework, named epigenetic game theory, for modeling sex-based epigenetic dynamics during embryogenesis from a new viewpoint of evolutionary game theory [1]. That is, epigenomes of sperms and oocytes may coordinate through either cooperation or competition, or both, to affect the fitness of embryos. The work uses a set of ordinary differential equations (ODEs) to describe longitudinal trajectories of DNA methylation levels in both parental and maternal gametes and their dependence on each other. The insights gained from this review, i.e. dynamic methylation profiles and their interaction are potentially important to many fields, such as biomedicine and agriculture.

Adaptive Tracking Control for Robots With an Interneural Computing Scheme.

PubMed

Tsai, Feng-Sheng; Hsu, Sheng-Yi; Shih, Mau-Hsiang

2018-04-01

Adaptive tracking control of mobile robots requires the ability to follow a trajectory generated by a moving target. The conventional analysis of adaptive tracking uses energy minimization to study the convergence and robustness of the tracking error when the mobile robot follows a desired trajectory. However, in the case that the moving target generates trajectories with uncertainties, a common Lyapunov-like function for energy minimization may be extremely difficult to determine. Here, to solve the adaptive tracking problem with uncertainties, we wish to implement an interneural computing scheme in the design of a mobile robot for behavior-based navigation. The behavior-based navigation adopts an adaptive plan of behavior patterns learning from the uncertainties of the environment. The characteristic feature of the interneural computing scheme is the use of neural path pruning with rewards and punishment interacting with the environment. On this basis, the mobile robot can be exploited to change its coupling weights in paths of neural connections systematically, which can then inhibit or enhance the effect of flow elimination in the dynamics of the evolutionary neural network. Such dynamical flow translation ultimately leads to robust sensory-to-motor transformations adapting to the uncertainties of the environment. A simulation result shows that the mobile robot with the interneural computing scheme can perform fault-tolerant behavior of tracking by maintaining suitable behavior patterns at high frequency levels.

The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation

PubMed Central

Hughes, Julie M.; Lohman, Brian K.; Deckert, Gail E.; Nichols, Eric P.; Settles, Matt; Abdo, Zaid; Top, Eva M.

2012-01-01

ABSTRACT Promiscuous plasmids replicate in a wide range of bacteria and therefore play a key role in the dissemination of various host-beneficial traits, including antibiotic resistance. Despite the medical relevance, little is known about the evolutionary dynamics through which drug resistance plasmids adapt to new hosts and thereby persist in the absence of antibiotics. We previously showed that the incompatibility group P-1 (IncP-1) minireplicon pMS0506 drastically improved its stability in novel host Shewanella oneidensis MR-1 after 1,000 generations under antibiotic selection for the plasmid. The only mutations found were those affecting the N terminus of the plasmid replication initiation protein TrfA1. Our aim in this study was to gain insight into the dynamics of plasmid evolution. Changes in stability and genotype frequencies of pMS0506 were monitored in evolving populations of MR-1 (pMS0506). Genotypes were determined by sequencing trfA1 amplicons from individual clones and by 454 pyrosequencing of whole plasmids from entire populations. Stability of pMS0506 drastically improved by generation 200. Many evolved plasmid genotypes with point mutations as well as in-frame and frameshift deletions and duplications in trfA1 were observed in all lineages with both sequencing methods. Strikingly, multiple genotypes were simultaneously present at high frequencies (>10%) in each population. Their relative abundances changed over time, but after 1,000 generations only one or two genotypes dominated the populations. This suggests that hosts with different plasmid genotypes were competing with each other, thus affecting the evolutionary trajectory. Plasmids can thus rapidly improve their stability, and clonal interference plays a significant role in plasmid-host adaptation dynamics. PMID:22761390

Religion and psychosis: a common evolutionary trajectory?

PubMed

Dein, Simon; Littlewood, Roland

2011-07-01

In this article we propose that schizophrenia and religious cognition engage cognate mental modules in the over-attribution of agency and the overextension of theory of mind. We argue similarities and differences between assumptions of ultrahuman agents with omniscient minds and certain ''pathological'' forms of thinking in schizophrenia: thought insertion, withdrawal and broadcasting, and delusions of reference. In everyday religious cognition agency detection and theory of mind modules function ''normally,'' whereas in schizophrenia both modules are impaired. It is suggested that religion and schizophrenia have perhaps had a related evolutionary trajectory.

How can we model selectively neutral density dependence in evolutionary games.

PubMed

Argasinski, Krzysztof; Kozłowski, Jan

2008-03-01

The problem of density dependence appears in all approaches to the modelling of population dynamics. It is pertinent to classic models (i.e., Lotka-Volterra's), and also population genetics and game theoretical models related to the replicator dynamics. There is no density dependence in the classic formulation of replicator dynamics, which means that population size may grow to infinity. Therefore the question arises: How is unlimited population growth suppressed in frequency-dependent models? Two categories of solutions can be found in the literature. In the first, replicator dynamics is independent of background fitness. In the second type of solution, a multiplicative suppression coefficient is used, as in a logistic equation. Both approaches have disadvantages. The first one is incompatible with the methods of life history theory and basic probabilistic intuitions. The logistic type of suppression of per capita growth rate stops trajectories of selection when population size reaches the maximal value (carrying capacity); hence this method does not satisfy selective neutrality. To overcome these difficulties, we must explicitly consider turn-over of individuals dependent on mortality rate. This new approach leads to two interesting predictions. First, the equilibrium value of population size is lower than carrying capacity and depends on the mortality rate. Second, although the phase portrait of selection trajectories is the same as in density-independent replicator dynamics, pace of selection slows down when population size approaches equilibrium, and then remains constant and dependent on the rate of turn-over of individuals.

Mega-evolutionary dynamics of the adaptive radiation of birds.

PubMed

Cooney, Christopher R; Bright, Jen A; Capp, Elliot J R; Chira, Angela M; Hughes, Emma C; Moody, Christopher J A; Nouri, Lara O; Varley, Zoë K; Thomas, Gavin H

2017-02-16

The origin and expansion of biological diversity is regulated by both developmental trajectories and limits on available ecological niches. As lineages diversify, an early and often rapid phase of species and trait proliferation gives way to evolutionary slow-downs as new species pack into ever more densely occupied regions of ecological niche space. Small clades such as Darwin's finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear. Here we address this problem on a global scale by analysing a crowdsourced dataset of three-dimensional scanned bill morphology from more than 2,000 species. We find that bill diversity expanded early in extant avian evolutionary history, before transitioning to a phase dominated by packing of morphological space. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare, but major, discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill-shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian and Simpsonian ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks.

Arctic biodiversity: Increasing richness accompanies shrinking refugia for a cold-associated tundra fauna

USGS Publications Warehouse

Hope, Andrew G.; Waltari, Eric; Malaney, Jason L.; Payer, David C.; Cook, J.A.; Talbot, Sandra L.

2015-01-01

As ancestral biodiversity responded dynamically to late-Quaternary climate changes, so are extant organisms responding to the warming trajectory of the Anthropocene. Ecological predictive modeling, statistical hypothesis tests, and genetic signatures of demographic change can provide a powerful integrated toolset for investigating these biodiversity responses to climate change, and relative resiliency across different communities. Within the biotic province of Beringia, we analyzed specimen localities and DNA sequences from 28 mammal species associated with boreal forest and Arctic tundra biomes to assess both historical distributional and evolutionary responses and then forecasted future changes based on statistical assessments of past and present trajectories, and quantified distributional and demographic changes in relation to major management regions within the study area. We addressed three sets of hypotheses associated with aspects of methodological, biological, and socio-political importance by asking (1) what is the consistency among implications of predicted changes based on the results of both ecological and evolutionary analyses; (2) what are the ecological and evolutionary implications of climate change considering either total regional diversity or distinct communities associated with major biomes; and (3) are there differences in management implications across regions? Our results indicate increasing Arctic richness through time that highlights a potential state shift across the Arctic landscape. However, within distinct ecological communities, we found a predicted decline in the range and effective population size of tundra species into several discrete refugial areas. Consistency in results based on a combination of both ecological and evolutionary approaches demonstrates increased statistical confidence by applying cross-discipline comparative analyses to conservation of biodiversity, particularly considering variable management regimes that seek to balance sustainable ecosystems with other anthropogenic values. Refugial areas for cold-adapted taxa appear to be persistent across both warm and cold climate phases and although fragmented, constitute vital regions for persistence of Arctic mammals.

Optimal lunar soft landing trajectories using taboo evolutionary programming

NASA Astrophysics Data System (ADS)

Mutyalarao, M.; Raj, M. Xavier James

A safe lunar landing is a key factor to undertake an effective lunar exploration. Lunar lander consists of four phases such as launch phase, the earth-moon transfer phase, circumlunar phase and landing phase. The landing phase can be either hard landing or soft landing. Hard landing means the vehicle lands under the influence of gravity without any deceleration measures. However, soft landing reduces the vertical velocity of the vehicle before landing. Therefore, for the safety of the astronauts as well as the vehicle lunar soft landing with an acceptable velocity is very much essential. So it is important to design the optimal lunar soft landing trajectory with minimum fuel consumption. Optimization of Lunar Soft landing is a complex optimal control problem. In this paper, an analysis related to lunar soft landing from a parking orbit around Moon has been carried out. A two-dimensional trajectory optimization problem is attempted. The problem is complex due to the presence of system constraints. To solve the time-history of control parameters, the problem is converted into two point boundary value problem by using the maximum principle of Pontrygen. Taboo Evolutionary Programming (TEP) technique is a stochastic method developed in recent years and successfully implemented in several fields of research. It combines the features of taboo search and single-point mutation evolutionary programming. Identifying the best unknown parameters of the problem under consideration is the central idea for many space trajectory optimization problems. The TEP technique is used in the present methodology for the best estimation of initial unknown parameters by minimizing objective function interms of fuel requirements. The optimal estimation subsequently results into an optimal trajectory design of a module for soft landing on the Moon from a lunar parking orbit. Numerical simulations demonstrate that the proposed approach is highly efficient and it reduces the minimum fuel consumption. The results are compared with the available results in literature shows that the solution of present algorithm is better than some of the existing algorithms. Keywords: soft landing, trajectory optimization, evolutionary programming, control parameters, Pontrygen principle.

Comparison of long-term evolutionary trajectories of two ephemeral channels after channel-forming extraordinary floods

NASA Astrophysics Data System (ADS)

Lotsari, Eliisa; House, Kyle; Alho, Petteri; Baker, Victor

2017-04-01

Analyses of the evolutionary trajectories of braided ephemeral channels enable identification of trends, magnitudes and periodicity of the processes that affect the channels. In addition to infrequent great floods, relatively frequent, small discharge events have been shown to be important for the evolution of ephemeral channels. However, evolutionary trajectories have rarely been studied in small ephemeral rivers, that predominantly transport gravel, cobles and boulders. Ephemeral tributary channels typify the Colorado River basin (USA), and two examples are Bronco Creek and Eldorado Canyon. These streams experienced extraordinary great floods in 1971 and 1974 respectively, and they are comparable to each other in both basin size, and climatic conditions. Annual precipitation is less than 50 cm, and the average temperature of each month is above 7°C. More importantly, earlier studies have shown similarities in the hydraulics and geomorphic characteristics of the extraordinary floods, which removed the pre-flood bar and braiding structure from the channels. Thus, these two channels are ideal for comparisons of their evolutionary trajecties. Moreover, the availability of high-resolutions aerial photographs for both channels since 1954 allowed for decadal analyses. Our research has analyzed and compared the long-term evolutionary trajectories of the two ephemeral channels within Colorado River Basin based on series of aerial photos and digital elevation models. (1) We detected the development and adjustment of braiding since the extraordinary floods. The detected parameters include the braiding index, bar area and number, channel area and width, confluence number and density, and the proportion of inactive and active areas. (2) We also analyzed the time required for the ephemeral river system to evolve back to its prior state before the high magnitude floods. Finally, (3) we analyzed whether these temporal changes in channel evolution can reveal new insights as to climatic and environmental conditions for these un-gauged basins.

Evolution and Vaccination of Influenza Virus.

PubMed

Lam, Ham Ching; Bi, Xuan; Sreevatsan, Srinand; Boley, Daniel

2017-08-01

In this study, we present an application paradigm in which an unsupervised machine learning approach is applied to the high-dimensional influenza genetic sequences to investigate whether vaccine is a driving force to the evolution of influenza virus. We first used a visualization approach to visualize the evolutionary paths of vaccine-controlled and non-vaccine-controlled influenza viruses in a low-dimensional space. We then quantified the evolutionary differences between their evolutionary trajectories through the use of within- and between-scatter matrices computation to provide the statistical confidence to support the visualization results. We used the influenza surface Hemagglutinin (HA) gene for this study as the HA gene is the major target of the immune system. The visualization is achieved without using any clustering methods or prior information about the influenza sequences. Our results clearly showed that the evolutionary trajectories between vaccine-controlled and non-vaccine-controlled influenza viruses are different and vaccine as an evolution driving force cannot be completely eliminated.

De novo inference of protein function from coarse-grained dynamics.

PubMed

Bhadra, Pratiti; Pal, Debnath

2014-10-01

Inference of molecular function of proteins is the fundamental task in the quest for understanding cellular processes. The task is getting increasingly difficult with thousands of new proteins discovered each day. The difficulty arises primarily due to lack of high-throughput experimental technique for assessing protein molecular function, a lacunae that computational approaches are trying hard to fill. The latter too faces a major bottleneck in absence of clear evidence based on evolutionary information. Here we propose a de novo approach to annotate protein molecular function through structural dynamics match for a pair of segments from two dissimilar proteins, which may share even <10% sequence identity. To screen these matches, corresponding 1 µs coarse-grained (CG) molecular dynamics trajectories were used to compute normalized root-mean-square-fluctuation graphs and select mobile segments, which were, thereafter, matched for all pairs using unweighted three-dimensional autocorrelation vectors. Our in-house custom-built forcefield (FF), extensively validated against dynamics information obtained from experimental nuclear magnetic resonance data, was specifically used to generate the CG dynamics trajectories. The test for correspondence of dynamics-signature of protein segments and function revealed 87% true positive rate and 93.5% true negative rate, on a dataset of 60 experimentally validated proteins, including moonlighting proteins and those with novel functional motifs. A random test against 315 unique fold/function proteins for a negative test gave >99% true recall. A blind prediction on a novel protein appears consistent with additional evidences retrieved therein. This is the first proof-of-principle of generalized use of structural dynamics for inferring protein molecular function leveraging our custom-made CG FF, useful to all. © 2014 Wiley Periodicals, Inc.

Critical Transition in Critical Zone of Intensively Managed Landscapes

NASA Astrophysics Data System (ADS)

Kumar, P.

2017-12-01

Intensification of industrial agriculture has resulted in severe unintended global impacts, including degradation of arable land and eutrophication of receiving water bodies. Modern agricultural practices rely on significant direct and indirect human energy inputs, which have created imbalances between increased rates of biogeochemical processes related to production and background rates of natural processes. These imbalances have cascaded through the deep inter-dependencies between carbon, soil, water, nutrient and ecological processes, resulting in a critical transition of the Critical Zone and creating emergent dynamics and evolutionary trajectories. Understanding of these novel organization and function of the Critical Zone is vital for developing sustainable agricultural practices.

The semaphorontic view of homology.

PubMed

Havstad, Joyce C; Assis, Leandro C S; Rieppel, Olivier

2015-11-01

The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra-organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter-species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity--ontogenetic (through development) and phylogenetic (via shared evolutionary history)--break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (-state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (-states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution Published by Wiley Periodicals, Inc.

Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.

PubMed

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into "species groups". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.

On the origin of biological construction, with a focus on multicellularity.

PubMed

van Gestel, Jordi; Tarnita, Corina E

2017-10-17

Biology is marked by a hierarchical organization: all life consists of cells; in some cases, these cells assemble into groups, such as endosymbionts or multicellular organisms; in turn, multicellular organisms sometimes assemble into yet other groups, such as primate societies or ant colonies. The construction of new organizational layers results from hierarchical evolutionary transitions, in which biological units (e.g., cells) form groups that evolve into new units of biological organization (e.g., multicellular organisms). Despite considerable advances, there is no bottom-up, dynamical account of how, starting from the solitary ancestor, the first groups originate and subsequently evolve the organizing principles that qualify them as new units. Guided by six central questions, we propose an integrative bottom-up approach for studying the dynamics underlying hierarchical evolutionary transitions, which builds on and synthesizes existing knowledge. This approach highlights the crucial role of the ecology and development of the solitary ancestor in the emergence and subsequent evolution of groups, and it stresses the paramount importance of the life cycle: only by evaluating groups in the context of their life cycle can we unravel the evolutionary trajectory of hierarchical transitions. These insights also provide a starting point for understanding the types of subsequent organizational complexity. The central research questions outlined here naturally link existing research programs on biological construction (e.g., on cooperation, multilevel selection, self-organization, and development) and thereby help integrate knowledge stemming from diverse fields of biology.

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

PubMed Central

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

Weight of fitness deviation governs strict physical chaos in replicator dynamics.

PubMed

Pandit, Varun; Mukhopadhyay, Archan; Chakraborty, Sagar

2018-03-01

Replicator equation-a paradigm equation in evolutionary game dynamics-mathematizes the frequency dependent selection of competing strategies vying to enhance their fitness (quantified by the average payoffs) with respect to the average fitnesses of the evolving population under consideration. In this paper, we deal with two discrete versions of the replicator equation employed to study evolution in a population where any two players' interaction is modelled by a two-strategy symmetric normal-form game. There are twelve distinct classes of such games, each typified by a particular ordinal relationship among the elements of the corresponding payoff matrix. Here, we find the sufficient conditions for the existence of asymptotic solutions of the replicator equations such that the solutions-fixed points, periodic orbits, and chaotic trajectories-are all strictly physical, meaning that the frequency of any strategy lies inside the closed interval zero to one at all times. Thus, we elaborate on which of the twelve types of games are capable of showing meaningful physical solutions and for which of the two types of replicator equation. Subsequently, we introduce the concept of the weight of fitness deviation that is the scaling factor in a positive affine transformation connecting two payoff matrices such that the corresponding one-shot games have exactly same Nash equilibria and evolutionary stable states. The weight also quantifies how much the excess of fitness of a strategy over the average fitness of the population affects the per capita change in the frequency of the strategy. Intriguingly, the weight's variation is capable of making the Nash equilibria and the evolutionary stable states, useless by introducing strict physical chaos in the replicator dynamics based on the normal-form game.

Decoupled evolution of floral traits and climatic preferences in a clade of Neotropical Gesneriaceae.

PubMed

Serrano-Serrano, Martha Liliana; Perret, Mathieu; Guignard, Maïté; Chautems, Alain; Silvestro, Daniele; Salamin, Nicolas

2015-11-10

Major factors influencing the phenotypic diversity of a lineage can be recognized by characterizing the extent and mode of trait evolution between related species. Here, we compared the evolutionary dynamics of traits associated with floral morphology and climatic preferences in a clade composed of the genera Codonanthopsis, Codonanthe and Nematanthus (Gesneriaceae). To test the mode and specific components that lead to phenotypic diversity in this group, we performed a Bayesian phylogenetic analysis of combined nuclear and plastid DNA sequences and modeled the evolution of quantitative traits related to flower shape and size and to climatic preferences. We propose an alternative approach to display graphically the complex dynamics of trait evolution along a phylogenetic tree using a wide range of evolutionary scenarios. Our results demonstrated heterogeneous trait evolution. Floral shapes displaced into separate regimes selected by the different pollinator types (hummingbirds versus insects), while floral size underwent a clade-specific evolution. Rates of evolution were higher for the clade that is hummingbird pollinated and experienced flower resupination, compared with species pollinated by bees, suggesting a relevant role of plant-pollinator interactions in lowland rainforest. The evolution of temperature preferences is best explained by a model with distinct selective regimes between the Brazilian Atlantic Forest and the other biomes, whereas differentiation along the precipitation axis was characterized by higher rates, compared with temperature, and no regime or clade-specific patterns. Our study shows different selective regimes and clade-specific patterns in the evolution of morphological and climatic components during the diversification of Neotropical species. Our new graphical visualization tool allows the representation of trait trajectories under parameter-rich models, thus contributing to a better understanding of complex evolutionary dynamics.

Evolutionary construction by staying together and coming together.

PubMed

Tarnita, Corina E; Taubes, Clifford H; Nowak, Martin A

2013-03-07

The evolutionary trajectory of life on earth is one of increasing size and complexity. Yet the standard equations of evolutionary dynamics describe mutation and selection among similar organisms that compete on the same level of organization. Here we begin to outline a mathematical theory that might help to explore how evolution can be constructive, how natural selection can lead from lower to higher levels of organization. We distinguish two fundamental operations, which we call 'staying together' and 'coming together'. Staying together means that individuals form larger units by not separating after reproduction, while coming together means that independent individuals form aggregates. Staying together can lead to specialization and division of labor, but the developmental program must evolve in the basic unit. Coming together can be creative by combining units with different properties. Both operations have been identified in the context of multicellularity, but they have been treated very similarly. Here we point out that staying together and coming together can be found at every level of biological construction and moreover that they face different evolutionary problems. The distinction is particularly clear in the context of cooperation and defection. For staying together the stability of cooperation takes the form of a developmental error threshold, while coming together leads to evolutionary games and requires a mechanism for the evolution of cooperation. We use our models to discuss simple aspects of the evolution of protocells, eukarya, multi-cellularity and animal societies. Copyright © 2012 Elsevier Ltd. All rights reserved.

Identifying predictors of time-inhomogeneous viral evolutionary processes.

PubMed

Bielejec, Filip; Baele, Guy; Rodrigo, Allen G; Suchard, Marc A; Lemey, Philippe

2016-07-01

Various factors determine the rate at which mutations are generated and fixed in viral genomes. Viral evolutionary rates may vary over the course of a single persistent infection and can reflect changes in replication rates and selective dynamics. Dedicated statistical inference approaches are required to understand how the complex interplay of these processes shapes the genetic diversity and divergence in viral populations. Although evolutionary models accommodating a high degree of complexity can now be formalized, adequately informing these models by potentially sparse data, and assessing the association of the resulting estimates with external predictors, remains a major challenge. In this article, we present a novel Bayesian evolutionary inference method, which integrates multiple potential predictors and tests their association with variation in the absolute rates of synonymous and non-synonymous substitutions along the evolutionary history. We consider clinical and virological measures as predictors, but also changes in population size trajectories that are simultaneously inferred using coalescent modelling. We demonstrate the potential of our method in an application to within-host HIV-1 sequence data sampled throughout the infection of multiple patients. While analyses of individual patient populations lack statistical power, we detect significant evidence for an abrupt drop in non-synonymous rates in late stage infection and a more gradual increase in synonymous rates over the course of infection in a joint analysis across all patients. The former is predicted by the immune relaxation hypothesis while the latter may be in line with increasing replicative fitness during the asymptomatic stage.

Mega-evolutionary dynamics of the adaptive radiation of birds

PubMed Central

Capp, Elliot J. R.; Chira, Angela M.; Hughes, Emma C.; Moody, Christopher J. A.; Nouri, Lara O.; Varley, Zoë K.; Thomas, Gavin H.

2017-01-01

The origin and expansion of biological diversity is regulated by both developmental trajectories1,2 and limits on available ecological niches3–7. As lineages diversify an early, often rapid, phase of species and trait proliferation gives way to evolutionary slowdowns as new species pack into ever more densely occupied regions of ecological niche space6,8. Small clades such as Darwin’s finches demonstrate that natural selection is the driving force of adaptive radiations, but how microevolutionary processes scale up to shape the expansion of phenotypic diversity over much longer evolutionary timescales is unclear9. Here we address this problem on a global scale by analysing a novel crowd-sourced dataset of 3D-scanned bill morphology from >2000 species. We find that bill diversity expanded early in extant avian evolutionary history before transitioning to a phase dominated by morphospace packing. However, this early phenotypic diversification is decoupled from temporal variation in evolutionary rate: rates of bill evolution vary among lineages but are comparatively stable through time. We find that rare but major discontinuities in phenotype emerge from rapid increases in rate along single branches, sometimes leading to depauperate clades with unusual bill morphologies. Despite these jumps between groups, the major axes of within-group bill shape evolution are remarkably consistent across birds. We reveal that macroevolutionary processes underlying global-scale adaptive radiations support Darwinian9 and Simpsonian4 ideas of microevolution within adaptive zones and accelerated evolution between distinct adaptive peaks. PMID:28146475

Time Series Expression Analyses Using RNA-seq: A Statistical Approach

PubMed Central

Oh, Sunghee; Song, Seongho; Grabowski, Gregory; Zhao, Hongyu; Noonan, James P.

2013-01-01

RNA-seq is becoming the de facto standard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis. PMID:23586021

Time series expression analyses using RNA-seq: a statistical approach.

PubMed

Oh, Sunghee; Song, Seongho; Grabowski, Gregory; Zhao, Hongyu; Noonan, James P

2013-01-01

RNA-seq is becoming the de facto standard approach for transcriptome analysis with ever-reducing cost. It has considerable advantages over conventional technologies (microarrays) because it allows for direct identification and quantification of transcripts. Many time series RNA-seq datasets have been collected to study the dynamic regulations of transcripts. However, statistically rigorous and computationally efficient methods are needed to explore the time-dependent changes of gene expression in biological systems. These methods should explicitly account for the dependencies of expression patterns across time points. Here, we discuss several methods that can be applied to model timecourse RNA-seq data, including statistical evolutionary trajectory index (SETI), autoregressive time-lagged regression (AR(1)), and hidden Markov model (HMM) approaches. We use three real datasets and simulation studies to demonstrate the utility of these dynamic methods in temporal analysis.

Does aquatic foraging impact head shape evolution in snakes?

PubMed Central

Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-01-01

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. PMID:27581887

De novo assembly and next-generation sequencing to analyse full-length gene variants from codon-barcoded libraries.

PubMed

Cho, Namjin; Hwang, Byungjin; Yoon, Jung-ki; Park, Sangun; Lee, Joongoo; Seo, Han Na; Lee, Jeewon; Huh, Sunghoon; Chung, Jinsoo; Bang, Duhee

2015-09-21

Interpreting epistatic interactions is crucial for understanding evolutionary dynamics of complex genetic systems and unveiling structure and function of genetic pathways. Although high resolution mapping of en masse variant libraries renders molecular biologists to address genotype-phenotype relationships, long-read sequencing technology remains indispensable to assess functional relationship between mutations that lie far apart. Here, we introduce JigsawSeq for multiplexed sequence identification of pooled gene variant libraries by combining a codon-based molecular barcoding strategy and de novo assembly of short-read data. We first validate JigsawSeq on small sub-pools and observed high precision and recall at various experimental settings. With extensive simulations, we then apply JigsawSeq to large-scale gene variant libraries to show that our method can be reliably scaled using next-generation sequencing. JigsawSeq may serve as a rapid screening tool for functional genomics and offer the opportunity to explore evolutionary trajectories of protein variants.

Allometry and Interspecific Differences in the Facial Cranium of Two Closely Related Macaque Species

PubMed Central

Ito, Tsuyoshi; Nishimura, Takeshi; Takai, Masanaru

2011-01-01

Interpreting evolutionary history of macaque monkeys from fossil evidence is difficult, because their evolutionary fluctuations in body size might have removed or formed important morphological features differently in each lineage. We employed geometric morphometrics to explore allometric trajectories of craniofacial shape in two closely related species, Macaca fascicularis and M. fuscata. These two species exhibit a single shared allometric trajectory in superoinferior deflection of the anterior face, indicating that the differences in this feature can be explained by size variation. In contrast, two parallel trajectories are demonstrated in craniofacial protrusion, indicating that even if they are comparable in size, M. fuscata has a higher and shorter face than M. fascicularis. The degree of facial protrusion is most likely a critical feature for phyletic evaluation in the fascicularis group. Such analyses in various macaques would help to resolve controversies regarding phyletic interpretations of fossil macaques. PMID:22567301

Life as a Cosmic Phenomenon: 2. the Panspermic Trajectory of Homo Sapiens

NASA Astrophysics Data System (ADS)

Tokoro, Gensuke; Wickramasinghe, N. Chandra

We discuss the origin and evolution of Homo sapiens in a cosmic context, and in relation to the Hoyle-Wickramasinghe theory of panspermia for which there is now overwhelming evidence. It is argued that the first bacteria (archea) incident on the Earth via the agency of comets 3.8-4 billion years ago continued at later times to be augmented by viral genes (DNA, RNA) from space that eventually led to the evolutionary patterns we see in present-day biology. We argue that the current evolutionary status of Homo sapiens as well as its future trajectory is circumscribed by evolutionary processes that were pre-determined on a cosmic scale -- over vast distances and enormous spans of cosmic time. Based on this teleological hypothesis we postulate that two distinct classes of cosmic viruses (cosmic viral genes) are involved in accounting for the facts relating to the evolution of life.

Evolution of a predator-induced, nonlinear reaction norm.

PubMed

Carter, Mauricio J; Lind, Martin I; Dennis, Stuart R; Hentley, William; Beckerman, Andrew P

2017-08-30

Inducible, anti-predator traits are a classic example of phenotypic plasticity. Their evolutionary dynamics depend on their genetic basis, the historical pattern of predation risk that populations have experienced and current selection gradients. When populations experience predators with contrasting hunting strategies and size preferences, theory suggests contrasting micro-evolutionary responses to selection. Daphnia pulex is an ideal species to explore the micro-evolutionary response of anti-predator traits because they face heterogeneous predation regimes, sometimes experiencing only invertebrate midge predators and other times experiencing vertebrate fish and invertebrate midge predators. We explored plausible patterns of adaptive evolution of a predator-induced morphological reaction norm. We combined estimates of selection gradients that characterize the various habitats that D. pulex experiences with detail on the quantitative genetic architecture of inducible morphological defences. Our data reveal a fine scale description of daphnid defensive reaction norms, and a strong covariance between the sensitivity to cues and the maximum response to cues. By analysing the response of the reaction norm to plausible, predator-specific selection gradients, we show how in the context of this covariance, micro-evolution may be more uniform than predicted from size-selective predation theory. Our results show how covariance between the sensitivity to cues and the maximum response to cues for morphological defence can shape the evolutionary trajectory of predator-induced defences in D. pulex . © 2017 The Authors.

Human drivers of ecological and evolutionary dynamics in emerging and disappearing infectious disease systems.

PubMed

Rogalski, Mary A; Gowler, Camden D; Shaw, Clara L; Hufbauer, Ruth A; Duffy, Meghan A

2017-01-19

Humans have contributed to the increased frequency and severity of emerging infectious diseases, which pose a significant threat to wild and domestic species, as well as human health. This review examines major pathways by which humans influence parasitism by altering (co)evolutionary interactions between hosts and parasites on ecological timescales. There is still much to learn about these interactions, but a few well-studied cases show that humans influence disease emergence every step of the way. Human actions significantly increase dispersal of host, parasite and vector species, enabling greater frequency of infection in naive host populations and host switches. Very dense host populations resulting from urbanization and agriculture can drive the evolution of more virulent parasites and, in some cases, more resistant host populations. Human activities that reduce host genetic diversity or impose abiotic stress can impair the ability of hosts to adapt to disease threats. Further, evolutionary responses of hosts and parasites can thwart disease management and biocontrol efforts. Finally, in rare cases, humans influence evolution by eradicating an infectious disease. If we hope to fully understand the factors driving disease emergence and potentially control these epidemics we must consider the widespread influence of humans on host and parasite evolutionary trajectories.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Author(s).

Risk of herbivore attack and heritability of ontogenetic trajectories in plant defense.

PubMed

Ochoa-López, Sofía; Rebollo, Roberto; Barton, Kasey E; Fornoni, Juan; Boege, Karina

2018-06-01

Ontogeny has been identified as a main source of variation in the expression of plant phenotypes. However, there is limited information on the mechanisms behind the evolution of ontogenetic trajectories in plant defense. We explored if risk of attack, herbivore damage, heritability, and phenotypic plasticity can promote or constrain the evolutionary potential of ontogenetic trajectories in three defensive traits. We exposed 20 genotypes of Turnera velutina to contrasting environments (shadehouse and field plots), and measured the cyanogenic potential, trichome density, and sugar content in extrafloral nectar in seedlings, juveniles and reproductive plants. We also assessed risk of attack through oviposition preferences, and quantified herbivore damage in the field. We estimated genetic variance, broad sense heritability, and evolvability of the defensive traits at each ontogenetic stage, and of the ontogenetic trajectories themselves. For plants growing in the shadehouse, we found genetic variation and broad sense heritability for cyanogenic potential in seedlings, and for trichome density at all ontogenetic stages. Genetic variation and heritability of ontogenetic trajectories was detected for trichome density only. These genetic pre-requisites for evolution, however, were not detected in the field, suggesting that environmental variation and phenotypic plastic responses mask any heritable variation. Finally, ontogenetic trajectories were found to be plastic, differing between shadehouse and field conditions for the same genetic families. Overall, we provide support for the idea that changes in herbivore pressure can be a mechanism behind the evolution of ontogenetic trajectories. This evolutionary potential, however, can be constrained by phenotypic plasticity expressed in heterogeneous environments.

The semaphorontic view of homology

PubMed Central

Assis, Leandro C.S.; Rieppel, Olivier

2015-01-01

ABSTRACT The relation of homology is generally characterized as an identity relation, or alternatively as a correspondence relation, both of which are transitive. We use the example of the ontogenetic development and evolutionary origin of the gnathostome jaw to discuss identity and transitivity of the homology relation under the transformationist and emergentist paradigms respectively. Token identity and consequent transitivity of homology relations are shown to be requirements that are too strong to allow the origin of genuine evolutionary novelties. We consequently introduce the concept of compositional identity that is grounded in relations prevailing between parts (organs and organ systems) of a whole (organism). We recognize an ontogenetic identity of parts within a whole throughout the sequence of successive developmental stages of those parts: this is an intra‐organismal character identity maintained throughout developmental trajectory. Correspondingly, we recognize a phylogenetic identity of homologous parts within two or more organisms of different species: this is an inter‐species character identity maintained throughout evolutionary trajectory. These different dimensions of character identity—ontogenetic (through development) and phylogenetic (via shared evolutionary history)—break the transitivity of homology relations. Under the transformationist paradigm, the relation of homology reigns over the entire character (‐state) transformation series, and thus encompasses the plesiomorphic as well as the apomorphic condition of form. In contrast, genuine evolutionary novelties originate not through transformation of ancestral characters (‐states), but instead through deviating developmental trajectories that result in alternate characters. Under the emergentist paradigm, homology is thus synonymous with synapomorphy. J. Exp. Zool. (Mol. Dev. Evol.) 324B: 578–587, 2015. © 2015 The Authors. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution published by Wiley Periodicals, Inc. PMID:26175214

Integrating animal movement with habitat suitability for estimating dynamic landscape connectivity

USGS Publications Warehouse

van Toor, Mariëlle L.; Kranstauber, Bart; Newman, Scott H.; Prosser, Diann J.; Takekawa, John Y.; Technitis, Georgios; Weibel, Robert; Wikelski, Martin; Safi, Kamran

2018-01-01

Context High-resolution animal movement data are becoming increasingly available, yet having a multitude of empirical trajectories alone does not allow us to easily predict animal movement. To answer ecological and evolutionary questions at a population level, quantitative estimates of a species’ potential to link patches or populations are of importance. Objectives We introduce an approach that combines movement-informed simulated trajectories with an environment-informed estimate of the trajectories’ plausibility to derive connectivity. Using the example of bar-headed geese we estimated migratory connectivity at a landscape level throughout the annual cycle in their native range. Methods We used tracking data of bar-headed geese to develop a multi-state movement model and to estimate temporally explicit habitat suitability within the species’ range. We simulated migratory movements between range fragments, and calculated a measure we called route viability. The results are compared to expectations derived from published literature. Results Simulated migrations matched empirical trajectories in key characteristics such as stopover duration. The viability of the simulated trajectories was similar to that of the empirical trajectories. We found that, overall, the migratory connectivity was higher within the breeding than in wintering areas, corroborating previous findings for this species. Conclusions We show how empirical tracking data and environmental information can be fused for meaningful predictions of animal movements throughout the year and even outside the spatial range of the available data. Beyond predicting migratory connectivity, our framework will prove useful for modelling ecological processes facilitated by animal movement, such as seed dispersal or disease ecology.

Increasingly diverse brain dynamics in the developmental arc: using Pareto-optimization to infer a mechanism

NASA Astrophysics Data System (ADS)

Tang, Evelyn; Giusti, Chad; Baum, Graham; Gu, Shi; Pollock, Eli; Kahn, Ari; Roalf, David; Moore, Tyler; Ruparel, Kosha; Gur, Ruben; Gur, Raquel; Satterthwaite, Theodore; Bassett, Danielle

Motivated by a recent demonstration that the network architecture of white matter supports emerging control of diverse neural dynamics as children mature into adults, we seek to investigate structural mechanisms that support these changes. Beginning from a network representation of diffusion imaging data, we simulate network evolution with a set of simple growth rules built on principles of network control. Notably, the optimal evolutionary trajectory displays a striking correspondence to the progression of child to adult brain, suggesting that network control is a driver of development. More generally, and in comparison to the complete set of available models, we demonstrate that all brain networks from child to adult are structured in a manner highly optimized for the control of diverse neural dynamics. Within this near-optimality, we observe differences in the predicted control mechanisms of the child and adult brains, suggesting that the white matter architecture in children has a greater potential to increasingly support brain state transitions, potentially underlying cognitive switching.

Global dynamics of non-equilibrium gliding in animals.

PubMed

Yeaton, Isaac J; Socha, John J; Ross, Shane D

2017-03-17

Gliding flight-moving horizontally downward through the air without power-has evolved in a broad diversity of taxa and serves numerous ecologically relevant functions such as predator escape, expanding foraging locations, and finding mates, and has been suggested as an evolutionary pathway to powered flight. Historically, gliding has been conceptualized using the idealized conditions of equilibrium, in which the net aerodynamic force on the glider balances its weight. While this assumption is appealing for its simplicity, recent studies of glide trajectories have shown that equilibrium gliding is not the norm for most species. Furthermore, equilibrium theory neglects the aerodynamic differences between species, as well as how a glider can modify its glide path using control. To investigate non-equilibrium glide behavior, we developed a reduced-order model of gliding that accounts for self-similarity in the equations of motion, such that the lift and drag characteristics alone determine the glide trajectory. From analysis of velocity polar diagrams of horizontal and vertical velocity from several gliding species, we find that pitch angle, the angle between the horizontal and chord line, is a control parameter that can be exploited to modulate glide angle and glide speed. Varying pitch results in changing locations of equilibrium glide configurations in the velocity polar diagram that govern passive glide dynamics. Such analyses provide a new mechanism of interspecies comparison and tools to understand experimentally-measured kinematics data and theory. In addition, this analysis suggests that the lift and drag characteristics of aerial and aquatic autonomous gliders can be engineered to passively alter glide trajectories with minimal control effort.

The evolution of lethal intergroup violence

PubMed Central

Kelly, Raymond C.

2005-01-01

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry. PMID:16129826

The evolution of lethal intergroup violence.

PubMed

Kelly, Raymond C

2005-10-25

Recent findings and analyses in evolutionary biology, archaeology, and ethnology provide a favorable conjuncture for examining the evolution of lethal intergroup violence among hominids during the 2.9-million-year Paleolithic time span. Here, I seek to identify and investigate the main turning points in this evolutionary trajectory and to delineate the periodization that follows from this inquiry.

Flying at no mechanical energy cost: disclosing the secret of wandering albatrosses.

PubMed

Sachs, Gottfried; Traugott, Johannes; Nesterova, Anna P; Dell'Omo, Giacomo; Kümmeth, Franz; Heidrich, Wolfgang; Vyssotski, Alexei L; Bonadonna, Francesco

2012-01-01

Albatrosses do something that no other birds are able to do: fly thousands of kilometres at no mechanical cost. This is possible because they use dynamic soaring, a flight mode that enables them to gain the energy required for flying from wind. Until now, the physical mechanisms of the energy gain in terms of the energy transfer from the wind to the bird were mostly unknown. Here we show that the energy gain is achieved by a dynamic flight manoeuvre consisting of a continually repeated up-down curve with optimal adjustment to the wind. We determined the energy obtained from the wind by analysing the measured trajectories of free flying birds using a new GPS-signal tracking method yielding a high precision. Our results reveal an evolutionary adaptation to an extreme environment, and may support recent biologically inspired research on robotic aircraft that might utilize albatrosses' flight technique for engineless propulsion.

Flying at No Mechanical Energy Cost: Disclosing the Secret of Wandering Albatrosses

PubMed Central

Sachs, Gottfried; Traugott, Johannes; Nesterova, Anna P.; Dell'Omo, Giacomo; Kümmeth, Franz; Heidrich, Wolfgang

2012-01-01

Albatrosses do something that no other birds are able to do: fly thousands of kilometres at no mechanical cost. This is possible because they use dynamic soaring, a flight mode that enables them to gain the energy required for flying from wind. Until now, the physical mechanisms of the energy gain in terms of the energy transfer from the wind to the bird were mostly unknown. Here we show that the energy gain is achieved by a dynamic flight manoeuvre consisting of a continually repeated up-down curve with optimal adjustment to the wind. We determined the energy obtained from the wind by analysing the measured trajectories of free flying birds using a new GPS-signal tracking method yielding a high precision. Our results reveal an evolutionary adaptation to an extreme environment, and may support recent biologically inspired research on robotic aircraft that might utilize albatrosses' flight technique for engineless propulsion. PMID:22957014

Does aquatic foraging impact head shape evolution in snakes?

PubMed

Segall, Marion; Cornette, Raphaël; Fabre, Anne-Claire; Godoy-Diana, Ramiro; Herrel, Anthony

2016-08-31

Evolutionary trajectories are often biased by developmental and historical factors. However, environmental factors can also impose constraints on the evolutionary trajectories of organisms leading to convergence of morphology in similar ecological contexts. The physical properties of water impose strong constraints on aquatic feeding animals by generating pressure waves that can alert prey and potentially push them away from the mouth. These hydrodynamic constraints have resulted in the independent evolution of suction feeding in most groups of secondarily aquatic tetrapods. Despite the fact that snakes cannot use suction, they have invaded the aquatic milieu many times independently. Here, we test whether the aquatic environment has constrained head shape evolution in snakes and whether shape converges on that predicted by biomechanical models. To do so, we used three-dimensional geometric morphometrics and comparative, phylogenetically informed analyses on a large sample of aquatic snake species. Our results show that aquatic snakes partially conform to our predictions and have a narrower anterior part of the head and dorsally positioned eyes and nostrils. This morphology is observed, irrespective of the phylogenetic relationships among species, suggesting that the aquatic environment does indeed drive the evolution of head shape in snakes, thus biasing the evolutionary trajectory of this group of animals. © 2016 The Author(s).

Fluctuating observation time ensembles in the thermodynamics of trajectories

NASA Astrophysics Data System (ADS)

Budini, Adrián A.; Turner, Robert M.; Garrahan, Juan P.

2014-03-01

The dynamics of stochastic systems, both classical and quantum, can be studied by analysing the statistical properties of dynamical trajectories. The properties of ensembles of such trajectories for long, but fixed, times are described by large-deviation (LD) rate functions. These LD functions play the role of dynamical free energies: they are cumulant generating functions for time-integrated observables, and their analytic structure encodes dynamical phase behaviour. This ‘thermodynamics of trajectories’ approach is to trajectories and dynamics what the equilibrium ensemble method of statistical mechanics is to configurations and statics. Here we show that, just like in the static case, there are a variety of alternative ensembles of trajectories, each defined by their global constraints, with that of trajectories of fixed total time being just one of these. We show how the LD functions that describe an ensemble of trajectories where some time-extensive quantity is constant (and large) but where total observation time fluctuates can be mapped to those of the fixed-time ensemble. We discuss how the correspondence between generalized ensembles can be exploited in path sampling schemes for generating rare dynamical trajectories.

Eco-evolutionary feedbacks, adaptive dynamics and evolutionary rescue theory

PubMed Central

Ferriere, Regis; Legendre, Stéphane

2013-01-01

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

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.

Querying databases of trajectories of differential equations: Data structures for trajectories

NASA Technical Reports Server (NTRS)

Grossman, Robert

1989-01-01

One approach to qualitative reasoning about dynamical systems is to extract qualitative information by searching or making queries on databases containing very large numbers of trajectories. The efficiency of such queries depends crucially upon finding an appropriate data structure for trajectories of dynamical systems. Suppose that a large number of parameterized trajectories gamma of a dynamical system evolving in R sup N are stored in a database. Let Eta is contained in set R sup N denote a parameterized path in Euclidean Space, and let the Euclidean Norm denote a norm on the space of paths. A data structure is defined to represent trajectories of dynamical systems, and an algorithm is sketched which answers queries.

Spatial connectivity, scaling, and temporal trajectories as emergent urban stormwater impacts

NASA Astrophysics Data System (ADS)

Jovanovic, T.; Gironas, J. A.; Hale, R. L.; Mejia, A.

2016-12-01

Urban watersheds are structurally complex systems comprised of multiple components (e.g., streets, pipes, ponds, vegetated swales, wetlands, riparian corridors, etc.). These multiple engineered components interact in unanticipated and nontrivial ways with topographic conditions, climate variability, land use/land cover changes, and the underlying eco-hydrogeomorphic dynamics. Such interactions can result in emergent urban stormwater impacts with cascading effects that can negatively influence the overall functioning of the urban watershed. For example, the interaction among many detention ponds has been shown, in some situations, to synchronize flow volumes and ultimately lead to downstream flow amplifications and increased pollutant mobilization. Additionally, interactions occur at multiple temporal and spatial scales requiring that urban stormwater dynamics be represented at the long-term temporal (decadal) and across spatial scales (from the single lot to the watershed scale). In this study, we develop and implement an event-based, high-resolution, network hydro-engineering model (NHEM), and demonstrate an approach to reconstruct the long-term regional infrastructure and land use/land cover conditions of an urban watershed. As the study area, we select an urban watershed in the metropolitan area of Scottsdale, Arizona. Using the reconstructed landscapes to drive the NHEM, we find that distinct surficial, hydrologic connectivity patterns result from the intersection of hydrologic processes, infrastructure, and land use/land cover arrangements. These spatial patters, in turn, exhibit scaling characteristics. For example, the scaling of urban watershed dispersion mechanisms shows altered scaling exponents with respect to pre-urban conditions. For example, the scaling exponent associated with geomorphic dispersion tends to increase for urban conditions, reflecting increased surficial path heterogeneity. Both the connectivity and scaling results can be used to delineate impact trajectories (i.e. the evolution of spatially referenced impacts over time). We find that the impact trajectories provide insight about the urban stormwater sustainability of watersheds as well as clues about the potential imprint of socio-environmental feedbacks in the evolutionary dynamics.

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

PubMed

Kasada, Minoru; Yamamichi, Masato; Yoshida, Takehito

2014-11-11

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

A multi-state trajectory method for non-adiabatic dynamics simulations

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

Tao, Guohua, E-mail: taogh@pkusz.edu.cn

2016-03-07

A multi-state trajectory approach is proposed to describe nuclear-electron coupled dynamics in nonadiabatic simulations. In this approach, each electronic state is associated with an individual trajectory, among which electronic transition occurs. The set of these individual trajectories constitutes a multi-state trajectory, and nuclear dynamics is described by one of these individual trajectories as the system is on the corresponding state. The total nuclear-electron coupled dynamics is obtained from the ensemble average of the multi-state trajectories. A variety of benchmark systems such as the spin-boson system have been tested and the results generated using the quasi-classical version of the method showmore » reasonably good agreement with the exact quantum calculations. Featured in a clear multi-state picture, high efficiency, and excellent numerical stability, the proposed method may have advantages in being implemented to realistic complex molecular systems, and it could be straightforwardly applied to general nonadiabatic dynamics involving multiple states.« less

A parametric interpretation of Bayesian Nonparametric Inference from Gene Genealogies: Linking ecological, population genetics and evolutionary processes.

PubMed

Ponciano, José Miguel

2017-11-22

Using a nonparametric Bayesian approach Palacios and Minin (2013) dramatically improved the accuracy, precision of Bayesian inference of population size trajectories from gene genealogies. These authors proposed an extension of a Gaussian Process (GP) nonparametric inferential method for the intensity function of non-homogeneous Poisson processes. They found that not only the statistical properties of the estimators were improved with their method, but also, that key aspects of the demographic histories were recovered. The authors' work represents the first Bayesian nonparametric solution to this inferential problem because they specify a convenient prior belief without a particular functional form on the population trajectory. Their approach works so well and provides such a profound understanding of the biological process, that the question arises as to how truly "biology-free" their approach really is. Using well-known concepts of stochastic population dynamics, here I demonstrate that in fact, Palacios and Minin's GP model can be cast as a parametric population growth model with density dependence and environmental stochasticity. Making this link between population genetics and stochastic population dynamics modeling provides novel insights into eliciting biologically meaningful priors for the trajectory of the effective population size. The results presented here also bring novel understanding of GP as models for the evolution of a trait. Thus, the ecological principles foundation of Palacios and Minin (2013)'s prior adds to the conceptual and scientific value of these authors' inferential approach. I conclude this note by listing a series of insights brought about by this connection with Ecology. Copyright © 2017 The Author. Published by Elsevier Inc. All rights reserved.

The coevolutionary dynamics of obligate ant social parasite systems--between prudence and antagonism.

PubMed

Brandt, Miriam; Foitzik, Susanne; Fischer-Blass, Birgit; Heinze, Jürgen

2005-05-01

In this synthesis we apply coevolutionary models to the interactions between socially parasitic ants and their hosts. Obligate social parasite systems are ideal models for coevolution, because the close phylogenetic relationship between these parasites and their hosts results in similar evolutionary potentials, thus making mutual adaptations in a stepwise fashion especially likely to occur. The evolutionary dynamics of host-parasite interactions are influenced by a number of parameters, for example the parasite's transmission mode and rate, the genetic structure of host and parasite populations, the antagonists' migration rates, and the degree of mutual specialisation. For the three types of obligate ant social parasites, queen-tolerant and queen-intolerant inquilines and slavemakers, several of these parameters, and thus the evolutionary trajectory, are likely to differ. Because of the fundamental differences in lifestyle between these social parasite systems, coevolution should further select for different traits in the parasites and their hosts. Queen-tolerant inquilines are true parasites that exert a low selection pressure on their host, because of their rarity and the fact that they do not conduct slave raids to replenish their labour force. Due to their high degree of specialisation and the potential for vertical transmission, coevolutionary theory would predict interactions between these workerless parasites and their hosts to become even more benign over time. Queen-intolerant inquilines that kill the host queen during colony take-over are best described as parasitoids, and their reproductive success is limited by the existing worker force of the invaded host nest. These parasites should therefore evolve strategies to best exploit this fixed resource. Slavemaking ants, by contrast, act as parasites only during colony foundation, while their frequent slave raids follow a predator prey dynamic. They often exploit a number of host species at a given site, and theory predicts that their associations are best described in terms of a highly antagonistic coevolutionary arms race.

Phase transitions in trajectories of a superconducting single-electron transistor coupled to a resonator.

PubMed

Genway, Sam; Garrahan, Juan P; Lesanovsky, Igor; Armour, Andrew D

2012-05-01

Recent progress in the study of dynamical phase transitions has been made with a large-deviation approach to study trajectories of stochastic jumps using a thermodynamic formalism. We study this method applied to an open quantum system consisting of a superconducting single-electron transistor, near the Josephson quasiparticle resonance, coupled to a resonator. We find that the dynamical behavior shown in rare trajectories can be rich even when the mean dynamical activity is small, and thus the formalism gives insights into the form of fluctuations. The structure of the dynamical phase diagram found from the quantum-jump trajectories of the resonator is studied, and we see that sharp transitions in the dynamical activity may be related to the appearance and disappearance of bistabilities in the state of the resonator as system parameters are changed. We also demonstrate that for a fast resonator, the trajectories of quasiparticles are similar to the resonator trajectories.

Evolutionary dynamics with fluctuating population sizes and strong mutualism.

PubMed

Chotibut, Thiparat; Nelson, David R

2015-08-01

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

Evolutionary dynamics with fluctuating population sizes and strong mutualism

NASA Astrophysics Data System (ADS)

Chotibut, Thiparat; Nelson, David R.

2015-08-01

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

Theoretical Approaches in Evolutionary Ecology: Environmental Feedback as a Unifying Perspective.

PubMed

Lion, Sébastien

2018-01-01

Evolutionary biology and ecology have a strong theoretical underpinning, and this has fostered a variety of modeling approaches. A major challenge of this theoretical work has been to unravel the tangled feedback loop between ecology and evolution. This has prompted the development of two main classes of models. While quantitative genetics models jointly consider the ecological and evolutionary dynamics of a focal population, a separation of timescales between ecology and evolution is assumed by evolutionary game theory, adaptive dynamics, and inclusive fitness theory. As a result, theoretical evolutionary ecology tends to be divided among different schools of thought, with different toolboxes and motivations. My aim in this synthesis is to highlight the connections between these different approaches and clarify the current state of theory in evolutionary ecology. Central to this approach is to make explicit the dependence on environmental dynamics of the population and evolutionary dynamics, thereby materializing the eco-evolutionary feedback loop. This perspective sheds light on the interplay between environmental feedback and the timescales of ecological and evolutionary processes. I conclude by discussing some potential extensions and challenges to our current theoretical understanding of eco-evolutionary dynamics.

Inactivation of tumor suppressor genes and cancer therapy: An evolutionary game theory approach.

PubMed

Khadem, Heydar; Kebriaei, Hamed; Veisi, Zahra

2017-06-01

Inactivation of alleles in tumor suppressor genes (TSG) is one of the important issues resulting in evolution of cancerous cells. In this paper, the evolution of healthy, one and two missed allele cells is modeled using the concept of evolutionary game theory and replicator dynamics. The proposed model also takes into account the interaction rates of the cells as designing parameters of the system. Different combinations of the equilibrium points of the parameterized nonlinear system is studied and categorized into some cases. In each case, the interaction rates' values are suggested in a way that the equilibrium points of the replicator dynamics are located on an appropriate region of the state space. Based on the suggested interaction rates, it is proved that the system doesn't have any undesirable interior equilibrium point as well. Therefore, the system will converge to the desirable region, where there is a scanty level of cancerous cells. In addition, the proposed conditions for interaction rates guarantee that, when a trajectory of the system reaches the boundaries, then it will stay there forever which is a desirable property since the equilibrium points have been already located on the boundaries, appropriately. The simulation results show the effectiveness of the suggestions in the elimination of the cancerous cells in different scenarios. Copyright © 2017 Elsevier Inc. All rights reserved.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.

PubMed

Hanski, Ilkka A

2011-08-30

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time.

Comparison of kinematic and dynamic leg trajectory optimization techniques for biped robot locomotion

NASA Astrophysics Data System (ADS)

Khusainov, R.; Klimchik, A.; Magid, E.

2017-01-01

The paper presents comparison analysis of two approaches in defining leg trajectories for biped locomotion. The first one operates only with kinematic limitations of leg joints and finds the maximum possible locomotion speed for given limits. The second approach defines leg trajectories from the dynamic stability point of view and utilizes ZMP criteria. We show that two methods give different trajectories and demonstrate that trajectories based on pure dynamic optimization cannot be realized due to joint limits. Kinematic optimization provides unstable solution which can be balanced by upper body movement.

Vector-Borne Pathogen and Host Evolution in a Structured Immuno-Epidemiological System.

PubMed

Gulbudak, Hayriye; Cannataro, Vincent L; Tuncer, Necibe; Martcheva, Maia

2017-02-01

Vector-borne disease transmission is a common dissemination mode used by many pathogens to spread in a host population. Similar to directly transmitted diseases, the within-host interaction of a vector-borne pathogen and a host's immune system influences the pathogen's transmission potential between hosts via vectors. Yet there are few theoretical studies on virulence-transmission trade-offs and evolution in vector-borne pathogen-host systems. Here, we consider an immuno-epidemiological model that links the within-host dynamics to between-host circulation of a vector-borne disease. On the immunological scale, the model mimics antibody-pathogen dynamics for arbovirus diseases, such as Rift Valley fever and West Nile virus. The within-host dynamics govern transmission and host mortality and recovery in an age-since-infection structured host-vector-borne pathogen epidemic model. By considering multiple pathogen strains and multiple competing host populations differing in their within-host replication rate and immune response parameters, respectively, we derive evolutionary optimization principles for both pathogen and host. Invasion analysis shows that the [Formula: see text] maximization principle holds for the vector-borne pathogen. For the host, we prove that evolution favors minimizing case fatality ratio (CFR). These results are utilized to compute host and pathogen evolutionary trajectories and to determine how model parameters affect evolution outcomes. We find that increasing the vector inoculum size increases the pathogen [Formula: see text], but can either increase or decrease the pathogen virulence (the host CFR), suggesting that vector inoculum size can contribute to virulence of vector-borne diseases in distinct ways.

Grouping and trajectories of neuropsychiatric symptoms in patients with Alzheimer's disease. Part II: two-year patient trajectories.

PubMed

Garre-Olmo, Josep; López-Pousa, Secundino; Vilalta-Franch, Joan; de Gracia Blanco, Manuel; Vilarrasa, Antoni Bulbena

2010-01-01

Behavioral and psychological symptoms of dementia (BPSD) are characterized by fluctuations in their frequency and severity as well as by differences in the concurrent presentation of different symptoms. The goal of the current study was to identify groups of patients with Alzheimer's disease (AD) that had similar trajectories in the expression of BPSD. Over a 24-month period, an observational study was conducted using a population of ambulatory patients with AD of mild or moderate severity. The Neuropsychiatric Inventory (NPI) was administered every 6 months to the patient's caregiver. To classify patients according to changes in the frequency and severity of BPSD, growth mixture models were fitted to the applied to the grouping of NPI subscales in the following three categories: psychotic syndrome (hallucinations and delusions), affective syndrome (depression, anxiety, irritability, and agitation), and behavioral syndrome (disinhibition, euphoria, apathy, and aberrant motor behavior). The sample population consisted of 491 patients (70.9% women) that had an average age of 75.2 years (SD=6.6). Different trajectory patterns were identified based on differences in changes over the time in the frequency (stable, increasing, decreasing, or fluctuating in course) and severity (low, moderate, or elevated severity) for psychotic syndrome, emotional syndrome, and behavior syndrome. Patients with AD display a high degree of variability in the evolutionary course of BPSD. It is possible to identify groups of patients with similar evolutionary trajectories in terms of changes in the frequency and severity of BPSD.

Character convergence under competition for nutritionally essential resources.

PubMed

Fox, Jeremy W; Vasseur, David A

2008-11-01

Resource competition is thought to drive divergence in resource use traits (character displacement) by generating selection favoring individuals able to use resources unavailable to others. However, this picture assumes nutritionally substitutable resources (e.g., different prey species). When species compete for nutritionally essential resources (e.g., different nutrients), theory predicts that selection drives character convergence. We used models of two species competing for two essential resources to address several issues not considered by existing theory. The models incorporated either slow evolutionary change in resource use traits or fast physiological or behavioral change. We report four major results. First, competition always generates character convergence, but differences in resource requirements prevent competitors from evolving identical resource use traits. Second, character convergence promotes coexistence. Competing species always attain resource use traits that allow coexistence, and adaptive trait change stabilizes the ecological equilibrium. In contrast, adaptation in allopatry never preadapts species to coexist in sympatry. Third, feedbacks between ecological dynamics and trait dynamics lead to surprising dynamical trajectories such as transient divergence in resource use traits followed by subsequent convergence. Fourth, under sufficiently slow trait change, ecological dynamics often drive one of the competitors to near extinction, which would prevent realization of long-term character convergence in practice.

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.

Multi-state trajectory approach to non-adiabatic dynamics: General formalism and the active state trajectory approximation

NASA Astrophysics Data System (ADS)

Tao, Guohua

2017-07-01

A general theoretical framework is derived for the recently developed multi-state trajectory (MST) approach from the time dependent Schrödinger equation, resulting in equations of motion for coupled nuclear-electronic dynamics equivalent to Hamilton dynamics or Heisenberg equation based on a new multistate Meyer-Miller (MM) model. The derived MST formalism incorporates both diabatic and adiabatic representations as limiting cases and reduces to Ehrenfest or Born-Oppenheimer dynamics in the mean-field or the single-state limits, respectively. In the general multistate formalism, nuclear dynamics is represented in terms of a set of individual state-specific trajectories, while in the active state trajectory (AST) approximation, only one single nuclear trajectory on the active state is propagated with its augmented images running on all other states. The AST approximation combines the advantages of consistent nuclear-coupled electronic dynamics in the MM model and the single nuclear trajectory in the trajectory surface hopping (TSH) treatment and therefore may provide a potential alternative to both Ehrenfest and TSH methods. The resulting algorithm features in a consistent description of coupled electronic-nuclear dynamics and excellent numerical stability. The implementation of the MST approach to several benchmark systems involving multiple nonadiabatic transitions and conical intersection shows reasonably good agreement with exact quantum calculations, and the results in both representations are similar in accuracy. The AST treatment also reproduces the exact results reasonably, sometimes even quantitatively well, with a better performance in the adiabatic representation.

From success to persistence: Identifying an evolutionary regime shift in the diverse Paleozoic aquatic arthropod group Eurypterida, driven by the Devonian biotic crisis.

PubMed

Lamsdell, James C; Selden, Paul A

2017-01-01

Mass extinctions have altered the trajectory of evolution a number of times over the Phanerozoic. During these periods of biotic upheaval a different selective regime appears to operate, although it is still unclear whether consistent survivorship rules apply across different extinction events. We compare variations in diversity and disparity across the evolutionary history of a major Paleozoic arthropod group, the Eurypterida. Using these data, we explore the group's transition from a successful, dynamic clade to a stagnant persistent lineage, pinpointing the Devonian as the period during which this evolutionary regime shift occurred. The late Devonian biotic crisis is potentially unique among the "Big Five" mass extinctions in exhibiting a drop in speciation rates rather than an increase in extinction. Our study reveals eurypterids show depressed speciation rates throughout the Devonian but no abnormal peaks in extinction. Loss of morphospace occupation is random across all Paleozoic extinction events; however, differential origination during the Devonian results in a migration and subsequent stagnation of occupied morphospace. This shift appears linked to an ecological transition from euryhaline taxa to freshwater species with low morphological diversity alongside a decrease in endemism. These results demonstrate the importance of the Devonian biotic crisis in reshaping Paleozoic ecosystems. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly

PubMed Central

Hanski, Ilkka A.

2011-01-01

Demographic population dynamics, gene flow, and local adaptation may influence each other and lead to coupling of ecological and evolutionary dynamics, especially in species inhabiting fragmented heterogeneous environments. Here, I review long-term research on eco-evolutionary spatial dynamics in the Glanville fritillary butterfly inhabiting a large network of approximately 4,000 meadows in Finland. The metapopulation persists in a balance between frequent local extinctions and recolonizations. The genetic spatial structure as defined by neutral markers is much more coarse-grained than the demographic spatial structure determined by the fragmented habitat, yet small-scale spatial structure has important consequences for the dynamics. I discuss three examples of eco-evolutionary spatial dynamics. (i) Extinction-colonization metapopulation dynamics influence allele frequency changes in the phosphoglucose isomerase (Pgi) gene, which leads to strong associations between genetic variation in Pgi and dispersal, recolonization, and local population dynamics. (ii) Inbreeding in local populations increases their risk for extinction, whereas reciprocal effects between inbreeding, population size, and emigration represent likely eco-evolutionary feedbacks. (iii) Genetically determined female oviposition preference for two host plant species exhibits a cline paralleling a gradient in host plant relative abundances, and host plant preference of dispersing females in relation to the host plant composition of habitat patches influences immigration (gene flow) and recolonization (founder events). Eco-evolutionary spatial dynamics in heterogeneous environments may not lead to directional evolutionary changes unless the environment itself changes, but eco-evolutionary dynamics may contribute to the maintenance of genetic variation attributable to fluctuating selection in space and time. PMID:21788506

When new human-modified habitats favour the expansion of an amphibian pioneer species: Evolutionary history of the natterjack toad (Bufo calamita) in a coal basin.

PubMed

Faucher, Leslie; Hénocq, Laura; Vanappelghem, Cédric; Rondel, Stéphanie; Quevillart, Robin; Gallina, Sophie; Godé, Cécile; Jaquiéry, Julie; Arnaud, Jean-François

2017-09-01

Human activities affect microevolutionary dynamics by inducing environmental changes. In particular, land cover conversion and loss of native habitats decrease genetic diversity and jeopardize the adaptive ability of populations. Nonetheless, new anthropogenic habitats can also promote the successful establishment of emblematic pioneer species. We investigated this issue by examining the population genetic features and evolutionary history of the natterjack toad (Bufo [Epidalea] calamita) in northern France, where populations can be found in native coastal habitats and coalfield habitats shaped by European industrial history, along with an additional set of European populations located outside this focal area. We predicted contrasting patterns of genetic structure, with newly settled coalfield populations departing from migration-drift equilibrium. As expected, coalfield populations showed a mosaic of genetically divergent populations with short-range patterns of gene flow, and native coastal populations indicated an equilibrium state with an isolation-by-distance pattern suggestive of postglacial range expansion. However, coalfield populations exhibited (i) high levels of genetic diversity, (ii) no evidence of local inbreeding or reduced effective population size and (iii) multiple maternal mitochondrial lineages, a genetic footprint depicting independent colonization events. Furthermore, approximate Bayesian computations suggested several evolutionary trajectories from ancient isolation in glacial refugia during the Pleistocene, with biogeographical signatures of recent expansion probably confounded by human-mediated mixing of different lineages. From an evolutionary and conservation perspective, this study highlights the ecological value of industrial areas, provided that ongoing regional gene flow is ensured within the existing lineage boundaries. © 2017 John Wiley & Sons Ltd.

Dose calculation of dynamic trajectory radiotherapy using Monte Carlo.

PubMed

Manser, P; Frauchiger, D; Frei, D; Volken, W; Terribilini, D; Fix, M K

2018-04-06

Using volumetric modulated arc therapy (VMAT) delivery technique gantry position, multi-leaf collimator (MLC) as well as dose rate change dynamically during the application. However, additional components can be dynamically altered throughout the dose delivery such as the collimator or the couch. Thus, the degrees of freedom increase allowing almost arbitrary dynamic trajectories for the beam. While the dose delivery of such dynamic trajectories for linear accelerators is technically possible, there is currently no dose calculation and validation tool available. Thus, the aim of this work is to develop a dose calculation and verification tool for dynamic trajectories using Monte Carlo (MC) methods. The dose calculation for dynamic trajectories is implemented in the previously developed Swiss Monte Carlo Plan (SMCP). SMCP interfaces the treatment planning system Eclipse with a MC dose calculation algorithm and is already able to handle dynamic MLC and gantry rotations. Hence, the additional dynamic components, namely the collimator and the couch, are described similarly to the dynamic MLC by defining data pairs of positions of the dynamic component and the corresponding MU-fractions. For validation purposes, measurements are performed with the Delta4 phantom and film measurements using the developer mode on a TrueBeam linear accelerator. These measured dose distributions are then compared with the corresponding calculations using SMCP. First, simple academic cases applying one-dimensional movements are investigated and second, more complex dynamic trajectories with several simultaneously moving components are compared considering academic cases as well as a clinically motivated prostate case. The dose calculation for dynamic trajectories is successfully implemented into SMCP. The comparisons between the measured and calculated dose distributions for the simple as well as for the more complex situations show an agreement which is generally within 3% of the maximum dose or 3mm. The required computation time for the dose calculation remains the same when the additional dynamic moving components are included. The results obtained for the dose comparisons for simple and complex situations suggest that the extended SMCP is an accurate dose calculation and efficient verification tool for dynamic trajectory radiotherapy. This work was supported by Varian Medical Systems. Copyright © 2018. Published by Elsevier GmbH.

Evolutionary inevitability of sexual antagonism.

PubMed

Connallon, Tim; Clark, Andrew G

2014-02-07

Sexual antagonism, whereby mutations are favourable in one sex and disfavourable in the other, is common in natural populations, yet the root causes of sexual antagonism are rarely considered in evolutionary theories of adaptation. Here, we explore the evolutionary consequences of sex-differential selection and genotype-by-sex interactions for adaptation in species with separate sexes. We show that sexual antagonism emerges naturally from sex differences in the direction of selection on phenotypes expressed by both sexes or from sex-by-genotype interactions affecting the expression of such phenotypes. Moreover, modest sex differences in selection or genotype-by-sex effects profoundly influence the long-term evolutionary trajectories of populations with separate sexes, as these conditions trigger the evolution of strong sexual antagonism as a by-product of adaptively driven evolutionary change. The theory demonstrates that sexual antagonism is an inescapable by-product of adaptation in species with separate sexes, whether or not selection favours evolutionary divergence between males and females.

Quantum trajectory phase transitions in the micromaser.

PubMed

Garrahan, Juan P; Armour, Andrew D; Lesanovsky, Igor

2011-08-01

We study the dynamics of the single-atom maser, or micromaser, by means of the recently introduced method of thermodynamics of quantum jump trajectories. We find that the dynamics of the micromaser displays multiple space-time phase transitions, i.e., phase transitions in ensembles of quantum jump trajectories. This rich dynamical phase structure becomes apparent when trajectories are classified by dynamical observables that quantify dynamical activity, such as the number of atoms that have changed state while traversing the cavity. The space-time transitions can be either first order or continuous, and are controlled not just by standard parameters of the micromaser but also by nonequilibrium "counting" fields. We discuss how the dynamical phase behavior relates to the better known stationary-state properties of the micromaser.

The origin and dynamic evolution of chemical information transfer

PubMed Central

Steiger, Sandra; Schmitt, Thomas; Schaefer, H. Martin

2011-01-01

Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general. PMID:21177681

Exploiting temporal collateral sensitivity in tumor clonal evolution

PubMed Central

Zhao, Boyang; Sedlak, Joseph C.; Srinivas, Raja; Creixell, Pau; Pritchard, Justin R.; Tidor, Bruce; Lauffenburger, Douglas A.; Hemann, Michael T.

2016-01-01

SUMMARY The prevailing approach to addressing secondary drug resistance in cancer focuses on treating the resistance mechanisms at relapse. However, the dynamic nature of clonal evolution, along with potential fitness costs and cost compensations, may present exploitable vulnerabilities; a notion that we term ‘temporal collateral sensitivity’. Using a combined pharmacological screen and drug resistance selection approach in a murine model of Ph+ acute lymphoblastic leukemia, we indeed find that temporal and/or persistent collateral sensitivity to non-classical BCR-ABL1 drugs arises in emergent tumor subpopulations during the evolution of resistance toward initial treatment with BCR-ABL1 targeted inhibitors. We determined the sensitization mechanism via genotypic, phenotypic, signaling, and binding measurements in combination with computational models, and demonstrated significant overall survival extension in mice. Additional stochastic mathematical models and small molecule screens extended our insights, indicating the value of focusing on evolutionary trajectories and pharmacological profiles to identify new strategies to treat dynamic tumor vulnerabilities. PMID:26924578

Exploiting Temporal Collateral Sensitivity in Tumor Clonal Evolution.

PubMed

Zhao, Boyang; Sedlak, Joseph C; Srinivas, Raja; Creixell, Pau; Pritchard, Justin R; Tidor, Bruce; Lauffenburger, Douglas A; Hemann, Michael T

2016-03-24

The prevailing approach to addressing secondary drug resistance in cancer focuses on treating the resistance mechanisms at relapse. However, the dynamic nature of clonal evolution, along with potential fitness costs and cost compensations, may present exploitable vulnerabilities-a notion that we term "temporal collateral sensitivity." Using a combined pharmacological screen and drug resistance selection approach in a murine model of Ph(+) acute lymphoblastic leukemia, we indeed find that temporal and/or persistent collateral sensitivity to non-classical BCR-ABL1 drugs arises in emergent tumor subpopulations during the evolution of resistance toward initial treatment with BCR-ABL1-targeted inhibitors. We determined the sensitization mechanism via genotypic, phenotypic, signaling, and binding measurements in combination with computational models and demonstrated significant overall survival extension in mice. Additional stochastic mathematical models and small-molecule screens extended our insights, indicating the value of focusing on evolutionary trajectories and pharmacological profiles to identify new strategies to treat dynamic tumor vulnerabilities. Copyright © 2016 Elsevier Inc. All rights reserved.

Empirical confirmation of creative destruction from world trade data.

PubMed

Klimek, Peter; Hausmann, Ricardo; Thurner, Stefan

2012-01-01

We show that world trade network datasets contain empirical evidence that the dynamics of innovation in the world economy indeed follows the concept of creative destruction, as proposed by J.A. Schumpeter more than half a century ago. National economies can be viewed as complex, evolving systems, driven by a stream of appearance and disappearance of goods and services. Products appear in bursts of creative cascades. We find that products systematically tend to co-appear, and that product appearances lead to massive disappearance events of existing products in the following years. The opposite-disappearances followed by periods of appearances-is not observed. This is an empirical validation of the dominance of cascading competitive replacement events on the scale of national economies, i.e., creative destruction. We find a tendency that more complex products drive out less complex ones, i.e., progress has a direction. Finally we show that the growth trajectory of a country's product output diversity can be understood by a recently proposed evolutionary model of Schumpeterian economic dynamics.

Empirical Confirmation of Creative Destruction from World Trade Data

PubMed Central

Klimek, Peter; Hausmann, Ricardo; Thurner, Stefan

2012-01-01

We show that world trade network datasets contain empirical evidence that the dynamics of innovation in the world economy indeed follows the concept of creative destruction, as proposed by J.A. Schumpeter more than half a century ago. National economies can be viewed as complex, evolving systems, driven by a stream of appearance and disappearance of goods and services. Products appear in bursts of creative cascades. We find that products systematically tend to co-appear, and that product appearances lead to massive disappearance events of existing products in the following years. The opposite–disappearances followed by periods of appearances–is not observed. This is an empirical validation of the dominance of cascading competitive replacement events on the scale of national economies, i.e., creative destruction. We find a tendency that more complex products drive out less complex ones, i.e., progress has a direction. Finally we show that the growth trajectory of a country’s product output diversity can be understood by a recently proposed evolutionary model of Schumpeterian economic dynamics. PMID:22719989

Tracking Genomic Cancer Evolution for Precision Medicine: The Lung TRACERx Study

PubMed Central

Jamal-Hanjani, Mariam; Hackshaw, Alan; Ngai, Yenting; Shaw, Jacqueline; Dive, Caroline; Quezada, Sergio; Middleton, Gary; de Bruin, Elza; Le Quesne, John; Shafi, Seema; Falzon, Mary; Horswell, Stuart; Blackhall, Fiona; Khan, Iftekhar; Janes, Sam; Nicolson, Marianne; Lawrence, David; Forster, Martin; Fennell, Dean; Lee, Siow-Ming; Lester, Jason; Kerr, Keith; Muller, Salli; Iles, Natasha; Smith, Sean; Murugaesu, Nirupa; Mitter, Richard; Salm, Max; Stuart, Aengus; Matthews, Nik; Adams, Haydn; Ahmad, Tanya; Attanoos, Richard; Bennett, Jonathan; Birkbak, Nicolai Juul; Booton, Richard; Brady, Ged; Buchan, Keith; Capitano, Arrigo; Chetty, Mahendran; Cobbold, Mark; Crosbie, Philip; Davies, Helen; Denison, Alan; Djearman, Madhav; Goldman, Jacki; Haswell, Tom; Joseph, Leena; Kornaszewska, Malgorzata; Krebs, Matthew; Langman, Gerald; MacKenzie, Mairead; Millar, Joy; Morgan, Bruno; Naidu, Babu; Nonaka, Daisuke; Peggs, Karl; Pritchard, Catrin; Remmen, Hardy; Rowan, Andrew; Shah, Rajesh; Smith, Elaine; Summers, Yvonne; Taylor, Magali; Veeriah, Selvaraju; Waller, David; Wilcox, Ben; Wilcox, Maggie; Woolhouse, Ian; McGranahan, Nicholas; Swanton, Charles

2014-01-01

The importance of intratumour genetic and functional heterogeneity is increasingly recognised as a driver of cancer progression and survival outcome. Understanding how tumour clonal heterogeneity impacts upon therapeutic outcome, however, is still an area of unmet clinical and scientific need. TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy [Rx]), a prospective study of patients with primary non-small cell lung cancer (NSCLC), aims to define the evolutionary trajectories of lung cancer in both space and time through multiregion and longitudinal tumour sampling and genetic analysis. By following cancers from diagnosis to relapse, tracking the evolutionary trajectories of tumours in relation to therapeutic interventions, and determining the impact of clonal heterogeneity on clinical outcomes, TRACERx may help to identify novel therapeutic targets for NSCLC and may also serve as a model applicable to other cancer types. PMID:25003521

Additive genetic variance and developmental plasticity in growth trajectories in a wild cooperative mammal.

PubMed

Huchard, E; Charmantier, A; English, S; Bateman, A; Nielsen, J F; Clutton-Brock, T

2014-09-01

Individual variation in growth is high in cooperative breeders and may reflect plastic divergence in developmental trajectories leading to breeding vs. helping phenotypes. However, the relative importance of additive genetic variance and developmental plasticity in shaping growth trajectories is largely unknown in cooperative vertebrates. This study exploits weekly sequences of body mass from birth to adulthood to investigate sources of variance in, and covariance between, early and later growth in wild meerkats (Suricata suricatta), a cooperative mongoose. Our results indicate that (i) the correlation between early growth (prior to nutritional independence) and adult mass is positive but weak, and there are frequent changes (compensatory growth) in post-independence growth trajectories; (ii) among parameters describing growth trajectories, those describing growth rate (prior to and at nutritional independence) show undetectable heritability while associated size parameters (mass at nutritional independence and asymptotic mass) are moderately heritable (0.09 ≤ h(2) < 0.3); and (iii) additive genetic effects, rather than early environmental effects, mediate the covariance between early growth and adult mass. These results reveal that meerkat growth trajectories remain plastic throughout development, rather than showing early and irreversible divergence, and that the weak effects of early growth on adult mass, an important determinant of breeding success, are partly genetic. In contrast to most cooperative invertebrates, the acquisition of breeding status is often determined after sexual maturity and strongly impacted by chance in many cooperative vertebrates, who may therefore retain the ability to adjust their morphology to environmental changes and social opportunities arising throughout their development, rather than specializing early. © 2014 The Authors. Journal of Evolutionary Biology © 2014 European Society For Evolutionary Biology.

A switching control law approach for cancer immunotherapy of an evolutionary tumor growth model.

PubMed

Doban, Alina I; Lazar, Mircea

2017-02-01

We propose a new approach for tumor immunotherapy which is based on a switching control strategy defined on domains of attraction of equilibria of interest. For this, we consider a recently derived model which captures the effects of the tumor cells on the immune system and viceversa, through predator-prey competition terms. Additionally, it incorporates the immune system's mechanism for producing hunting immune cells, which makes the model suitable for immunotherapy strategies analysis and design. For computing domains of attraction for the tumor nonlinear dynamics, and thus, for deriving immunotherapeutic strategies we employ rational Lyapunov functions. Finally, we apply the switching control strategy to destabilize an invasive tumor equilibrium and steer the system trajectories to tumor dormancy. Copyright © 2016 Elsevier Inc. All rights reserved.

Experimental Evidence for a Structural-Dynamical Transition in Trajectory Space.

PubMed

Pinchaipat, Rattachai; Campo, Matteo; Turci, Francesco; Hallett, James E; Speck, Thomas; Royall, C Patrick

2017-07-14

Among the key insights into the glass transition has been the identification of a nonequilibrium phase transition in trajectory space which reveals phase coexistence between the normal supercooled liquid (active phase) and a glassy state (inactive phase). Here, we present evidence that such a transition occurs in experiments. In colloidal hard spheres, we find a non-Gaussian distribution of trajectories leaning towards those rich in locally favored structures (LFSs), associated with the emergence of slow dynamics. This we interpret as evidence for a nonequilibrium transition to an inactive LFS-rich phase. Reweighting trajectories reveals a first-order phase transition in trajectory space between a normal liquid and a LFS-rich phase. We also find evidence for a purely dynamical transition in trajectory space.

Plastic and evolutionary responses of plankton to environmental change are influenced by drift in ocean currents

NASA Astrophysics Data System (ADS)

Doblin, M.; van Sebille, E.

2016-02-01

The analytical framework for understanding fluctuations in ocean habitats has typically involved a Eulerian view. However, for marine microbes, this framework does not take into account their transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Using a modelling approach, we show that generations of upper ocean microbes experience along-trajectory temperature variability up to 10°C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents contributes to environmental fluctuation experienced by microbes and suggests that microbial populations may be adapted to upstream rather than local conditions. In an empirical test, we demonstrate that microbes in a warm, poleward flowing western boundary current (East Australian Current) have a different thermal response curve to microbes in coastal water at the same latitude (p < 0.05). Our findings suggest that advection has the capacity to influence microbial community assemblies such that water masses with relatively small thermal fluctuations select for thermal specialists, and communities with broad temperature performance curves are found in locations where ocean currents are strong or along-trajectory temperature variation is high.

Generalized Gaussian wave packet dynamics: Integrable and chaotic systems.

PubMed

Pal, Harinder; Vyas, Manan; Tomsovic, Steven

2016-01-01

The ultimate semiclassical wave packet propagation technique is a complex, time-dependent Wentzel-Kramers-Brillouin method known as generalized Gaussian wave packet dynamics (GGWPD). It requires overcoming many technical difficulties in order to be carried out fully in practice. In its place roughly twenty years ago, linearized wave packet dynamics was generalized to methods that include sets of off-center, real trajectories for both classically integrable and chaotic dynamical systems that completely capture the dynamical transport. The connections between those methods and GGWPD are developed in a way that enables a far more practical implementation of GGWPD. The generally complex saddle-point trajectories at its foundation are found using a multidimensional Newton-Raphson root search method that begins with the set of off-center, real trajectories. This is possible because there is a one-to-one correspondence. The neighboring trajectories associated with each off-center, real trajectory form a path that crosses a unique saddle; there are exceptions that are straightforward to identify. The method is applied to the kicked rotor to demonstrate the accuracy improvement as a function of ℏ that comes with using the saddle-point trajectories.

Preserving correlations between trajectories for efficient path sampling

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

Gingrich, Todd R.; Geissler, Phillip L.; Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720

2015-06-21

Importance sampling of trajectories has proved a uniquely successful strategy for exploring rare dynamical behaviors of complex systems in an unbiased way. Carrying out this sampling, however, requires an ability to propose changes to dynamical pathways that are substantial, yet sufficiently modest to obtain reasonable acceptance rates. Satisfying this requirement becomes very challenging in the case of long trajectories, due to the characteristic divergences of chaotic dynamics. Here, we examine schemes for addressing this problem, which engineer correlation between a trial trajectory and its reference path, for instance using artificial forces. Our analysis is facilitated by a modern perspective onmore » Markov chain Monte Carlo sampling, inspired by non-equilibrium statistical mechanics, which clarifies the types of sampling strategies that can scale to long trajectories. Viewed in this light, the most promising such strategy guides a trial trajectory by manipulating the sequence of random numbers that advance its stochastic time evolution, as done in a handful of existing methods. In cases where this “noise guidance” synchronizes trajectories effectively, as the Glauber dynamics of a two-dimensional Ising model, we show that efficient path sampling can be achieved for even very long trajectories.« less

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

NASA Astrophysics Data System (ADS)

Cucchi, T.; Mohaseb, A.; Peigné, S.; Debue, K.; Orlando, L.; Mashkour, M.

2017-04-01

The Plio-Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys.

The sex-specific region of sex chromosomes in animals and plants.

PubMed

Gschwend, Andrea R; Weingartner, Laura A; Moore, Richard C; Ming, Ray

2012-01-01

Our understanding of the evolution of sex chromosomes has increased greatly in recent years due to a number of molecular evolutionary investigations in divergent sex chromosome systems, and these findings are reshaping theories of sex chromosome evolution. In particular, the dynamics of the sex-determining region (SDR) have been demonstrated by recent findings in ancient and incipient sex chromosomes. Radical changes in genomic structure and gene content in the male specific region of the Y chromosome between human and chimpanzee indicated rapid evolution in the past 6 million years, defying the notion that the pace of evolution in the SDR was fast at early stages but slowed down overtime. The chicken Z and the human X chromosomes appeared to have acquired testis-expressed genes and expanded in intergenic regions. Transposable elements greatly contributed to SDR expansion and aided the trafficking of genes in the SDR and its X or Z counterpart through retrotransposition. Dosage compensation is not a destined consequence of sex chromosomes as once thought. Most X-linked microRNA genes escape silencing and are expressed in testis. Collectively, these findings are challenging many of our preconceived ideas of the evolutionary trajectory and fates of sex chromosomes.

Detecting taxonomic and phylogenetic signals in equid cheek teeth: towards new palaeontological and archaeological proxies

PubMed Central

Mohaseb, A.; Peigné, S.; Debue, K.; Orlando, L.; Mashkour, M.

2017-01-01

The Plio–Pleistocene evolution of Equus and the subsequent domestication of horses and donkeys remains poorly understood, due to the lack of phenotypic markers capable of tracing this evolutionary process in the palaeontological/archaeological record. Using images from 345 specimens, encompassing 15 extant taxa of equids, we quantified the occlusal enamel folding pattern in four mandibular cheek teeth with a single geometric morphometric protocol. We initially investigated the protocol accuracy by assigning each tooth to its correct anatomical position and taxonomic group. We then contrasted the phylogenetic signal present in each tooth shape with an exome-wide phylogeny from 10 extant equine species. We estimated the strength of the phylogenetic signal using a Brownian motion model of evolution with multivariate K statistic, and mapped the dental shape along the molecular phylogeny using an approach based on squared-change parsimony. We found clear evidence for the relevance of dental phenotypes to accurately discriminate all modern members of the genus Equus and capture their phylogenetic relationships. These results are valuable for both palaeontologists and zooarchaeologists exploring the spatial and temporal dynamics of the evolutionary history of the horse family, up to the latest domestication trajectories of horses and donkeys. PMID:28484618

Heterostyly accelerates diversification via reduced extinction in primroses.

PubMed

de Vos, Jurriaan M; Hughes, Colin E; Schneeweiss, Gerald M; Moore, Brian R; Conti, Elena

2014-06-07

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower-pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification.

Heterostyly accelerates diversification via reduced extinction in primroses

PubMed Central

de Vos, Jurriaan M.; Hughes, Colin E.; Schneeweiss, Gerald M.; Moore, Brian R.; Conti, Elena

2014-01-01

The exceptional species diversity of flowering plants, exceeding that of their sister group more than 250-fold, is especially evident in floral innovations, interactions with pollinators and sexual systems. Multiple theories, emphasizing flower–pollinator interactions, genetic effects of mating systems or high evolvability, predict that floral evolution profoundly affects angiosperm diversification. However, consequences for speciation and extinction dynamics remain poorly understood. Here, we investigate trajectories of species diversification focusing on heterostyly, a remarkable floral syndrome where outcrossing is enforced via cross-compatible floral morphs differing in placement of their respective sexual organs. Heterostyly evolved at least 20 times independently in angiosperms. Using Darwin's model for heterostyly, the primrose family, we show that heterostyly accelerates species diversification via decreasing extinction rates rather than increasing speciation rates, probably owing to avoidance of the negative genetic effects of selfing. However, impact of heterostyly appears to differ over short and long evolutionary time-scales: the accelerating effect of heterostyly on lineage diversification is manifest only over long evolutionary time-scales, whereas recent losses of heterostyly may prompt ephemeral bursts of speciation. Our results suggest that temporal or clade-specific conditions may ultimately determine the net effects of specific traits on patterns of species diversification. PMID:24759859

Convergent evolution at the pathway level: predictable regulatory changes during flower color transitions.

PubMed

Larter, Maximilian; Dunbar-Wallis, Amy; Berardi, Andrea E; Smith, Stacey D

2018-06-07

The predictability of evolution, or whether lineages repeatedly follow the same evolutionary trajectories during phenotypic convergence remains an open question of evolutionary biology. In this study, we investigate evolutionary convergence at the biochemical pathway level and test the predictability of evolution using floral anthocyanin pigmentation, a trait with a well-understood genetic and regulatory basis. We reconstructed the evolution of floral anthocyanin content across 28 species of the Andean clade Iochrominae (Solanaceae) and investigated how shifts in pigmentation are related to changes in expression of 7 key anthocyanin pathway genes. We used phylogenetic multivariate analysis of gene expression to test for phenotypic and developmental convergence at a macroevolutionary scale. Our results show that the four independent losses of the ancestral pigment delphinidin involved convergent losses of expression of the three late pathway genes (F3'5'h, Dfr and Ans). Transitions between pigment types affecting floral hue (e.g. blue to red) involve changes to the expression of branching genes F3'h and F3'5'h, while the expression levels of early steps of the pathway are strongly conserved in all species. These patterns support the idea that the macroevolution of floral pigmentation follows predictable evolutionary trajectories to reach convergent phenotype space, repeatedly involving regulatory changes. This is likely driven by constraints at the pathway level, such as pleiotropy and regulatory structure.

Global DNA cytosine methylation as an evolving trait: phylogenetic signal and correlated evolution with genome size in angiosperms

PubMed Central

Alonso, Conchita; Pérez, Ricardo; Bazaga, Pilar; Herrera, Carlos M.

2015-01-01

DNA cytosine methylation is a widespread epigenetic mechanism in eukaryotes, and plant genomes commonly are densely methylated. Genomic methylation can be associated with functional consequences such as mutational events, genomic instability or altered gene expression, but little is known on interspecific variation in global cytosine methylation in plants. In this paper, we compare global cytosine methylation estimates obtained by HPLC and use a phylogenetically-informed analytical approach to test for significance of evolutionary signatures of this trait across 54 angiosperm species in 25 families. We evaluate whether interspecific variation in global cytosine methylation is statistically related to phylogenetic distance and also whether it is evolutionarily correlated with genome size (C-value). Global cytosine methylation varied widely between species, ranging between 5.3% (Arabidopsis) and 39.2% (Narcissus). Differences between species were related to their evolutionary trajectories, as denoted by the strong phylogenetic signal underlying interspecific variation. Global cytosine methylation and genome size were evolutionarily correlated, as revealed by the significant relationship between the corresponding phylogenetically independent contrasts. On average, a ten-fold increase in genome size entailed an increase of about 10% in global cytosine methylation. Results show that global cytosine methylation is an evolving trait in angiosperms whose evolutionary trajectory is significantly linked to changes in genome size, and suggest that the evolutionary implications of epigenetic mechanisms are likely to vary between plant lineages. PMID:25688257

Y chromosome evolution: emerging insights into processes of Y chromosome degeneration

PubMed Central

Bachtrog, Doris

2014-01-01

The human Y chromosome is intriguing not only because it harbours the master-switch gene determining gender but also because of its unusual evolutionary trajectory. Previously an autosome, Y chromosome evolution has been characterized by massive gene decay. Recent whole-genome and transcriptome analyses of Y chromosomes in humans and other primates, in Drosophila species as well as in plants have shed light on the current gene content of the Y, its origins and its long-term fate. Comparative analysis of young and old Y chromosomes have given further insights into the evolutionary and molecular forces triggering Y degeneration and its evolutionary destiny. PMID:23329112

Quantum dynamics modeled by interacting trajectories

NASA Astrophysics Data System (ADS)

Cruz-Rodríguez, L.; Uranga-Piña, L.; Martínez-Mesa, A.; Meier, C.

2018-03-01

We present quantum dynamical simulations based on the propagation of interacting trajectories where the effect of the quantum potential is mimicked by effective pseudo-particle interactions. The method is applied to several quantum systems, both for bound and scattering problems. For the bound systems, the quantum ground state density and zero point energy are shown to be perfectly obtained by the interacting trajectories. In the case of time-dependent quantum scattering, the Eckart barrier and uphill ramp are considered, with transmission coefficients in very good agreement with standard quantum calculations. Finally, we show that via wave function synthesis along the trajectories, correlation functions and energy spectra can be obtained based on the dynamics of interacting trajectories.

Lane changing trajectory planning and tracking control for intelligent vehicle on curved road.

PubMed

Wang, Lukun; Zhao, Xiaoying; Su, Hao; Tang, Gongyou

2016-01-01

This paper explores lane changing trajectory planning and tracking control for intelligent vehicle on curved road. A novel arcs trajectory is planned for the desired lane changing trajectory. A kinematic controller and a dynamics controller are designed to implement the trajectory tracking control. Firstly, the kinematic model and dynamics model of intelligent vehicle with non-holonomic constraint are established. Secondly, two constraints of lane changing on curved road in practice (LCCP) are proposed. Thirdly, two arcs with same curvature are constructed for the desired lane changing trajectory. According to the geometrical characteristics of arcs trajectory, equations of desired state can be calculated. Finally, the backstepping method is employed to design a kinematic trajectory tracking controller. Then the sliding-mode dynamics controller is designed to ensure that the motion of the intelligent vehicle can follow the desired velocity generated by kinematic controller. The stability of control system is proved by Lyapunov theory. Computer simulation demonstrates that the desired arcs trajectory and state curves with B-spline optimization can meet the requirements of LCCP constraints and the proposed control schemes can make tracking errors to converge uniformly.

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories

NASA Astrophysics Data System (ADS)

Kaźmierkiewicz, R.; Czaplewski, C.; Lammek, B.; Ciarkowski, J.

1999-01-01

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.

Design and Optimization of Low-thrust Orbit Transfers Using Q-law and Evolutionary Algorithms

NASA Technical Reports Server (NTRS)

Lee, Seungwon; vonAllmen, Paul; Fink, Wolfgang; Petropoulos, Anastassios; Terrile, Richard

2005-01-01

Future space missions will depend more on low-thrust propulsion (such as ion engines) thanks to its high specific impulse. Yet, the design of low-thrust trajectories is complex and challenging. Third-body perturbations often dominate the thrust, and a significant change to the orbit requires a long duration of thrust. In order to guide the early design phases, we have developed an efficient and efficacious method to obtain approximate propellant and flight-time requirements (i.e., the Pareto front) for orbit transfers. A search for the Pareto-optimal trajectories is done in two levels: optimal thrust angles and locations are determined by Q-law, while the Q-law is optimized with two evolutionary algorithms: a genetic algorithm and a simulated-annealing-related algorithm. The examples considered are several types of orbit transfers around the Earth and the asteroid Vesta.

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

NASA Astrophysics Data System (ADS)

Zhai, Weiwei; Lim, Tony Kiat-Hon; Zhang, Tong; Phang, Su-Ting; Tiang, Zenia; Guan, Peiyong; Ng, Ming-Hwee; Lim, Jia Qi; Yao, Fei; Li, Zheng; Ng, Poh Yong; Yan, Jie; Goh, Brian K.; Chung, Alexander Yaw-Fui; Choo, Su-Pin; Khor, Chiea Chuen; Soon, Wendy Wei-Jia; Sung, Ken Wing-Kin; Foo, Roger Sik-Yin; Chow, Pierce Kah-Hoe

2017-02-01

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy.

Experimental test of an eco-evolutionary dynamic feedback loop between evolution and population density in the green peach aphid.

PubMed

Turcotte, Martin M; Reznick, David N; Daniel Hare, J

2013-05-01

An eco-evolutionary feedback loop is defined as the reciprocal impacts of ecology on evolutionary dynamics and evolution on ecological dynamics on contemporary timescales. We experimentally tested for an eco-evolutionary feedback loop in the green peach aphid, Myzus persicae, by manipulating initial densities and evolution. We found strong evidence that initial aphid density alters the rate and direction of evolution, as measured by changes in genotype frequencies through time. We also found that evolution of aphids within only 16 days, or approximately three generations, alters the rate of population growth and predicts density compared to nonevolving controls. The impact of evolution on population dynamics also depended on density. In one evolution treatment, evolution accelerated population growth by up to 10.3% at high initial density or reduced it by up to 6.4% at low initial density. The impact of evolution on population growth was as strong as or stronger than that caused by a threefold change in intraspecific density. We found that, taken together, ecological condition, here intraspecific density, alters evolutionary dynamics, which in turn alter concurrent population growth rate (ecological dynamics) in an eco-evolutionary feedback loop. Our results suggest that ignoring evolution in studies predicting population dynamics might lead us to over- or underestimate population density and that we cannot predict the evolutionary outcome within aphid populations without considering population size.

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.

Trajectory optimization for the National Aerospace Plane

NASA Technical Reports Server (NTRS)

Lu, Ping

1993-01-01

The objective of this second phase research is to investigate the optimal ascent trajectory for the National Aerospace Plane (NASP) from runway take-off to orbital insertion and address the unique problems associated with the hypersonic flight trajectory optimization. The trajectory optimization problem for an aerospace plane is a highly challenging problem because of the complexity involved. Previous work has been successful in obtaining sub-optimal trajectories by using energy-state approximation and time-scale decomposition techniques. But it is known that the energy-state approximation is not valid in certain portions of the trajectory. This research aims at employing full dynamics of the aerospace plane and emphasizing direct trajectory optimization methods. The major accomplishments of this research include the first-time development of an inverse dynamics approach in trajectory optimization which enables us to generate optimal trajectories for the aerospace plane efficiently and reliably, and general analytical solutions to constrained hypersonic trajectories that has wide application in trajectory optimization as well as in guidance and flight dynamics. Optimal trajectories in abort landing and ascent augmented with rocket propulsion and thrust vectoring control were also investigated. Motivated by this study, a new global trajectory optimization tool using continuous simulated annealing and a nonlinear predictive feedback guidance law have been under investigation and some promising results have been obtained, which may well lead to more significant development and application in the near future.

A variational approach to niche construction.

PubMed

Constant, Axel; Ramstead, Maxwell J D; Veissière, Samuel P L; Campbell, John O; Friston, Karl J

2018-04-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. © 2018 The Authors.

A variational approach to niche construction

PubMed Central

Ramstead, Maxwell J. D.; Veissière, Samuel P. L.; Campbell, John O.; Friston, Karl J.

2018-01-01

In evolutionary biology, niche construction is sometimes described as a genuine evolutionary process whereby organisms, through their activities and regulatory mechanisms, modify their environment such as to steer their own evolutionary trajectory, and that of other species. There is ongoing debate, however, on the extent to which niche construction ought to be considered a bona fide evolutionary force, on a par with natural selection. Recent formulations of the variational free-energy principle as applied to the life sciences describe the properties of living systems, and their selection in evolution, in terms of variational inference. We argue that niche construction can be described using a variational approach. We propose new arguments to support the niche construction perspective, and to extend the variational approach to niche construction to current perspectives in various scientific fields. PMID:29643221

Validation of a Low-Thrust Mission Design Tool Using Operational Navigation Software

NASA Technical Reports Server (NTRS)

Englander, Jacob A.; Knittel, Jeremy M.; Williams, Ken; Stanbridge, Dale; Ellison, Donald H.

2017-01-01

Design of flight trajectories for missions employing solar electric propulsion requires a suitably high-fidelity design tool. In this work, the Evolutionary Mission Trajectory Generator (EMTG) is presented as a medium-high fidelity design tool that is suitable for mission proposals. EMTG is validated against the high-heritage deep-space navigation tool MIRAGE, demonstrating both the accuracy of EMTG's model and an operational mission design and navigation procedure using both tools. The validation is performed using a benchmark mission to the Jupiter Trojans.

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

PubMed

Iyer, Swami; Killingback, Timothy

2014-10-01

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

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

NASA Astrophysics Data System (ADS)

Iyer, Swami; Killingback, Timothy

2014-10-01

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

Growth and patterning are evolutionarily dissociated in the vestigial wing discs of workers of the red imported fire ant, Solenopsis invicta.

PubMed

Bowsher, Julia H; Wray, Gregory A; Abouheif, Ehab

2007-12-15

Over the last decade, it has become clear that organismal form is largely determined by developmental and evolutionary changes in the growth and pattern formation of tissues. Yet, there is little known about how these two integrated processes respond to environmental cues or how they evolve relative to one another. Here, we present the discovery of vestigial wing imaginal discs in worker larvae of the red imported fire ant, Solenopsis invicta. These vestigial wing discs are present in all worker larvae, which is uncommon for a species with a large worker size distribution. Furthermore, the growth trajectory of these vestigial discs is distinct from all of the ant species examined to date because they grow at a rate slower than the leg discs. We predicted that the growth trajectory of the vestigial wing discs would be mirrored by evolutionary changes in their patterning. We tested this prediction by examining the expression of three patterning genes, extradenticle, ultrabithorax, and engrailed, known to underlie the wing polyphenism in ants. Surprisingly, the expression patterns of these three genes in the vestigial wing discs was the same as those found in ant species with different worker size distributions and wing disc growth than fire ants. We conclude that growth and patterning are evolutionarily dissociated in the vestigial wing discs of S. invicta because patterning in these discs is conserved, whereas their growth trajectories are not. The evolutionary dissociation of growth and patterning may be an important feature of gene networks that underlie polyphenic traits. 2007 Wiley-Liss, Inc

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

PubMed Central

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

2014-01-01

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

Cocoa/Cotton Comparative Genomics

USDA-ARS?s Scientific Manuscript database

With genome sequence from two members of the Malvaceae family recently made available, we are exploring syntenic relationships, gene content, and evolutionary trajectories between the cacao and cotton genomes. An assembly of cacao (Theobroma cacao) using Illumina and 454 sequence technology yielded ...

Trajectory phase transitions and dynamical Lee-Yang zeros of the Glauber-Ising chain.

PubMed

Hickey, James M; Flindt, Christian; Garrahan, Juan P

2013-07-01

We examine the generating function of the time-integrated energy for the one-dimensional Glauber-Ising model. At long times, the generating function takes on a large-deviation form and the associated cumulant generating function has singularities corresponding to continuous trajectory (or "space-time") phase transitions between paramagnetic trajectories and ferromagnetically or antiferromagnetically ordered trajectories. In the thermodynamic limit, the singularities make up a whole curve of critical points in the complex plane of the counting field. We evaluate analytically the generating function by mapping the generator of the biased dynamics to a non-Hermitian Hamiltonian of an associated quantum spin chain. We relate the trajectory phase transitions to the high-order cumulants of the time-integrated energy which we use to extract the dynamical Lee-Yang zeros of the generating function. This approach offers the possibility to detect continuous trajectory phase transitions from the finite-time behavior of measurable quantities.

Trajectory control method of stratospheric airship based on the sliding mode control and prediction in wind field

NASA Astrophysics Data System (ADS)

Zhang, Jia-shi; Yang, Xi-xiang

2017-11-01

The stratospheric airship has the characteristics of large inertia, long time delay and large disturbance of wind field , so the trajectory control is very difficult .Build the lateral three degrees of freedom dynamic model which consider the wind interference , the dynamics equation is linearized by the small perturbation theory, propose a trajectory control method Combine with the sliding mode control and prediction, design the trajectory controller , takes the HAA airship as the reference to carry out simulation analysis. Results show that the improved sliding mode control with front-feedback method not only can solve well control problems of airship trajectory in wind field, but also can effectively improve the control accuracy of the traditional sliding mode control method, solved problems that using the traditional sliding mode control to control. It provides a useful reference for dynamic modeling and trajectory control of stratospheric airship.

Visualizing global properties of a molecular dynamics trajectory.

PubMed

Zhou, Hao; Li, Shangyang; Makowski, Lee

2016-01-01

Molecular dynamics (MD) trajectories are very large data sets that contain substantial information about the dynamic behavior of a protein. Condensing these data into a form that can provide intuitively useful understanding of the molecular behavior during the trajectory is a substantial challenge that has received relatively little attention. Here, we introduce the sigma-r plot, a plot of the standard deviation of intermolecular distances as a function of that distance. This representation of global dynamics contains within a single, one-dimensional plot, the average range of motion between pairs of atoms within a macromolecule. Comparison of sigma-r plots calculated from 10 ns trajectories of proteins representing the four major SCOP fold classes indicates diversity of dynamic behaviors which are recognizably different among the four classes. Differences in domain structure and molecular weight also produce recognizable features in sigma-r plots, reflective of differences in global dynamics. Plots generated from trajectories with progressively increasing simulation time reflect the increased sampling of the structural ensemble as a function of time. Single amino acid replacements can give rise to changes in global dynamics detectable through comparison of sigma-r plots. Dynamic behavior of substructures can be monitored by careful choice of interatomic vectors included in the calculation. These examples provide demonstrations of the utility of the sigma-r plot to provide a simple measure of the global dynamics of a macromolecule. © 2015 Wiley Periodicals, Inc.

Understanding Past Population Dynamics: Bayesian Coalescent-Based Modeling with Covariates

PubMed Central

Gill, Mandev S.; Lemey, Philippe; Bennett, Shannon N.; Biek, Roman; Suchard, Marc A.

2016-01-01

Effective population size characterizes the genetic variability in a population and is a parameter of paramount importance in population genetics and evolutionary biology. Kingman’s coalescent process enables inference of past population dynamics directly from molecular sequence data, and researchers have developed a number of flexible coalescent-based models for Bayesian nonparametric estimation of the effective population size as a function of time. Major goals of demographic reconstruction include identifying driving factors of effective population size, and understanding the association between the effective population size and such factors. Building upon Bayesian nonparametric coalescent-based approaches, we introduce a flexible framework that incorporates time-varying covariates that exploit Gaussian Markov random fields to achieve temporal smoothing of effective population size trajectories. To approximate the posterior distribution, we adapt efficient Markov chain Monte Carlo algorithms designed for highly structured Gaussian models. Incorporating covariates into the demographic inference framework enables the modeling of associations between the effective population size and covariates while accounting for uncertainty in population histories. Furthermore, it can lead to more precise estimates of population dynamics. We apply our model to four examples. We reconstruct the demographic history of raccoon rabies in North America and find a significant association with the spatiotemporal spread of the outbreak. Next, we examine the effective population size trajectory of the DENV-4 virus in Puerto Rico along with viral isolate count data and find similar cyclic patterns. We compare the population history of the HIV-1 CRF02_AG clade in Cameroon with HIV incidence and prevalence data and find that the effective population size is more reflective of incidence rate. Finally, we explore the hypothesis that the population dynamics of musk ox during the Late Quaternary period were related to climate change. [Coalescent; effective population size; Gaussian Markov random fields; phylodynamics; phylogenetics; population genetics. PMID:27368344

Modelling and strategy optimisation for a kind of networked evolutionary games with memories under the bankruptcy mechanism

NASA Astrophysics Data System (ADS)

Fu, Shihua; Li, Haitao; Zhao, Guodong

2018-05-01

This paper investigates the evolutionary dynamic and strategy optimisation for a kind of networked evolutionary games whose strategy updating rules incorporate 'bankruptcy' mechanism, and the situation that each player's bankruptcy is due to the previous continuous low profits gaining from the game is considered. First, by using semi-tensor product of matrices method, the evolutionary dynamic of this kind of games is expressed as a higher order logical dynamic system and then converted into its algebraic form, based on which, the evolutionary dynamic of the given games can be discussed. Second, the strategy optimisation problem is investigated, and some free-type control sequences are designed to maximise the total payoff of the whole game. Finally, an illustrative example is given to show that our new results are very effective.

Mutation rate evolution in replicator dynamics.

PubMed

Allen, Benjamin; Rosenbloom, Daniel I Scholes

2012-11-01

The mutation rate of an organism is itself evolvable. In stable environments, if faithful replication is costless, theory predicts that mutation rates will evolve to zero. However, positive mutation rates can evolve in novel or fluctuating environments, as analytical and empirical studies have shown. Previous work on this question has focused on environments that fluctuate independently of the evolving population. Here we consider fluctuations that arise from frequency-dependent selection in the evolving population itself. We investigate how the dynamics of competing traits can induce selective pressure on the rates of mutation between these traits. To address this question, we introduce a theoretical framework combining replicator dynamics and adaptive dynamics. We suppose that changes in mutation rates are rare, compared to changes in the traits under direct selection, so that the expected evolutionary trajectories of mutation rates can be obtained from analysis of pairwise competition between strains of different rates. Depending on the nature of frequency-dependent trait dynamics, we demonstrate three possible outcomes of this competition. First, if trait frequencies are at a mutation-selection equilibrium, lower mutation rates can displace higher ones. Second, if trait dynamics converge to a heteroclinic cycle-arising, for example, from "rock-paper-scissors" interactions-mutator strains succeed against non-mutators. Third, in cases where selection alone maintains all traits at positive frequencies, zero and nonzero mutation rates can coexist indefinitely. Our second result suggests that relatively high mutation rates may be observed for traits subject to cyclical frequency-dependent dynamics.

Clustering molecular dynamics trajectories for optimizing docking experiments.

PubMed

De Paris, Renata; Quevedo, Christian V; Ruiz, Duncan D; Norberto de Souza, Osmar; Barros, Rodrigo C

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand.

A case study of bats and white-nose syndrome demonstrating how to model population viability with evolutionary effects.

PubMed

Maslo, Brooke; Fefferman, Nina H

2015-08-01

Ecological factors generally affect population viability on rapid time scales. Traditional population viability analyses (PVA) therefore focus on alleviating ecological pressures, discounting potential evolutionary impacts on individual phenotypes. Recent studies of evolutionary rescue (ER) focus on cases in which severe, environmentally induced population bottlenecks trigger a rapid evolutionary response that can potentially reverse demographic threats. ER models have focused on shifting genetics and resulting population recovery, but no one has explored how to incorporate those findings into PVA. We integrated ER into PVA to identify the critical decision interval for evolutionary rescue (DIER) under which targeted conservation action should be applied to buffer populations undergoing ER against extinction from stochastic events and to determine the most appropriate vital rate to target to promote population recovery. We applied this model to little brown bats (Myotis lucifugus) affected by white-nose syndrome (WNS), a fungal disease causing massive declines in several North American bat populations. Under the ER scenario, the model predicted that the DIER period for little brown bats was within 11 years of initial WNS emergence, after which they stabilized at a positive growth rate (λ = 1.05). By comparing our model results with population trajectories of multiple infected hibernacula across the WNS range, we concluded that ER is a potential explanation of observed little brown bat population trajectories across multiple hibernacula within the affected range. Our approach provides a tool that can be used by all managers to provide testable hypotheses regarding the occurrence of ER in declining populations, suggest empirical studies to better parameterize the population genetics and conservation-relevant vital rates, and identify the DIER period during which management strategies will be most effective for species conservation. © 2015 Society for Conservation Biology.

Evo-devo of human adolescence: beyond disease models of early puberty

PubMed Central

2013-01-01

Despite substantial heritability in pubertal development, much variation remains to be explained, leaving room for the influence of environmental factors to adjust its phenotypic trajectory in the service of fitness goals. Utilizing evolutionary development biology (evo-devo), we examine adolescence as an evolutionary life-history stage in its developmental context. We show that the transition from the preceding stage of juvenility entails adaptive plasticity in response to energy resources, other environmental cues, social needs of adolescence and maturation toward youth and adulthood. Using the evolutionary theory of socialization, we show that familial psychosocial stress fosters a fast life history and reproductive strategy rather than early maturation being just a risk factor for aggression and delinquency. Here we explore implications of an evolutionary-developmental-endocrinological-anthropological framework for theory building, while illuminating new directions for research. PMID:23627891

Entangled trajectories Hamiltonian dynamics for treating quantum nuclear effects

NASA Astrophysics Data System (ADS)

Smith, Brendan; Akimov, Alexey V.

2018-04-01

A simple and robust methodology, dubbed Entangled Trajectories Hamiltonian Dynamics (ETHD), is developed to capture quantum nuclear effects such as tunneling and zero-point energy through the coupling of multiple classical trajectories. The approach reformulates the classically mapped second-order Quantized Hamiltonian Dynamics (QHD-2) in terms of coupled classical trajectories. The method partially enforces the uncertainty principle and facilitates tunneling. The applicability of the method is demonstrated by studying the dynamics in symmetric double well and cubic metastable state potentials. The methodology is validated using exact quantum simulations and is compared to QHD-2. We illustrate its relationship to the rigorous Bohmian quantum potential approach, from which ETHD can be derived. Our simulations show a remarkable agreement of the ETHD calculation with the quantum results, suggesting that ETHD may be a simple and inexpensive way of including quantum nuclear effects in molecular dynamics simulations.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity.

PubMed

Frickel, Jens; Theodosiou, Loukas; Becks, Lutz

2017-10-17

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus-host and prey-predator) with a more complex three-species system (virus-host-predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host-virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host-virus coevolution in the complex system and that the virus' effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species.

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

PubMed

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

2017-07-01

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

The challenges of modelling antibody repertoire dynamics in HIV infection

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

Luo, Shishi; Perelson, Alan S.

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

The challenges of modelling antibody repertoire dynamics in HIV infection

DOE PAGES

Luo, Shishi; Perelson, Alan S.

2015-07-20

Antibody affinity maturation by somatic hypermutation of B-cell immunoglobulin variable region genes has been studied for decades in various model systems using well-defined antigens. While much is known about the molecular details of the process, our understanding of the selective forces that generate affinity maturation are less well developed, particularly in the case of a co-evolving pathogen such as HIV. Despite this gap in understanding, high-throughput antibody sequence data are increasingly being collected to investigate the evolutionary trajectories of antibody lineages in HIV-infected individuals. Here, we review what is known in controlled experimental systems about the mechanisms underlying antibody selectionmore » and compare this to the observed temporal patterns of antibody evolution in HIV infection. In addition, we describe how our current understanding of antibody selection mechanisms leaves questions about antibody dynamics in HIV infection unanswered. Without a mechanistic understanding of antibody selection in the context of a co-evolving viral population, modelling and analysis of antibody sequences in HIV-infected individuals will be limited in their interpretation and predictive ability.« less

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

PubMed

Frickel, Jens; Sieber, Michael; Becks, Lutz

2016-04-01

Eco-evolutionary dynamics have been shown to be important for understanding population and community stability and their adaptive potential. However, coevolution in the framework of eco-evolutionary theory has not been addressed directly. Combining experiments with an algal host and its viral parasite, and mathematical model analyses we show eco-evolutionary dynamics in antagonistic coevolving populations. The interaction between antagonists initially resulted in arms race dynamics (ARD) with selective sweeps, causing oscillating host-virus population dynamics. However, ARD ended and populations stabilised after the evolution of a general resistant host, whereas a trade-off between host resistance and growth then maintained host diversity over time (trade-off driven dynamics). Most importantly, our study shows that the interaction between ecology and evolution had important consequences for the predictability of the mode and tempo of adaptive change and for the stability and adaptive potential of populations. © 2016 John Wiley & Sons Ltd/CNRS.

On the evolution of specialization with a mechanistic underpinning in structured metapopulations.

PubMed

Nurmi, Tuomas; Parvinen, Kalle

2008-03-01

We analyze the evolution of specialization in resource utilization in a discrete-time metapopulation model using the adaptive dynamics approach. The local dynamics in the metapopulation are based on the Beverton-Holt model with mechanistic underpinnings. The consumer faces a trade-off in the abilities to consume two resources that are spatially heterogeneously distributed to patches that are prone to local catastrophes. We explore the factors favoring the spread of generalist or specialist strategies. Increasing fecundity or decreasing catastrophe probability favors the spread of the generalist strategy and increasing environmental heterogeneity enlarges the parameter domain where the evolutionary branching is possible. When there are no catastrophes, increasing emigration diminishes the parameter domain where the evolutionary branching may occur. Otherwise, the effect of emigration on evolutionary dynamics is non-monotonous: both small and large values of emigration probability favor the spread of the specialist strategies whereas the parameter domain where evolutionary branching may occur is largest when the emigration probability has intermediate values. We compare how different forms of spatial heterogeneity and different models of local growth affect the evolutionary dynamics. We show that even small changes in the resource dynamics may have outstanding evolutionary effects to the consumers.

An inverse dynamics approach to trajectory optimization for an aerospace plane

NASA Technical Reports Server (NTRS)

Lu, Ping

1992-01-01

An inverse dynamics approach for trajectory optimization is proposed. This technique can be useful in many difficult trajectory optimization and control problems. The application of the approach is exemplified by ascent trajectory optimization for an aerospace plane. Both minimum-fuel and minimax types of performance indices are considered. When rocket augmentation is available for ascent, it is shown that accurate orbital insertion can be achieved through the inverse control of the rocket in the presence of disturbances.

Mutation Supply and Relative Fitness Shape the Genotypes of Ciprofloxacin-Resistant Escherichia coli.

PubMed

Huseby, Douglas L; Pietsch, Franziska; Brandis, Gerrit; Garoff, Linnéa; Tegehall, Angelica; Hughes, Diarmaid

2017-05-01

Ciprofloxacin is an important antibacterial drug targeting Type II topoisomerases, highly active against Gram-negatives including Escherichia coli. The evolution of resistance to ciprofloxacin in E. coli always requires multiple genetic changes, usually including mutations affecting two different drug target genes, gyrA and parC. Resistant mutants selected in vitro or in vivo can have many different mutations in target genes and efflux regulator genes that contribute to resistance. Among resistant clinical isolates the genotype, gyrA S83L D87N, parC S80I is significantly overrepresented suggesting that it has a selective advantage. However, the evolutionary or functional significance of this high frequency resistance genotype is not fully understood. By combining experimental data and mathematical modeling, we addressed the reasons for the predominance of this specific genotype. The experimental data were used to model trajectories of mutational resistance evolution under different conditions of drug exposure and population bottlenecks. We identified the order in which specific mutations are selected in the clinical genotype, showed that the high frequency genotype could be selected over a range of drug selective pressures, and was strongly influenced by the relative fitness of alternative mutations and factors affecting mutation supply. Our data map for the first time the fitness landscape that constrains the evolutionary trajectories taken during the development of clinical resistance to ciprofloxacin and explain the predominance of the most frequently selected genotype. This study provides strong support for the use of in vitro competition assays as a tool to trace evolutionary trajectories, not only in the antibiotic resistance field. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Anharmonic quantum mechanical systems do not feature phase space trajectories

NASA Astrophysics Data System (ADS)

Oliva, Maxime; Kakofengitis, Dimitris; Steuernagel, Ole

2018-07-01

Phase space dynamics in classical mechanics is described by transport along trajectories. Anharmonic quantum mechanical systems do not allow for a trajectory-based description of their phase space dynamics. This invalidates some approaches to quantum phase space studies. We first demonstrate the absence of trajectories in general terms. We then give an explicit proof for all quantum phase space distributions with negative values: we show that the generation of coherences in anharmonic quantum mechanical systems is responsible for the occurrence of singularities in their phase space velocity fields, and vice versa. This explains numerical problems repeatedly reported in the literature, and provides deeper insight into the nature of quantum phase space dynamics.

Ecological transition predictably associated with gene degeneration.

PubMed

Wessinger, Carolyn A; Rausher, Mark D

2015-02-01

Gene degeneration or loss can significantly contribute to phenotypic diversification, but may generate genetic constraints on future evolutionary trajectories, potentially restricting phenotypic reversal. Such constraints may manifest as directional evolutionary trends when parallel phenotypic shifts consistently involve gene degeneration or loss. Here, we demonstrate that widespread parallel evolution in Penstemon from blue to red flowers predictably involves the functional inactivation and degeneration of the enzyme flavonoid 3',5'-hydroxylase (F3'5'H), an anthocyanin pathway enzyme required for the production of blue floral pigments. Other types of genetic mutations do not consistently accompany this phenotypic shift. This pattern may be driven by the relatively large mutational target size of degenerative mutations to this locus and the apparent lack of associated pleiotropic effects. The consistent degeneration of F3'5'H may provide a mechanistic explanation for the observed asymmetry in the direction of flower color evolution in Penstemon: Blue to red transitions are common, but reverse transitions have not been observed. Although phenotypic shifts in this system are likely driven by natural selection, internal constraints may generate predictable genetic outcomes and may restrict future evolutionary trajectories. © The Author 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Rapid Preliminary Design of Interplanetary Trajectories Using the Evolutionary Mission Trajectory Generator

NASA Technical Reports Server (NTRS)

Englander, Jacob

2016-01-01

Preliminary design of interplanetary missions is a highly complex process. The mission designer must choose discrete parameters such as the number of flybys, the bodies at which those flybys are performed, and in some cases the final destination. In addition, a time-history of control variables must be chosen that defines the trajectory. There are often many thousands, if not millions, of possible trajectories to be evaluated. This can be a very expensive process in terms of the number of human analyst hours required. An automated approach is therefore very desirable. This work presents such an approach by posing the mission design problem as a hybrid optimal control problem. The method is demonstrated on notional high-thrust chemical and low-thrust electric propulsion missions. In the low-thrust case, the hybrid optimal control problem is augmented to include systems design optimization.

A computational intelligence approach to the Mars Precision Landing problem

NASA Astrophysics Data System (ADS)

Birge, Brian Kent, III

Various proposed Mars missions, such as the Mars Sample Return Mission (MRSR) and the Mars Smart Lander (MSL), require precise re-entry terminal position and velocity states. This is to achieve mission objectives including rendezvous with a previous landed mission, or reaching a particular geographic landmark. The current state of the art footprint is in the magnitude of kilometers. For this research a Mars Precision Landing is achieved with a landed footprint of no more than 100 meters, for a set of initial entry conditions representing worst guess dispersions. Obstacles to reducing the landed footprint include trajectory dispersions due to initial atmospheric entry conditions (entry angle, parachute deployment height, etc.), environment (wind, atmospheric density, etc.), parachute deployment dynamics, unavoidable injection error (propagated error from launch on), etc. Weather and atmospheric models have been developed. Three descent scenarios have been examined. First, terminal re-entry is achieved via a ballistic parachute with concurrent thrusting events while on the parachute, followed by a gravity turn. Second, terminal re-entry is achieved via a ballistic parachute followed by gravity turn to hover and then thrust vector to desired location. Third, a guided parafoil approach followed by vectored thrusting to reach terminal velocity is examined. The guided parafoil is determined to be the best architecture. The purpose of this study is to examine the feasibility of using a computational intelligence strategy to facilitate precision planetary re-entry, specifically to take an approach that is somewhat more intuitive and less rigid, and see where it leads. The test problems used for all research are variations on proposed Mars landing mission scenarios developed by NASA. A relatively recent method of evolutionary computation is Particle Swarm Optimization (PSO), which can be considered to be in the same general class as Genetic Algorithms. An improvement over the regular PSO algorithm, allowing tracking of nonstationary error functions is detailed. Continued refinement of PSO in the larger research community comes from attempts to understand human-human social interaction as well as analysis of the emergent behavior. Using PSO and the parafoil scenario, optimized reference trajectories are created for an initial condition set of 76 states, representing the convex hull of 2001 states from an early Monte Carlo analysis. The controls are a set series of bank angles followed by a set series of 3DOF thrust vectoring. The reference trajectories are used to train an Artificial Neural Network Reference Trajectory Generator (ANNTraG), with the (marginal) ability to generalize a trajectory from initial conditions it has never been presented. The controls here allow continuous change in bank angle as well as thrust vector. The optimized reference trajectories represent the best achievable trajectory given the initial condition. Steps toward a closed loop neural controller with online learning updates are examined. The inner loop of the simulation employs the Program to Optimize Simulated Trajectories (POST) as the basic model, containing baseline dynamics and state generation. This is controlled from a MATLAB shell that directs the optimization, learning, and control strategy. Using mainly bank angle guidance coupled with CI strategies, the set of achievable reference trajectories are shown to be 88% under 10 meters, a significant improvement in the state of the art. Further, the automatic real-time generation of realistic reference trajectories in the presence of unknown initial conditions is shown to have promise. The closed loop CI guidance strategy is outlined. An unexpected advance came from the effort to optimize the optimization, where the PSO algorithm was improved with the capability for tracking a changing error environment.

[A delayed motor production of open chains of linear strokes presented visually in static and dynamic modes: a comparison between 9 to 11 years old children and adults].

PubMed

Antonova, A A; Absatova, K A; Korneev, A A; Kurgansky, A V

2015-01-01

The production of drawing movements was studied in 29 right-handed children of 9-to-11 years old. The movements were the sequences of horizontal and vertical linear stokes conjoined at right angle (open polygonal chains) referred to throughout the paper as trajectories. The length of a trajectory varied from 4 to 6. The trajectories were presented visually to a subject in static (linedrawing) and dynamic (moving cursor that leaves no trace) modes. The subjects were asked to draw (copy) a trajectory in response to delayed go-signal (short click) as fast as possible without lifting the pen. The production latency time, the average movement duration along a trajectory segment, and overall number of errors committed by a subject during trajectory production were analyzed. A comparison of children's data with similar data in adults (16 subjects) shows the following. First, a substantial reduction in error rate is observed in the age range between 9 and 11 years old for both static and dynamic modes of trajectory presentation, with children of 11 still committing more error than adults. Second, the averaged movement duration shortens with age while the latency time tends to increase. Third, unlike the adults, the children of 9-11 do not show any difference in latency time between static and dynamic modes of visual presentation of trajectories. The difference in trajectory production between adult and children is attributed to the predominant involvement of on-line programming in children and pre-programming in adults.

Falsification of matching theory and confirmation of an evolutionary theory of behavior dynamics in a critical experiment.

PubMed

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

2017-07-01

Two competing predictions of matching theory and an evolutionary theory of behavior dynamics, and one additional prediction of the evolutionary theory, were tested in a critical experiment in which human participants worked on concurrent schedules for money (Dallery et al., 2005). The three predictions concerned the descriptive adequacy of matching theory equations, and of equations describing emergent equilibria of the evolutionary theory. Tests of the predictions falsified matching theory and supported the evolutionary theory. Copyright © 2017 Elsevier B.V. All rights reserved.

Flight Dynamics Operations: Methods and Lessons Learned from Space Shuttle Orbit Operations

NASA Technical Reports Server (NTRS)

Cutri-Kohart, Rebecca M.

2011-01-01

The Flight Dynamics Officer is responsible for trajectory maintenance of the Space Shuttle. This paper will cover high level operational considerations, methodology, procedures, and lessons learned involved in performing the functions of orbit and rendezvous Flight Dynamics Officer and leading the team of flight dynamics specialists during different phases of flight. The primary functions that will be address are: onboard state vector maintenance, ground ephemeris maintenance, calculation of ground and spacecraft acquisitions, collision avoidance, burn targeting for the primary mission, rendezvous, deorbit and contingencies, separation sequences, emergency deorbit preparation, mass properties coordination, payload deployment planning, coordination with the International Space Station, and coordination with worldwide trajectory customers. Each of these tasks require the Flight Dynamics Officer to have cognizance of the current trajectory state as well as the impact of future events on the trajectory plan in order to properly analyze and react to real-time changes. Additionally, considerations are made to prepare flexible alternative trajectory plans in the case timeline changes or a systems failure impact the primary plan. The evolution of the methodology, procedures, and techniques used by the Flight Dynamics Officer to perform these tasks will be discussed. Particular attention will be given to how specific Space Shuttle mission and training simulation experiences, particularly off-nominal or unexpected events such as shortened mission durations, tank failures, contingency deorbit, navigation errors, conjunctions, and unexpected payload deployments, have influenced the operational procedures and training for performing Space Shuttle flight dynamics operations over the history of the program. These lessons learned can then be extended to future vehicle trajectory operations.

Actuarial senescence in a long-lived orchid challenges our current understanding of ageing

PubMed Central

Colchero, Fernando; Jones, Owen R.; Øien, Dag-Inge; Moen, Asbjørn; Sletvold, Nina

2016-01-01

The dominant evolutionary theory of actuarial senescence—an increase in death rate with advancing age—is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study of Dactylorhiza lapponica that replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival–reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics. PMID:27852801

Actuarial senescence in a long-lived orchid challenges our current understanding of ageing.

PubMed

Dahlgren, Johan Petter; Colchero, Fernando; Jones, Owen R; Øien, Dag-Inge; Moen, Asbjørn; Sletvold, Nina

2016-11-16

The dominant evolutionary theory of actuarial senescence-an increase in death rate with advancing age-is based on the concept of a germ cell line that is separated from the somatic cells early in life. However, such a separation is not clear in all organisms. This has been suggested to explain the paucity of evidence for actuarial senescence in plants. We used a 32 year study of Dactylorhiza lapponica that replaces its organs each growing season, to test whether individuals of this tuberous orchid senesce. We performed a Bayesian survival trajectory analysis accounting for reproductive investment, for individuals under two types of land use, in two climatic regions. The mortality trajectory was best approximated by a Weibull model, showing clear actuarial senescence. Rates of senescence in this model declined with advancing age, but were slightly higher in mown plots and in the more benign climatic region. At older ages, senescence was evident only when accounting for a positive effect of reproductive investment on mortality. Our results demonstrate actuarial senescence as well as a survival-reproduction trade-off in plants, and indicate that environmental context may influence senescence rates. This knowledge is crucial for understanding the evolution of demographic senescence and for models of plant population dynamics. © 2016 The Author(s).

The evolutionary rate dynamically tracks changes in HIV-1 epidemics

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

Maljkovic-berry, Irina; Athreya, Gayathri; Daniels, Marcus

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

Unravelling the dynamical origin of below- and near-threshold harmonic generation of H 2 + in an intense NIR laser field

DOE PAGES

Heslar, John; Chu, Shih-I.

2016-11-24

Recently, the study of near- and below- threshold regime harmonics as a potential source of intense coherent vacuum-ultraviolet radiation has received considerable attention. However, the dynamical origin of these lower harmonics, particularly for the molecular systems, is less understood and largely unexplored. Here we perform the first fully ab initio and high precision 3D quantum study of the below- and near-threshold harmonic generation of H 2 + molecules in an intense 800-nm near-infrared (NIR) laser field. Furthermore, combining with a synchrosqueezing transform of the quantum time-frequency spectrum and an extended semiclassical analysis, we explore in-depth the roles of various quantummore » trajectories, including short- and long trajectories, multiphoton trajectories, resonance-enhanced trajectories, and multiple rescattering trajectories of the below- and near- threshold harmonic generation processes. Our results shed new light on the dynamical origin of the below- and near-threshold harmonic generation and various quantum trajectories for diatomic molecules for the first time.« less

EVOLUTIONARY TRAJECTORIES OF ULTRACOMPACT 'BLACK WIDOW' PULSARS WITH VERY LOW MASS COMPANIONS

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

Benvenuto, O. G.; De Vito, M. A.; Horvath, J. E., E-mail: obenvenu@fcaglp.unlp.edu.ar, E-mail: adevito@fcaglp.unlp.edu.ar, E-mail: foton@astro.iag.usp.br

The existence of millisecond pulsars with planet-mass companions in close orbits is challenging from the stellar evolution point of view. We calculate in detail the evolution of binary systems self-consistently, including mass transfer, evaporation, and irradiation of the donor by X-ray feedback, demonstrating the existence of a new evolutionary path leading to short periods and compact donors as required by the observations of PSR J1719-1438. We also point out the alternative of an exotic nature of the companion planet-mass star.

Biased Brownian dynamics for rate constant calculation.

PubMed

Zou, G; Skeel, R D; Subramaniam, S

2000-08-01

An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force.

The Roles of Standing Genetic Variation and Evolutionary History in Determining the Evolvability of Anti-Predator Strategies

PubMed Central

Dworkin, Ian; Wagner, Aaron P.

2014-01-01

Standing genetic variation and the historical environment in which that variation arises (evolutionary history) are both potentially significant determinants of a population's capacity for evolutionary response to a changing environment. Using the open-ended digital evolution software Avida, we evaluated the relative importance of these two factors in influencing evolutionary trajectories in the face of sudden environmental change. We examined how historical exposure to predation pressures, different levels of genetic variation, and combinations of the two, affected the evolvability of anti-predator strategies and competitive abilities in the presence or absence of threats from new, invasive predator populations. We show that while standing genetic variation plays some role in determining evolutionary responses, evolutionary history has the greater influence on a population's capacity to evolve anti-predator traits, i.e. traits effective against novel predators. This adaptability likely reflects the relative ease of repurposing existing, relevant genes and traits, and the broader potential value of the generation and maintenance of adaptively flexible traits in evolving populations. PMID:24955847

Tangled trios? Characterizing a hybrid zone in Castilleja (Orobanchaceae)

Treesearch

Erika l. Hersch-Green; Richard Cronn

2009-01-01

Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here...

The spatial organization of intra-tumour heterogeneity and evolutionary trajectories of metastases in hepatocellular carcinoma

PubMed Central

Zhai, Weiwei; Lim, Tony Kiat-Hon; Zhang, Tong; Phang, Su-Ting; Tiang, Zenia; Guan, Peiyong; Ng, Ming-Hwee; Lim, Jia Qi; Yao, Fei; Li, Zheng; Ng, Poh Yong; Yan, Jie; Goh, Brian K.; Chung, Alexander Yaw-Fui; Choo, Su-Pin; Khor, Chiea Chuen; Soon, Wendy Wei-Jia; Sung, Ken Wing-Kin; Foo, Roger Sik-Yin; Chow, Pierce Kah-Hoe

2017-01-01

Hepatocellular carcinoma (HCC) has one of the poorest survival rates among cancers. Using multi-regional sampling of nine resected HCC with different aetiologies, here we construct phylogenetic relationships of these sectors, showing diverse levels of genetic sharing, spanning early to late diversification. Unlike the variegated pattern found in colorectal cancers, a large proportion of HCC display a clear isolation-by-distance pattern where spatially closer sectors are genetically more similar. Two resected intra-hepatic metastases showed genetic divergence occurring before and after primary tumour diversification, respectively. Metastatic tumours had much higher variability than their primary tumours, suggesting that intra-hepatic metastasis is accompanied by rapid diversification at the distant location. The presence of co-existing mutations offers the possibility of drug repositioning for HCC treatment. Taken together, these insights into intra-tumour heterogeneity allow for a comprehensive understanding of the evolutionary trajectories of HCC and suggest novel avenues for personalized therapy. PMID:28240289

An evolutionary game approach for determination of the structural conflicts in signed networks

PubMed Central

Tan, Shaolin; Lü, Jinhu

2016-01-01

Social or biochemical networks can often divide into two opposite alliances in response to structural conflicts between positive (friendly, activating) and negative (hostile, inhibiting) interactions. Yet, the underlying dynamics on how the opposite alliances are spontaneously formed to minimize the structural conflicts is still unclear. Here, we demonstrate that evolutionary game dynamics provides a felicitous possible tool to characterize the evolution and formation of alliances in signed networks. Indeed, an evolutionary game dynamics on signed networks is proposed such that each node can adaptively adjust its choice of alliances to maximize its own fitness, which yet leads to a minimization of the structural conflicts in the entire network. Numerical experiments show that the evolutionary game approach is universally efficient in quality and speed to find optimal solutions for all undirected or directed, unweighted or weighted signed networks. Moreover, the evolutionary game approach is inherently distributed. These characteristics thus suggest the evolutionary game dynamic approach as a feasible and effective tool for determining the structural conflicts in large-scale on-line signed networks. PMID:26915581

Fast optimization of glide vehicle reentry trajectory based on genetic algorithm

NASA Astrophysics Data System (ADS)

Jia, Jun; Dong, Ruixing; Yuan, Xuejun; Wang, Chuangwei

2018-02-01

An optimization method of reentry trajectory based on genetic algorithm is presented to meet the need of reentry trajectory optimization for glide vehicle. The dynamic model for the glide vehicle during reentry period is established. Considering the constraints of heat flux, dynamic pressure, overload etc., the optimization of reentry trajectory is investigated by utilizing genetic algorithm. The simulation shows that the method presented by this paper is effective for the optimization of reentry trajectory of glide vehicle. The efficiency and speed of this method is comparative with the references. Optimization results meet all constraints, and the on-line fast optimization is potential by pre-processing the offline samples.

Clustering Molecular Dynamics Trajectories for Optimizing Docking Experiments

PubMed Central

De Paris, Renata; Quevedo, Christian V.; Ruiz, Duncan D.; Norberto de Souza, Osmar; Barros, Rodrigo C.

2015-01-01

Molecular dynamics simulations of protein receptors have become an attractive tool for rational drug discovery. However, the high computational cost of employing molecular dynamics trajectories in virtual screening of large repositories threats the feasibility of this task. Computational intelligence techniques have been applied in this context, with the ultimate goal of reducing the overall computational cost so the task can become feasible. Particularly, clustering algorithms have been widely used as a means to reduce the dimensionality of molecular dynamics trajectories. In this paper, we develop a novel methodology for clustering entire trajectories using structural features from the substrate-binding cavity of the receptor in order to optimize docking experiments on a cloud-based environment. The resulting partition was selected based on three clustering validity criteria, and it was further validated by analyzing the interactions between 20 ligands and a fully flexible receptor (FFR) model containing a 20 ns molecular dynamics simulation trajectory. Our proposed methodology shows that taking into account features of the substrate-binding cavity as input for the k-means algorithm is a promising technique for accurately selecting ensembles of representative structures tailored to a specific ligand. PMID:25873944

Comparative diversification dynamics among palaeocontinents during the Ordovician Radiation

NASA Technical Reports Server (NTRS)

Miller, A. I.

1997-01-01

The Ordovician Radiation was among the most extensive intervals of diversification in the history of life. However, a delineation of the proximal cause(s) of the Radiation remains elusive. Any such determination should involve an analysis of geographic overprints on diversification: did the Radiation occur randomly around the world or, alternatively, was it focused in particular geographic or depositional regimes? Here, I present a comparative evaluation of Ordovician diversification among several palaeocontinents to determine whether biotas associated with certain palaeocontinents exhibited different diversification patterns than others; in part, this involves a numerical "correction" to raw diversity trajectories. Clear disparities among palaeocontinents are indicated by the data, which appear to reflect differences in the extent of siliciclastic input partly in association with tectonic activity. Further testing will be required to fully substantiate the implication that siliciclastic influx was a predominant factor in the Ordovician Radiation, affecting a variety of higher taxa among all three Phanerozoic evolutionary faunas.

Insecticide Resistance and Malaria Vector Control: The Importance of Fitness Cost Mechanisms in Determining Economically Optimal Control Trajectories

PubMed Central

Brown, Zachary S.; Dickinson, Katherine L.; Kramer, Randall A.

2014-01-01

The evolutionary dynamics of insecticide resistance in harmful arthropods has economic implications, not only for the control of agricultural pests (as has been well studied), but also for the control of disease vectors, such as malaria-transmitting Anopheles mosquitoes. Previous economic work on insecticide resistance illustrates the policy relevance of knowing whether insecticide resistance mutations involve fitness costs. Using a theoretical model, this article investigates economically optimal strategies for controlling malaria-transmitting mosquitoes when there is the potential for mosquitoes to evolve resistance to insecticides. Consistent with previous literature, we find that fitness costs are a key element in the computation of economically optimal resistance management strategies. Additionally, our models indicate that different biological mechanisms underlying these fitness costs (e.g., increased adult mortality and/or decreased fecundity) can significantly alter economically optimal resistance management strategies. PMID:23448053

Riding across the selection landscape: fitness consequences of annual variation in reproductive characteristics

PubMed Central

Tremblay, Raymond L.; Ackerman, James D.; Pérez, Maria-Eglée

2010-01-01

Evolutionary models estimating phenotypic selection in character size usually assume that the character is invariant across reproductive bouts. We show that variation in the size of reproductive traits may be large over multiple events and can influence fitness in organisms where these traits are produced anew each season. With data from populations of two orchid species, Caladenia valida and Tolumnia variegata, we used Bayesian statistics to investigate the effect on the distribution in fitness of individuals when the fitness landscape is not flat and when characters vary across reproductive bouts. Inconsistency in character size across reproductive periods within an individual increases the uncertainty of mean fitness and, consequently, the uncertainty in individual fitness. The trajectory of selection is likely to be muddled as a consequence of variation in morphology of individuals across reproductive bouts. The frequency and amplitude of such changes will certainly affect the dynamics between selection and genetic drift. PMID:20047875

Adaptive evolution of body size subject to indirect effect in trophic cascade system.

PubMed

Wang, Xin; Fan, Meng; Hao, Lina

2017-09-01

Trophic cascades represent a classic example of indirect effect and are wide-spread in nature. Their ecological impact are well established, but the evolutionary consequences have received even less theoretical attention. We theoretically and numerically investigate the trait (i.e., body size of consumer) evolution in response to indirect effect in a trophic cascade system. By applying the quantitative trait evolutionary theory and the adaptive dynamic theory, we formulate and explore two different types of eco-evolutionary resource-consumer-predator trophic cascade model. First, an eco-evolutionary model incorporating the rapid evolution is formulated to investigate the effect of rapid evolution of the consumer's body size, and to explore the impact of density-mediate indirect effect on the population dynamics and trait dynamics. Next, by employing the adaptive dynamic theory, a long-term evolutionary model of consumer body size is formulated to evaluate the effect of long-term evolution on the population dynamics and the effect of trait-mediate indirect effect. Those models admit rich dynamics that has not been observed yet in empirical studies. It is found that, both in the trait-mediated and density-mediated system, the body size of consumer in predator-consumer-resource interaction (indirect effect) evolves smaller than that in consumer-resource and predator-consumer interaction (direct effect). Moreover, in the density-mediated system, we found that the evolution of consumer body size contributes to avoiding consumer extinction (i.e., evolutionary rescue). The trait-mediate and density-mediate effects may produce opposite evolutionary response. This study suggests that the trophic cascade indirect effect affects consumer evolution, highlights a more comprehensive mechanistic understanding of the intricate interplay between ecological and evolutionary force. The modeling approaches provide avenue for study on indirect effects from an evolutionary perspective. Copyright © 2017 Elsevier B.V. All rights reserved.

Rapid evolution of hosts begets species diversity at the cost of intraspecific diversity

PubMed Central

Frickel, Jens; Theodosiou, Loukas

2017-01-01

Ecosystems are complex food webs in which multiple species interact and ecological and evolutionary processes continuously shape populations and communities. Previous studies on eco-evolutionary dynamics have shown that the presence of intraspecific diversity affects community structure and function, and that eco-evolutionary feedback dynamics can be an important driver for its maintenance. Within communities, feedbacks are, however, often indirect, and they can feed back over many generations. Here, we studied eco-evolutionary feedbacks in evolving communities over many generations and compared two-species systems (virus–host and prey–predator) with a more complex three-species system (virus–host–predator). Both indirect density- and trait-mediated effects drove the dynamics in the complex system, where host–virus coevolution facilitated coexistence of predator and virus, and where coexistence, in return, lowered intraspecific diversity of the host population. Furthermore, ecological and evolutionary dynamics were significantly altered in the three-species system compared with the two-species systems. We found that the predator slowed host–virus coevolution in the complex system and that the virus’ effect on the overall population dynamics was negligible when the three species coexisted. Overall, we show that a detailed understanding of the mechanism driving eco-evolutionary feedback dynamics is necessary for explaining trait and species diversity in communities, even in communities with only three species. PMID:28973943

J.A. Schumpeter and T.B. Veblen on economic evolution: the dichotomy between statics and dynamics

PubMed Central

Schütz, Marlies; Rainer, Andreas

2016-01-01

Abstract At present, the discussion on the dichotomy between statics and dynamics is resolved by concentrating on its mathematical meaning. Yet, a simple formalisation masks the underlying methodological discussion. Overcoming this limitation, the paper discusses Schumpeter's and Veblen's viewpoint on dynamic economic systems as systems generating change from within. It contributes to an understanding on their ideas of how economics could become an evolutionary science and on their contributions to elaborate an evolutionary economics. It confronts Schumpeter's with Veblen's perspective on evolutionary economics and provides insight into their evolutionary economic theorising by discussing their ideas on the evolution of capitalism. PMID:28057981

Goddard trajectory determination subsystem: Mathematical specifications

NASA Technical Reports Server (NTRS)

Wagner, W. E. (Editor); Velez, C. E. (Editor)

1972-01-01

The mathematical specifications of the Goddard trajectory determination subsystem of the flight dynamics system are presented. These specifications include the mathematical description of the coordinate systems, dynamic and measurement model, numerical integration techniques, and statistical estimation concepts.

Fitness costs and benefits of novel herbicide tolerance in a noxious weed

PubMed Central

Baucom, Regina S.; Mauricio, Rodney

2004-01-01

Glyphosate, the active ingredient in the herbicide RoundUp, has increased dramatically in use over the past decade and constitutes a potent anthropogenic source of selection. In the southeastern United States, weedy morning glories have begun to develop tolerance to glyphosate, representing a unique opportunity to examine the evolutionary genetics of a novel trait. We found genetic variation for tolerance, indicating the potential for the population to respond to selection by glyphosate. However, the following significant evolutionary constraint exists: in the absence of glyphosate, tolerant genotypes produced fewer seeds than susceptible genotypes. The combination of strong positive directional selection in the presence of glyphosate and strong negative directional selection in its absence may indicate that the selective landscape of land use could drive the evolutionary trajectory of glyphosate tolerance. Understanding these evolutionary forces is imperative for devising comprehensive management strategies to help slow the rate of the evolution of tolerance. PMID:15326309

Extending Bell's beables to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories

NASA Astrophysics Data System (ADS)

Lorenzen, F.; de Ponte, M. A.; Moussa, M. H. Y.

2009-09-01

In this paper, employing the Itô stochastic Schrödinger equation, we extend Bell’s beable interpretation of quantum mechanics to encompass dissipation, decoherence, and the quantum-to-classical transition through quantum trajectories. For a particular choice of the source of stochasticity, the one leading to a dissipative Lindblad-type correction to the Hamiltonian dynamics, we find that the diffusive terms in Nelsons stochastic trajectories are naturally incorporated into Bohm’s causal dynamics, yielding a unified Bohm-Nelson theory. In particular, by analyzing the interference between quantum trajectories, we clearly identify the decoherence time, as estimated from the quantum formalism. We also observe the quantum-to-classical transition in the convergence of the infinite ensemble of quantum trajectories to their classical counterparts. Finally, we show that our extended beables circumvent the problems in Bohm’s causal dynamics regarding stationary states in quantum mechanics.

Trajectory tracking control for underactuated stratospheric airship

NASA Astrophysics Data System (ADS)

Zheng, Zewei; Huo, Wei; Wu, Zhe

2012-10-01

Stratospheric airship is a new kind of aerospace system which has attracted worldwide developing interests for its broad application prospects. Based on the trajectory linearization control (TLC) theory, a novel trajectory tracking control method for an underactuated stratospheric airship is presented in this paper. Firstly, the TLC theory is described sketchily, and the dynamic model of the stratospheric airship is introduced with kinematics and dynamics equations. Then, the trajectory tracking control strategy is deduced in detail. The designed control system possesses a cascaded structure which consists of desired attitude calculation, position control loop and attitude control loop. Two sub-loops are designed for the position and attitude control loops, respectively, including the kinematics control loop and dynamics control loop. Stability analysis shows that the controlled closed-loop system is exponentially stable. Finally, simulation results for the stratospheric airship to track typical trajectories are illustrated to verify effectiveness of the proposed approach.

Advanced launch system trajectory optimization using suboptimal control

NASA Technical Reports Server (NTRS)

Shaver, Douglas A.; Hull, David G.

1993-01-01

The maximum-final mass trajectory of a proposed configuration of the Advanced Launch System is presented. A model for the two-stage rocket is given; the optimal control problem is formulated as a parameter optimization problem; and the optimal trajectory is computed using a nonlinear programming code called VF02AD. Numerical results are presented for the controls (angle of attack and velocity roll angle) and the states. After the initial rotation, the angle of attack goes to a positive value to keep the trajectory as high as possible, returns to near zero to pass through the transonic regime and satisfy the dynamic pressure constraint, returns to a positive value to keep the trajectory high and to take advantage of minimum drag at positive angle of attack due to aerodynamic shading of the booster, and then rolls off to negative values to satisfy the constraints. Because the engines cannot be throttled, the maximum dynamic pressure occurs at a single point; there is no maximum dynamic pressure subarc. To test approximations for obtaining analytical solutions for guidance, two additional optimal trajectories are computed: one using untrimmed aerodynamics and one using no atmospheric effects except for the dynamic pressure constraint. It is concluded that untrimmed aerodynamics has a negligible effect on the optimal trajectory and that approximate optimal controls should be able to be obtained by treating atmospheric effects as perturbations.

Early arrival and climatically-linked geographic expansion of New World monkeys from tiny African ancestors.

PubMed

Silvestro, Daniele; Tejedor, Marcelo F; Serrano-Serrano, Martha L; Loiseau, Oriane; Rossier, Victor; Rolland, Jonathan; Zizka, Alexander; Höhna, Sebastian; Antonelli, Alexandre; Salamin, Nicolas

2018-06-20

New World monkeys (platyrrhines) are one of the most diverse groups of primates, occupying today a wide range of ecosystems in the American tropics and exhibiting large variations in ecology, morphology, and behavior. Although the relationships among the almost 200 living species are relatively well understood, we lack robust estimates of the timing of origin, ancestral morphology, and geographic range evolution of the clade. Here we integrate paleontological and molecular evidence to assess the evolutionary dynamics of extinct and extant platyrrhines. We develop novel analytical frameworks to infer the evolution of body mass, changes in latitudinal ranges through time, and species diversification rates using a phylogenetic tree of living and fossil taxa. Our results show that platyrrhines originated 5-10 million years earlier than previously assumed, dating back to the Middle Eocene. The estimated ancestral platyrrhine was small - weighing 0.4 kg - and matched the size of their presumed African ancestors. As the three platyrrhine families diverged, we recover a rapid change in body mass range. During the Miocene Climatic Optimum, fossil diversity peaked and platyrrhines reached their widest latitudinal range, expanding as far South as Patagonia, favored by warm and humid climate and the lower elevation of the Andes. Finally, global cooling and aridification after the middle Miocene triggered a geographic contraction of New World monkeys and increased their extinction rates. These results unveil the full evolutionary trajectory of an iconic and ecologically important radiation of monkeys and showcase the necessity of integrating fossil and molecular data for reliably estimating evolutionary rates and trends.

Chaotic trajectories in the standard map. The concept of anti-integrability

NASA Astrophysics Data System (ADS)

Aubry, Serge; Abramovici, Gilles

1990-07-01

A rigorous proof is given in the standard map (associated with a Frenkel-Kontorowa model) for the existence of chaotic trajectories with unbounded momenta for large enough coupling constant k > k0. These chaotic trajectories (with finite entropy per site) are coded by integer sequences { mi} such that the sequence bi = |m i+1 + m i-1-2m i| be bounded by some integer b. The bound k0 in k depends on b and can be lowered for coding sequences { mi} fulfilling more restrictive conditions. The obtained chaotic trajectories correspond to stationary configurations of the Frenkel-Kontorowa model with a finite (non-zero) photon gap (called gap parameter in dimensionless units). This property implies that the trajectory (or the configuration { ui}) can be uniquely continued as a uniformly continuous function of the model parameter k in some neighborhood of the initial configuration. A non-zero gap parameter implies that the Lyapunov coefficient is strictly positive (when it is defined). In addition, the existence of dilating and contracting manifolds is proven for these chaotic trajectories. “Exotic” trajectories such as ballistic trajectories are also proven to exist as a consequence of these theorems. The concept of anti-integrability emerges from these theorems. In the anti-integrable limit which can be only defined for a discrete time dynamical system, the coordinates of the trajectory at time i do not depend on the coordinates at time i - 1. Thus, at this singular limit, the existence of chaotic trajectories is trivial and the dynamical system reduces to a Bernoulli shift. It is well known that the KAM tori of symplectic dynamical originates by continuity from the invariant tori which exists in the integrible limit (under certain conditions). In a similar way, it appears that the chaotic trajectories of dynamical systems originate by continuity from those which exists at the anti-integrable limits (also under certain conditions).

Evolutionary trajectory of Pack-MULEs is determined by their epigenetic status

USDA-ARS?s Scientific Manuscript database

Acquisition and rearrangement of host genes by transposable elements is one mechanism to increase gene diversity. The rice genome is replete in such sequences and while ~3,000 Pack- Mutator-like transposable elements containing gene sequences (Pack-MULEs) have been identified, their function remains...

Gene evolutionary trajectories and GC patterns driven by recombination in Zea mays

USDA-ARS?s Scientific Manuscript database

Recombination occurring during meiosis is critical for creating genetic variation and plays an essential role in plant evolution. In addition to creating novel gene combinations, recombination can affect genome structure through altering GC patterns. In maize (Zea mays) and other grasses, another in...

Interpolating moving least-squares methods for fitting potential energy surfaces: using classical trajectories to explore configuration space.

PubMed

Dawes, Richard; Passalacqua, Alessio; Wagner, Albert F; Sewell, Thomas D; Minkoff, Michael; Thompson, Donald L

2009-04-14

We develop two approaches for growing a fitted potential energy surface (PES) by the interpolating moving least-squares (IMLS) technique using classical trajectories. We illustrate both approaches by calculating nitrous acid (HONO) cis-->trans isomerization trajectories under the control of ab initio forces from low-level HF/cc-pVDZ electronic structure calculations. In this illustrative example, as few as 300 ab initio energy/gradient calculations are required to converge the isomerization rate constant at a fixed energy to approximately 10%. Neither approach requires any preliminary electronic structure calculations or initial approximate representation of the PES (beyond information required for trajectory initial conditions). Hessians are not required. Both approaches rely on the fitting error estimation properties of IMLS fits. The first approach, called IMLS-accelerated direct dynamics, propagates individual trajectories directly with no preliminary exploratory trajectories. The PES is grown "on the fly" with the computation of new ab initio data only when a fitting error estimate exceeds a prescribed tight tolerance. The second approach, called dynamics-driven IMLS fitting, uses relatively inexpensive exploratory trajectories to both determine and fit the dynamically accessible configuration space. Once exploratory trajectories no longer find configurations with fitting error estimates higher than the designated accuracy, the IMLS fit is considered to be complete and usable in classical trajectory calculations or other applications.

Complex quantum Hamilton-Jacobi equation with Bohmian trajectories: Application to the photodissociation dynamics of NOCl

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

Chou, Chia-Chun, E-mail: ccchou@mx.nthu.edu.tw

2014-03-14

The complex quantum Hamilton-Jacobi equation-Bohmian trajectories (CQHJE-BT) method is introduced as a synthetic trajectory method for integrating the complex quantum Hamilton-Jacobi equation for the complex action function by propagating an ensemble of real-valued correlated Bohmian trajectories. Substituting the wave function expressed in exponential form in terms of the complex action into the time-dependent Schrödinger equation yields the complex quantum Hamilton-Jacobi equation. We transform this equation into the arbitrary Lagrangian-Eulerian version with the grid velocity matching the flow velocity of the probability fluid. The resulting equation describing the rate of change in the complex action transported along Bohmian trajectories is simultaneouslymore » integrated with the guidance equation for Bohmian trajectories, and the time-dependent wave function is readily synthesized. The spatial derivatives of the complex action required for the integration scheme are obtained by solving one moving least squares matrix equation. In addition, the method is applied to the photodissociation of NOCl. The photodissociation dynamics of NOCl can be accurately described by propagating a small ensemble of trajectories. This study demonstrates that the CQHJE-BT method combines the considerable advantages of both the real and the complex quantum trajectory methods previously developed for wave packet dynamics.« less

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

Quantum trajectory analysis of multimode subsystem-bath dynamics.

PubMed

Wyatt, Robert E; Na, Kyungsun

2002-01-01

The dynamics of a swarm of quantum trajectories is investigated for systems involving the interaction of an active mode (the subsystem) with an M-mode harmonic reservoir (the bath). Equations of motion for the position, velocity, and action function for elements of the probability fluid are integrated in the Lagrangian (moving with the fluid) picture of quantum hydrodynamics. These fluid elements are coupled through the Bohm quantum potential and as a result evolve as a correlated ensemble. Wave function synthesis along the trajectories permits an exact description of the quantum dynamics for the evolving probability fluid. The approach is fully quantum mechanical and does not involve classical or semiclassical approximations. Computational results are presented for three systems involving the interaction on an active mode with M=1, 10, and 15 bath modes. These results include configuration space trajectory evolution, flux analysis of the evolving ensemble, wave function synthesis along trajectories, and energy partitioning along specific trajectories. These results demonstrate the feasibility of using a small number of quantum trajectories to obtain accurate quantum results on some types of open quantum systems that are not amenable to standard quantum approaches involving basis set expansions or Eulerian space-fixed grids.

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

NASA Astrophysics Data System (ADS)

Zhou, Da; Qian, Hong

2011-09-01

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

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence

PubMed Central

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D.

2015-01-01

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. PMID:25761710

IRVE-II Post-Flight Trajectory Reconstruction

NASA Technical Reports Server (NTRS)

O'Keefe, Stephen A.; Bose, David M.

2010-01-01

NASA s Inflatable Re-entry Vehicle Experiment (IRVE) II successfully demonstrated an inflatable aerodynamic decelerator after being launched aboard a sounding rocket from Wallops Flight Facility (WFF). Preliminary day of flight data compared well with pre-flight Monte Carlo analysis, and a more complete trajectory reconstruction performed with an Extended Kalman Filter (EKF) approach followed. The reconstructed trajectory and comparisons to an attitude solution provided by NASA Sounding Rocket Operations Contract (NSROC) personnel at WFF are presented. Additional comparisons are made between the reconstructed trajectory and pre and post-flight Monte Carlo trajectory predictions. Alternative observations of the trajectory are summarized which leverage flight accelerometer measurements, the pre-flight aerodynamic database, and on-board flight video. Finally, analysis of the payload separation and aeroshell deployment events are presented. The flight trajectory is reconstructed to fidelity sufficient to assess overall project objectives related to flight dynamics and overall, IRVE-II flight dynamics are in line with expectations

Nonlinear dynamic analysis and optimal trajectory planning of a high-speed macro-micro manipulator

NASA Astrophysics Data System (ADS)

Yang, Yi-ling; Wei, Yan-ding; Lou, Jun-qiang; Fu, Lei; Zhao, Xiao-wei

2017-09-01

This paper reports the nonlinear dynamic modeling and the optimal trajectory planning for a flexure-based macro-micro manipulator, which is dedicated to the large-scale and high-speed tasks. In particular, a macro- micro manipulator composed of a servo motor, a rigid arm and a compliant microgripper is focused. Moreover, both flexure hinges and flexible beams are considered. By combining the pseudorigid-body-model method, the assumed mode method and the Lagrange equation, the overall dynamic model is derived. Then, the rigid-flexible-coupling characteristics are analyzed by numerical simulations. After that, the microscopic scale vibration excited by the large-scale motion is reduced through the trajectory planning approach. Especially, a fitness function regards the comprehensive excitation torque of the compliant microgripper is proposed. The reference curve and the interpolation curve using the quintic polynomial trajectories are adopted. Afterwards, an improved genetic algorithm is used to identify the optimal trajectory by minimizing the fitness function. Finally, the numerical simulations and experiments validate the feasibility and the effectiveness of the established dynamic model and the trajectory planning approach. The amplitude of the residual vibration reduces approximately 54.9%, and the settling time decreases 57.1%. Therefore, the operation efficiency and manipulation stability are significantly improved.

Geometric quadratic stochastic operator on countable infinite set

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

Ganikhodjaev, Nasir; Hamzah, Nur Zatul Akmar

2015-02-03

In this paper we construct the family of Geometric quadratic stochastic operators defined on the countable sample space of nonnegative integers and investigate their trajectory behavior. Such operators can be reinterpreted in terms of of evolutionary operator of free population. We show that Geometric quadratic stochastic operators are regular transformations.

Evolutionary genetics of maternal effects

PubMed Central

Wolf, Jason B.; Wade, Michael J.

2016-01-01

Maternal genetic effects (MGEs), where genes expressed by mothers affect the phenotype of their offspring, are important sources of phenotypic diversity in a myriad of organisms. We use a single‐locus model to examine how MGEs contribute patterns of heritable and nonheritable variation and influence evolutionary dynamics in randomly mating and inbreeding populations. We elucidate the influence of MGEs by examining the offspring genotype‐phenotype relationship, which determines how MGEs affect evolutionary dynamics in response to selection on offspring phenotypes. This approach reveals important results that are not apparent from classic quantitative genetic treatments of MGEs. We show that additive and dominance MGEs make different contributions to evolutionary dynamics and patterns of variation, which are differentially affected by inbreeding. Dominance MGEs make the offspring genotype‐phenotype relationship frequency dependent, resulting in the appearance of negative frequency‐dependent selection, while additive MGEs contribute a component of parent‐of‐origin dependent variation. Inbreeding amplifies the contribution of MGEs to the additive genetic variance and, therefore enhances their evolutionary response. Considering evolutionary dynamics of allele frequency change on an adaptive landscape, we show that this landscape differs from the mean fitness surface, and therefore, under some condition, fitness peaks can exist but not be “available” to the evolving population. PMID:26969266

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence

PubMed Central

McLeish, Tom C. B.

2015-01-01

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity—the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity—essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution. PMID:26640648

Are there ergodic limits to evolution? Ergodic exploration of genome space and convergence.

PubMed

McLeish, Tom C B

2015-12-06

We examine the analogy between evolutionary dynamics and statistical mechanics to include the fundamental question of ergodicity-the representative exploration of the space of possible states (in the case of evolution this is genome space). Several properties of evolutionary dynamics are identified that allow a generalization of the ergodic dynamics, familiar in dynamical systems theory, to evolution. Two classes of evolved biological structure then arise, differentiated by the qualitative duration of their evolutionary time scales. The first class has an ergodicity time scale (the time required for representative genome exploration) longer than available evolutionary time, and has incompletely explored the genotypic and phenotypic space of its possibilities. This case generates no expectation of convergence to an optimal phenotype or possibility of its prediction. The second, more interesting, class exhibits an evolutionary form of ergodicity-essentially all of the structural space within the constraints of slower evolutionary variables have been sampled; the ergodicity time scale for the system evolution is less than the evolutionary time. In this case, some convergence towards similar optima may be expected for equivalent systems in different species where both possess ergodic evolutionary dynamics. When the fitness maximum is set by physical, rather than co-evolved, constraints, it is additionally possible to make predictions of some properties of the evolved structures and systems. We propose four structures that emerge from evolution within genotypes whose fitness is induced from their phenotypes. Together, these result in an exponential speeding up of evolution, when compared with complete exploration of genomic space. We illustrate a possible case of application and a prediction of convergence together with attaining a physical fitness optimum in the case of invertebrate compound eye resolution.

Multiobjective Optimization of Low-Energy Trajectories Using Optimal Control on Dynamical Channels

NASA Technical Reports Server (NTRS)

Coffee, Thomas M.; Anderson, Rodney L.; Lo, Martin W.

2011-01-01

We introduce a computational method to design efficient low-energy trajectories by extracting initial solutions from dynamical channels formed by invariant manifolds, and improving these solutions through variational optimal control. We consider trajectories connecting two unstable periodic orbits in the circular restricted 3-body problem (CR3BP). Our method leverages dynamical channels to generate a range of solutions, and approximates the areto front for impulse and time of flight through a multiobjective optimization of these solutions based on primer vector theory. We demonstrate the application of our method to a libration orbit transfer in the Earth-Moon system.

Individual heterogeneity in life histories and eco-evolutionary dynamics

PubMed Central

Vindenes, Yngvild; Langangen, Øystein

2015-01-01

Individual heterogeneity in life history shapes eco-evolutionary processes, and unobserved heterogeneity can affect demographic outputs characterising life history and population dynamical properties. Demographic frameworks like matrix models or integral projection models represent powerful approaches to disentangle mechanisms linking individual life histories and population-level processes. Recent developments have provided important steps towards their application to study eco-evolutionary dynamics, but so far individual heterogeneity has largely been ignored. Here, we present a general demographic framework that incorporates individual heterogeneity in a flexible way, by separating static and dynamic traits (discrete or continuous). First, we apply the framework to derive the consequences of ignoring heterogeneity for a range of widely used demographic outputs. A general conclusion is that besides the long-term growth rate lambda, all parameters can be affected. Second, we discuss how the framework can help advance current demographic models of eco-evolutionary dynamics, by incorporating individual heterogeneity. For both applications numerical examples are provided, including an empirical example for pike. For instance, we demonstrate that predicted demographic responses to climate warming can be reversed by increased heritability. We discuss how applications of this demographic framework incorporating individual heterogeneity can help answer key biological questions that require a detailed understanding of eco-evolutionary dynamics. PMID:25807980

Unexpected Nongenetic Individual Heterogeneity and Trait Covariance in Daphnia and Its Consequences for Ecological and Evolutionary Dynamics.

PubMed

Cressler, Clayton E; Bengtson, Stefan; Nelson, William A

2017-07-01

Individual differences in genetics, age, or environment can cause tremendous differences in individual life-history traits. This individual heterogeneity generates demographic heterogeneity at the population level, which is predicted to have a strong impact on both ecological and evolutionary dynamics. However, we know surprisingly little about the sources of individual heterogeneity for particular taxa or how different sources scale up to impact ecological and evolutionary dynamics. Here we experimentally study the individual heterogeneity that emerges from both genetic and nongenetic sources in a species of freshwater zooplankton across a large gradient of food quality. Despite the tight control of environment, we still find that the variation from nongenetic sources is greater than that from genetic sources over a wide range of food quality and that this variation has strong positive covariance between growth and reproduction. We evaluate the general consequences of genetic and nongenetic covariance for ecological and evolutionary dynamics theoretically and find that increasing nongenetic variation slows evolution independent of the correlation in heritable life-history traits but that the impact on ecological dynamics depends on both nongenetic and genetic covariance. Our results demonstrate that variation in the relative magnitude of nongenetic versus genetic sources of variation impacts the predicted ecological and evolutionary dynamics.

The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy.

PubMed

Trauner, Andrej; Liu, Qingyun; Via, Laura E; Liu, Xin; Ruan, Xianglin; Liang, Lili; Shi, Huimin; Chen, Ying; Wang, Ziling; Liang, Ruixia; Zhang, Wei; Wei, Wang; Gao, Jingcai; Sun, Gang; Brites, Daniela; England, Kathleen; Zhang, Guolong; Gagneux, Sebastien; Barry, Clifton E; Gao, Qian

2017-04-19

Combination therapy is one of the most effective tools for limiting the emergence of drug resistance in pathogens. Despite the widespread adoption of combination therapy across diseases, drug resistance rates continue to rise, leading to failing treatment regimens. The mechanisms underlying treatment failure are well studied, but the processes governing successful combination therapy are poorly understood. We address this question by studying the population dynamics of Mycobacterium tuberculosis within tuberculosis patients undergoing treatment with different combinations of antibiotics. By combining very deep whole genome sequencing (~1000-fold genome-wide coverage) with sequential sputum sampling, we were able to detect transient genetic diversity driven by the apparently continuous turnover of minor alleles, which could serve as the source of drug-resistant bacteria. However, we report that treatment efficacy has a clear impact on the population dynamics: sufficient drug pressure bears a clear signature of purifying selection leading to apparent genetic stability. In contrast, M. tuberculosis populations subject to less drug pressure show markedly different dynamics, including cases of acquisition of additional drug resistance. Our findings show that for a pathogen like M. tuberculosis, which is well adapted to the human host, purifying selection constrains the evolutionary trajectory to resistance in effectively treated individuals. Nonetheless, we also report a continuous turnover of minor variants, which could give rise to the emergence of drug resistance in cases of drug pressure weakening. Monitoring bacterial population dynamics could therefore provide an informative metric for assessing the efficacy of novel drug combinations.

An Energy-Aware Trajectory Optimization Layer for sUAS

NASA Astrophysics Data System (ADS)

Silva, William A.

The focus of this work is the implementation of an energy-aware trajectory optimization algorithm that enables small unmanned aircraft systems (sUAS) to operate in unknown, dynamic severe weather environments. The software is designed as a component of an Energy-Aware Dynamic Data Driven Application System (EA-DDDAS) for sUAS. This work addresses the challenges of integrating and executing an online trajectory optimization algorithm during mission operations in the field. Using simplified aircraft kinematics, the energy-aware algorithm enables extraction of kinetic energy from measured winds to optimize thrust use and endurance during flight. The optimization layer, based upon a nonlinear program formulation, extracts energy by exploiting strong wind velocity gradients in the wind field, a process known as dynamic soaring. The trajectory optimization layer extends the energy-aware path planner developed by Wenceslao Shaw-Cortez te{Shaw-cortez2013} to include additional mission configurations, simulations with a 6-DOF model, and validation of the system with flight testing in June 2015 in Lubbock, Texas. The trajectory optimization layer interfaces with several components within the EA-DDDAS to provide an sUAS with optimal flight trajectories in real-time during severe weather. As a result, execution timing, data transfer, and scalability are considered in the design of the software. Severe weather also poses a measure of unpredictability to the system with respect to communication between systems and available data resources during mission operations. A heuristic mission tree with different cost functions and constraints is implemented to provide a level of adaptability to the optimization layer. Simulations and flight experiments are performed to assess the efficacy of the trajectory optimization layer. The results are used to assess the feasibility of flying dynamic soaring trajectories with existing controllers as well as to verify the interconnections between EA-DDDAS components. Results also demonstrate the usage of the trajectory optimization layer in conjunction with a lattice-based path planner as a method of guiding the optimization layer and stitching together subsequent trajectories.

Fractional dynamics using an ensemble of classical trajectories

NASA Astrophysics Data System (ADS)

Sun, Zhaopeng; Dong, Hao; Zheng, Yujun

2018-01-01

A trajectory-based formulation for fractional dynamics is presented and the trajectories are generated deterministically. In this theoretical framework, we derive a new class of estimators in terms of confluent hypergeometric function (F11) to represent the Riesz fractional derivative. Using this method, the simulation of free and confined Lévy flight are in excellent agreement with the exact numerical and analytical results. In addition, the barrier crossing in a bistable potential driven by Lévy noise of index α is investigated. In phase space, the behavior of trajectories reveal the feature of Lévy flight in a better perspective.

The evolutionary time machine: forecasting how populations can adapt to changing environments using dormant propagules

PubMed Central

Orsini, Luisa; Schwenk, Klaus; De Meester, Luc; Colbourne, John K.; Pfrender, Michael E.; Weider, Lawrence J.

2013-01-01

Evolutionary changes are determined by a complex assortment of ecological, demographic and adaptive histories. Predicting how evolution will shape the genetic structures of populations coping with current (and future) environmental challenges has principally relied on investigations through space, in lieu of time, because long-term phenotypic and molecular data are scarce. Yet, dormant propagules in sediments, soils and permafrost are convenient natural archives of population-histories from which to trace adaptive trajectories along extended time periods. DNA sequence data obtained from these natural archives, combined with pioneering methods for analyzing both ecological and population genomic time-series data, are likely to provide predictive models to forecast evolutionary responses of natural populations to environmental changes resulting from natural and anthropogenic stressors, including climate change. PMID:23395434

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.

Classification and Lineage Tracing of SH2 Domains Throughout Eukaryotes.

PubMed

Liu, Bernard A

2017-01-01

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

Evolutionary models of interstellar chemistry

NASA Technical Reports Server (NTRS)

Prasad, Sheo S.

1987-01-01

The goal of evolutionary models of interstellar chemistry is to understand how interstellar clouds came to be the way they are, how they will change with time, and to place them in an evolutionary sequence with other celestial objects such as stars. An improved Mark II version of an earlier model of chemistry in dynamically evolving clouds is presented. The Mark II model suggests that the conventional elemental C/O ratio less than one can explain the observed abundances of CI and the nondetection of O2 in dense clouds. Coupled chemical-dynamical models seem to have the potential to generate many observable discriminators of the evolutionary tracks. This is exciting, because, in general, purely dynamical models do not yield enough verifiable discriminators of the predicted tracks.

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

Optimization of fixed-range trajectories for supersonic transport aircraft

NASA Astrophysics Data System (ADS)

Windhorst, Robert Dennis

1999-11-01

This thesis develops near-optimal guidance laws that generate minimum fuel, time, or direct operating cost fixed-range trajectories for supersonic transport aircraft. The approach uses singular perturbation techniques to time-scale de-couple the equations of motion into three sets of dynamics, two of which are analyzed in the main body of this thesis and one of which is analyzed in the Appendix. The two-point-boundary-value-problems obtained by application of the maximum principle to the dynamic systems are solved using the method of matched asymptotic expansions. Finally, the two solutions are combined using the matching principle and an additive composition rule to form a uniformly valid approximation of the full fixed-range trajectory. The approach is used on two different time-scale formulations. The first holds weight constant, and the second allows weight and range dynamics to propagate on the same time-scale. Solutions for the first formulation are only carried out to zero order in the small parameter, while solutions for the second formulation are carried out to first order. Calculations for a HSCT design were made to illustrate the method. Results show that the minimum fuel trajectory consists of three segments: a minimum fuel energy-climb, a cruise-climb, and a minimum drag glide. The minimum time trajectory also has three segments: a maximum dynamic pressure ascent, a constant altitude cruise, and a maximum dynamic pressure glide. The minimum direct operating cost trajectory is an optimal combination of the two. For realistic costs of fuel and flight time, the minimum direct operating cost trajectory is very similar to the minimum fuel trajectory. Moreover, the HSCT has three local optimum cruise speeds, with the globally optimum cruise point at the highest allowable speed, if range is sufficiently long. The final range of the trajectory determines which locally optimal speed is best. Ranges of 500 to 6,000 nautical miles, subsonic and supersonic mixed flight, and varying fuel efficiency cases are analyzed. Finally, the payload-range curve of the HSCT design is determined.

Mapping quantum-classical Liouville equation: projectors and trajectories.

PubMed

Kelly, Aaron; van Zon, Ramses; Schofield, Jeremy; Kapral, Raymond

2012-02-28

The evolution of a mixed quantum-classical system is expressed in the mapping formalism where discrete quantum states are mapped onto oscillator states, resulting in a phase space description of the quantum degrees of freedom. By defining projection operators onto the mapping states corresponding to the physical quantum states, it is shown that the mapping quantum-classical Liouville operator commutes with the projection operator so that the dynamics is confined to the physical space. It is also shown that a trajectory-based solution of this equation can be constructed that requires the simulation of an ensemble of entangled trajectories. An approximation to this evolution equation which retains only the Poisson bracket contribution to the evolution operator does admit a solution in an ensemble of independent trajectories but it is shown that this operator does not commute with the projection operators and the dynamics may take the system outside the physical space. The dynamical instabilities, utility, and domain of validity of this approximate dynamics are discussed. The effects are illustrated by simulations on several quantum systems.

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles.

PubMed

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F; Perez, Danny

2017-10-21

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Cluster analysis of accelerated molecular dynamics simulations: A case study of the decahedron to icosahedron transition in Pt nanoparticles

NASA Astrophysics Data System (ADS)

Huang, Rao; Lo, Li-Ta; Wen, Yuhua; Voter, Arthur F.; Perez, Danny

2017-10-01

Modern molecular-dynamics-based techniques are extremely powerful to investigate the dynamical evolution of materials. With the increase in sophistication of the simulation techniques and the ubiquity of massively parallel computing platforms, atomistic simulations now generate very large amounts of data, which have to be carefully analyzed in order to reveal key features of the underlying trajectories, including the nature and characteristics of the relevant reaction pathways. We show that clustering algorithms, such as the Perron Cluster Cluster Analysis, can provide reduced representations that greatly facilitate the interpretation of complex trajectories. To illustrate this point, clustering tools are used to identify the key kinetic steps in complex accelerated molecular dynamics trajectories exhibiting shape fluctuations in Pt nanoclusters. This analysis provides an easily interpretable coarse representation of the reaction pathways in terms of a handful of clusters, in contrast to the raw trajectory that contains thousands of unique states and tens of thousands of transitions.

Optimization of dynamic soaring maneuvers to enhance endurance of a versatile UAV

NASA Astrophysics Data System (ADS)

Mir, Imran; Maqsood, Adnan; Akhtar, Suhail

2017-06-01

Dynamic soaring is a process of acquiring energy available in atmospheric wind shears and is commonly exhibited by soaring birds to perform long distance flights. This paper aims to demonstrate a viable algorithm which can be implemented in near real time environment to formulate optimal trajectories for dynamic soaring maneuvers for a small scale Unmanned Aerial Vehicle (UAV). The objective is to harness maximum energy from atmosphere wind shear to improve loiter time for Intelligence, Surveillance and Reconnaissance (ISR) missions. Three-dimensional point-mass UAV equations of motion and linear wind gradient profile are used to model flight dynamics. Utilizing UAV states, controls, operational constraints, initial and terminal conditions that enforce a periodic flight, dynamic soaring problem is formulated as an optimal control problem. Optimized trajectories of the maneuver are subsequently generated employing pseudo spectral techniques against distant UAV performance parameters. The discussion also encompasses the requirement for generation of optimal trajectories for dynamic soaring in real time environment and the ability of the proposed algorithm for speedy solution generation. Coupled with the fact that dynamic soaring is all about immediately utilizing the available energy from the wind shear encountered, the proposed algorithm promises its viability for practical on board implementations requiring computation of trajectories in near real time.

Zero-Point Energy Constraint for Unimolecular Dissociation Reactions. Giving Trajectories Multiple Chances To Dissociate Correctly.

PubMed

Paul, Amit K; Hase, William L

2016-01-28

A zero-point energy (ZPE) constraint model is proposed for classical trajectory simulations of unimolecular decomposition and applied to CH4* → H + CH3 decomposition. With this model trajectories are not allowed to dissociate unless they have ZPE in the CH3 product. If not, they are returned to the CH4* region of phase space and, if necessary, given additional opportunities to dissociate with ZPE. The lifetime for dissociation of an individual trajectory is the time it takes to dissociate with ZPE in CH3, including multiple possible returns to CH4*. With this ZPE constraint the dissociation of CH4* is exponential in time as expected for intrinsic RRKM dynamics and the resulting rate constant is in good agreement with the harmonic quantum value of RRKM theory. In contrast, a model that discards trajectories without ZPE in the reaction products gives a CH4* → H + CH3 rate constant that agrees with the classical and not quantum RRKM value. The rate constant for the purely classical simulation indicates that anharmonicity may be important and the rate constant from the ZPE constrained classical trajectory simulation may not represent the complete anharmonicity of the RRKM quantum dynamics. The ZPE constraint model proposed here is compared with previous models for restricting ZPE flow in intramolecular dynamics, and connecting product and reactant/product quantum energy levels in chemical dynamics simulations.

Trajectory design strategies that incorporate invariant manifolds and swingby

NASA Technical Reports Server (NTRS)

Guzman, J. J.; Cooley, D. S.; Howell, K. C.; Folta, D. C.

1998-01-01

Libration point orbits serve as excellent platforms for scientific investigations involving the Sun as well as planetary environments. Trajectory design in support of such missions is increasingly challenging as more complex missions are envisioned in the next few decades. Software tools for trajectory design in this regime must be further developed to incorporate better understanding of the solution space and, thus, improve the efficiency and expand the capabilities of current approaches. Only recently applied to trajectory design, dynamical systems theory now offers new insights into the natural dynamics associated with the multi-body problem. The goal of this effort is the blending of analysis from dynamical systems theory with the well established NASA Goddard software program SWINGBY to enhance and expand the capabilities for mission design. Basic knowledge concerning the solution space is improved as well.

Demographic source-sink dynamics restrict local adaptation in Elliott's blueberry (Vaccinium elliottii).

PubMed

Anderson, Jill T; Geber, Monica A

2010-02-01

In heterogeneous landscapes, divergent selection can favor the evolution of locally adapted ecotypes, especially when interhabitat gene flow is minimal. However, if habitats differ in size or quality, source-sink dynamics can shape evolutionary trajectories. Upland and bottomland forests of the southeastern USA differ in water table depth, light availability, edaphic conditions, and plant community. We conducted a multiyear reciprocal transplant experiment to test whether Elliott's blueberry (Vaccinium elliottii) is locally adapted to these contrasting environments. Additionally, we exposed seedlings and cuttings to prolonged drought and flooding in the greenhouse to assess fitness responses to abiotic stress. Contrary to predictions of local adaptation, V. elliottii families exhibited significantly higher survivorship and growth in upland than in bottomland forests and under drought than flooded conditions, regardless of habitat of origin. Neutral population differentiation was minimal, suggesting widespread interhabitat migration. Population density, reproductive output, and genetic diversity were all significantly greater in uplands than in bottomlands. These disparities likely result in asymmetric gene flow from uplands to bottomlands. Thus, adaptation to a marginal habitat can be constrained by small populations, limited fitness, and immigration from a benign habitat. Our study highlights the importance of demography and genetic diversity in the evolution of local (mal)adaptation.

Bio-inspired energy-harvesting mechanisms and patterns of dynamic soaring.

PubMed

Liu, Duo-Neng; Hou, Zhong-Xi; Guo, Zheng; Yang, Xi-Xiang; Gao, Xian-Zhong

2017-01-30

Albatrosses can make use of the dynamic soaring technique extracting energy from the wind field to achieve large-scale movement without a flap, which stimulates interest in effortless flight with small unmanned aerial vehicles (UAVs). However, mechanisms of energy harvesting in terms of the energy transfer from the wind to the flyer (albatross or UAV) are still indeterminate and controversial when using different reference frames in previous studies. In this paper, the classical four-phase Rayleigh cycle, includes sequentially upwind climb, downwind turn, downwind dive and upwind turn, is introduced in analyses of energy gain with the albatross's equation of motions and the simulated trajectory in dynamic soaring. Analytical and numerical results indicate that the energy gain in the air-relative frame mostly originates from large wind gradients at lower part of the climb and dive, while the energy gain in the inertial frame comes from the lift vector inclined to the wind speed direction during the climb, dive and downwind turn at higher altitude. These two energy-gain mechanisms are not equivalent in terms of energy sources and reference frames but have to be simultaneously satisfied in terms of the energy-neutral dynamic soaring cycle. For each reference frame, energy-loss phases are necessary to connect energy-gain ones. Based on these four essential phases in dynamic soaring and the albatrosses' flight trajectory, different dynamic soaring patterns are schematically depicted and corresponding optimal trajectories are computed. The optimal dynamic soaring trajectories are classified into two closed patterns including 'O' shape and '8' shape, and four travelling patterns including 'Ω' shape, 'α' shape, 'C' shape and 'S' shape. The correlation among these patterns are analysed and discussed. The completeness of the classification for different patterns is confirmed by listing and summarising dynamic soaring trajectories shown in studies over the past decades.

Evolutionary Trajectories in School Assessment Systems: The Case of Bhutan

ERIC Educational Resources Information Center

Maxwell, Tom W.; Rinchen, Phub; Cooksey, Ray

2010-01-01

The purpose of this paper is to trace the evolution of school assessment in Bhutan, briefly, as a background to considering the present and future school assessment issues especially as they relate to quality concerns and educational improvement in Bhutan. A benchmark for Bhutan, the National Educational Assessment (NEA) programme in Bhutan was…

Experimental evidence for the evolution of indirect genetic effects: changes in the interaction effect coefficient, psi (Psi), due to sexual selection.

PubMed

Chenoweth, Stephen F; Rundle, Howard D; Blows, Mark W

2010-06-01

Indirect genetics effects (IGEs)--when the genotype of one individual affects the phenotypic expression of a trait in another--may alter evolutionary trajectories beyond that predicted by standard quantitative genetic theory as a consequence of genotypic evolution of the social environment. For IGEs to occur, the trait of interest must respond to one or more indicator traits in interacting conspecifics. In quantitative genetic models of IGEs, these responses (reaction norms) are termed interaction effect coefficients and are represented by the parameter psi (Psi). The extent to which Psi exhibits genetic variation within a population, and may therefore itself evolve, is unknown. Using an experimental evolution approach, we provide evidence for a genetic basis to the phenotypic response caused by IGEs on sexual display traits in Drosophila serrata. We show that evolution of the response is affected by sexual but not natural selection when flies adapt to a novel environment. Our results indicate a further mechanism by which IGEs can alter evolutionary trajectories--the evolution of interaction effects themselves.

Evolutionary Maps: A new model for the analysis of conceptual development, with application to the diurnal cycle

NASA Astrophysics Data System (ADS)

Navarro, Manuel

2014-05-01

This paper presents a model of how children generate concrete concepts from perception through processes of differentiation and integration. The model informs the design of a novel methodology (evolutionary maps or emaps), whose implementation on certain domains unfolds the web of itineraries that children may follow in the construction of concrete conceptual knowledge and pinpoints, for each conception, the architecture of the conceptual change that leads to the scientific concept. Remarkably, the generative character of its syntax yields conceptions that, if unknown, amount to predictions that can be tested experimentally. Its application to the diurnal cycle (including the sun's trajectory in the sky) indicates that the model is correct and the methodology works (in some domains). Specifically, said emap predicts a number of exotic trajectories of the sun in the sky that, in the experimental work, were drawn spontaneously both on paper and a dome. Additionally, the application of the emaps theoretical framework in clinical interviews has provided new insight into other cognitive processes. The field of validity of the methodology and its possible applications to science education are discussed.

Emulation of rocket trajectory based on a six degree of freedom model

NASA Astrophysics Data System (ADS)

Zhang, Wenpeng; Li, Fan; Wu, Zhong; Li, Rong

2008-10-01

In this paper, a 6-DOF motion mathematical model is discussed. It is consisted of body dynamics and kinematics block, aero dynamics block and atmosphere block. Based on Simulink, the whole rocket trajectory mathematical model is developed. In this model, dynamic system simulation becomes easy and visual. The method of modularization design gives more convenience to transplant. At last, relevant data is given to be validated by Monte Carlo means. Simulation results show that the flight trajectory of the rocket can be simulated preferably by means of this model, and it also supplies a necessary simulating tool for the development of control system.

Trajectories of Depressive Symptoms Among a Population of HIV-Infected Men and Women in Routine HIV Care in the United States.

PubMed

Bengtson, Angela M; Pence, Brian W; Powers, Kimberly A; Weaver, Mark A; Mimiaga, Matthew J; Gaynes, Bradley N; O'Cleirigh, Conall; Christopoulos, Katerina; Christopher Mathews, W; Crane, Heidi; Mugavero, Michael

2018-04-06

Depressive symptoms vary in severity and chronicity. We used group-based trajectory models to describe trajectories of depressive symptoms (measured using the Patient Health Questionnaire-9) and predictors of trajectory group membership among 1493 HIV-infected men (84%) and 292 HIV-infected women (16%). At baseline, 29% of women and 26% of men had depressive symptoms. Over a median of 30 months of follow-up, we identified four depressive symptom trajectories for women (labeled "low" [experienced by 56% of women], "mild/moderate" [24%], "improving" [14%], and "severe" [6%]) and five for men ("low" [61%], "mild/moderate" [14%], "rebounding" [5%], "improving" [13%], and "severe" [7%]). Baseline antidepressant prescription, panic symptoms, and prior mental health diagnoses were associated with more severe or dynamic depressive symptom trajectories. Nearly a quarter of participants experienced some depressive symptoms, highlighting the need for improved depression management. Addressing more severe or dynamic depressive symptom trajectories may require interventions that additionally address mental health comorbidities.

Direct dynamics trajectory study of the reaction of formaldehyde cation with D2: vibrational and zero-point energy effects on quasiclassical trajectories.

PubMed

Liu, Jianbo; Song, Kihyung; Hase, William L; Anderson, Scott L

2005-12-22

Quasiclassical, direct dynamics trajectories have been used to study the reaction of formaldehyde cation with molecular hydrogen, simulating the conditions in an experimental study of H2CO+ vibrational effects on this reaction. Effects of five different H2CO+ modes were probed, and we also examined different approaches to treating zero-point energy in quasiclassical trajectories. The calculated absolute cross-sections are in excellent agreement with experiments, and the results provide insight into the reaction mechanism, product scattering behavior, and energy disposal, and how they vary with impact parameter and reactant state. The reaction is sharply orientation-dependent, even at high collision energies, and both trajectories and experiment find that H2CO+ vibration inhibits reaction. On the other hand, the trajectories do not reproduce the anomalously strong effect of nu2(+) (the CO stretch). The origin of the discrepancy and approaches for minimizing such problems in quasiclassical trajectories are discussed.

Convergence analysis of sliding mode trajectories in multi-objective neural networks learning.

PubMed

Costa, Marcelo Azevedo; Braga, Antonio Padua; de Menezes, Benjamin Rodrigues

2012-09-01

The Pareto-optimality concept is used in this paper in order to represent a constrained set of solutions that are able to trade-off the two main objective functions involved in neural networks supervised learning: data-set error and network complexity. The neural network is described as a dynamic system having error and complexity as its state variables and learning is presented as a process of controlling a learning trajectory in the resulting state space. In order to control the trajectories, sliding mode dynamics is imposed to the network. It is shown that arbitrary learning trajectories can be achieved by maintaining the sliding mode gains within their convergence intervals. Formal proofs of convergence conditions are therefore presented. The concept of trajectory learning presented in this paper goes further beyond the selection of a final state in the Pareto set, since it can be reached through different trajectories and states in the trajectory can be assessed individually against an additional objective function. Copyright © 2012 Elsevier Ltd. All rights reserved.

Genetic implications of bottleneck effects of differing severities on genetic diversity in naturally recovering populations: An example from Hawaiian coot and Hawaiian gallinule

USGS Publications Warehouse

Sonsthagen, Sarah A.; Wilson, Robert E.; Underwood, Jared G.

2017-01-01

The evolutionary trajectory of populations through time is influenced by the interplay of forces (biological, evolutionary, and anthropogenic) acting on the standing genetic variation. We used microsatellite and mitochondrial loci to examine the influence of population declines, of varying severity, on genetic diversity within two Hawaiian endemic waterbirds, the Hawaiian coot and Hawaiian gallinule, by comparing historical (samples collected in the late 1800s and early 1900s) and modern (collected in 2012–2013) populations. Population declines simultaneously experienced by Hawaiian coots and Hawaiian gallinules differentially shaped the evolutionary trajectory of these two populations. Within Hawaiian coot, large reductions (between −38.4% and −51.4%) in mitochondrial diversity were observed, although minimal differences were observed in the distribution of allelic and haplotypic frequencies between sampled time periods. Conversely, for Hawaiian gallinule, allelic frequencies were strongly differentiated between time periods, signatures of a genetic bottleneck were detected, and biases in means of the effective population size were observed at microsatellite loci. The strength of the decline appears to have had a greater influence on genetic diversity within Hawaiian gallinule than Hawaiian coot, coincident with the reduction in census size. These species exhibit similar life history characteristics and generation times; therefore, we hypothesize that differences in behavior and colonization history are likely playing a large role in how allelic and haplotypic frequencies are being shaped through time. Furthermore, differences in patterns of genetic diversity within Hawaiian coot and Hawaiian gallinule highlight the influence of demographic and evolutionary processes in shaping how species respond genetically to ecological stressors.

Optimization of Insertion Cost for Transfer Trajectories to Libration Point Orbits

NASA Technical Reports Server (NTRS)

Howell, K. C.; Wilson, R. S.; Lo, M. W.

1999-01-01

The objective of this work is the development of efficient techniques to optimize the cost associated with transfer trajectories to libration point orbits in the Sun-Earth-Moon four body problem, that may include lunar gravity assists. Initially, dynamical systems theory is used to determine invariant manifolds associated with the desired libration point orbit. These manifolds are employed to produce an initial approximation to the transfer trajectory. Specific trajectory requirements such as, transfer injection constraints, inclusion of phasing loops, and targeting of a specified state on the manifold are then incorporated into the design of the transfer trajectory. A two level differential corrections process is used to produce a fully continuous trajectory that satisfies the design constraints, and includes appropriate lunar and solar gravitational models. Based on this methodology, and using the manifold structure from dynamical systems theory, a technique is presented to optimize the cost associated with insertion onto a specified libration point orbit.

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

Heslar, John; Chu, Shih-I.

Recently, the study of near- and below- threshold regime harmonics as a potential source of intense coherent vacuum-ultraviolet radiation has received considerable attention. However, the dynamical origin of these lower harmonics, particularly for the molecular systems, is less understood and largely unexplored. Here we perform the first fully ab initio and high precision 3D quantum study of the below- and near-threshold harmonic generation of H 2 + molecules in an intense 800-nm near-infrared (NIR) laser field. Furthermore, combining with a synchrosqueezing transform of the quantum time-frequency spectrum and an extended semiclassical analysis, we explore in-depth the roles of various quantummore » trajectories, including short- and long trajectories, multiphoton trajectories, resonance-enhanced trajectories, and multiple rescattering trajectories of the below- and near- threshold harmonic generation processes. Our results shed new light on the dynamical origin of the below- and near-threshold harmonic generation and various quantum trajectories for diatomic molecules for the first time.« less

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs.

PubMed

Stollmeier, Frank; Nagler, Jan

2018-02-02

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair," meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the prisoner's dilemma, and an unexpected selection reversal in the hawk-dove game.

Unfair and Anomalous Evolutionary Dynamics from Fluctuating Payoffs

NASA Astrophysics Data System (ADS)

Stollmeier, Frank; Nagler, Jan

2018-02-01

Evolution occurs in populations of reproducing individuals. Reproduction depends on the payoff a strategy receives. The payoff depends on the environment that may change over time, on intrinsic uncertainties, and on other sources of randomness. These temporal variations in the payoffs can affect which traits evolve. Understanding evolutionary game dynamics that are affected by varying payoffs remains difficult. Here we study the impact of arbitrary amplitudes and covariances of temporally varying payoffs on the dynamics. The evolutionary dynamics may be "unfair," meaning that, on average, two coexisting strategies may persistently receive different payoffs. This mechanism can induce an anomalous coexistence of cooperators and defectors in the prisoner's dilemma, and an unexpected selection reversal in the hawk-dove game.

Principles and Algorithms for Natural and Engineered Systems

DTIC Science & Technology

2014-12-16

Toolbox for MATLAB into C/C++. The target for the calibration is a 2D black and white checkerboard pattern. In a typical set of calibration images...errors the dynamic clusters typically contain entangled trajectories i.e. links form between two different dynamic clusters (see Figures 8 and 9). To...all dynamic clusters is L, and the average number of trajectories a given dynamic cluster are entangled with for its entire length is known as the

Observing Clonal Dynamics across Spatiotemporal Axes: A Prelude to Quantitative Fitness Models for Cancer.

PubMed

McPherson, Andrew W; Chan, Fong Chun; Shah, Sohrab P

2018-02-01

The ability to accurately model evolutionary dynamics in cancer would allow for prediction of progression and response to therapy. As a prelude to quantitative understanding of evolutionary dynamics, researchers must gather observations of in vivo tumor evolution. High-throughput genome sequencing now provides the means to profile the mutational content of evolving tumor clones from patient biopsies. Together with the development of models of tumor evolution, reconstructing evolutionary histories of individual tumors generates hypotheses about the dynamics of evolution that produced the observed clones. In this review, we provide a brief overview of the concepts involved in predicting evolutionary histories, and provide a workflow based on bulk and targeted-genome sequencing. We then describe the application of this workflow to time series data obtained for transformed and progressed follicular lymphomas (FL), and contrast the observed evolutionary dynamics between these two subtypes. We next describe results from a spatial sampling study of high-grade serous (HGS) ovarian cancer, propose mechanisms of disease spread based on the observed clonal mixtures, and provide examples of diversification through subclonal acquisition of driver mutations and convergent evolution. Finally, we state implications of the techniques discussed in this review as a necessary but insufficient step on the path to predictive modelling of disease dynamics. Copyright © 2018 Cold Spring Harbor Laboratory Press; all rights reserved.

Swing-leg trajectory of running guinea fowl suggests task-level priority of force regulation rather than disturbance rejection.

PubMed

Blum, Yvonne; Vejdani, Hamid R; Birn-Jeffery, Aleksandra V; Hubicki, Christian M; Hurst, Jonathan W; Daley, Monica A

2014-01-01

To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait) versus regulation of leg loading (for injury avoidance and economy). Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i) constant peak force, ii) constant axial impulse, or iii) perfect disturbance rejection (steady gait) in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii), and do not match the simulations optimized for disturbance rejection (priority iii). The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait. Swing-leg trajectory optimized for load regulation may facilitate economy and injury avoidance in uneven terrain.

WE-AB-209-06: Dynamic Collimator Trajectory Algorithm for Use in VMAT Treatment Deliveries

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

MacDonald, L; Thomas, C; Syme, A

2016-06-15

Purpose: To develop advanced dynamic collimator positioning algorithms for optimal beam’s-eye-view (BEV) fitting of targets in VMAT procedures, including multiple metastases stereotactic radiosurgery procedures. Methods: A trajectory algorithm was developed, which can dynamically modify the angle of the collimator as a function of VMAT control point to provide optimized collimation of target volume(s). Central to this algorithm is a concept denoted “whitespace”, defined as area within the jaw-defined BEV field, outside of the PTV, and not shielded by the MLC when fit to the PTV. Calculating whitespace at all collimator angles and every control point, a two-dimensional topographical map depictingmore » the tightness-of-fit of the MLC was generated. A variety of novel searching algorithms identified a number of candidate trajectories of continuous collimator motion. Ranking these candidate trajectories according to their accrued whitespace value produced an optimal solution for navigation of this map. Results: All trajectories were normalized to minimum possible (i.e. calculated without consideration of collimator motion constraints) accrued whitespace. On an acoustic neuroma case, a random walk algorithm generated a trajectory with 151% whitespace; random walk including a mandatory anchor point improved this to 148%; gradient search produced a trajectory with 137%; and bi-directional gradient search generated a trajectory with 130% whitespace. For comparison, a fixed collimator angle of 30° and 330° accumulated 272% and 228% of whitespace, respectively. The algorithm was tested on a clinical case with two metastases (single isocentre) and identified collimator angles that allow for simultaneous irradiation of the PTVs while minimizing normal tissue irradiation. Conclusion: Dynamic collimator trajectories have the potential to improve VMAT deliveries through increased efficiency and reduced normal tissue dose, especially in treatment of multiple cranial metastases, without significant safety concerns that hinder immediate clinical implementation.« less

Swing-Leg Trajectory of Running Guinea Fowl Suggests Task-Level Priority of Force Regulation Rather than Disturbance Rejection

PubMed Central

Blum, Yvonne; Vejdani, Hamid R.; Birn-Jeffery, Aleksandra V.; Hubicki, Christian M.; Hurst, Jonathan W.; Daley, Monica A.

2014-01-01

To achieve robust and stable legged locomotion in uneven terrain, animals must effectively coordinate limb swing and stance phases, which involve distinct yet coupled dynamics. Recent theoretical studies have highlighted the critical influence of swing-leg trajectory on stability, disturbance rejection, leg loading and economy of walking and running. Yet, simulations suggest that not all these factors can be simultaneously optimized. A potential trade-off arises between the optimal swing-leg trajectory for disturbance rejection (to maintain steady gait) versus regulation of leg loading (for injury avoidance and economy). Here we investigate how running guinea fowl manage this potential trade-off by comparing experimental data to predictions of hypothesis-based simulations of running over a terrain drop perturbation. We use a simple model to predict swing-leg trajectory and running dynamics. In simulations, we generate optimized swing-leg trajectories based upon specific hypotheses for task-level control priorities. We optimized swing trajectories to achieve i) constant peak force, ii) constant axial impulse, or iii) perfect disturbance rejection (steady gait) in the stance following a terrain drop. We compare simulation predictions to experimental data on guinea fowl running over a visible step down. Swing and stance dynamics of running guinea fowl closely match simulations optimized to regulate leg loading (priorities i and ii), and do not match the simulations optimized for disturbance rejection (priority iii). The simulations reinforce previous findings that swing-leg trajectory targeting disturbance rejection demands large increases in stance leg force following a terrain drop. Guinea fowl negotiate a downward step using unsteady dynamics with forward acceleration, and recover to steady gait in subsequent steps. Our results suggest that guinea fowl use swing-leg trajectory consistent with priority for load regulation, and not for steadiness of gait. Swing-leg trajectory optimized for load regulation may facilitate economy and injury avoidance in uneven terrain. PMID:24979750

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.

The population genetics of X-autosome synthetic lethals and steriles.

PubMed

Lachance, Joseph; Johnson, Norman A; True, John R

2011-11-01

Epistatic interactions are widespread, and many of these interactions involve combinations of alleles at different loci that are deleterious when present in the same individual. The average genetic environment of sex-linked genes differs from that of autosomal genes, suggesting that the population genetics of interacting X-linked and autosomal alleles may be complex. Using both analytical theory and computer simulations, we analyzed the evolutionary trajectories and mutation-selection balance conditions for X-autosome synthetic lethals and steriles. Allele frequencies follow a set of fundamental trajectories, and incompatible alleles are able to segregate at much higher frequencies than single-locus expectations. Equilibria exist, and they can involve fixation of either autosomal or X-linked alleles. The exact equilibrium depends on whether synthetic alleles are dominant or recessive and whether fitness effects are seen in males, females, or both sexes. When single-locus fitness effects and synthetic incompatibilities are both present, population dynamics depend on the dominance of alleles and historical contingency (i.e., whether X-linked or autosomal mutations occur first). Recessive synthetic lethality can result in high-frequency X-linked alleles, and dominant synthetic lethality can result in high-frequency autosomal alleles. Many X-autosome incompatibilities in natural populations may be cryptic, appearing to be single-locus effects because one locus is fixed. We also discuss the implications of these findings with respect to standing genetic variation and the origins of Haldane's rule.

Deterministic Evolutionary Trajectories Influence Primary Tumor Growth: TRACERx Renal.

PubMed

Turajlic, Samra; Xu, Hang; Litchfield, Kevin; Rowan, Andrew; Horswell, Stuart; Chambers, Tim; O'Brien, Tim; Lopez, Jose I; Watkins, Thomas B K; Nicol, David; Stares, Mark; Challacombe, Ben; Hazell, Steve; Chandra, Ashish; Mitchell, Thomas J; Au, Lewis; Eichler-Jonsson, Claudia; Jabbar, Faiz; Soultati, Aspasia; Chowdhury, Simon; Rudman, Sarah; Lynch, Joanna; Fernando, Archana; Stamp, Gordon; Nye, Emma; Stewart, Aengus; Xing, Wei; Smith, Jonathan C; Escudero, Mickael; Huffman, Adam; Matthews, Nik; Elgar, Greg; Phillimore, Ben; Costa, Marta; Begum, Sharmin; Ward, Sophia; Salm, Max; Boeing, Stefan; Fisher, Rosalie; Spain, Lavinia; Navas, Carolina; Grönroos, Eva; Hobor, Sebastijan; Sharma, Sarkhara; Aurangzeb, Ismaeel; Lall, Sharanpreet; Polson, Alexander; Varia, Mary; Horsfield, Catherine; Fotiadis, Nicos; Pickering, Lisa; Schwarz, Roland F; Silva, Bruno; Herrero, Javier; Luscombe, Nick M; Jamal-Hanjani, Mariam; Rosenthal, Rachel; Birkbak, Nicolai J; Wilson, Gareth A; Pipek, Orsolya; Ribli, Dezso; Krzystanek, Marcin; Csabai, Istvan; Szallasi, Zoltan; Gore, Martin; McGranahan, Nicholas; Van Loo, Peter; Campbell, Peter; Larkin, James; Swanton, Charles

2018-04-19

The evolutionary features of clear-cell renal cell carcinoma (ccRCC) have not been systematically studied to date. We analyzed 1,206 primary tumor regions from 101 patients recruited into the multi-center prospective study, TRACERx Renal. We observe up to 30 driver events per tumor and show that subclonal diversification is associated with known prognostic parameters. By resolving the patterns of driver event ordering, co-occurrence, and mutual exclusivity at clone level, we show the deterministic nature of clonal evolution. ccRCC can be grouped into seven evolutionary subtypes, ranging from tumors characterized by early fixation of multiple mutational and copy number drivers and rapid metastases to highly branched tumors with >10 subclonal drivers and extensive parallel evolution associated with attenuated progression. We identify genetic diversity and chromosomal complexity as determinants of patient outcome. Our insights reconcile the variable clinical behavior of ccRCC and suggest evolutionary potential as a biomarker for both intervention and surveillance. Copyright © 2018 Francis Crick Institute. Published by Elsevier Inc. All rights reserved.

Eco-genetic modeling of contemporary life-history evolution.

PubMed

Dunlop, Erin S; Heino, Mikko; Dieckmann, Ulf

2009-10-01

We present eco-genetic modeling as a flexible tool for exploring the course and rates of multi-trait life-history evolution in natural populations. We build on existing modeling approaches by combining features that facilitate studying the ecological and evolutionary dynamics of realistically structured populations. In particular, the joint consideration of age and size structure enables the analysis of phenotypically plastic populations with more than a single growth trajectory, and ecological feedback is readily included in the form of density dependence and frequency dependence. Stochasticity and life-history trade-offs can also be implemented. Critically, eco-genetic models permit the incorporation of salient genetic detail such as a population's genetic variances and covariances and the corresponding heritabilities, as well as the probabilistic inheritance and phenotypic expression of quantitative traits. These inclusions are crucial for predicting rates of evolutionary change on both contemporary and longer timescales. An eco-genetic model can be tightly coupled with empirical data and therefore may have considerable practical relevance, in terms of generating testable predictions and evaluating alternative management measures. To illustrate the utility of these models, we present as an example an eco-genetic model used to study harvest-induced evolution of multiple traits in Atlantic cod. The predictions of our model (most notably that harvesting induces a genetic reduction in age and size at maturation, an increase or decrease in growth capacity depending on the minimum-length limit, and an increase in reproductive investment) are corroborated by patterns observed in wild populations. The predicted genetic changes occur together with plastic changes that could phenotypically mask the former. Importantly, our analysis predicts that evolutionary changes show little signs of reversal following a harvest moratorium. This illustrates how predictions offered by eco-genetic models can enable and guide evolutionarily sustainable resource management.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2017-11-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Natural Selection as Coarsening

NASA Astrophysics Data System (ADS)

Smerlak, Matteo

2018-07-01

Analogies between evolutionary dynamics and statistical mechanics, such as Fisher's second-law-like "fundamental theorem of natural selection" and Wright's "fitness landscapes", have had a deep and fruitful influence on the development of evolutionary theory. Here I discuss a new conceptual link between evolution and statistical physics. I argue that natural selection can be viewed as a coarsening phenomenon, similar to the growth of domain size in quenched magnets or to Ostwald ripening in alloys and emulsions. In particular, I show that the most remarkable features of coarsening—scaling and self-similarity—have strict equivalents in evolutionary dynamics. This analogy has three main virtues: it brings a set of well-developed mathematical tools to bear on evolutionary dynamics; it suggests new problems in theoretical evolution; and it provides coarsening physics with a new exactly soluble model.

Effects of environmental variation on host-parasite interaction in three-spined sticklebacks (Gasterosteus aculeatus).

PubMed

Scharsack, Jörn P; Franke, Frederik; Erin, Noémi I; Kuske, Andra; Büscher, Janine; Stolz, Hendrik; Samonte, Irene E; Kurtz, Joachim; Kalbe, Martin

2016-08-01

Recent research provides accumulating evidence that the evolutionary dynamics of host-parasite adaptations strongly depend on environmental variation. In this context, the three-spined stickleback (Gasterosteus aculeatus) has become an important research model since it is distributed all over the northern hemisphere and lives in very different habitat types, ranging from marine to freshwater, were it is exposed to a huge diversity of parasites. While a majority of studies start from explorations of sticklebacks in the wild, only relatively few investigations have continued under laboratory conditions. Accordingly, it has often been described that sticklebacks differ in parasite burden between habitats, but the underlying co-evolutionary trajectories are often not well understood. With the present review, we give an overview of the most striking examples of stickleback-parasite-environment interactions discovered in the wild and discuss two model parasites which have received some attention in laboratory studies: the eye fluke Diplostomum pseudospathacaeum, for which host fish show habitat-specific levels of resistance, and the tapeworm Schistocephalus solidus, which manipulates immunity and behavior of its stickleback host to its advantage. Finally, we will concentrate on an important environmental variable, namely temperature, which has prominent effects on the activity of the immune system of ectothermic hosts and on parasite growth rates. Copyright © 2016 The Authors. Published by Elsevier GmbH.. All rights reserved.

Evolutionary Potential of an RNA Virus

PubMed Central

Makeyev, Eugene V.; Bamford, Dennis H.

2004-01-01

RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, φ6, containing a β-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another β-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for β-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins. PMID:14747576

Evolutionary potential of an RNA virus.

PubMed

Makeyev, Eugene V; Bamford, Dennis H

2004-02-01

RNA viruses are remarkably adaptable to changing environments. This is medically important because it enables pathogenic viruses to escape the immune response and chemotherapy and is of considerable theoretical interest since it allows the investigation of evolutionary processes within convenient time scales. A number of earlier studies have addressed the dynamics of adapting RNA virus populations. However, it has been difficult to monitor the trajectory of molecular changes in RNA genomes in response to selective pressures. To address the problem, we developed a novel in vitro evolution system based on a recombinant double-stranded RNA bacteriophage, phi 6, containing a beta-lactamase (bla) gene marker. Carrier-state bacterial cells are resistant to ampicillin, and after several passages, they become resistant to high concentrations of another beta-lactam antibiotic, cefotaxime, due to mutations in the virus-borne bla gene. We monitored the changes in bla cDNAs induced by cefotaxime selection and observed an initial explosion in sequence variants with multiple mutations throughout the gene. After four passages, a stable, homogeneous population of bla sequences containing three specific nonsynonymous mutations was established. Of these, two mutations (E104K and G238S) have been previously reported for beta-lactamases from cefotaxime-resistant bacterial isolates. These results extend our understanding of the molecular mechanisms of viral adaptation and also demonstrate the possibility of using an RNA virus as a vehicle for directed evolution of heterologous proteins.

Exploring Regularities and Dynamic Systems in L2 Development

ERIC Educational Resources Information Center

Lenzing, Anke

2015-01-01

This article focuses on a theoretical and empirical exploration of developmental trajectories and individual learner variation in second language (L2) acquisition. Taking a processability perspective, I view learner language as a dynamic system that includes predictable universal developmental trajectories as well as individual learner variation,…

Using ancient protein kinases to unravel a modern cancer drug's mechanism

DOE PAGES

Wilson, C.; Agafonov, R. V.; Hoemberger, M.; ...

2015-02-19

Macromolecular function is rooted in energy landscapes, where sequence determines not a single structure but an ensemble of conformations. Hence, evolution modifies a protein’s function by altering its energy landscape. Consequently, we recreate the evolutionary pathway between two modern human oncogenes, Src and Abl, by reconstructing their common ancestors. Our evolutionary reconstruction combined with x-ray structures of the common ancestor and pre–steady-state kinetics reveals a detailed atomistic mechanism for selectivity of the successful cancer drug Gleevec. Gleevec affinity is gained during the evolutionary trajectory toward Abl and lost toward Src, primarily by shifting an induced-fit equilibrium that is also disruptedmore » in the clinical T315I resistance mutation. Lastly, this work reveals the mechanism of Gleevec specificity while offering insights into how energy landscapes evolve.« less

Exploring the application of an evolutionary educational complex systems framework to teaching and learning about issues in the science and technology classroom

NASA Astrophysics Data System (ADS)

Yoon, Susan Anne

Understanding the world through a complex systems lens has recently garnered a great deal of interest in many knowledge disciplines. In the educational arena, interactional studies, through their focus on understanding patterns of system behaviour including the dynamical processes and trajectories of learning, lend support for investigating how a complex systems approach can inform educational research. This study uses previously existing literature and tools for complex systems applications and seeks to extend this research base by exploring learning outcomes of a complex systems framework when applied to curriculum and instruction. It is argued that by applying the evolutionary dynamics of variation, interaction and selection, complexity may be harnessed to achieve growth in both the social and cognitive systems of the classroom. Furthermore, if the goal of education, i.e., the social system under investigation, is to teach for understanding, conceptual knowledge of the kind described in Popper's (1972; 1976) World 3, needs to evolve. Both the study of memetic processes and knowledge building pioneered by Bereiter (cf. Bereiter, 2002) draw on the World 3 notion of ideas existing as conceptual artifacts that can be investigated as products outside of the individual mind providing an educational lens from which to proceed. The curricular topic addressed is the development of an ethical understanding of the scientific and technological issues of genetic engineering. 11 grade 8 students are studied as they proceed through 40 hours of curricular instruction based on the complex systems evolutionary framework. Results demonstrate growth in both complex systems thinking and content knowledge of the topic of genetic engineering. Several memetic processes are hypothesized to have influenced how and why ideas change. Categorized by factors influencing either reflective or non-reflective selection, these processes appear to have exerted differential effects on students' abilities to think and act in complex ways at various points throughout the study. Finally, an analysis of winner and loser memes is offered that is intended to reveal information about the conceptual system---its strengths and deficiencies---that can help educators assess curricular goals and organize and construct additional educational activities.

Gravity-Assist Trajectories to the Ice Giants: An Automated Method to Catalog Mass- Or Time-Optimal Solutions

NASA Technical Reports Server (NTRS)

Hughes, Kyle M.; Knittel, Jeremy M.; Englander, Jacob A.

2017-01-01

This work presents an automated method of calculating mass (or time) optimal gravity-assist trajectories without a priori knowledge of the flyby-body combination. Since gravity assists are particularly crucial for reaching the outer Solar System, we use the Ice Giants, Uranus and Neptune, as example destinations for this work. Catalogs are also provided that list the most attractive trajectories found over launch dates ranging from 2024 to 2038. The tool developed to implement this method, called the Python EMTG Automated Trade Study Application (PEATSA), iteratively runs the Evolutionary Mission Trajectory Generator (EMTG), a NASA Goddard Space Flight Center in-house trajectory optimization tool. EMTG finds gravity-assist trajectories with impulsive maneuvers using a multiple-shooting structure along with stochastic methods (such as monotonic basin hopping) and may be run with or without an initial guess provided. PEATSA runs instances of EMTG in parallel over a grid of launch dates. After each set of runs completes, the best results within a neighborhood of launch dates are used to seed all other cases in that neighborhood-allowing the solutions across the range of launch dates to improve over each iteration. The results here are compared against trajectories found using a grid-search technique, and PEATSA is found to outperform the grid-search results for most launch years considered.

Gravity-Assist Trajectories to the Ice Giants: An Automated Method to Catalog Mass-or Time-Optimal Solutions

NASA Technical Reports Server (NTRS)

Hughes, Kyle M.; Knittel, Jeremy M.; Englander, Jacob A.

2017-01-01

This work presents an automated method of calculating mass (or time) optimal gravity-assist trajectories without a priori knowledge of the flyby-body combination. Since gravity assists are particularly crucial for reaching the outer Solar System, we use the Ice Giants, Uranus and Neptune, as example destinations for this work. Catalogs are also provided that list the most attractive trajectories found over launch dates ranging from 2024 to 2038. The tool developed to implement this method, called the Python EMTG Automated Trade Study Application (PEATSA), iteratively runs the Evolutionary Mission Trajectory Generator (EMTG), a NASA Goddard Space Flight Center in-house trajectory optimization tool. EMTG finds gravity-assist trajectories with impulsive maneuvers using a multiple-shooting structure along with stochastic methods (such as monotonic basin hopping) and may be run with or without an initial guess provided. PEATSA runs instances of EMTG in parallel over a grid of launch dates. After each set of runs completes, the best results within a neighborhood of launch dates are used to seed all other cases in that neighborhood---allowing the solutions across the range of launch dates to improve over each iteration. The results here are compared against trajectories found using a grid-search technique, and PEATSA is found to outperform the grid-search results for most launch years considered.

Analysis of self-overlap reveals trade-offs in plankton swimming trajectories

PubMed Central

Bianco, Giuseppe; Mariani, Patrizio; Visser, Andre W.; Mazzocchi, Maria Grazia; Pigolotti, Simone

2014-01-01

Movement is a fundamental behaviour of organisms that not only brings about beneficial encounters with resources and mates, but also at the same time exposes the organism to dangerous encounters with predators. The movement patterns adopted by organisms should reflect a balance between these contrasting processes. This trade-off can be hypothesized as being evident in the behaviour of plankton, which inhabit a dilute three-dimensional environment with few refuges or orienting landmarks. We present an analysis of the swimming path geometries based on a volumetric Monte Carlo sampling approach, which is particularly adept at revealing such trade-offs by measuring the self-overlap of the trajectories. Application of this method to experimentally measured trajectories reveals that swimming patterns in copepods are shaped to efficiently explore volumes at small scales, while achieving a large overlap at larger scales. Regularities in the observed trajectories make the transition between these two regimes always sharper than in randomized trajectories or as predicted by random walk theory. Thus, real trajectories present a stronger separation between exploration for food and exposure to predators. The specific scale and features of this transition depend on species, gender and local environmental conditions, pointing at adaptation to state and stage-dependent evolutionary trade-offs. PMID:24789560

Analysis of Video-Based Microscopic Particle Trajectories Using Kalman Filtering

PubMed Central

Wu, Pei-Hsun; Agarwal, Ashutosh; Hess, Henry; Khargonekar, Pramod P.; Tseng, Yiider

2010-01-01

Abstract The fidelity of the trajectories obtained from video-based particle tracking determines the success of a variety of biophysical techniques, including in situ single cell particle tracking and in vitro motility assays. However, the image acquisition process is complicated by system noise, which causes positioning error in the trajectories derived from image analysis. Here, we explore the possibility of reducing the positioning error by the application of a Kalman filter, a powerful algorithm to estimate the state of a linear dynamic system from noisy measurements. We show that the optimal Kalman filter parameters can be determined in an appropriate experimental setting, and that the Kalman filter can markedly reduce the positioning error while retaining the intrinsic fluctuations of the dynamic process. We believe the Kalman filter can potentially serve as a powerful tool to infer a trajectory of ultra-high fidelity from noisy images, revealing the details of dynamic cellular processes. PMID:20550894

Breeding biology and the evolution of dynamic sexual dichromatism in frogs.

PubMed

Bell, R C; Webster, G N; Whiting, M J

2017-12-01

Dynamic sexual dichromatism is a temporary colour change between the sexes and has evolved independently in a wide range of anurans, many of which are explosive breeders wherein males physically compete for access to females. Behavioural studies in a few species indicate that dynamic dichromatism functions as a visual signal in large breeding aggregations; however, the prevalence of this trait and the social and environmental factors underlying its expression are poorly understood. We compiled a database of 178 anurans with dynamic dichromatism that include representatives from 15 families and subfamilies. Dynamic dichromatism is common in two of the three subfamilies of hylid treefrogs. Phylogenetic comparative analyses of 355 hylid species (of which 95 display dynamic dichromatism) reveal high transition rates between dynamic dichromatism, ontogenetic (permanent) dichromatism and monochromatism reflecting the high evolutionary lability of this trait. Correlated evolution in hylids between dynamic dichromatism and forming large breeding aggregations indicates that the evolution of large breeding aggregations precedes the evolution of dynamic dichromatism. Multivariate phylogenetic logistic regression recovers the interaction between biogeographic distribution and forming breeding aggregations as a significant predictor of dynamic dichromatism in hylids. Accounting for macroecological differences between temperate and tropical regions, such as seasonality and the availability of breeding sites, may improve our understanding of ecological contexts in which dynamic dichromatism is likely to arise in tropical lineages and why it is retained in some temperate species and lost in others. © 2017 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2017 European Society For Evolutionary Biology.

Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory.

PubMed

Hasselmo, Michael E; Giocomo, Lisa M; Brandon, Mark P; Yoshida, Motoharu

2010-12-31

Understanding the mechanisms of episodic memory requires linking behavioral data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action. Copyright © 2010 Elsevier B.V. All rights reserved.

Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory

PubMed Central

Hasselmo, Michael E.; Giocomo, Lisa M.; Yoshida, Motoharu

2010-01-01

Understanding the mechanisms of episodic memory requires linking behavioural data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within these brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action. PMID:20018213

The evolutionary dynamics of canid and mongoose rabies virus in Southern Africa.

PubMed

Davis, P L; Rambaut, A; Bourhy, H; Holmes, E C

2007-01-01

Two variants of rabies virus (RABV) currently circulate in southern Africa: canid RABV, mainly associated with dogs, jackals, and bat-eared foxes, and mongoose RABV. To investigate the evolutionary dynamics of these variants, we performed coalescent-based analyses of the G-L inter-genic region, allowing for rate variation among viral lineages through the use of a relaxed molecular clock. This revealed that mongoose RABV is evolving more slowly than canid RABV, with mean evolutionary rates of 0.826 and 1.676 x 10(-3) nucleotide substitutions per site, per year, respectively. Additionally, mongoose RABV exhibits older genetic diversity than canid RABV, with common ancestors dating to 73 and 30 years, respectively, and while mongoose RABV has experienced exponential population growth over its evolutionary history in Africa, populations of canid RABV have maintained a constant size. Hence, despite circulating in the same geographic region, these two variants of RABV exhibit striking differences in evolutionary dynamics which are likely to reflect differences in their underlying ecology.

Asynchronous spatial evolutionary games.

PubMed

Newth, David; Cornforth, David

2009-02-01

Over the past 50 years, much attention has been given to the Prisoner's Dilemma as a metaphor for problems surrounding the evolution and maintenance of cooperative and altruistic behavior. The bulk of this work has dealt with the successfulness and robustness of various strategies. Nowak and May (1992) considered an alternative approach to studying evolutionary games. They assumed that players were distributed across a two-dimensional (2D) lattice, interactions between players occurred locally, rather than at long range as in the well mixed situation. The resulting spatial evolutionary games display dynamics not seen in their well-mixed counterparts. An assumption underlying much of the work on spatial evolutionary games is that the state of all players is updated in unison or in synchrony. Using the framework outlined in Nowak and May (1992), we examine the effect of various asynchronous updating schemes on the dynamics of spatial evolutionary games. There are potential implications for the dynamics of a wide variety of spatially extended systems in biology, physics and chemistry.

A dynamic eco-evolutionary model predicts slow response of alpine plants to climate warming.

PubMed

Cotto, Olivier; Wessely, Johannes; Georges, Damien; Klonner, Günther; Schmid, Max; Dullinger, Stefan; Thuiller, Wilfried; Guillaume, Frédéric

2017-05-05

Withstanding extinction while facing rapid climate change depends on a species' ability to track its ecological niche or to evolve a new one. Current methods that predict climate-driven species' range shifts use ecological modelling without eco-evolutionary dynamics. Here we present an eco-evolutionary forecasting framework that combines niche modelling with individual-based demographic and genetic simulations. Applying our approach to four endemic perennial plant species of the Austrian Alps, we show that accounting for eco-evolutionary dynamics when predicting species' responses to climate change is crucial. Perennial species persist in unsuitable habitats longer than predicted by niche modelling, causing delayed range losses; however, their evolutionary responses are constrained because long-lived adults produce increasingly maladapted offspring. Decreasing population size due to maladaptation occurs faster than the contraction of the species range, especially for the most abundant species. Monitoring of species' local abundance rather than their range may likely better inform on species' extinction risks under climate change.

A phenomenological approach to modeling chemical dynamics in nonlinear and two-dimensional spectroscopy.

PubMed

Ramasesha, Krupa; De Marco, Luigi; Horning, Andrew D; Mandal, Aritra; Tokmakoff, Andrei

2012-04-07

We present an approach for calculating nonlinear spectroscopic observables, which overcomes the approximations inherent to current phenomenological models without requiring the computational cost of performing molecular dynamics simulations. The trajectory mapping method uses the semi-classical approximation to linear and nonlinear response functions, and calculates spectra from trajectories of the system's transition frequencies and transition dipole moments. It rests on identifying dynamical variables important to the problem, treating the dynamics of these variables stochastically, and then generating correlated trajectories of spectroscopic quantities by mapping from the dynamical variables. This approach allows one to describe non-Gaussian dynamics, correlated dynamics between variables of the system, and nonlinear relationships between spectroscopic variables of the system and the bath such as non-Condon effects. We illustrate the approach by applying it to three examples that are often not adequately treated by existing analytical models--the non-Condon effect in the nonlinear infrared spectra of water, non-Gaussian dynamics inherent to strongly hydrogen bonded systems, and chemical exchange processes in barrier crossing reactions. The methods described are generally applicable to nonlinear spectroscopy throughout the optical, infrared and terahertz regions.

Trajectory optimization for the National aerospace plane

NASA Technical Reports Server (NTRS)

Lu, Ping

1993-01-01

While continuing the application of the inverse dynamics approach in obtaining the optimal numerical solutions, the research during the past six months has been focused on the formulation and derivation of closed-form solutions for constrained hypersonic flight trajectories. Since it was found in the research of the first year that a dominant portion of the optimal ascent trajectory of the aerospace plane is constrained by dynamic pressure and heating constraints, the application of the analytical solutions significantly enhances the efficiency in trajectory optimization, provides a better insight to understanding of the trajectory and conceivably has great potential in guidance of the vehicle. Work of this period has been reported in four technical papers. Two of the papers were presented in the AIAA Guidance, Navigation, and Control Conference (Hilton Head, SC, August, 1992) and Fourth International Aerospace Planes Conference (Orlando, FL, December, 1992). The other two papers have been accepted for publication by Journal of Guidance, Control, and Dynamics, and will appear in 1993. This report briefly summarizes the work done in the past six months and work currently underway.

Coupled forward-backward trajectory approach for nonequilibrium electron-ion dynamics

NASA Astrophysics Data System (ADS)

Sato, Shunsuke A.; Kelly, Aaron; Rubio, Angel

2018-04-01

We introduce a simple ansatz for the wave function of a many-body system based on coupled forward and backward propagating semiclassical trajectories. This method is primarily aimed at, but not limited to, treating nonequilibrium dynamics in electron-phonon systems. The time evolution of the system is obtained from the Euler-Lagrange variational principle, and we show that this ansatz yields Ehrenfest mean-field theory in the limit that the forward and backward trajectories are orthogonal, and in the limit that they coalesce. We investigate accuracy and performance of this method by simulating electronic relaxation in the spin-boson model and the Holstein model. Although this method involves only pairs of semiclassical trajectories, it shows a substantial improvement over mean-field theory, capturing quantum coherence of nuclear dynamics as well as electron-nuclear correlations. This improvement is particularly evident in nonadiabatic systems, where the accuracy of this coupled trajectory method extends well beyond the perturbative electron-phonon coupling regime. This approach thus provides an attractive route forward to the ab initio description of relaxation processes, such as thermalization, in condensed phase systems.

Cancer Evolution: Mathematical Models and Computational Inference

PubMed Central

Beerenwinkel, Niko; Schwarz, Roland F.; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. PMID:25293804

Post-Flight Assessment of Low Density Supersonic Decelerator Flight Dynamics Test 2 Simulation

NASA Technical Reports Server (NTRS)

Dutta, Soumyo; Bowes, Angela L.; White, Joseph P.; Striepe, Scott A.; Queen, Eric M.; O'Farrel, Clara; Ivanov, Mark C.

2016-01-01

NASA's Low Density Supersonic Decelerator (LDSD) project conducted its second Supersonic Flight Dynamics Test (SFDT-2) on June 8, 2015. The Program to Optimize Simulated Trajectories II (POST2) was one of the flight dynamics tools used to simulate and predict the flight performance and was a major tool used in the post-flight assessment of the flight trajectory. This paper compares the simulation predictions with the reconstructed trajectory. Additionally, off-nominal conditions seen during flight are modeled in the simulation to reconcile the predictions with flight data. These analyses are beneficial to characterize the results of the flight test and to improve the simulation and targeting of the subsequent LDSD flights.

Low-Thrust Many-Revolution Trajectory Optimization via Differential Dynamic Programming and a Sundman Transformation

NASA Astrophysics Data System (ADS)

Aziz, Jonathan D.; Parker, Jeffrey S.; Scheeres, Daniel J.; Englander, Jacob A.

2018-01-01

Low-thrust trajectories about planetary bodies characteristically span a high count of orbital revolutions. Directing the thrust vector over many revolutions presents a challenging optimization problem for any conventional strategy. This paper demonstrates the tractability of low-thrust trajectory optimization about planetary bodies by applying a Sundman transformation to change the independent variable of the spacecraft equations of motion to an orbit angle and performing the optimization with differential dynamic programming. Fuel-optimal geocentric transfers are computed with the transfer duration extended up to 2000 revolutions. The flexibility of the approach to higher fidelity dynamics is shown with Earth's J 2 perturbation and lunar gravity included for a 500 revolution transfer.

Mystic: Implementation of the Static Dynamic Optimal Control Algorithm for High-Fidelity, Low-Thrust Trajectory Design

NASA Technical Reports Server (NTRS)

Whiffen, Gregory J.

2006-01-01

Mystic software is designed to compute, analyze, and visualize optimal high-fidelity, low-thrust trajectories, The software can be used to analyze inter-planetary, planetocentric, and combination trajectories, Mystic also provides utilities to assist in the operation and navigation of low-thrust spacecraft. Mystic will be used to design and navigate the NASA's Dawn Discovery mission to orbit the two largest asteroids, The underlying optimization algorithm used in the Mystic software is called Static/Dynamic Optimal Control (SDC). SDC is a nonlinear optimal control method designed to optimize both 'static variables' (parameters) and dynamic variables (functions of time) simultaneously. SDC is a general nonlinear optimal control algorithm based on Bellman's principal.

Low-Thrust Many-Revolution Trajectory Optimization via Differential Dynamic Programming and a Sundman Transformation

NASA Astrophysics Data System (ADS)

Aziz, Jonathan D.; Parker, Jeffrey S.; Scheeres, Daniel J.; Englander, Jacob A.

2018-06-01

Low-thrust trajectories about planetary bodies characteristically span a high count of orbital revolutions. Directing the thrust vector over many revolutions presents a challenging optimization problem for any conventional strategy. This paper demonstrates the tractability of low-thrust trajectory optimization about planetary bodies by applying a Sundman transformation to change the independent variable of the spacecraft equations of motion to an orbit angle and performing the optimization with differential dynamic programming. Fuel-optimal geocentric transfers are computed with the transfer duration extended up to 2000 revolutions. The flexibility of the approach to higher fidelity dynamics is shown with Earth's J 2 perturbation and lunar gravity included for a 500 revolution transfer.

Using Static Percentiles of AE9/AP9 to Approximate Dynamic Monte Carlo Runs for Radiation Analysis of Spiral Transfer Orbits

NASA Astrophysics Data System (ADS)

Kwan, Betty P.; O'Brien, T. Paul

2015-06-01

The Aerospace Corporation performed a study to determine whether static percentiles of AE9/AP9 can be used to approximate dynamic Monte Carlo runs for radiation analysis of spiral transfer orbits. Solar panel degradation is a major concern for solar-electric propulsion because solar-electric propulsion depends on the power output of the solar panel. Different spiral trajectories have different radiation environments that could lead to solar panel degradation. Because the spiral transfer orbits only last weeks to months, an average environment does not adequately address the possible transient enhancements of the radiation environment that must be accounted for in optimizing the transfer orbit trajectory. Therefore, to optimize the trajectory, an ensemble of Monte Carlo simulations of AE9/AP9 would normally be run for every spiral trajectory to determine the 95th percentile radiation environment. To avoid performing lengthy Monte Carlo dynamic simulations for every candidate spiral trajectory in the optimization, we found a static percentile that would be an accurate representation of the full Monte Carlo simulation for a representative set of spiral trajectories. For 3 LEO to GEO and 1 LEO to MEO trajectories, a static 90th percentile AP9 is a good approximation of the 95th percentile fluence with dynamics for 4-10 MeV protons, and a static 80th percentile AE9 is a good approximation of the 95th percentile fluence with dynamics for 0.5-2 MeV electrons. While the specific percentiles chosen cannot necessarily be used in general for other orbit trade studies, the concept of determining a static percentile as a quick approximation to a full Monte Carlo ensemble of simulations can likely be applied to other orbit trade studies. We expect the static percentile to depend on the region of space traversed, the mission duration, and the radiation effect considered.

The role of invariant manifolds in lowthrust trajectory design (part III)

NASA Technical Reports Server (NTRS)

Lo, Martin W.; Anderson, Rodney L.; Lam, Try; Whiffen, Greg

2006-01-01

This paper is the third in a series to explore the role of invariant manifolds in the design of low thrust trajectories. In previous papers, we analyzed an impulsive thrust resonant gravity assist flyby trajectory to capture into Europa orbit using the invariant manifolds of unstable resonant periodic orbits and libration orbits. The energy savings provided by the gravity assist may be interpreted dynamically as the result of a finite number of intersecting invariant manifolds. In this paper we demonstrate that the same dynamics is at work for low thrust trajectories with resonant flybys and low energy capture. However, in this case, the flybys and capture are effected by continuous families of intersecting invariant manifolds.

Attractors of equations of non-Newtonian fluid dynamics

NASA Astrophysics Data System (ADS)

Zvyagin, V. G.; Kondrat'ev, S. K.

2014-10-01

This survey describes a version of the trajectory-attractor method, which is applied to study the limit asymptotic behaviour of solutions of equations of non-Newtonian fluid dynamics. The trajectory-attractor method emerged in papers of the Russian mathematicians Vishik and Chepyzhov and the American mathematician Sell under the condition that the corresponding trajectory spaces be invariant under the translation semigroup. The need for such an approach was caused by the fact that for many equations of mathematical physics for which the Cauchy initial-value problem has a global (weak) solution with respect to the time, the uniqueness of such a solution has either not been established or does not hold. In particular, this is the case for equations of fluid dynamics. At the same time, trajectory spaces invariant under the translation semigroup could not be constructed for many equations of non-Newtonian fluid dynamics. In this connection, a different approach to the construction of trajectory attractors for dissipative systems was proposed in papers of Zvyagin and Vorotnikov without using invariance of trajectory spaces under the translation semigroup and is based on the topological lemma of Shura-Bura. This paper presents examples of equations of non-Newtonian fluid dynamics (the Jeffreys system describing movement of the Earth's crust, the model of motion of weak aqueous solutions of polymers, a system with memory) for which the aforementioned construction is used to prove the existence of attractors in both the autonomous and the non-autonomous cases. At the beginning of the paper there is also a brief exposition of the results of Ladyzhenskaya on the existence of attractors of the two-dimensional Navier-Stokes system and the result of Vishik and Chepyzhov for the case of attractors of the three-dimensional Navier-Stokes system. Bibliography: 34 titles.

The evolutionary dynamics of language.

PubMed

Steels, Luc; Szathmáry, Eörs

2018-02-01

The well-established framework of evolutionary dynamics can be applied to the fascinating open problems how human brains are able to acquire and adapt language and how languages change in a population. Schemas for handling grammatical constructions are the replicating unit. They emerge and multiply with variation in the brains of individuals and undergo selection based on their contribution to needed expressive power, communicative success and the reduction of cognitive effort. Adopting this perspective has two major benefits. (i) It makes a bridge to neurobiological models of the brain that have also adopted an evolutionary dynamics point of view, thus opening a new horizon for studying how human brains achieve the remarkably complex competence for language. And (ii) it suggests a new foundation for studying cultural language change as an evolutionary dynamics process. The paper sketches this novel perspective, provides references to empirical data and computational experiments, and points to open problems. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Evolutionary Dynamics and Diversity in Microbial Populations

NASA Astrophysics Data System (ADS)

Thompson, Joel; Fisher, Daniel

2013-03-01

Diseases such as flu and cancer adapt at an astonishing rate. In large part, viruses and cancers are so difficult to prevent because they are continually evolving. Controlling such ``evolutionary diseases'' requires a better understanding of the underlying evolutionary dynamics. It is conventionally assumed that adaptive mutations are rare and therefore will occur and sweep through the population in succession. Recent experiments using modern sequencing technologies have illuminated the many ways in which real population sequence data does not conform to the predictions of conventional theory. We consider a very simple model of asexual evolution and perform simulations in a range of parameters thought to be relevant for microbes and cancer. Simulation results reveal complex evolutionary dynamics typified by competition between lineages with different sets of adaptive mutations. This dynamical process leads to a distribution of mutant gene frequencies different than expected under the conventional assumption that adaptive mutations are rare. Simulated gene frequencies share several conspicuous features with data collected from laboratory-evolved yeast and the worldwide population of influenza.

Optimizing Mars Airplane Trajectory with the Application Navigation System

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Riley, Derek

2004-01-01

Planning complex missions requires a number of programs to be executed in concert. The Application Navigation System (ANS), developed in the NAS Division, can execute many interdependent programs in a distributed environment. We show that the ANS simplifies user effort and reduces time in optimization of the trajectory of a martian airplane. We use a software package, Cart3D, to evaluate trajectories and a shortest path algorithm to determine the optimal trajectory. ANS employs the GridScape to represent the dynamic state of the available computer resources. Then, ANS uses a scheduler to dynamically assign ready task to machine resources and the GridScape for tracking available resources and forecasting completion time of running tasks. We demonstrate system capability to schedule and run the trajectory optimization application with efficiency exceeding 60% on 64 processors.

A Probabilistic Framework for Constructing Temporal Relations in Replica Exchange Molecular Trajectories.

PubMed

Chattopadhyay, Aditya; Zheng, Min; Waller, Mark Paul; Priyakumar, U Deva

2018-05-23

Knowledge of the structure and dynamics of biomolecules is essential for elucidating the underlying mechanisms of biological processes. Given the stochastic nature of many biological processes, like protein unfolding, it's almost impossible that two independent simulations will generate the exact same sequence of events, which makes direct analysis of simulations difficult. Statistical models like Markov Chains, transition networks etc. help in shedding some light on the mechanistic nature of such processes by predicting long-time dynamics of these systems from short simulations. However, such methods fall short in analyzing trajectories with partial or no temporal information, for example, replica exchange molecular dynamics or Monte Carlo simulations. In this work we propose a probabilistic algorithm, borrowing concepts from graph theory and machine learning, to extract reactive pathways from molecular trajectories in the absence of temporal data. A suitable vector representation was chosen to represent each frame in the macromolecular trajectory (as a series of interaction and conformational energies) and dimensionality reduction was performed using principal component analysis (PCA). The trajectory was then clustered using a density-based clustering algorithm, where each cluster represents a metastable state on the potential energy surface (PES) of the biomolecule under study. A graph was created with these clusters as nodes with the edges learnt using an iterative expectation maximization algorithm. The most reactive path is conceived as the widest path along this graph. We have tested our method on RNA hairpin unfolding trajectory in aqueous urea solution. Our method makes the understanding of the mechanism of unfolding in RNA hairpin molecule more tractable. As this method doesn't rely on temporal data it can be used to analyze trajectories from Monte Carlo sampling techniques and replica exchange molecular dynamics (REMD).

Genetic recapture identifies long-distance breeding dispersal in Greater Sage-Grouse (Centrocercus urophasianus)

Treesearch

Todd B. Cross; David E. Naugle; John C. Carlson; Michael K. Schwartz

2017-01-01

Dispersal can strongly influence the demographic and evolutionary trajectory of populations. For many species, little is known about dispersal, despite its importance to conservation. The Greater Sage-Grouse (Centrocercus urophasianus) is a species of conservation concern that ranges across 11 western U.S. states and 2 Canadian provinces. To investigate dispersal...

Assessing intra- and inter-regional climate effects on Douglas-fir biomass dynamics in Oregon and Washington, USA

Treesearch

David M. Bell; Andrew N. Gray

2016-01-01

While ecological succession shapes contemporary forest structure and dynamics, other factors like forest structure (dense vs. sparse canopies) and climate may alter structural trajectories. To assess potential sources of variation in structural trajectories, we examined proportional biomass change for a regionally dominant tree species, Douglas-fir (...

A walk through the approximations of ab initio multiple spawning

NASA Astrophysics Data System (ADS)

Mignolet, Benoit; Curchod, Basile F. E.

2018-04-01

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Application of dynamic programming to control khuzestan water resources system

USGS Publications Warehouse

Jamshidi, M.; Heidari, M.

1977-01-01

An approximate optimization technique based on discrete dynamic programming called discrete differential dynamic programming (DDDP), is employed to obtain the near optimal operation policies of a water resources system in the Khuzestan Province of Iran. The technique makes use of an initial nominal state trajectory for each state variable, and forms corridors around the trajectories. These corridors represent a set of subdomains of the entire feasible domain. Starting with such a set of nominal state trajectories, improvements in objective function are sought within the corridors formed around them. This leads to a set of new nominal trajectories upon which more improvements may be sought. Since optimization is confined to a set of subdomains, considerable savings in memory and computer time are achieved over that of conventional dynamic programming. The Kuzestan water resources system considered in this study is located in southwest Iran, and consists of two rivers, three reservoirs, three hydropower plants, and three irrigable areas. Data and cost benefit functions for the analysis were obtained either from the historical records or from similar studies. ?? 1977.

A walk through the approximations of ab initio multiple spawning.

PubMed

Mignolet, Benoit; Curchod, Basile F E

2018-04-07

Full multiple spawning offers an in principle exact framework for excited-state dynamics, where nuclear wavefunctions in different electronic states are represented by a set of coupled trajectory basis functions that follow classical trajectories. The couplings between trajectory basis functions can be approximated to treat molecular systems, leading to the ab initio multiple spawning method which has been successfully employed to study the photochemistry and photophysics of several molecules. However, a detailed investigation of its approximations and their consequences is currently missing in the literature. In this work, we simulate the explicit photoexcitation and subsequent excited-state dynamics of a simple system, LiH, and we analyze (i) the effect of the ab initio multiple spawning approximations on different observables and (ii) the convergence of the ab initio multiple spawning results towards numerically exact quantum dynamics upon a progressive relaxation of these approximations. We show that, despite the crude character of the approximations underlying ab initio multiple spawning for this low-dimensional system, the qualitative excited-state dynamics is adequately captured, and affordable corrections can further be applied to ameliorate the coupling between trajectory basis functions.

Tracing evolutionary relicts of positive selection on eight malaria-related immune genes in mammals.

PubMed

Huang, Bing-Hong; Liao, Pei-Chun

2015-07-01

Plasmodium-induced malaria widely infects primates and other mammals. Multiple past studies have revealed that positive selection could be the main evolutionary force triggering the genetic diversity of anti-malaria resistance-associated genes in human or primates. However, researchers focused most of their attention on the infra-generic and intra-specific genome evolution rather than analyzing the complete evolutionary history of mammals. Here we extend previous research by testing the evolutionary link of natural selection on eight candidate genes associated with malaria resistance in mammals. Three of the eight genes were detected to be affected by recombination, including TNF-α, iNOS and DARC. Positive selection was detected in the rest five immunogenes multiple times in different ancestral lineages of extant species throughout the mammalian evolution. Signals of positive selection were exposed in four malaria-related immunogenes in primates: CCL2, IL-10, HO1 and CD36. However, selection signals of G6PD have only been detected in non-primate eutherians. Significantly higher evolutionary rates and more radical amino acid replacement were also detected in primate CD36, suggesting its functional divergence from other eutherians. Prevalent positive selection throughout the evolutionary trajectory of mammalian malaria-related genes supports the arms race evolutionary hypothesis of host genetic response of mammalian immunogenes to infectious pathogens. © The Author(s) 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

Dynamic heterogeneity in the folding/unfolding transitions of FiP35

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

Mori, Toshifumi, E-mail: mori@ims.ac.jp; Saito, Shinji, E-mail: shinji@ims.ac.jp

Molecular dynamics simulations have become an important tool in studying protein dynamics over the last few decades. Atomistic simulations on the order of micro- to milliseconds are becoming feasible and are used to study the state-of-the-art experiments in atomistic detail. Yet, analyzing the high-dimensional-long-temporal trajectory data is still a challenging task and sometimes leads to contradictory results depending on the analyses. To reveal the dynamic aspect of the trajectory, here we propose a simple approach which uses a time correlation function matrix and apply to the folding/unfolding trajectory of FiP35 WW domain [Shaw et al., Science 330, 341 (2010)]. Themore » approach successfully characterizes the slowest mode corresponding to the folding/unfolding transitions and determines the free energy barrier indicating that FiP35 is not an incipient downhill folder. The transition dynamics analysis further reveals that the folding/unfolding transition is highly heterogeneous, e.g., the transition path time varies by ∼100 fold. We identify two misfolded states and show that the dynamic heterogeneity in the folding/unfolding transitions originates from the trajectory being trapped in the misfolded and half-folded intermediate states rather than the diffusion driven by a thermal noise. The current results help reconcile the conflicting interpretations of the folding mechanism and highlight the complexity in the folding dynamics. This further motivates the need to understand the transition dynamics beyond a simple free energy picture using simulations and single-molecule experiments.« less

An evolutionary perspective on leaf economics: phylogenetics of leaf mass per area in vascular plants

PubMed Central

Flores, Olivier; Garnier, Eric; Wright, Ian J; Reich, Peter B; Pierce, Simon; Dìaz, Sandra; Pakeman, Robin J; Rusch, Graciela M; Bernard-Verdier, Maud; Testi, Baptiste; Bakker, Jan P; Bekker, Renée M; Cerabolini, Bruno E L; Ceriani, Roberta M; Cornu, Guillaume; Cruz, Pablo; Delcamp, Matthieu; Dolezal, Jiri; Eriksson, Ove; Fayolle, Adeline; Freitas, Helena; Golodets, Carly; Gourlet-Fleury, Sylvie; Hodgson, John G; Brusa, Guido; Kleyer, Michael; Kunzmann, Dieter; Lavorel, Sandra; Papanastasis, Vasilios P; Pérez-Harguindeguy, Natalia; Vendramini, Fernanda; Weiher, Evan

2014-01-01

In plant leaves, resource use follows a trade-off between rapid resource capture and conservative storage. This “worldwide leaf economics spectrum” consists of a suite of intercorrelated leaf traits, among which leaf mass per area, LMA, is one of the most fundamental as it indicates the cost of leaf construction and light-interception borne by plants. We conducted a broad-scale analysis of the evolutionary history of LMA across a large dataset of 5401 vascular plant species. The phylogenetic signal in LMA displayed low but significant conservatism, that is, leaf economics tended to be more similar among close relatives than expected by chance alone. Models of trait evolution indicated that LMA evolved under weak stabilizing selection. Moreover, results suggest that different optimal phenotypes evolved among large clades within which extremes tended to be selected against. Conservatism in LMA was strongly related to growth form, as were selection intensity and phenotypic evolutionary rates: woody plants showed higher conservatism in relation to stronger stabilizing selection and lower evolutionary rates compared to herbaceous taxa. The evolutionary history of LMA thus paints different evolutionary trajectories of vascular plant species across clades, revealing the coordination of leaf trait evolution with growth forms in response to varying selection regimes. PMID:25165520

Making evolutionary history count: biodiversity planning for coral reef fishes and the conservation of evolutionary processes

NASA Astrophysics Data System (ADS)

von der Heyden, Sophie

2017-03-01

Anthropogenic activities are having devastating impacts on marine systems with numerous knock-on effects on trophic functioning, species interactions and an accelerated loss of biodiversity. Establishing conservation areas can not only protect biodiversity, but also confer resilience against changes to coral reefs and their inhabitants. Planning for protection and conservation in marine systems is complex, but usually focuses on maintaining levels of biodiversity and protecting special and unique landscape features while avoiding negative impacts to socio-economic benefits. Conversely, the integration of evolutionary processes that have shaped extant species assemblages is rarely taken into account. However, it is as important to protect processes as it is to protect patterns for maintaining the evolutionary trajectories of populations and species. This review focuses on different approaches for integrating genetic analyses, such as phylogenetic diversity, phylogeography and the delineation of management units, temporal and spatial monitoring of genetic diversity and quantification of adaptive variation for protecting evolutionary resilience, into marine spatial planning, specifically for coral reef fishes. Many of these concepts are not yet readily applied to coral reef fish studies, but this synthesis highlights their potential and the importance of including historical processes into systematic biodiversity planning for conserving not only extant, but also future, biodiversity and its evolutionary potential.

Aspiration dynamics of multi-player games in finite populations

PubMed Central

Du, Jinming; Wu, Bin; Altrock, Philipp M.; Wang, Long

2014-01-01

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics. PMID:24598208

Aspiration dynamics of multi-player games in finite populations.

PubMed

Du, Jinming; Wu, Bin; Altrock, Philipp M; Wang, Long

2014-05-06

On studying strategy update rules in the framework of evolutionary game theory, one can differentiate between imitation processes and aspiration-driven dynamics. In the former case, individuals imitate the strategy of a more successful peer. In the latter case, individuals adjust their strategies based on a comparison of their pay-offs from the evolutionary game to a value they aspire, called the level of aspiration. Unlike imitation processes of pairwise comparison, aspiration-driven updates do not require additional information about the strategic environment and can thus be interpreted as being more spontaneous. Recent work has mainly focused on understanding how aspiration dynamics alter the evolutionary outcome in structured populations. However, the baseline case for understanding strategy selection is the well-mixed population case, which is still lacking sufficient understanding. We explore how aspiration-driven strategy-update dynamics under imperfect rationality influence the average abundance of a strategy in multi-player evolutionary games with two strategies. We analytically derive a condition under which a strategy is more abundant than the other in the weak selection limiting case. This approach has a long-standing history in evolutionary games and is mostly applied for its mathematical approachability. Hence, we also explore strong selection numerically, which shows that our weak selection condition is a robust predictor of the average abundance of a strategy. The condition turns out to differ from that of a wide class of imitation dynamics, as long as the game is not dyadic. Therefore, a strategy favoured under imitation dynamics can be disfavoured under aspiration dynamics. This does not require any population structure, and thus highlights the intrinsic difference between imitation and aspiration dynamics.

Expression of parasite genetic variation changes over the course of infection: implications of within-host dynamics for the evolution of virulence.

PubMed

Clerc, Melanie; Ebert, Dieter; Hall, Matthew D

2015-04-07

How infectious disease agents interact with their host changes during the course of infection and can alter the expression of disease-related traits. Yet by measuring parasite life-history traits at one or few moments during infection, studies have overlooked the impact of variable parasite growth trajectories on disease evolution. Here we show that infection-age-specific estimates of host and parasite fitness components can reveal new insight into the evolution of parasites. We do so by characterizing the within-host dynamics over an entire infection period for five genotypes of the castrating bacterial parasite Pasteuria ramosa infecting the crustacean Daphnia magna. Our results reveal that genetic variation for parasite-induced gigantism, host castration and parasite spore loads increases with the age of infection. Driving these patterns appears to be variation in how well the parasite maintains control of host reproduction late in the infection process. We discuss the evolutionary consequences of this finding with regard to natural selection acting on different ages of infection and the mechanism underlying the maintenance of castration efficiency. Our results highlight how elucidating within-host dynamics can shed light on the selective forces that shape infection strategies and the evolution of virulence. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

The Role of Family Income Dynamics in Predicting Trajectories of Internalizing and Externalizing Problems.

PubMed

Miller, Portia; Votruba-Drzal, Elizabeth

2017-04-01

Economic disparities in children's behavioral functioning have been observed in prior research. Yet, studies have ignored important perspectives from developmental psychopathology and have not delineated how aspects of income dynamics (i.e., cumulative family income versus income volatility) differentially relate to behavior problems. To address these limitations, the current study examined how both cumulative income and income volatility predict trajectories of children's internalizing and externalizing problems from kindergarten through fifth grade in a nationally representative sample of 10,900 children (51.4 % male). Results showed four distinct trajectories of internalizing problems and five distinct externalizing trajectories. Family income dynamics were related to trajectory group membership. Specifically, increased cumulative income decreased risk of membership in mid-increasing and mid-stable internalizing groups, and children whose families experienced multiple waves of income loss were 2.4 times as likely to be in the mid-increasing group instead of the low-stable group. With respect to externalizing, higher cumulative income increased the likelihood of belonging in the group exhibiting stably low externalizing problems. Experiencing income loss increased the risk of belonging in the trajectory group exhibiting chronically high externalizing behaviors. These results enhance our knowledge of the role of family income in the development of behavior problems.

Enhanced sampling by multiple molecular dynamics trajectories: carbonmonoxy myoglobin 10 micros A0-->A(1-3) transition from ten 400 picosecond simulations.

PubMed

Loccisano, Anne E; Acevedo, Orlando; DeChancie, Jason; Schulze, Brita G; Evanseck, Jeffrey D

2004-05-01

The utility of multiple trajectories to extend the time scale of molecular dynamics simulations is reported for the spectroscopic A-states of carbonmonoxy myoglobin (MbCO). Experimentally, the A0-->A(1-3) transition has been observed to be 10 micros at 300 K, which is beyond the time scale of standard molecular dynamics simulations. To simulate this transition, 10 short (400 ps) and two longer time (1.2 ns) molecular dynamics trajectories, starting from five different crystallographic and solution phase structures with random initial velocities centered in a 37 A radius sphere of water, have been used to sample the native-fold of MbCO. Analysis of the ensemble of structures gathered over the cumulative 5.6 ns reveals two biomolecular motions involving the side chains of His64 and Arg45 to explain the spectroscopic states of MbCO. The 10 micros A0-->A(1-3) transition involves the motion of His64, where distance between His64 and CO is found to vary up to 8.8 +/- 1.0 A during the transition of His64 from the ligand (A(1-3)) to bulk solvent (A0). The His64 motion occurs within a single trajectory only once, however the multiple trajectories populate the spectroscopic A-states fully. Consequently, multiple independent molecular dynamics simulations have been found to extend biomolecular motion from 5 ns of total simulation to experimental phenomena on the microsecond time scale.

Optimization design and dynamic analysis on the drive mechanisms of flapping-wing air vehicles based on flapping trajectories

NASA Astrophysics Data System (ADS)

Xie, Lingwang; Zhang, Xingwei; Luo, Pan; Huang, Panpan

2017-10-01

The optimization designs and dynamic analysis on the driving mechanism of flapping-wing air vehicles on base of flapping trajectory patterns is carried out in this study. Three different driving mechanisms which are spatial double crank-rocker, plane five-bar and gear-double slider, are systematically optimized and analysed by using the Mat lab and Adams software. After a series debugging on the parameter, the comparatively ideal flapping trajectories are obtained by the simulation of Adams. Present results indicate that different drive mechanisms output different flapping trajectories and have their unique characteristic. The spatial double crank-rocker mechanism can only output the arc flapping trajectory and it has the advantages of small volume, high flexibility and efficient space utilization. Both planar five-bar mechanism and gear-double slider mechanism can output the oval, figure of eight and double eight flapping trajectories. Nevertheless, the gear-double slider mechanism has the advantage of convenient parameter setting and better performance in output double eight flapping trajectory. This study can provide theoretical basis and helpful reference for the design of the drive mechanisms of flapping-wing air vehicles with different output flapping trajectories.

Langevin synchronization in a time-dependent, harmonic basin: An exact solution in 1D

NASA Astrophysics Data System (ADS)

Cadilhe, A.; Voter, Arthur F.

2018-02-01

The trajectories of two particles undergoing Langevin dynamics while sharing a common noise sequence can merge into a single (master) trajectory. Here, we present an exact solution for a particle undergoing Langevin dynamics in a harmonic, time-dependent potential, thus extending the idea of synchronization to nonequilibrium systems. We calculate the synchronization level, i.e., the mismatch between two trajectories sharing a common noise sequence, in the underdamped, critically damped, and overdamped regimes. Finally, we provide asymptotic expansions in various limiting cases and compare to the time independent case.

Gut Microbiome and Infant Health: Brain-Gut-Microbiota Axis and Host Genetic Factors.

PubMed

Cong, Xiaomei; Xu, Wanli; Romisher, Rachael; Poveda, Samantha; Forte, Shaina; Starkweather, Angela; Henderson, Wendy A

2016-09-01

The development of the neonatal gut microbiome is influenced by multiple factors, such as delivery mode, feeding, medication use, hospital environment, early life stress, and genetics. The dysbiosis of gut microbiota persists during infancy, especially in high-risk preterm infants who experience lengthy stays in the Neonatal intensive care unit (NICU). Infant microbiome evolutionary trajectory is essentially parallel with the host (infant) neurodevelopmental process and growth. The role of the gut microbiome, the brain-gut signaling system, and its interaction with the host genetics have been shown to be related to both short and long term infant health and bio-behavioral development. The investigation of potential dysbiosis patterns in early childhood is still lacking and few studies have addressed this host-microbiome co-developmental process. Further research spanning a variety of fields of study is needed to focus on the mechanisms of brain-gut-microbiota signaling system and the dynamic host-microbial interaction in the regulation of health, stress and development in human newborns.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung.

PubMed

O'Brien, Siobhán; Fothergill, Joanne L

2017-08-15

Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome. © FEMS 2017.

The role of multispecies social interactions in shaping Pseudomonas aeruginosa pathogenicity in the cystic fibrosis lung

PubMed Central

Fothergill, Joanne L.

2017-01-01

Abstract Pseudomonas aeruginosa is a major pathogen in the lungs of cystic fibrosis (CF) patients. However, it is now recognised that a diverse microbial community exists in the airways comprising aerobic and anaerobic bacteria as well as fungi and viruses. This rich soup of microorganisms provides ample opportunity for interspecies interactions, particularly when considering secreted compounds. Here, we discuss how P. aeruginosa-secreted products can have community-wide effects, with the potential to ultimately shape microbial community dynamics within the lung. We focus on three well-studied traits associated with worsening clinical outcome in CF: phenazines, siderophores and biofilm formation, and discuss how secretions can shape interactions between P. aeruginosa and other commonly encountered members of the lung microbiome: Staphylococcus aureus, the Burkholderia cepacia complex, Candida albicans and Aspergillus fumigatus. These interactions may shape the evolutionary trajectory of P. aeruginosa while providing new opportunities for therapeutic exploitation of the CF lung microbiome. PMID:28859314

A dynamic parking charge optimal control model under perspective of commuters' evolutionary game behavior

NASA Astrophysics Data System (ADS)

Lin, XuXun; Yuan, PengCheng

2018-01-01

In this research we consider commuters' dynamic learning effect by modeling the trip mode choice behavior from a new perspective of dynamic evolutionary game theory. We explore the behavior pattern of different types of commuters and study the evolution path and equilibrium properties under different traffic conditions. We further establish a dynamic parking charge optimal control (referred to as DPCOC) model to alter commuters' trip mode choice while minimizing the total social cost. Numerical tests show. (1) Under fixed parking fee policy, the evolutionary results are completely decided by the travel time and the only method for public transit induction is to increase the parking charge price. (2) Compared with fixed parking fee policy, DPCOC policy proposed in this research has several advantages. Firstly, it can effectively turn the evolutionary path and evolutionary stable strategy to a better situation while minimizing the total social cost. Secondly, it can reduce the sensitivity of trip mode choice behavior to traffic congestion and improve the ability to resist interferences and emergencies. Thirdly, it is able to control the private car proportion to a stable state and make the trip behavior more predictable for the transportation management department. The research results can provide theoretical basis and decision-making references for commuters' mode choice prediction, dynamic setting of urban parking charge prices and public transit induction.

Dynamic characteristics of a pump-turbine during hydraulic transients of a model pumped-storage system: 3D CFD simulation

NASA Astrophysics Data System (ADS)

Zhang, X. X.; Cheng, Y. G.; Xia, L. S.; Yang, J. D.

2014-03-01

The runaway process in a model pumped-storage system was simulated for analyzing the dynamic characteristics of a pump-turbine. The simulation was adopted by coupling 1D (One Dimensional) pipeline MOC (Method of Characteristics) equations with a 3D (Three Dimensional) pump-turbine CFD (Computational Fluid Dynamics) model, in which the water hammer wave in the 3D zone was defined by giving a pressure dependent density. We found from the results that the dynamic performances of the pump-turbine do not coincide with the static operating points, especially in the S-shaped characteristics region, where the dynamic trajectories follow ring-shaped curves. Specifically, the transient operating points with the same Q11 and M11 in different moving directions of the dynamic trajectories give different n11. The main reason of this phenomenon is that the transient flow patterns inside the pump-turbine are influenced by the ones in the previous time step, which leads to different flow patterns between the points with the same Q11 and M11 in different moving directions of the dynamic trajectories.

Genetic algorithm for investigating flight MH370 in Indian Ocean using remotely sensed data

NASA Astrophysics Data System (ADS)

Marghany, Maged; Mansor, Shattri; Shariff, Abdul Rashid Bin Mohamed

2016-06-01

This study utilized Genetic algorithm (GA) for automatic detection and simulation trajectory movements of flight MH370 debris. In doing so, the Ocean Surface Topography Mission(OSTM) on the Jason- 2 satellite have been used within 1 and half year covers data to simulate the pattern of Flight MH370 debris movements across the southern Indian Ocean. Further, multi-objectives evolutionary algorithm also used to discriminate uncertainty of flight MH370 imagined and detection. The study shows that the ocean surface current speed is 0.5 m/s. This current patterns have developed a large anticlockwise gyre over a water depth of 8,000 m. The multi-objectives evolutionary algorithm suggested that objects are existed on satellite data are not flight MH370 debris. In addition, multiobjectives evolutionary algorithm suggested that the difficulties to acquire the exact location of flight MH370 due to complicated hydrodynamic movements across the southern Indian Ocean.

Evolutionary Computation for the Identification of Emergent Behavior in Autonomous Systems

NASA Technical Reports Server (NTRS)

Terrile, Richard J.; Guillaume, Alexandre

2009-01-01

Over the past several years the Center for Evolutionary Computation and Automated Design at the Jet Propulsion Laboratory has developed a technique based on Evolutionary Computational Methods (ECM) that allows for the automated optimization of complex computationally modeled systems. An important application of this technique is for the identification of emergent behaviors in autonomous systems. Mobility platforms such as rovers or airborne vehicles are now being designed with autonomous mission controllers that can find trajectories over a solution space that is larger than can reasonably be tested. It is critical to identify control behaviors that are not predicted and can have surprising results (both good and bad). These emergent behaviors need to be identified, characterized and either incorporated into or isolated from the acceptable range of control characteristics. We use cluster analysis of automatically retrieved solutions to identify isolated populations of solutions with divergent behaviors.

Evolution of cyclohexadienyl dehydratase from an ancestral solute-binding protein.

PubMed

Clifton, Ben E; Kaczmarski, Joe A; Carr, Paul D; Gerth, Monica L; Tokuriki, Nobuhiko; Jackson, Colin J

2018-04-23

The emergence of enzymes through the neofunctionalization of noncatalytic proteins is ultimately responsible for the extraordinary range of biological catalysts observed in nature. Although the evolution of some enzymes from binding proteins can be inferred by homology, we have a limited understanding of the nature of the biochemical and biophysical adaptations along these evolutionary trajectories and the sequence in which they occurred. Here we reconstructed and characterized evolutionary intermediate states linking an ancestral solute-binding protein to the extant enzyme cyclohexadienyl dehydratase. We show how the intrinsic reactivity of a desolvated general acid was harnessed by a series of mutations radiating from the active site, which optimized enzyme-substrate complementarity and transition-state stabilization and minimized sampling of noncatalytic conformations. Our work reveals the molecular evolutionary processes that underlie the emergence of enzymes de novo, which are notably mirrored by recent examples of computational enzyme design and directed evolution.

Eocene evolution of whale hearing.

PubMed

Nummela, Sirpa; Thewissen, J G M; Bajpai, Sunil; Hussain, S Taseer; Kumar, Kishor

2004-08-12

The origin of whales (order Cetacea) is one of the best-documented examples of macroevolutionary change in vertebrates. As the earliest whales became obligately marine, all of their organ systems adapted to the new environment. The fossil record indicates that this evolutionary transition took less than 15 million years, and that different organ systems followed different evolutionary trajectories. Here we document the evolutionary changes that took place in the sound transmission mechanism of the outer and middle ear in early whales. Sound transmission mechanisms change early on in whale evolution and pass through a stage (in pakicetids) in which hearing in both air and water is unsophisticated. This intermediate stage is soon abandoned and is replaced (in remingtonocetids and protocetids) by a sound transmission mechanism similar to that in modern toothed whales. The mechanism of these fossil whales lacks sophistication, and still retains some of the key elements that land mammals use to hear airborne sound.

Bridging Developmental Systems Theory and Evolutionary Psychology Using Dynamic Optimization

ERIC Educational Resources Information Center

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

2013-01-01

Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic…

Evolutionary Dynamics of Digitized Organizational Routines

ERIC Educational Resources Information Center

Liu, Peng

2013-01-01

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

Ecological and evolutionary approaches to managing honeybee disease.

PubMed

Brosi, Berry J; Delaplane, Keith S; Boots, Michael; de Roode, Jacobus C

2017-09-01

Honeybee declines are a serious threat to global agricultural security and productivity. Although multiple factors contribute to these declines, parasites are a key driver. Disease problems in honeybees have intensified in recent years, despite increasing attention to addressing them. Here we argue that we must focus on the principles of disease ecology and evolution to understand disease dynamics, assess the severity of disease threats, and control these threats via honeybee management. We cover the ecological context of honeybee disease, including both host and parasite factors driving current transmission dynamics, and then discuss evolutionary dynamics including how beekeeping management practices may drive selection for more virulent parasites. We then outline how ecological and evolutionary principles can guide disease mitigation in honeybees, including several practical management suggestions for addressing short- and long-term disease dynamics and consequences.

Space shuttle launch vehicle performance trajectory, exchange ratios, and dispersion analysis

NASA Technical Reports Server (NTRS)

Toelle, R. G.; Blackwell, D. L.; Lott, L. N.

1973-01-01

A baseline space shuttle performance trajectory for Mission 3A launched from WTR has been generated. Design constraints of maximum dynamic pressure, longitudinal acceleration, and delivered payload were satisfied. Payload exchange ratios are presented with explanation on use. Design envelopes of dynamic pressure, SRB staging point, aerodynamic heating and flight performance reserves are calculated and included.

A dynamical systems approach to actin-based motility in Listeria monocytogenes

NASA Astrophysics Data System (ADS)

Hotton, S.

2010-11-01

A simple kinematic model for the trajectories of Listeria monocytogenes is generalized to a dynamical system rich enough to exhibit the resonant Hopf bifurcation structure of excitable media and simple enough to be studied geometrically. It is shown how L. monocytogenes trajectories and meandering spiral waves are organized by the same type of attracting set.

Comparing Classical Water Models Using Molecular Dynamics to Find Bulk Properties

ERIC Educational Resources Information Center

Kinnaman, Laura J.; Roller, Rachel M.; Miller, Carrie S.

2018-01-01

A computational chemistry exercise for the undergraduate physical chemistry laboratory is described. In this exercise, students use the molecular dynamics package Amber to generate trajectories of bulk liquid water for 4 different water models (TIP3P, OPC, SPC/E, and TIP4Pew). Students then process the trajectory to calculate structural (radial…

Laboratory evolution of protein conformational dynamics.

PubMed

Campbell, Eleanor C; Correy, Galen J; Mabbitt, Peter D; Buckle, Ashley M; Tokuriki, Nobuhiko; Jackson, Colin J

2017-11-08

This review focuses on recent work that has begun to establish specific functional roles for protein conformational dynamics, specifically how the conformational landscapes that proteins can sample can evolve under laboratory based evolutionary selection. We discuss recent technical advances in computational and biophysical chemistry, which have provided us with new ways to dissect evolutionary processes. Finally, we offer some perspectives on the emerging view of conformational dynamics and evolution, and the challenges that we face in rationally engineering conformational dynamics. Copyright © 2017 Elsevier Ltd. All rights reserved.

Trajectory optimization for the National Aerospace Plane

NASA Technical Reports Server (NTRS)

Lu, Ping

1992-01-01

The primary objective of this research is to develop an efficient and robust trajectory optimization tool for the optimal ascent problem of the National Aerospace Plane (NASP). This report is organized in the following order to summarize the complete work: Section two states the formulation and models of the trajectory optimization problem. An inverse dynamics approach to the problem is introduced in Section three. Optimal trajectories corresponding to various conditions and performance parameters are presented in Section four. A midcourse nonlinear feedback controller is developed in Section five. Section six demonstrates the performance of the inverse dynamics approach and midcourse controller during disturbances. Section seven discusses rocket assisted ascent which may be beneficial when orbital altitude is high. Finally, Section eight recommends areas of future research.

A practical six-degree of freedom solar sail dynamics model for optimizing solar sail trajectories with torque constraints

NASA Technical Reports Server (NTRS)

Lisano, Michael E.

2004-01-01

Controlled flight of a solar sail-propelled spacecraft ('sailcraft') is a six-degree-of-freedom dynamics problem. Current state-of-the-art tools that simulate and optimize the trajectories flown by sailcraft do not treat the full kinetic (i.e. force and torque-constrained) motion, instead treating a discrete history of commanded sail attitudes, and either neglecting the sail attitude motion over an integration timestep, or treating the attitude evolution kinematically with a spline or similar treatment. The present paper discusses an aspect of developing a next generation sailcraf trajectory designing optimization tool JPL, for NASA's Solar Sail Spaceflight Simulation Software (SS). The aspect discussed in an experimental approach to modeling full six-degree-of-freedom kinetic motion of a solar sail in a trajectory propagator. Early results from implementing this approach in a new trajectory propagation tool are given.

The Price Equation, Gradient Dynamics, and Continuous Trait Game Theory.

PubMed

Lehtonen, Jussi

2018-01-01

A recent article convincingly nominated the Price equation as the fundamental theorem of evolution and used it as a foundation to derive several other theorems. A major section of evolutionary theory that was not addressed is that of game theory and gradient dynamics of continuous traits with frequency-dependent fitness. Deriving fundamental results in these fields under the unifying framework of the Price equation illuminates similarities and differences between approaches and allows a simple, unified view of game-theoretical and dynamic concepts. Using Taylor polynomials and the Price equation, I derive a dynamic measure of evolutionary change, a condition for singular points, the convergence stability criterion, and an alternative interpretation of evolutionary stability. Furthermore, by applying the Price equation to a multivariable Taylor polynomial, the direct fitness approach to kin selection emerges. Finally, I compare these results to the mean gradient equation of quantitative genetics and the canonical equation of adaptive dynamics.

Neuronal boost to evolutionary dynamics.

PubMed

de Vladar, Harold P; Szathmáry, Eörs

2015-12-06

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

Evolutionary branching under multi-dimensional evolutionary constraints.

PubMed

Ito, Hiroshi; Sasaki, Akira

2016-10-21

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

Selection on Network Dynamics Drives Differential Rates of Protein Domain Evolution

PubMed Central

Mannakee, Brian K.; Gutenkunst, Ryan N.

2016-01-01

The long-held principle that functionally important proteins evolve slowly has recently been challenged by studies in mice and yeast showing that the severity of a protein knockout only weakly predicts that protein’s rate of evolution. However, the relevance of these studies to evolutionary changes within proteins is unknown, because amino acid substitutions, unlike knockouts, often only slightly perturb protein activity. To quantify the phenotypic effect of small biochemical perturbations, we developed an approach to use computational systems biology models to measure the influence of individual reaction rate constants on network dynamics. We show that this dynamical influence is predictive of protein domain evolutionary rate within networks in vertebrates and yeast, even after controlling for expression level and breadth, network topology, and knockout effect. Thus, our results not only demonstrate the importance of protein domain function in determining evolutionary rate, but also the power of systems biology modeling to uncover unanticipated evolutionary forces. PMID:27380265

The one-third law of evolutionary dynamics.

PubMed

Ohtsuki, Hisashi; Bordalo, Pedro; Nowak, Martin A

2007-11-21

Evolutionary game dynamics in finite populations provide a new framework for studying selection of traits with frequency-dependent fitness. Recently, a "one-third law" of evolutionary dynamics has been described, which states that strategy A fixates in a B-population with selective advantage if the fitness of A is greater than that of B when A has a frequency 13. This relationship holds for all evolutionary processes examined so far, from the Moran process to games on graphs. However, the origin of the "number"13 is not understood. In this paper we provide an intuitive explanation by studying the underlying stochastic processes. We find that in one invasion attempt, an individual interacts on average with B-players twice as often as with A-players, which yields the one-third law. We also show that the one-third law implies that the average Malthusian fitness of A is positive.

Learning State Space Dynamics in Recurrent Networks

NASA Astrophysics Data System (ADS)

Simard, Patrice Yvon

Fully recurrent (asymmetrical) networks can be used to learn temporal trajectories. The network is unfolded in time, and backpropagation is used to train the weights. The presence of recurrent connections creates internal states in the system which vary as a function of time. The resulting dynamics can provide interesting additional computing power but learning is made more difficult by the existence of internal memories. This study first exhibits the properties of recurrent networks in terms of convergence when the internal states of the system are unknown. A new energy functional is provided to change the weights of the units in order to the control the stability of the fixed points of the network's dynamics. The power of the resultant algorithm is illustrated with the simulation of a content addressable memory. Next, the more general case of time trajectories on a recurrent network is studied. An application is proposed in which trajectories are generated to draw letters as a function of an input. In another application of recurrent systems, a neural network certain temporal properties observed in human callosally sectioned brains. Finally the proposed algorithm for stabilizing dynamics around fixed points is extended to one for stabilizing dynamics around time trajectories. Its effects are illustrated on a network which generates Lisajous curves.

Trajectories of Identity Formation Modes and Their Personality Context in Adolescence.

PubMed

Topolewska-Siedzik, Ewa; Cieciuch, Jan

2018-04-01

Identity formation is a dynamic process during adolescence. Trajectories of identity formation were assessed longitudinally in early and middle adolescents, taking into account the personality underpinnings of this process. Identity formation was conceptualized according to the circumplex of identity formation modes. The model distinguishes basic modes rooted in Marcia's categories of exploration and commitment. Plasticity and stability, the two higher order Big Five meta-traits, were used to assess personality underpinnings. This study includes five measurement waves over 1.5 years and involves 1,839 Polish participants; 914 early adolescents (53.9% girls) and 925 middle adolescents (63.8% girls). The results suggest that (1) the four identity formation modes change dynamically, showing linear and curvilinear growth and that (2) identity formation mode trajectories are more dynamic in middle adolescence than in early adolescence. The results also showed that, in the conditional model, (3) the higher-order personality factors and gender affect the growth factors of identity formation modes. Overall, trajectories of identity formation modes are more linear during early adolescence and more curvilinear during middle adolescence. The initial levels in identity trajectories are influenced by the personality metatraits but only plasticity is related to change among early adolescents.

Direct dynamics simulations of the unimolecular dissociation of dioxetane: Probing the non-RRKM dynamics

NASA Astrophysics Data System (ADS)

Malpathak, Shreyas; Ma, Xinyou; Hase, William L.

2018-04-01

In a previous UB3LYP/6-31G* direct dynamics simulation, non-Rice-Ramsperger-Kassel-Marcus (RRKM) unimolecular dynamics was found for vibrationally excited 1,2-dioxetane (DO); [R. Sun et al., J. Chem. Phys. 137, 044305 (2012)]. In the work reported here, these dynamics are studied in more detail using the same direct dynamics method. Vibrational modes of DO were divided into 4 groups, based on their characteristic motions, and each group excited with the same energy. To compare with the dynamics of these groups, an additional group of trajectories comprising a microcanonical ensemble was also simulated. The results of these simulations are consistent with the previous study. The dissociation probability, N(t)/N(0), for these excitation groups were all different. Groups A, B, and C, without initial excitation in the O-O stretch reaction coordinate, had a time lag to of 0.25-1.0 ps for the first dissociation to occur. Somewhat surprisingly, the C-H stretch Group A and out-of-plane motion Group C excitations had exponential dissociation probabilities after to, with a rate constant ˜2 times smaller than the anharmonic RRKM value. Groups B and D, with excitation of the H-C-H bend and wag, and ring bend and stretch modes, respectively, had bi-exponential dissociation probabilities. For Group D, with excitation localized in the reaction coordinate, the initial rate constant is ˜7 times larger than the anharmonic RRKM value, substantial apparent non-RRKM dynamics. N(t)/N(0) for the random excitation trajectories was non-exponential, indicating intrinsic non-RRKM dynamics. For the trajectory integration time of 13.5 ps, 9% of these trajectories did not dissociate in comparison to the RRKM prediction of 0.3%. Classical power spectra for these trajectories indicate they have regular intramolecular dynamics. The N(t)/N(0) for the excitation groups are well described by a two-state coupled phase space model. From the intercept of N(t)/N(0) with random excitation, the anharmonic correction to the RRKM rate constant is approximately a factor of 1.5.

Moyal dynamics and trajectories

NASA Astrophysics Data System (ADS)

Braunss, G.

2010-01-01

We give first an approximation of the operator δh: f → δhf := h*planckf - f*planckh in terms of planck2n, n >= 0, where h\\equiv h(p,q), (p,q)\\in {\\mathbb R}^{2 n} , is a Hamilton function and *planck denotes the star product. The operator, which is the generator of time translations in a *planck-algebra, can be considered as a canonical extension of the Liouville operator Lh: f → Lhf := {h, f}Poisson. Using this operator we investigate the dynamics and trajectories of some examples with a scheme that extends the Hamilton-Jacobi method for classical dynamics to Moyal dynamics. The examples we have chosen are Hamiltonians with a one-dimensional quartic potential and two-dimensional radially symmetric nonrelativistic and relativistic Coulomb potentials, and the Hamiltonian for a Schwarzschild metric. We further state a conjecture concerning an extension of the Bohr-Sommerfeld formula for the calculation of the exact eigenvalues for systems with classically periodic trajectories.

Trajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter

PubMed Central

Sikorski, Johannes; Bunk, Boyke; Scheuner, Carmen; Meier-Kolthoff, Jan P; Spröer, Cathrin; Gram, Lone; Overmann, Jörg

2017-01-01

Abstract The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists. PMID:29194520

Evolutionary trend toward kinetic stability in the folding trajectory of RNases H

PubMed Central

Lim, Shion A.; Hart, Kathryn M.; Marqusee, Susan

2016-01-01

Proper folding of proteins is critical to producing the biological machinery essential for cellular function. The rates and energetics of a protein’s folding process, which is described by its energy landscape, are encoded in the amino acid sequence. Over the course of evolution, this landscape must be maintained such that the protein folds and remains folded over a biologically relevant time scale. How exactly a protein’s energy landscape is maintained or altered throughout evolution is unclear. To study how a protein’s energy landscape changed over time, we characterized the folding trajectories of ancestral proteins of the ribonuclease H (RNase H) family using ancestral sequence reconstruction to access the evolutionary history between RNases H from mesophilic and thermophilic bacteria. We found that despite large sequence divergence, the overall folding pathway is conserved over billions of years of evolution. There are robust trends in the rates of protein folding and unfolding; both modern RNases H evolved to be more kinetically stable than their most recent common ancestor. Finally, our study demonstrates how a partially folded intermediate provides a readily adaptable folding landscape by allowing the independent tuning of kinetics and thermodynamics. PMID:27799545

Evolution of neuroarchitecture, multi-level analyses and calibrative reductionism

PubMed Central

Berntson, Gary G.; Norman, Greg J.; Hawkley, Louise C.; Cacioppo, John T.

2012-01-01

Evolution has sculpted the incredibly complex human nervous system, among the most complex functions of which extend beyond the individual to an intricate social structure. Although these functions are deterministic, those determinants are legion, heavily interacting and dependent on a specific evolutionary trajectory. That trajectory was directed by the adaptive significance of quasi-random genetic variations, but was also influenced by chance and caprice. With a different evolutionary pathway, the same neural elements could subserve functions distinctly different from what they do in extant human brains. Consequently, the properties of higher level neural networks cannot be derived readily from the properties of the lower level constituent elements, without studying these elements in the aggregate. Thus, a multi-level approach to integrative neuroscience may offer an optimal strategy. Moreover, the process of calibrative reductionism, by which concepts and understandings from one level of organization or analysis can mutually inform and ‘calibrate’ those from other levels (both higher and lower), may represent a viable approach to the application of reductionism in science. This is especially relevant in social neuroscience, where the basic subject matter of interest is defined by interacting organisms across diverse environments. PMID:23386961

The impact of rapid evolution on population dynamics in the wild: experimental test of eco-evolutionary dynamics.

PubMed

Turcotte, Martin M; Reznick, David N; Hare, J Daniel

2011-11-01

Rapid evolution challenges the assumption that evolution is too slow to impact short-term ecological dynamics. This insight motivates the study of 'Eco-Evolutionary Dynamics' or how evolution and ecological processes reciprocally interact on short time scales. We tested how rapid evolution impacts concurrent population dynamics using an aphid (Myzus persicae) and an undomesticated host (Hirschfeldia incana) in replicated wild populations. We manipulated evolvability by creating non-evolving (single clone) and potentially evolving (two-clone) aphid populations that contained genetic variation in intrinsic growth rate. We observed significant evolution in two-clone populations whether or not they were exposed to predators and competitors. Evolving populations grew up to 42% faster and attained up to 67% higher density, compared with non-evolving control populations but only in treatments exposed to competitors and predators. Increased density also correlates with relative fitness of competing clones suggesting a full eco-evolutionary dynamic cycle defined as reciprocal interactions between evolution and density. © 2011 Blackwell Publishing Ltd/CNRS.

Trajectory Adjustments Underlying Task-Specific Intermittent Force Behaviors and Muscular Rhythms

PubMed Central

Chen, Yi-Ching; Lin, Yen-Ting; Huang, Chien-Ting; Shih, Chia-Li; Yang, Zong-Ru; Hwang, Ing-Shiou

2013-01-01

Force intermittency is one of the major causes of motor variability. Focusing on the dynamics of force intermittency, this study was undertaken to investigate how force trajectory is fine-tuned for static and dynamic force-tracking of a comparable physical load. Twenty-two healthy adults performed two unilateral resistance protocols (static force-tracking at 75% maximal effort and dynamic force-tracking in the range of 50%–100% maximal effort) using the left hand. The electromyographic activity and force profile of the designated hand were monitored. Gripping force was off-line decomposed into a primary movement spectrally identical to the target motion and a force intermittency profile containing numerous force pulses. The results showed that dynamic force-tracking exhibited greater intermittency amplitude and force pulse but a smaller amplitude ratio of primary movement to force intermittency than static force-tracking. Multi-scale entropy analysis revealed that force intermittency during dynamic force-tracking was more complex on a low time scale but more regular on a high time scale than that of static force-tracking. Together with task-dependent force intermittency properties, dynamic force-tracking exhibited a smaller 8–12 Hz muscular oscillation but a more potentiated muscular oscillation at 35–50 Hz than static force-tracking. In conclusion, force intermittency reflects differing trajectory controls for static and dynamic force-tracking. The target goal of dynamic tracking is achieved through trajectory adjustments that are more intricate and more frequent than those of static tracking, pertaining to differing organizations and functioning of muscular oscillations in the alpha and gamma bands. PMID:24098640

Limits in the evolution of biological form: a theoretical morphologic perspective.

PubMed

McGhee, George R

2015-12-06

Limits in the evolution of biological form can be empirically demonstrated by using theoretical morphospace analyses, and actual analytic examples are given for univalved ammonoid shell form, bivalved brachiopod shell form and helical bryozoan colony form. Limits in the evolution of form in these animal groups can be shown to be due to functional and developmental constraints on possible evolutionary trajectories in morphospace. Future evolutionary-limit research is needed to analyse the possible existence of temporal constraint in the evolution of biological form on Earth, and in the search for the possible existence of functional alien life forms on Titan and Triton that are developmentally impossible for Earth life.

Trajectory optimization of spacecraft high-thrust orbit transfer using a modified evolutionary algorithm

NASA Astrophysics Data System (ADS)

Shirazi, Abolfazl

2016-10-01

This article introduces a new method to optimize finite-burn orbital manoeuvres based on a modified evolutionary algorithm. Optimization is carried out based on conversion of the orbital manoeuvre into a parameter optimization problem by assigning inverse tangential functions to the changes in direction angles of the thrust vector. The problem is analysed using boundary delimitation in a common optimization algorithm. A method is introduced to achieve acceptable values for optimization variables using nonlinear simulation, which results in an enlarged convergence domain. The presented algorithm benefits from high optimality and fast convergence time. A numerical example of a three-dimensional optimal orbital transfer is presented and the accuracy of the proposed algorithm is shown.

Evolutionary Inference across Eukaryotes Identifies Specific Pressures Favoring Mitochondrial Gene Retention.

PubMed

Johnston, Iain G; Williams, Ben P

2016-02-24

Since their endosymbiotic origin, mitochondria have lost most of their genes. Although many selective mechanisms underlying the evolution of mitochondrial genomes have been proposed, a data-driven exploration of these hypotheses is lacking, and a quantitatively supported consensus remains absent. We developed HyperTraPS, a methodology coupling stochastic modeling with Bayesian inference, to identify the ordering of evolutionary events and suggest their causes. Using 2015 complete mitochondrial genomes, we inferred evolutionary trajectories of mtDNA gene loss across the eukaryotic tree of life. We find that proteins comprising the structural cores of the electron transport chain are preferentially encoded within mitochondrial genomes across eukaryotes. A combination of high GC content and high protein hydrophobicity is required to explain patterns of mtDNA gene retention; a model that accounts for these selective pressures can also predict the success of artificial gene transfer experiments in vivo. This work provides a general method for data-driven inference of the ordering of evolutionary and progressive events, here identifying the distinct features shaping mitochondrial genomes of present-day species. Copyright © 2016 Elsevier Inc. All rights reserved.

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.

Emerging Concepts of Data Integration in Pathogen Phylodynamics.

PubMed

Baele, Guy; Suchard, Marc A; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics.

Emerging Concepts of Data Integration in Pathogen Phylodynamics

PubMed Central

Baele, Guy; Suchard, Marc A.; Rambaut, Andrew; Lemey, Philippe

2017-01-01

Phylodynamics has become an increasingly popular statistical framework to extract evolutionary and epidemiological information from pathogen genomes. By harnessing such information, epidemiologists aim to shed light on the spatio-temporal patterns of spread and to test hypotheses about the underlying interaction of evolutionary and ecological dynamics in pathogen populations. Although the field has witnessed a rich development of statistical inference tools with increasing levels of sophistication, these tools initially focused on sequences as their sole primary data source. Integrating various sources of information, however, promises to deliver more precise insights in infectious diseases and to increase opportunities for statistical hypothesis testing. Here, we review how the emerging concept of data integration is stimulating new advances in Bayesian evolutionary inference methodology which formalize a marriage of statistical thinking and evolutionary biology. These approaches include connecting sequence to trait evolution, such as for host, phenotypic and geographic sampling information, but also the incorporation of covariates of evolutionary and epidemic processes in the reconstruction procedures. We highlight how a full Bayesian approach to covariate modeling and testing can generate further insights into sequence evolution, trait evolution, and population dynamics in pathogen populations. Specific examples demonstrate how such approaches can be used to test the impact of host on rabies and HIV evolutionary rates, to identify the drivers of influenza dispersal as well as the determinants of rabies cross-species transmissions, and to quantify the evolutionary dynamics of influenza antigenicity. Finally, we briefly discuss how data integration is now also permeating through the inference of transmission dynamics, leading to novel insights into tree-generative processes and detailed reconstructions of transmission trees. [Bayesian inference; birth–death models; coalescent models; continuous trait evolution; covariates; data integration; discrete trait evolution; pathogen phylodynamics. PMID:28173504

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

Treesearch

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

2012-01-01

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

Spatial evolutionary epidemiology of spreading epidemics

PubMed Central

2016-01-01

Most spatial models of host–parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. PMID:27798295

Spatial evolutionary epidemiology of spreading epidemics.

PubMed

Lion, S; Gandon, S

2016-10-26

Most spatial models of host-parasite interactions either neglect the possibility of pathogen evolution or consider that this process is slow enough for epidemiological dynamics to reach an equilibrium on a fast timescale. Here, we propose a novel approach to jointly model the epidemiological and evolutionary dynamics of spatially structured host and pathogen populations. Starting from a multi-strain epidemiological model, we use a combination of spatial moment equations and quantitative genetics to analyse the dynamics of mean transmission and virulence in the population. A key insight of our approach is that, even in the absence of long-term evolutionary consequences, spatial structure can affect the short-term evolution of pathogens because of the build-up of spatial differentiation in mean virulence. We show that spatial differentiation is driven by a balance between epidemiological and genetic effects, and this quantity is related to the effect of kin competition discussed in previous studies of parasite evolution in spatially structured host populations. Our analysis can be used to understand and predict the transient evolutionary dynamics of pathogens and the emergence of spatial patterns of phenotypic variation. © 2016 The Author(s).

A Smoluchowski model of crystallization dynamics of small colloidal clusters

NASA Astrophysics Data System (ADS)

Beltran-Villegas, Daniel J.; Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.; Bevan, Michael A.

2011-10-01

We investigate the dynamics of colloidal crystallization in a 32-particle system at a fixed value of interparticle depletion attraction that produces coexisting fluid and solid phases. Free energy landscapes (FELs) and diffusivity landscapes (DLs) are obtained as coefficients of 1D Smoluchowski equations using as order parameters either the radius of gyration or the average crystallinity. FELs and DLs are estimated by fitting the Smoluchowski equations to Brownian dynamics (BD) simulations using either linear fits to locally initiated trajectories or global fits to unbiased trajectories using Bayesian inference. The resulting FELs are compared to Monte Carlo Umbrella Sampling results. The accuracy of the FELs and DLs for modeling colloidal crystallization dynamics is evaluated by comparing mean first-passage times from BD simulations with analytical predictions using the FEL and DL models. While the 1D models accurately capture dynamics near the free energy minimum fluid and crystal configurations, predictions near the transition region are not quantitatively accurate. A preliminary investigation of ensemble averaged 2D order parameter trajectories suggests that 2D models are required to capture crystallization dynamics in the transition region.

Properties of the optimal trajectories for coplanar, aeroassisted orbital transfer

NASA Technical Reports Server (NTRS)

Miele, A.; Wang, T.; Deaton, A. W.

1990-01-01

The optimization of trajectories for coplaner, aeroassisted orbital transfer (AOT) from a high Earth orbit (HEO) to a low Earth orbit (LEO) is examined. In particular, HEO can be a geosynchronous Earth orbit (GEO). It is assumed that the initial and final orbits are circular, that the gravitational field is central and is governed by the inverse square law, and that two impulses are employed, one at HEO exit and one at LEO entry. During the atmospheric pass, the trajectory is controlled via the lift coefficient in such a way that the total characteristic velocity is minimized. First, an ideal optimal trajectory is determined analytically for lift coefficient unbounded. This trajectory is called grazing trajectory, because the atmospheric pass is made by flying at constant altitude along the edge of the atmosphere until the excess velocity is depleted. For the grazing trajectory, the lift coefficient varies in such a way that the lift, the centrifugal force due to the Earth's curvature, the weight, and the Coriolis force due to the Earth's rotation are in static balance. Also, the grazing trajectory minimizes the total characteristic velocity and simultaneously nearly minimizes the peak values of the altitude drop, dynamic pressure, and heating rate. Next, starting from the grazing trajectory results, a real optimal trajectory is determined numerically for the lift coefficient bounded from both below and above. This trajectory is characterized by atmospheric penetration with the smallest possible entry angle, followed by flight at the lift coefficient lower bound. Consistently with the grazing trajectory behavior, the real optimal trajectory minimizes the total characteristic velocity and simultaneously nearly minimizes the peak values of the altitude drop, the dynamic pressure, and the heating rate.

Implementation of optimal trajectory control of series resonant converter

NASA Technical Reports Server (NTRS)

Oruganti, Ramesh; Yang, James J.; Lee, Fred C.

1987-01-01

Due to the presence of a high-frequency LC tank circuit, the dynamics of a resonant converter are unpredictable. There is often a large surge of tank energy during transients. Using state-plane analysis technique, an optimal trajectory control utilizing the desired solution trajectory as the control law was previously proposed for the series resonant converters. The method predicts the fastest response possible with minimum energy surge in the resonant tank. The principle of the control and its experimental implementation are described here. The dynamics of the converter are shown to be close to time-optimal.

Trajectory Design Strategies for the NGST L2 Libration Point Mission

NASA Technical Reports Server (NTRS)

Folta, David; Cooley, Steven; Howell, Kathleen; Bauer, Frank H.

2001-01-01

The Origins' Next Generation Space Telescope (NGST) trajectory design is addressed in light of improved methods for attaining constrained orbit parameters and their control at the exterior collinear libration point, L2. The use of a dynamical systems approach, state-space equations for initial libration orbit control, and optimization to achieve constrained orbit parameters are emphasized. The NGST trajectory design encompasses a direct transfer and orbit maintenance under a constant acceleration. A dynamical systems approach can be used to provide a biased orbit and stationkeeping maintenance method that incorporates the constraint of a single axis correction scheme.

Low-Thrust Many-Revolution Trajectory Optimization via Differential Dynamic Programming and a Sundman Transformation

NASA Technical Reports Server (NTRS)

Aziz, Jonathan D.; Parker, Jeffrey S.; Scheeres, Daniel J.; Englander, Jacob A.

2017-01-01

Low-thrust trajectories about planetary bodies characteristically span a high count of orbital revolutions. Directing the thrust vector over many revolutions presents a challenging optimization problem for any conventional strategy. This paper demonstrates the tractability of low-thrust trajectory optimization about planetary bodies by applying a Sundman transformation to change the independent variable of the spacecraft equations of motion to the eccentric anomaly and performing the optimization with differential dynamic programming. Fuel-optimal geocentric transfers are shown in excess of 1000 revolutions while subject to Earths J2 perturbation and lunar gravity.

Life history determines genetic structure and evolutionary potential of host–parasite interactions

PubMed Central

Barrett, Luke G.; Thrall, Peter H.; Burdon, Jeremy J.; Linde, Celeste C.

2009-01-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns. PMID:18947899

Life history determines genetic structure and evolutionary potential of host-parasite interactions.

PubMed

Barrett, Luke G; Thrall, Peter H; Burdon, Jeremy J; Linde, Celeste C

2008-12-01

Measures of population genetic structure and diversity of disease-causing organisms are commonly used to draw inferences regarding their evolutionary history and potential to generate new variation in traits that determine interactions with their hosts. Parasite species exhibit a range of population structures and life-history strategies, including different transmission modes, life-cycle complexity, off-host survival mechanisms and dispersal ability. These are important determinants of the frequency and predictability of interactions with host species. Yet the complex causal relationships between spatial structure, life history and the evolutionary dynamics of parasite populations are not well understood. We demonstrate that a clear picture of the evolutionary potential of parasitic organisms and their demographic and evolutionary histories can only come from understanding the role of life history and spatial structure in influencing population dynamics and epidemiological patterns.

Cancer evolution: mathematical models and computational inference.

PubMed

Beerenwinkel, Niko; Schwarz, Roland F; Gerstung, Moritz; Markowetz, Florian

2015-01-01

Cancer is a somatic evolutionary process characterized by the accumulation of mutations, which contribute to tumor growth, clinical progression, immune escape, and drug resistance development. Evolutionary theory can be used to analyze the dynamics of tumor cell populations and to make inference about the evolutionary history of a tumor from molecular data. We review recent approaches to modeling the evolution of cancer, including population dynamics models of tumor initiation and progression, phylogenetic methods to model the evolutionary relationship between tumor subclones, and probabilistic graphical models to describe dependencies among mutations. Evolutionary modeling helps to understand how tumors arise and will also play an increasingly important prognostic role in predicting disease progression and the outcome of medical interventions, such as targeted therapy. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society of Systematic Biologists.

Wigner flow reveals topological order in quantum phase space dynamics.

PubMed

Steuernagel, Ole; Kakofengitis, Dimitris; Ritter, Georg

2013-01-18

The behavior of classical mechanical systems is characterized by their phase portraits, the collections of their trajectories. Heisenberg's uncertainty principle precludes the existence of sharply defined trajectories, which is why traditionally only the time evolution of wave functions is studied in quantum dynamics. These studies are quite insensitive to the underlying structure of quantum phase space dynamics. We identify the flow that is the quantum analog of classical particle flow along phase portrait lines. It reveals hidden features of quantum dynamics and extra complexity. Being constrained by conserved flow winding numbers, it also reveals fundamental topological order in quantum dynamics that has so far gone unnoticed.

Large deviations in the presence of cooperativity and slow dynamics

NASA Astrophysics Data System (ADS)

Whitelam, Stephen

2018-06-01

We study simple models of intermittency, involving switching between two states, within the dynamical large-deviation formalism. Singularities appear in the formalism when switching is cooperative or when its basic time scale diverges. In the first case the unbiased trajectory distribution undergoes a symmetry breaking, leading to a change in shape of the large-deviation rate function for a particular dynamical observable. In the second case the symmetry of the unbiased trajectory distribution remains unbroken. Comparison of these models suggests that singularities of the dynamical large-deviation formalism can signal the dynamical equivalent of an equilibrium phase transition but do not necessarily do so.

A coupling of homology modeling with multiple molecular dynamics simulation for identifying representative conformation of GPCR structures: a case study on human bombesin receptor subtype-3.

PubMed

Nowroozi, Amin; Shahlaei, Mohsen

2017-02-01

In this study, a computational pipeline was therefore devised to overcome homology modeling (HM) bottlenecks. The coupling of HM with molecular dynamics (MD) simulation is useful in that it tackles the sampling deficiency of dynamics simulations by providing good-quality initial guesses for the native structure. Indeed, HM also relaxes the severe requirement of force fields to explore the huge conformational space of protein structures. In this study, the interaction between the human bombesin receptor subtype-3 and MK-5046 was investigated integrating HM, molecular docking, and MD simulations. To improve conformational sampling in typical MD simulations of GPCRs, as in other biomolecules, multiple trajectories with different initial conditions can be employed rather than a single long trajectory. Multiple MD simulations of human bombesin receptor subtype-3 with different initial atomic velocities are applied to sample conformations in the vicinity of the structure generated by HM. The backbone atom conformational space distribution of replicates is analyzed employing principal components analysis. As a result, the averages of structural and dynamic properties over the twenty-one trajectories differ significantly from those obtained from individual trajectories.

Turbulence and the Stabilization Principle

NASA Technical Reports Server (NTRS)

Zak, Michail

2010-01-01

Further results of research, reported in several previous NASA Tech Briefs articles, were obtained on a mathematical formalism for postinstability motions of a dynamical system characterized by exponential divergences of trajectories leading to chaos (including turbulence). To recapitulate: Fictitious control forces are introduced to couple the dynamical equations with a Liouville equation that describes the evolution of the probability density of errors in initial conditions. These forces create a powerful terminal attractor in probability space that corresponds to occurrence of a target trajectory with probability one. The effect in ordinary perceived three-dimensional space is to suppress exponential divergences of neighboring trajectories without affecting the target trajectory. Con sequently, the postinstability motion is represented by a set of functions describing the evolution of such statistical quantities as expectations and higher moments, and this representation is stable. The previously reported findings are analyzed from the perspective of the authors Stabilization Principle, according to which (1) stability is recognized as an attribute of mathematical formalism rather than of underlying physics and (2) a dynamical system that appears unstable when modeled by differentiable functions only can be rendered stable by modifying the dynamical equations to incorporate intrinsic stochasticity.

Complexity Science Applications to Dynamic Trajectory Management: Research Strategies

NASA Technical Reports Server (NTRS)

Sawhill, Bruce; Herriot, James; Holmes, Bruce J.; Alexandrov, Natalia

2009-01-01

The promise of the Next Generation Air Transportation System (NextGen) is strongly tied to the concept of trajectory-based operations in the national airspace system. Existing efforts to develop trajectory management concepts are largely focused on individual trajectories, optimized independently, then de-conflicted among each other, and individually re-optimized, as possible. The benefits in capacity, fuel, and time are valuable, though perhaps could be greater through alternative strategies. The concept of agent-based trajectories offers a strategy for automation of simultaneous multiple trajectory management. The anticipated result of the strategy would be dynamic management of multiple trajectories with interacting and interdependent outcomes that satisfy multiple, conflicting constraints. These constraints would include the business case for operators, the capacity case for the Air Navigation Service Provider (ANSP), and the environmental case for noise and emissions. The benefits in capacity, fuel, and time might be improved over those possible under individual trajectory management approaches. The proposed approach relies on computational agent-based modeling (ABM), combinatorial mathematics, as well as application of "traffic physics" concepts to the challenge, and modeling and simulation capabilities. The proposed strategy could support transforming air traffic control from managing individual aircraft behaviors to managing systemic behavior of air traffic in the NAS. A system built on the approach could provide the ability to know when regions of airspace approach being "full," that is, having non-viable local solution space for optimizing trajectories in advance.

Ecological and evolutionary approaches to managing honey bee disease

PubMed Central

Brosi, Berry J.; Delaplane, Keith S.; Boots, Michael; de Roode, Jacobus C.

2017-01-01

Honey bee declines are a serious threat to global agricultural security and productivity. While multiple factors contribute to these declines, parasites are a key driver. Disease problems in honey bees have intensified in recent years, despite increasing attention to addressing them. Here we argue that we must focus on the principles of disease ecology and evolution to understand disease dynamics, assess the severity of disease threats, and manage these threats via honey bee management. We cover the ecological context of honey bee disease, including both host and parasite factors driving current transmission dynamics, and then discuss evolutionary dynamics including how beekeeping management practices may drive selection for more virulent parasites. We then outline how ecological and evolutionary principles can guide disease mitigation in honey bees, including several practical management suggestions for addressing short- and long-term disease dynamics and consequences. PMID:29046562

Determining individual variation in growth and its implication for life-history and population processes using the empirical Bayes method.

PubMed

Vincenzi, Simone; Mangel, Marc; Crivelli, Alain J; Munch, Stephan; Skaug, Hans J

2014-09-01

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and L∞ (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish.

Drift in ocean currents impacts intergenerational microbial exposure to temperature.

PubMed

Doblin, Martina A; van Sebille, Erik

2016-05-17

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034-1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming.

Antecedents of transition patterns of depressive symptom trajectories from adolescence to young adulthood.

PubMed

Lee, Tae Kyoung; Wickrama, Kandauda A S; Kwon, Josephine A; Lorenz, Frederick O; Oshri, Assaf

2017-11-01

This study examined (a) transition patterns from adolescent-specific depressive symptom trajectory classes to young adult-specific trajectory classes (N = 537; 15-26 years) and (b) identified risk factors associated with these transition patterns. The latent classes and transition analyses identified three transitional patterns of depressive symptom trajectories, including a deteriorating pattern (8.2%), a recovering pattern (22.5%), and a consistently low pattern (69.3%). Additionally, the results showed that contextual risk factors (i.e., negative economic events, negative romantic relationships, and low college enrolment rates) in the transition period to young adulthood were more positively associated with deteriorated or recovered transition patterns of depressive symptom trajectories than with the consistently low transition patterns even after taking into account the effects of adolescent risk factors. The identification of dynamic transition patterns in depressive symptom trajectories from adolescence to young adulthood and risk factors provide useful tools for preventive and intervention efforts. Statement of contribution What is already known on this subject? Heterogeneous trajectories of depressive symptoms across adolescence and young adulthood have been reported. Psychosocial characteristics differentiate trajectories of depressive symptoms from adolescence to young adulthood. What does this study add? Dynamic transition patterns of depressive symptom trajectories are found between adolescence and young adulthood. Life experiences in the transition period are uniquely associated with the transition patterns of depressive symptom trajectories even after adjusting the effects of adolescent characteristics. © 2017 The British Psychological Society.

Evolution and social epidemiology.

PubMed

Nishi, Akihiro

2015-11-01

Evolutionary biology, which aims to explain the dynamic process of shaping the diversity of life, has not yet significantly affected thinking in social epidemiology. Current challenges in social epidemiology include understanding how social exposures can affect our biology, explaining the dynamics of society and health, and designing better interventions that are mindful of the impact of exposures during critical periods. I review how evolutionary concepts and tools, such as fitness gradient in cultural evolution, evolutionary game theory, and contemporary evolution in cancer, can provide helpful insights regarding social epidemiology. Copyright © 2015 Elsevier Ltd. All rights reserved.

Observing single quantum trajectories of a superconducting qubit: ensemble properties and driven dynamics

NASA Astrophysics Data System (ADS)

Weber, Steven; Murch, K. W.; Chantasri, A.; Dressel, J.; Jordan, A. N.; Siddiqi, I.

2014-03-01

We use weak measurements to track individual quantum trajectories of a superconducting qubit embedded in a microwave cavity. Using a near-quantum-limited parametric amplifier, we selectively measure either the phase or amplitude of the cavity field, and thereby confine trajectories to either the equator or a meridian of the Bloch sphere. We analyze ensembles of trajectories to determine statistical properties such as the most likely path and most likely time connecting pre and post-selected quantum states. We compare our results with theoretical predictions derived from an action principle for continuous quantum measurement. Furthermore, by introducing a qubit drive, we investigate the interplay between unitary state evolution and non-unitary measurement dynamics. This work was supported by the IARPA CSQ program and the ONR.

Classical-trajectory simulation of accelerating neutral atoms with polarized intense laser pulses

NASA Astrophysics Data System (ADS)

Xia, Q. Z.; Fu, L. B.; Liu, J.

2013-03-01

In the present paper, we perform the classical trajectory Monte Carlo simulation of the complex dynamics of accelerating neutral atoms with linearly or circularly polarized intense laser pulses. Our simulations involve the ion motion as well as the tunneling ionization and the scattering dynamics of valence electron in the combined Coulomb and electromagnetic fields, for both helium (He) and magnesium (Mg). We show that for He atoms, only linearly polarized lasers can effectively accelerate the atoms, while for Mg atoms, we find that both linearly and circularly polarized lasers can successively accelerate the atoms. The underlying mechanism is discussed and the subcycle dynamics of accelerating trajectories is investigated. We have compared our theoretical results with a recent experiment [Eichmann Nature (London)NATUAS0028-083610.1038/nature08481 461, 1261 (2009)].

Phase space trajectories and Lyapunov exponents in the dynamics of an alpha-helical protein lattice with intra- and inter-spine interactions

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

Angelin Jeba, K.; Latha, M. M., E-mail: lathaisaac@yahoo.com; Jain, Sudhir R.

2015-11-15

The nonlinear dynamics of intra- and inter-spine interaction models of alpha-helical proteins is investigated by proposing a Hamiltonian using the first quantized operators. Hamilton's equations of motion are derived, and the dynamics is studied by constructing the trajectories and phase space plots in both cases. The phase space plots display a chaotic behaviour in the dynamics, which opens questions about the relationship between the chaos and exciton-exciton and exciton-phonon interactions. This is verified by plotting the Lyapunov characteristic exponent curves.

African wildlife conservation and the evolution of hunting institutions

NASA Astrophysics Data System (ADS)

't Sas-Rolfes, Michael

2017-11-01

Hunting regulation presents a significant challenge for contemporary global conservation governance. Motivated by various incentives, hunters may act legally or illegally, for or against the interests of conservation. Hunter incentives are shaped by the interactions between unevenly evolving formal and informal institutions, embedded in socio-ecological systems. To work effectively for conservation, regulatory interventions must take these evolving institutional interactions into account. Drawing on analytical tools from evolutionary institutional economics, this article examines the trajectory of African hunting regulation and its consequences. Concepts of institutional dynamics, fit, scale, and interplay are applied to case studies of rhinoceros and lion hunting to highlight issues of significance to conservation outcomes. These include important links between different forms of hunting and dynamic interplay with institutions of trade. The case studies reveal that inappropriate formal regulatory approaches may be undermined by adaptive informal market responses. Poorly regulated hunting may lead to calls for stricter regulations or bans, but such legal restrictions may in turn perversely lead to more intensified and organised illegal hunting activity, further undermining conservation objectives. I conclude by offering insights and recommendations to guide more effective future regulatory interventions and priorities for further research. Specifically, I advocate approaches that move beyond simplistic regulatory interventions toward more complex, but supportive, institutional arrangements that align formal and informal institutions through inclusive stakeholder engagement.

Using experimental evolution to identify druggable targets that could inhibit the evolution of antimicrobial resistance

PubMed Central

Mehta, Heer H.; Prater, Amy G.; Shamoo, Yousif

2017-01-01

With multi-drug and pan-drug resistant bacteria becoming increasingly common in hospitals, antibiotic resistance has threatened to return us to a pre-antibiotic era that would completely undermine modern medicine. There is an urgent need to develop new antibiotics and strategies to combat resistance that are substantially different from earlier drug discovery efforts. One such strategy that would complement current and future antibiotics would be a class of co-drugs that target the evolution of resistance and thereby extend the efficacy of specific classes of antibiotics. A critical step in the development of such strategies lies in understanding the critical evolutionary trajectories responsible for resistance and which proteins or biochemical pathways within those trajectories would be good candidates for co-drug discovery. We identify the most important steps in the evolution of resistance for a specific pathogen and antibiotic combination by evolving highly polymorphic populations of pathogens to resistance in a novel bioreactor that favors biofilm development. As the populations evolve to increasing drug concentrations, we use deep sequencing to elucidate the network of genetic changes responsible for resistance and subsequent in vitro biochemistry and often structure determination to determine how the adaptive mutations produce resistance. Importantly, the identification of the molecular steps, their frequency within the populations and their chronology within the evolutionary trajectory toward resistance is critical to assessing their relative importance. In this work, we discuss findings from the evolution of the ESKAPE pathogen, Pseudomonas aeruginosa to the drug of last resort, colistin to illustrate the power of this approach. PMID:28928474

The Effects of Auditory Information on 4-Month-Old Infants' Perception of Trajectory Continuity

ERIC Educational Resources Information Center

Bremner, J. Gavin; Slater, Alan M.; Johnson, Scott P.; Mason, Uschi C.; Spring, Jo

2012-01-01

Young infants perceive an object's trajectory as continuous across occlusion provided the temporal or spatial gap in perception is small. In 3 experiments involving 72 participants the authors investigated the effects of different forms of auditory information on 4-month-olds' perception of trajectory continuity. Provision of dynamic auditory…

Revealing nonergodic dynamics in living cells from a single particle trajectory

NASA Astrophysics Data System (ADS)

Lanoiselée, Yann; Grebenkov, Denis S.

2016-05-01

We propose the improved ergodicity and mixing estimators to identify nonergodic dynamics from a single particle trajectory. The estimators are based on the time-averaged characteristic function of the increments and can thus capture additional information on the process as compared to the conventional time-averaged mean-square displacement. The estimators are first investigated and validated for several models of anomalous diffusion, such as ergodic fractional Brownian motion and diffusion on percolating clusters, and nonergodic continuous-time random walks and scaled Brownian motion. The estimators are then applied to two sets of earlier published trajectories of mRNA molecules inside live Escherichia coli cells and of Kv2.1 potassium channels in the plasma membrane. These statistical tests did not reveal nonergodic features in the former set, while some trajectories of the latter set could be classified as nonergodic. Time averages along such trajectories are thus not representative and may be strongly misleading. Since the estimators do not rely on ensemble averages, the nonergodic features can be revealed separately for each trajectory, providing a more flexible and reliable analysis of single-particle tracking experiments in microbiology.

Feedback Integrators

NASA Astrophysics Data System (ADS)

Chang, Dong Eui; Jiménez, Fernando; Perlmutter, Matthew

2016-12-01

A new method is proposed to numerically integrate a dynamical system on a manifold such that the trajectory stably remains on the manifold and preserves the first integrals of the system. The idea is that given an initial point in the manifold we extend the dynamics from the manifold to its ambient Euclidean space and then modify the dynamics outside the intersection of the manifold and the level sets of the first integrals containing the initial point such that the intersection becomes a unique local attractor of the resultant dynamics. While the modified dynamics theoretically produces the same trajectory as the original dynamics, it yields a numerical trajectory that stably remains on the manifold and preserves the first integrals. The big merit of our method is that the modified dynamics can be integrated with any ordinary numerical integrator such as Euler or Runge-Kutta. We illustrate this method by applying it to three famous problems: the free rigid body, the Kepler problem and a perturbed Kepler problem with rotational symmetry. We also carry out simulation studies to demonstrate the excellence of our method and make comparisons with the standard projection method, a splitting method and Störmer-Verlet schemes.

Dynamic prediction in functional concurrent regression with an application to child growth.

PubMed

Leroux, Andrew; Xiao, Luo; Crainiceanu, Ciprian; Checkley, William

2018-04-15

In many studies, it is of interest to predict the future trajectory of subjects based on their historical data, referred to as dynamic prediction. Mixed effects models have traditionally been used for dynamic prediction. However, the commonly used random intercept and slope model is often not sufficiently flexible for modeling subject-specific trajectories. In addition, there may be useful exposures/predictors of interest that are measured concurrently with the outcome, complicating dynamic prediction. To address these problems, we propose a dynamic functional concurrent regression model to handle the case where both the functional response and the functional predictors are irregularly measured. Currently, such a model cannot be fit by existing software. We apply the model to dynamically predict children's length conditional on prior length, weight, and baseline covariates. Inference on model parameters and subject-specific trajectories is conducted using the mixed effects representation of the proposed model. An extensive simulation study shows that the dynamic functional regression model provides more accurate estimation and inference than existing methods. Methods are supported by fast, flexible, open source software that uses heavily tested smoothing techniques. © 2017 The Authors. Statistics in Medicine Published by John Wiley & Sons Ltd.

Evolutionary rescue from extinction is contingent on a lower rate of environmental change.

PubMed

Lindsey, Haley A; Gallie, Jenna; Taylor, Susan; Kerr, Benjamin

2013-02-28

The extinction rate of populations is predicted to rise under increasing rates of environmental change. If a population experiencing increasingly stressful conditions lacks appropriate phenotypic plasticity or access to more suitable habitats, then genetic change may be the only way to avoid extinction. Evolutionary rescue from extinction occurs when natural selection enriches a population for more stress-tolerant genetic variants. Some experimental studies have shown that lower rates of environmental change lead to more adapted populations or fewer extinctions. However, there has been little focus on the genetic changes that underlie evolutionary rescue. Here we demonstrate that some evolutionary trajectories are contingent on a lower rate of environmental change. We allowed hundreds of populations of Escherichia coli to evolve under variable rates of increase in concentration of the antibiotic rifampicin. We then genetically engineered all combinations of mutations from isolates evolved under lower rates of environmental change. By assessing fitness of these engineered strains across a range of drug concentrations, we show that certain genotypes are evolutionarily inaccessible under rapid environmental change. Rapidly deteriorating environments not only limit mutational opportunities by lowering population size, but they can also eliminate sets of mutations as evolutionary options. As anthropogenic activities are leading to environmental change at unprecedented rapidity, it is critical to understand how the rate of environmental change affects both demographic and genetic underpinnings of evolutionary rescue.

Allowable Trajectory Variations for Space Shuttle Orbiter Entry-Aeroheating CFD

NASA Technical Reports Server (NTRS)

Wood, William A.; Alter, Stephen J.

2008-01-01

Reynolds-number criteria are developed for acceptable variations in Space Shuttle Orbiter entry trajectories for use in computational aeroheating analyses. The criteria determine if an existing computational fluid dynamics solution for a particular trajectory can be extrapolated to a different trajectory. The criteria development begins by estimating uncertainties for seventeen types of computational aeroheating data, such as boundary layer thickness, at exact trajectory conditions. For each type of datum, the allowable uncertainty contribution due to trajectory variation is set to be half of the value of the estimated exact-trajectory uncertainty. Then, for the twelve highest-priority datum types, Reynolds-number relations between trajectory variation and output uncertainty are determined. From these relations the criteria are established for the maximum allowable trajectory variations. The most restrictive criterion allows a 25% variation in Reynolds number at constant Mach number between trajectories.

River channel adjustments in Southern Italy over the past 150 years and implications for channel recovery

NASA Astrophysics Data System (ADS)

Scorpio, Vittoria; Aucelli, Pietro P. C.; Giano, Salvatore I.; Pisano, Luca; Robustelli, Gaetano; Rosskopf, Carmen M.; Schiattarella, Marcello

2015-12-01

Multi-temporal GIS analysis of topographic maps and aerial photographs along with topographic and geomorphological surveys are used to assess evolutionary trends and key control factors of channel adjustments for five major rivers in southern Italy (the Trigno, Biferno, Volturno, Sinni and Crati rivers) to support assessment of channel recovery and river restoration. Three distinct phases of channel adjustment are identified over the past 150 years primarily driven by human disturbances. Firstly, slight channel widening dominated from the last decades of the nineteenth century to the 1950s. Secondly, from the 1950s to the end of the 1990s, altered sediment fluxes induced by in-channel mining and channel works brought about moderate to very intense incision (up to 6-7 m) accompanied by strong channel narrowing (up to 96%) and changes in channel configuration from multi-threaded to single-threaded patterns. Thirdly, the period from around 2000 to 2015 has been characterized by channel stabilization and local widening. Evolutionary trajectories of the rivers studied are quite similar to those reconstructed for other Italian rivers, particularly regarding the second phase of channel adjustments and ongoing transitions towards channel recovery in some reaches. Analyses of river dynamics, recovery potential and connectivity with sediment sources of the study reaches, framed in their catchment context, can be used as part of a wider interdisciplinary approach that views effective river restoration alongside sustainable and risk-reduced river management.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

PubMed

Hanson-Smith, Victor; Johnson, Alexander

2016-07-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories

PubMed Central

Hanson-Smith, Victor; Johnson, Alexander

2016-01-01

The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and “resurrect” (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server. PMID:27472806

Dynamic Adaptive Neural Network Arrays: A Neuromorphic Architecture

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

Disney, Adam; Reynolds, John

2015-01-01

Dynamic Adaptive Neural Network Array (DANNA) is a neuromorphic hardware implementation. It differs from most other neuromorphic projects in that it allows for programmability of structure, and it is trained or designed using evolutionary optimization. This paper describes the DANNA structure, how DANNA is trained using evolutionary optimization, and an application of DANNA to a very simple classification task.

An Evolutionary Complex Systems Decision-Support Tool for the Management of Operations

NASA Astrophysics Data System (ADS)

Baldwin, J. S.; Allen, P. M.; Ridgway, K.

2011-12-01

This research aimed to add both to the development of complex systems thinking in the subject area of Operations and Production Management and to the limited number of applications of computational models and simulations from the science of complex systems. The latter potentially offer helpful decision-support tools for operations and production managers. A mechanical engineering firm was used as a case study where a combined qualitative and quantitative methodological approach was employed to extract the required data from four senior managers. Company performance measures as well as firm technologies, practices and policies, and their relation and interaction with one another, were elicited. The data were subjected to an evolutionary complex systems model resulting in a series of simulations. The findings included both reassuring and some unexpected results. The simulation based on the CEO's opinions led the most cohesive and synergistic collection of practices describing the firm, closely followed by the Marketing and R&D Managers. The Manufacturing Manager's responses led to the most extreme evolutionary trajectory where the integrity of the entire firm came into question particularly when considering how employees were utilised. By drawing directly from the opinions and views of managers rather than from logical 'if-then' rules and averaged mathematical representations of agents that characterise agent-based and other self-organisational models, this work builds on previous applications by capturing a micro-level description of diversity and a learning effect that has been problematical not only in terms of theory but also in application. This approach can be used as a decision-support tool for operations and other managers providing a forum with which to explore a) the strengths, weaknesses and consequences of different decision-making capacities within the firm; b) the introduction of new manufacturing technologies, practices and policies; and, c) the different evolutionary trajectories that a firm can take.

Integrating protein structural dynamics and evolutionary analysis with Bio3D.

PubMed

Skjærven, Lars; Yao, Xin-Qiu; Scarabelli, Guido; Grant, Barry J

2014-12-10

Popular bioinformatics approaches for studying protein functional dynamics include comparisons of crystallographic structures, molecular dynamics simulations and normal mode analysis. However, determining how observed displacements and predicted motions from these traditionally separate analyses relate to each other, as well as to the evolution of sequence, structure and function within large protein families, remains a considerable challenge. This is in part due to the general lack of tools that integrate information of molecular structure, dynamics and evolution. Here, we describe the integration of new methodologies for evolutionary sequence, structure and simulation analysis into the Bio3D package. This major update includes unique high-throughput normal mode analysis for examining and contrasting the dynamics of related proteins with non-identical sequences and structures, as well as new methods for quantifying dynamical couplings and their residue-wise dissection from correlation network analysis. These new methodologies are integrated with major biomolecular databases as well as established methods for evolutionary sequence and comparative structural analysis. New functionality for directly comparing results derived from normal modes, molecular dynamics and principal component analysis of heterogeneous experimental structure distributions is also included. We demonstrate these integrated capabilities with example applications to dihydrofolate reductase and heterotrimeric G-protein families along with a discussion of the mechanistic insight provided in each case. The integration of structural dynamics and evolutionary analysis in Bio3D enables researchers to go beyond a prediction of single protein dynamics to investigate dynamical features across large protein families. The Bio3D package is distributed with full source code and extensive documentation as a platform independent R package under a GPL2 license from http://thegrantlab.org/bio3d/ .

Dynamic multipopulation and density dependent evolutionary games related to replicator dynamics. A metasimplex concept.

PubMed

Argasinski, Krzysztof

2006-07-01

This paper contains the basic extensions of classical evolutionary games (multipopulation and density dependent models). It is shown that classical bimatrix approach is inconsistent with other approaches because it does not depend on proportion between populations. The main conclusion is that interspecific proportion parameter is important and must be considered in multipopulation models. The paper provides a synthesis of both extensions (a metasimplex concept) which solves the problem intrinsic in the bimatrix model. It allows us to model interactions among any number of subpopulations including density dependence effects. We prove that all modern approaches to evolutionary games are closely related. All evolutionary models (except classical bimatrix approaches) can be reduced to a single population general model by a simple change of variables. Differences between classic bimatrix evolutionary games and a new model which is dependent on interspecific proportion are shown by examples.

A piecewise smooth model of evolutionary game for residential mobility and segregation

NASA Astrophysics Data System (ADS)

Radi, D.; Gardini, L.

2018-05-01

The paper proposes an evolutionary version of a Schelling-type dynamic system to model the patterns of residential segregation when two groups of people are involved. The payoff functions of agents are the individual preferences for integration which are empirically grounded. Differently from Schelling's model, where the limited levels of tolerance are the driving force of segregation, in the current setup agents benefit from integration. Despite the differences, the evolutionary model shows a dynamics of segregation that is qualitatively similar to the one of the classical Schelling's model: segregation is always a stable equilibrium, while equilibria of integration exist only for peculiar configurations of the payoff functions and their asymptotic stability is highly sensitive to parameter variations. Moreover, a rich variety of integrated dynamic behaviors can be observed. In particular, the dynamics of the evolutionary game is regulated by a one-dimensional piecewise smooth map with two kink points that is rigorously analyzed using techniques recently developed for piecewise smooth dynamical systems. The investigation reveals that when a stable internal equilibrium exists, the bimodal shape of the map leads to several different kinds of bifurcations, smooth, and border collision, in a complicated interplay. Our global analysis can give intuitions to be used by a social planner to maximize integration through social policies that manipulate people's preferences for integration.

Multiscale structure in eco-evolutionary dynamics

NASA Astrophysics Data System (ADS)

Stacey, Blake C.

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

Evolutionary game based control for biological systems with applications in drug delivery.

PubMed

Li, Xiaobo; Lenaghan, Scott C; Zhang, Mingjun

2013-06-07

Control engineering and analysis of biological systems have become increasingly important for systems and synthetic biology. Unfortunately, no widely accepted control framework is currently available for these systems, especially at the cell and molecular levels. This is partially due to the lack of appropriate mathematical models to describe the unique dynamics of biological systems, and the lack of implementation techniques, such as ultra-fast and ultra-small devices and corresponding control algorithms. This paper proposes a control framework for biological systems subject to dynamics that exhibit adaptive behavior under evolutionary pressures. The control framework was formulated based on evolutionary game based modeling, which integrates both the internal dynamics and the population dynamics. In the proposed control framework, the adaptive behavior was characterized as an internal dynamic, and the external environment was regarded as an external control input. The proposed open-interface control framework can be integrated with additional control algorithms for control of biological systems. To demonstrate the effectiveness of the proposed framework, an optimal control strategy was developed and validated for drug delivery using the pathogen Giardia lamblia as a test case. In principle, the proposed control framework can be applied to any biological system exhibiting adaptive behavior under evolutionary pressures. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards.

PubMed

Hagey, Travis J; Uyeda, Josef C; Crandell, Kristen E; Cheney, Jorn A; Autumn, Kellar; Harmon, Luke J

2017-10-01

Understanding macroevolutionary dynamics of trait evolution is an important endeavor in evolutionary biology. Ecological opportunity can liberate a trait as it diversifies through trait space, while genetic and selective constraints can limit diversification. While many studies have examined the dynamics of morphological traits, diverse morphological traits may yield the same or similar performance and as performance is often more proximately the target of selection, examining only morphology may give an incomplete understanding of evolutionary dynamics. Here, we ask whether convergent evolution of pad-bearing lizards has followed similar evolutionary dynamics, or whether independent origins are accompanied by unique constraints and selective pressures over macroevolutionary time. We hypothesized that geckos and anoles each have unique evolutionary tempos and modes. Using performance data from 59 species, we modified Brownian motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated origins estimated using Bayesian ancestral state reconstructions. We discovered that adhesive performance in geckos evolved in a fashion consistent with Brownian motion with a trend, whereas anoles evolved in bounded performance space consistent with more constrained evolution (an Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes can have quite distinctive evolutionary patterns, likely as a result of idiosyncratic constraints or ecological opportunities. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

Evolutionary dynamics of a smoothed war of attrition game.

PubMed

Iyer, Swami; Killingback, Timothy

2016-05-07

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

Testing for a genetic response to sexual selection in a wild Drosophila population.

PubMed

Gosden, T P; Thomson, J R; Blows, M W; Schaul, A; Chenoweth, S F

2016-06-01

In accordance with the consensus that sexual selection is responsible for the rapid evolution of display traits on macroevolutionary scales, microevolutionary studies suggest sexual selection is a widespread and often strong form of directional selection in nature. However, empirical evidence for the contemporary evolution of sexually selected traits via sexual rather than natural selection remains weak. In this study, we used a novel application of quantitative genetic breeding designs to test for a genetic response to sexual selection on eight chemical display traits from a field population of the fly, Drosophila serrata. Using our quantitative genetic approach, we were able to detect a genetically based difference in means between groups of males descended from fathers who had either successfully sired offspring or were randomly collected from the same wild population for one of these display traits, the diene (Z,Z)-5,9-C27 : 2 . Our experimental results, in combination with previous laboratory studies on this system, suggest that both natural and sexual selection may be influencing the evolutionary trajectories of these traits in nature, limiting the capacity for a contemporary evolutionary response. © 2016 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2016 European Society For Evolutionary Biology.

Making the case for orthogenesis: the popularization of definitely directed evolution (1890-1926).

PubMed

Ulett, Mark A

2014-03-01

Throughout the history of evolutionary theory a number of scientists have argued that evolution proceeds along a limited number of definite trajectories, a concept and group of theories known as "orthogenesis". Beginning in the 1880s, influential evolutionists including Theodor Eimer, Edward Drinker Cope, and Leo Berg argued that a fully causal explanation of evolution must take into account the origin and nature of variation, an idea that implied orthogenesis in their views. This paper argues that these orthogenesis developed theories that were more than highly technical and theoretically dubious hypotheses accessible only to elite specialists, as certain histories of these ideas might suggest. Some orthogenesists made their case to a non-specialist audience to gain support for their ideas in the face of widespread controversy over evolutionary theory. Through a case study analysis of three major books by Eimer, Cope, and Berg, this paper contends that they sought to re-orient the central tenets of the science of evolution to include the causal impact of variation on evolutionary outcomes. These orthogenesists developed novel and synthetic evolutionary theories in a publishing platform suited for non-specialist audiences in an effort to impact the debates over evolutionary causation prevalent in the late-19th and early 20th centuries. Copyright © 2013 Elsevier Ltd. All rights reserved.

Laboratory evolution of the migratory polymorphism in the sand cricket: combining physiology with quantitative genetics.

PubMed

Roff, Derek A; Fairbairn, Daphne J

2007-01-01

Predicting evolutionary change is the central goal of evolutionary biology because it is the primary means by which we can test evolutionary hypotheses. In this article, we analyze the pattern of evolutionary change in a laboratory population of the wing-dimorphic sand cricket Gryllus firmus resulting from relaxation of selection favoring the migratory (long-winged) morph. Based on a well-characterized trade-off between fecundity and flight capability, we predict that evolution in the laboratory environment should result in a reduction in the proportion of long-winged morphs. We also predict increased fecundity and reduced functionality and weight of the major flight muscles in long-winged females but little change in short-winged (flightless) females. Based on quantitative genetic theory, we predict that the regression equation describing the trade-off between ovary weight and weight of the major flight muscles will show a change in its intercept but not in its slope. Comparisons across generations verify all of these predictions. Further, using values of genetic parameters estimated from previous studies, we show that a quantitative genetic simulation model can account for not only the qualitative changes but also the evolutionary trajectory. These results demonstrate the power of combining quantitative genetic and physiological approaches for understanding the evolution of complex traits.

Hyper-X Stage Separation Trajectory Validation Studies

NASA Technical Reports Server (NTRS)

Tartabini, Paul V.; Bose, David M.; McMinn, John D.; Martin, John G.; Strovers, Brian K.

2003-01-01

An independent twelve degree-of-freedom simulation of the X-43A separation trajectory was created with the Program to Optimize Simulated trajectories (POST II). This simulation modeled the multi-body dynamics of the X-43A and its booster and included the effect of two pyrotechnically actuated pistons used to push the vehicles apart as well as aerodynamic interaction forces and moments between the two vehicles. The simulation was developed to validate trajectory studies conducted with a 14 degree-of-freedom simulation created early in the program using the Automatic Dynamic Analysis of Mechanics Systems (ADAMS) simulation software. The POST simulation was less detailed than the official ADAMS-based simulation used by the Project, but was simpler, more concise and ran faster, while providing similar results. The increase in speed provided by the POST simulation provided the Project with an alternate analysis tool. This tool was ideal for performing separation control logic trade studies that required the running of numerous Monte Carlo trajectories.

A new bio-inspired, population-level approach to the socioeconomic evolution of dynamic spectrum access services

NASA Astrophysics Data System (ADS)

Horvath, Denis; Gazda, Juraj; Brutovsky, Branislav

Evolutionary species and quasispecies models provide the universal and flexible basis for a large-scale description of the dynamics of evolutionary systems, which can be built conceived as a constraint satisfaction dynamics. It represents a general framework to design and study many novel, technologically contemporary models and their variants. Here, we apply the classical quasispecies concept to model the emerging dynamic spectrum access (DSA) markets. The theory describes the mechanisms of mimetic transfer, competitive interactions between socioeconomic strata of the end-users, their perception of the utility and inter-operator switching in the variable technological environments of the operators offering the wireless spectrum services. The algorithmization and numerical modeling demonstrate the long-term evolutionary socioeconomic changes which reflect the end-user preferences and results of the majorization of their irrational decisions in the same manner as the prevailing tendencies which are embodied in the efficient market hypothesis.

Neuronal boost to evolutionary dynamics

PubMed Central

de Vladar, Harold P.; Szathmáry, Eörs

2015-01-01

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

Evolution of intrinsic disorder in eukaryotic proteins.

PubMed

Ahrens, Joseph B; Nunez-Castilla, Janelle; Siltberg-Liberles, Jessica

2017-09-01

Conformational flexibility conferred though regions of intrinsic structural disorder allows proteins to behave as dynamic molecules. While it is well-known that intrinsically disordered regions can undergo disorder-to-order transitions in real-time as part of their function, we also are beginning to learn more about the dynamics of disorder-to-order transitions along evolutionary time-scales. Intrinsically disordered regions endow proteins with functional promiscuity, which is further enhanced by the ability of some of these regions to undergo real-time disorder-to-order transitions. Disorder content affects gene retention after whole genome duplication, but it is not necessarily conserved. Altered patterns of disorder resulting from evolutionary disorder-to-order transitions indicate that disorder evolves to modify function through refining stability, regulation, and interactions. Here, we review the evolution of intrinsically disordered regions in eukaryotic proteins. We discuss the interplay between secondary structure and disorder on evolutionary time-scales, the importance of disorder for eukaryotic proteome expansion and functional divergence, and the evolutionary dynamics of disorder.

Why evolutionary biologists should get seriously involved in ecological monitoring and applied biodiversity assessment programs

PubMed Central

Brodersen, Jakob; Seehausen, Ole

2014-01-01

While ecological monitoring and biodiversity assessment programs are widely implemented and relatively well developed to survey and monitor the structure and dynamics of populations and communities in many ecosystems, quantitative assessment and monitoring of genetic and phenotypic diversity that is important to understand evolutionary dynamics is only rarely integrated. As a consequence, monitoring programs often fail to detect changes in these key components of biodiversity until after major loss of diversity has occurred. The extensive efforts in ecological monitoring have generated large data sets of unique value to macro-scale and long-term ecological research, but the insights gained from such data sets could be multiplied by the inclusion of evolutionary biological approaches. We argue that the lack of process-based evolutionary thinking in ecological monitoring means a significant loss of opportunity for research and conservation. Assessment of genetic and phenotypic variation within and between species needs to be fully integrated to safeguard biodiversity and the ecological and evolutionary dynamics in natural ecosystems. We illustrate our case with examples from fishes and conclude with examples of ongoing monitoring programs and provide suggestions on how to improve future quantitative diversity surveys. PMID:25553061

Eco-evolutionary effects on population recovery following catastrophic disturbance

PubMed Central

Weese, Dylan J; Schwartz, Amy K; Bentzen, Paul; Hendry, Andrew P; Kinnison, Michael T

2011-01-01

Fine-scale genetic diversity and contemporary evolution can theoretically influence ecological dynamics in the wild. Such eco-evolutionary effects might be particularly relevant to the persistence of populations facing acute or chronic environmental change. However, experimental data on wild populations is currently lacking to support this notion. One way that ongoing evolution might influence the dynamics of threatened populations is through the role that selection plays in mediating the ‘rescue effect’, the ability of migrants to contribute to the recovery of populations facing local disturbance and decline. Here, we combine experiments with natural catastrophic events to show that ongoing evolution is a major determinant of migrant contributions to population recovery in Trinidadian guppies (Poecilia reticulata). These eco-evolutionary limits on migrant contributions appear to be mediated by the reinforcing effects of natural and sexual selection against migrants, despite the close geographic proximity of migrant sources. These findings show that ongoing adaptive evolution can be a double-edged sword for population persistence, maintaining local fitness at a cost to demographic risk. Our study further serves as a potent reminder that significant evolutionary and eco-evolutionary dynamics might be at play even where the phenotypic status quo is largely maintained generation to generation. PMID:25567978

POLYANA-A tool for the calculation of molecular radial distribution functions based on Molecular Dynamics trajectories

NASA Astrophysics Data System (ADS)

Dimitroulis, Christos; Raptis, Theophanes; Raptis, Vasilios

2015-12-01

We present an application for the calculation of radial distribution functions for molecular centres of mass, based on trajectories generated by molecular simulation methods (Molecular Dynamics, Monte Carlo). When designing this application, the emphasis was placed on ease of use as well as ease of further development. In its current version, the program can read trajectories generated by the well-known DL_POLY package, but it can be easily extended to handle other formats. It is also very easy to 'hack' the program so it can compute intermolecular radial distribution functions for groups of interaction sites rather than whole molecules.

Preparation and Relaxation of Very Stable Glassy States of a Simulated Liquid

NASA Astrophysics Data System (ADS)

Jack, Robert L.; Hedges, Lester O.; Garrahan, Juan P.; Chandler, David

2011-12-01

We prepare metastable glassy states in a model glass former made of Lennard-Jones particles by sampling biased ensembles of trajectories with low dynamical activity. These trajectories form an inactive dynamical phase whose “fast” vibrational degrees of freedom are maintained at thermal equilibrium by contact with a heat bath, while the “slow” structural degrees of freedom are located in deep valleys of the energy landscape. We examine the relaxation to equilibrium and the vibrational properties of these metastable states. The glassy states we prepare by our trajectory sampling method are very stable to thermal fluctuations and also more mechanically rigid than low-temperature equilibrated configurations.

An Earth-Moon System Trajectory Design Reference Catalog

NASA Technical Reports Server (NTRS)

Folta, David; Bosanac, Natasha; Guzzetti, Davide; Howell, Kathleen C.

2014-01-01

As demonstrated by ongoing concept designs and the recent ARTEMIS mission, there is, currently, significant interest in exploiting three-body dynamics in the design of trajectories for both robotic and human missions within the Earth-Moon system. The concept of an interactive and 'dynamic' catalog of potential solutions in the Earth-Moon system is explored within this paper and analyzed as a framework to guide trajectory design. Characterizing and compiling periodic and quasi-periodic solutions that exist in the circular restricted three-body problem may offer faster and more efficient strategies for orbit design, while also delivering innovative mission design parameters for further examination.

A Segment-Based Trajectory Similarity Measure in the Urban Transportation Systems.

PubMed

Mao, Yingchi; Zhong, Haishi; Xiao, Xianjian; Li, Xiaofang

2017-03-06

With the rapid spread of built-in GPS handheld smart devices, the trajectory data from GPS sensors has grown explosively. Trajectory data has spatio-temporal characteristics and rich information. Using trajectory data processing techniques can mine the patterns of human activities and the moving patterns of vehicles in the intelligent transportation systems. A trajectory similarity measure is one of the most important issues in trajectory data mining (clustering, classification, frequent pattern mining, etc.). Unfortunately, the main similarity measure algorithms with the trajectory data have been found to be inaccurate, highly sensitive of sampling methods, and have low robustness for the noise data. To solve the above problems, three distances and their corresponding computation methods are proposed in this paper. The point-segment distance can decrease the sensitivity of the point sampling methods. The prediction distance optimizes the temporal distance with the features of trajectory data. The segment-segment distance introduces the trajectory shape factor into the similarity measurement to improve the accuracy. The three kinds of distance are integrated with the traditional dynamic time warping algorithm (DTW) algorithm to propose a new segment-based dynamic time warping algorithm (SDTW). The experimental results show that the SDTW algorithm can exhibit about 57%, 86%, and 31% better accuracy than the longest common subsequence algorithm (LCSS), and edit distance on real sequence algorithm (EDR) , and DTW, respectively, and that the sensitivity to the noise data is lower than that those algorithms.

An Improved Co-evolutionary Particle Swarm Optimization for Wireless Sensor Networks with Dynamic Deployment

PubMed Central

Wang, Xue; Wang, Sheng; Ma, Jun-Jie

2007-01-01

The effectiveness of wireless sensor networks (WSNs) depends on the coverage and target detection probability provided by dynamic deployment, which is usually supported by the virtual force (VF) algorithm. However, in the VF algorithm, the virtual force exerted by stationary sensor nodes will hinder the movement of mobile sensor nodes. Particle swarm optimization (PSO) is introduced as another dynamic deployment algorithm, but in this case the computation time required is the big bottleneck. This paper proposes a dynamic deployment algorithm which is named “virtual force directed co-evolutionary particle swarm optimization” (VFCPSO), since this algorithm combines the co-evolutionary particle swarm optimization (CPSO) with the VF algorithm, whereby the CPSO uses multiple swarms to optimize different components of the solution vectors for dynamic deployment cooperatively and the velocity of each particle is updated according to not only the historical local and global optimal solutions, but also the virtual forces of sensor nodes. Simulation results demonstrate that the proposed VFCPSO is competent for dynamic deployment in WSNs and has better performance with respect to computation time and effectiveness than the VF, PSO and VFPSO algorithms.

Decentralized adaptive control of manipulators - Theory, simulation, and experimentation

NASA Technical Reports Server (NTRS)

Seraji, Homayoun

1989-01-01

The author presents a simple decentralized adaptive-control scheme for multijoint robot manipulators based on the independent joint control concept. The control objective is to achieve accurate tracking of desired joint trajectories. The proposed control scheme does not use the complex manipulator dynamic model, and each joint is controlled simply by a PID (proportional-integral-derivative) feedback controller and a position-velocity-acceleration feedforward controller, both with adjustable gains. Simulation results are given for a two-link direct-drive manipulator under adaptive independent joint control. The results illustrate trajectory tracking under coupled dynamics and varying payload. The proposed scheme is implemented on a MicroVAX II computer for motion control of the three major joints of a PUMA 560 arm. Experimental results are presented to demonstrate that trajectory tracking is achieved despite coupled nonlinear joint dynamics.

Schrödinger–Langevin equation with quantum trajectories for photodissociation dynamics

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

Chou, Chia-Chun, E-mail: ccchou@mx.nthu.edu.tw

The Schrödinger–Langevin equation is integrated to study the wave packet dynamics of quantum systems subject to frictional effects by propagating an ensemble of quantum trajectories. The equations of motion for the complex action and quantum trajectories are derived from the Schrödinger–Langevin equation. The moving least squares approach is used to evaluate the spatial derivatives of the complex action required for the integration of the equations of motion. Computational results are presented and analyzed for the evolution of a free Gaussian wave packet, a two-dimensional barrier model, and the photodissociation dynamics of NOCl. The absorption spectrum of NOCl obtained from themore » Schrödinger–Langevin equation displays a redshift when frictional effects increase. This computational result agrees qualitatively with the experimental results in the solution-phase photochemistry of NOCl.« less

Cyclohexane isomerization. Unimolecular dynamics of the twist-boat intermediate.

PubMed

Kakhiani, Khatuna; Lourderaj, Upakarasamy; Hu, Wenfang; Birney, David; Hase, William L

2009-04-23

Direct dynamics simulations were performed at the HF/6-31G level of theory to investigate the intramolecular and unimolecuar dynamics of the twist-boat (TB) intermediate on the cyclohexane potential energy surface (PES). Additional calculations were performed at the MP2/aug-cc-pVDZ level of theory to further characterize the PES's stationary points. The trajectories were initiated at the C(1) and C(2) half-chair transition states (TSs) connecting a chair conformer with a TB intermediate, via an intrinsic reaction coordinate (IRC). Energy was added in accord with a microcanonical ensemble at the average energy for experiments at 263 K. Important nontransition state theory (TST), non-IRC, and non-RRKM dynamics were observed in the simulations. Trajectories initially directed toward the chair conformer had a high probability of recrossing the TS, with approximately 30% forming a TB intermediate instead of accessing the potential energy well for the conformer. The TB intermediate initially formed was not necessarily the one connected to the TS via the IRC. Of the trajectories initiated at the C(2) half-chair TS and initially directed toward the chair conformer, 35% formed a TB intermediate instead of the chair conformer. Also, of the trajectories forming a TB intermediate, only 16% formed the TB intermediate connected with the C(2) TS via the IRC. Up to eight consecutive TB --> TB isomerizations were followed, and non-RRKM behavior was observed in their dynamics. A TB can isomerize to two different TBs, one by a clockwise rotation of C-C-C-C dihedral angles and the other by a counterclockwise rotation. In contrast to RRKM theory, which predicts equivalent probabilities for these rotations, the trajectory dynamics show they are not equivalent and depend on whether the C(1) or C(2) half-chair TS is initially excited. Non-RRKM dynamics is also observed in the isomerization of the TB intermediates to the chair conformers. RRKM theory assumes equivalent probabilities for isomerizing to the two chair conformers. In contrast, for the first and following TB intermediate formed, there is a preference to isomerize to the chair conformer connected to the TS at which the trajectories were initiated. For the first TB intermediate formed, approximately 30% of the isomerization is to a chair conformer, but this fraction decreases for the later formed TB intermediates and becomes approximately 10% for the eighth consecutive TB intermediate formed.

Evolutionary dynamics of fearfulness and boldness.

PubMed

Ji, Ting; Zhang, Boyu; Sun, Yuehua; Tao, Yi

2009-02-21

A negative relationship between reproductive effort and survival is consistent with life-history. Evolutionary dynamics and evolutionarily stable strategy (ESS) for the trade-off between survival and reproduction are investigated using a simple model with two phenotypes, fearfulness and boldness. The dynamical stability of the pure strategy model and analysis of ESS conditions reveal that: (i) the simple coexistence of fearfulness and boldness is impossible; (ii) a small population size is favorable to fearfulness, but a large population size is favorable to boldness, i.e., neither fearfulness, nor boldness is always favored by natural selection; and (iii) the dynamics of population density is crucial for a proper understanding of the strategy dynamics.

Anosov C-systems and random number generators

NASA Astrophysics Data System (ADS)

Savvidy, G. K.

2016-08-01

We further develop our previous proposal to use hyperbolic Anosov C-systems to generate pseudorandom numbers and to use them for efficient Monte Carlo calculations in high energy particle physics. All trajectories of hyperbolic dynamical systems are exponentially unstable, and C-systems therefore have mixing of all orders, a countable Lebesgue spectrum, and a positive Kolmogorov entropy. These exceptional ergodic properties follow from the C-condition introduced by Anosov. This condition defines a rich class of dynamical systems forming an open set in the space of all dynamical systems. An important property of C-systems is that they have a countable set of everywhere dense periodic trajectories and their density increases exponentially with entropy. Of special interest are the C-systems defined on higher-dimensional tori. Such C-systems are excellent candidates for generating pseudorandom numbers that can be used in Monte Carlo calculations. An efficient algorithm was recently constructed that allows generating long C-system trajectories very rapidly. These trajectories have good statistical properties and can be used for calculations in quantum chromodynamics and in high energy particle physics.

Metadynamics Enhanced Markov Modeling of Protein Dynamics.

PubMed

Biswas, Mithun; Lickert, Benjamin; Stock, Gerhard

2018-05-31

Enhanced sampling techniques represent a versatile approach to account for rare conformational transitions in biomolecules. A particularly promising strategy is to combine massive parallel computing of short molecular dynamics (MD) trajectories (to sample the free energy landscape of the system) with Markov state modeling (to rebuild the kinetics from the sampled data). To obtain well-distributed initial structures for the short trajectories, it is proposed to employ metadynamics MD, which quickly sweeps through the entire free energy landscape of interest. Being only used to generate initial conformations, the implementation of metadynamics can be simple and fast. The conformational dynamics of helical peptide Aib 9 is adopted to discuss various technical issues of the approach, including metadynamics settings, minimal number and length of short MD trajectories, and the validation of the resulting Markov models. Using metadynamics to launch some thousands of nanosecond trajectories, several Markov state models are constructed that reveal that previous unbiased MD simulations of in total 16 μs length cannot provide correct equilibrium populations or qualitative features of the pathway distribution of the short peptide.

Simulations of High Speed Fragment Trajectories

NASA Astrophysics Data System (ADS)

Yeh, Peter; Attaway, Stephen; Arunajatesan, Srinivasan; Fisher, Travis

2017-11-01

Flying shrapnel from an explosion are capable of traveling at supersonic speeds and distances much farther than expected due to aerodynamic interactions. Predicting the trajectories and stable tumbling modes of arbitrary shaped fragments is a fundamental problem applicable to range safety calculations, damage assessment, and military technology. Traditional approaches rely on characterizing fragment flight using a single drag coefficient, which may be inaccurate for fragments with large aspect ratios. In our work we develop a procedure to simulate trajectories of arbitrary shaped fragments with higher fidelity using high performance computing. We employ a two-step approach in which the force and moment coefficients are first computed as a function of orientation using compressible computational fluid dynamics. The force and moment data are then input into a six-degree-of-freedom rigid body dynamics solver to integrate trajectories in time. Results of these high fidelity simulations allow us to further understand the flight dynamics and tumbling modes of a single fragment. Furthermore, we use these results to determine the validity and uncertainty of inexpensive methods such as the single drag coefficient model.

Refining Markov state models for conformational dynamics using ensemble-averaged data and time-series trajectories

NASA Astrophysics Data System (ADS)

Matsunaga, Y.; Sugita, Y.

2018-06-01

A data-driven modeling scheme is proposed for conformational dynamics of biomolecules based on molecular dynamics (MD) simulations and experimental measurements. In this scheme, an initial Markov State Model (MSM) is constructed from MD simulation trajectories, and then, the MSM parameters are refined using experimental measurements through machine learning techniques. The second step can reduce the bias of MD simulation results due to inaccurate force-field parameters. Either time-series trajectories or ensemble-averaged data are available as a training data set in the scheme. Using a coarse-grained model of a dye-labeled polyproline-20, we compare the performance of machine learning estimations from the two types of training data sets. Machine learning from time-series data could provide the equilibrium populations of conformational states as well as their transition probabilities. It estimates hidden conformational states in more robust ways compared to that from ensemble-averaged data although there are limitations in estimating the transition probabilities between minor states. We discuss how to use the machine learning scheme for various experimental measurements including single-molecule time-series trajectories.

Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach

NASA Astrophysics Data System (ADS)

Pizzolato, Nicola; Valenti, Davide; Adorno, Dominique Persano; Spagnolo, Bernardo

2009-09-01

The evolutionary dynamics of a system of cancerous cells in a model of chronic myeloid leukemia (CML) is investigated by a statistical approach. Cancer progression is explored by applying a Monte Carlo method to simulate the stochastic behavior of cell reproduction and death in a population of blood cells which can experience genetic mutations. In CML front line therapy is represented by the tyrosine kinase inhibitor imatinib which strongly affects the reproduction of leukemic cells only. In this work, we analyze the effects of a targeted therapy on the evolutionary dynamics of normal, first-mutant and cancerous cell populations. Several scenarios of the evolutionary dynamics of imatinib-treated leukemic cells are described as a consequence of the efficacy of the different modelled therapies. We show how the patient response to the therapy changes when a high value of the mutation rate from healthy to cancerous cells is present. Our results are in agreement with clinical observations. Unfortunately, development of resistance to imatinib is observed in a fraction of patients, whose blood cells are characterized by an increasing number of genetic alterations. We find that the occurrence of resistance to the therapy can be related to a progressive increase of deleterious mutations.

Antibiotic resistance in the wild: an eco-evolutionary perspective.

PubMed

Hiltunen, Teppo; Virta, Marko; Laine, Anna-Liisa

2017-01-19

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently.This article is part of the themed issue 'Human influences on evolution, and the ecological and societal consequences'. © 2016 The Authors.

Fixation of competing strategies when interacting agents differ in the time scale of strategy updating

NASA Astrophysics Data System (ADS)

Zhang, Jianlei; Weissing, Franz J.; Cao, Ming

2016-09-01

A commonly used assumption in evolutionary game theory is that natural selection acts on individuals in the same time scale; e.g., players use the same frequency to update their strategies. Variation in learning rates within populations suggests that evolutionary game theory may not necessarily be restricted to uniform time scales associated with the game interaction and strategy adaption evolution. In this study, we remove this restricting assumption by dividing the population into fast and slow groups according to the players' strategy updating frequencies and investigate how different strategy compositions of one group influence the evolutionary outcome of the other's fixation probabilities of strategies within its own group. Analytical analysis and numerical calculations are performed to study the evolutionary dynamics of strategies in typical classes of two-player games (prisoner's dilemma game, snowdrift game, and stag-hunt game). The introduction of the heterogeneity in strategy-update time scales leads to substantial changes in the evolution dynamics of strategies. We provide an approximation formula for the fixation probability of mutant types in finite populations and study the outcome of strategy evolution under the weak selection. We find that although heterogeneity in time scales makes the collective evolutionary dynamics more complicated, the possible long-run evolutionary outcome can be effectively predicted under technical assumptions when knowing the population composition and payoff parameters.

Antibiotic resistance in the wild: an eco-evolutionary perspective

PubMed Central

Virta, Marko

2017-01-01

The legacy of the use and misuse of antibiotics in recent decades has left us with a global public health crisis: antibiotic-resistant bacteria are on the rise, making it harder to treat infections. At the same time, evolution of antibiotic resistance is probably the best-documented case of contemporary evolution. To date, research on antibiotic resistance has largely ignored the complexity of interactions that bacteria engage in. However, in natural populations, bacteria interact with other species; for example, competition and grazing are import interactions influencing bacterial population dynamics. Furthermore, antibiotic leakage to natural environments can radically alter bacterial communities. Overall, we argue that eco-evolutionary feedback loops in microbial communities can be modified by residual antibiotics and evolution of antibiotic resistance. The aim of this review is to connect some of the well-established key concepts in evolutionary biology and recent advances in the study of eco-evolutionary dynamics to research on antibiotic resistance. We also identify some key knowledge gaps related to eco-evolutionary dynamics of antibiotic resistance, and review some of the recent technical advantages in molecular microbiology that offer new opportunities for tackling these questions. Finally, we argue that using the full potential of evolutionary theory and active communication across the different fields is needed for solving this global crisis more efficiently. This article is part of the themed issue ‘Human influences on evolution, and the ecological and societal consequences'. PMID:27920384

Timing of transients: quantifying reaching times and transient behavior in complex systems

NASA Astrophysics Data System (ADS)

Kittel, Tim; Heitzig, Jobst; Webster, Kevin; Kurths, Jürgen

2017-08-01

In dynamical systems, one may ask how long it takes for a trajectory to reach the attractor, i.e. how long it spends in the transient phase. Although for a single trajectory the mathematically precise answer may be infinity, it still makes sense to compare different trajectories and quantify which of them approaches the attractor earlier. In this article, we categorize several problems of quantifying such transient times. To treat them, we propose two metrics, area under distance curve and regularized reaching time, that capture two complementary aspects of transient dynamics. The first, area under distance curve, is the distance of the trajectory to the attractor integrated over time. It measures which trajectories are ‘reluctant’, i.e. stay distant from the attractor for long, or ‘eager’ to approach it right away. Regularized reaching time, on the other hand, quantifies the additional time (positive or negative) that a trajectory starting at a chosen initial condition needs to approach the attractor as compared to some reference trajectory. A positive or negative value means that it approaches the attractor by this much ‘earlier’ or ‘later’ than the reference, respectively. We demonstrated their substantial potential for application with multiple paradigmatic examples uncovering new features.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data

PubMed Central

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll.

2016-01-01

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. PMID:26612862

Sensitivity of peptide conformational dynamics on clustering of a classical molecular dynamics trajectory

NASA Astrophysics Data System (ADS)

Jensen, Christian H.; Nerukh, Dmitry; Glen, Robert C.

2008-03-01

We investigate the sensitivity of a Markov model with states and transition probabilities obtained from clustering a molecular dynamics trajectory. We have examined a 500ns molecular dynamics trajectory of the peptide valine-proline-alanine-leucine in explicit water. The sensitivity is quantified by varying the boundaries of the clusters and investigating the resulting variation in transition probabilities and the average transition time between states. In this way, we represent the effect of clustering using different clustering algorithms. It is found that in terms of the investigated quantities, the peptide dynamics described by the Markov model is sensitive to the clustering; in particular, the average transition times are found to vary up to 46%. Moreover, inclusion of nonphysical sparsely populated clusters can lead to serious errors of up to 814%. In the investigation, the time step used in the transition matrix is determined by the minimum time scale on which the system behaves approximately Markovian. This time step is found to be about 100ps. It is concluded that the description of peptide dynamics with transition matrices should be performed with care, and that using standard clustering algorithms to obtain states and transition probabilities may not always produce reliable results.

Evolution of Courtship Songs in Xenopus : Vocal Pattern Generation and Sound Production.

PubMed

Leininger, Elizabeth C; Kelley, Darcy B

2015-01-01

The extant species of African clawed frogs (Xenopus and Silurana) provide an opportunity to link the evolution of vocal characters to changes in the responsible cellular and molecular mechanisms. In this review, we integrate several robust lines of research: evolutionary trajectories of Xenopus vocalizations, cellular and circuit-level mechanisms of vocalization in selected Xenopus model species, and Xenopus evolutionary history and speciation mechanisms. Integrating recent findings allows us to generate and test specific hypotheses about the evolution of Xenopus vocal circuits. We propose that reduced vocal sex differences in some Xenopus species result from species-specific losses of sexually differentiated neural and neuromuscular features. Modification of sex-hormone-regulated developmental mechanisms is a strong candidate mechanism for reduced vocal sex differences.

Understanding transient uncoupling induced synchronization through modified dynamic coupling

NASA Astrophysics Data System (ADS)

Ghosh, Anupam; Godara, Prakhar; Chakraborty, Sagar

2018-05-01

An important aspect of the recently introduced transient uncoupling scheme is that it induces synchronization for large values of coupling strength at which the coupled chaotic systems resist synchronization when continuously coupled. However, why this is so is an open problem? To answer this question, we recall the conventional wisdom that the eigenvalues of the Jacobian of the transverse dynamics measure whether a trajectory at a phase point is locally contracting or diverging with respect to another nearby trajectory. Subsequently, we go on to highlight a lesser appreciated fact that even when, under the corresponding linearised flow, the nearby trajectory asymptotically diverges away, its distance from the reference trajectory may still be contracting for some intermediate period. We term this phenomenon transient decay in line with the phenomenon of the transient growth. Using these facts, we show that an optimal coupling region, i.e., a region of the phase space where coupling is on, should ideally be such that at any of the constituent phase point either the maximum of the real parts of the eigenvalues is negative or the magnitude of the positive maximum is lesser than that of the negative minimum. We also invent and employ a modified dynamics coupling scheme—a significant improvement over the well-known dynamic coupling scheme—as a decisive tool to justify our results.

Controlled recovery of phylogenetic communities from an evolutionary model using a network approach

NASA Astrophysics Data System (ADS)

Sousa, Arthur M. Y. R.; Vieira, André P.; Prado, Carmen P. C.; Andrade, Roberto F. S.

2016-04-01

This works reports the use of a complex network approach to produce a phylogenetic classification tree of a simple evolutionary model. This approach has already been used to treat proteomic data of actual extant organisms, but an investigation of its reliability to retrieve a traceable evolutionary history is missing. The used evolutionary model includes key ingredients for the emergence of groups of related organisms by differentiation through random mutations and population growth, but purposefully omits other realistic ingredients that are not strictly necessary to originate an evolutionary history. This choice causes the model to depend only on a small set of parameters, controlling the mutation probability and the population of different species. Our results indicate that for a set of parameter values, the phylogenetic classification produced by the used framework reproduces the actual evolutionary history with a very high average degree of accuracy. This includes parameter values where the species originated by the evolutionary dynamics have modular structures. In the more general context of community identification in complex networks, our model offers a simple setting for evaluating the effects, on the efficiency of community formation and identification, of the underlying dynamics generating the network itself.

Molecular dynamics studies of a DNA-binding protein: 2. An evaluation of implicit and explicit solvent models for the molecular dynamics simulation of the Escherichia coli trp repressor.

PubMed Central

Guenot, J.; Kollman, P. A.

1992-01-01

Although aqueous simulations with periodic boundary conditions more accurately describe protein dynamics than in vacuo simulations, these are computationally intensive for most proteins. Trp repressor dynamic simulations with a small water shell surrounding the starting model yield protein trajectories that are markedly improved over gas phase, yet computationally efficient. Explicit water in molecular dynamics simulations maintains surface exposure of protein hydrophilic atoms and burial of hydrophobic atoms by opposing the otherwise asymmetric protein-protein forces. This properly orients protein surface side chains, reduces protein fluctuations, and lowers the overall root mean square deviation from the crystal structure. For simulations with crystallographic waters only, a linear or sigmoidal distance-dependent dielectric yields a much better trajectory than does a constant dielectric model. As more water is added to the starting model, the differences between using distance-dependent and constant dielectric models becomes smaller, although the linear distance-dependent dielectric yields an average structure closer to the crystal structure than does a constant dielectric model. Multiplicative constants greater than one, for the linear distance-dependent dielectric simulations, produced trajectories that are progressively worse in describing trp repressor dynamics. Simulations of bovine pancreatic trypsin were used to ensure that the trp repressor results were not protein dependent and to explore the effect of the nonbonded cutoff on the distance-dependent and constant dielectric simulation models. The nonbonded cutoff markedly affected the constant but not distance-dependent dielectric bovine pancreatic trypsin inhibitor simulations. As with trp repressor, the distance-dependent dielectric model with a shell of water surrounding the protein produced a trajectory in better agreement with the crystal structure than a constant dielectric model, and the physical properties of the trajectory average structure, both with and without a nonbonded cutoff, were comparable. PMID:1304396

Understanding rapid evolution in predator‐prey interactions using the theory of fast‐slow dynamical systems.

PubMed

Cortez, Michael H; Ellner, Stephen P

2010-11-01

The accumulation of evidence that ecologically important traits often evolve at the same time and rate as ecological dynamics (e.g., changes in species' abundances or spatial distributions) has outpaced theory describing the interplay between ecological and evolutionary processes with comparable timescales. The disparity between experiment and theory is partially due to the high dimensionality of models that include both evolutionary and ecological dynamics. Here we show how the theory of fast-slow dynamical systems can be used to reduce model dimension, and we use that body of theory to study a general predator-prey system exhibiting fast evolution in either the predator or the prey. Our approach yields graphical methods with predictive power about when new and unique dynamics (e.g., completely out-of-phase oscillations and cryptic dynamics) can arise in ecological systems exhibiting fast evolution. In addition, we derive analytical expressions for determining when such behavior arises and how evolution affects qualitative properties of the ecological dynamics. Finally, while the theory requires a separation of timescales between the ecological and evolutionary processes, our approach yields insight into systems where the rates of those processes are comparable and thus is a step toward creating a general ecoevolutionary theory.

Constraints, Trade-offs and the Currency of Fitness.

PubMed

Acerenza, Luis

2016-03-01

Understanding evolutionary trajectories remains a difficult task. This is because natural evolutionary processes are simultaneously affected by various types of constraints acting at the different levels of biological organization. Of particular importance are constraints where correlated changes occur in opposite directions, called trade-offs. Here we review and classify the main evolutionary constraints and trade-offs, operating at all levels of trait hierarchy. Special attention is given to life history trade-offs and the conflict between the survival and reproduction components of fitness. Cellular mechanisms underlying fitness trade-offs are described. At the metabolic level, a linear trade-off between growth and flux variability was found, employing bacterial genome-scale metabolic reconstructions. Its analysis indicates that flux variability can be considered as the currency of fitness. This currency is used for fitness transfer between fitness components during adaptations. Finally, a discussion is made regarding the constraints which limit the increase in the amount of fitness currency during evolution, suggesting that occupancy constraints are probably the main restrictions.

Peregrine and saker falcon genome sequences provide insights into evolution of a predatory lifestyle.

PubMed

Zhan, Xiangjiang; Pan, Shengkai; Wang, Junyi; Dixon, Andrew; He, Jing; Muller, Margit G; Ni, Peixiang; Hu, Li; Liu, Yuan; Hou, Haolong; Chen, Yuanping; Xia, Jinquan; Luo, Qiong; Xu, Pengwei; Chen, Ying; Liao, Shengguang; Cao, Changchang; Gao, Shukun; Wang, Zhaobao; Yue, Zhen; Li, Guoqing; Yin, Ye; Fox, Nick C; Wang, Jun; Bruford, Michael W

2013-05-01

As top predators, falcons possess unique morphological, physiological and behavioral adaptations that allow them to be successful hunters: for example, the peregrine is renowned as the world's fastest animal. To examine the evolutionary basis of predatory adaptations, we sequenced the genomes of both the peregrine (Falco peregrinus) and saker falcon (Falco cherrug), and we present parallel, genome-wide evidence for evolutionary innovation and selection for a predatory lifestyle. The genomes, assembled using Illumina deep sequencing with greater than 100-fold coverage, are both approximately 1.2 Gb in length, with transcriptome-assisted prediction of approximately 16,200 genes for both species. Analysis of 8,424 orthologs in both falcons, chicken, zebra finch and turkey identified consistent evidence for genome-wide rapid evolution in these raptors. SNP-based inference showed contrasting recent demographic trajectories for the two falcons, and gene-based analysis highlighted falcon-specific evolutionary novelties for beak development and olfaction and specifically for homeostasis-related genes in the arid environment-adapted saker.

A systems approach to physiologic evolution: From micelles to consciousness.

PubMed

Torday, John S; Miller, William B

2018-01-01

A systems approach to evolutionary biology offers the promise of an improved understanding of the fundamental principles of life through the effective integration of many biologic disciplines. It is presented that any critical integrative approach to evolutionary development involves a paradigmatic shift in perspective, more than just the engagement of a large number of disciplines. Critical to this differing viewpoint is the recognition that all biological processes originate from the unicellular state and remain permanently anchored to that phase throughout evolutionary development despite their macroscopic appearances. Multicellular eukaryotic development can, therefore, be viewed as a series of connected responses to epiphenomena that proceeds from that base in continuous iterative maintenance of collective cellular homeostatic equipoise juxtaposed against an ever-changing and challenging environment. By following this trajectory of multicellular eukaryotic evolution from within unicellular First Principles of Physiology forward, the mechanistic nature of complex physiology can be identified through a step-wise analysis of a continuous arc of vertebrate evolution based upon serial exaptations. © 2017 Wiley Periodicals, Inc.

Evolutionary trends in arvicolids and the endemic murid Mikrotia - New data and a critical overview

NASA Astrophysics Data System (ADS)

Maul, Lutz C.; Masini, Federico; Parfitt, Simon A.; Rekovets, Leonid; Savorelli, Andrea

2014-07-01

The study of evolutionary rates dates back to the work of Simpson and Haldane in the 1940s. Small mammals, especially Plio-Pleistocene arvicolids (voles and lemmings), are particularly suited for such studies because they have an unusually complete fossil record and exhibit significant evolutionary change through time. In recent decades, arvicolids have been the focus of intensive research devoted to the tempo and mode of evolutionary change and the identification of trends in dental evolution that can be used to correlate and date fossil sites. These studies have raised interesting questions about whether voles and lemmings had unique evolutionary trajectories, or show convergent evolutionary patterns with other hypsodont rodents. Here we review evolutionary patterns in selected arvicolid lineages and endemic Messinian murids (Mikrotia spp.) and discuss reasons for convergence in dental morphology in these two groups of hypsodont rodents. The results substantiate previously detected patterns, but the larger dataset shows that some trends are less regular than previous studies have suggested. With the exception of a pervasive and sustained trend towards increased hypsodonty, our results show that other features do not follow consistent patterns in all lineages, exhibiting a mosaic pattern comprising stasis, variable rate evolution and gradual unidirectional change through time. Evidence for higher evolutionary rates is found in lineages apparently undergoing adaptations to new ecological niches. In the case of Mikrotia, Microtus voles and the water vole (Mimomys-Arvicola) lineage, a shift to a fossorial lifestyle appears to have been an important driving force in their evolution. For other characters, different causes can be invoked; for example a shift to a semi-aquatic lifestyle may be responsible for the trend towards increasing size in Arvicola. Biochronological application of the data should take into account the complexity and biases of the data.

A New Theory of Trajectory Design and NASA's Vision

NASA Technical Reports Server (NTRS)

Folta, David

2006-01-01

This new theory is defined as the use of chaos to design trajectories and orbits that can be used to meet complex mission goals. The benefits are; a) minimizes fuel costs; b) optimizes trajectory profiles; c) provides non-standard and new orbit designs; and d) mitigates operational risks. Other synonymous terms include dynamical systems, invariant manifolds, capture orbits and ballistic orbits.

Operator-assisted planning and execution of proximity operations subject to operational constraints

NASA Technical Reports Server (NTRS)

Grunwald, Arthur J.; Ellis, Stephen R.

1991-01-01

Future multi-vehicle operations will involve multiple scenarios that will require a planning tool for the rapid, interactive creation of fuel-efficient trajectories. The planning process must deal with higher-order, non-linear processes involving dynamics that are often counter-intuitive. The optimization of resulting trajectories can be difficult to envision. An interaction proximity operations planning system is being developed to provide the operator with easily interpreted visual feedback of trajectories and constraints. This system is hosted on an IRIS 4D graphics platform and utilizes the Clohessy-Wiltshire equations. An inverse dynamics algorithm is used to remove non-linearities while the trajectory maneuvers are decoupled and separated in a geometric spreadsheet. The operator has direct control of the position and time of trajectory waypoints to achieve the desired end conditions. Graphics provide the operator with visualization of satisfying operational constraints such as structural clearance, plume impingement, approach velocity limits, and arrival or departure corridors. Primer vector theory is combined with graphical presentation to improve operator understanding of suggested automated system solutions and to allow the operator to review, edit, or provide corrective action to the trajectory plan.

Testability of evolutionary game dynamics based on experimental economics data

NASA Astrophysics Data System (ADS)

Wang, Yijia; Chen, Xiaojie; Wang, Zhijian

2017-11-01

Understanding the dynamic processes of a real game system requires an appropriate dynamics model, and rigorously testing a dynamics model is nontrivial. In our methodological research, we develop an approach to testing the validity of game dynamics models that considers the dynamic patterns of angular momentum and speed as measurement variables. Using Rock-Paper-Scissors (RPS) games as an example, we illustrate the geometric patterns in the experiment data. We then derive the related theoretical patterns from a series of typical dynamics models. By testing the goodness-of-fit between the experimental and theoretical patterns, we show that the validity of these models can be evaluated quantitatively. Our approach establishes a link between dynamics models and experimental systems, which is, to the best of our knowledge, the most effective and rigorous strategy for ascertaining the testability of evolutionary game dynamics models.

Intermittency and dynamical Lee-Yang zeros of open quantum systems.

PubMed

Hickey, James M; Flindt, Christian; Garrahan, Juan P

2014-12-01

We use high-order cumulants to investigate the Lee-Yang zeros of generating functions of dynamical observables in open quantum systems. At long times the generating functions take on a large-deviation form with singularities of the associated cumulant generating functions-or dynamical free energies-signifying phase transitions in the ensemble of dynamical trajectories. We consider a driven three-level system as well as the dissipative Ising model. Both systems exhibit dynamical intermittency in the statistics of quantum jumps. From the short-time behavior of the dynamical Lee-Yang zeros, we identify critical values of the counting field which we attribute to the observed intermittency and dynamical phase coexistence. Furthermore, for the dissipative Ising model we construct a trajectory phase diagram and estimate the value of the transverse field where the stationary state changes from being ferromagnetic (inactive) to paramagnetic (active).

Population-level effects of fitness costs associated with repressible female-lethal transgene insertions in two pest insects

PubMed Central

Harvey-Samuel, Tim; Ant, Thomas; Gong, Hongfei; Morrison, Neil I; Alphey, Luke

2014-01-01

Genetic control strategies offer great potential for the sustainable and effective control of insect pests. These strategies involve the field release of transgenic insects with the aim of introducing engineered alleles into wild populations, either permanently or transiently. Their efficacy can therefore be reduced if transgene-associated fitness costs reduce the relative performance of released insects. We describe a method of measuring the fitness costs associated with transgenes by analyzing their evolutionary trajectories when placed in competition with wild-type alleles in replicated cage populations. Using this method, we estimated lifetime fitness costs associated with two repressible female-lethal transgenes in the diamondback moth and olive fly as being acceptable for field suppression programs. Furthermore, using these estimates of genotype-level fitness costs, we were able to project longer-term evolutionary trajectories for the transgenes investigated. Results from these projections demonstrate that although transgene-associated fitness costs will ultimately cause these transgenes to become extinct, even when engineered lethality is repressed, they may persist for varying periods of time before doing so. This implies that tetracycline-mediated transgene field persistence in these strains is unlikely and suggests that realistic estimates of transgene-associated fitness costs may be useful in trialing ‘uncoupled’ gene drive system components in the field. PMID:24944572

Convergent and parallel evolution in life habit of the scallops (Bivalvia: Pectinidae)

PubMed Central

2011-01-01

Background We employed a phylogenetic framework to identify patterns of life habit evolution in the marine bivalve family Pectinidae. Specifically, we examined the number of independent origins of each life habit and distinguished between convergent and parallel trajectories of life habit evolution using ancestral state estimation. We also investigated whether ancestral character states influence the frequency or type of evolutionary trajectories. Results We determined that temporary attachment to substrata by byssal threads is the most likely ancestral condition for the Pectinidae, with subsequent transitions to the five remaining habit types. Nearly all transitions between life habit classes were repeated in our phylogeny and the majority of these transitions were the result of parallel evolution from byssate ancestors. Convergent evolution also occurred within the Pectinidae and produced two additional gliding clades and two recessing lineages. Furthermore, our analysis indicates that byssal attaching gave rise to significantly more of the transitions than any other life habit and that the cementing and nestling classes are only represented as evolutionary outcomes in our phylogeny, never as progenitor states. Conclusions Collectively, our results illustrate that both convergence and parallelism generated repeated life habit states in the scallops. Bias in the types of habit transitions observed may indicate constraints due to physical or ontogenetic limitations of particular phenotypes. PMID:21672233

Population-level effects of fitness costs associated with repressible female-lethal transgene insertions in two pest insects.

PubMed

Harvey-Samuel, Tim; Ant, Thomas; Gong, Hongfei; Morrison, Neil I; Alphey, Luke

2014-05-01

Genetic control strategies offer great potential for the sustainable and effective control of insect pests. These strategies involve the field release of transgenic insects with the aim of introducing engineered alleles into wild populations, either permanently or transiently. Their efficacy can therefore be reduced if transgene-associated fitness costs reduce the relative performance of released insects. We describe a method of measuring the fitness costs associated with transgenes by analyzing their evolutionary trajectories when placed in competition with wild-type alleles in replicated cage populations. Using this method, we estimated lifetime fitness costs associated with two repressible female-lethal transgenes in the diamondback moth and olive fly as being acceptable for field suppression programs. Furthermore, using these estimates of genotype-level fitness costs, we were able to project longer-term evolutionary trajectories for the transgenes investigated. Results from these projections demonstrate that although transgene-associated fitness costs will ultimately cause these transgenes to become extinct, even when engineered lethality is repressed, they may persist for varying periods of time before doing so. This implies that tetracycline-mediated transgene field persistence in these strains is unlikely and suggests that realistic estimates of transgene-associated fitness costs may be useful in trialing 'uncoupled' gene drive system components in the field.

A Case-by-Case Evolutionary Analysis of Four Imprinted Retrogenes

PubMed Central

McCole, Ruth B; Loughran, Noeleen B; Chahal, Mandeep; Fernandes, Luis P; Roberts, Roland G; Fraternali, Franca; O'Connell, Mary J; Oakey, Rebecca J

2011-01-01

Retroposition is a widespread phenomenon resulting in the generation of new genes that are initially related to a parent gene via very high coding sequence similarity. We examine the evolutionary fate of four retrogenes generated by such an event; mouse Inpp5f_v2, Mcts2, Nap1l5, and U2af1-rs1. These genes are all subject to the epigenetic phenomenon of parental imprinting. We first provide new data on the age of these retrogene insertions. Using codon-based models of sequence evolution, we show these retrogenes have diverse evolutionary trajectories, including divergence from the parent coding sequence under positive selection pressure, purifying selection pressure maintaining parent-retrogene similarity, and neutral evolution. Examination of the expression pattern of retrogenes shows an atypical, broad pattern across multiple tissues. Protein 3D structure modeling reveals that a positively selected residue in U2af1-rs1, not shared by its parent, may influence protein conformation. Our case-by-case analysis of the evolution of four imprinted retrogenes reveals that this interesting class of imprinted genes, while similar in regulation and sequence characteristics, follow very varied evolutionary paths. PMID:21166792

Evolutionary ecology of virus emergence.

PubMed

Dennehy, John J

2017-02-01

The cross-species transmission of viruses into new host populations, termed virus emergence, is a significant issue in public health, agriculture, wildlife management, and related fields. Virus emergence requires overlap between host populations, alterations in virus genetics to permit infection of new hosts, and adaptation to novel hosts such that between-host transmission is sustainable, all of which are the purview of the fields of ecology and evolution. A firm understanding of the ecology of viruses and how they evolve is required for understanding how and why viruses emerge. In this paper, I address the evolutionary mechanisms of virus emergence and how they relate to virus ecology. I argue that, while virus acquisition of the ability to infect new hosts is not difficult, limited evolutionary trajectories to sustained virus between-host transmission and the combined effects of mutational meltdown, bottlenecking, demographic stochasticity, density dependence, and genetic erosion in ecological sinks limit most emergence events to dead-end spillover infections. Despite the relative rarity of pandemic emerging viruses, the potential of viruses to search evolutionary space and find means to spread epidemically and the consequences of pandemic viruses that do emerge necessitate sustained attention to virus research, surveillance, prophylaxis, and treatment. © 2016 New York Academy of Sciences.

Co-niche construction between hosts and symbionts: ideas and evidence.

PubMed

Borges, Renee M

2017-07-01

Symbiosis is a process that can generate evolutionary novelties and can extend the phenotypic niche space of organisms. Symbionts can act together with their hosts to co-construct host organs, within which symbionts are housed. Once established within hosts, symbionts can also influence various aspects of host phenotype, such as resource acquisition, protection from predation by acquisition of toxicity, as well as behaviour. Once symbiosis is established, its fidelity between generations must be ensured. Hosts evolve various mechanisms to screen unwanted symbionts and to facilitate faithful transmission of mutualistic partners between generations. Microbes are the most important symbionts that have influenced plant and animal phenotypes; multicellular organisms engage in developmental symbioses with microbes at many stages in ontogeny. The co-construction of niches may result in composite organisms that are physically nested within each other. While it has been advocated that these composite organisms need new evolutionary theories and perspectives to describe their properties and evolutionary trajectories, it appears that standard evolutionary theories are adequate to explore selection pressures on their composite or individual traits. Recent advances in our understanding of composite organisms open up many important questions regarding the stability and transmission of these units.

Hierarchical relaxation dynamics in a tilted two-band Bose-Hubbard model

NASA Astrophysics Data System (ADS)

Cosme, Jayson G.

2018-04-01

We numerically examine slow and hierarchical relaxation dynamics of interacting bosons described by a tilted two-band Bose-Hubbard model. The system is found to exhibit signatures of quantum chaos within the spectrum and the validity of the eigenstate thermalization hypothesis for relevant physical observables is demonstrated for certain parameter regimes. Using the truncated Wigner representation in the semiclassical limit of the system, dynamics of relevant observables reveal hierarchical relaxation and the appearance of prethermalized states is studied from the perspective of statistics of the underlying mean-field trajectories. The observed prethermalization scenario can be attributed to different stages of glassy dynamics in the mode-time configuration space due to dynamical phase transition between ergodic and nonergodic trajectories.

Evolutionary toxicology: Meta-analysis of evolutionary events in response to chemical stressors.

PubMed

M Oziolor, Elias; De Schamphelaere, Karel; Matson, Cole W

2016-12-01

The regulatory decision-making process regarding chemical safety is most often informed by evidence based on ecotoxicity tests that consider growth, reproduction and survival as end-points, which can be quantitatively linked to short-term population outcomes. Changes in these end-points resulting from chemical exposure can cause alterations in micro-evolutionary forces (mutation, drift, selection and gene flow) that control the genetic composition of populations. With multi-generation exposures, anthropogenic contamination can lead to a population with an altered genetic composition, which may respond differently to future stressors. These evolutionary changes are rarely discussed in regulatory or risk assessment frameworks, but the growing body of literature that documents their existence suggests that these important population-level impacts should be considered. In this meta-analysis we have compared existing contamination levels of polychlorinated biphenyls (PCBs) and polycyclic aromatic hydrocarbons (PAHs) that have been documented to be associated with evolutionary changes in resident aquatic organisms to regulatory benchmarks for these contaminants. The original intent of this project was to perform a meta-analysis on evolutionary events associated with PCB and PAH contamination. However, this effort was hindered by a lack of consistency in congener selection for "total" PCB or PAH measurements. We expanded this manuscript to include a discussion of methods used to determine PCB and PAH total contamination in addition to comparing regulatory guidelines and contamination that has caused evolutionary effects. Micro-evolutionary responses often lead populations onto unique and unpredictable trajectories. Therefore, to better understand the risk of population-wide alterations occurring, we need to improve comparisons of chemical contamination between affected locations. In this manuscript we offer several possibilities to unify chemical comparisons for PCBs and PAHs that would improve comparability among evolutionary toxicology investigations, and with regulatory guidelines. In addition, we identify studies documenting evolutionary change in the presence of PCB and PAH contamination levels below applicable regulatory benchmarks.

Simulation of wave packet tunneling of interacting identical particles

NASA Astrophysics Data System (ADS)

Lozovik, Yu. E.; Filinov, A. V.; Arkhipov, A. S.

2003-02-01

We demonstrate a different method of simulation of nonstationary quantum processes, considering the tunneling of two interacting identical particles, represented by wave packets. The used method of quantum molecular dynamics (WMD) is based on the Wigner representation of quantum mechanics. In the context of this method ensembles of classical trajectories are used to solve quantum Wigner-Liouville equation. These classical trajectories obey Hamiltonian-like equations, where the effective potential consists of the usual classical term and the quantum term, which depends on the Wigner function and its derivatives. The quantum term is calculated using local distribution of trajectories in phase space, therefore, classical trajectories are not independent, contrary to classical molecular dynamics. The developed WMD method takes into account the influence of exchange and interaction between particles. The role of direct and exchange interactions in tunneling is analyzed. The tunneling times for interacting particles are calculated.

Non-adiabatic molecular dynamics with complex quantum trajectories. I. The diabatic representation.

PubMed

Zamstein, Noa; Tannor, David J

2012-12-14

We extend a recently developed quantum trajectory method [Y. Goldfarb, I. Degani, and D. J. Tannor, J. Chem. Phys. 125, 231103 (2006)] to treat non-adiabatic transitions. Each trajectory evolves on a single surface according to Newton's laws with complex positions and momenta. The transfer of amplitude between surfaces stems naturally from the equations of motion, without the need for surface hopping. In this paper we derive the equations of motion and show results in the diabatic representation, which is rarely used in trajectory methods for calculating non-adiabatic dynamics. We apply our method to the first two benchmark models introduced by Tully [J. Chem. Phys. 93, 1061 (1990)]. Besides giving the probability branching ratios between the surfaces, the method also allows the reconstruction of the time-dependent wavepacket. Our results are in quantitative agreement with converged quantum mechanical calculations.

Neural coordination during reach-to-grasp

PubMed Central

Vaidya, Mukta; Kording, Konrad; Saleh, Maryam; Takahashi, Kazutaka

2015-01-01

When reaching to grasp, we coordinate how we preshape the hand with how we move it. To ask how motor cortical neurons participate in this coordination, we examined the interactions between reach- and grasp-related neuronal ensembles while monkeys reached to grasp a variety of different objects in different locations. By describing the dynamics of these two ensembles as trajectories in a low-dimensional state space, we examined their coupling in time. We found evidence for temporal compensation across many different reach-to-grasp conditions such that if one neural trajectory led in time the other tended to catch up, reducing the asynchrony between the trajectories. Granger causality revealed bidirectional interactions between reach and grasp neural trajectories beyond that which could be attributed to the joint kinematics that were consistently stronger in the grasp-to-reach direction. Characterizing cortical coordination dynamics provides a new framework for understanding the functional interactions between neural populations. PMID:26224773

3D Visualization of Cooperative Trajectories

NASA Technical Reports Server (NTRS)

Schaefer, John A.

2014-01-01

Aerodynamicists and biologists have long recognized the benefits of formation flight. When birds or aircraft fly in the upwash region of the vortex generated by leaders in a formation, induced drag is reduced for the trail bird or aircraft, and efficiency improves. The major consequence of this is that fuel consumption can be greatly reduced. When two aircraft are separated by a large enough longitudinal distance, the aircraft are said to be flying in a cooperative trajectory. A simulation has been developed to model autonomous cooperative trajectories of aircraft; however it does not provide any 3D representation of the multi-body system dynamics. The topic of this research is the development of an accurate visualization of the multi-body system observable in a 3D environment. This visualization includes two aircraft (lead and trail), a landscape for a static reference, and simplified models of the vortex dynamics and trajectories at several locations between the aircraft.

Nonlinear maneuver autopilot for the F-15 aircraft

NASA Technical Reports Server (NTRS)

Menon, P. K. A.; Badgett, M. E.; Walker, R. A.

1989-01-01

A methodology is described for the development of flight test trajectory control laws based on singular perturbation methodology and nonlinear dynamic modeling. The control design methodology is applied to a detailed nonlinear six degree-of-freedom simulation of the F-15 and results for a level accelerations, pushover/pullup maneuver, zoom and pushover maneuver, excess thrust windup turn, constant thrust windup turn, and a constant dynamic pressure/constant load factor trajectory are presented.

A rapid and robust gradient measurement technique using dynamic single-point imaging.

PubMed

Jang, Hyungseok; McMillan, Alan B

2017-09-01

We propose a new gradient measurement technique based on dynamic single-point imaging (SPI), which allows simple, rapid, and robust measurement of k-space trajectory. To enable gradient measurement, we utilize the variable field-of-view (FOV) property of dynamic SPI, which is dependent on gradient shape. First, one-dimensional (1D) dynamic SPI data are acquired from a targeted gradient axis, and then relative FOV scaling factors between 1D images or k-spaces at varying encoding times are found. These relative scaling factors are the relative k-space position that can be used for image reconstruction. The gradient measurement technique also can be used to estimate the gradient impulse response function for reproducible gradient estimation as a linear time invariant system. The proposed measurement technique was used to improve reconstructed image quality in 3D ultrashort echo, 2D spiral, and multi-echo bipolar gradient-echo imaging. In multi-echo bipolar gradient-echo imaging, measurement of the k-space trajectory allowed the use of a ramp-sampled trajectory for improved acquisition speed (approximately 30%) and more accurate quantitative fat and water separation in a phantom. The proposed dynamic SPI-based method allows fast k-space trajectory measurement with a simple implementation and no additional hardware for improved image quality. Magn Reson Med 78:950-962, 2017. © 2016 International Society for Magnetic Resonance in Medicine. © 2016 International Society for Magnetic Resonance in Medicine.

Singularity-free backstepping controller for model helicopters.

PubMed

Zou, Yao; Huo, Wei

2016-11-01

This paper develops a backstepping controller for model helicopters to achieve trajectory tracking without singularity, which occurs in the attitude representation when the roll or pitch reaches ±π2. Based on a simplified model with unmodeled dynamics, backstepping technique is introduced to exploit the controller and hyperbolic tangent functions are utilized to compensate the unmodeled dynamics. Firstly, a position loop controller is designed for the position tracking, where an auxiliary dynamic system with suitable parameters is introduced to warrant the singularity-free requirement for the extracted command attitude. Then, a novel attitude loop controller is proposed to obviate singularity. It is demonstrated that, based on the established criteria for selecting controller parameters and desired trajectories, the proposed controller realizes the singularity-free trajectory tracking of the model helicopter. Simulations confirm the theoretical results. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

The Influence of Life History and Sexual Dimorphism on Entheseal Changes in Modern Humans and African Great Apes

PubMed Central

Milella, Marco

2014-01-01

Entheseal changes have been widely studied with regard to their correlation to biomechanical stress and their usefulness for biocultural reconstructions. However, anthropological and medical studies have demonstrated the marked influence of both age and sex on the development of these features. Studies of entheseal changes are mostly aimed in testing functional hypotheses and are mostly focused on modern humans, with few data available for non-human primates. The lack of comparative studies on the effect of age and sex on entheseal changes represent a gap in our understanding of the evolutionary basis of both development and degeneration of the human musculoskeletal system. The aim of the present work is to compare age trajectories and patterns of sexual dimorphism in entheseal changes between modern humans and African great apes. To this end we analyzed 23 postcranial entheses in a human contemporary identified skeletal collection (N = 484) and compared the results with those obtained from the analysis of Pan (N = 50) and Gorilla (N = 47) skeletal specimens. Results highlight taxon-specific age trajectories possibly linked to differences in life history schedules and phyletic relationships. Robusticity trajectories separate Pan and modern humans from Gorilla, whereas enthesopathic patterns are unique in modern humans and possibly linked to their extended potential lifespan. Comparisons between sexes evidence a decreasing dimorphism in robusticity from Gorilla, to modern humans to Pan, which is likely linked to the role played by size, lifespan and physical activity on robusticity development. The present study confirms previous hypotheses on the possible relevance of EC in the study of life history, pointing moreover to their usefulness in evolutionary studies. PMID:25251439

Australian black field crickets show changes in neural gene expression associated with socially-induced morphological, life-history, and behavioral plasticity.

PubMed

Kasumovic, Michael M; Chen, Zhiliang; Wilkins, Marc R

2016-10-24

Ecological and evolutionary model organisms have provided extensive insight into the ecological triggers, adaptive benefits, and evolution of life-history driven developmental plasticity. Despite this, we still have a poor understanding of the underlying genetic changes that occur during shifts towards different developmental trajectories. The goal of this study is to determine whether we can identify underlying gene expression patterns that can describe the different life-history trajectories individuals follow in response to social cues of competition. To do this, we use the Australian black field cricket (Teleogryllus commodus), a species with sex-specific developmental trajectories moderated by the density and quality of calls heard during immaturity. In this study, we manipulated the social information males and females could hear by rearing individuals in either calling or silent treatments. We next used RNA-Seq to develop a reference transcriptome to study changes in brain gene expression at two points prior to sexual maturation. We show accelerated development in both sexes when exposed to calling; changes were also seen in growth, lifespan, and reproductive effort. Functional relationships between genes and phenotypes were apparent from ontological enrichment analysis. We demonstrate that increased investment towards traits such as growth and reproductive effort were often associated with the expression of a greater number of genes with similar effect, thus providing a suite of candidate genes for future research in this and other invertebrate organisms. Our results provide interesting insight into the genomic underpinnings of developmental plasticity and highlight the potential of a genomic exploration of other evolutionary theories such as condition dependence and sex-specific developmental strategies.

The influence of life history and sexual dimorphism on entheseal changes in modern humans and African great apes.

PubMed

Milella, Marco

2014-01-01

Entheseal changes have been widely studied with regard to their correlation to biomechanical stress and their usefulness for biocultural reconstructions. However, anthropological and medical studies have demonstrated the marked influence of both age and sex on the development of these features. Studies of entheseal changes are mostly aimed in testing functional hypotheses and are mostly focused on modern humans, with few data available for non-human primates. The lack of comparative studies on the effect of age and sex on entheseal changes represent a gap in our understanding of the evolutionary basis of both development and degeneration of the human musculoskeletal system. The aim of the present work is to compare age trajectories and patterns of sexual dimorphism in entheseal changes between modern humans and African great apes. To this end we analyzed 23 postcranial entheses in a human contemporary identified skeletal collection (N = 484) and compared the results with those obtained from the analysis of Pan (N = 50) and Gorilla (N = 47) skeletal specimens. Results highlight taxon-specific age trajectories possibly linked to differences in life history schedules and phyletic relationships. Robusticity trajectories separate Pan and modern humans from Gorilla, whereas enthesopathic patterns are unique in modern humans and possibly linked to their extended potential lifespan. Comparisons between sexes evidence a decreasing dimorphism in robusticity from Gorilla, to modern humans to Pan, which is likely linked to the role played by size, lifespan and physical activity on robusticity development. The present study confirms previous hypotheses on the possible relevance of EC in the study of life history, pointing moreover to their usefulness in evolutionary studies.

The possibility of evaluating turbo-set bearing misalignment defects on the basis of bearing trajectory features

NASA Astrophysics Data System (ADS)

Rybczyński, Józef

2011-02-01

This paper presents the results of computer simulation of bearing misalignment defects in a power turbogenerator. This malfunction is typical for great multi-rotor and multi-bearing rotating machines and very common in power turbo-sets. Necessary calculations were carried out by the computer code system MESWIR, developed and used at the IFFM in Gdansk for calculating dynamics of rotors supported on oil bearings. The results are presented in the form of a set of journal and bush trajectories of all turbo-set bearings. Our analysis focuses on the vibrational effects of displacing the two most vulnerable machine bearings in horizontal and vertical directions by the maximum acceptable range calculated with regard to bearing vibration criterion. This assumption required preliminary assessment of the maximum values for the permissible bearing dislocations. We show the relations between the attributes of the particular bearing trajectories and the bearing displacements in relation to their base design position. The shape and dimensions of bearing trajectories are interpreted based on the theory of hydrodynamic lubrication of oil bearings. It was shown that the relative journal trajectories and absolute bush trajectories carry much important information about the dynamic state of the machine, indicating also the way in which bearings are loaded. Therefore, trajectories can be a source of information about the position and direction of bearing misalignments. This article indicates the potential of using trajectory patterns for diagnosing misalignment defects in rotating machines and suggests including sets of trajectory patterns to the knowledge base of a machine diagnostic system.

Fitness landscape transformation through a single amino acid change in the rho terminator.

PubMed

Freddolino, Peter L; Goodarzi, Hani; Tavazoie, Saeed

2012-05-01

Regulatory networks allow organisms to match adaptive behavior to the complex and dynamic contingencies of their native habitats. Upon a sudden transition to a novel environment, the mismatch between the native behavior and the new niche provides selective pressure for adaptive evolution through mutations in elements that control gene expression. In the case of core components of cellular regulation and metabolism, with broad control over diverse biological processes, such mutations may have substantial pleiotropic consequences. Through extensive phenotypic analyses, we have characterized the systems-level consequences of one such mutation (rho*) in the global transcriptional terminator Rho of Escherichia coli. We find that a single amino acid change in Rho results in a massive change in the fitness landscape of the cell, with widely discrepant fitness consequences of identical single locus perturbations in rho* versus rho(WT) backgrounds. Our observations reveal the extent to which a single regulatory mutation can transform the entire fitness landscape of the cell, causing a massive change in the interpretation of individual mutations and altering the evolutionary trajectories which may be accessible to a bacterial population.

Climate and demography in early prehistory: using calibrated (14)C dates as population proxies.

PubMed

Riede, Felix

2009-04-01

Although difficult to estimate for prehistoric hunter-gatherer populations, demographic variables-population size, density, and the connectedness of demes-are critical for a better understanding of the processes of material culture change, especially in deep prehistory. Demography is the middle-range link between climatic changes and both biological and cultural evolutionary trajectories of human populations. Much of human material culture functions as a buffer against climatic changes, and the study of prehistoric population dynamics, estimated through changing frequencies of calibrated radiocarbon dates, therefore affords insights into how effectively such buffers operated and when they failed. In reviewing a number of case studies (Mesolithic Ireland, the origin of the Bromme culture, and the earliest late glacial human recolonization of southern Scandinavia), I suggest that a greater awareness of demographic processes, and in particular of demographic declines, provides many fresh insights into what structured the archaeological record. I argue that we cannot sideline climatic and environmental factors or extreme geophysical events in our reconstructions of prehistoric culture change. The implications of accepting demographic variability as a departure point for evaluating the archaeological record are discussed.

Prediction of human gait trajectories during the SSP using a neuromusculoskeletal modeling: A challenge for parametric optimization.

PubMed

Seyed, Mohammadali Rahmati; Mostafa, Rostami; Borhan, Beigzadeh

2018-04-27

The parametric optimization techniques have been widely employed to predict human gait trajectories; however, their applications to reveal the other aspects of gait are questionable. The aim of this study is to investigate whether or not the gait prediction model is able to justify the movement trajectories for the higher average velocities. A planar, seven-segment model with sixteen muscle groups was used to represent human neuro-musculoskeletal dynamics. At first, the joint angles, ground reaction forces (GRFs) and muscle activations were predicted and validated for normal average velocity (1.55 m/s) in the single support phase (SSP) by minimizing energy expenditure, which is subject to the non-linear constraints of the gait. The unconstrained system dynamics of extended inverse dynamics (USDEID) approach was used to estimate muscle activations. Then by scaling time and applying the same procedure, the movement trajectories were predicted for higher average velocities (from 2.07 m/s to 4.07 m/s) and compared to the pattern of movement with fast walking speed. The comparison indicated a high level of compatibility between the experimental and predicted results, except for the vertical position of the center of gravity (COG). It was concluded that the gait prediction model can be effectively used to predict gait trajectories for higher average velocities.

Trajectory NG: portable, compressed, general molecular dynamics trajectories.

PubMed

Spångberg, Daniel; Larsson, Daniel S D; van der Spoel, David

2011-10-01

We present general algorithms for the compression of molecular dynamics trajectories. The standard ways to store MD trajectories as text or as raw binary floating point numbers result in very large files when efficient simulation programs are used on supercomputers. Our algorithms are based on the observation that differences in atomic coordinates/velocities, in either time or space, are generally smaller than the absolute values of the coordinates/velocities. Also, it is often possible to store values at a lower precision. We apply several compression schemes to compress the resulting differences further. The most efficient algorithms developed here use a block sorting algorithm in combination with Huffman coding. Depending on the frequency of storage of frames in the trajectory, either space, time, or combinations of space and time differences are usually the most efficient. We compare the efficiency of our algorithms with each other and with other algorithms present in the literature for various systems: liquid argon, water, a virus capsid solvated in 15 mM aqueous NaCl, and solid magnesium oxide. We perform tests to determine how much precision is necessary to obtain accurate structural and dynamic properties, as well as benchmark a parallelized implementation of the algorithms. We obtain compression ratios (compared to single precision floating point) of 1:3.3-1:35 depending on the frequency of storage of frames and the system studied.

Non-adiabatic dynamics around a conical intersection with surface-hopping coupled coherent states

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

Humeniuk, Alexander; Mitrić, Roland, E-mail: roland.mitric@uni-wuerzburg.de

A surface-hopping extension of the coupled coherent states-method [D. Shalashilin and M. Child, Chem. Phys. 304, 103-120 (2004)] for simulating non-adiabatic dynamics with quantum effects of the nuclei is put forward. The time-dependent Schrödinger equation for the motion of the nuclei is solved in a moving basis set. The basis set is guided by classical trajectories, which can hop stochastically between different electronic potential energy surfaces. The non-adiabatic transitions are modelled by a modified version of Tully’s fewest switches algorithm. The trajectories consist of Gaussians in the phase space of the nuclei (coherent states) combined with amplitudes for an electronicmore » wave function. The time-dependent matrix elements between different coherent states determine the amplitude of each trajectory in the total multistate wave function; the diagonal matrix elements determine the hopping probabilities and gradients. In this way, both interference effects and non-adiabatic transitions can be described in a very compact fashion, leading to the exact solution if convergence with respect to the number of trajectories is achieved and the potential energy surfaces are known globally. The method is tested on a 2D model for a conical intersection [A. Ferretti, J. Chem. Phys. 104, 5517 (1996)], where a nuclear wavepacket encircles the point of degeneracy between two potential energy surfaces and interferes with itself. These interference effects are absent in classical trajectory-based molecular dynamics but can be fully incorpo rated if trajectories are replaced by surface hopping coupled coherent states.« less

Evolutionary suicide through a non-catastrophic bifurcation: adaptive dynamics of pathogens with frequency-dependent transmission.

PubMed

Boldin, Barbara; Kisdi, Éva

2016-03-01

Evolutionary suicide is a riveting phenomenon in which adaptive evolution drives a viable population to extinction. Gyllenberg and Parvinen (Bull Math Biol 63(5):981-993, 2001) showed that, in a wide class of deterministic population models, a discontinuous transition to extinction is a necessary condition for evolutionary suicide. An implicit assumption of their proof is that the invasion fitness of a rare strategy is well-defined also in the extinction state of the population. Epidemic models with frequency-dependent incidence, which are often used to model the spread of sexually transmitted infections or the dynamics of infectious diseases within herds, violate this assumption. In these models, evolutionary suicide can occur through a non-catastrophic bifurcation whereby pathogen adaptation leads to a continuous decline of host (and consequently pathogen) population size to zero. Evolutionary suicide of pathogens with frequency-dependent transmission can occur in two ways, with pathogen strains evolving either higher or lower virulence.

Evolution of dispersal and life history interact to drive accelerating spread of an invasive species.

PubMed

Perkins, T Alex; Phillips, Benjamin L; Baskett, Marissa L; Hastings, Alan

2013-08-01

Populations on the edge of an expanding range are subject to unique evolutionary pressures acting on their life-history and dispersal traits. Empirical evidence and theory suggest that traits there can evolve rapidly enough to interact with ecological dynamics, potentially giving rise to accelerating spread. Nevertheless, which of several evolutionary mechanisms drive this interaction between evolution and spread remains an open question. We propose an integrated theoretical framework for partitioning the contributions of different evolutionary mechanisms to accelerating spread, and we apply this model to invasive cane toads in northern Australia. In doing so, we identify a previously unrecognised evolutionary process that involves an interaction between life-history and dispersal evolution during range shift. In roughly equal parts, life-history evolution, dispersal evolution and their interaction led to a doubling of distance spread by cane toads in our model, highlighting the potential importance of multiple evolutionary processes in the dynamics of range expansion. © 2013 John Wiley & Sons Ltd/CNRS.

Ab Initio Molecular Dynamics Studies on Substitution vs. Electron Transfer Reactions of Substituted Ketyl Radical Anions with Chloroalkanes: How Do the Two Products Form in a Borderline Mechanism?

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

Yamataka, H.; Aida, Misako; Dupuis, Michel

We present a qualitative analysis, based on ab initio molecular dynamics (MD) calculations, of the SN2/ET mechanistic spectrum for three reactions: (1) HC(CN)=O.- + CH3Cl, (2) HC(CN)=O.- + (CH3)2CHCl, and (3) H2C=O.- + CH3Cl, passing through their SN2-like transition states. The finite temperature (298 K) direct-MD simulations indicate that the trajectories for reaction 1 appear to have a propensity towards SN2 products, the propensity for trajectories for reaction 2 seems to be towards ET products, whereas trajectories for reaction 3 appear to show no particular propensity towards either ET or SN2 products. The mechanistic diversity is consistent with the electronmore » donating ability of the ketyl species and steric bulkiness of chloroalkanes. We find that the trajectories have characteristics that reflect strongly the types of process (SN2 trajectories in reactions 1 and 3 vs. ET trajectories in reactions 2 and 3). Trajectories that lead to SN2 products are simple with C-C bond formation and C-Cl bond breaking essentially completed within 50 fs. By contrast, trajectories leading to ET products are more complex with a sudden electron reorganization taking place within 15 - 30 fs and the major bonding changes and electron and spin reorganizations completed after 250 fs.« less

Construction of multiple trade-offs to obtain arbitrary singularities of adaptive dynamics.

PubMed

Kisdi, Éva

2015-04-01

Evolutionary singularities are central to the adaptive dynamics of evolving traits. The evolutionary singularities are strongly affected by the shape of any trade-off functions a model assumes, yet the trade-off functions are often chosen in an ad hoc manner, which may unjustifiably constrain the evolutionary dynamics exhibited by the model. To avoid this problem, critical function analysis has been used to find a trade-off function that yields a certain evolutionary singularity such as an evolutionary branching point. Here I extend this method to multiple trade-offs parameterized with a scalar strategy. I show that the trade-off functions can be chosen such that an arbitrary point in the viability domain of the trait space is a singularity of an arbitrary type, provided (next to certain non-degeneracy conditions) that the model has at least two environmental feedback variables and at least as many trade-offs as feedback variables. The proof is constructive, i.e., it provides an algorithm to find trade-off functions that yield the desired singularity. I illustrate the construction of trade-offs with an example where the virulence of a pathogen evolves in a small ecosystem of a host, its pathogen, a predator that attacks the host and an alternative prey of the predator.

Relative importance of evolutionary dynamics depends on the composition of microbial predator-prey community.

PubMed

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-06-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities.

Relative importance of evolutionary dynamics depends on the composition of microbial predator–prey community

PubMed Central

Friman, Ville-Petri; Dupont, Alessandra; Bass, David; Murrell, David J; Bell, Thomas

2016-01-01

Community dynamics are often studied in subsets of pairwise interactions. Scaling pairwise interactions back to the community level is, however, problematic because one given interaction might not reflect ecological and evolutionary outcomes of other functionally similar species interactions or capture the emergent eco-evolutionary dynamics arising only in more complex communities. Here we studied this experimentally by exposing Pseudomonas fluorescens SBW25 prey bacterium to four different protist predators (Tetrahymena pyriformis, Tetrahymena vorax, Chilomonas paramecium and Acanthamoeba polyphaga) in all possible single-predator, two-predator and four-predator communities for hundreds of prey generations covering both ecological and evolutionary timescales. We found that only T. pyriformis selected for prey defence in single-predator communities. Although T. pyriformis selection was constrained in the presence of the intraguild predator, T. vorax, T. pyriformis selection led to evolution of specialised prey defence strategies in the presence of C. paramecium or A. polyphaga. At the ecological level, adapted prey populations were phenotypically more diverse, less stable and less productive compared with non-adapted prey populations. These results suggest that predator community composition affects the relative importance of ecological and evolutionary processes and can crucially determine when rapid evolution has the potential to change ecological properties of microbial communities. PMID:26684728

Bipartite graphs as models of population structures in evolutionary multiplayer games.

PubMed

Peña, Jorge; Rochat, Yannick

2012-01-01

By combining evolutionary game theory and graph theory, "games on graphs" study the evolutionary dynamics of frequency-dependent selection in population structures modeled as geographical or social networks. Networks are usually represented by means of unipartite graphs, and social interactions by two-person games such as the famous prisoner's dilemma. Unipartite graphs have also been used for modeling interactions going beyond pairwise interactions. In this paper, we argue that bipartite graphs are a better alternative to unipartite graphs for describing population structures in evolutionary multiplayer games. To illustrate this point, we make use of bipartite graphs to investigate, by means of computer simulations, the evolution of cooperation under the conventional and the distributed N-person prisoner's dilemma. We show that several implicit assumptions arising from the standard approach based on unipartite graphs (such as the definition of replacement neighborhoods, the intertwining of individual and group diversity, and the large overlap of interaction neighborhoods) can have a large impact on the resulting evolutionary dynamics. Our work provides a clear example of the importance of construction procedures in games on graphs, of the suitability of bigraphs and hypergraphs for computational modeling, and of the importance of concepts from social network analysis such as centrality, centralization and bipartite clustering for the understanding of dynamical processes occurring on networked population structures.

Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain

NASA Astrophysics Data System (ADS)

Huizhong, Dong; Hongli, Song

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

Energy conserving, linear scaling Born-Oppenheimer molecular dynamics.

PubMed

Cawkwell, M J; Niklasson, Anders M N

2012-10-07

Born-Oppenheimer molecular dynamics simulations with long-term conservation of the total energy and a computational cost that scales linearly with system size have been obtained simultaneously. Linear scaling with a low pre-factor is achieved using density matrix purification with sparse matrix algebra and a numerical threshold on matrix elements. The extended Lagrangian Born-Oppenheimer molecular dynamics formalism [A. M. N. Niklasson, Phys. Rev. Lett. 100, 123004 (2008)] yields microcanonical trajectories with the approximate forces obtained from the linear scaling method that exhibit no systematic drift over hundreds of picoseconds and which are indistinguishable from trajectories computed using exact forces.

Long-time Dynamics of Stochastic Wave Breaking

NASA Astrophysics Data System (ADS)

Restrepo, J. M.; Ramirez, J. M.; Deike, L.; Melville, K.

2017-12-01

A stochastic parametrization is proposed for the dynamics of wave breaking of progressive water waves. The model is shown to agree with transport estimates, derived from the Lagrangian path of fluid parcels. These trajectories are obtained numerically and are shown to agree well with theory in the non-breaking regime. Of special interest is the impact of wave breaking on transport, momentum exchanges and energy dissipation, as well as dispersion of trajectories. The proposed model, ensemble averaged to larger time scales, is compared to ensemble averages of the numerically generated parcel dynamics, and is then used to capture energy dissipation and path dispersion.

Non-recursive augmented Lagrangian algorithms for the forward and inverse dynamics of constrained flexible multibodies

NASA Technical Reports Server (NTRS)

Bayo, Eduardo; Ledesma, Ragnar

1993-01-01

A technique is presented for solving the inverse dynamics of flexible planar multibody systems. This technique yields the non-causal joint efforts (inverse dynamics) as well as the internal states (inverse kinematics) that produce a prescribed nominal trajectory of the end effector. A non-recursive global Lagrangian approach is used in formulating the equations for motion as well as in solving the inverse dynamics equations. Contrary to the recursive method previously presented, the proposed method solves the inverse problem in a systematic and direct manner for both open-chain as well as closed-chain configurations. Numerical simulation shows that the proposed procedure provides an excellent tracking of the desired end effector trajectory.

An inverse dynamics approach to trajectory optimization and guidance for an aerospace plane

NASA Technical Reports Server (NTRS)

Lu, Ping

1992-01-01

The optimal ascent problem for an aerospace planes is formulated as an optimal inverse dynamic problem. Both minimum-fuel and minimax type of performance indices are considered. Some important features of the optimal trajectory and controls are used to construct a nonlinear feedback midcourse controller, which not only greatly simplifies the difficult constrained optimization problem and yields improved solutions, but is also suited for onboard implementation. Robust ascent guidance is obtained by using combination of feedback compensation and onboard generation of control through the inverse dynamics approach. Accurate orbital insertion can be achieved with near-optimal control of the rocket through inverse dynamics even in the presence of disturbances.

Evolutionary Dynamic Multiobjective Optimization Via Kalman Filter Prediction.

PubMed

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

2016-12-01

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

Towards a physics of evolution: Critical diversity dynamics at the edges of collapse and bursts of diversification

NASA Astrophysics Data System (ADS)

Hanel, Rudolf; Kauffman, Stuart A.; Thurner, Stefan

2007-09-01

Systems governed by the standard mechanisms of biological or technological evolution are often described by catalytic evolution equations. We study the structure of these equations and find an analogy with classical thermodynamic systems. In particular, we can demonstrate the existence of several distinct phases of evolutionary dynamics: a phase of fast growing diversity, one of stationary, finite diversity, and one of rapidly decaying diversity. While the first two phases have been subject to previous work, here we focus on the destructive aspects—in particular the phase diagram—of evolutionary dynamics. The main message is that within a critical region, massive loss of diversity can be triggered by very small external fluctuations. We further propose a dynamical model of diversity which captures spontaneous creation and destruction processes fully respecting the phase diagrams of evolutionary systems. The emergent time series show rich diversity dynamics, including power laws as observed in actual economical data, e.g., firm bankruptcy data. We believe the present model presents a possibility to cast the famous qualitative picture of Schumpeterian economic evolution, into a quantifiable and testable framework.

Dynamic trajectory-based couch motion for improvement of radiation therapy trajectories in cranial SRT

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

MacDonald, R. Lee; Thomas, Christopher G., E-mail: Chris.Thomas@cdha.nshealth.ca; Department of Medical Physics, Nova Scotia Cancer Centre, Queen Elizabeth II Health Sciences Centre, Halifax, Nova Scotia B3H 1V7

2015-05-15

Purpose: To investigate potential improvement in external beam stereotactic radiation therapy plan quality for cranial cases using an optimized dynamic gantry and patient support couch motion trajectory, which could minimize exposure to sensitive healthy tissue. Methods: Anonymized patient anatomy and treatment plans of cranial cancer patients were used to quantify the geometric overlap between planning target volumes and organs-at-risk (OARs) based on their two-dimensional projection from source to a plane at isocenter as a function of gantry and couch angle. Published dose constraints were then used as weighting factors for the OARs to generate a map of couch-gantry coordinate space,more » indicating degree of overlap at each point in space. A couch-gantry collision space was generated by direct measurement on a linear accelerator and couch using an anthropomorphic solid-water phantom. A dynamic, fully customizable algorithm was written to generate a navigable ideal trajectory for the patient specific couch-gantry space. The advanced algorithm can be used to balance the implementation of absolute minimum values of overlap with the clinical practicality of large-scale couch motion and delivery time. Optimized cranial cancer treatment trajectories were compared to conventional treatment trajectories. Results: Comparison of optimized treatment trajectories with conventional treatment trajectories indicated an average decrease in mean dose to the OARs of 19% and an average decrease in maximum dose to the OARs of 12%. Degradation was seen for homogeneity index (6.14% ± 0.67%–5.48% ± 0.76%) and conformation number (0.82 ± 0.02–0.79 ± 0.02), but neither was statistically significant. Removal of OAR constraints from volumetric modulated arc therapy optimization reveals that reduction in dose to OARs is almost exclusively due to the optimized trajectory and not the OAR constraints. Conclusions: The authors’ study indicated that simultaneous couch and gantry motion during radiation therapy to minimize the geometrical overlap in the beams-eye-view of target volumes and the organs-at-risk can have an appreciable dose reduction to organs-at-risk.« less

UAV Trajectory Modeling Using Neural Networks

NASA Technical Reports Server (NTRS)

Xue, Min

2017-01-01

Large amount of small Unmanned Aerial Vehicles (sUAVs) are projected to operate in the near future. Potential sUAV applications include, but not limited to, search and rescue, inspection and surveillance, aerial photography and video, precision agriculture, and parcel delivery. sUAVs are expected to operate in the uncontrolled Class G airspace, which is at or below 500 feet above ground level (AGL), where many static and dynamic constraints exist, such as ground properties and terrains, restricted areas, various winds, manned helicopters, and conflict avoidance among sUAVs. How to enable safe, efficient, and massive sUAV operations at the low altitude airspace remains a great challenge. NASA's Unmanned aircraft system Traffic Management (UTM) research initiative works on establishing infrastructure and developing policies, requirement, and rules to enable safe and efficient sUAVs' operations. To achieve this goal, it is important to gain insights of future UTM traffic operations through simulations, where the accurate trajectory model plays an extremely important role. On the other hand, like what happens in current aviation development, trajectory modeling should also serve as the foundation for any advanced concepts and tools in UTM. Accurate models of sUAV dynamics and control systems are very important considering the requirement of the meter level precision in UTM operations. The vehicle dynamics are relatively easy to derive and model, however, vehicle control systems remain unknown as they are usually kept by manufactures as a part of intellectual properties. That brings challenges to trajectory modeling for sUAVs. How to model the vehicle's trajectories with unknown control system? This work proposes to use a neural network to model a vehicle's trajectory. The neural network is first trained to learn the vehicle's responses at numerous conditions. Once being fully trained, given current vehicle states, winds, and desired future trajectory, the neural network should be able to predict the vehicle's future states at next time step. A complete 4-D trajectory are then generated step by step using the trained neural network. Experiments in this work show that the neural network can approximate the sUAV's model and predict the trajectory accurately.

High-Fidelity Multi-Rotor Unmanned Aircraft System Simulation Development for Trajectory Prediction Under Off-Nominal Flight Dynamics

NASA Technical Reports Server (NTRS)

Foster, John V.; Hartman, David C.

2017-01-01

The NASA Unmanned Aircraft System (UAS) Traffic Management (UTM) project is conducting research to enable civilian low-altitude airspace and UAS operations. A goal of this project is to develop probabilistic methods to quantify risk during failures and off nominal flight conditions. An important part of this effort is the reliable prediction of feasible trajectories during off-nominal events such as control failure, atmospheric upsets, or navigation anomalies that can cause large deviations from the intended flight path or extreme vehicle upsets beyond the normal flight envelope. Few examples of high-fidelity modeling and prediction of off-nominal behavior for small UAS (sUAS) vehicles exist, and modeling requirements for accurately predicting flight dynamics for out-of-envelope or failure conditions are essentially undefined. In addition, the broad range of sUAS aircraft configurations already being fielded presents a significant modeling challenge, as these vehicles are often very different from one another and are likely to possess dramatically different flight dynamics and resultant trajectories and may require different modeling approaches to capture off-nominal behavior. NASA has undertaken an extensive research effort to define sUAS flight dynamics modeling requirements and develop preliminary high fidelity six degree-of-freedom (6-DOF) simulations capable of more closely predicting off-nominal flight dynamics and trajectories. This research has included a literature review of existing sUAS modeling and simulation work as well as development of experimental testing methods to measure and model key components of propulsion, airframe and control characteristics. The ultimate objective of these efforts is to develop tools to support UTM risk analyses and for the real-time prediction of off-nominal trajectories for use in the UTM Risk Assessment Framework (URAF). This paper focuses on modeling and simulation efforts for a generic quad-rotor configuration typical of many commercial vehicles in use today. An overview of relevant off-nominal multi-rotor behaviors will be presented to define modeling goals and to identify the prediction capability lacking in simplified models of multi-rotor performance. A description of recent NASA wind tunnel testing of multi-rotor propulsion and airframe components will be presented illustrating important experimental and data acquisition methods, and a description of preliminary propulsion and airframe models will be presented. Lastly, examples of predicted off-nominal flight dynamics and trajectories from the simulation will be presented.

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data.

PubMed

Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra, Yolanda; Dans, Pablo D; Battistini, Federica; Torres, Jordi; Goñi, Ramón; Orozco, Modesto; Gelpí, Josep Ll

2016-01-04

Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories are obtained after months of calculations, analysed in situ, and in practice forgotten. Several projects to generate stable trajectory databases have been developed for proteins, but no equivalence exists in the nucleic acids world. We present here a novel database system to store MD trajectories and analyses of nucleic acids. The initial data set available consists mainly of the benchmark of the new molecular dynamics force-field, parmBSC1. It contains 156 simulations, with over 120 μs of total simulation time. A deposition protocol is available to accept the submission of new trajectory data. The database is based on the combination of two NoSQL engines, Cassandra for storing trajectories and MongoDB to store analysis results and simulation metadata. The analyses available include backbone geometries, helical analysis, NMR observables and a variety of mechanical analyses. Individual trajectories and combined meta-trajectories can be downloaded from the portal. The system is accessible through http://mmb.irbbarcelona.org/BIGNASim/. Supplementary Material is also available on-line at http://mmb.irbbarcelona.org/BIGNASim/SuppMaterial/. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Significance of specific force models in two applications: Solar sails to sun-earth L4/L5 and grail data analysis suggesting lava tubes and buried craters on the moon

NASA Astrophysics Data System (ADS)

Sood, Rohan

In the trajectory design process, gravitational interaction between the bodies of interest plays a key role in developing the over-arching force model. However, non-gravitational forces, such as solar radiation pressure (SRP), can significantly influence the motion of a spacecraft. Incorporating SRP within the dynamical model can assist in estimating the trajectory of a spacecraft with greater precision, in particular, for a spacecraft with a large area-to-mass ratio, i.e., solar sails. Subsequently, in the trajectory design process, solar radiation pressure can be leveraged to maneuver the sail-based spacecraft. First, to construct low energy transfers, the invariant manifolds are explored that form an important tool in the computation and design of complex trajectories. The focus is the investigation of trajectory design options, incorporating solar sail dynamics, from the Earth parking orbit to the vicinity of triangular Lagrange points. Thereafter, an optimization scheme assisted in investigating the ?V requirement to depart from the Earth parking orbit. Harnessing the solar radiation pressure, the spacecraft is delivered to the vicinity of the displaced Lagrange point and maintains a trajectory close to the artificial libration point with the help of the solar sail. However, these trajectories are converged in a model formulated as a three-body problem with additional acceleration from solar radiation pressure. Thus, the trajectories are transitioned to higher fidelity ephemeris model to account for additional perturbing accelerations that may dominate the sail-craft dynamics and improve upon the trajectory design process. Alternatively, precise knowledge of the motion of a spacecraft about a central body and the contribution of the SRP can assist in deriving a highly accurate gravity field model. The high resolution gravity data can potentially assist in exploring the surface and subsurface properties of a particular body. With the goal of expanding human presence beyond Earth, sub-surface empty lava tubes on other worlds form ideal candidates for creating a permanent habitation environment safe from cosmic radiation, micrometeorite impacts and temperature extremes. In addition, gravitational analysis has also revealed large buried craters under thick piles of mare basalt, shedding light on Moon's dynamic and hostile past. In this work, gravity mapping observations from NASA's Gravity Recovery and Interior Laboratory (GRAIL) are employed to detect the presence of potential empty lava tubes and large impact craters buried beneath the lunar maria.

Drift in ocean currents impacts intergenerational microbial exposure to temperature

PubMed Central

Doblin, Martina A.; van Sebille, Erik

2016-01-01

Microbes are the foundation of marine ecosystems [Falkowski PG, Fenchel T, Delong EF (2008) Science 320(5879):1034–1039]. Until now, the analytical framework for understanding the implications of ocean warming on microbes has not considered thermal exposure during transport in dynamic seascapes, implying that our current view of change for these critical organisms may be inaccurate. Here we show that upper-ocean microbes experience along-trajectory temperature variability up to 10 °C greater than seasonal fluctuations estimated in a static frame, and that this variability depends strongly on location. These findings demonstrate that drift in ocean currents can increase the thermal exposure of microbes and suggests that microbial populations with broad thermal tolerance will survive transport to distant regions of the ocean and invade new habitats. Our findings also suggest that advection has the capacity to influence microbial community assemblies, such that regions with strong currents and large thermal fluctuations select for communities with greatest plasticity and evolvability, and communities with narrow thermal performance are found where ocean currents are weak or along-trajectory temperature variation is low. Given that fluctuating environments select for individual plasticity in microbial lineages, and that physiological plasticity of ancestors can predict the magnitude of evolutionary responses of subsequent generations to environmental change [Schaum CE, Collins S (2014) Proc Biol Soc 281(1793):20141486], our findings suggest that microbial populations in the sub-Antarctic (∼40°S), North Pacific, and North Atlantic will have the most capacity to adapt to contemporary ocean warming. PMID:27140608

Determining Individual Variation in Growth and Its Implication for Life-History and Population Processes Using the Empirical Bayes Method

PubMed Central

Vincenzi, Simone; Mangel, Marc; Crivelli, Alain J.; Munch, Stephan; Skaug, Hans J.

2014-01-01

The differences in demographic and life-history processes between organisms living in the same population have important consequences for ecological and evolutionary dynamics. Modern statistical and computational methods allow the investigation of individual and shared (among homogeneous groups) determinants of the observed variation in growth. We use an Empirical Bayes approach to estimate individual and shared variation in somatic growth using a von Bertalanffy growth model with random effects. To illustrate the power and generality of the method, we consider two populations of marble trout Salmo marmoratus living in Slovenian streams, where individually tagged fish have been sampled for more than 15 years. We use year-of-birth cohort, population density during the first year of life, and individual random effects as potential predictors of the von Bertalanffy growth function's parameters k (rate of growth) and (asymptotic size). Our results showed that size ranks were largely maintained throughout marble trout lifetime in both populations. According to the Akaike Information Criterion (AIC), the best models showed different growth patterns for year-of-birth cohorts as well as the existence of substantial individual variation in growth trajectories after accounting for the cohort effect. For both populations, models including density during the first year of life showed that growth tended to decrease with increasing population density early in life. Model validation showed that predictions of individual growth trajectories using the random-effects model were more accurate than predictions based on mean size-at-age of fish. PMID:25211603

Generalized correlation integral vectors: A distance concept for chaotic dynamical systems

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

Haario, Heikki, E-mail: heikki.haario@lut.fi; Kalachev, Leonid, E-mail: KalachevL@mso.umt.edu; Hakkarainen, Janne

2015-06-15

Several concepts of fractal dimension have been developed to characterise properties of attractors of chaotic dynamical systems. Numerical approximations of them must be calculated by finite samples of simulated trajectories. In principle, the quantities should not depend on the choice of the trajectory, as long as it provides properly distributed samples of the underlying attractor. In practice, however, the trajectories are sensitive with respect to varying initial values, small changes of the model parameters, to the choice of a solver, numeric tolerances, etc. The purpose of this paper is to present a statistically sound approach to quantify this variability. Wemore » modify the concept of correlation integral to produce a vector that summarises the variability at all selected scales. The distribution of this stochastic vector can be estimated, and it provides a statistical distance concept between trajectories. Here, we demonstrate the use of the distance for the purpose of estimating model parameters of a chaotic dynamic model. The methodology is illustrated using computational examples for the Lorenz 63 and Lorenz 95 systems, together with a framework for Markov chain Monte Carlo sampling to produce posterior distributions of model parameters.« less

Photodissociation Dynamics of Phenol: Multistate Trajectory Simulations including Tunneling

DOE PAGES

Xu, Xuefei; Zheng, Jingjing; Yang, Ke R.; ...

2014-10-27

We report multistate trajectory simulations, including coherence, decoherence, and multidimensional tunneling, of phenol photodissociation dynamics. The calculations are based on full-dimensional anchor-points reactive potential surfaces and state couplings fit to electronic structure calculations including dynamical correlation with an augmented correlation-consistent polarized valence double-ζ basis set. The calculations successfully reproduce the experimentally observed bimodal character of the total kinetic energy release spectra and confirm the interpretation of the most recent experiments that the photodissociation process is dominated by tunneling. Analysis of the trajectories uncovers an unexpected dissociation pathway for one quantum excitation of the O–H stretching mode of the S 1more » state, namely, tunneling in a coherent mixture of states starting in a smaller R OH (~0.9–1.0 Å) region than has previously been invoked. The simulations also show that most trajectories do not pass close to the S 1–S 2 conical intersection (they have a minimum gap greater than 0.6 eV), they provide statistics on the out-of-plane angles at the locations of the minimum energy adiabatic gap, and they reveal information about which vibrational modes are most highly activated in the products.« less

Cluster Analysis of Atmospheric Dynamics and Pollution Transport in a Coastal Area

NASA Astrophysics Data System (ADS)

Sokolov, Anton; Dmitriev, Egor; Maksimovich, Elena; Delbarre, Hervé; Augustin, Patrick; Gengembre, Cyril; Fourmentin, Marc; Locoge, Nadine

2016-11-01

Summertime atmospheric dynamics in the coastal zone of the industrialized Dunkerque agglomeration in northern France was characterized by a cluster analysis of back trajectories in the context of pollution transport. The MESO-NH atmospheric model was used to simulate the local dynamics at multiple scales with horizontal resolution down to 500 m, and for the online calculation of the Lagrangian backward trajectories with 30-min temporal resolution. Airmass transport was performed along six principal pathways obtained by the weighted k-means clustering technique. Four of these centroids corresponded to a range of wind speeds over the English Channel: two for wind directions from the north-east and two from the south-west. Another pathway corresponded to a south-westerly continental transport. The backward trajectories of the largest and most dispersed sixth cluster contained low wind speeds, including sea-breeze circulations. Based on analyses of meteorological data and pollution measurements, the principal atmospheric pathways were related to local air-contamination events. Continuous air quality and meteorological data were collected during the Benzene-Toluene-Ethylbenzene-Xylene 2006 campaign. The sites of the pollution measurements served as the endpoints for the backward trajectories. Pollutant transport pathways corresponding to the highest air contamination were defined.

The amazing evolutionary dynamics of non-linear optical systems with feedback

NASA Astrophysics Data System (ADS)

Yaroslavsky, Leonid

2013-09-01

Optical systems with feedback are, generally, non-linear dynamic systems. As such, they exhibit evolutionary behavior. In the paper we present results of experimental investigation of evolutionary dynamics of several models of such systems. The models are modifications of the famous mathematical "Game of Life". The modifications are two-fold: "Game of Life" rules are made stochastic and mutual influence of cells is made spatially non-uniform. A number of new phenomena in the evolutionary dynamics of the models are revealed: - "Ordering of chaos". Formation, from seed patterns, of stable maze-like patterns with chaotic "dislocations" that resemble natural patterns, such as skin patterns of some animals and fishes, see shell, fingerprints, magnetic domain patterns and alike, which one can frequently find in the nature. These patterns and their fragments exhibit a remarkable capability of unlimited growth. - "Self-controlled growth" of chaotic "live" formations into "communities" bounded, depending on the model, by a square, hexagon or octagon, until they reach a certain critical size, after which the growth stops. - "Eternal life in a bounded space" of "communities" after reaching a certain size and shape. - "Coherent shrinkage" of "mature", after reaching a certain size, "communities" into one of stable or oscillating patterns preserving in this process isomorphism of their bounding shapes until the very end.

Evolutionary perspectives on ageing.

PubMed

Reichard, Martin

2017-10-01

From an evolutionary perspective, ageing is a decrease in fitness with chronological age - expressed by an increase in mortality risk and/or decline in reproductive success and mediated by deterioration of functional performance. While this makes ageing intuitively paradoxical - detrimental to individual fitness - evolutionary theory offers answers as to why ageing has evolved. In this review, I first briefly examine the classic evolutionary theories of ageing and their empirical tests, and highlight recent findings that have advanced our understanding of the evolution of ageing (condition-dependent survival, positive pleiotropy). I then provide an overview of recent theoretical extensions and modifications that accommodate those new discoveries. I discuss the role of indeterminate (asymptotic) growth for lifetime increases in fecundity and ageing trajectories. I outline alternative views that challenge a universal existence of senescence - namely the lack of a germ-soma distinction and the ability of tissue replacement and retrogression to younger developmental stages in modular organisms. I argue that rejuvenation at the organismal level is plausible, but includes a return to a simple developmental stage. This may exempt a particular genotype from somatic defects but, correspondingly, removes any information acquired during development. A resolution of the question of whether a rejuvenated individual is the same entity is central to the recognition of whether current evolutionary theories of ageing, with their extensions and modifications, can explain the patterns of ageing across the Tree of Life. Copyright © 2017 Elsevier Ltd. All rights reserved.

Applying evolutionary concepts to wildlife disease ecology and management

PubMed Central

Vander Wal, Eric; Garant, Dany; Calmé, Sophie; Chapman, Colin A; Festa-Bianchet, Marco; Millien, Virginie; Rioux-Paquette, Sébastien; Pelletier, Fanie

2014-01-01

Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host–pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment–disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management. PMID:25469163

The role of evolutionary biology in research and control of liver flukes in Southeast Asia.

PubMed

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F; Wilcox, Bruce A

2016-09-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. Copyright © 2016 Elsevier B.V. All rights reserved.

The Role of Evolutionary Biology in Research and Control of Liver Flukes in Southeast Asia

PubMed Central

Echaubard, Pierre; Sripa, Banchob; Mallory, Frank F.; Wilcox, Bruce A.

2016-01-01

Stimulated largely by the availability of new technology, biomedical research at the molecular-level and chemical-based control approaches arguably dominate the field of infectious diseases. Along with this, the proximate view of disease etiology predominates to the exclusion of the ultimate, evolutionary biology-based, causation perspective. Yet, historically and up to today, research in evolutionary biology has provided much of the foundation for understanding the mechanisms underlying disease transmission dynamics, virulence, and the design of effective integrated control strategies. Here we review the state of knowledge regarding the biology of Asian liver Fluke-host relationship, parasitology, phylodynamics, drug-based interventions and liver Fluke-related cancer etiology from an evolutionary biology perspective. We consider how evolutionary principles, mechanisms and research methods could help refine our understanding of clinical disease associated with infection by Liver Flukes as well as their transmission dynamics. We identify a series of questions for an evolutionary biology research agenda for the liver Fluke that should contribute to an increased understanding of liver Fluke-associated diseases. Finally, we describe an integrative evolutionary medicine approach to liver Fluke prevention and control highlighting the need to better contextualize interventions within a broader human health and sustainable development framework. PMID:27197053

Applying evolutionary concepts to wildlife disease ecology and management.

PubMed

Vander Wal, Eric; Garant, Dany; Calmé, Sophie; Chapman, Colin A; Festa-Bianchet, Marco; Millien, Virginie; Rioux-Paquette, Sébastien; Pelletier, Fanie

2014-08-01

Existing and emerging infectious diseases are among the most pressing global threats to biodiversity, food safety and human health. The complex interplay between host, pathogen and environment creates a challenge for conserving species, communities and ecosystem functions, while mediating the many known ecological and socio-economic negative effects of disease. Despite the clear ecological and evolutionary contexts of host-pathogen dynamics, approaches to managing wildlife disease remain predominantly reactionary, focusing on surveillance and some attempts at eradication. A few exceptional studies have heeded recent calls for better integration of ecological concepts in the study and management of wildlife disease; however, evolutionary concepts remain underused. Applied evolution consists of four principles: evolutionary history, genetic and phenotypic variation, selection and eco-evolutionary dynamics. In this article, we first update a classical framework for understanding wildlife disease to integrate better these principles. Within this framework, we explore the evolutionary implications of environment-disease interactions. Subsequently, we synthesize areas where applied evolution can be employed in wildlife disease management. Finally, we discuss some future directions and challenges. Here, we underscore that despite some evolutionary principles currently playing an important role in our understanding of disease in wild animals, considerable opportunities remain for fostering the practice of evolutionarily enlightened wildlife disease management.

Querying databases of trajectories of differential equations 2: Index functions

NASA Technical Reports Server (NTRS)

Grossman, Robert

1991-01-01

Suppose that a large number of parameterized trajectories (gamma) of a dynamical system evolving in R sup N are stored in a database. Let eta is contained R sup N denote a parameterized path in Euclidean space, and let parallel to center dot parallel to denote a norm on the space of paths. A data structures and indices for trajectories are defined and algorithms are given to answer queries of the following forms: Query 1. Given a path eta, determine whether eta occurs as a subtrajectory of any trajectory gamma from the database. If so, return the trajectory; otherwise, return null. Query 2. Given a path eta, return the trajectory gamma from the database which minimizes the norm parallel to eta - gamma parallel.

Mapping the evolutionary trajectories of morbilliviruses: what, where and whither.

PubMed

Nambulli, Sham; Sharp, Claire R; Acciardo, Andrew S; Drexler, J Felix; Duprex, W Paul

2016-02-01

Morbilliviruses are pathogens of humans and other animals. Live attenuated morbillivirus vaccines have been used to end endemic transmission of measles virus (MV) in many parts of the developed world and to eradicate rinderpest virus. Entry is mediated by two different receptors which govern virus lymphotropism and epitheliotropism. Morbillivirus transmissibility is unparalleled and MV represents the most infectious human pathogen on earth. Their evolutionary origins remain obscure and their potential for adaption to new hosts is poorly understood. It has been suggested that MV could be eradicated. Therefore it is imperative to dissect barriers which restrict cross species infections. This is important as ecological studies identify novel morbilliviruses in a vast number of small mammals and carnivorous predators. Copyright © 2016 Elsevier B.V. All rights reserved.

Adaptive Capacity: An Evolutionary Neuroscience Model Linking Exercise, Cognition, and Brain Health.

PubMed

Raichlen, David A; Alexander, Gene E

2017-07-01

The field of cognitive neuroscience was transformed by the discovery that exercise induces neurogenesis in the adult brain, with the potential to improve brain health and stave off the effects of neurodegenerative disease. However, the basic mechanisms underlying exercise-brain connections are not well understood. We use an evolutionary neuroscience approach to develop the adaptive capacity model (ACM), detailing how and why physical activity improves brain function based on an energy-minimizing strategy. Building on studies showing a combined benefit of exercise and cognitive challenge to enhance neuroplasticity, our ACM addresses two fundamental questions: (i) what are the proximate and ultimate mechanisms underlying age-related brain atrophy, and (ii) how do lifestyle changes influence the trajectory of healthy and pathological aging? Copyright © 2017 Elsevier Ltd. All rights reserved.

Integrating Competition for Food, Hosts, or Mates via Experimental Evolution.

PubMed

Rodrigues, Leonor R; Duncan, Alison B; Clemente, Salomé H; Moya-Laraño, Jordi; Magalhães, Sara

2016-02-01

Competitive interactions shape the evolution of organisms. However, often it is not clear whether competition is the driving force behind the patterns observed. The recent use of experimental evolution in competitive environments can help establish such causality. Unfortunately, this literature is scattered, as competition for food, mates, and hosts are subject areas that belong to different research fields. Here, we group these bodies of literature, extract common processes and patterns concerning the role of competition in shaping evolutionary trajectories, and suggest perspectives stemming from an integrative view of competition across these research fields. This review reinstates the power of experimental evolution in addressing the evolutionary consequences of competition, but highlights potential pitfalls in the design of such experiments. Copyright © 2015 Elsevier Ltd. All rights reserved.

Understanding sequence similarity and framework analysis between centromere proteins using computational biology.

PubMed

Doss, C George Priya; Chakrabarty, Chiranjib; Debajyoti, C; Debottam, S

2014-11-01

Certain mysteries pointing toward their recruitment pathways, cell cycle regulation mechanisms, spindle checkpoint assembly, and chromosome segregation process are considered the centre of attraction in cancer research. In modern times, with the established databases, ranges of computational platforms have provided a platform to examine almost all the physiological and biochemical evidences in disease-associated phenotypes. Using existing computational methods, we have utilized the amino acid residues to understand the similarity within the evolutionary variance of different associated centromere proteins. This study related to sequence similarity, protein-protein networking, co-expression analysis, and evolutionary trajectory of centromere proteins will speed up the understanding about centromere biology and will create a road map for upcoming researchers who are initiating their work of clinical sequencing using centromere proteins.

Dynamics of essential collective motions in proteins: Theory

NASA Astrophysics Data System (ADS)

Stepanova, Maria

2007-11-01

A general theoretical background is introduced for characterization of conformational motions in protein molecules, and for building reduced coarse-grained models of proteins, based on the statistical analysis of their phase trajectories. Using the projection operator technique, a system of coupled generalized Langevin equations is derived for essential collective coordinates, which are generated by principal component analysis of molecular dynamic trajectories. The number of essential degrees of freedom is not limited in the theory. An explicit analytic relation is established between the generalized Langevin equation for essential collective coordinates and that for the all-atom phase trajectory projected onto the subspace of essential collective degrees of freedom. The theory introduced is applied to identify correlated dynamic domains in a macromolecule and to construct coarse-grained models representing the conformational motions in a protein through a few interacting domains embedded in a dissipative medium. A rigorous theoretical background is provided for identification of dynamic correlated domains in a macromolecule. Examples of domain identification in protein G are given and employed to interpret NMR experiments. Challenges and potential outcomes of the theory are discussed.

Principal component analysis for protein folding dynamics.

PubMed

Maisuradze, Gia G; Liwo, Adam; Scheraga, Harold A

2009-01-09

Protein folding is considered here by studying the dynamics of the folding of the triple beta-strand WW domain from the Formin-binding protein 28. Starting from the unfolded state and ending either in the native or nonnative conformational states, trajectories are generated with the coarse-grained united residue (UNRES) force field. The effectiveness of principal components analysis (PCA), an already established mathematical technique for finding global, correlated motions in atomic simulations of proteins, is evaluated here for coarse-grained trajectories. The problems related to PCA and their solutions are discussed. The folding and nonfolding of proteins are examined with free-energy landscapes. Detailed analyses of many folding and nonfolding trajectories at different temperatures show that PCA is very efficient for characterizing the general folding and nonfolding features of proteins. It is shown that the first principal component captures and describes in detail the dynamics of a system. Anomalous diffusion in the folding/nonfolding dynamics is examined by the mean-square displacement (MSD) and the fractional diffusion and fractional kinetic equations. The collisionless (or ballistic) behavior of a polypeptide undergoing Brownian motion along the first few principal components is accounted for.

Probing the dynamics of restriction endonuclease NgoMIV-DNA interaction by single-molecule FRET.

PubMed

Tutkus, Marijonas; Sasnauskas, Giedrius; Rutkauskas, Danielis

2017-12-01

Many type II restriction endonucleases require two copies of their recognition sequence for optimal activity. Concomitant binding of two DNA sites by such an enzyme produces a DNA loop. Here we exploit single-molecule Förster resonance energy transfer (smFRET) of surface-immobilized DNA fragments to study the dynamics of DNA looping induced by tetrameric endonuclease NgoMIV. We have employed a DNA fragment with two NgoMIV recognition sites and a FRET dye pair such that upon protein-induced DNA looping the dyes are brought to close proximity resulting in a FRET signal. The dynamics of DNA-NgoMIV interactions proved to be heterogeneous, with individual smFRET trajectories exhibiting broadly different average looped state durations. Distinct types of the dynamics were attributed to different types of DNA-protein complexes, mediated either by one NgoMIV tetramer simultaneously bound to two specific sites ("slow" trajectories) or by semi-specific interactions of two DNA-bound NgoMIV tetramers ("fast" trajectories), as well as to conformational heterogeneity of individual NgoMIV molecules. © 2017 Wiley Periodicals, Inc.

Motion Tree Delineates Hierarchical Structure of Protein Dynamics Observed in Molecular Dynamics Simulation

PubMed Central

Moritsugu, Kei; Koike, Ryotaro; Yamada, Kouki; Kato, Hiroaki; Kidera, Akinori

2015-01-01

Molecular dynamics (MD) simulations of proteins provide important information to understand their functional mechanisms, which are, however, likely to be hidden behind their complicated motions with a wide range of spatial and temporal scales. A straightforward and intuitive analysis of protein dynamics observed in MD simulation trajectories is therefore of growing significance with the large increase in both the simulation time and system size. In this study, we propose a novel description of protein motions based on the hierarchical clustering of fluctuations in the inter-atomic distances calculated from an MD trajectory, which constructs a single tree diagram, named a “Motion Tree”, to determine a set of rigid-domain pairs hierarchically along with associated inter-domain fluctuations. The method was first applied to the MD trajectory of substrate-free adenylate kinase to clarify the usefulness of the Motion Tree, which illustrated a clear-cut dynamics picture of the inter-domain motions involving the ATP/AMP lid and the core domain together with the associated amplitudes and correlations. The comparison of two Motion Trees calculated from MD simulations of ligand-free and -bound glutamine binding proteins clarified changes in inherent dynamics upon ligand binding appeared in both large domains and a small loop that stabilized ligand molecule. Another application to a huge protein, a multidrug ATP binding cassette (ABC) transporter, captured significant increases of fluctuations upon binding a drug molecule observed in both large scale inter-subunit motions and a motion localized at a transmembrane helix, which may be a trigger to the subsequent structural change from inward-open to outward-open states to transport the drug molecule. These applications demonstrated the capabilities of Motion Trees to provide an at-a-glance view of various sizes of functional motions inherent in the complicated MD trajectory. PMID:26148295

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout.

PubMed

Muhlfeld, Clint C; Kovach, Ryan P; Al-Chokhachy, Robert; Amish, Stephen J; Kershner, Jeffrey L; Leary, Robb F; Lowe, Winsor H; Luikart, Gordon; Matson, Phil; Schmetterling, David A; Shepard, Bradley B; Westley, Peter A H; Whited, Diane; Whiteley, Andrew; Allendorf, Fred W

2017-11-01

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multidecade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world's most widely introduced invasive fish, across the Northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11°C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially nonhybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories. © 2017 John Wiley & Sons Ltd.

Population genomics of a symbiont in the early stages of a pest invasion.

PubMed

Brown, Amanda M V; Huynh, Lynn Y; Bolender, Caitlin M; Nelson, Kelly G; McCutcheon, John P

2014-03-01

Invasive species often depend on microbial symbionts, but few studies have examined the evolutionary dynamics of symbionts during the early stages of an invasion. The insect Megacopta cribraria and its bacterial nutritional symbiont Candidatus Ishikawaella capsulata invaded the southeastern US in 2009. While M. cribraria was initially discovered on wild kudzu plants, it was found as a pest on soybeans within 1 year of infestation. Because prior research suggests Ishikawaella confers the pest status--that is, the ability to thrive on soybeans--in some Megacopta species, we performed a genomic study on Ishikawaella from US. Megacopta cribraria populations to understand the role of the symbiont in driving host plant preferences. We included Ishikawaella samples collected in the first days of the invasion in 2009 and from 23 locations across the insect's 2011 US range. The 0.75 Mb symbiont genome revealed only 47 fixed differences from the pest-conferring Ishikawaella in Japan, with only one amino acid change in a nutrition-provisioning gene. This similarity, along with a lack of fixed substitutions in the US symbiont population, indicates that Ishikawella likely arrived in the US capable of being a soybean pest. Analyses of allele frequency changes between 2009 and 2011 uncover signatures of both positive and negative selection and suggest that symbionts on soybeans and kudzu experience differential selection for genes related to nutrient provisioning. Our data reveal the evolutionary trajectory of an important insect-bacteria symbiosis in the early stages of an invasion, highlighting the role microbial symbionts may play in the spread of invasive species. © 2013 John Wiley & Sons Ltd.

Mechanistic Explanations for Restricted Evolutionary Paths That Emerge from Gene Regulatory Networks

PubMed Central

Cotterell, James; Sharpe, James

2013-01-01

The extent and the nature of the constraints to evolutionary trajectories are central issues in biology. Constraints can be the result of systems dynamics causing a non-linear mapping between genotype and phenotype. How prevalent are these developmental constraints and what is their mechanistic basis? Although this has been extensively explored at the level of epistatic interactions between nucleotides within a gene, or amino acids within a protein, selection acts at the level of the whole organism, and therefore epistasis between disparate genes in the genome is expected due to their functional interactions within gene regulatory networks (GRNs) which are responsible for many aspects of organismal phenotype. Here we explore epistasis within GRNs capable of performing a common developmental function – converting a continuous morphogen input into discrete spatial domains. By exploring the full complement of GRN wiring designs that are able to perform this function, we analyzed all possible mutational routes between functional GRNs. Through this study we demonstrate that mechanistic constraints are common for GRNs that perform even a simple function. We demonstrate a common mechanistic cause for such a constraint involving complementation between counter-balanced gene-gene interactions. Furthermore we show how such constraints can be bypassed by means of “permissive” mutations that buffer changes in a direct route between two GRN topologies that would normally be unviable. We show that such bypasses are common and thus we suggest that unlike what was observed in protein sequence-function relationships, the “tape of life” is less reproducible when one considers higher levels of biological organization. PMID:23613807

Restricted Gene Flow among Hospital Subpopulations of Enterococcus faecium

PubMed Central

Willems, Rob J. L.; Top, Janetta; van Schaik, Willem; Leavis, Helen; Bonten, Marc; Sirén, Jukka; Hanage, William P.; Corander, Jukka

2012-01-01

ABSTRACT Enterococcus faecium has recently emerged as an important multiresistant nosocomial pathogen. Defining population structure in this species is required to provide insight into the existence, distribution, and dynamics of specific multiresistant or pathogenic lineages in particular environments, like the hospital. Here, we probe the population structure of E. faecium using Bayesian-based population genetic modeling implemented in Bayesian Analysis of Population Structure (BAPS) software. The analysis involved 1,720 isolates belonging to 519 sequence types (STs) (491 for E. faecium and 28 for Enterococcus faecalis). E. faecium isolates grouped into 13 BAPS (sub)groups, but the large majority (80%) of nosocomial isolates clustered in two subgroups (2-1 and 3-3). Phylogenetic and eBURST analysis of BAPS groups 2 and 3 confirmed the existence of three separate hospital lineages (17, 18, and 78), highlighting different evolutionary trajectories for BAPS 2-1 (lineage 78) and 3-3 (lineage 17 and lineage 18) isolates. Phylogenomic analysis of 29 E. faecium isolates showed agreement between BAPS assignment of STs and their relative positions in the phylogenetic tree. Odds ratio calculation confirmed the significant association between hospital isolates with BAPS 3-3 and lineages 17, 18, and 78. Admixture analysis showed a scarce number of recombination events between the different BAPS groups. For the E. faecium hospital population, we propose an evolutionary model in which strains with a high propensity to colonize and infect hospitalized patients arise through horizontal gene transfer. Once adapted to the distinct hospital niche, this subpopulation becomes isolated, and recombination with other populations declines. PMID:22807567

Legacy introductions and climatic variation explain spatiotemporal patterns of invasive hybridization in a native trout

USGS Publications Warehouse

Muhlfeld, Clint C.; Kovach, Ryan P.; Al-Chokhachy, Robert K.; Amish, Stephen J.; Kershner, Jeffrey L.; Leary, Robb F.; Lowe, Winsor H.; Luikart, Gordon; Matson, Phil; Schmetterling, David A.; Shepard, Bradley B.; Westley, Peter A. H.; Whited, Diane; Whiteley, Andrew R.; Allendorf, Fred W.

2017-01-01

Hybridization between invasive and native species, a significant threat to worldwide biodiversity, is predicted to increase due to climate-induced expansions of invasive species. Long-term research and monitoring are crucial for understanding the ecological and evolutionary processes that modulate the effects of invasive species. Using a large, multi-decade genetics dataset (N = 582 sites, 12,878 individuals) with high-resolution climate predictions and extensive stocking records, we evaluate the spatiotemporal dynamics of hybridization between native cutthroat trout and invasive rainbow trout, the world’s most widely introduced invasive fish, across the northern Rocky Mountains of the United States. Historical effects of stocking and contemporary patterns of climatic variation were strongly related to the spread of hybridization across space and time. The probability of occurrence, extent of, and temporal changes in hybridization increased at sites in close proximity to historical stocking locations with greater rainbow trout propagule pressure, warmer water temperatures, and lower spring precipitation. Although locations with warmer water temperatures were more prone to hybridization, cold sites were not protected from invasion; 58% of hybridized sites had cold mean summer water temperatures (<11°C). Despite cessation of stocking over 40 years ago, hybridization increased over time at half (50%) of the locations with long-term data, the vast majority of which (74%) were initially non-hybridized, emphasizing the chronic, negative impacts of human-mediated hybridization. These results show that effects of climate change on biodiversity must be analyzed in the context of historical human impacts that set ecological and evolutionary trajectories.

An evolutionary perspective on the history of flap reconstruction in the upper extremity.

PubMed

Fang, Frank; Chung, Kevin C

2014-05-01

Examining the evolution of flap reconstruction of the upper extremity is similar to studying the evolution of biological species. This analogy provides a perspective to appreciate the contributing factors that led to the development of the current arsenal of techniques. It shows the trajectory for the future and provides a glimpse of the factors that that will be influential in the future. Copyright © 2014 Elsevier Inc. All rights reserved.

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

NASA Astrophysics Data System (ADS)

Ma, Zhanshan (Sam)

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

Control and trajectory design of a highly flexible air vehicle with a distributed sensing architecture

NASA Astrophysics Data System (ADS)

Pachikara, Abraham James

Next generational aircraft are becoming very flexible due to efforts to reduce weight and increase aerodynamic efficiency. As a result, flight control systems and trajectories that were designed with traditional rigid body assumptions may no longer become valid. When an aircraft becomes more flexible, the shape of the aircraft can deform significantly due to the aeroservoelastic dynamics. No longer are few sensors located at the CG and elsewhere will be enough to maximize performance. Instead, a full suite of sensors will be needed all throughout the aircraft to accurately measure the complete aerodynamic distribution and dynamics. First, a parametric study will be conducted to understand how flexibility impacts both the open-loop and closed-loop dynamics of a generic micro air vehicle (MAV). Once the impact of flexibility on the MAV's aeroservoelastic dynamics is well understood, an aeroservoelastic flight controller will be designed that leverages a "Fly-By-Feel" sensor architecture. A sensor architecture will be developed that uses several sensors to estimate the MAV's full aerodynamic and inertial distribution along with inertial sensors at the CG. A modal filtering approach will be used for the relevant sensor management and to extract useful modal characteristics from the sensor data. Once that is done, a controller will be designed for maneuver tracking. Once a flight controller has been designed, a set of representative motion primitives for the MAV can be developed that model how the aircraft moves for trajectory generation. Then trajectories can be developed for the flexible vehicle. Analysis will then be conducted to understand how flexibility impacts the creation of trajectories and MAV performance metrics.

Thermal boundaries analysis program document

NASA Technical Reports Server (NTRS)

Evans, M. E.

1975-01-01

The digital program TBAP has been developed to provide thermal boundaries in the DD/M-relative velocity (D-V), dynamic pressure-relative velocity (q-V), and altitude-relative velocity (h-V) planes. These thermal boundaries are used to design and/or analyze shuttle orbiter entry trajectories. The TBAP has been used extensively in supporting the Flight Performance Branch of NASA in evaluating candidate trajectories for the thermal protection system design trajectory.

LDSD POST2 Simulation and SFDT-1 Pre-Flight Launch Operations Analyses

NASA Technical Reports Server (NTRS)

Bowes, Angela L.; Davis, Jody L.; Dutta, Soumyo; Striepe, Scott A.; Ivanov, Mark C.; Powell, Richard W.; White, Joseph

2015-01-01

The Low-Density Supersonic Decelerator (LDSD) Project's first Supersonic Flight Dynamics Test (SFDT-1) occurred June 28, 2014. Program to Optimize Simulated Trajectories II (POST2) was utilized to develop trajectory simulations characterizing all SFDT-1 flight phases from drop to splashdown. These POST2 simulations were used to validate the targeting parameters developed for SFDT- 1, predict performance and understand the sensitivity of the vehicle and nominal mission designs, and to support flight test operations with trajectory performance and splashdown location predictions for vehicle recovery. This paper provides an overview of the POST2 simulations developed for LDSD and presents the POST2 simulation flight dynamics support during the SFDT-1 launch, operations, and recovery.