Evolutionary Algorithms and Dynamic Programming
Doerr, Benjamin; Eremeev, Anton; Neumann, Frank; Theile, Madeleine; Thyssen, Christian
2013-01-01
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which enables them to construct solutions in a dynamic programming fashion. We take a general approach and relate the construction of such algorithms to the development of algorithms using dynamic programming techniques. Thereby, we give general guidelines on how ...
Neuronal boost to evolutionary dynamics
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
Modeling tumor evolutionary dynamics
Directory of Open Access Journals (Sweden)
Beatriz eStransky
2013-02-01
Full Text Available Tumorigenesis can be seen as an evolutionary process, in which the transformation of a normal cell into a tumor cell involves a number of limiting genetic and epigenetic events, occurring in a series of discrete stages. However, not all mutations in a cell are directly involved in cancer development and it is likely that most of them (passenger mutations do not contribute in any way to tumorigenesis. Moreover, the process of tumor evolution is punctuated by selection of advantageous (driver mutations and clonal expansions. Regarding these driver mutations, it is uncertain how many limiting events are required and / or sufficient to promote a tumorigenic process or what are the values associated with the adaptive advantage of different driver mutations. In spite of the availability of high-quality cancer data, several assumptions about the mechanistic process of cancer initiation and development remain largely untested, both mathematically and statistically. Here we review the development of mathematical/computational models where some assumptions were tested and discuss the impact of these models to the field of tumor biology.
Evolutionary dynamics of mammalian karyotypes
Directory of Open Access Journals (Sweden)
Carlo Alberto Redi
2012-12-01
Full Text Available This special volume of Cytogenetic and Genome Research (edited by Roscoe Stanyon, University of Florence and Alexander Graphodatsky, Siberian division of the Russian Academy of Sciences is dedicated to the fascinating long search of the forces behind the evolutionary dynamics of mammalian karyotypes, revealed after the hypotonic miracle of the 1950s....
Organisations’ evolutionary dynamics: a group dynamics approach
Directory of Open Access Journals (Sweden)
Germán Eduardo Vargas
2010-04-01
Full Text Available Colombian entrepreneurs’ straggling, reactionary and inertial orientation has been inconsistently lustified by the availability of internal and leveraged resources, a concept intensifying deficient technological capacity. Company activity (seen as being a socioeconomic unit has been integrally orientated within an evolutionary framework by company identity and cohesion as well as adaptation and evolutionary mechanisms. The present document uses a group dynamics’ model to illustrate how knowledge-based strategic orientation and integration for innovation have become an imperative for development, from slight leverage, distinguishing between two evolutionary company forms: traditional economic (inertial, as they introduce sporadic incremental improvements and modern companies (dynamic and radical innovators. Revealing conclusions obtained from such model may be used for intervening in and modernising company activity.
Dynamics of a Simple Evolutionary Process
Stauffer, Dietrich; Newman, M. E. J.
We study the simple evolutionary process in which we repeatedly find the least fit agent in a population of agents and give it a new fitness, which is chosen independently at random from a specified distribution. We show that many of the average properties of this process can be calculated exactly using analytic methods. In particular, we find the distribution of fitnesses at arbitrary time, and the distribution of the lengths of runs of hits on the same agent, the latter being found to follow a power law with exponent -1, similar to the distribution of times between evolutionary events in the Bak-Sneppen model and models based on the so-called record dynamics. We confirm our analytic results with extensive numerical simulations.
Evolutionary dynamics of group fairness.
Santos, Fernando P; Santos, Francisco C; Paiva, Ana; Pacheco, Jorge M
2015-08-01
The emergence and impact of fairness is commonly studied in the context of 2-person games, notably the Ultimatum Game. Often, however, humans face problems of collective action involving more than two individuals where fairness is known to play a very important role, and whose dynamics cannot be inferred from what is known from 2-person games. Here, we propose a generalization of the Ultimatum Game for an arbitrary number of players--the Multiplayer Ultimatum Game. Proposals are made to a group of responders who must individually reject or accept the proposal. If the total number of individual acceptances stands below a given threshold, the offer will be rejected; otherwise, the offer will be accepted, and equally shared by all responders. We investigate the evolution of fairness in populations of individuals by means of evolutionary game theory, providing both analytical insights and results from numerical simulations. We show how imposing stringent consensuses significantly increases the value of the proposals, leading to fairer outcomes and more tolerant players. Furthermore, we show how stochastic effects--such as imitation errors and/or errors when assessing the fitness of others--may further enhance the overall success in reaching fair collective action. PMID:25936348
Stochastic evolutionary dynamics of direct reciprocity
Lorens A. Imhof; Nowak, Martin A.
2009-01-01
Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the reside...
On evolutionary ray-projection dynamics
Joosten, Reinoud; Roorda, Berend
2011-01-01
We introduce the ray-projection dynamics in evolutionary game theory by employing a ray projection of the relative fitness (vector) function, i.e., a projection unto the unit simplex along a ray through the origin. Ray-projection dynamics are weakly compatible in the terminology of Friedman (Econome
Evolutionary Dynamics of Nationalism and Migration
André Barreira da Silva Rocha
2012-01-01
I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modelled using replicator dynamics (...
On the Dynamic Foundation of Evolutionary Stability in Continuous Models
Oechssler, Jörg; Riedel, Frank
2000-01-01
We show in this paper that none of the existing static evolutionary stability concepts (ESS, CSS, uninvadability, NIS) is sufficient to guarantee dynamic stability in the weak topology with respect to standard evolutionary dynamics if the strategy space is continuous. We propose a new concept, evolutionary robustness, which is stronger than the previous concepts. Evolutionary robustness ensures dynamic stability for replicator dynamics in doubly symmetric games.
Multiscale structure in eco-evolutionary dynamics
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.
A Simple General Model of Evolutionary Dynamics
Thurner, Stefan
Evolution is a process in which some variations that emerge within a population (of, e.g., biological species or industrial goods) get selected, survive, and proliferate, whereas others vanish. Survival probability, proliferation, or production rates are associated with the "fitness" of a particular variation. We argue that the notion of fitness is an a posteriori concept in the sense that one can assign higher fitness to species or goods that survive but one can generally not derive or predict fitness per se. Whereas proliferation rates can be measured, fitness landscapes, that is, the inter-dependence of proliferation rates, cannot. For this reason we think that in a physical theory of evolution such notions should be avoided. Here we review a recent quantitative formulation of evolutionary dynamics that provides a framework for the co-evolution of species and their fitness landscapes (Thurner et al., 2010, Physica A 389, 747; Thurner et al., 2010, New J. Phys. 12, 075029; Klimek et al., 2009, Phys. Rev. E 82, 011901 (2010). The corresponding model leads to a generic evolutionary dynamics characterized by phases of relative stability in terms of diversity, followed by phases of massive restructuring. These dynamical modes can be interpreted as punctuated equilibria in biology, or Schumpeterian business cycles (Schumpeter, 1939, Business Cycles, McGraw-Hill, London) in economics. We show that phase transitions that separate phases of high and low diversity can be approximated surprisingly well by mean-field methods. We demonstrate that the mathematical framework is suited to understand systemic properties of evolutionary systems, such as their proneness to collapse, or their potential for diversification. The framework suggests that evolutionary processes are naturally linked to self-organized criticality and to properties of production matrices, such as their eigenvalue spectra. Even though the model is phrased in general terms it is also practical in the sense
Molecular Dynamics Calculations
1996-01-01
The development of thermodynamics and statistical mechanics is very important in the history of physics, and it underlines the difficulty in dealing with systems involving many bodies, even if those bodies are identical. Macroscopic systems of atoms typically contain so many particles that it would be virtually impossible to follow the behavior of all of the particles involved. Therefore, the behavior of a complete system can only be described or predicted in statistical ways. Under a grant to the NASA Lewis Research Center, scientists at the Case Western Reserve University have been examining the use of modern computing techniques that may be able to investigate and find the behavior of complete systems that have a large number of particles by tracking each particle individually. This is the study of molecular dynamics. In contrast to Monte Carlo techniques, which incorporate uncertainty from the outset, molecular dynamics calculations are fully deterministic. Although it is still impossible to track, even on high-speed computers, each particle in a system of a trillion trillion particles, it has been found that such systems can be well simulated by calculating the trajectories of a few thousand particles. Modern computers and efficient computing strategies have been used to calculate the behavior of a few physical systems and are now being employed to study important problems such as supersonic flows in the laboratory and in space. In particular, an animated video (available in mpeg format--4.4 MB) was produced by Dr. M.J. Woo, now a National Research Council fellow at Lewis, and the G-VIS laboratory at Lewis. This video shows the behavior of supersonic shocks produced by pistons in enclosed cylinders by following exactly the behavior of thousands of particles. The major assumptions made were that the particles involved were hard spheres and that all collisions with the walls and with other particles were fully elastic. The animated video was voted one of two
Calculation of Triggering Angle of Thyristor Rectifiers with Evolutionary Algorithms
Directory of Open Access Journals (Sweden)
Fahri VATANSEVER
2015-05-01
Full Text Available Rectifier circuits have important role in electrical energy systems. Especially in thyristor rectifiers which have capability of generating multiple voltage level, determining/calculating the optimal trigger angle and applying trigger signal at this angles are among the main process. In this study, desired level of average output voltage according to trigger angles is obtained both classically (mathematically solving of equations and using evolutionary algorithms which are genetic algorithms and differential evolutions. In this way, a software can be used in educational purposes which can calculate optimal trigger angles using both mathematically and heuristically, show results and many properties/parameters of circuit graphically and numerically is developed. Analysis/simulations performed with the designed software indicates that evolutionary algorithms can be used in this field effectively and efficiently.
Eco-evolutionary dynamics in a changing world.
Hanski, Ilkka
2012-02-01
Fast evolutionary changes are common in natural populations, though episodes of rapid evolution do not generally last for long and are typically associated with changing environments. During such periods, evolutionary dynamics may influence ecological population dynamics and vice versa. This review is concerned with spatial eco-evolutionary dynamics with a focus on the occurrence of species in marginal habitats and on metapopulations inhabiting heterogeneous environments. Dispersal and gene flow are key processes in both cases, linking demographic and evolutionary dynamics to each other, facilitating but also constraining the expansion of the current niche and the geographical range of species and determining the spatial scale and pattern of adaptation in heterogeneous environments. An eco-evolutionary metapopulation model helps explain the contrasting responses of species to habitat loss and fragmentation. Eco-evolutionary dynamics may facilitate the persistence of species in changing environments, but typically the evolutionary response only partially compensates for the negative ecological consequences of adverse environmental changes. PMID:22335524
Transition matrix model for evolutionary game dynamics
Ermentrout, G. Bard; Griffin, Christopher; Belmonte, Andrew
2016-03-01
We study an evolutionary game model based on a transition matrix approach, in which the total change in the proportion of a population playing a given strategy is summed directly over contributions from all other strategies. This general approach combines aspects of the traditional replicator model, such as preserving unpopulated strategies, with mutation-type dynamics, which allow for nonzero switching to unpopulated strategies, in terms of a single transition function. Under certain conditions, this model yields an endemic population playing non-Nash-equilibrium strategies. In addition, a Hopf bifurcation with a limit cycle may occur in the generalized rock-scissors-paper game, unlike the replicator equation. Nonetheless, many of the Folk Theorem results are shown to hold for this model.
Evolutionary dynamics with fluctuating population sizes and strong mutualism
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.
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. PMID:26382443
Evolutionary dynamics of nationalism and migration
Barreira da Silva Rocha, André
2013-08-01
I present a dynamic evolutionary game model to address the relation between nationalism against immigrants and assimilation of the latter into the host country culture. I assume a country composed of two different large polymorphic populations, one of native citizens and the other of immigrants. A native citizen may behave nationalistically or may welcome immigrants. Immigrants may have an interest in learning the host country language or not. Evolution is modeled using replicator dynamics (RD). I also account for the presence of an enclave of immigrants in the host country. In the RD, the latter represents the immigrants’ own population effect, which contribution to fitness is controlled using a parameter ρ, 0≤ρ≤1, that represents the enclave size. In line with the empirical literature on migration, the existence of an enclave of immigrants makes assimilation less likely to occur. For large values of ρ, complete assimilation may not occur even if immigrants and natives share very close cultures and norms. Government policy regarding nationalism is modeled both exogenously and endogenously. A single or multiple asymptotically stable states exist for all cases studied but one in which the dynamics is similar to that found in the predator-prey model of Lotka-Volterra for competing species.
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
Compared with ellipse cavity, the spoke cavity has many advantages, especially for the low and medium beam energy. It will be used in the superconductor accelerator popular in the future. Based on the spoke cavity, we design and calculate an accelerator
Quantifying Slow Evolutionary Dynamics in RNA Fitness Landscapes
Sulc, P; Wagner, A.; Martin, O. C.
2009-01-01
We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an inverse power of the evolutionary time. In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. In particular, the distribution of genotypes is close to that arising during equilibriu...
Dynamical characteristics of software trustworthiness and their evolutionary complexity
Institute of Scientific and Technical Information of China (English)
ZHENG ZhiMing; MA ShiLong; LI Wei; WEI Wei; JIANG Xin; ZHANG ZhanLi; GUO BingHui
2009-01-01
Developing trusted $oftwares has become an important trend and a natural choice In the development of software technology and applications, and software trustworthiness modeling has become a prerequisite and necessary means. To discuss and explain the basic scientific problems in software trustworthiness and to establish theoretical foundations for software trustworthiness measurement, combining the Ideas of dynamical system study, this paper studies evolutionary laws of software trustworthiness and the dynamical mechanism under the effect of various internal and external factors, and proposes dynamical models for software trustworthiness, thus, software trustworthiness can be considered as the statistical characteristics of behaviors of software systems in the dynamical and open environment. By analyzing two simple examples, the paper explains the relationship between the limit evolutionary behaviors of software trustworthiness attributes and dynamical system characteristics, and interprets the dynamical characteristics of software trustworthiness and their evolutionary complexity.
Eco-evolutionary spatial dynamics in the Glanville fritillary butterfly.
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. PMID:21788506
An evolutionary dynamics model adapted to eusocial insects.
Directory of Open Access Journals (Sweden)
Louise van Oudenhove
Full Text Available This study aims to better understand the evolutionary processes allowing species coexistence in eusocial insect communities. We develop a mathematical model that applies adaptive dynamics theory to the evolutionary dynamics of eusocial insects, focusing on the colony as the unit of selection. The model links long-term evolutionary processes to ecological interactions among colonies and seasonal worker production within the colony. Colony population dynamics is defined by both worker production and colony reproduction. Random mutations occur in strategies, and mutant colonies enter the community. The interactions of colonies at the ecological timescale drive the evolution of strategies at the evolutionary timescale by natural selection. This model is used to study two specific traits in ants: worker body size and the degree of collective foraging. For both traits, trade-offs in competitive ability and other fitness components allows to determine conditions in which selection becomes disruptive. Our results illustrate that asymmetric competition underpins diversity in ant communities.
Quantifying slow evolutionary dynamics in RNA fitness landscapes.
Sulc, Petr; Wagner, Andreas; Martin, Olivier C
2010-12-01
We re-examine the evolutionary dynamics of RNA secondary structures under directional selection towards an optimum RNA structure. We find that the punctuated equilibria lead to a very slow approach to the optimum, following on average an inverse power of the evolutionary time. In addition, our study of the trajectories shows that the out-of-equilibrium effects due to the evolutionary process are very weak. In particular, the distribution of genotypes is close to that arising during equilibrium stabilizing selection. As a consequence, the evolutionary dynamics leave almost no measurable out-of-equilibrium trace, only the transition genotypes (close to the border between different periods of stasis) have atypical mutational properties. PMID:21121025
The evolutionary rate dynamically tracks changes in HIV-1 epidemics
Energy Technology Data Exchange (ETDEWEB)
Maljkovic-berry, Irina [Los Alamos National Laboratory; Athreya, Gayathri [Los Alamos National Laboratory; Daniels, Marcus [Los Alamos National Laboratory; Bruno, William [Los Alamos National Laboratory; Korber, Bette [Los Alamos National Laboratory; Kuiken, Carla [Los Alamos National Laboratory; Ribeiro, Ruy M [Los Alamos National Laboratory
2009-01-01
Large-sequence datasets provide an opportunity to investigate the dynamics of pathogen epidemics. Thus, a fast method to estimate the evolutionary rate from large and numerous phylogenetic trees becomes necessary. Based on minimizing tip height variances, we optimize the root in a given phylogenetic tree to estimate the most homogenous evolutionary rate between samples from at least two different time points. Simulations showed that the method had no bias in the estimation of evolutionary rates and that it was robust to tree rooting and topological errors. We show that the evolutionary rates of HIV-1 subtype B and C epidemics have changed over time, with the rate of evolution inversely correlated to the rate of virus spread. For subtype B, the evolutionary rate slowed down and tracked the start of the HAART era in 1996. Subtype C in Ethiopia showed an increase in the evolutionary rate when the prevalence increase markedly slowed down in 1995. Thus, we show that the evolutionary rate of HIV-1 on the population level dynamically tracks epidemic events.
Evolutionary Dynamics of Chronic Myeloid Leukemia
Dingli, David; Traulsen, Arne; Lenaerts, Tom; Pacheco, Jorge M.
2010-01-01
Cancer is an evolutionary process that arises due to mutations and expands through the selection of clones with higher reproductive success that will outcompete their peers. Most tumors require many mutations to explain the cancer phenotype, making it difficult to identify the gene(s) that confer the reproductive fitness to the clone. Moreover, the impact of any oncogene is context dependent: it can increase the fitness of particular stages of cell differentiation but not other stages. In add...
HIV evolutionary dynamics within and among hosts.
Lemey, Philippe; Rambaut, Andrew; Pybus, Oliver G
2006-01-01
The HIV evolutionary processes continuously unfold, leaving a measurable footprint in viral gene sequences. A variety of statistical models and inference techniques have been developed to reconstruct the HIV evolutionary history and to investigate the population genetic processes that shape viral diversity. Remarkably different population genetic forces are at work within and among hosts. Population-level HIV phylogenies are mainly shaped by selectively neutral epidemiologic processes, implying that genealogy-based population genetic inference can be useful to study the HIV epidemic history. Such evolutionary analyses have shed light on the origins of HIV, and on the epidemic spread of viral variants in different geographic locations and in different populations. The HIV genealogies reconstructed from within-host sequences indicate the action of selection pressure. In addition, recombination has a significant impact on HIV genetic diversity. Accurately quantifying both the adaptation rate and the population recombination rate of HIV will contribute to a better understanding of immune escape and drug resistance. Characterizing the impact of HIV transmission on viral genetic diversity will be a key factor in reconciling the different population genetic processes within and among hosts. PMID:17078483
Spatial effect on stochastic dynamics of bistable evolutionary games
International Nuclear Information System (INIS)
We consider the lifetimes of metastable states in bistable evolutionary games (coordination games), and examine how they are affected by spatial structure. A semiclassical approximation based on a path integral method is applied to stochastic evolutionary game dynamics with and without spatial structure, and the lifetimes of the metastable states are evaluated. It is shown that the population dependence of the lifetimes is qualitatively different in these two models. Our result indicates that spatial structure can accelerate the transitions between metastable states. (paper)
Evolutionary dynamics of group interactions on structured populations: A review
Perc, Matjaz; Szolnoki, Attila; Floría, Luis M; Moreno, Yamir; 10.1098/rsif.2012.0997
2013-01-01
Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and nonliving matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proven valuable for studying pattern formation, equilibrium selection, and self-organisation in evolutionary games. Here we review recent advances in the study of evolutionary dynamics of group interactions on structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory...
Saakian, David B
2009-01-01
The parallel mutation-selection evolutionary dynamics, in which mutation and replication are independent events, is solved exactly in the case that the Malthusian fitnesses associated to the genomes are described by the Random Energy Model (REM) and by a ferromagnetic version of the REM. The solution method uses the mapping of the evolutionary dynamics into a quantum Ising chain in a transverse field and the Suzuki-Trotter formalism to calculate the transition probabilities between configurations at different times. We find that in the case of the REM landscape the dynamics can exhibit three distinct regimes: pure diffusion or stasis for short times, depending on the fitness of the initial configuration, and a spin-glass regime for large times. The dynamic transition between these dynamical regimes is marked by discontinuities in the mean-fitness as well as in the overlap with the initial reference sequence. The relaxation to equilibrium is described by an inverse time decay. In the ferromagnetic REM, we find...
Emergence of structured communities through evolutionary dynamics.
Shtilerman, Elad; Kessler, David A; Shnerb, Nadav M
2015-10-21
Species-rich communities, in which many competing species coexist in a single trophic level, are quite frequent in nature, but pose a formidable theoretical challenge. In particular, it is known that complex competitive systems become unstable and unfeasible when the number of species is large. Recently, many studies have attributed the stability of natural communities to the structure of the interspecific interaction network, yet the nature of such structures and the underlying mechanisms responsible for them remain open questions. Here we introduce an evolutionary model, based on the generic Lotka-Volterra competitive framework, from which a stable, structured, diverse community emerges spontaneously. The modular structure of the competition matrix reflects the phylogeny of the community, in agreement with the hierarchial taxonomic classification. Closely related species tend to have stronger niche overlap and weaker fitness differences, as opposed to pairs of species from different modules. The competitive-relatedness hypothesis and the idea of emergent neutrality are discussed in the context of this evolutionary model. PMID:26231415
Dynamic Ising model: reconstruction of evolutionary trees
International Nuclear Information System (INIS)
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. ‘Species’ here is a general denomination for biological species, spoken languages or any other entity which evolves through heredity. From the N currently alive species within a clade, distances are measured through pairwise comparisons made by geneticists, linguists, etc. The larger is such a distance that, for a pair of species, the older is their last common ancestor. The aim is to reconstruct the previously unknown bifurcations, i.e. the whole clade, from knowledge of the N(N − 1)/2 quoted distances, which are taken for granted. A mechanical method is presented and its applicability is discussed. (paper)
Eco-evolutionary dynamics of dispersal in spatially heterogeneous environments.
Hanski, Ilkka; Mononen, Tommi
2011-10-01
Ecology Letters (2011) 14: 1025-1034 ABSTRACT: Evolutionary changes in natural populations are often so fast that the evolutionary dynamics may influence ecological population dynamics and vice versa. Here we construct an eco-evolutionary model for dispersal by combining a stochastic patch occupancy metapopulation model with a model for changes in the frequency of fast-dispersing individuals in local populations. We test the model using data on allelic variation in the gene phosphoglucose isomerase (Pgi), which is strongly associated with dispersal rate in the Glanville fritillary butterfly. Population-specific measures of immigration and extinction rates and the frequency of fast-dispersing individuals among the immigrants explained 40% of spatial variation in Pgi allele frequency among 97 local populations. The model clarifies the roles of founder events and gene flow in dispersal evolution and resolves a controversy in the literature about the consequences of habitat loss and fragmentation on the evolution of dispersal. PMID:21794053
Bridging Developmental Systems Theory and Evolutionary Psychology Using Dynamic Optimization
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…
A stochastic evolutionary model for survival dynamics
Fenner, Trevor; Loizou, George
2014-01-01
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in different contexts. Here we propose a generative model to capture the essential dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. In our model, the only implicit assumption made is that the longer an actor has been in the system, the more likely it is to have failed. We derive a power-law distribution for the process and provide preliminary empirical evidence for the validity of the model from two well-known survival analysis data sets.
Evolutionary dynamics of a smoothed war of attrition game.
Iyer, Swami; Killingback, Timothy
2016-05-01
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. PMID:26903203
Temporal and evolutionary dynamics of two-component signaling pathways.
Salazar, Michael E; Laub, Michael T
2015-04-01
Bacteria sense and respond to numerous environmental signals through two-component signaling pathways. Typically, a given stimulus will activate a sensor histidine kinase to autophosphorylate and then phosphotransfer to a cognate response regulator, which can mount an appropriate response. Although these signaling pathways often appear to be simple switches, they can also orchestrate surprisingly sophisticated and complex responses. These temporal dynamics arise from several key regulatory features, including the bifunctionality of histidine kinases as well as positive and negative feedback loops. Two-component signaling pathways are also dynamic on evolutionary time-scales, expanding dramatically in many species through gene duplication and divergence. Here, we review recent work probing the temporal and evolutionary dynamics of two-component signaling systems. PMID:25589045
Evolutionary Dynamics of the World Wide Web
Bernardo A. Huberman; Adamic, Lada A.
1999-01-01
We present a theory for the growth dynamics of the World Wide Web that takes into account the wide range of stochastic growth rates in the number of pages per site, as well as the fact that new sites are created at different times. This leads to the prediction of a universal power law in the distribution of the number of pages per site which we confirm experimentally by analyzing data from large crawls made by the search engines Alexa and Infoseek. The existence of this power law not only imp...
Reconstructing the Nonlinear Dynamical Systems by Evolutionary Computation Techniques
Institute of Scientific and Technical Information of China (English)
LIU Minzhong; KANG Lishan
2006-01-01
We introduce a new dynamical evolutionary algorithm(DEA) based on the theory of statistical mechanics and investigate the reconstruction problem for the nonlinear dynamical systems using observation data. The convergence of the algorithm is discussed. We make the numerical experiments and test our model using the two famous chaotic systems (mainly the Lorenz and Chen systems ). The results show the relatively accurate reconstruction of these chaotic systems based on observational data can be obtained. Therefore we may conclude that there are broad prospects using our method to model the nonlinear dynamical systems.
Adversarial Scheduling in Evolutionary Game Dynamics
Istrate, Gabriel; Ravi, S S
2008-01-01
Consider a system in which players at nodes of an underlying graph G repeatedly play Prisoner's Dilemma against their neighbors. The players adapt their strategies based on the past behavior of their opponents by applying the so-called win-stay lose-shift strategy. This dynamics has been studied in (Kittock 94), (Dyer et al. 2002), (Mossel and Roch, 2006). With random scheduling, starting from any initial configuration with high probability the system reaches the unique fixed point in which all players cooperate. This paper investigates the validity of this result under various classes of adversarial schedulers. Our results can be sumarized as follows: 1. An adversarial scheduler that can select both participants to the game can preclude the system from reaching the unique fixed point on most graph topologies. 2. A nonadaptive scheduler that is only allowed to choose one of the participants is no more powerful than a random scheduler. With this restriction even an adaptive scheduler is not significantly more ...
Evolutionary dynamics of collective index insurance.
Pacheco, Jorge M; Santos, Francisco C; Levin, Simon A
2016-03-01
Index-based insurances offer promising opportunities for climate-risk investments in developing countries. Indeed, contracts conditional on, e.g., weather or livestock indexes can be cheaper to set up than conventional indemnity-based insurances, while offering a safety net to vulnerable households, allowing them to eventually escape poverty traps. Moreover, transaction costs by insurance companies may be additionally reduced if contracts, instead of arranged with single households, are endorsed by collectives of households that bear the responsibility of managing the division of the insurance coverage by its members whenever the index is surpassed, allowing for additional flexibility in what concerns risk-sharing and also allowing insurance companies to avoid the costs associated with moral hazard. Here we resort to a population dynamics framework to investigate under which conditions household collectives may find collective index insurances attractive, when compared with individual index insurances. We assume risk sharing among the participants of each collective, and model collective action in terms of an N-person threshold game. Compared to less affordable individual index insurances, we show how collective index insurances lead to a coordination problem in which the adoption of index insurances may become the optimal decision, spreading index insurance coverage to the entire population. We further investigate the role of risk-averse and risk-prone behaviors, as well as the role of partial correlation between insurance coverage and actual loss of crops, and in which way these affect the original coordination thresholds. PMID:26486802
Evolutionary history of Pacific salmon in dynamic environments
Waples, Robin S.; George R. Pess; Beechie, Tim
2008-01-01
Contemporary evolution of Pacific salmon (Oncorhynchus spp.) is best viewed in the context of the evolutionary history of the species and the dynamic ecosystems they inhabit. Speciation was complete by the late Miocene, leaving c. six million years for intraspecific diversification. Following the most recent glacial maximum, large areas became available for recolonization. Current intraspecific diversity is thus the product of recent evolution overlaid onto divergent historical lineages forge...
Evolutionary dynamics of bacteria in a human host environment
Lei YANG; Jelsbak, Lars; Marvig, Rasmus Lykke; Damkiær, Søren; Workman, Christopher T; Rau, Martin Holm; Hansen, Susse Kirkelund; Folkesson, Anders; Johansen, Helle Krogh; Ciofu, Oana; Høiby, Niels; Morten O. A. Sommer; Molin, Søren
2011-01-01
Laboratory evolution experiments have led to important findings relating organism adaptation and genomic evolution. However, continuous monitoring of long-term evolution has been lacking for natural systems, limiting our understanding of these processes in situ. Here we characterize the evolutionary dynamics of a lineage of a clinically important opportunistic bacterial pathogen, Pseudomonas aeruginosa, as it adapts to the airways of several individual cystic fibrosis patients over 200,000 ba...
Evolutionary dynamics in a simple model of self-assembly
Johnston, Iain G.; Ahnert, Sebastian E.; Doye, Jonathan P. K.; Louis, Ard A.
2011-06-01
We investigate the evolutionary dynamics of an idealized model for the robust self-assembly of two-dimensional structures called polyominoes. The model includes rules that encode interactions between sets of square tiles that drive the self-assembly process. The relationship between the model’s rule set and its resulting self-assembled structure can be viewed as a genotype-phenotype map and incorporated into a genetic algorithm. The rule sets evolve under selection for specified target structures. The corresponding complex fitness landscape generates rich evolutionary dynamics as a function of parameters such as the population size, search space size, mutation rate, and method of recombination. Furthermore, these systems are simple enough that in some cases the associated model genome space can be completely characterized, shedding light on how the evolutionary dynamics depends on the detailed structure of the fitness landscape. Finally, we apply the model to study the emergence of the preference for dihedral over cyclic symmetry observed for homomeric protein tetramers.
An Evolutionary Dynamic Clustering based Colour Image Segmentation
Directory of Open Access Journals (Sweden)
Amiya Halder, Nilvra Pathak
2011-02-01
Full Text Available We have presented a novel Dynamic Colour Image Segmentation (DCISSystem for colour image. In this paper, we have proposed an efficient colourimage segmentation algorithm based on evolutionary approach i.e. dynamic GAbased clustering (GADCIS. The proposed technique automatically determinesthe optimum number of clusters for colour images. The optimal number ofclusters is obtained by using cluster validity criterion with the help of Gaussiandistribution. The advantage of this method is that no a priori knowledge isrequired to segment the color image. The proposed algorithm is evaluated onwell known natural images and its performance is compared to other clusteringtechniques. Experimental results show the performance of the proposedalgorithm producing comparable segmentation results.
DeLong, John P; Gibert, Jean P
2016-02-01
Heritable trait variation is a central and necessary ingredient of evolution. Trait variation also directly affects ecological processes, generating a clear link between evolutionary and ecological dynamics. Despite the changes in variation that occur through selection, drift, mutation, and recombination, current eco-evolutionary models usually fail to track how variation changes through time. Moreover, eco-evolutionary models assume fitness functions for each trait and each ecological context, which often do not have empirical validation. We introduce a new type of model, Gillespie eco-evolutionary models (GEMs), that resolves these concerns by tracking distributions of traits through time as eco-evolutionary dynamics progress. This is done by allowing change to be driven by the direct fitness consequences of model parameters within the context of the underlying ecological model, without having to assume a particular fitness function. GEMs work by adding a trait distribution component to the standard Gillespie algorithm - an approach that models stochastic systems in nature that are typically approximated through ordinary differential equations. We illustrate GEMs with the Rosenzweig-MacArthur consumer-resource model. We show not only how heritable trait variation fuels trait evolution and influences eco-evolutionary dynamics, but also how the erosion of variation through time may hinder eco-evolutionary dynamics in the long run. GEMs can be developed for any parameter in any ordinary differential equation model and, furthermore, can enable modeling of multiple interacting traits at the same time. We expect GEMs will open the door to a new direction in eco-evolutionary and evolutionary modeling by removing long-standing modeling barriers, simplifying the link between traits, fitness, and dynamics, and expanding eco-evolutionary treatment of a greater diversity of ecological interactions. These factors make GEMs much more than a modeling advance, but an important
Iterative Dynamic Diversity Evolutionary Algorithm for Constrained Optimization
Institute of Scientific and Technical Information of China (English)
GAO Wei-Shang; SHAO Cheng
2014-01-01
Evolutionary algorithms (EAs) were shown to be effective for complex constrained optimization problems. However, inflexible exploration in general EAs would lead to losing the global optimum nearby the ill-convergence regions. In this paper, we propose an iterative dynamic diversity evolutionary algorithm (IDDEA) with contractive subregions guiding exploitation through local extrema to the global optimum in suitable steps. In IDDEA, a novel optimum estimation strategy with multi-agents evolving diversely is suggested to eﬃciently compute dominance trend and establish a subregion. In addition, a subregion converging iteration is designed to redistrict a smaller subregion in current subregion for next iteration, which is based on a special dominance estimation scheme. Meanwhile, an infimum penalty function is embedded into IDDEA to judge agents and penalize adaptively the unfeasible agents with the lowest fitness of feasible agents. Furthermore, several engineering design optimization problems taken from the specialized literature are successfully solved by the present algorithm with high reliable solutions.
Dynamics Calculation of Travel Wave Tube
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
During the dynamics calculating of the travel tube, we must obtain the field map in the tube. The field map can be affected by not only the beam loading, but also the attenuation coefficient. The calculation of the attenuation coefficient
Evolutionary network games: Imitation and Best-Response dynamics
Cimini, Giulio; Sánchez, Angel
2014-01-01
We consider games of strategic substitutes and strategic complements on networks. We introduce two different evolutionary dynamics in order to refine their multiplicity of equilibria, that can be related to alternative informational contexts. We find that for the best-shot game, taken as a model for substitutes, a replicator-like dynamics does not lead to Nash equilibria, whereas it leads to unique equilibria (full cooperation or full defection, depending on the initial condition and the game parameter) for complements, represented by a coordination game. On the other hand, when the dynamics becomes more cognitively demanding in the form of a best response evolution, predictions are always Nash equilibria (at least when individuals are fully rational): For the best-shot game we find equilibria with a definite value of the fraction of contributors, whereas for the coordination game symmetric equilibria arise only for low or high initial fractions of cooperators. We also consider extensions of the natural incom...
Evolutionary dynamics of time-resolved social interactions
Cardillo, Alessio; Nicosia, Vincenzo; Sinatra, Roberta; Gómez-Gardeñes, Jesús; Latora, Vito
2013-01-01
Cooperation among unrelated individuals is frequently observed in social groups when their members join efforts and resources to obtain a shared benefit which is unachievable by singles. However, understanding why cooperation arises despite the natural tendency of individuals towards selfish behaviors is still an open problem and represents one of the most fascinating challenges in volutionary dynamics. Very recently, the structural characterization of the networks upon which social interactions take place has shed some light on the mechanisms by which cooperative behaviours emerge and eventually overcome the individual temptation to defect. In particular, it has been found that the heterogeneity in the number of social ties and the presence of tightly-knit communities lead to a significant increase of cooperation as compared with the unstructured and homogeneous connection patterns considered in classical evolutionary dynamics. Here we investigate the role of social ties dynamics for the emergence of coopera...
Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.
Directory of Open Access Journals (Sweden)
Guillaume Chevereau
Full Text Available The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the "morbidostat", a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations-an almost paradoxical behavior since this drug causes DNA damage and increases the mutation
A quantitative evolutionary theory of adaptive behavior dynamics.
McDowell, J J
2013-10-01
The idea that behavior is selected by its consequences in a process analogous to organic evolution has been discussed for over 100 years. A recently proposed theory instantiates this idea by means of a genetic algorithm that operates on a population of potential behaviors. Behaviors in the population are represented by numbers in decimal integer (phenotypic) and binary bit string (genotypic) forms. One behavior from the population is emitted at random each time tick, after which a new population of potential behaviors is constructed by recombining parent behavior bit strings. If the emitted behavior produced a benefit to the organism, then parents are chosen on the basis of their phenotypic similarity to the emitted behavior; otherwise, they are chosen at random. After parent behavior recombination, the population is subjected to a small amount of mutation by flipping random bits in the population's bit strings. The behavior generated by this process of selection, reproduction, and mutation reaches equilibrium states that conform to every empirically valid equation of matching theory, exactly and without systematic error. These equations are known to describe the behavior of many vertebrate species, including humans, in a variety of experimental, naturalistic, natural, and social environments. The evolutionary theory also generates instantaneous dynamics and patterns of preference change in constantly changing environments that are consistent with the dynamics of live-organism behavior. These findings support the assertion that the world of behavior we observe and measure is generated by evolutionary dynamics. PMID:24219847
Evolutionary dynamics of N-person snowdrift game
Sui, Xiukai; Cong, Rui; Li, Kun; Wang, Long
2015-12-01
In this letter, we investigate the evolutionary dynamics of N-person snowdrift game in both well-mixed and structured populations. For well-mixed populations, we construct a double-threshold model considering both the necessary and the minimum cost players should pay for completing the task. We have explored the influences of these thresholds on both equilibrium points in infinite populations and the fixation probabilities in finite populations. Results present complicated behaviors that show characteristics of both stag-hunt game and snowdrift game. For structured populations, we use pair approximation and diffusion approximation to derive the critical benefit-to-cost ratio in favor of cooperation.
The Dynamic Evolutionary History of Pancrustacean Eyes and Opsins.
Henze, Miriam J; Oakley, Todd H
2015-11-01
Pancrustacea (Hexapoda plus Crustacea) display an enormous diversity of eye designs, including multiple types of compound eyes and single-chambered eyes, often with color vision and/or polarization vision. Although the eyes of some pancrustaceans are well-studied, there is still much to learn about the evolutionary paths to this amazing visual diversity. Here, we examine the evolutionary history of eyes and opsins across the principle groups of Pancrustacea. First, we review the distribution of lateral and median eyes, which are found in all major pancrustacean clades (Oligostraca, Multicrustacea, and Allotriocarida). At the same time, each of those three clades has taxa that lack lateral and/or median eyes. We then compile data on the expression of visual r-opsins (rhabdomeric opsins) in lateral and median eyes across Pancrustacea and find no evidence for ancient opsin clades expressed in only one type of eye. Instead, opsin clades with eye-specific expression are products of recent gene duplications, indicating a dynamic past, during which opsins often changed expression from one type of eye to another. We also investigate the evolutionary history of peropsins and r-opsins, which are both known to be expressed in eyes of arthropods. By searching published transcriptomes, we discover for the first time crustacean peropsins and suggest that previously reported odonate opsins may also be peropsins. Finally, from analyzing a reconciled, phylogenetic tree of arthropod r-opsins, we infer that the ancestral pancrustacean had four visual opsin genes, which we call LW2, MW1, MW2, and SW. These are the progenitors of opsin clades that later were variously duplicated or lost during pancrustacean evolution. Together, our results reveal a particularly dynamic history, with losses of eyes, duplication and loss of opsin genes, and changes in opsin expression between types of eyes. PMID:26319405
Bidirectional Dynamic Diversity Evolutionary Algorithm for Constrained Optimization
Directory of Open Access Journals (Sweden)
Weishang Gao
2013-01-01
Full Text Available Evolutionary algorithms (EAs were shown to be effective for complex constrained optimization problems. However, inflexible exploration-exploitation and improper penalty in EAs with penalty function would lead to losing the global optimum nearby or on the constrained boundary. To determine an appropriate penalty coefficient is also difficult in most studies. In this paper, we propose a bidirectional dynamic diversity evolutionary algorithm (Bi-DDEA with multiagents guiding exploration-exploitation through local extrema to the global optimum in suitable steps. In Bi-DDEA potential advantage is detected by three kinds of agents. The scale and the density of agents will change dynamically according to the emerging of potential optimal area, which play an important role of flexible exploration-exploitation. Meanwhile, a novel double optimum estimation strategy with objective fitness and penalty fitness is suggested to compute, respectively, the dominance trend of agents in feasible region and forbidden region. This bidirectional evolving with multiagents can not only effectively avoid the problem of determining penalty coefficient but also quickly converge to the global optimum nearby or on the constrained boundary. By examining the rapidity and veracity of Bi-DDEA across benchmark functions, the proposed method is shown to be effective.
Lattice Dynamics Calculation in MGB2
International Nuclear Information System (INIS)
In Present report, We have introduced a new theoretical results for MgB2 by using home design programme Lattice Dynamics. we have calculated partial and total density of states (PDOS, TDOS), infrared and Raman spectrums and specific heat capacity. Dispersion curves in different symmetry points are calculated and found that there is agreement with other calculations. Also we have tried to investigate the Boron Isotope effect on the calculated properties
Evolutionary dynamics of plants and animals: a comparative approach
Valentine, J. W.; Tiffney, B. H.; Sepkoski, J. J. Jr; Sepkoski JJ, J. r. (Principal Investigator)
1991-01-01
Patterns of longevity and rate of appearance of taxa in the fossil record indicate a different evolutionary dynamic between land plants and marine invertebrates. Among marine invertebrates, rates of taxonomic turnover declined through the Phanerozoic, with increasingly extinction-resistant, long-lived, clades coming to dominate. Among terrestrial vascular plants, rates of turnover increased through the Phanerozoic, with short-lived, extinction-prone clades coming to dominate from the Devonian to the present. Terrestrial vertebrates appear to approximate the marine invertebrate pattern more closely than the plant record. We identify two features which individually or jointly may have influenced this distinction. First, land plants continuously invaded stressful environments during their evolution, while marine invertebrates and terrestrial vertebrates did not. Second, the relative structural simplicity and indeterminate mode of plant growth vs. the relative structural complexity and determinate mode of animal growth may have influenced the timing of major clade origin in the two groups.
The mathematical law of evolutionary information dynamics and an observer's evolution regularities
Lerner, Vladimir S
2011-01-01
An interactive stochastics, evaluated by an entropy functional (EF) of a random field and informational process' path functional (IPF), allows us modeling the evolutionary information processes and revealing regularities of evolution dynamics. Conventional Shannon's information measure evaluates a sequence of the process' static events for each information state and do not reveal hidden dynamic connections between these events. The paper formulates the mathematical forms of the information regularities, based on a minimax variation principle (VP) for IPF, applied to the evolution's both random microprocesses and dynamic macroprocesses. The paper shows that the VP single form of the mathematical law leads to the following evolutionary regularities: -creation of the order from stochastics through the evolutionary macrodynamics, described by a gradient of dynamic potential, evolutionary speed and the evolutionary conditions of a fitness and diversity; -the evolutionary hierarchy with growing information values a...
A New, Efficient Stellar Evolution Code for Calculating Complete Evolutionary Tracks
Kovetz, Attay; Prialnik, Dina
2008-01-01
We present a new stellar evolution code and a set of results, demonstrating its capability at calculating full evolutionary tracks for a wide range of masses and metallicities. The code is fast and efficient, and is capable of following through all evolutionary phases, without interruption or human intervention. It is meant to be used also in the context of modeling the evolution of dense stellar systems, for performing live calculations for both normal star models and merger-products. The code is based on a fully implicit, adaptive-grid numerical scheme that solves simultaneously for structure, mesh and chemical composition. Full details are given for the treatment of convection, equation of state, opacity, nuclear reactions and mass loss. Results of evolutionary calculations are shown for a solar model that matches the characteristics of the present sun to an accuracy of better than 1%; a $1 \\Msun$ model for a wide range of metallicities; a series of models of stellar populations I and II, for the mass rang...
Ribosome dynamics and the evolutionary history of ribosomes
Fox, George E.; Paci, Maxim; Tran, Quyen; Petrov, Anton S.; Williams, Loren D.
2015-09-01
The ribosome is a dynamic nanomachine responsible for coded protein synthesis. Its major subsystems were essentially in place at the time of the last universal common ancestor (LUCA). Ribosome evolutionary history thus potentially provides a window into the pre- LUCA world. This history begins with the origins of the peptidyl transferase center where the actual peptide is synthesized and then continues over an extended timeframe as additional functional centers including the GTPase center are added. The large ribosomal RNAs (rRNAs) have grown over time by an accretion process and a model exists that proposes a relative age of each accreted element. We have compared atomic resolution ribosome structures before and after EF-G bound GTP hydrolysis and thereby identified the location of 23 pivot points in the large rRNAs that facilitate ribosome dynamics. Pivots in small subunit helices h28 and h44 appear to be especially central to the process and according to the accretion model significantly older than the other helices containing pivots. Overall, the results suggest that ribosomal dynamics occurred in two phases. In the first phase, an inherently mobile h28/h44 combination provided the flexibility needed to create a dynamic ribosome that was essentially a Brownian machine. This addition likely made coded peptide synthesis possible by facilitating movement of a primitive mRNA. During the second phase, addition of pivoting elements and the creation of a factor binding site allowed the regulation of the inherent motion created by h28/h44. All of these events likely occurred before LUCA.
Evolutionary dynamics of general group interactions in structured populations
Li, Aming; Broom, Mark; Du, Jinming; Wang, Long
2016-02-01
The evolution of populations is influenced by many factors, and the simple classical models have been developed in a number of important ways. Both population structure and multiplayer interactions have been shown to significantly affect the evolution of important properties, such as the level of cooperation or of aggressive behavior. Here we combine these two key factors and develop the evolutionary dynamics of general group interactions in structured populations represented by regular graphs. The traditional linear and threshold public goods games are adopted as models to address the dynamics. We show that for linear group interactions, population structure can favor the evolution of cooperation compared to the well-mixed case, and we see that the more neighbors there are, the harder it is for cooperators to persist in structured populations. We further show that threshold group interactions could lead to the emergence of cooperation even in well-mixed populations. Here population structure sometimes inhibits cooperation for the threshold public goods game, where depending on the benefit to cost ratio, the outcomes are bistability or a monomorphic population of defectors or cooperators. Our results suggest, counterintuitively, that structured populations are not always beneficial for the evolution of cooperation for nonlinear group interactions.
Modeling Evolutionary Dynamics of Lurking in Social Networks
Javarone, Marco Alberto; Tagarelli, Andrea
2016-01-01
Lurking is a complex user-behavioral phenomenon that occurs in all large-scale online communities and social networks. It generally refers to the behavior characterizing users that benefit from the information produced by others in the community without actively contributing back to the production of social content. The amount and evolution of lurkers may strongly affect an online social environment, therefore understanding the lurking dynamics and identifying strategies to curb this trend are relevant problems. In this regard, we introduce the Lurker Game, i.e., a model for analyzing the transitions from a lurking to a non-lurking (i.e., active) user role, and vice versa, in terms of evolutionary game theory. We evaluate the proposed Lurker Game by arranging agents on complex networks and analyzing the system evolution, seeking relations between the network topology and the final equilibrium of the game. Results suggest that the Lurker Game is suitable to model the lurking dynamics, showing how the adoption ...
Nuclear Research Center IRT reactor dynamics calculation
International Nuclear Information System (INIS)
The main features of the code DIRT, for dynamical calculations are described in the paper. With the results obtained by the program, an analysis of the dynamic behaviour of the Research Reactor IRT of the Nuclear Research Center (CIN) is performed. Different transitories were considered such as variation of the system reactivity, coolant inlet temperature variation and also variations of the coolant velocity through the reactor core. 3 refs
Evolutionary game dynamics of controlled and automatic decision-making
Toupo, Danielle F. P.; Strogatz, Steven H.; Cohen, Jonathan D.; Rand, David G.
2015-07-01
We integrate dual-process theories of human cognition with evolutionary game theory to study the evolution of automatic and controlled decision-making processes. We introduce a model in which agents who make decisions using either automatic or controlled processing compete with each other for survival. Agents using automatic processing act quickly and so are more likely to acquire resources, but agents using controlled processing are better planners and so make more effective use of the resources they have. Using the replicator equation, we characterize the conditions under which automatic or controlled agents dominate, when coexistence is possible and when bistability occurs. We then extend the replicator equation to consider feedback between the state of the population and the environment. Under conditions in which having a greater proportion of controlled agents either enriches the environment or enhances the competitive advantage of automatic agents, we find that limit cycles can occur, leading to persistent oscillations in the population dynamics. Critically, however, these limit cycles only emerge when feedback occurs on a sufficiently long time scale. Our results shed light on the connection between evolution and human cognition and suggest necessary conditions for the rise and fall of rationality.
Computational complexity of ecological and evolutionary spatial dynamics.
Ibsen-Jensen, Rasmus; Chatterjee, Krishnendu; Nowak, Martin A
2015-12-22
There are deep, yet largely unexplored, connections between computer science and biology. Both disciplines examine how information proliferates in time and space. Central results in computer science describe the complexity of algorithms that solve certain classes of problems. An algorithm is deemed efficient if it can solve a problem in polynomial time, which means the running time of the algorithm is a polynomial function of the length of the input. There are classes of harder problems for which the fastest possible algorithm requires exponential time. Another criterion is the space requirement of the algorithm. There is a crucial distinction between algorithms that can find a solution, verify a solution, or list several distinct solutions in given time and space. The complexity hierarchy that is generated in this way is the foundation of theoretical computer science. Precise complexity results can be notoriously difficult. The famous question whether polynomial time equals nondeterministic polynomial time (i.e., P = NP) is one of the hardest open problems in computer science and all of mathematics. Here, we consider simple processes of ecological and evolutionary spatial dynamics. The basic question is: What is the probability that a new invader (or a new mutant) will take over a resident population? We derive precise complexity results for a variety of scenarios. We therefore show that some fundamental questions in this area cannot be answered by simple equations (assuming that P is not equal to NP). PMID:26644569
Behavioral variability in an evolutionary theory of behavior dynamics.
Popa, Andrei; McDowell, J J
2016-03-01
McDowell's evolutionary theory of behavior dynamics (McDowell, 2004) instantiates populations of behaviors (abstractly represented by integers) that evolve under the selection pressure of the environment in the form of positive reinforcement. Each generation gives rise to the next via low-level Darwinian processes of selection, recombination, and mutation. The emergent patterns can be analyzed and compared to those produced by biological organisms. The purpose of this project was to explore the effects of high mutation rates on behavioral variability in environments that arranged different reinforcer rates and magnitudes. Behavioral variability increased with the rate of mutation. High reinforcer rates and magnitudes reduced these effects; low reinforcer rates and magnitudes augmented them. These results are in agreement with live-organism research on behavioral variability. Various combinations of mutation rates, reinforcer rates, and reinforcer magnitudes produced similar high-level outcomes (equifinality). These findings suggest that the independent variables that describe an experimental condition interact; that is, they do not influence behavior independently. These conclusions have implications for the interpretation of high levels of variability, mathematical undermatching, and the matching theory. The last part of the discussion centers on a potential biological counterpart for the rate of mutation, namely spontaneous fluctuations in the brain's default mode network. PMID:27002687
Evolutionary Voluntary Prisoner’s Dilemma Game under Deterministic and Stochastic Dynamics
Directory of Open Access Journals (Sweden)
Qian Yu
2015-03-01
Full Text Available The voluntary prisoner’s dilemma (VPD game has sparked interest from various fields since it was proposed as an effective mechanism to incentivize cooperative behavior. Current studies show that the inherent cyclic dominance of the strategies of the VPD game results in periodic oscillations in population. This paper investigated the influence of the level of individual rationality and the size of a population on the evolutionary dynamics of the VPD game. Different deterministic dynamics, such as the replicator dynamic, the Smith dynamic, the Brown-von Neumann-Nash (BNN dynamic and the best response (BR dynamic, for the evolutionary VPD game were modeled and simulated. The stochastic evolutionary dynamics based on quasi birth and death (QBD process was proposed for the evolutionary VPD game and compared with deterministic dynamics. The results indicated that with the increase of the loners’ fixed payoff, the loner is more likely to remain in the stable state of a VPD game under any of the dynamics mentioned above. However, the different speeds of motion under the dynamics in the cycle dominance proved to be diverse under different evolutionary dynamics and also highly sensitive to the rationality of individuals in a population. Furthermore, in QBD stochastic dynamics, the size of the population has a remarkable effect on the possibility distribution. When the population size increases, the limited distribution of the QBD process will be in accordance with the results in the deterministic dynamics.
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.
Directory of Open Access Journals (Sweden)
Andrea Sottoriva
2011-05-01
Full Text Available The cancer stem cell (CSC concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of CSCs. Our results demonstrate that epigenetic mutations that occur during mitosis display highly altered dynamics in CSC-driven malignancies compared to a classical, non-hierarchical model of growth. In particular, the heterogeneity observed in CSC-driven tumors is considerably higher. We speculate that this feature could be used in combination with epigenetic (methylation sequencing studies of human malignancies to prove or refute the CSC hypothesis in established tumors without the need for transplantation. Moreover our tumor growth simulations indicate that CSC-driven tumors display evolutionary features that can be considered beneficial during tumor progression. Besides an increased heterogeneity they also exhibit properties that allow the escape of clones from local fitness peaks. This leads to more aggressive phenotypes in the long run and makes the neoplasm more adaptable to stringent selective forces such as cancer treatment. Indeed when therapy is applied the clone landscape of the regrown tumor is more aggressive with respect to the primary tumor, whereas the classical model demonstrated similar patterns before and after therapy. Understanding these often counter-intuitive fundamental properties of (non-hierarchically organized malignancies is a crucial step in validating the CSC concept as well as providing insight into the therapeutical consequences of this model.
Modeling viral evolutionary dynamics after telaprevir-based treatment.
Directory of Open Access Journals (Sweden)
Eric L Haseltine
2014-08-01
Full Text Available For patients infected with hepatitis C virus (HCV, the combination of the direct-acting antiviral agent telaprevir, pegylated-interferon alfa (Peg-IFN, and ribavirin (RBV significantly increases the chances of sustained virologic response (SVR over treatment with Peg-IFN and RBV alone. If patients do not achieve SVR with telaprevir-based treatment, their viral population is often significantly enriched with telaprevir-resistant variants at the end of treatment. We sought to quantify the evolutionary dynamics of these post-treatment resistant variant populations. Previous estimates of these dynamics were limited by analyzing only population sequence data (20% sensitivity, qualitative resistance information from 388 patients enrolled in Phase 3 clinical studies. Here we add clonal sequence analysis (5% sensitivity, quantitative for a subset of these patients. We developed a computational model which integrates both the qualitative and quantitative sequence data, and which forms a framework for future analyses of drug resistance. The model was qualified by showing that deep-sequence data (1% sensitivity from a subset of these patients are consistent with model predictions. When determining the median time for viral populations to revert to 20% resistance in these patients, the model predicts 8.3 (95% CI: 7.6, 8.4 months versus 10.7 (9.9, 12.8 months estimated using solely population sequence data for genotype 1a, and 1.0 (0.0, 1.4 months versus 0.9 (0.0, 2.7 months for genotype 1b. For each individual patient, the time to revert to 20% resistance predicted by the model was typically comparable to or faster than that estimated using solely population sequence data. Furthermore, the model predicts a median of 11.0 and 2.1 months after treatment failure for viral populations to revert to 99% wild-type in patients with HCV genotypes 1a or 1b, respectively. Our modeling approach provides a framework for projecting accurate, quantitative assessment of
Evolutionary aspects of gift-giving dynamics among Norwegian students
2007-01-01
Data from questionnaires filled out by 336 students during a nine day period in January and February 1999 at the University of Oslo, Norway was analyzed to find patterns in gift-giving behavior corresponding to predicted evolutionary biological and evolutionary psychological hypotheses. Gifts given and received, people given to and received from, monetary value of gifts given and estimated monetary value of gifts received were tallied. We tested the effects of four main factors: kin and non-k...
Bias in Dynamic Monte Carlo Alpha Calculations
Energy Technology Data Exchange (ETDEWEB)
Sweezy, Jeremy Ed [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nolen, Steven Douglas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Adams, Terry R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Trahan, Travis John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2015-02-06
A 1/N bias in the estimate of the neutron time-constant (commonly denoted as α) has been seen in dynamic neutronic calculations performed with MCATK. In this paper we show that the bias is most likely caused by taking the logarithm of a stochastic quantity. We also investigate the known bias due to the particle population control method used in MCATK. We conclude that this bias due to the particle population control method is negligible compared to other sources of bias.
The co-evolutionary dynamics of directed network of spin market agents
Horvath, D.; Z. Kuscsik; Gmitra, M.
2005-01-01
The spin market model [S. Bornholdt, Int.J.Mod.Phys. C 12 (2001) 667] is extended into co-evolutionary version, where strategies of interacting and competitive traders are represented by local and global couplings between the nodes of dynamic directed stochastic network. The co-evolutionary principles are applied in the frame of Bak - Sneppen self-organized dynamics [P. Bak, K. Sneppen, Phys. Rev. Letter 71 (1993) 4083] that includes the processes of selection and extinction actuated by the l...
Eco-evolutionary dynamics in a coevolving host-virus system.
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. PMID:26898162
EVOLUTIONARY DYNAMIC MODEL OF POPULATION WITH NICHE CONSTRUCTION AND ITS APPLICATION RESEARCH
Institute of Scientific and Technical Information of China (English)
无
2006-01-01
Based on the theories and approaches in biomechanics, the mechanism and pattern of niche construction were discussed systematically. Through establishing the spatial pattern of niche and its measuring-fitness formula, and the dynamic system models of single- and two-population with niche construction, including corresponding theoretical analysis and numerical simulation on their evolutionary dynamics of population and the mechanism of competitive coexistence, the co-evolutionary relationship between organisms and their environments was revealed. The results indicate that population dynamics is governed by positive feedback between primary ecological factors and resource content.Niche construction generates an evolutionary effect in system by influencing the fitness of population. A threshold effect exists in single population dynamic system. In dynamic system of two competitive populations, niche construction can lead to alternative competitive consequences, which may be a potential mechanism to explain the competitive coexistence of species.
Design games: A conceptual framework for dynamic evolutionary design
Sönmez, N.O.; Erdem, A.
2014-01-01
Most evolutionary computation (EC) applications in design fields either assume simplified, static, performance-oriented procedures for design or focus on well-defined sub-problems, to be able to impose problem-solving and optimization schemes on design tasks, which render known EC techniques directl
Despotism, Democracy, and the Evolutionary Dynamics of Leadership and Followership
Van Vugt, Mark
2009-01-01
Responds to comments made by George B. Graen and Stephen J. Guastello on the current author's article Leadership, followership, and evolution: Some lessons from the past by Van Vugt, Hogan, and Kaiser. In the original article my co-authors and I proposed a new way of thinking about leadership, informed by evolutionary (neo-Darwinian) theory. In…
Electrostatic Energy Calculations for Molecular Dynamics
Love, M J; Comment, Henri J.F. Jansen; Love, Michael J.
1995-01-01
The evaluation of Coulomb forces is a difficult task. The summations that are involved converge only conditionally and care has to be taken in selecting the appropriate procedure to define the limits. The Ewald method is a standard method for obtaining Coulomb forces, but this method is rather slow, since it depends on the square of the number of atoms in a unit cell. In this paper we have adapted the plane-wise summation method for the evaluation of Coulomb forces. The use of this method allows for larger computational cells in molecular dynamics calculations.
Stochastic evolutionary dynamics of minimum-effort coordination games
Li, Kun; Wang, Long
2016-01-01
The minimum-effort coordination game, having potentially important implications in both evolutionary biology and sociology, draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classic game theory. In the framework of classic game theory, any common effort level is a strict and trembling hand perfect Nash equilibrium, so that no desideratum is provided for selecting among them. Behavior experiments, however, show that the effort levels employed by subjects are inversely related to the effort costs. Here, we combine coalescence theory and evolutionary game theory to investigate this game in finite populations. Both analytic results and individual-based simulations show that effort costs play a key role in the evolution of contribution levels, which is in good agreement with those observed experimentally. Besides well-mixed populations, set structured populations, where the population structure itself is a consequence of the evolutio...
Eco-evolutionary metapopulation dynamics and the spatial scale of adaptation.
Hanski, Ilkka; Mononen, Tommi; Ovaskainen, Otso
2011-01-01
We construct a model that combines extinction-colonization dynamics with the dynamics of local adaptation in a network of habitat patches of dissimilar qualities. We derive a deterministic approximation for the stochastic model that allows the calculation of patch-specific incidences of occupancy and levels of adaptation at steady state. Depending on (i) the strength of local selection, (ii) the amount of genetic variance, (iii) the demographic cost of maladaptation, (iv) the spatial scale of gene flow, and (v) the amount of habitat heterogeneity, the model predicts adaptation at different spatial scales. Local adaptation is predicted when there is much genetic variance and strong selection, while network-level adaptation occurs when the demographic cost of maladaptation is low. For little genetic variance and high cost of maladaptation, the model predicts network-level habitat specialization in species with long-range migration but an intermediate scale of adaptation (mosaic specialization) in species with short-range migration. In fragmented landscapes, the evolutionary dynamics of adaptation may both decrease and enhance metapopulation viability in comparison with no evolution. The model can be applied to real patch networks with given sizes, qualities, and spatial positions of habitat patches. PMID:21090992
The stability concept of evolutionary game theory a dynamic approach
1992-01-01
These Notes grew from my research in evolutionary biology, specifically on the theory of evolutionarily stable strategies (ESS theory), over the past ten years. Personally, evolutionary game theory has given me the opportunity to transfer my enthusiasm for abstract mathematics to more practical pursuits. I was fortunate to have entered this field in its infancy when many biologists recognized its potential but were not prepared to grant it general acceptance. This is no longer the case. ESS theory is now a rapidly expanding (in both applied and theoretical directions) force that no evolutionary biologist can afford to ignore. Perhaps, to continue the life-cycle metaphor, ESS theory is now in its late adolescence and displays much of the optimism and exuberance of this exciting age. There are dangers in writing a text about a theory at this stage of development. A comprehensive treatment would involve too many loose ends for the reader to appreciate the central message. On the other hand, the current central m...
An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game
Moshe Hoffman; Sigrid Suetens; Uri Gneezy; Nowak, Martin A.
2015-01-01
Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium (NE), which is motivated by perfect rationality. NE specifies a strategy for everyone, such that no one would benefit by deviating unilaterally from his/her strategy. Another powerful tool available to game theorists are evolutionary dynamics (ED). Motivated by evolutionary and learning processes, ED specify changes in...
Female polymorphism, frequency dependence, and rapid evolutionary dynamics in natural populations
Svensson, Erik; Abbott, Jessica; Härdling, Roger
2005-01-01
Rapid evolutionary change over a few generations has been documented in natural populations. Such changes are observed as organisms invade new environments, and they are often triggered by changed interspecific interactions, such as differences in predation regimes. However, in spite of increased recognition of antagonistic male-female mating interactions, there is very limited evidence that such intraspecific interactions could cause rapid evolutionary dynamics in nature. This is because eco...
Improving the accuracy of dynamic mass calculation
Directory of Open Access Journals (Sweden)
Oleksandr F. Dashchenko
2015-06-01
Full Text Available With the acceleration of goods transporting, cargo accounting plays an important role in today's global and complex environment. Weight is the most reliable indicator of the materials control. Unlike many other variables that can be measured indirectly, the weight can be measured directly and accurately. Using strain-gauge transducers, weight value can be obtained within a few milliseconds; such values correspond to the momentary load, which acts on the sensor. Determination of the weight of moving transport is only possible by appropriate processing of the sensor signal. The aim of the research is to develop a methodology for weighing freight rolling stock, which increases the accuracy of the measurement of dynamic mass, in particular wagon that moves. Apart from time-series methods, preliminary filtration for improving the accuracy of calculation is used. The results of the simulation are presented.
Stochastic evolutionary dynamics in minimum-effort coordination games
Li, Kun; Cong, Rui; Wang, Long
2016-08-01
The minimum-effort coordination game draws recently more attention for the fact that human behavior in this social dilemma is often inconsistent with the predictions of classical game theory. Here, we combine evolutionary game theory and coalescence theory to investigate this game in finite populations. Both analytic results and individual-based simulations show that effort costs play a key role in the evolution of contribution levels, which is in good agreement with those observed experimentally. Besides well-mixed populations, set structured populations have also been taken into consideration. Therein we find that large number of sets and moderate migration rate greatly promote effort levels, especially for high effort costs.
Eco-evolutionary dynamics, coding structure and the information threshold
Directory of Open Access Journals (Sweden)
Hogeweg Paulien
2010-11-01
Full Text Available Abstract Background The amount of information that can be maintained in an evolutionary system of replicators is limited by genome length, the number of errors during replication (mutation rate and various external factors that influence the selection pressure. To date, this phenomenon, known as the information threshold, has been studied (both genotypically and phenotypically in a constant environment and with respect to maintenance (as opposed to accumulation of information. Here we take a broader perspective on this problem by studying the accumulation of information in an ecosystem, given an evolvable coding structure. Moreover, our setup allows for individual based as well as ecosystem based solutions. That is, all functions can be performed by individual replicators, or complementing functions can be performed by different replicators. In this setup, where both the ecosystem and the individual genomes can evolve their structure, we study how populations cope with high mutation rates and accordingly how the information threshold might be alleviated. Results We observe that the first response to increased mutation rates is a change in coding structure. At moderate mutation rates evolution leads to longer genomes with a higher diversity than at high mutation rates. Thus, counter-intuitively, at higher mutation rates diversity is reduced and the efficacy of the evolutionary process is decreased. Therefore, moderate mutation rates allow for more degrees of freedom in exploring genotype space during the evolutionary trajectory, facilitating the emergence of solutions. When an individual based solution cannot be attained due to high mutation rates, spatial structuring of the ecosystem can accommodate the evolution of ecosystem based solutions. Conclusions We conclude that the evolutionary freedom (eg. the number of genotypes that can be reached by evolution is increasingly restricted by higher mutation rates. In the case of such severe mutation
Geomedium as a nonlinear dynamic system. An evolutionary concept of earthquake development
Energy Technology Data Exchange (ETDEWEB)
Makarov, Pavel V., E-mail: pvm@ispms.tsc.ru [National Research Tomsk State University, Tomsk, 634050, Russia and Institute of Strength Physics and Materials Science SB RAS, Tomsk, 634055 (Russian Federation)
2014-11-14
An evolutionary approach to earthquake development is proposed. A medium under loading is treated as a multiscale nonlinear dynamic system. Its failure involves a number of stages typical of any dynamic system: dynamic chaos, self-organized criticality, and global stability loss in the final stage of its evolution. In the latter stage, the system evolves in a blow-up mode accompanied by catastrophic superfast movements of the elements of this geomedium.
Directory of Open Access Journals (Sweden)
Shahamatnia Ehsan
2016-01-01
Full Text Available Developing specialized software tools is essential to support studies of solar activity evolution. With new space missions such as Solar Dynamics Observatory (SDO, solar images are being produced in unprecedented volumes. To capitalize on that huge data availability, the scientific community needs a new generation of software tools for automatic and efficient data processing. In this paper a prototype of a modular framework for solar feature detection, characterization, and tracking is presented. To develop an efficient system capable of automatic solar feature tracking and measuring, a hybrid approach combining specialized image processing, evolutionary optimization, and soft computing algorithms is being followed. The specialized hybrid algorithm for tracking solar features allows automatic feature tracking while gathering characterization details about the tracked features. The hybrid algorithm takes advantages of the snake model, a specialized image processing algorithm widely used in applications such as boundary delineation, image segmentation, and object tracking. Further, it exploits the flexibility and efficiency of Particle Swarm Optimization (PSO, a stochastic population based optimization algorithm. PSO has been used successfully in a wide range of applications including combinatorial optimization, control, clustering, robotics, scheduling, and image processing and video analysis applications. The proposed tool, denoted PSO-Snake model, was already successfully tested in other works for tracking sunspots and coronal bright points. In this work, we discuss the application of the PSO-Snake algorithm for calculating the sidereal rotational angular velocity of the solar corona. To validate the results we compare them with published manual results performed by an expert.
Shahamatnia, Ehsan; Dorotovič, Ivan; Fonseca, Jose M.; Ribeiro, Rita A.
2016-03-01
Developing specialized software tools is essential to support studies of solar activity evolution. With new space missions such as Solar Dynamics Observatory (SDO), solar images are being produced in unprecedented volumes. To capitalize on that huge data availability, the scientific community needs a new generation of software tools for automatic and efficient data processing. In this paper a prototype of a modular framework for solar feature detection, characterization, and tracking is presented. To develop an efficient system capable of automatic solar feature tracking and measuring, a hybrid approach combining specialized image processing, evolutionary optimization, and soft computing algorithms is being followed. The specialized hybrid algorithm for tracking solar features allows automatic feature tracking while gathering characterization details about the tracked features. The hybrid algorithm takes advantages of the snake model, a specialized image processing algorithm widely used in applications such as boundary delineation, image segmentation, and object tracking. Further, it exploits the flexibility and efficiency of Particle Swarm Optimization (PSO), a stochastic population based optimization algorithm. PSO has been used successfully in a wide range of applications including combinatorial optimization, control, clustering, robotics, scheduling, and image processing and video analysis applications. The proposed tool, denoted PSO-Snake model, was already successfully tested in other works for tracking sunspots and coronal bright points. In this work, we discuss the application of the PSO-Snake algorithm for calculating the sidereal rotational angular velocity of the solar corona. To validate the results we compare them with published manual results performed by an expert.
The Ecology and Evolutionary Dynamics of Meiotic Drive.
Lindholm, Anna K; Dyer, Kelly A; Firman, Renée C; Fishman, Lila; Forstmeier, Wolfgang; Holman, Luke; Johannesson, Hanna; Knief, Ulrich; Kokko, Hanna; Larracuente, Amanda M; Manser, Andri; Montchamp-Moreau, Catherine; Petrosyan, Varos G; Pomiankowski, Andrew; Presgraves, Daven C; Safronova, Larisa D; Sutter, Andreas; Unckless, Robert L; Verspoor, Rudi L; Wedell, Nina; Wilkinson, Gerald S; Price, Tom A R
2016-04-01
Meiotic drivers are genetic variants that selfishly manipulate the production of gametes to increase their own rate of transmission, often to the detriment of the rest of the genome and the individual that carries them. This genomic conflict potentially occurs whenever a diploid organism produces a haploid stage, and can have profound evolutionary impacts on gametogenesis, fertility, individual behaviour, mating system, population survival, and reproductive isolation. Multiple research teams are developing artificial drive systems for pest control, utilising the transmission advantage of drive to alter or exterminate target species. Here, we review current knowledge of how natural drive systems function, how drivers spread through natural populations, and the factors that limit their invasion. PMID:26920473
Directory of Open Access Journals (Sweden)
Alvaro Sanchez
Full Text Available The evolutionary spread of cheater strategies can destabilize populations engaging in social cooperative behaviors, thus demonstrating that evolutionary changes can have profound implications for population dynamics. At the same time, the relative fitness of cooperative traits often depends upon population density, thus leading to the potential for bi-directional coupling between population density and the evolution of a cooperative trait. Despite the potential importance of these eco-evolutionary feedback loops in social species, they have not yet been demonstrated experimentally and their ecological implications are poorly understood. Here, we demonstrate the presence of a strong feedback loop between population dynamics and the evolutionary dynamics of a social microbial gene, SUC2, in laboratory yeast populations whose cooperative growth is mediated by the SUC2 gene. We directly visualize eco-evolutionary trajectories of hundreds of populations over 50-100 generations, allowing us to characterize the phase space describing the interplay of evolution and ecology in this system. Small populations collapse despite continual evolution towards increased cooperative allele frequencies; large populations with a sufficient number of cooperators "spiral" to a stable state of coexistence between cooperator and cheater strategies. The presence of cheaters does not significantly affect the equilibrium population density, but it does reduce the resilience of the population as well as its ability to adapt to a rapidly deteriorating environment. Our results demonstrate the potential ecological importance of coupling between evolutionary dynamics and the population dynamics of cooperatively growing organisms, particularly in microbes. Our study suggests that this interaction may need to be considered in order to explain intraspecific variability in cooperative behaviors, and also that this feedback between evolution and ecology can critically affect the
Evolutionary Fates and Dynamic Functionalization of Young Duplicate Genes in Arabidopsis Genomes.
Wang, Jun; Tao, Feng; Marowsky, Nicholas C; Fan, Chuanzhu
2016-09-01
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883
Wang, Baokui; Wang, Long
2014-01-01
The world in which we are living is a huge network of networks and should be described by interdependent networks. The interdependence between networks significantly affects the evolutionary dynamics of cooperation on them. Meanwhile, due to the diversity and complexity of social and biological systems, players on different networks may not interact with each other by the same way, which should be described by multiple models in evolutionary game theory, such as the Prisoner's Dilemma and Snowdrift Game. We therefore study the evolutionary dynamics of cooperation on two interdependent networks playing different games respectively. We clearly evidence that, with the increment of network interdependence, the evolution of cooperation is dramatically promoted on the network playing Prisoner's Dilemma. The cooperation level of the network playing Snowdrift Game reduces correspondingly, although it is almost invisible. In particular, there exists an optimal intermediate region of network interdependence maximizing ...
System dynamics of behaviour-evolutionary mix-game models
Institute of Scientific and Technical Information of China (English)
Gou Cheng-Ling; Gao Jie-Ping; Chen Fang
2010-01-01
In real financial markets there are two kinds of traders:one is fundamentalist,and the other is a trend-follower.The mix-game model is proposed to mimic such phenomena.In a mix-game model there are two groups of agents:Group 1 plays the majority game and Group 2 plays the minority game.In this paper,we investigate such a case that some traders in real financial markets could change their investment behaviours by assigning the evolutionary abilities to agents:if the winning rates of agents are smaller than a threshold,they will join the other group;and agents will repeat such an evolution at certain time intervals.Through the simulations,we obtain the following findings:(i) the volatilities of systems increase with the increase of the number of agents in Group 1 and the times of behavioural changes of all agents;(ii) the performances of agents in both groups and the stabilities of systems become better if all agents take more time to observe their new investment behaviours;(iii) there are two-phase zones of market and non-market and two-phase zones of evolution and non-evolution;(iv) parameter configurations located within the cross areas between the zones of markets and the zones of evolution are suited for simulating the financial markets.
System dynamics of behaviour-evolutionary mix-game models
Gou, Cheng-Ling; Gao, Jie-Ping; Chen, Fang
2010-11-01
In real financial markets there are two kinds of traders: one is fundamentalist, and the other is a trend-follower. The mix-game model is proposed to mimic such phenomena. In a mix-game model there are two groups of agents: Group 1 plays the majority game and Group 2 plays the minority game. In this paper, we investigate such a case that some traders in real financial markets could change their investment behaviours by assigning the evolutionary abilities to agents: if the winning rates of agents are smaller than a threshold, they will join the other group; and agents will repeat such an evolution at certain time intervals. Through the simulations, we obtain the following findings: (i) the volatilities of systems increase with the increase of the number of agents in Group 1 and the times of behavioural changes of all agents; (ii) the performances of agents in both groups and the stabilities of systems become better if all agents take more time to observe their new investment behaviours; (iii) there are two-phase zones of market and non-market and two-phase zones of evolution and non-evolution; (iv) parameter configurations located within the cross areas between the zones of markets and the zones of evolution are suited for simulating the financial markets.
Non-Payoff Monotonic Dynamics in an Evolutionary Game of Courtship
Chacoma, Andrés; Zanette, Damián H
2015-01-01
We propose an evolutionary coordination game to formalize a simplified model of the evolution of strategies during human courtship. The dynamics, derived from the consideration of experimental observations on human social behavior driven by self-esteem, turns out to be non-payoff monotonic. This property gives rise to nontrivial evolution in the players' strategies, which we study both numerically and analytically.
A stochastic evolutionary model for capturing human dynamics
Fenner, Trevor; Loizou, George
2015-01-01
The recent interest in human dynamics has led researchers to investigate the stochastic processes that explain human behaviour in various contexts. Here we propose a generative model to capture the dynamics of survival analysis, traditionally employed in clinical trials and reliability analysis in engineering. We derive a general solution for the model in the form of a product, and then a continuous approximation to the solution via the renewal equation describing age-structured population dynamics. This enables us to model a wide rage of survival distributions, according to the choice of the mortality distribution. We provide empirical evidence for the validity of the model from a longitudinal data set of popular search engine queries over 114 months, showing that the survival function of these queries is closely matched by the solution for our model with power-law mortality.
Dynamic evolutionary community detection algorithms based on the modularity matrix
International Nuclear Information System (INIS)
Motivated by the relationship of the dynamic behaviors and network structure, in this paper, we present two efficient dynamic community detection algorithms. The phases of the nodes in the network can evolve according to our proposed differential equations. In each iteration, the phases of the nodes are controlled by several parameters. It is found that the phases of the nodes are ultimately clustered into several communities after a short period of evolution. They can be adopted to detect the communities successfully. The second differential equation can dynamically adjust several parameters, so it can obtain satisfactory detection results. Simulations on some test networks have verified the efficiency of the presented algorithms. (interdisciplinary physics and related areas of science and technology)
Dynamic Waste Management (DWM):Towards an evolutionary decision-making approach
Rojo, Gabriel; Glaus, Mathias; Hausler, Robert; Laforest, Valérie; Bourgois, Jacques
2013-01-01
To guarantee sustainable and dynamic waste management, the dynamic waste management approach (DWM) suggests an evolutionary new approach that maintains a constant flow towards the most favourable waste treatment processes (facilities) within a system. To that end, DWM is based on the law of conservation of energy, which allows the balancing of a network, while considering the constraints of incoming (h1) and outgoing (h2) loads, as well as the distribution network (ΔH) characteristics. The de...
The Tangled Nature Model of evolutionary dynamics reconsidered
DEFF Research Database (Denmark)
Andersen, Christian Walther; Sibani, Paolo
2016-01-01
elephant. To bring out the structural and dynamical effects of trait inheritance , we introduce and numerically analyze a family of TNM models where a positive integer $K$ parametrises correlations between the interactions of an agent and those of its mutated offspring. For $K=1$ a single point mutation...
Achieving Reliability in Master-worker Computing via Evolutionary Dynamics
Christoforou, Evgenia; Fernández Anta, Antonio; Georgiou, Chryssis; Mosteiro, Miguel A.; Sánchez, Angel
2012-01-01
This work considers Internet-based task computations in which a master process assigns tasks, over the Internet, to rational workers and collect their responses. The objective is for the master to obtain the correct task outcomes. For this purpose we formulate and study the dynamics of evolution of Internet-based master-worker computations through reinforcement learning.
Bandy, D. K.; Hall, J. R.; Denker, M. E.
2015-07-01
We show that the role of the Lyapunov exponents can be extended beyond the customary local instability, such as limit cycle behavior, to include its use as an evolutionary predictor of the dynamics of a laser with injected signal (LIS). Numerical studies of LIS reveal that as a function of the input-signal strength the evolution of two nonzero Lyapunov exponents (generally equal) distinctively predicts the evolutionary trend of the fundamental frequency of the laser output signal (an important dynamic characteristic of the LIS) even with the presence of some noise. This globally predictive behavior of the Lyapunov exponents includes also the dynamic behavior of the individual coexisting attractors. Different coexisting attractors of LIS and configurations of Lyapunov exponents for both individual attractors and the global system are reported. Two LIS case studies are considered: (I) a high-gain system with a rich history of nonlinear behavior but not experimentally accessible, and (II) a low-gain system that has complex dynamics and is experimentally accessible for Class B lasers. Universality arguments support the thesis that these different configurations and the extended role of the Lyapunov exponents as an evolutionary predictor of the dynamics will be observed in other nonlinear, dynamic dissipative systems as well.
Directory of Open Access Journals (Sweden)
Pesole Graziano
2009-09-01
Full Text Available Abstract Background The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the annotation of newly sequenced genomes. In the context of recent findings that the number non-coding transcripts in higher organisms is likely to be much higher than previously imagined, discrimination between conserved coding and non-coding sequences is a topic of considerable interest. Additionally, it should be considered desirable to discriminate between coding and non-coding conserved sequences without recourse to the use of sequence similarity searches of protein databases as such approaches exclude the identification of novel conserved proteins without characterized homologs and may be influenced by the presence in databases of sequences which are erroneously annotated as coding. Results Here we present a machine learning-based approach for the discrimination of conserved coding sequences. Our method calculates various statistics related to the evolutionary dynamics of two aligned sequences. These features are considered by a Support Vector Machine which designates the alignment coding or non-coding with an associated probability score. Conclusion We show that our approach is both sensitive and accurate with respect to comparable methods and illustrate several situations in which it may be applied, including the identification of conserved coding regions in genome sequences and the discrimination of coding from non-coding cDNA sequences.
Temporal and Evolutionary Dynamics of Two-Component Signaling Pathways
Salazar, Michael E.; Laub, Michael T.
2015-01-01
Bacteria sense and respond to numerous environmental signals through two-component signaling pathways. Typically, a given stimulus will activate a sensor histidine kinase to autophosphorylate and then phosphotransfer to a cognate response regulator, which can mount an appropriate response. Although these signaling pathways often appear to be simple switches, they can also orchestrate surprisingly sophisticated and complex responses. These temporal dynamics arise from several key regulatory fe...
Modeling evolutionary dynamics of epigenetic mutations in hierarchically organized tumors.
Andrea Sottoriva; Louis Vermeulen; Simon Tavaré
2011-01-01
The cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of ...
Modeling Evolutionary Dynamics of Epigenetic Mutations in Hierarchically Organized Tumors
Sottoriva, A.; Vermeulen, L; Tavare, S
2011-01-01
The cancer stem cell (CSC) concept is a highly debated topic in cancer research. While experimental evidence in favor of the cancer stem cell theory is apparently abundant, the results are often criticized as being difficult to interpret. An important reason for this is that most experimental data that support this model rely on transplantation studies. In this study we use a novel cellular Potts model to elucidate the dynamics of established malignancies that are driven by a small subset of ...
Eco-evolutionary feedback promotes Red Queen dynamics and selects for sex in predator populations.
Haafke, Julia; Abou Chakra, Maria; Becks, Lutz
2016-03-01
Although numerous hypotheses exist to explain the overwhelming presence of sexual reproduction across the tree of life, we still cannot explain its prevalence when considering all inherent costs involved. The Red Queen hypothesis states that sex is maintained because it can create novel genotypes with a selective advantage. This occurs when the interactions between species induce frequent environmental change. Here, we investigate whether coevolution and eco-evolutionary feedback dynamics in a predator-prey system allows for indirect selection and maintenance of sexual reproduction in the predator. Combining models and chemostat experiments of a rotifer-algae system we show a continuous feedback between population and trait change along with recurrent shifts from selection by predation and competition for a limited resource. We found that a high propensity for sex was indirectly selected and was maintained in rotifer populations within environments containing these eco-evolutionary dynamics; whereas within environments under constant conditions, predators evolved rapidly to lower levels of sex. Thus, our results indicate that the influence of eco-evolutionary feedback dynamics on the overall evolutionary change has been underestimated. PMID:26899793
Calculation of dynamics of silver sorption by zirconium phosphate
International Nuclear Information System (INIS)
The experimental and calculation data on kinetics and dynamics of silver ions sorption by zirconium phosphate are considered in present article. The evaluation of sorption process in dynamic conditions is carried out.
Dynamic calculations of pressurized water reactor internals
International Nuclear Information System (INIS)
A mathematical model is briefly described for the calculation of oscillations in the WWER-440 reactor internals. The model was developed for improved safety of the type of reactors. It allows calculating vibrations resistance of reactor components, mainly during accidents, such as loss of coolant accidents. Some results are given of the calculation of forces acting in the rupture of the reactor inlet and outlet pipes. (Z.M.)
How the Magnitude of Prey Genetic Variation Alters Predator-Prey Eco-Evolutionary Dynamics.
Cortez, Michael H
2016-09-01
Evolution can alter the stability and dynamics of ecological communities; for example, prey evolution can drive cyclic dynamics in predator-prey systems that are not possible in the absence of evolution. However, it is unclear how the magnitude of additive genetic variation in the evolving species mediates those effects. In this study, I explore how the magnitude of prey additive genetic variation determines what effects prey evolution has on the dynamics and stability of predator-prey systems. I use linear stability analysis to decompose the stability of a general eco-evolutionary predator-prey model into components representing the stabilities of the ecological and evolutionary subsystems as well as the interactions between those subsystems. My results show that with low genetic variation, the cyclic dynamics and stability of the system are determined by the ecological subsystem. With increased genetic variation, disruptive selection always destabilizes stable communities, stabilizing selection can stabilize or destabilize communities, and prey evolution can alter predator-prey phase lags. Stability changes occur approximately when the magnitude of genetic variation balances the (in)stabilities of the ecological and evolutionary subsystems. I discuss the connections between my stability results and prior results from the theory of adaptive dynamics. PMID:27501090
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. PMID:26684728
Evolutionary dynamics on stochastic evolving networks for multiple-strategy games
Wu, Bin; Zhou, Da; Wang, Long
2011-10-01
Evolutionary game theory on dynamical networks has received much attention. Most of the work has been focused on 2×2 games such as prisoner's dilemma and snowdrift, with general n×n games seldom addressed. In particular, analytical methods are still lacking. Here we generalize the stochastic linking dynamics proposed by Wu, Zhou, Fu, Luo, Wang, and Traulsen [PLoS ONEBSYMBO1932-620310.1371/journal.pone.0011187 5, e11187 (2010)] to n×n games. We analytically obtain that the fast linking dynamics results in the replicator dynamics with a rescaled payoff matrix. In the rescaled matrix, intuitively, each entry is the product of the original entry and the average duration time of the corresponding link. This result is shown to be robust to a wide class of imitation processes. As applications, we show both analytically and numerically that the biodiversity, modeled as the stability of a zero-sum rock-paper-scissors game, cannot be altered by the fast linking dynamics. In addition, we show that the fast linking dynamics can stabilize tit-for-tat as an evolutionary stable strategy in the repeated prisoner's dilemma game provided the interaction between the identical strategies happens sufficiently often. Our method paves the way for an analytical study of the multiple-strategy coevolutionary dynamics.
Evolutionary calculations of carbon dredge-up in helium envelope white dwarfs
Macdonald, James; Hernanz, Margarita; José, Jordi
1998-01-01
We investigate the evolution of cooling helium atmosphere white dwarfs using a full evolutionary code, specifically developed for following the effects of element diffusion and gravitational settling on white dwarf cooling. The major difference between this work and previous work is that we use more recent opacity data from the OPAL project. Since, in general, these opacities are higher than those available ten years ago, at a given effective temperature, convection zones go deeper than in mo...
Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014
Xiang Yong Oong; Kim Tien Ng; Tommy Tsan-Yuk Lam; Yong Kek Pang; Kok Gan Chan; Nik Sherina Hanafi; Adeeba Kamarulzaman; Kok Keng Tee
2015-01-01
Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1%) patients infected with at least one respira...
Mutation-selection dynamics and error threshold in an evolutionary model for Turing Machines
Musso, Fabio; Feverati, Giovanni
2011-01-01
We investigate the mutation-selection dynamics for an evolutionary computation model based on Turing Machines that we introduced in a previous article. The use of Turing Machines allows for very simple mechanisms of code growth and code activation/inactivation through point mutations. To any value of the point mutation probability corresponds a maximum amount of active code that can be maintained by selection and the Turing machines that reach it are said to be at the error threshold. Simulat...
The Role of Clonal Interference in the Evolutionary Dynamics of Plasmid-Host Adaptation
Hughes, Julie M; Lohman, Brian K.; Deckert, Gail E.; Nichols, Eric P.; Settles, Matt; Abdo, Zaid; Eva M. Top
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 i...
Evolutionary supervision of a dynamical neural network allows learning with on-going weights
Meunier, David; Paugam-Moisy, Hélène
2005-01-01
Recent electrophysiological data show that synaptic weights are highly influenced by electrical activities displayed by neurons. Weights are not stable as assumed in classical neural network models. What is the nature of engrams, if not stored in synaptic weights? Adopting the theory of dynamical systems, which allows an implicit form of memory, we propose a new framework for learning, where synaptic weights are continuously adapted. Evolutionary computation has been applied to a population o...
Senerchia, Natacha; Wicker, Thomas; Felber, François; Parisod, Christian
2013-01-01
Transposable elements (TEs) represent a major fraction of plant genomes and drive their evolution. An improved understanding of genome evolution requires the dynamics of a large number of TE families to be considered. We put forward an approach bypassing the required step of a complete reference genome to assess the evolutionary trajectories of high copy number TE families from genome snapshot with high-throughput sequencing. Low coverage sequencing of the complex genomes of Aegilops cylindri...
Bando, Kathy J.
2005-01-01
Dwarf eelgrass (Zostera japonica) and smooth cordgrass (Spartina alterniflora) are ecologically important invaders of intertidal mudflats in the eastern Pacific. S. alterniflora and Z. japonica invasions alter estuarine nutrient dynamics, cause sediment and infaunal community changes, and modify waterfowl foraging habitats. Ecological and evolutionary mechanisms of the invasion success of Z. japonica and S. alterniflora were addressed with a combination of experimental and observational field...
Macroecology meets macroevolution: evolutionary niche dynamics in the seaweed Halimeda
Verbruggen, H.; Tyberghein, L.; Pauly, K.; C. Vlaeminck; VAN NIEUWENHUYZE, K; Kooistra, W.H.C.F.; Leliaert, F.; De Clerck, O
2011-01-01
Aim Because of their broad distribution in geographical and ecological dimensions, seaweeds (marine macroalgae) offer great potential as models for marine biogeographical inquiry and exploration of the interface between macroecology and macroevolution. This study aims to characterize evolutionary niche dynamics in the common green seaweed genus Halimeda, use the observed insights to gain understanding of the biogeographical history of the genus and predict habitats that can be targeted for t...
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. PMID:27140640
Evolutionary dynamics of imatinib-treated leukemic cells by stochastic approach
Pizzolato, Nicola; Valenti, Davide; Adorno, Dominique; 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.
The amazing evolutionary dynamics of non-linear optical systems with feedback
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.
Ito, Takashi; Pilat, Marcin L; Suzuki, Reiji; Arita, Takaya
2016-01-01
Recent studies have reported that population dynamics and evolutionary dynamics, occurring at different time scales, can be affected by each other. Our purpose is to explore the interaction between population and evolutionary dynamics using an artificial life approach based on a 3D physically simulated environment in the context of predator-prey and morphology-behavior coevolution. The morphologies and behaviors of virtual prey creatures are evolved using a genetic algorithm based on the predation interactions between predators and prey. Both population sizes are also changed, depending on the fitness. We observe two types of cyclic behaviors, corresponding to short-term and long-term dynamics. The former can be interpreted as a simple population dynamics of Lotka-Volterra type. It is shown that the latter cycle is based on the interaction between the changes in the prey strategy against predators and the long-term change in both population sizes, resulting partly from a tradeoff between their defensive success and the cost of defense. PMID:26934093
Dynamical collective calculation of supernova neutrino signals.
Gava, Jérôme; Kneller, James; Volpe, Cristina; McLaughlin, G C
2009-08-14
We present the first calculations with three flavors of collective and shock wave effects for neutrino propagation in core-collapse supernovae using hydrodynamical density profiles and the S matrix formalism. We explore the interplay between the neutrino-neutrino interaction and the effects of multiple resonances upon the time signal of positrons in supernova observatories. A specific signature is found for the inverted hierarchy and a large third neutrino mixing angle and we predict, in this case, a dearth of lower energy positrons in Cherenkov detectors midway through the neutrino signal and the simultaneous revelation of valuable information about the original fluxes. We show that this feature is also observable with current generation neutrino detectors at the level of several sigmas. PMID:19792628
Analysis of Ant Colony Optimization and Population-Based Evolutionary Algorithms on Dynamic Problems
DEFF Research Database (Denmark)
Lissovoi, Andrei
exist more complex oscillations that cannot be tracked with a polynomial-size colony. MMAS and (μ+1) EA on Maze We analyse the behaviour of a (μ + 1) EA with genotype diversity on a dynamic fitness function Maze, extended to a finite-alphabet search space. We prove that the (μ + 1) EA is able to track...... the dynamic optimum for finite alphabets up to size μ, while MMAS is able to do so for any finite alphabet size. Parallel Evolutionary Algorithms on Maze. We prove that while a (1 + λ) EA is unable to track the optimum of the dynamic fitness function Maze for offspring population size up to λ = O(n1-ε...... analysis showing how closely the EA can track the dynamically moving optimum over time. These results are also extended to a finite-alphabet search space....
Evolutionary Design of Both Topologies and Parameters of a Hybrid Dynamical System
DEFF Research Database (Denmark)
Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik
2012-01-01
This paper investigates the issue of evolutionary design of open-ended plants for hybrid dynamical systems--i.e. both their topologies and parameters. Hybrid bond graphs are used to represent dynamical systems involving both continuous and discrete system dynamics. Genetic programming, with some...... special mechanisms incorporated, is used as a search tool to explore the open-ended design space of hybrid bond graphs. Combination of these two tools--i.e., hybrid bond graphs (HGBs) and genetic programming (GP)--leads to an approach called HBGGP that can automatically generate viable design candidates...... of hybrid dynamical systems that fulfill predefined design specifications. A comprehensive investigation of a case study of DC-DC converter design demonstrates the feasibility and effectiveness of the HBGGP approach. Important characteristics of the approach are also discussed, with some future...
Dynamics of evolutionary rescue in changing environments and the emergence of antibiotic resistance.
Wu, Yue; Saddler, Clare A; Valckenborgh, Frank; Tanaka, Mark M
2014-01-01
Populations can go extinct when their environments deteriorate, but evolutionary rescue occurs when a shrinking population adapts to the new environmental conditions. The emergence of resistance from a drug sensitive bacterial population under treatment can be regarded as an instance of evolutionary rescue. Understanding evolutionary rescue in a particular context such as drug resistance requires knowledge of how the environment changes and how selection coefficients change as a result. In this study, we propose a model for evolutionary rescue under three different scenarios of environmental change: abrupt change, periodic fluctuation and gradual decay. The model makes use of the notion of reaction norms to describe fitness values that depend on both genotype and environmental state. We find that although drug sensitive bacterial populations may be large, allowing them to generate resistant mutants frequently, a harsh abrupt change due to the drug usually drives them extinct. Evolutionary rescue occurs far more frequently under the milder forms of environmental change we investigated. Rescue is favoured when the absolute fitnesses of individuals remain sufficiently high over the range of environment qualities experienced by the population. The minimum environment quality, which is inversely related to drug dose in the antibiotic context, is thus an important factor. Interestingly, in the periodic fluctuation model, the inter-dose period is less influential in promoting rescue through resistance unless the minimum environment quality is in a particular range. We also investigated fitness trade-offs across environments including the case of a resistant allele not subject to any trade-off (a "superbug"). This fitness trade-off affects the probability of rescue in decaying environments, but surprisingly has only a weak effect in the periodic fluctuation scenario. Finally, we use the model to show how niche construction, whereby organisms are the source of environmental
Ancient origin of the tryptophan operon and the dynamics of evolutionary change.
Xie, Gary; Keyhani, Nemat O; Bonner, Carol A; Jensen, Roy A
2003-09-01
The seven conserved enzymatic domains required for tryptophan (Trp) biosynthesis are encoded in seven genetic regions that are organized differently (whole-pathway operons, multiple partial-pathway operons, and dispersed genes) in prokaryotes. A comparative bioinformatics evaluation of the conservation and organization of the genes of Trp biosynthesis in prokaryotic operons should serve as an excellent model for assessing the feasibility of predicting the evolutionary histories of genes and operons associated with other biochemical pathways. These comparisons should provide a better understanding of possible explanations for differences in operon organization in different organisms at a genomics level. These analyses may also permit identification of some of the prevailing forces that dictated specific gene rearrangements during the course of evolution. Operons concerned with Trp biosynthesis in prokaryotes have been in a dynamic state of flux. Analysis of closely related organisms among the Bacteria at various phylogenetic nodes reveals many examples of operon scission, gene dispersal, gene fusion, gene scrambling, and gene loss from which the direction of evolutionary events can be deduced. Two milestone evolutionary events have been mapped to the 16S rRNA tree of Bacteria, one splitting the operon in two, and the other rejoining it by gene fusion. The Archaea, though less resolved due to a lesser genome representation, appear to exhibit more gene scrambling than the Bacteria. The trp operon appears to have been an ancient innovation; it was already present in the common ancestor of Bacteria and Archaea. Although the operon has been subjected, even in recent times, to dynamic changes in gene rearrangement, the ancestral gene order can be deduced with confidence. The evolutionary history of the genes of the pathway is discernible in rough outline as a vertical line of descent, with events of lateral gene transfer or paralogy enriching the analysis as interesting
Beam dynamics calculations for fault-tolerance
International Nuclear Information System (INIS)
The European Transmutation Demonstration requires a high-power proton accelerator operating in CW mode. This accelerator is also expected to have a very limited number of unexpected beam interruptions per year. To reach such an ambitious goal, it is clear that reliability-oriented design practices need to be followed from the early stage of components design and fault-tolerance capabilities have to be introduced to the maximum extent. The goal of this document is precisely to investigate in more details the fault-tolerance capability of the XT-ADS linac. From previous analysis, it appears that if nothing is done, a cavity's failure leads in nearly all the cases to a complete beam loss, due to the non-relativistic varying velocity of the particles. To avoid such a total beam loss, it is clear that some kind of retuning has to be performed to compensate the lack of acceleration due to the faulty cavity. We have to identify and develop fast failure recovery scenarios to ensure that such retuning can be performed in less than 1 second. 2 ways are investigated. The first way is to stop the beam to achieve the retuning (Scenario 1). The other way is to try to perform the retuning without stopping the beam (Scenario 2). The present analysis demonstrates on the beam dynamics point of view that a fast retuning procedure can be envisaged without stopping the beam (Scenario 2). Nevertheless, this Scenario 2 implies stringent specifications, especially on: - the fault detection time, that has to be extremely short (order of magnitude: 100 μs) and - the margins required on the accelerating field and RF power point of view, that are higher than in Scenario 1
On the calculation of dynamic derivatives using computational fluid dynamics
Da Ronch, Andrea
2012-01-01
In this thesis, the exploitation of computational fluid dynamics (CFD) methods for the flight dynamics of manoeuvring aircraft is investigated. It is demonstrated that CFD can now be used in a reasonably routine fashion to generate stability and control databases. Different strategies to create CFD-derived simulation models across the flight envelope are explored, ranging from combined low-fidelity/high-fidelity methods to reduced-order modelling. For the representation of the unsteady aerody...
Monte Carlo dose calculations for dynamic IMRT treatments
International Nuclear Information System (INIS)
Dose calculations for intensity modulated radiation therapy (IMRT) face new challenges due to the complex leaf geometry and time dependent nature of the delivery. A fast method of particle transport through a dynamic multileaf collimator (MLC) geometry that accounts for photon attenuation and first-scattered Compton photon production has been incorporated into an existing Monte Carlo code used for patient dose calculations. Dosimetric agreement between calculation and measurement for two photon energies and MLC types is within experimental error for the sliding window tests. For a patient IMRT field, the Monte Carlo calculations are closer to measured dose than similar superposition or pencil beam calculations. (author)
International Nuclear Information System (INIS)
This paper proposes a new hybrid approach based on nonlinear chaotic dynamics and evolutionary strategy to forecast electricity loads and prices. The main idea is to develop a new training or identification stage in a nonlinear chaotic dynamic based predictor. In the training stage five optimal parameters for a chaotic based predictor are searched through an optimization model based on evolutionary strategy. The objective function of the optimization model is the mismatch minimization between the multi-step-ahead forecasting of predictor and observed data such as it is done in identification problems. The first contribution of this paper is that the proposed approach is capable of capturing the complex dynamic of demand and price time series considered resulting in a more accuracy forecasting. The second contribution is that the proposed approach run on-line manner, i.e. the optimal set of parameters and prediction is executed automatically which can be used to prediction in real-time, it is an advantage in comparison with other models, where the choice of their input parameters are carried out off-line, following qualitative/experience-based recipes. A case study of load and price forecasting is presented using data from New England, Alberta, and Spain. A comparison with other methods such as autoregressive integrated moving average (ARIMA) and artificial neural network (ANN) is shown. The results show that the proposed approach provides a more accurate and effective forecasting than ARIMA and ANN methods. (author)
An experimental investigation of evolutionary dynamics in the Rock-Paper-Scissors game.
Hoffman, Moshe; Suetens, Sigrid; Gneezy, Uri; Nowak, Martin A
2015-01-01
Game theory describes social behaviors in humans and other biological organisms. By far, the most powerful tool available to game theorists is the concept of a Nash Equilibrium (NE), which is motivated by perfect rationality. NE specifies a strategy for everyone, such that no one would benefit by deviating unilaterally from his/her strategy. Another powerful tool available to game theorists are evolutionary dynamics (ED). Motivated by evolutionary and learning processes, ED specify changes in strategies over time in a population, such that more successful strategies typically become more frequent. A simple game that illustrates interesting ED is the generalized Rock-Paper-Scissors (RPS) game. The RPS game extends the children's game to situations where winning or losing can matter more or less relative to tying. Here we investigate experimentally three RPS games, where the NE is always to randomize with equal probability, but the evolutionary stability of this strategy changes. Consistent with the prediction of ED we find that aggregate behavior is far away from NE when it is evolutionarily unstable. Our findings add to the growing literature that demonstrates the predictive validity of ED in large-scale incentivized laboratory experiments with human subjects. PMID:25743257
Qian, Hong
2012-01-01
The study of biological cells in terms of mesoscopic, nonequilibrium, nonlinear, stochastic dynamics of open chemical systems provides a paradigm for other complex, self-organizing systems with ultra-fast stochastic fluctuations, short-time deterministic nonlinear dynamics, and long-time evolutionary behavior with exponentially distributed rare events, discrete jumps among punctuated equilibria, and catastrophe.
Evolutionary dynamics of public goods games with diverse contributions in finite populations
Wang, Jing; Wu, Bin; Chen, Xiaojie; Wang, Long
2010-05-01
The public goods game is a powerful metaphor for exploring the maintenance of social cooperative behavior in a group of interactional selfish players. Here we study the emergence of cooperation in the public goods games with diverse contributions in finite populations. The theory of stochastic process is innovatively adopted to investigate the evolutionary dynamics of the public goods games involving a diversity of contributions. In the limit of rare mutations, the general stationary distribution of this stochastic process can be analytically approximated by means of diffusion theory. Moreover, we demonstrate that increasing the diversity of contributions greatly reduces the probability of finding the population in a homogeneous state full of defectors. This increase also raises the expectation of the total contribution in the entire population and thus promotes social cooperation. Furthermore, by investigating the evolutionary dynamics of optional public goods games with diverse contributions, we find that nonparticipation can assist players who contribute more in resisting invasion and taking over individuals who contribute less. In addition, numerical simulations are performed to confirm our analytical results. Our results may provide insight into the effect of diverse contributions on cooperative behaviors in the real world.
The co-evolutionary dynamics of directed network of spin market agents
Horváth, Denis; Kuscsik, Zoltán; Gmitra, Martin
2006-09-01
The spin market model [S. Bornholdt, Int. J. Mod. Phys. C 12 (2001) 667] is generalized by employing co-evolutionary principles, where strategies of the interacting and competitive traders are represented by local and global couplings between the nodes of dynamic directed stochastic network. The co-evolutionary principles are applied in the frame of Bak-Sneppen self-organized dynamics [P. Bak, K. Sneppen, Phys. Rev. Lett. 71 (1993) 4083] that includes the processes of selection and extinction actuated by the local (node) fitness. The local fitness is related to orientation of spin agent with respect to the instant magnetization. The stationary regime is formed due to the interplay of self-organization and adaptivity effects. The fat tailed distributions of log-price returns are identified numerically. The non-trivial model consequence is the evidence of the long time market memory indicated by the power-law range of the autocorrelation function of volatility with exponent smaller than one. The simulations yield network topology with broad-scale node degree distribution characterized by the range of exponents 1.3<γin<3 coinciding with social networks.
Two-stage evolutionary algorithm for dynamic multicast routing in mesh network
Institute of Scientific and Technical Information of China (English)
Li ZHU; Zhi-shu LI; Liang-yin CHEN; Yan-hong CHENG
2008-01-01
In order to share multimedia transmissions in mesh networks and optimize the utilization of network resources, this paper presents a Two-stage Evolutionary Algorithm (TEA), i.e., unicast routing evolution and multicast path composition, for dynamic multicast routing. The TEA uses a novel link-duplicate-degree encoding, which can encode a multicast path in the link-duplicate-degree and decode the path as a link vector easily. A dynamic algorithm for adding nodes to or removing nodes from a multicast group and a repairing algorithm are also covered in this paper. As the TEA is based on global evaluation, the quality of the multicast path remains stabilized without degradation when multicast members change over time. Therefore, it is not necessary to rearrange the multicast path during the life cycle of the multicast sessions. Simulation results show that the TEA is efficient and convergent.
Evolutionary systemic risk: Fisher information flow metric in financial network dynamics
Khashanah, Khaldoun; Yang, Hanchao
2016-03-01
Recently the topic of financial network dynamics has gained renewed interest from researchers in the field of empirical systemic risk measurements. We refer to this type of network analysis as information flow networks analysis (IFNA). This paper proposes a new method that applies Fisher information metric to the evolutionary dynamics of financial networks using IFNA. Our paper is the first to apply the Fisher information metric to a set of financial time series. We introduce Evolution Index (EI) as a measure of systemic risk in financial networks. It is shown, for concrete networks with actual data of several stock markets, that the EI can be implemented as a measure of fitness of the stock market and as a leading indicator of systemic risk.
A New Multiobjective Evolutionary Algorithm for Community Detection in Dynamic Complex Networks
Directory of Open Access Journals (Sweden)
Guoqiang Chen
2013-01-01
Full Text Available Community detection in dynamic networks is an important research topic and has received an enormous amount of attention in recent years. Modularity is selected as a measure to quantify the quality of the community partition in previous detection methods. But, the modularity has been exposed to resolution limits. In this paper, we propose a novel multiobjective evolutionary algorithm for dynamic networks community detection based on the framework of nondominated sorting genetic algorithm. Modularity density which can address the limitations of modularity function is adopted to measure the snapshot cost, and normalized mutual information is selected to measure temporal cost, respectively. The characteristics knowledge of the problem is used in designing the genetic operators. Furthermore, a local search operator was designed, which can improve the effectiveness and efficiency of community detection. Experimental studies based on synthetic datasets show that the proposed algorithm can obtain better performance than the compared algorithms.
Multi CPU clusters and calculations by molecular dynamics method
International Nuclear Information System (INIS)
The technical characteristics of multi CPU (Central Processor Unit) clusters in Institute of Ion-Plasma and Laser Technologies AS RUz and Institute of Mathematics and Information Technologies AS RUz are described. There is detail information about cluster s architecture, installed programs and their productivity for decision of molecular dynamics tasks. Molecular dynamics program packages GROMACS, OPENMX and AutoDock-4.2.3 are described. The results of calculations using these program packages are presented. (author)
Quantum parallelism as a tool for ensemble spin dynamics calculations
Alvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.
2007-01-01
Efficient simulations of quantum evolutions of spin-1/2 systems are relevant for ensemble quantum computation as well as in typical NMR experiments. We propose an efficient method to calculate the dynamics of an observable provided that the initial excitation is "local". It resorts a single entangled pure initial state built as a superposition, with random phases, of the pure elements that compose the mixture. This ensures self-averaging of any observable, drastically reducing the calculation...
Self-consistent calculation of spin transport and magnetization dynamics
International Nuclear Information System (INIS)
A spin-polarized current transfers its spin-angular momentum to a local magnetization, exciting various types of current-induced magnetization dynamics. So far, most studies in this field have focused on the direct effect of spin transport on magnetization dynamics, but ignored the feedback from the magnetization dynamics to the spin transport and back to the magnetization dynamics. Although the feedback is usually weak, there are situations when it can play an important role in the dynamics. In such situations, simultaneous, self-consistent calculations of the magnetization dynamics and the spin transport can accurately describe the feedback. This review describes in detail the feedback mechanisms, and presents recent progress in self-consistent calculations of the coupled dynamics. We pay special attention to three representative examples, where the feedback generates non-local effective interactions for the magnetization after the spin accumulation has been integrated out. Possibly the most dramatic feedback example is the dynamic instability in magnetic nanopillars with a single magnetic layer. This instability does not occur without non-local feedback. We demonstrate that full self-consistent calculations generate simulation results in much better agreement with experiments than previous calculations that addressed the feedback effect approximately. The next example is for more typical spin valve nanopillars. Although the effect of feedback is less dramatic because even without feedback the current can make stationary states unstable and induce magnetization oscillation, the feedback can still have important consequences. For instance, we show that the feedback can reduce the linewidth of oscillations, in agreement with experimental observations. A key aspect of this reduction is the suppression of the excitation of short wavelength spin waves by the non-local feedback. Finally, we consider nonadiabatic electron transport in narrow domain walls. The non
Fe IX CALCULATIONS FOR THE SOLAR DYNAMICS OBSERVATORY
International Nuclear Information System (INIS)
New calculations of the energy levels, radiative transition rates, and collisional excitation rates of Fe IX have been carried out using the Flexible Atomic Code, paying close attention to experimentally identified levels and extending existing calculations to higher energy levels. For lower levels, R-matrix collisional excitation rates from earlier work have been used. Significant emission is predicted by these calculations in the 5f-3d transitions, which will impact analysis of Solar Dynamics Observatory Atmospheric Imaging Assembly observations using the 94 A filter.
Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily
Directory of Open Access Journals (Sweden)
Bagnato S
2014-04-01
Full Text Available Evolutionary dynamics of birch (Betula aetnensis Rafin coppices on the Mount Etna (Sicily. The aim of this paper is to evaluate the dynamics of Etna birch stands (Betula aetnensis Rafin following the cessation of silvicultural activities in the Etna Regional Park (Sicily. We investigated forest structure, natural regeneration, vegetation and deadwood in different forest types. Our findings highlighted three different dynamics for birch populations: stable birch stands in the high mountain area which might represent an edapho-climax forest; progressive dynamic birch stands in the intermediate mountain area, showing a gradual depletion of birch and a concomitant replacement with monospecific stands (calabrian pine, beech, oaks or mixed ones (with birch; pure birch stands (typical that tend to be regressive - especially under stressful conditions - and to be replaced by xerophilous grasslands. Following the cessation of coppicing and with stand ageing, the stumps transformation into more homogeneous stand structures have been increasing. Within the context of protected areas the restoration of coppice selection system (with appropriate adaptations could help to maintain the traditional forest landscape, acting as a silvicultural technique with low environmental and landscape impact.
Directory of Open Access Journals (Sweden)
2015-03-01
Full Text Available The dynamic economic load dispatch is one of the main problems of power systems generation and operation. The objective is to schedule power generation for units over a certain period of time, while satisfying operating constraints and load demand in each interval. Wind farms, as renewable energy resources are playing an increasing role in electricity generation. In this paper, a computational framework is presented to solve the dynamic economic emission dispatch problem with inclusion of wind farms considering their associated constraints. An optimization algorithm called modified co-evolutionary particle swarm optimization (MCPSO is proposed to solve the problem. In the proposed algorithm, two kinds of swarms evolve interactively where one of them is used to calculate the penalty factors (constraints handling and the other is used for searching good solutions (optimization process. In addition, some modifications such as using an inertia weight that decreases linearly during the simulation are made to improve the performance of the algorithm. Finally, the validity and superiority of the proposed method are demonstrated by simulation results on a modiﬁed IEEE benchmark system including six thermal units and two wind farms.
Directory of Open Access Journals (Sweden)
Yao Yao
Full Text Available One of the important challenges in the field of evolutionary robotics is the development of systems that can adapt to a changing environment. However, the ability to adapt to unknown and fluctuating environments is not straightforward. Here, we explore the adaptive potential of simulated swarm robots that contain a genomic encoding of a bio-inspired gene regulatory network (GRN. An artificial genome is combined with a flexible agent-based system, representing the activated part of the regulatory network that transduces environmental cues into phenotypic behaviour. Using an artificial life simulation framework that mimics a dynamically changing environment, we show that separating the static from the conditionally active part of the network contributes to a better adaptive behaviour. Furthermore, in contrast with most hitherto developed ANN-based systems that need to re-optimize their complete controller network from scratch each time they are subjected to novel conditions, our system uses its genome to store GRNs whose performance was optimized under a particular environmental condition for a sufficiently long time. When subjected to a new environment, the previous condition-specific GRN might become inactivated, but remains present. This ability to store 'good behaviour' and to disconnect it from the novel rewiring that is essential under a new condition allows faster re-adaptation if any of the previously observed environmental conditions is reencountered. As we show here, applying these evolutionary-based principles leads to accelerated and improved adaptive evolution in a non-stable environment.
Directory of Open Access Journals (Sweden)
Matos Margarida
2009-06-01
Full Text Available Abstract Here we present a correction to our article "Evolutionary dynamics of molecular markers during local adaptation: a case study in Drosophila subobscura". We have recently detected an error concerning the application of the Ln RH formula – a test to detect positive selection – to our microsatellite data. Here we provide the corrected data and discuss its implications for our overall findings. The corrections presented here have produced some changes relative to our previous results, namely in a locus (dsub14 that presents indications of being affected by positive selection. In general, our populations present less consistent indications of positive selection for this particular locus in both periods studied – between generations 3 and 14 and between generation 14 and 40 of laboratory adaptation. Despite this, the main findings of our study regarding the possibility of positive selection acting on that particular microsatellite still hold. As previously concluded in our article, further studies should be performed on this specific microsatellite locus (and neighboring areas to elucidate in greater detail the evolutionary forces acting on this specific region of the O chromosome of Drosophila subobscura.
Bardella, Vanessa Bellini; Fernandes, José Antônio Marin; Cabral-de-Mello, Diogo Cavalcanti
2016-10-01
Previous chromosome mapping of multigene families in Pentatomomorpha (Heteroptera) insects, which was restricted to the major rDNA, revealed remarkable conservation of number of clusters and chromosomal positions. Aiming to understand the chromosomal organization and evolutionary patterns of multigene families in karyotypes of Heteroptera, we performed a chromosomal mapping using four distinct multigene families in representatives of Coreidae (ten species) and Pentatomidae (five species). A single pair of the major rDNA cluster (18S rDNA probe) and a single pair of the minor rDNA cluster (5S rDNA probe), both terminally located were primarily observed, being, in most species, located in distinct chromosomes. However, some alternative patterns were also observed. In species in which the U2 snDNA and H4 gene clusters were mapped, they were mainly located in one autosomal pair each, wherein the H4 gene cluster was located in different positions. Our data suggest that the karyotype diversity reported in Coreidae is not reflected in the distribution diversity of multigene families. This contrasts with the data for Pentatomidae, with a conserved gross karyotype but a discrete diversity in the location of the clusters of multigene families, indicating genome dynamics for these markers. The findings are discussed to shed light on the possible causes for the conservation or variation observed and to assist in understanding the chromosomal evolutionary trends in the group. PMID:27380138
Effect of Recombination in the Evolutionary Dynamics of HIV under the Surveillance of Immune System
Peng, Weiqun; Yang, Wenjing; Wang, Guanyu
2009-03-01
Human immunodeficiency virus (HIV) is a retrovirus that causes acquired immunodeficiency syndrome (AIDS), which has become one of the most destructive pandemics in history. The fact that HIV virus evolves very fast plays a central role in AIDS immunopathogenesis and the difficulty we face in finding a cure or a vaccine for AIDS. A distinguishing feature of HIV is its high frequency of recombination. The effect of recombination in the HIV evolution is not clear. We establish a mathematical model of the evolutionary dynamics. This model incorporates both point mutation and recombination for genetic diversity, and employs a fitness function developed by Wang and Deem (PRL 97, 188106, 2006) that accounts for the effect of immune system. Using this model, we explore the role of recombination in the battle between the virus population and the immune system, with a special focus on the condition under which recombination helps the virus population to escape from the immune system.
Rocha, M. C.; Saraiva, J. T.
2012-10-01
The basic objective of Transmission Expansion Planning (TEP) is to schedule a number of transmission projects along an extended planning horizon minimizing the network construction and operational costs while satisfying the requirement of delivering power safely and reliably to load centres along the horizon. This principle is quite simple, but the complexity of the problem and the impact on society transforms TEP on a challenging issue. This paper describes a new approach to solve the dynamic TEP problem, based on an improved discrete integer version of the Evolutionary Particle Swarm Optimization (EPSO) meta-heuristic algorithm. The paper includes sections describing in detail the EPSO enhanced approach, the mathematical formulation of the TEP problem, including the objective function and the constraints, and a section devoted to the application of the developed approach to this problem. Finally, the use of the developed approach is illustrated using a case study based on the IEEE 24 bus 38 branch test system.
Directory of Open Access Journals (Sweden)
Saraiva J. T.
2012-10-01
Full Text Available The basic objective of Transmission Expansion Planning (TEP is to schedule a number of transmission projects along an extended planning horizon minimizing the network construction and operational costs while satisfying the requirement of delivering power safely and reliably to load centres along the horizon. This principle is quite simple, but the complexity of the problem and the impact on society transforms TEP on a challenging issue. This paper describes a new approach to solve the dynamic TEP problem, based on an improved discrete integer version of the Evolutionary Particle Swarm Optimization (EPSO meta-heuristic algorithm. The paper includes sections describing in detail the EPSO enhanced approach, the mathematical formulation of the TEP problem, including the objective function and the constraints, and a section devoted to the application of the developed approach to this problem. Finally, the use of the developed approach is illustrated using a case study based on the IEEE 24 bus 38 branch test system.
An Evolutionary Algorithm Approach to Link Prediction in Dynamic Social Networks
Bliss, Catherine A; Danforth, Christopher M; Dodds, Peter Sheridan
2013-01-01
Many real world, complex phenomena have underlying structures of evolving networks where nodes and links are added and removed over time. A central scientific challenge is the description and explanation of network dynamics, with a key test being the prediction of short and long term changes. For the problem of short-term link prediction, existing methods attempt to determine neighborhood metrics that correlate with the appearance of a link in the next observation period. Recent work has suggested that the incorporation of user-specific metadata and usage patterns can improve link prediction, however methodologies for doing so in a systematic way are largely unexplored in the literature. Here, we provide an approach to predicting future links by applying an evolutionary algorithm to weights which are used in a linear combination of sixteen neighborhood and node similarity indices. We examine Twitter reciprocal reply networks constructed at the time scale of weeks, both as a test of our general method and as a...
Evolutionary genetic optimization of the injector beam dynamics for the ERL test facility at IHEP
Yi, Jiao
2013-01-01
The energy recovery linac test facility (ERL-TF), a compact ERL-FEL (free electron laser) two-purpose machine, was proposed at the Institute of High Energy Physics, Beijing. As one important component of the ERL-TF, the photo-injector started with a photocathode direct-current gun was designed and preliminarily optimized. In this paper an evolutionary genetic method, non-dominated sorting genetic algorithm II, is applied to optimize the injector beam dynamics, especially in the high-charge operation mode. Study shows that using an incident laser with rms transverse size of 1~1.2 mm, the normalized emittance of the electron beam can be kept below 1 mm.mrad at the end of the injector. This work, together with the previous optimization for the low-charge operation mode by using the iterative scan method, provides guidance and confidence for future constructing and commissioning of the ERL-TF injector.
VERIFICATION OF TORSIONAL OSCILLATING MECHANICAL SYSTEM DYNAMIC CALCULATION RESULTS
Directory of Open Access Journals (Sweden)
Peter KAŠŠAY
2014-09-01
Full Text Available On our department we deal with optimization and tuning of torsional oscillating mechanical systems. When solving these problems we often use results of dynamic calculation. The goal of this article is to compare values obtained by computation and experimentally. For this purpose, a mechanical system built in our laboratory was used. At first, classical HARDY type flexible coupling has been applied into the system, then we used a pneumatic flexible shaft coupling developed by us. The main difference of these couplings over conventional flexible couplings is that they can change their dynamic properties during operation, by changing the pressure of the gaseous medium in their flexible elements.
Dissipative Particle Dynamics interaction parameters from ab initio calculations
Sepehr, Fatemeh; Paddison, Stephen J.
2016-02-01
Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.
Quantum Parallelism as a Tool for Ensemble Spin Dynamics Calculations
Álvarez, Gonzalo A.; Danieli, Ernesto P.; Levstein, Patricia R.; Pastawski, Horacio M.
2008-09-01
Efficient simulations of quantum evolutions of spin-1/2 systems are relevant for ensemble quantum computation as well as in typical NMR experiments. We propose an efficient method to calculate the dynamics of an observable provided that the initial excitation is “local.” It resorts to a single entangled pure initial state built as a superposition, with random phases, of the pure elements that compose the mixture. This ensures self-averaging of any observable, drastically reducing the calculation time. The procedure is tested for two representative systems: a spin star (cluster with random long range interactions) and a spin ladder.
DEFF Research Database (Denmark)
Tian, Yihui; Govindan, Kannan; Zhu, Qinghua
2014-01-01
In this study, a system dynamics (SD) model is developed to guide the subsidy policies to promote the diffusion of green supply chain management (GSCM) in China. The relationships of stakeholders such as government, enterprises and consumers are analyzed through evolutionary game theory. Finally...
Calculation of the dynamic air flow resistivity of fibre materials
DEFF Research Database (Denmark)
Tarnow, Viggo
1997-01-01
The acoustic attenuation of acoustic fiber materials is mainly determined by the dynamic resistivity to an oscillating air flow. The dynamic resistance is calculated for a model with geometry close to the geometry of real fibre material. The model constists of parallel cylinders placed randomly....... Two case are treated: flow perpendicular to the cylinder axes, and flow parallel to the axes. In each case two new approximate procedures were used. In the first procedure, one solves the equation of flow in a Voronoi cell around the fiber, and averages over the distribution of the Voronoi cells.......The second procedure is an extension to oscillating air flow of the Brinkman self-consistent procedure for dc flow. The procedures are valid for volume concentrations of cylinders less than 0.1. The calculations show that for the density of fibers of interest for acoustic fibre materials the simple self...
Andersen, Christian Walther; Sibani, Paolo
2016-05-01
Based on the stochastic dynamics of interacting agents which reproduce, mutate, and die, the tangled nature model (TNM) describes key emergent features of biological and cultural ecosystems' evolution. While trait inheritance is not included in many applications, i.e., the interactions of an agent and those of its mutated offspring are taken to be uncorrelated, in the family of TNMs introduced in this work correlations of varying strength are parametrized by a positive integer K . We first show that the interactions generated by our rule are nearly independent of K . Consequently, the structural and dynamical effects of trait inheritance can be studied independently of effects related to the form of the interactions. We then show that changing K strengthens the core structure of the ecology, leads to population abundance distributions better approximated by log-normal probability densities, and increases the probability that a species extant at time tw also survives at t >tw . Finally, survival probabilities of species are shown to decay as powers of the ratio t /tw , a so-called pure aging behavior usually seen in glassy systems of physical origin. We find a quantitative dynamical effect of trait inheritance, namely, that increasing the value of K numerically decreases the decay exponent of the species survival probability.
Tennessen, Jacob A; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron
2014-12-01
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes. PMID:25477420
Helbing, Dirk; Johansson, Anders
2010-01-01
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination or cooperation of interacting entities will occur, be it spins, particles, bacteria, animals, or humans. Here, we analyze the case, where the entities are heterogeneous, particularly the case of two populations with conflicting interactions and two possible states. For such systems, explicit mathematical formulas will be determined for the stationary solutions and the associated eigenvalues, which determine their stability. In this way, four different types of system dynamics can be classified and the various kinds of phase transitions between them will be discussed. While these results are interesting from a physics point of view, they are also relevant for social, economic, and biological systems, as they allow one to understand conditions for (1) the breakdown of cooperation, (2) the coexistence of different behaviors (“subcultures”), (3) the evolution of commonly shared behaviors (“norms”), and (4) the occurrence of polarization or conflict. We point out that norms have a similar function in social systems that forces have in physics.
Directory of Open Access Journals (Sweden)
Jingjing Ma
2014-01-01
Full Text Available Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.
Random and non-random mating populations: Evolutionary dynamics in meiotic drive.
Sarkar, Bijan
2016-01-01
Game theoretic tools are utilized to analyze a one-locus continuous selection model of sex-specific meiotic drive by considering nonequivalence of the viabilities of reciprocal heterozygotes that might be noticed at an imprinted locus. The model draws attention to the role of viability selections of different types to examine the stable nature of polymorphic equilibrium. A bridge between population genetics and evolutionary game theory has been built up by applying the concept of the Fundamental Theorem of Natural Selection. In addition to pointing out the influences of male and female segregation ratios on selection, configuration structure reveals some noted results, e.g., Hardy-Weinberg frequencies hold in replicator dynamics, occurrence of faster evolution at the maximized variance fitness, existence of mixed Evolutionarily Stable Strategy (ESS) in asymmetric games, the tending evolution to follow not only a 1:1 sex ratio but also a 1:1 different alleles ratio at particular gene locus. Through construction of replicator dynamics in the group selection framework, our selection model introduces a redefining bases of game theory to incorporate non-random mating where a mating parameter associated with population structure is dependent on the social structure. Also, the model exposes the fact that the number of polymorphic equilibria will depend on the algebraic expression of population structure. PMID:26524140
Directory of Open Access Journals (Sweden)
Mia T Levine
Full Text Available Heterochromatin is the gene-poor, satellite-rich eukaryotic genome compartment that supports many essential cellular processes. The functional diversity of proteins that bind and often epigenetically define heterochromatic DNA sequence reflects the diverse functions supported by this enigmatic genome compartment. Moreover, heterogeneous signatures of selection at chromosomal proteins often mirror the heterogeneity of evolutionary forces that act on heterochromatic DNA. To identify new such surrogates for dissecting heterochromatin function and evolution, we conducted a comprehensive phylogenomic analysis of the Heterochromatin Protein 1 gene family across 40 million years of Drosophila evolution. Our study expands this gene family from 5 genes to at least 26 genes, including several uncharacterized genes in Drosophila melanogaster. The 21 newly defined HP1s introduce unprecedented structural diversity, lineage-restriction, and germline-biased expression patterns into the HP1 family. We find little evidence of positive selection at these HP1 genes in both population genetic and molecular evolution analyses. Instead, we find that dynamic evolution occurs via prolific gene gains and losses. Despite this dynamic gene turnover, the number of HP1 genes is relatively constant across species. We propose that karyotype evolution drives at least some HP1 gene turnover. For example, the loss of the male germline-restricted HP1E in the obscura group coincides with one episode of dramatic karyotypic evolution, including the gain of a neo-Y in this lineage. This expanded compendium of ovary- and testis-restricted HP1 genes revealed by our study, together with correlated gain/loss dynamics and chromosome fission/fusion events, will guide functional analyses of novel roles supported by germline chromatin.
Electronic Structure and Molecular Dynamics Calculations for KBH4
Papaconstantopoulos, Dimitrios; Shabaev, Andrew; Hoang, Khang; Mehl, Michael; Kioussis, Nicholas
2012-02-01
In the search for hydrogen storage materials, alkali borohydrides MBH4 (M=Li, Na, K) are especially interesting because of their light weight and the high number of hydrogen atoms per metal atom. Electronic structure calculations can give insights into the properties of these complex hydrides and provide understanding of the structural properties and of the bonding of hydrogen. We have performed first-principles density-functional theory (DFT) and tight-binding (TB) calculations for KBH4 in both the high temperature (HT) and low temperature (LT) phases to understand its electronic and structural properties. Our DFT calculations were carried out using the VASP code. The results were then used as a database to develop a tight-binding Hamiltonian using the NRL-TB method. This approach allowed for computationally efficient calculations of phonon frequencies and elastic constants using the static module of the NRL-TB, and also using the molecular dynamics module to calculate mean-square displacements and formation energies of hydrogen vacancies.
A cascade of evolutionary change alters consumer-resource dynamics and ecosystem function
Walsh, Matthew R.; DeLong, John P.; Hanley, Torrance C.; Post, David M
2012-01-01
It is becoming increasingly clear that intraspecific evolutionary divergence influences the properties of populations, communities and ecosystems. The different ecological impacts of phenotypes and genotypes may alter selection on many species and promote a cascade of ecological and evolutionary change throughout the food web. Theory predicts that evolutionary interactions across trophic levels may contribute to hypothesized feedbacks between ecology and evolution. However, the importance of ...
Mueller, Georg P.
2012-01-01
This article analyzes different cultures of corruption with regard to their evolutionary stability, i.e. their ability to annihilate small disturbances in the equilibria between corrupt and noncorrupt agents. The article starts with the development of an evolutionary model of the interactions between corrupt and noncorrupt citizens and functionaries of the state, which is subsequently explored by formal analyses and computer simulation. It turns out that zero-corruption is always evolutionari...
VTT Energy's calculation system for reactor physics and dynamics
International Nuclear Information System (INIS)
VTT Energy has a comprehensive and independent calculation system for reactor physics and dynamics analyses. The system is widely utilized in contract research for the nuclear safety authorities and power companies. The four Finnish reactors, some foreign plants and potential new plant concepts have been studied. The system is being modernized all the time both by own development work and by international cooperation. The reactor physics codes are upgraded and new codes and methods are developed and acquired for calculations and safety evaluations of new, increasingly complicated fuel assembly types and fuel-loading schemes, as well as for criticality and dose rate studies. The reactor dynamics methods are developed and new sophisticated models are created for tasks related to increased safety requirements. The primary aim is to realistically simulate reactor stability and complicated reactivity accidents with three-dimensional core models. For thermal hydraulics calculations, an accurate general flow model based on a new solution method has been developed. (orig.) (30 refs., 3 figs.)
METHOD FOR CALCULATION OF STRESSED STATE SUBSTANTIATED BY DYNAMIC MICROTWIN
Directory of Open Access Journals (Sweden)
V. V. Vlashevich
2015-01-01
Full Text Available Method for calculation of the stressed state in a dynamic twin has been developed on the basis of a non-thin non-coherent micro-twin model with continuous distribution of twinning dislocations at twin boundaries. In this case there is no additional generation with the help of twinning dislocation source. The model takes into account that the twin has coherent and noncoherent boundary sections. The developed model has made it possible to take into consideration a form of non-coherent sections of twinning boundaries in calculations of stressed and deformed state at dynamic twins. It has been established that localized stresses are migrating together with non-coherent sections of the twin. Normal stresses σxx change their sign in relation to direction of the twin development. Shear stresses σxy are alternating in signs in relation to an axis which is perpendicular to the direction of the twin development and which is passing through a mid-point of non-coherent twin section. Distribution of stresses σyy и σyz has similar configuration. Stresses σzx in the second and fourth quarters of XOY plane are negative and the stresses in the first and third quarters are positive. Distribution of stresses σzz practically does not differ from distribution of stresses σyy according to configuration but numerical values of stress tensor component data are different.The results have been obtained without thin twin model that permits to consider only elastic stage of the twinning process. The executed stress calculations at dynamic twin are important for forecasting at the accumulation stage of damage origination which is caused by twinning destruction and permit to improve forecasting accuracy of technical system resources on the basis of twinning materials such as alloys based on iron, copper, zinc, aluminium, titanium.
Advanced Dynamics Analytical and Numerical Calculations with MATLAB
Marghitu, Dan B
2012-01-01
Advanced Dynamics: Analytical and Numerical Calculations with MATLAB provides a thorough, rigorous presentation of kinematics and dynamics while using MATLAB as an integrated tool to solve problems. Topics presented are explained thoroughly and directly, allowing fundamental principles to emerge through applications from areas such as multibody systems, robotics, spacecraft and design of complex mechanical devices. This book differs from others in that it uses symbolic MATLAB for both theory and applications. Special attention is given to solutions that are solved analytically and numerically using MATLAB. The illustrations and figures generated with MATLAB reinforce visual learning while an abundance of examples offer additional support. This book also: Provides solutions analytically and numerically using MATLAB Illustrations and graphs generated with MATLAB reinforce visual learning for students as they study Covers modern technical advancements in areas like multibody systems, robotics, spacecraft and des...
Evolutionary history and spatiotemporal dynamics of dengue virus type 1 in Asia.
Sun, Yan; Meng, Shengli
2013-06-01
Previous studies showed that DENV-1 transmitted from monkeys to humans approximately 125 years ago. However, there is no comprehensive analysis about phylogeography and population dynamics of Asian DENV-1. Here, we adopt a Bayesian phylogeographic approach to investigate the evolutionary history and phylogeography of Asian DENV-1 using envelope (E) protein gene sequences of 450 viruses isolated from 1954 to 2010 throughout 18 Asian countries and regions. Bayesian phylogeographic analyses indicate that the high rates of viral migration possibly follows long-distance travel for humans in Southeast Asia. Our study highlights that Southeast Asian countries have acted as the main viral sources of the dengue epidemics in East Asia. The results reveal that the time to the most recent common ancestor (TMRCA) of Asian DENV-1 is 1906 (95% HPD, years 1897-1915). We show that the spatial dissemination of virus is the major source of DENV-1 outbreaks in the different localities and leads to subsequent establishment and expansion of the virus in these areas. PMID:23395769
Evolutionary dynamics of strategic behavior in a collective-risk dilemma.
Abou Chakra, Maria; Traulsen, Arne
2012-01-01
A collective-risk social dilemma arises when a group must cooperate to reach a common target in order to avoid the risk of collective loss while each individual is tempted to free-ride on the contributions of others. In contrast to the prisoners' dilemma or public goods games, the collective-risk dilemma encompasses the risk that all individuals lose everything. These characteristics have potential relevance for dangerous climate change and other risky social dilemmas. Cooperation is costly to the individual and it only benefits all individuals if the common target is reached. An individual thus invests without guarantee that the investment is worthwhile for anyone. If there are several subsequent stages of investment, it is not clear when individuals should contribute. For example, they could invest early, thereby signaling their willingness to cooperate in the future, constantly invest their fair share, or wait and compensate missing contributions. To investigate the strategic behavior in such situations, we have simulated the evolutionary dynamics of such collective-risk dilemmas in a finite population. Contributions depend individually on the stage of the game and on the sum of contributions made so far. Every individual takes part in many games and successful behaviors spread in the population. It turns out that constant contributors, such as constant fair sharers, quickly lose out against those who initially do not contribute, but compensate this in later stages of the game. In particular for high risks, such late contributors are favored. PMID:22927807
Evolutionary dynamics of strategic behavior in a collective-risk dilemma.
Directory of Open Access Journals (Sweden)
Maria Abou Chakra
Full Text Available A collective-risk social dilemma arises when a group must cooperate to reach a common target in order to avoid the risk of collective loss while each individual is tempted to free-ride on the contributions of others. In contrast to the prisoners' dilemma or public goods games, the collective-risk dilemma encompasses the risk that all individuals lose everything. These characteristics have potential relevance for dangerous climate change and other risky social dilemmas. Cooperation is costly to the individual and it only benefits all individuals if the common target is reached. An individual thus invests without guarantee that the investment is worthwhile for anyone. If there are several subsequent stages of investment, it is not clear when individuals should contribute. For example, they could invest early, thereby signaling their willingness to cooperate in the future, constantly invest their fair share, or wait and compensate missing contributions. To investigate the strategic behavior in such situations, we have simulated the evolutionary dynamics of such collective-risk dilemmas in a finite population. Contributions depend individually on the stage of the game and on the sum of contributions made so far. Every individual takes part in many games and successful behaviors spread in the population. It turns out that constant contributors, such as constant fair sharers, quickly lose out against those who initially do not contribute, but compensate this in later stages of the game. In particular for high risks, such late contributors are favored.
The effect of network structure on innovation initiation process: an evolutionary dynamics approach
Jafari, Afshin; Zolfagharzadeh, Mohammad Mahdi; Mohammadi, Mehdi
2016-01-01
In this paper we have proposed a basic agent-based model based on evolutionary dynamics for investigating innovation initiation process. In our model we suppose each agent will represent a firm which is interacting with other firms through a given network structure. We consider a two-hit process for presenting a potentially successful innovation in this model and therefore at each time step each firm can be in on of three different stages which are respectively, Ordinary, Innovative, and Successful. We design different experiments in order to investigate how different interaction networks may affect the process of presenting a successful innovation to the market. In this experiments, we use five different network structures, i.e. Erd\\H{o}s and R\\'enyi, Ring Lattice, Small World, Scale-Free and Distance-Based networks. According to the results of the simulations, for less frequent innovations like radical innovation, local structures are showing a better performance comparing to Scale-Free and Erd\\H{o}s and R\\...
Evolutionary Dynamics of MERS-CoV: Potential Recombination, Positive Selection and Transmission.
Zhang, Zhao; Shen, Libing; Gu, Xun
2016-01-01
Middle East respiratory syndrome coronavirus (MERS-CoV) belongs to beta group of coronavirus and was first discovered in 2012. MERS-CoV can infect multiple host species and cause severe diseases in human. We conducted a series of phylogenetic and bioinformatic analyses to study the evolution dynamics of MERS-CoV among different host species with genomic data. Our analyses show: 1) 28 potential recombinant sequences were detected and they can be classified into seven potential recombinant types; 2) The spike (S) protein of MERS-CoV was under strong positive selection when MERS-CoV transmitted from their natural host to human; 3) Six out of nine positive selection sites detected in spike (S) protein are located in its receptor-binding domain which is in direct contact with host cells; 4) MERS-CoV frequently transmitted back and forth between human and camel after it had acquired the human-camel infection capability. Together, these results suggest that potential recombination events might have happened frequently during MERS-CoV's evolutionary history and the positive selection sites in MERS-CoV's S protein might enable it to infect human. PMID:27142087
The evolutionary dynamics of the Helena retrotransposon revealed by sequenced Drosophila genomes
Directory of Open Access Journals (Sweden)
Carareto Claudia MA
2009-07-01
Full Text Available Abstract Background Several studies have shown that genomes contain a mixture of transposable elements, some of which are still active and others ancient relics that have degenerated. This is true for the non-LTR retrotransposon Helena, of which only degenerate sequences have been shown to be present in some species (Drosophila melanogaster, whereas putatively active sequences are present in others (D. simulans. Combining experimental and population analyses with the sequence analysis of the 12 Drosophila genomes, we have investigated the evolution of Helena, and propose a possible scenario for the evolution of this element. Results We show that six species of Drosophila have the Helena transposable element at different stages of its evolution. The copy number is highly variable among these species, but most of them are truncated at the 5' ends and also harbor several internal deletions and insertions suggesting that they are inactive in all species, except in D. mojavensis in which quantitative RT-PCR experiments have identified a putative active copy. Conclusion Our data suggest that Helena was present in the common ancestor of the Drosophila genus, which has been vertically transmitted to the derived lineages, but that it has been lost in some of them. The wide variation in copy number and sequence degeneration in the different species suggest that the evolutionary dynamics of Helena depends on the genomic environment of the host species.
Dynamic calculation of structures in seismic zones. 2. ed.
International Nuclear Information System (INIS)
The aims of this book are both didactic and practical. It is therefore addressed to both experienced engineers and students. Some general information about earthquakes and their occurrence is first given. The problem of a simple oscillator is presented. In this way, the reader is provided with an insight into undestanding the dynamic phenomena taking place and is introduced to the concept of response spectra and to an intuitive comprehension of the behavior of structures during earthquakes. The next chapter is devoted to the cases most frequently encountered with multiple oscillator structures. Theoretical studies are based on the usual modal decomposition method. The various practical methods of calculation employed are then examined, emphasis being given to the various different stages involved and to which of them is the best suited for a particular type of structure. Advise is given on how to select the model whose behavior best describes the real structure, both manual and computer methods of calculation being envisaged
Molecular dynamics calculations for sodium using pseudopotential theory
International Nuclear Information System (INIS)
The equation of state of sodium is studied using the molecular dynamics technique whereby the classical motion of a system of ions is solved with the aid of computers. The interaction potential between pairs of sodium ions consists of Coulomb and Born-Mayer repulsion terms and an effective ion-ion interaction derived from pseudopotential theory. This theory includes the effects of electron gas screening, exchange, and correlation. A model pseudopotential with parameters fit to experimental low-temperature data is used. By using this technique, an atomic description of a simple metal proceeds to the calculation of macroscopic thermodynamic properties
Approximate dynamic fault tree calculations for modelling water supply risks
International Nuclear Information System (INIS)
Traditional fault tree analysis is not always sufficient when analysing complex systems. To overcome the limitations dynamic fault tree (DFT) analysis is suggested in the literature as well as different approaches for how to solve DFTs. For added value in fault tree analysis, approximate DFT calculations based on a Markovian approach are presented and evaluated here. The approximate DFT calculations are performed using standard Monte Carlo simulations and do not require simulations of the full Markov models, which simplifies model building and in particular calculations. It is shown how to extend the calculations of the traditional OR- and AND-gates, so that information is available on the failure probability, the failure rate and the mean downtime at all levels in the fault tree. Two additional logic gates are presented that make it possible to model a system's ability to compensate for failures. This work was initiated to enable correct analyses of water supply risks. Drinking water systems are typically complex with an inherent ability to compensate for failures that is not easily modelled using traditional logic gates. The approximate DFT calculations are compared to results from simulations of the corresponding Markov models for three water supply examples. For the traditional OR- and AND-gates, and one gate modelling compensation, the errors in the results are small. For the other gate modelling compensation, the error increases with the number of compensating components. The errors are, however, in most cases acceptable with respect to uncertainties in input data. The approximate DFT calculations improve the capabilities of fault tree analysis of drinking water systems since they provide additional and important information and are simple and practically applicable.
Dynamical calculations of nuclear fission and heavy-ion reactions
International Nuclear Information System (INIS)
With the goal of determining the magnitude and mechanism of nuclear dissipation from comparisons of predictions with experimental data, we describe recent calculations in a unified macroscopic-microscopic approach to large-amplitude collective nuclear motion such as occurs in fission and heavy-ion reactions. We describe the time dependence of the distribution function in phase space of collective coordinates and momenta by a generalized Fokker-Planck equation. The nuclear potential energy of deformation is calculated as the sum of repulsive Coulomb and centrifugal energies and an attractive Yukawa-plus-exponential potential, the inertia tensor is calculated for a superposition of rigid-body rotation and incompressible, nearly irrotational flow by use of the Werner-Wheeler method, and the dissipation ensor that describes the conversion of collective energy into single-particle excitation energy is calculated for two prototype mechanisms that represent opposite extremes of large and small dissipation. We solve the generalized Hamilton equations of motion for the first moments of the distribution function to obtain the mean translational fission-fragment kinetic energy and mass of a third fragment that sometimes forms between the two end fragments, as well as dynamical thresholds, capture cross sections, and ternary events in heavy-ion reactions. 33 references
Neotropical fish-fruit interactions: eco-evolutionary dynamics and conservation.
Correa, Sandra Bibiana; Costa-Pereira, Raul; Fleming, Theodore; Goulding, Michael; Anderson, Jill T
2015-11-01
Frugivorous fish play a prominent role in seed dispersal and reproductive dynamics of plant communities in riparian and floodplain habitats of tropical regions worldwide. In Neotropical wetlands, many plant species have fleshy fruits and synchronize their fruiting with the flood season, when fruit-eating fish forage in forest and savannahs for periods of up to 7 months. We conducted a comprehensive analysis to examine the evolutionary origin of fish-fruit interactions, describe fruit traits associated with seed dispersal and seed predation, and assess the influence of fish size on the effectiveness of seed dispersal by fish (ichthyochory). To date, 62 studies have documented 566 species of fruits and seeds from 82 plant families in the diets of 69 Neotropical fish species. Fish interactions with flowering plants are likely to be as old as 70 million years in the Neotropics, pre-dating most modern bird-fruit and mammal-fruit interactions, and contributing to long-distance seed dispersal and possibly the radiation of early angiosperms. Ichthyochory occurs across the angiosperm phylogeny, and is more frequent among advanced eudicots. Numerous fish species are capable of dispersing small seeds, but only a limited number of species can disperse large seeds. The size of dispersed seeds and the probability of seed dispersal both increase with fish size. Large-bodied species are the most effective seed dispersal agents and remain the primary target of fishing activities in the Neotropics. Thus, conservation efforts should focus on these species to ensure continuity of plant recruitment dynamics and maintenance of plant diversity in riparian and floodplain ecosystems. PMID:25599800
Agoti, Charles N.; Gitahi, Caroline W.; Bett, Ann; Ngama, Mwanajuma; Medley, Graham F.; Cane, Patricia A.; Nokes, D. James
2016-01-01
ABSTRACT The characteristic recurrent epidemics of human respiratory syncytial virus (RSV) within communities may result from the genetic variability of the virus and associated evolutionary adaptation, reducing the efficiency of preexisting immune responses. We analyzed the molecular evolutionary changes in the attachment (G) glycoprotein of RSV-A viruses collected over 13 epidemic seasons (2000 to 2012) in Kilifi (n = 649), Kenya, and contemporaneous sequences (n = 1,131) collected elsewhere within Kenya and 28 other countries. Genetic diversity in the G gene in Kilifi was dynamic both within and between epidemics, characterized by frequent new variant introductions and limited variant persistence between consecutive epidemics. Four RSV-A genotypes were detected in Kilifi: ON1 (11.9%), GA2 (75.5%), GA5 (12.3%), and GA3 (0.3%), with predominant genotype replacement of GA5 by GA2 and then GA2 by ON1. Within these genotypes, there was considerable variation in potential N-glycosylation sites, with GA2 and ON1 viruses showing up to 15 different patterns involving eight possible sites. Further, we identified 15 positively selected and 34 genotype-distinguishing codon sites, with six of these sites exhibiting both characteristics. The mean substitution rate of the G ectodomain for the Kilifi data set was estimated at 3.58 × 10−3 (95% highest posterior density interval = 3.04 to 4.16) nucleotide substitutions/site/year. Kilifi viruses were interspersed in the global phylogenetic tree, clustering mostly with Kenyan and European sequences. Our findings highlight ongoing genetic evolution and high diversity of circulating RSV-A strains, locally and globally, with potential antigenic differences. Taken together, these provide a possible explanation on the nature of recurrent local RSV epidemics. IMPORTANCE The mechanisms underlying recurrent epidemics of RSV are poorly understood. We observe high genetic diversity in circulating strains within and between epidemics in
Directory of Open Access Journals (Sweden)
José Alexandre F. Diniz-Filho
2013-10-01
Full Text Available Macroecology focuses on ecological questions at broad spatial and temporal scales, providing a statistical description of patterns in species abundance, distribution and diversity. More recently, historical components of these patterns have begun to be investigated more deeply. We tentatively refer to the practice of explicitly taking species history into account, both analytically and conceptually, as ‘evolutionary macroecology’. We discuss how the evolutionary dimension can be incorporated into macroecology through two orthogonal and complementary data types: fossils and phylogenies. Research traditions dealing with these data have developed more‐or‐less independently over the last 20–30 years, but merging them will help elucidate the historical components of diversity gradients and the evolutionary dynamics of species’ traits. Here we highlight conceptual and methodological advances in merging these two research traditions and review the viewpoints and toolboxes that can, in combination, help address patterns and unveil processes at temporal and spatial macro‐scales.
International Nuclear Information System (INIS)
In this study either cluster fragmentation, using a time-dependent Hartree-Fock formulation, or cluster deposition, based on classical molecular dynamics, have been studied. An exhaustive analysis has been performed on the many parameters acting on the two processes. Fragmentation calculations show a primary dependence on the input energy whereas the interatomic forces play a primary role in deposition. However the central result of this study is the essential agreement between the classical and quantum mechanical calculation
Biopolymers under large external forces and mean-field RNA virus evolutionary dynamics
Ahsan, Syed Amir
The modeling of the mechanical response of single-molecules of DNA and RNA under large external forces through statistical mechanical methods is central to this thesis with a small portion devoted to modeling the evolutionary dynamics of positive-sense single-stranded RNA viruses. In order to develop and test models of biopolymer mechanics and illuminate the mechanisms underlying biological processes where biopolymers undergo changes in energy on the order of the thermal energy, , entails measuring forces and lengths on the scale of piconewtons (pN) and nanometers (nm), respectively. A capacity achieved in the past two decades at the single-molecule level through the development of micromanipulation techniques such as magnetic and optical tweezers, atomic force microscopy, coupled with advances in micro- and nanofabrication. The statistical mechanical models of biopolymers developed in this dissertation are dependent upon and the outcome of these advancements and resulting experiments. The dissertation begins in chapter 1 with an introduction to the structure and thermodynamics of DNA and RNA, highlighting the importance and effectiveness of simple, two-state models in their description as a prelude to the emergence of two-state models in the research manuscripts. In chapter 2 the standard models of the elasticity of polymers and of a polymer gel are reviewed, characterizing the continuum and mean-field models, including the scaling behavior of DNA in confined spaces. The research manuscript presented in the last section of chapter 2 (section 2.5), subsequent to a review of a Flory gel and in contrast to it, is a model of the elasticity of RNA as a gel, with viral RNA illustrating an instance of such a network, and shown to exhibit anomalous elastic behavior, a negative Poisson ratio, and capable of facilitating viral RNA encapsidation with further context provided in section 5.1. In chapter 3 the experimental methods and behavior of DNA and RNA under mechanical
Wolfe, Alexander P.; Siver, Peter A.
2013-12-01
Chrysophyte algae are common in the plankton of oligotrophic lakes and produce a rich microfossil record of siliceous cysts and scales. Paleolimnological investigations and phytoplankton records suggest that chrysophyte populations are increasing in a wide range of boreal and arctic lakes, ultimately representing one component of the limnological response to contemporary global changes. However, the exact mechanisms responsible for widespread increases of chrysophyte populations remain elusive. We hypothesize that recent increases in chrysophytes are related to rising pCO2 in lakes, in part because these algae lack carbon concentrating mechanisms and therefore rely on diffusive entry of CO2 to Rubisco during photosynthesis. We assessed the abundance of modern sediment chrysophyte microfossils in relation to summer CO2 relative saturation in 46 New England (USA) lakes, revealing significant positive relationships for both cysts and scales. These observations imply that correlations between chrysophytes and limnological conditions including low pH, oligotrophy, and elevated dissolved organic matter are ultimately underscored by the high pCO2 associated with these conditions. In lakes where chrysophyte populations have expanded over recent decades, we infer that increasingly heterotrophic conditions with respect to CO2 have stimulated production by these organisms. This linkage is supported by the remarkable abundance and diversity of chrysophytes from middle Eocene lake sediments, deposited under atmospheric CO2 concentrations significantly higher than present. The Eocene assemblages suggest that any chrysophyte-CO2 connection borne out of results from modern and sub-recent sediments also operated on evolutionary time scales, and thus the absence of carbon concentrating mechanisms appears to be an ancient feature within the group. Chrysophyte microfossils may potentially provide important insights concerning the temporal dynamics of carbon cycling in aquatic
Beam dynamics calculations and particle tracking using massively parallel processors
International Nuclear Information System (INIS)
During the past decade massively parallel processors (MPPs) have slowly gained acceptance within the scientific community. At present these machines typically contain a few hundred to one thousand off-the-shelf microprocessors and a total memory of up to 32 GBytes. The potential performance of these machines is illustrated by the fact that a month long job on a high end workstation might require only a few hours on an MPP. The acceptance of MPPs has been slow for a variety of reasons. For example, some algorithms are not easily parallelizable. Also, in the past these machines were difficult to program. But in recent years the development of Fortran-like languages such as CM Fortran and High Performance Fortran have made MPPs much easier to use. In the following we will describe how MPPs can be used for beam dynamics calculations and long term particle tracking
Flux-vector splitting for unsteady calculations on dynamic meshes
Anderson, W. Kyle; Thomas, James L.; Rumsey, Christopher L.
1989-01-01
The method of flux vector splitting used is that of Van Leer. The fluxes split in this manner have the advantage of being continuously differentiable at eigenvalue sign changes and this allows normal shocks to be captured with at most two interior zones, although in practice only one zone is usually observed. The fluxes as originally derived, however did not include the necessary terms appropriate for calculations on a dynamic mesh. The extension of the splitting to include these terms while retaining the advantages of the original splitting is the main purpose of this investigation. In addition, the use of multiple grids to reduce the computer time is investigated. A subiterative procedure to eliminate factorization and linearization error so that larger time steps can be used is also investigated.
Automating the parallel processing of fluid and structural dynamics calculations
Arpasi, Dale J.; Cole, Gary L.
1987-01-01
The NASA Lewis Research Center is actively involved in the development of expert system technology to assist users in applying parallel processing to computational fluid and structural dynamic analysis. The goal of this effort is to eliminate the necessity for the physical scientist to become a computer scientist in order to effectively use the computer as a research tool. Programming and operating software utilities have previously been developed to solve systems of ordinary nonlinear differential equations on parallel scalar processors. Current efforts are aimed at extending these capabilties to systems of partial differential equations, that describe the complex behavior of fluids and structures within aerospace propulsion systems. This paper presents some important considerations in the redesign, in particular, the need for algorithms and software utilities that can automatically identify data flow patterns in the application program and partition and allocate calculations to the parallel processors. A library-oriented multiprocessing concept for integrating the hardware and software functions is described.
Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.
Directory of Open Access Journals (Sweden)
Xiang Yong Oong
Full Text Available Epidemiological and evolutionary dynamics of influenza B Victoria and Yamagata lineages remained poorly understood in the tropical Southeast Asia region, despite causing seasonal outbreaks worldwide. From 2012-2014, nasopharyngeal swab samples collected from outpatients experiencing acute upper respiratory tract infection symptoms in Kuala Lumpur, Malaysia, were screened for influenza viruses using a multiplex RT-PCR assay. Among 2,010/3,935 (51.1% patients infected with at least one respiratory virus, 287 (14.3% and 183 (9.1% samples were tested positive for influenza A and B viruses, respectively. Influenza-positive cases correlate significantly with meteorological factors-total amount of rainfall, relative humidity, number of rain days, ground temperature and particulate matter (PM10. Phylogenetic reconstruction of haemagglutinin (HA gene from 168 influenza B viruses grouped them into Yamagata Clade 3 (65, 38.7%, Yamagata Clade 2 (48, 28.6% and Victoria Clade 1 (55, 32.7%. With neuraminidase (NA phylogeny, 30 intra-clade (29 within Yamagata Clade 3, 1 within Victoria Clade 1 and 1 inter-clade (Yamagata Clade 2-HA/Yamagata Clade 3-NA reassortants were identified. Study of virus temporal dynamics revealed a lineage shift from Victoria to Yamagata (2012-2013, and a clade shift from Yamagata Clade 2 to Clade 3 (2013-2014. Yamagata Clade 3 predominating in 2014 consisted of intra-clade reassortants that were closely related to a recent WHO vaccine candidate strain (B/Phuket/3073/2013, with the reassortment event occurred approximately 2 years ago based on Bayesian molecular clock estimation. Malaysian Victoria Clade 1 viruses carried H274Y substitution in the active site of neuraminidase, which confers resistance to oseltamivir. Statistical analyses on clinical and demographic data showed Yamagata-infected patients were older and more likely to experience headache while Victoria-infected patients were more likely to experience nasal congestion and
Directory of Open Access Journals (Sweden)
Colin J Worby
Full Text Available Genome sequencing is an increasingly common component of infectious disease outbreak investigations. However, the relationship between pathogen transmission and observed genetic data is complex, and dependent on several uncertain factors. As such, simulation of pathogen dynamics is an important tool for interpreting observed genomic data in an infectious disease outbreak setting, in order to test hypotheses and to explore the range of outcomes consistent with a given set of parameters. We introduce 'seedy', an R package for the simulation of evolutionary and epidemiological dynamics (http://cran.r-project.org/web/packages/seedy/. Our software implements stochastic models for the accumulation of mutations within hosts, as well as individual-level disease transmission. By allowing variables such as the transmission bottleneck size, within-host effective population size and population mixing rates to be specified by the user, our package offers a flexible framework to investigate evolutionary dynamics during disease outbreaks. Furthermore, our software provides theoretical pairwise genetic distance distributions to provide a likelihood of person-to-person transmission based on genomic observations, and using this framework, implements transmission route assessment for genomic data collected during an outbreak. Our open source software provides an accessible platform for users to explore pathogen evolution and outbreak dynamics via simulation, and offers tools to assess observed genomic data in this context.
TRAWA, LWR Dynamic by Coupled Neutron Diffusion and Thermohydraulics Calculation
International Nuclear Information System (INIS)
1 - Description of problem or function: The purpose of the program is to study reactor dynamics in thermal water-cooled reactors. It treats the core as one or a few axially one-dimensional subregions. The two group neutron diffusion equations are solved simultaneously with the heat conduction equations and the two-phase hydraulic equations for one or more channels. Neither thermal nor hydraulic mixing appear between channels. Doppler, coolant density, coolant temperature, and soluble poison density feedbacks due to the thermo- hydraulics of the channels are described by using polynomial expansions for the group constants. The hydraulic circuit outside the reactor core consists of by-pass channels and risers with two- phase flow and of pump lines with incompressible flow. Various transients can be calculated by applying external disturbances. They can affect e.g. on movements of control rods, core inlet hydraulic conditions, system pressure or coefficients of neutronic shape function expansion between subregions. 2 - Method of solution: Nontrivial implicit methods are employed in the discretization of the equations to allow for sparse spatial mesh and flexible choice of time steps. The same spatial and temporal discretization is used for neutronics and thermohydraulics. 3 - Restrictions on the complexity of the problem: The dimensions of the program variable tables can easily be extended. Now the main dimensions are: 52 axial mesh points in core; 3 subregions; 10 axial regions with different fuel compositions; 7 radial mesh points in fuel rod; 6 delayed neutron groups; 6 coupled legs in pressure balance calculation; No flow reversals are allowed
Roaming dynamics in the MgH + H→Mg + H 2 reaction: Quantum dynamics calculations
Takayanagi, Toshiyuki; Tanaka, Tomokazu
2011-03-01
Reaction mechanisms of the MgH + H→Mg + H 2 reaction have been investigated using quantum reactive scattering methods on a global ab initio potential energy surface. There exist two microscopic mechanisms in the dynamics of this reaction. One is a direct hydrogen abstraction reaction and the other proceeds via initial formation of a HMgH complex in the deep potential well. The result of the present quantum dynamics calculations suggests that the HMgH complex formed in the reaction mainly decays into the Mg + H 2 channel via a 'roaming mechanism' without going through the saddle point region.
Self-consistent calculation of spin transport and magnetization dynamics
Lee, Kyung-Jin; Stiles, M. D.; Lee, Hyun-Woo; Moon, Jung-Hwan; Kim, Kyoung-Whan; Lee, Seo-Won
2013-01-01
A spin-polarized current transfers its spin-angular momentum to a local magnetization, exciting current-induced magnetization dynamics. So far, most studies in this field have focused on the direct effect of spin transport on magnetization dynamics, but ignored the feedback from the magnetization dynamics to the spin transport and back to the magnetization dynamics. Although the feedback is usually weak, there are situations when it can play an important role in the dynamics. In such situatio...
DEFF Research Database (Denmark)
Neumann, Frank; Witt, Carsten
combinatorial optimization problem, namely makespan scheduling. We study the model of a strong adversary which is allowed to change one job at regular intervals. Furthermore, we investigate the setting of random changes. Our results show that randomized local search and a simple evolutionary algorithm are very...
Synthesizing mixed H2/H-infinity dynamic controller using evolutionary algorithms
DEFF Research Database (Denmark)
Pedersen, Gerulf; Langballe, A.S.; Wisniewski, Rafal
2001-01-01
This paper covers the design of an Evolutionary Algorithm (EA), which should be able to synthesize a mixed H2/H-infinity. It will be shown how a system can be expressed as Matrix Inequalities (MI) and these will then be used in the design of the EA. The main objective is to examine whether a mixed...
An evolutionary Algorithm for Structural Subjected to Dynamic Loading With Random Excitation
International Nuclear Information System (INIS)
This paper presents an evolutionary algorithm for optimization of structures subjected to random excitation. The new iteration scheme in conjunction with multi-population genetic strategy, entropy-based searching technique with narrowing down space and the quasi-exactness penalty function is developed to ensure rapid and steady convergence. Numerical example shows that proposed method has good accuracy and efficiency
Synthesizing multi-objective H2/H-infinity dynamic controller using evolutionary algorithms
DEFF Research Database (Denmark)
Pedersen, Gerulf; Langballe, A.S.; Wisniewski, Rafal
This paper covers the design of an Evolutionary Algorithm (EA), which should be able to synthesize a mixed H2/H-infinity. It will be shown how a system can be expressed as Matrix Inequalities (MI) and these will then be used in the design of the EA. The main objective is to examine whether a mixed...
Zheng, Chaozhi; Ovaskainen, Otso; Hanski, Ilkka
2009-01-01
Dispersal comprises a complex life-history syndrome that influences the demographic dynamics of especially those species that live in fragmented landscapes, the structure of which may in turn be expected to impose selection on dispersal. We have constructed an individual-based evolutionary sexual model of dispersal for species occurring as metapopulations in habitat patch networks. The model assumes correlated random walk dispersal with edge-mediated behaviour (habitat selection) and spatially correlated stochastic local dynamics. The model is parametrized with extensive data for the Glanville fritillary butterfly. Based on empirical results for a single nucleotide polymorphism (SNP) in the phosphoglucose isomerase (Pgi) gene, we assume that dispersal rate in the landscape matrix, fecundity and survival are affected by a locus with two alleles, A and C, individuals with the C allele being more mobile. The model was successfully tested with two independent empirical datasets on spatial variation in Pgi allele frequency. First, at the level of local populations, the frequency of the C allele is the highest in newly established isolated populations and the lowest in old isolated populations. Second, at the level of sub-networks with dissimilar numbers and connectivities of patches, the frequency of C increases with decreasing network size and hence with decreasing average metapopulation size. The frequency of C is the highest in landscapes where local extinction risk is high and where there are abundant opportunities to establish new populations. Our results indicate that the strength of the coupling of the ecological and evolutionary dynamics depends on the spatial scale and is asymmetric, demographic dynamics having a greater immediate impact on genetic dynamics than vice versa. PMID:19414467
Evolutionary dynamics of human autoimmune disease genes and malfunctioned immunological genes
Directory of Open Access Journals (Sweden)
Podder Soumita
2012-01-01
Full Text Available Abstract Background One of the main issues of molecular evolution is to divulge the principles in dictating the evolutionary rate differences among various gene classes. Immunological genes have received considerable attention in evolutionary biology as candidates for local adaptation and for studying functionally important polymorphisms. The normal structure and function of immunological genes will be distorted when they experience mutations leading to immunological dysfunctions. Results Here, we examined the fundamental differences between the genes which on mutation give rise to autoimmune or other immune system related diseases and the immunological genes that do not cause any disease phenotypes. Although the disease genes examined are analogous to non-disease genes in product, expression, function, and pathway affiliation, a statistically significant decrease in evolutionary rate has been found in autoimmune disease genes relative to all other immune related diseases and non-disease genes. Possible ways of accumulation of mutation in the three steps of the central dogma (DNA-mRNA-Protein have been studied to trace the mutational effects predisposed to disease consequence and acquiring higher selection pressure. Principal Component Analysis and Multivariate Regression Analysis have established the predominant role of single nucleotide polymorphisms in guiding the evolutionary rate of immunological disease and non-disease genes followed by m-RNA abundance, paralogs number, fraction of phosphorylation residue, alternatively spliced exon, protein residue burial and protein disorder. Conclusions Our study provides an empirical insight into the etiology of autoimmune disease genes and other immunological diseases. The immediate utility of our study is to help in disease gene identification and may also help in medicinal improvement of immune related disease.
Directory of Open Access Journals (Sweden)
Jiaqin Shi
Full Text Available Despite their ubiquity and functional importance, microsatellites have been largely ignored in comparative genomics, mostly due to the lack of genomic information. In the current study, microsatellite distribution was characterized and compared in the whole genomes and both the coding and non-coding DNA sequences of the sequenced Brassica, Arabidopsis and other angiosperm species to investigate their evolutionary dynamics in plants. The variation in the microsatellite frequencies of these angiosperm species was much smaller than those for their microsatellite numbers and genome sizes, suggesting that microsatellite frequency may be relatively stable in plants. The microsatellite frequencies of these angiosperm species were significantly negatively correlated with both their genome sizes and transposable elements contents. The pattern of microsatellite distribution may differ according to the different genomic regions (such as coding and non-coding sequences. The observed differences in many important microsatellite characteristics (especially the distribution with respect to motif length, type and repeat number of these angiosperm species were generally accordant with their phylogenetic distance, which suggested that the evolutionary dynamics of microsatellite distribution may be generally consistent with plant divergence/evolution. Importantly, by comparing these microsatellite characteristics (especially the distribution with respect to motif type the angiosperm species (aside from a few species all clustered into two obviously different groups that were largely represented by monocots and dicots, suggesting a complex and generally dichotomous evolutionary pattern of microsatellite distribution in angiosperms. Polyploidy may lead to a slight increase in microsatellite frequency in the coding sequences and a significant decrease in microsatellite frequency in the whole genome/non-coding sequences, but have little effect on the microsatellite
Costa, Gideão Wagner Werneck Félix da; Cioffi, Marcelo de Bello; Bertollo, Luiz Antonio Carlos; Molina, Wagner Franco
2016-03-01
Lutjanidae is a family of primarily marine and carnivorous fishes distributed in the Atlantic, Indian, and Pacific oceans, with enormous economic and ecological importance. In order to better clarify the conservative chromosomal evolution of Lutjanidae, we analyzed the evolutionary dynamics of 5 repetitive DNA classes in 5 Lutjanus and in 1 Ocyurus species from the Western Atlantic. The ribosomal 18S sites were generally located in a single chromosome pair, except for L. jocu and L. alexandrei where they are found in 2 pairs. In turn, the 5S rDNA sites are unique, terminal and nonsyntenic with the 18S rDNA sites. In 3 species analyzed, H3 hisDNA genes were found in 1 chromosomal pair. However, while L. jocu presented 2 H3 sites, O. chrysurus showed a noteworthy dispersion of this gene in almost all chromosomes of the karyotype. Retrotransposons Rex1 and Rex3 do not exhibit any association with the explosive distribution of H3 sequences in O. chrysurus. The low compartmentalization of Rex elements, in addition to the general nondynamic distribution of ribosomal and H3 genes, corroborate the karyotype conservatism in Lutjanidae species, also at the microstructural level. However, some "disturbing evolutionary waves" can break down this conservative scenario, as evidenced by the massive random dispersion of H3 hisDNA in the genome of O. chrysurus. The implication of the genomic expansion of H3 histone genes and their functionality remain unknown, although suggesting that they have higher evolutionary dynamics than previously thought. PMID:26792596
Diversity, abundance, and evolutionary dynamics of Pong-like transposable elements in Triticeae.
Markova, Dragomira N; Mason-Gamer, Roberta J
2015-12-01
Pong-like elements are members of the PIF/Harbinger superfamily of DNA transposons that has been described in many plants, animals, and fungi. Most Pong elements contain two open reading frames (ORFs). One encodes a transposase (ORF2) that catalyzes transposition of Pong and related non-autonomous elements, while the function of the second is unknown. Little is known about the evolutionary history of Pong elements in flowering plants. In this work, we present the first comprehensive analysis of the diversity, abundance, and evolution of the Pong-like transposase gene in the genomes of 21 diploid species from the wheat tribe, Triticeae, and we present the first convincing evidence of horizontal transfer of nuclear-encoded Pong elements in any organism. A phylogenetic analysis of nearly 300 Pong sequences based on a conserved region of the transposase domain revealed a complex evolutionary history of Pong elements that can be best explained by ancestral polymorphism, followed by differential evolutionary success of some transposase lineages, and by occasional horizontal transfer between phylogenetically distant genera. In addition, we used transposon display to estimate the abundance of the transposase gene within Triticeae genomes, and our results revealed varying levels of Pong proliferation, with numbers of transposase copies ranging from 22 to 92. Comparisons of Pong transposase abundance to flow cytometry estimates of genome size revealed that larger Triticeae genome size was not correlated with transposase abundance. PMID:26206730
Dynamic model for calculating heating patterns during microwave sintering
International Nuclear Information System (INIS)
In this paper the authors describe a thermal model that calculates the temperature distribution in ceramic samples and insulation under realistic sintering conditions. The calculation process involves a two-step procedure. The first step is to calculate the microwave power deposition in the sample and surrounding insulation. 3D FDTD calculations described in a companion paper are used for this purpose. The other step involves calculation of the temperature distribution using a 3D finite-difference heat-transfer program developed in our department. Results illustrating the effect of thickness of insulation and the placement of SiC rods in picket-fence arrangement are presented
DEFF Research Database (Denmark)
Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea; Schiøtt, Birgit; Nielsen, Niels Christian; Vosegaard, Thomas
2014-01-01
We present a method to calculate 31P solid-state NMR spectra based on the dynamic input from extended molecular dynamics (MD) simulations. The dynamic information confered by MD simulations is much more comprehensive than the information provided by traditional NMR dynamics models based on, for...... example, order parameters. Therefore, valuable insight into the dynamics of biomolecules may be achieved by the present method. We have applied this method to study the dynamics of lipid bilayers containing the antimicrobial peptide alamethicin, and we show that the calculated 31P spectra obtained with...
A comparison of techniques for calculating protein essential dynamics
van Aalten, D.M.F.; de Groot, B.L.; Findlay, J.B.C.; Berendsen, H.J.C.; Amadei, A
1997-01-01
Recently the basic theory of essential dynamics, a method for extracting large concerted motions from protein molecular dynamics trajectories, was described. Here, we introduce and test new aspects. A method for diagonalizing large covariance matrices is presented. We show that it is possible to per
Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein–Protein Interactions
Bartlett, Madelaine; Thompson, Beth; Brabazon, Holly; Del Gizzi, Robert; Zhang, Thompson; Whipple, Clinton
2016-01-01
Protein–protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PIL) and AP3-like (AP3L) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PIL protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PIL homodimerization is an anomaly or indicative of broader trends, we characterized PIL dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PIL homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PIL homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PIL protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PIL dimerization activity. Furthermore, ectopic expression of a Joinvillea PIL homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner. PMID:26908583
Evolutionary Dynamics of Floral Homeotic Transcription Factor Protein-Protein Interactions.
Bartlett, Madelaine; Thompson, Beth; Brabazon, Holly; Del Gizzi, Robert; Zhang, Thompson; Whipple, Clinton
2016-06-01
Protein-protein interactions (PPIs) have widely acknowledged roles in the regulation of development, but few studies have addressed the timing and mechanism of shifting PPIs over evolutionary history. The B-class MADS-box transcription factors, PISTILLATA (PI) and APETALA3 (AP3) are key regulators of floral development. PI-like (PI(L)) and AP3-like (AP3(L)) proteins from a number of plants, including Arabidopsis thaliana (Arabidopsis) and the grass Zea mays (maize), bind DNA as obligate heterodimers. However, a PI(L) protein from the grass relative Joinvillea can bind DNA as a homodimer. To ascertain whether Joinvillea PI(L) homodimerization is an anomaly or indicative of broader trends, we characterized PI(L) dimerization across the Poales and uncovered unexpected evolutionary lability. Both obligate B-class heterodimerization and PI(L) homodimerization have evolved multiple times in the order, by distinct molecular mechanisms. For example, obligate B-class heterodimerization in maize evolved very recently from PI(L) homodimerization. A single amino acid change, fixed during domestication, is sufficient to toggle one maize PI(L) protein between homodimerization and obligate heterodimerization. We detected a signature of positive selection acting on residues preferentially clustered in predicted sites of contact between MADS-box monomers and dimers, and in motifs that mediate MADS PPI specificity in Arabidopsis. Changing one positively selected residue can alter PI(L) dimerization activity. Furthermore, ectopic expression of a Joinvillea PI(L) homodimer in Arabidopsis can homeotically transform sepals into petals. Our results provide a window into the evolutionary remodeling of PPIs, and show that novel interactions have the potential to alter plant form in a context-dependent manner. PMID:26908583
Two sexes, one genome: the evolutionary dynamics of intralocus sexual conflict
Pennell, Tanya M.; Morrow, Edward H.
2013-01-01
As the evolutionary interests of males and females are frequently divergent, a trait value that is optimal for the fitness of one sex is often not optimal for the other. A shared genome also means that the same genes may underlie the same trait in both sexes. This can give rise to a form of sexual antagonism, known as intralocus sexual conflict (IASC). Here, a tug-of-war over allelic expression can occur, preventing the sexes from reaching optimal trait values, thereby causing sex-specific re...
Directory of Open Access Journals (Sweden)
Tassos Patokos
2014-01-01
Full Text Available The paper presents an evolutionary model, based on the assumption that agents may revise their current strategies if they previously failed to attain the maximum level of potential payoffs. We offer three versions of this reflexive mechanism, each one of which describes a distinct type: spontaneous agents, rigid players, and ‘satisficers’. We use simulations to examine the performance of these types. Agents who change their strategies relatively easily tend to perform better in coordination games, but antagonistic games generally lead to more favorable outcomes if the individuals only change their strategies when disappointment from previous rounds surpasses some predefined threshold.
Fabre, Frédéric; Montarry, Josselin; Coville, Jérôme; Senoussi, Rachid; Simon, Vincent; Moury, Benoît
2012-01-01
Uncovering how natural selection and genetic drift shape the evolutionary dynamics of virus populations within their hosts can pave the way to a better understanding of virus emergence. Mathematical models already play a leading role in these studies and are intended to predict future emergences. Here, using high-throughput sequencing, we analyzed the within-host population dynamics of four Potato virus Y (PVY) variants differing at most by two substitutions involved in pathogenicity properties. Model selection procedures were used to compare experimental results to six hypotheses regarding competitiveness and intensity of genetic drift experienced by viruses during host plant colonization. Results indicated that the frequencies of variants were well described using Lotka-Volterra models where the competition coefficients β(ij) exerted by variant j on variant i are equal to their fitness ratio, r(j)/r(i). Statistical inference allowed the estimation of the effect of each mutation on fitness, revealing slight (s = -0.45%) and high (s = -13.2%) fitness costs and a negative epistasis between them. Results also indicated that only 1 to 4 infectious units initiated the population of one apical leaf. The between-host variances of the variant frequencies were described using Dirichlet-multinomial distributions whose scale parameters, closely related to the fixation index F(ST), were shown to vary with time. The genetic differentiation of virus populations among plants increased from 0 to 10 days post-inoculation and then decreased until 35 days. Overall, this study showed that mathematical models can accurately describe both selection and genetic drift processes shaping the evolutionary dynamics of viruses within their hosts. PMID:22532800
Fe IX Calculations for the Solar Dynamics Observatory
Foster, Adam R
2011-01-01
New calculations of the energy levels, radiative transition rates and collisional excitation rates of \\ion{Fe}{ix} have been carried out using the Flexible Atomic Code, paying close attention to experimentally identified levels and extending existing calculations to higher energy levels. For lower levels, R-matrix collisional excitation rates from earlier work have been used. Significant emission is predicted by these calculations in the 5f-3d transitions, which will impact analysis of SDO AIA observations using the 94\\AA\\ filter.
Dynamic Calculation Method of Beam System Under Low Velocity Impact
Institute of Scientific and Technical Information of China (English)
LI Wen-pei; WANG De-rong; SONG Chun-ming; WANG Ming-yang
2008-01-01
The beating beams and the supporting beams under low velocity impact may be in four different strain stages of deformation depending on the impact intensity and beam structure strength. Based on the different judging conditions of deformation stages, the corresponding calculation models are proposed, the calculation formulae for the determination of the impact force and the beam's lateral displacement are obtained. Calculation shows that the beam's total deflection is small when the flexibility of the supporting component is high and the effect of diminishing deflection disappears almost when the stiffness of the supporting component is high.
Hapuarachchi, Hapuarachchige Chanditha; Koo, Carmen; Kek, Relus; Xu, Helen; Lai, Yee Ling; Liu, Lilac; Kok, Suet Yheng; Shi, Yuan; Chuen, Raphael Lee Tze; Lee, Kim-Sung; Maurer-Stroh, Sebastian; Ng, Lee Ching
2016-01-01
Dengue virus (DENV) is currently the most prevalent mosquito-borne viral pathogen. DENVs naturally exist as highly heterogeneous populations. Even though the descriptions on DENV diversity are plentiful, only a few studies have narrated the dynamics of intra-epidemic virus diversity at a fine scale. Such accounts are important to decipher the reciprocal relationship between viral evolutionary dynamics and disease transmission that shape dengue epidemiology. In the current study, we present a micro-scale genetic analysis of a monophyletic lineage of DENV-1 genotype III (epidemic lineage) detected from November 2012 to May 2014. The lineage was involved in an unprecedented dengue epidemic in Singapore during 2013-2014. Our findings showed that the epidemic lineage was an ensemble of mutants (variants) originated from an initial mixed viral population. The composition of mutant spectrum was dynamic and positively correlated with case load. The close interaction between viral evolution and transmission intensity indicated that tracking genetic diversity through time is potentially a useful tool to infer DENV transmission dynamics and thereby, to assess the epidemic risk in a disease control perspective. Moreover, such information is salient to understand the viral basis of clinical outcome and immune response variations that is imperative to effective vaccine design. PMID:26940650
Directory of Open Access Journals (Sweden)
Jing Chen
2013-01-01
Full Text Available Due to high efficiency and good scalability, hierarchical hybrid P2P architecture has drawn more and more attention in P2P streaming research and application fields recently. The problem about super peer selection, which is the key problem in hybrid heterogeneous P2P architecture, is becoming highly challenging because super peers must be selected from a huge and dynamically changing network. A distributed super peer selection (SPS algorithm for hybrid heterogeneous P2P streaming system based on evolutionary game is proposed in this paper. The super peer selection procedure is modeled based on evolutionary game framework firstly, and its evolutionarily stable strategies are analyzed. Then a distributed Q-learning algorithm (ESS-SPS according to the mixed strategies by analysis is proposed for the peers to converge to the ESSs based on its own payoff history. Compared to the traditional randomly super peer selection scheme, experiments results show that the proposed ESS-SPS algorithm achieves better performance in terms of social welfare and average upload rate of super peers and keeps the upload capacity of the P2P streaming system increasing steadily with the number of peers increasing.
Atienza, David; Baloukas, Christos; Papadopoulos, Lazaros; Poucet, Christophe; Mamagkakis, Stylianos; Hidalgo, Jose I.; Catthoor, Francky; Soudris, Dimitrios; Lanchares, Juan
2007-01-01
Embedded consumer devices are increasing their capabilities and can now implement new multimedia applications reserved only for powerful desktops a few years ago. These applications share complex and intensive dynamic memory use. Thus, dynamic memory optimizations are a requirement when porting these applications. Within these optimizations, the refinement of the Dynamically (de)allocated Data Type (or DDT) implementations is one of the most important and difficult parts for an efficient mapp...
Between Pleasure and Contentment: Evolutionary Dynamics of Some Possible Parameters of Happiness
Gao, Yue; Edelman, Shimon
2016-01-01
We offer and test a simple operationalization of hedonic and eudaimonic well-being (“happiness”) as mediating variables that link outcomes to motivation. In six evolutionary agent-based simulation experiments, we compared the relative performance of agents endowed with different combinations of happiness-related traits (parameter values), under four types of environmental conditions. We found (i) that the effects of attaching more weight to longer-term than to momentary happiness and of extending the memory for past happiness are both stronger in an environment where food is scarce; (ii) that in such an environment “relative consumption,” in which the agent’s well-being is negatively affected by that of its neighbors, is more detrimental to survival when food is scarce; and (iii) that having a positive outlook, under which agents’ longer-term happiness is increased by positive events more than it is decreased by negative ones, is generally advantageous. PMID:27144982
The evolutionary dynamics of a population model with a strong Allee effect.
Cushing, Jim M
2015-08-01
An evolutionary game theoretic model for a population subject to predation and a strong Allee threshold of extinction is analyzed using, among other methods, Poincaré-Bendixson theory. The model is a nonlinear, plane autonomous system whose state variables are population density and the mean of a phenotypic trait, which is subject to Darwinian evolution, that determines the population's inherent (low density) growth rate (fitness). A trade-off is assumed in that an increase in the inherent growth rate results in a proportional increase in the predator's attack rate. The main results are that orbits equilibrate (there are no cycles or cycle chains of saddles), that the extinction set (or Allee basin) shrinks when evolution occurs, and that the meant trait component of survival equilibria occur at maxima of the inherent growth rate (as a function of the trait). PMID:25974340
Between Pleasure and Contentment: Evolutionary Dynamics of Some Possible Parameters of Happiness.
Gao, Yue; Edelman, Shimon
2016-01-01
We offer and test a simple operationalization of hedonic and eudaimonic well-being ("happiness") as mediating variables that link outcomes to motivation. In six evolutionary agent-based simulation experiments, we compared the relative performance of agents endowed with different combinations of happiness-related traits (parameter values), under four types of environmental conditions. We found (i) that the effects of attaching more weight to longer-term than to momentary happiness and of extending the memory for past happiness are both stronger in an environment where food is scarce; (ii) that in such an environment "relative consumption," in which the agent's well-being is negatively affected by that of its neighbors, is more detrimental to survival when food is scarce; and (iii) that having a positive outlook, under which agents' longer-term happiness is increased by positive events more than it is decreased by negative ones, is generally advantageous. PMID:27144982
Dynamic instability of cooperation due to diverse activity patterns in evolutionary social dilemmas
Xia, Cheng-Yi; Perc, Matjaz; Moreno, Yamir
2015-01-01
Individuals might abstain from participating in an instance of an evolutionary game for various reasons, ranging from lack of interest to risk aversion. In order to understand the consequences of such diverse activity patterns on the evolution of cooperation, we study a weak prisoner's dilemma where each player's participation is probabilistic rather than certain. Players that do not participate get a null payoff and are unable to replicate. We show that inactivity introduces cascading failures of cooperation, which are particularly severe on scale-free networks with frequently inactive hubs. The drops in the fraction of cooperators are sudden, while the spatiotemporal reorganization of compact cooperative clusters, and thus the recovery, takes time. Nevertheless, if the activity of players is directly proportional to their degree, or if the interaction network is not strongly heterogeneous, the overall evolution of cooperation is not impaired. This is because inactivity negatively affects the potency of low-...
Dynamic simulation of flash drums using rigorous physical property calculations
Directory of Open Access Journals (Sweden)
F. M. Gonçalves
2007-06-01
Full Text Available The dynamics of flash drums is simulated using a formulation adequate for phase modeling with equations of state (EOS. The energy and mass balances are written as differential equations for the internal energy and the number of moles of each species. The algebraic equations of the model, solved at each time step, are those of a flash with specified internal energy, volume and mole numbers (UVN flash. A new aspect of our dynamic simulations is the use of direct iterations in phase volumes (instead of pressure for solving the algebraic equations. It was also found that an iterative procedure previously suggested in the literature for UVN flashes becomes unreliable close to phase boundaries and a new alternative is proposed. Another unusual aspect of this work is that the model expressions, including the physical properties and their analytical derivatives, were quickly implemented using computer algebra.
A dynamical collective calculation of supernova neutrino signals
Gava, J.; Kneller, J.; Volpe, C.; McLaughlin, G.C.
2009-01-01
We present the first calculations with three flavors of collective and shock wave effects for neutrino propagation in core-collapse supernovae using hydroynamical density profiles and the S matrix formalism. We explore the interplay between the neutrino-neutrino interaction and the effects of multiple resonances upon the time signal of positrons in supernova observatories. A specific signature is found for the inverted hierarchy and a large third neutrino mixing angle and we predict, in this ...
Development of a dynamic calculation tool forsimulation of ditching
Pilorget, Marc
2011-01-01
The present document is the final master thesis report written by Marc PILORGET,student at SUPAERO (home institution) and KTH (Royal Institute of Technology,Exchange University). This six months internship was done at DASSAULT AVIATION(Airframe engineering department) based in Saint-Cloud, France. It spanned from the 5thof July to the 23rd of December. The thesis work aims at developing an SPH (SmoothParticle Hydrodynamics) calculation method for ditching and implementing it in the finiteelem...
Hydraulic calculation and dynamic analysis of columnar reversing gate
Directory of Open Access Journals (Sweden)
You-an HU
2011-09-01
Full Text Available According to the hydraulic calculation principles of the orifice outflow, the discharge capacity of the columnar reversing gate under the partial opening condition was calculated and checked. Using ANSYS, a large finite element analysis software, the discharge process was simulated. The distribution rule of the velocities in the gate chamber and downstream channel was obtained. An FEM model of the columnar reversing gate was built, and the natural vibration properties of the gate were analyzed. Based on the Westergaard added mass method, the added mass caused by the fluid-structure coupling motion was taken into account, and the effects of the coupling interaction were discussed. The results show that the size of the small gates meets the demand for discharge capacity, the current in the gate chamber is quite turbulent, the trunnion and arms are obviously impacted by flow, and the effects of water on vibration characteristics are remarkable. The study provides a reference for the design and calculation of gates of the same type.
International Nuclear Information System (INIS)
In the present paper we report a theoretical study on mechanistic photodissociation of acetaldehyde (CH3CHO). Stationary structures for H2 and CO eliminations in the ground state (S0) have been optimized with density functional theory method, which is followed by the intrinsic reaction coordinate and ab initio molecular dynamics calculations to confirm the elimination mechanism. Equilibrium geometries, transition states, and intersection structures for the C-C and C-H dissociations in excited states were determined by the complete-active-space self-consistent field (CASSCF) method. Based on the CASSCF optimized structures, the potential energy profiles for the dissociations were refined by performing the single-point calculations using the multireference configuration interaction method. Upon the low-energy irradiation of CH3CHO (265 nm1 C-C bond fission following intersystem crossing from the S1 state is the predominant channel and the minor channel, the ground-state elimination to CH4+CO after internal conversion (IC) from S1 to S0, could not be excluded. With the photon energy increasing, another pathway of IC, achieved via an S1/S0 intersection point resulting from the S1 C-C bond fission, becomes accessible and increases the yield of CH4+CO.
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs.
Mai, Guoqin; Ge, Ruiquan; Sun, Guoquan; Meng, Qinghan; Zhou, Fengfeng
2016-01-01
Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas) gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history. PMID:27195295
A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs
Directory of Open Access Journals (Sweden)
Guoqin Mai
2016-01-01
Full Text Available Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.
Evolutionary history of chordate PAX genes: dynamics of change in a complex gene family.
Directory of Open Access Journals (Sweden)
Vanessa Rodrigues Paixão-Côrtes
Full Text Available Paired box (PAX genes are transcription factors that play important roles in embryonic development. Although the PAX gene family occurs in animals only, it is widely distributed. Among the vertebrates, its 9 genes appear to be the product of complete duplication of an original set of 4 genes, followed by an additional partial duplication. Although some studies of PAX genes have been conducted, no comprehensive survey of these genes across the entire taxonomic unit has yet been attempted. In this study, we conducted a detailed comparison of PAX sequences from 188 chordates, which revealed restricted variation. The absence of PAX4 and PAX8 among some species of reptiles and birds was notable; however, all 9 genes were present in all 74 mammalian genomes investigated. A search for signatures of selection indicated that all genes are subject to purifying selection, with a possible constraint relaxation in PAX4, PAX7, and PAX8. This result indicates asymmetric evolution of PAX family genes, which can be associated with the emergence of adaptive novelties in the chordate evolutionary trajectory.
Calculated dynamical scattering in a fibrous protein structure
International Nuclear Information System (INIS)
The effects of dynamical electron scattering on the amplitudes and phases diffracted by the microcrystals of an alpha-helical coiled-coil protein have been investigated by computer simulation using a model structure derived from relatively low resolution data recorded at liquid nitrogen temperature. The projected potential of this model show only small departure from the weak-phase-object approximation predictions, with amplitudes increasing almost linearly with thickness and phases nearly constant up to thickness of 200 Angstroems. 4 refs., 3 figs
Non-linear calculation of PCRV using dynamic relaxation
International Nuclear Information System (INIS)
A brief review is presented of a numerical method called the dynamic relaxation method for stress analysis of the concrete in prestressed concrete pressure vessels. By this method the three-dimensional elliptic differential equations of the continuum are changed into the four-dimensional hyperbolic differential equations known as wave equations. The boundary value problem of the static system is changed into an initial and boundary value problem for which a solution exists if the physical system is defined at time t=0. The effect of non-linear stress-strain behaviour of the material as well as creep and cracking are considered
Parallel beam dynamics calculations on high performance computers
International Nuclear Information System (INIS)
Faced with a backlog of nuclear waste and weapons plutonium, as well as an ever-increasing public concern about safety and environmental issues associated with conventional nuclear reactors, many countries are studying new, accelerator-driven technologies that hold the promise of providing safe and effective solutions to these problems. Proposed projects include accelerator transmutation of waste (ATW), accelerator-based conversion of plutonium (ABC), accelerator-driven energy production (ADEP), and accelerator production of tritium (APT). Also, next-generation spallation neutron sources based on similar technology will play a major role in materials science and biological science research. The design of accelerators for these projects will require a major advance in numerical modeling capability. For example, beam dynamics simulations with approximately 100 million particles will be needed to ensure that extremely stringent beam loss requirements (less than a nanoampere per meter) can be met. Compared with typical present-day modeling using 10,000-100,000 particles, this represents an increase of 3-4 orders of magnitude. High performance computing (HPC) platforms make it possible to perform such large scale simulations, which require 10's of GBytes of memory. They also make it possible to perform smaller simulations in a matter of hours that would require months to run on a single processor workstation. This paper will describe how HPC platforms can be used to perform the numerically intensive beam dynamics simulations required for development of these new accelerator-driven technologies
Sumathy, K; Ella, Krishna M
2012-03-01
The genetic diversity of Chikungunya virus (CHIKV) causing recurring outbreaks in India since 2006 was studied. The 2006 epidemic was caused by a virus strain of the East, Central and South African (ECSA) genotype with 226A in the E1 glycoprotein. The variant strain with E1-A226V mutation caused outbreaks since 2007 in the state of Kerala where Aedes albopictus is the abundant mosquito vector. Molecular epidemiology data since 2007 is scarce from other regions of the country. RT-PCR, sequencing and phylogenetic analyses of CHIKV isolates from the 2009 to 2010 epidemics in the States of Tamil Nadu and Andhra Pradesh placed them in a separate clade within the ECSA lineage. The isolates of the study had 226A in the E1 glycoprotein. The isolates had a novel E1-K211E mutation that was under significant positive selection. E1-211E is highly conserved in the Asian genotype of the virus circulated by Aedes aegypti. Unique mutations in E2 glycoprotein were identified. The two sub-lineages of ECSA genotype circulating in India parallel the abundance of Ae. albopictus and Ae. aegypti. Novel mutations in the envelope glycoproteins suggest adaptive evolution of the virus to local vector abundance. Cross neutralization of the virus isolates from recurring Indian epidemics indicated that no distinct serotypes had evolved. The study has provided insights into the origin, distribution and evolutionary adaptation of the virus to local vector abundance in the region that has reportedly, the highest incidence of CHIKV infection in the world. PMID:22246833
Toward a Mechanics of Adaptive Behavior: Evolutionary Dynamics and Matching Theory Statics
McDowell, J. J.; Popa, Andrei
2010-01-01
One theory of behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of reinforcement. This computational theory implements Darwinian principles of selection, reproduction, and mutation, which operate on a population of potential behaviors by means of a genetic algorithm.…
Ordway, Stephen; King, Dawn; Bahar, Sonya
Reaction-diffusion processes, such as branching-coalescing random walks, can be used to describe the underlying dynamics of nonequilibrium phase transitions. In an agent-based, neutral model of evolutionary dynamics, we have previously shown that our system undergoes a continuous, nonequilibrium phase transition, from extinction to survival, as various system parameters were tuned. This model was shown to belong to the directed percolation (DP) universality class, by measuring the critical exponents corresponding to correlation length ξ⊥, correlation time ξ| |, and particle density β. The fourth critical exponent that defines the DP universality class is β', which measures the survival probability of growth from a single seed organism. Since DP universality is theorized to have time-reversal symmetry, it is assumed that β = β '. In order to confirm the existence of time-reversal symmetry in our model, we evaluate the system growth from a single asexually reproducing organism. Importantly, the critical exponent β' could be useful for comparison to experimental studies of phase transitions in biological systems, since observing growth of microbial populations is significantly easier than observing death. This research was supported by funding from the James S. McDonnell Foundation.
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
Directory of Open Access Journals (Sweden)
Ana Zafra Ruano
2016-05-01
Full Text Available Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis.
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors.
Zafra Ruano, Ana; Cilia, Elisa; Couceiro, José R; Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic; Luque, Irene; Lenaerts, Tom
2016-05-01
Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis. PMID:27213566
From Binding-Induced Dynamic Effects in SH3 Structures to Evolutionary Conserved Sectors
Ruiz Sanz, Javier; Schymkowitz, Joost; Rousseau, Frederic
2016-01-01
Src Homology 3 domains are ubiquitous small interaction modules known to act as docking sites and regulatory elements in a wide range of proteins. Prior experimental NMR work on the SH3 domain of Src showed that ligand binding induces long-range dynamic changes consistent with an induced fit mechanism. The identification of the residues that participate in this mechanism produces a chart that allows for the exploration of the regulatory role of such domains in the activity of the encompassing protein. Here we show that a computational approach focusing on the changes in side chain dynamics through ligand binding identifies equivalent long-range effects in the Src SH3 domain. Mutation of a subset of the predicted residues elicits long-range effects on the binding energetics, emphasizing the relevance of these positions in the definition of intramolecular cooperative networks of signal transduction in this domain. We find further support for this mechanism through the analysis of seven other publically available SH3 domain structures of which the sequences represent diverse SH3 classes. By comparing the eight predictions, we find that, in addition to a dynamic pathway that is relatively conserved throughout all SH3 domains, there are dynamic aspects specific to each domain and homologous subgroups. Our work shows for the first time from a structural perspective, which transduction mechanisms are common between a subset of closely related and distal SH3 domains, while at the same time highlighting the differences in signal transduction that make each family member unique. These results resolve the missing link between structural predictions of dynamic changes and the domain sectors recently identified for SH3 domains through sequence analysis. PMID:27213566
Phase diagram of kaolinite from Molecular Dynamics calculations
International Nuclear Information System (INIS)
Structural and thermal behaviors of uncharged 1:1 phyllosilicates kaolinite were investigated from molecular dynamics simulations based on the CLAYFF force field. The focus is on the variation of structural properties including bulk modulus with pressure from 0 to 20 GPa under various range of temperature. The largest bulk modulus between the pressures of 200 and 800 MPa varies from 80 GPa at 298 K to 50 GPa at 1473 K. The obtained value of Cp varies between 7.8 and 13.6 Kcal mol-1 K-1 in the pressure range of 0.1 MPa-20 GPa. Besides, a huge difference was noticed regarding the computed properties at the superheating point. Finally, we show the relationship between superheating point temperature and pressure leading to a phase diagram of kaolinite.
Parallel beam dynamics calculations on high performance computers
International Nuclear Information System (INIS)
Faced with a backlog of nuclear waste and weapons plutonium, as well as an ever-increasing public concern about safety and environmental issues associated with conventional nuclear reactors, many countries are studying new, accelerator-driven technologies that hold the promise of providing safe and effective solutions to these problems. Proposed projects include accelerator transmutation of waste (ATW), accelerator-based conversion of plutonium (ABC), accelerator-driven energy production (ADEP), and accelerator production of tritium (APT). Also, next-generation spallation neutron sources based on similar technology will play a major role in materials science and biological science research. The design of accelerators for these projects will require a major advance in numerical modeling capability. For example, beam dynamics simulations with approximately 100 million particles will be needed to ensure that extremely stringent beam loss requirements (less than a nanoampere per meter) can be met. Compared with typical present-day modeling using 10,000 endash 100,000 particles, this represents an increase of 3 endash 4 orders of magnitude. High performance computing (HPC) platforms make it possible to perform such large scale simulations, which require 10 close-quote s of GBytes of memory. They also make it possible to perform smaller simulations in a matter of hours that would require months to run on a single processor workstation. This paper will describe how HPC platforms can be used to perform the numerically intensive beam dynamics simulations required for development of these new accelerator-driven technologies. copyright 1997 American Institute of Physics
Body drop into a fluid tank and dynamic loads calculation
Directory of Open Access Journals (Sweden)
Komarov Aleksandr Andreevich
2014-05-01
Full Text Available The theory of a body striking a fluid began intensively developing due to the tasks of hydroplanes landing. For the recent years the study of a stroke and submersion of bodies into fluid became even more current. We face them in the process of strength calculation of ship hulls and other structures in modern technology. These tasks solution represents great mathematical difficulty even in case of the mentioned simplifications. These difficulties emerge due to the unsteady character of fluid motion in case of body submersion, and also jet and spray phenomena, which lead to discontinuous motions. On the basis of G.V. Logvinovich’s concept the problem of loads determination with consideration for air gap is solved for both a body and reservoir enclosing structures when a body falls into a fluid. Numerical method is based on the decay of an arbitrary discontinuity.
Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm
Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew
2000-01-01
One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous
Sorokin, Valery A.; Gelfand, Mikhail S.; Artamonova, Irena I.
2010-01-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic ...
Lande, Russell; Engen, Steinar; Sæther, Bernt-Erik
2009-01-01
The evolution of population dynamics in a stochastic environment is analysed under a general form of density-dependence with genetic variation in r and K, the intrinsic rate of increase and carrying capacity in the average environment, and in σe2, the environmental variance of population growth rate. The continuous-time model assumes a large population size and a stationary distribution of environments with no autocorrelation. For a given population density, N, and genotype frequency, p, the ...
Sexual selection and the evolutionary dynamics of the major histocompatibility complex
Jan Ejsmond, Maciej; Radwan, Jacek; Wilson, Anthony B
2014-01-01
The genes of the major histocompatibility complex (MHC) are a key component of the adaptive immune system and among the most variable loci in the vertebrate genome. Pathogen-mediated natural selection and MHC-based disassortative mating are both thought to structure MHC polymorphism, but their effects have proven difficult to discriminate in natural systems. Using the first model of MHC dynamics incorporating both survival and reproduction, we demonstrate that natural and sexual selection pro...
Co-Evolutionary Mechanisms of Emotional Bursts in Online Social Dynamics and Networks
Directory of Open Access Journals (Sweden)
Bosiljka Tadić
2013-11-01
Full Text Available Collective emotional behavior of users is frequently observed on various Web portals; however, its complexity and the role of emotions in the acting mechanisms are still not thoroughly understood. In this work, using the empirical data and agent-based modeling, a parallel analysis is performed of two archetypal systems—Blogs and Internet-Relayed-Chats—both of which maintain self-organized dynamics but not the same communication rules and time scales. The emphasis is on quantifying the collective emotions by means of fractal analysis of the underlying processes as well as topology of social networks, which arise and co-evolve in these stochastic processes. The results reveal that two distinct mechanisms, which are based on different use of emotions (an emotion is characterized by two components, arousal and valence, are intrinsically associated with two classes of emergent social graphs. Their hallmarks are the evolution of communities in accordance with the excess of the negative emotions on popular Blogs, on one side, and smooth spreading of the Bot’s emotional impact over the entire hierarchical network of chats, on the other. Another emphasis of this work is on the understanding of nonextensivity of the emotion dynamics; it was found that, in its own way, each mechanism leads to a reduced phase space of the emotion components when the collective dynamics takes place. That a non-additive entropy describes emotion dynamics, is further confirmed by computing the q-generalized Kolmogorov-Sinai entropy rate in the empirical data of chats as well as in the simulations of interacting emotional agents and Bots.
Ab initio molecular dynamics calculations of ion hydration free energies
International Nuclear Information System (INIS)
We apply ab initio molecular dynamics (AIMD) methods in conjunction with the thermodynamic integration or 'λ-path' technique to compute the intrinsic hydration free energies of Li+, Cl-, and Ag+ ions. Using the Perdew-Burke-Ernzerhof functional, adapting methods developed for classical force field applications, and with consistent assumptions about surface potential (φ) contributions, we obtain absolute AIMD hydration free energies (ΔGhyd) within a few kcal/mol, or better than 4%, of Tissandier et al.'s [J. Phys. Chem. A 102, 7787 (1998)] experimental values augmented with the SPC/E water model φ predictions. The sums of Li+/Cl- and Ag+/Cl- AIMD ΔGhyd, which are not affected by surface potentials, are within 2.6% and 1.2 % of experimental values, respectively. We also report the free energy changes associated with the transition metal ion redox reaction Ag++Ni+→Ag+Ni2+ in water. The predictions for this reaction suggest that existing estimates of ΔGhyd for unstable radiolysis intermediates such as Ni+ may need to be extensively revised.
Pion dose distribution calculations and measurements for dynamic radiotherapy
International Nuclear Information System (INIS)
Routine three dimensional conformation therapy with negative pions is done with the PIOTRON at SIN since two years. More than 60 patients have been treated by spot scan with the 60 converging beams for deep seated tumors in the pelvic region. Extensive measurements have been performed on various phantoms, homogeneous and anthropomorphic, to investigate the influence of tissue inhomogeneities and verify treatment planning calculations. Total dose has been measured by T.E. ionization chambers and TLD, two dimensional stop distributions exposed in planes between phantom slices. In vivo measurements with ionization chambers, as well as catheters filled with /sup 7/LiF TLD's and rolled Al foils, introduced in bladder or rectum, have been used to confirm dose distributions in patients. To check predictions of differences of RBE due to variations in treatment volumes or beam configuration, treatment plans, reflecting typical situation in therapy, have been created for radiobiological investigations. Various user groups have measured biological effects by cell survival experiments with mammalian cells or with mouse intestinal crypt cell assay
Evolutionary dynamics in the Bak-Sneppen model on small-world networks
Kulkarni, R. V.; Almaas, E.; Stroud, D.
1999-01-01
We study the dynamics of the Bak-Sneppen model on small-world networks. For each site in the network, we define a ``connectance,'' which measures the distance to all other sites. We find radically different patterns of activity for different sites, depending on their connectance and also on the topology of the network. For a given network, the site with the minimal connectance shows long periods of stasis interrupted by much smaller periods of activity. In contrast, the activity pattern for t...
Evolutionary dynamics of immune-related genes and pathways in disease-vector mosquitoes.
Waterhouse, Robert M; Kriventseva, Evgenia V; Meister, Stephan; Xi, Zhiyong; Alvarez, Kanwal S; Bartholomay, Lyric C; Barillas-Mury, Carolina; Bian, Guowu; Blandin, Stephanie; Christensen, Bruce M; Dong, Yuemei; Jiang, Haobo; Kanost, Michael R; Koutsos, Anastasios C; Levashina, Elena A; Li, Jianyong; Ligoxygakis, Petros; Maccallum, Robert M; Mayhew, George F; Mendes, Antonio; Michel, Kristin; Osta, Mike A; Paskewitz, Susan; Shin, Sang Woon; Vlachou, Dina; Wang, Lihui; Wei, Weiqi; Zheng, Liangbiao; Zou, Zhen; Severson, David W; Raikhel, Alexander S; Kafatos, Fotis C; Dimopoulos, George; Zdobnov, Evgeny M; Christophides, George K
2007-06-22
Mosquitoes are vectors of parasitic and viral diseases of immense importance for public health. The acquisition of the genome sequence of the yellow fever and Dengue vector, Aedes aegypti (Aa), has enabled a comparative phylogenomic analysis of the insect immune repertoire: in Aa, the malaria vector Anopheles gambiae (Ag), and the fruit fly Drosophila melanogaster (Dm). Analysis of immune signaling pathways and response modules reveals both conservative and rapidly evolving features associated with different functional gene categories and particular aspects of immune reactions. These dynamics reflect in part continuous readjustment between accommodation and rejection of pathogens and suggest how innate immunity may have evolved. PMID:17588928
Evolutionary Dynamics of Immune-Related Genes and Pathways in Disease-Vector Mosquitoes
Waterhouse, Robert M.; Kriventseva, Evgenia V.; Meister, Stephan; Xi, Zhiyong; Alvarez, Kanwal S.; Bartholomay, Lyric C.; Barillas-Mury, Carolina; Bian, Guowu; Blandin, Stephanie; Christensen, Bruce M.; Dong, Yuemei; Jiang, Haobo; Kanost, Michael R.; Koutsos, Anastasios C.; Levashina, Elena A.; Li, Jianyong; Ligoxygakis, Petros; MacCallum, Robert M.; Mayhew, George F.; Mendes, Antonio; Michel, Kristin; Osta, Mike A.; Paskewitz, Susan; Shin, Sang Woon; Vlachou, Dina; Wang, Lihui; Wei, Weiqi; Zheng, Liangbiao; Zou, Zhen; Severson, David W.; Raikhel, Alexander S.; Kafatos, Fotis C.; Dimopoulos, George; Zdobnov, Evgeny M.; Christophides, George K.
2007-01-01
Mosquitoes are vectors of parasitic and viral diseases of immense importance for public health. The acquisition of the genome sequence of the yellow fever and Dengue vector, Aedes aegypti (Aa), has enabled a comparative phylogenomic analysis of the insect immune repertoire: in Aa, the malaria vector Anopheles gambiae (Ag), and the fruit fly Drosophila melanogaster (Dm). Analysis of immune signaling pathways and response modules reveals both conservative and rapidly evolving features associated with different functional gene categories and particular aspects of immune reactions. These dynamics reflect in part continuous readjustment between accommodation and rejection of pathogens and suggest how innate immunity may have evolved. PMID:17588928
Jaffe, Klaus
2016-01-01
W.D. Hamilton's Inclusive Fitness Theory explains the conditions that favor the emergence and maintenance of social cooperation. Today we know that these include direct and indirect benefits an agent obtains by its actions, and through interactions with kin and with genetically unrelated individuals. That is, in addition to kin-selection, assortation or homophily, and social synergies drive the evolution of cooperation. An Extended Inclusive Fitness Theory (EIFT) synthesizes the natural selection forces acting on biological evolution and on human economic interactions by assuming that natural selection driven by inclusive fitness produces agents with utility functions that exploit assortation and synergistic opportunities. This formulation allows to estimate sustainable cost/benefit threshold ratios of cooperation among organisms and/or economic agents, using existent analytical tools, illuminating our understanding of the dynamic nature of society, the evolution of cooperation among kin and non-kin, inter-specific cooperation, co-evolution, symbioses, division of labor and social synergies. EIFT helps to promote an interdisciplinary cross fertilization of the understanding of synergy by, for example, allowing to describe the role for division of labor in the emergence of social synergies, providing an integrated framework for the study of both, biological evolution of social behavior and economic market dynamics. Another example is a bio-economic understanding of the motivations of terrorists, which identifies different forms of terrorism. PMID:27468393
A recursive genetic framework for evolutionary decision-making in problems with high dynamism
Pashaei, Kaveh; Taghiyareh, Fattaneh; Badie, Kambiz
2015-11-01
Communication and coordination are the main cores for reaching a constructive agreement among multi-agent systems (MASs). Dividing the overall performance of MAS to individual agents may lead to group learning as opposed to individual learning, which is one of the weak points of MASs. This paper proposes a recursive genetic framework for solving problems with high dynamism. In this framework, a combination of genetic algorithm and multi-agent capabilities is utilised to accelerate team learning and accurate credit assignment. The argumentation feature is used to accomplish agent learning and the negotiation features of MASs are used to achieve a credit assignment. The proposed framework is quite general and its recursive hierarchical structure could be extended. We have dedicated one special controlling module for increasing convergence time. Due to the complexity of blackjack, we have applied it as a possible test bed to evaluate the system's performance. The learning rate of agents is measured as well as their credit assignment. The analysis of the obtained results led us to believe that our robust framework with the proposed negotiation operator is a promising methodology to solve similar problems in other areas with high dynamism.
The population and evolutionary dynamics of phage and bacteria with CRISPR-mediated immunity.
Directory of Open Access Journals (Sweden)
Bruce R Levin
Full Text Available Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR, together with associated genes (cas, form the CRISPR-cas adaptive immune system, which can provide resistance to viruses and plasmids in bacteria and archaea. Here, we use mathematical models, population dynamic experiments, and DNA sequence analyses to investigate the host-phage interactions in a model CRISPR-cas system, Streptococcus thermophilus DGCC7710 and its virulent phage 2972. At the molecular level, the bacteriophage-immune mutant bacteria (BIMs and CRISPR-escape mutant phage (CEMs obtained in this study are consistent with those anticipated from an iterative model of this adaptive immune system: resistance by the addition of novel spacers and phage evasion of resistance by mutation in matching sequences or flanking motifs. While CRISPR BIMs were readily isolated and CEMs generated at high rates (frequencies in excess of 10(-6, our population studies indicate that there is more to the dynamics of phage-host interactions and the establishment of a BIM-CEM arms race than predicted from existing assumptions about phage infection and CRISPR-cas immunity. Among the unanticipated observations are: (i the invasion of phage into populations of BIMs resistant by the acquisition of one (but not two spacers, (ii the survival of sensitive bacteria despite the presence of high densities of phage, and (iii the maintenance of phage-limited communities due to the failure of even two-spacer BIMs to become established in populations with wild-type bacteria and phage. We attribute (i to incomplete resistance of single-spacer BIMs. Based on the results of additional modeling and experiments, we postulate that (ii and (iii can be attributed to the phage infection-associated production of enzymes or other compounds that induce phenotypic phage resistance in sensitive bacteria and kill resistant BIMs. We present evidence in support of these hypotheses and discuss the implications of these
DEFF Research Database (Denmark)
Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew
experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated the...... free energy changes of the initial tetramer dissociation under different conditions and in the presence of thyroxine....
Jackson, Andrew P.
2014-05-05
Babesia spp. are tick-borne, intraerythrocytic hemoparasites that use antigenic variation to resist host immunity, through sequential modification of the parasite-derived variant erythrocyte surface antigen (VESA) expressed on the infected red blood cell surface. We identified the genomic processes driving antigenic diversity in genes encoding VESA (ves1) through comparative analysis within and between three Babesia species, (B. bigemina, B. divergens and B. bovis). Ves1 structure diverges rapidly after speciation, notably through the evolution of shortened forms (ves2) from 5? ends of canonical ves1 genes. Phylogenetic analyses show that ves1 genes are transposed between loci routinely, whereas ves2 genes are not. Similarly, analysis of sequence mosaicism shows that recombination drives variation in ves1 sequences, but less so for ves2, indicating the adoption of different mechanisms for variation of the two families. Proteomic analysis of the B. bigemina PR isolate shows that two dominant VESA1 proteins are expressed in the population, whereas numerous VESA2 proteins are co-expressed, consistent with differential transcriptional regulation of each family. Hence, VESA2 proteins are abundant and previously unrecognized elements of Babesia biology, with evolutionary dynamics consistently different to those of VESA1, suggesting that their functions are distinct. 2014 The Author(s) 2014.
Radzvilavicius, Arunas L
2016-09-01
Sexual reproduction is a trait shared by all complex life, but the complete account of its origin is missing. Virtually all theoretical work on the evolution of sex has been centered around the benefits of reciprocal recombination among nuclear genes, paying little attention to the evolutionary dynamics of multi-copy mitochondrial genomes. Here I develop a mathematical model to study the evolution of nuclear alleles inducing cell fusion in an ancestral population of clonal proto-eukaryotes. Segregational drift maintains high mitochondrial variance between clonally reproducing hosts, but the effect of segregation is opposed by cytoplasmic mixing which tends to reduce variation between cells in favor of higher heterogeneity within the cell. Despite the reduced long-term population fitness, alleles responsible for sexual cell fusion can spread to fixation. The evolution of sex requires negative epistatic interactions between mitochondrial mutations under strong purifying selection, low mutation load and weak mitochondrial-nuclear associations. I argue that similar conditions could have been maintained during the late stages of eukaryogenesis, facilitating the evolution of sexual cell fusion and meiotic recombination without compromising the stability of the emerging complex cell. PMID:27266671
Universal effect of dynamical reinforcement learning mechanism in spatial evolutionary games
International Nuclear Information System (INIS)
One of the prototypical mechanisms in understanding the ubiquitous cooperation in social dilemma situations is the win–stay, lose–shift rule. In this work, a generalized win–stay, lose–shift learning model—a reinforcement learning model with dynamic aspiration level—is proposed to describe how humans adapt their social behaviors based on their social experiences. In the model, the players incorporate the information of the outcomes in previous rounds with time-dependent aspiration payoffs to regulate the probability of choosing cooperation. By investigating such a reinforcement learning rule in the spatial prisoner's dilemma game and public goods game, a most noteworthy viewpoint is that moderate greediness (i.e. moderate aspiration level) favors best the development and organization of collective cooperation. The generality of this observation is tested against different regulation strengths and different types of network of interaction as well. We also make comparisons with two recently proposed models to highlight the importance of the mechanism of adaptive aspiration level in supporting cooperation in structured populations
Evolutionary and transmission dynamics of reassortant H5N1 influenza virus in Indonesia.
Directory of Open Access Journals (Sweden)
Tommy Tsan-Yuk Lam
Full Text Available H5N1 highly pathogenic avian influenza (HPAI viruses have seriously affected the Asian poultry industry since their recurrence in 2003. The viruses pose a threat of emergence of a global pandemic influenza through point mutation or reassortment leading to a strain that can effectively transmit among humans. In this study, we present phylogenetic evidences for the interlineage reassortment among H5N1 HPAI viruses isolated from humans, cats, and birds in Indonesia, and identify the potential genetic parents of the reassorted genome segments. Parsimony analyses of viral phylogeography suggest that the reassortant viruses may have originated from greater Jakarta and surroundings, and subsequently spread to other regions in the West Java province. In addition, Bayesian methods were used to elucidate the genetic diversity dynamics of the reassortant strain and one of its genetic parents, which revealed a more rapid initial growth of genetic diversity in the reassortant viruses relative to their genetic parent. These results demonstrate that interlineage exchange of genetic information may play a pivotal role in determining viral genetic diversity in a focal population. Moreover, our study also revealed significantly stronger diversifying selection on the M1 and PB2 genes in the lineages preceding and subsequent to the emergence of the reassortant viruses, respectively. We discuss how the corresponding mutations might drive the adaptation and onward transmission of the newly formed reassortant viruses.
Directory of Open Access Journals (Sweden)
Niimura Yoshihito
2009-12-01
Full Text Available Abstract Olfaction is essential for the survival of animals. Versatile odour molecules in the environment are received by olfactory receptors (ORs, which form the largest multigene family in vertebrates. Identification of the entire repertories of OR genes using bioinformatics methods from the whole-genome sequences of diverse organisms revealed that the numbers of OR genes vary enormously, ranging from ~1,200 in rats and ~400 in humans to ~150 in zebrafish and ~15 in pufferfish. Most species have a considerable fraction of pseudogenes. Extensive phylogenetic analyses have suggested that the numbers of gene gains and losses are extremely large in the OR gene family, which is a striking example of the birth-and-death evolution. It appears that OR gene repertoires change dynamically, depending on each organism's living environment. For example, higher primates equipped with a well-developed vision system have lost a large number of OR genes. Moreover, two groups of OR genes for detecting airborne odorants greatly expanded after the time of terrestrial adaption in the tetrapod lineage, whereas fishes retain diverse repertoires of genes that were present in aquatic ancestral species. The origin of vertebrate OR genes can be traced back to the common ancestor of all chordate species, but insects, nematodes and echinoderms utilise distinctive families of chemoreceptors, suggesting that chemoreceptor genes have evolved many times independently in animal evolution.
Kruijssen, J M Diederik; Longmore, Steven N
2014-01-01
We recently proposed that the star-forming potential of dense molecular clouds in the Central Molecular Zone (CMZ, i.e. the central few 100 pc) of the Milky Way is linked to their orbital dynamics, potentially giving rise to an absolute-time sequence of star-forming clouds. In this paper, we present an orbital model for the gas stream(s) observed in the CMZ. The model is obtained by integrating orbits in the observed gravitational potential and represents a good fit to the distribution of dense gas, reproducing all of its key properties. The orbit is also consistent with observational constraints not included in the fitting process, such as the velocities of Sgr B2 and the Arches and Quintuplet clusters. It differs from previous models: (1) the orbit is open rather than closed due to the extended mass distribution in the CMZ, (2) its orbital velocity is twice as high as in previous models, and (3) Sgr A$^*$ coincides with the focus of the (eccentric) orbit rather than being offset. Our orbital solution suppor...
Precise integration method without inverse matrix calculation for structural dynamic equations
Institute of Scientific and Technical Information of China (English)
Wang Mengfu; F. T. K. Au
2007-01-01
The precise integration method proposed for linear time-invariant homogeneous dynamic systems can provide accurate numerical results that approach an exact solution at integration points. However, difficulties arise when the algorithm is used for non-homogeneous dynamic systems due to the inverse matrix calculation required. In this paper, the structural dynamic equalibrium equations are converted into a special form, the inverse matrix calculation is replaced by the Crout decomposition method to solve the dynamic equilibrium equations, and the precise integration method without the inverse matrix calculation is obtained. The new algorithm enhances the present precise integration method by improving both the computational accuracy and efficiency. Two numerical examples are given to demonstrate the validity and efficiency of the proposed algorithm.
Evolutionary dynamics of viral escape under antibodies stress: A biophysical model.
Chéron, Nicolas; Serohijos, Adrian W R; Choi, Jeong-Mo; Shakhnovich, Eugene I
2016-07-01
Viruses constantly face the selection pressure of antibodies, either from innate immune response of the host or from administered antibodies for treatment. We explore the interplay between the biophysical properties of viral proteins and the population and demographic variables in the viral escape. The demographic and population genetics aspect of the viral escape have been explored before; however one important assumption was the a priori distribution of fitness effects (DFE). Here, we relax this assumption by instead considering a realistic biophysics-based genotype-phenotype relationship for RNA viruses escaping antibodies stress. In this model the DFE is itself an evolvable property that depends on the genetic background (epistasis) and the distribution of biophysical effects of mutations, which is informed by biochemical experiments and theoretical calculations in protein engineering. We quantitatively explore in silico the viability of viral populations under antibodies pressure and derive the phase diagram that defines the fate of the virus population (extinction or escape from stress) in a range of viral mutation rates and antibodies concentrations. We find that viruses are most resistant to stress at an optimal mutation rate (OMR) determined by the competition between supply of beneficial mutation to facilitate escape from stressors and lethal mutagenesis caused by excess of destabilizing mutations. We then show the quantitative dependence of the OMR on genome length and viral burst size. We also recapitulate the experimental observation that viruses with longer genomes have smaller mutation rate per nucleotide. PMID:26939576
Evolutionary Theorizing in Economics
Richard R. Nelson; Winter, Sidney G.
2002-01-01
This paper reviews the case for an evolutionary approach to problems of economic analysis, ranging from the details of individual firm behavior in the short run through industrial dynamics to the historical evolution of institutions and technologies. We draw upon a substantial body of recent research contributions. We characterize micro behavior as governed by skills and routines that are shaped by learning and selection. We then consider major areas of application of evolutionary thinking, i...
Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids
Directory of Open Access Journals (Sweden)
Fernandes António MG
2008-10-01
Full Text Available Abstract Background Segmental duplications (SDs are euchromatic portions of genomic DNA (≥ 1 kb that occur at more than one site within the genome, and typically share a high level of sequence identity (>90%. Approximately 5% of the human genome is composed of such duplicated sequences. Here we report the detailed investigation of CHEK2 duplications. CHEK2 is a multiorgan cancer susceptibility gene encoding a cell cycle checkpoint kinase acting in the DNA-damage response signalling pathway. The continuous presence of the CHEK2 gene in all eukaryotes and its important role in maintaining genome stability prompted us to investigate the duplicative evolution and phylogeny of CHEK2 and its paralogs during anthropoid evolution. Results To study CHEK2 duplicon evolution in anthropoids we applied a combination of comparative FISH and in silico analyses. Our comparative FISH results with a CHEK2 fosmid probe revealed the single-copy status of CHEK2 in New World monkeys, Old World monkeys and gibbons. Whereas a single CHEK2 duplication was detected in orangutan, a multi-site signal pattern indicated a burst of duplication in African great apes and human. Phylogenetic analysis of paralogous and ancestral CHEK2 sequences in human, chimpanzee and rhesus macaque confirmed this burst of duplication, which occurred after the radiation of orangutan and African great apes. In addition, we used inter-species quantitative PCR to determine CHEK2 copy numbers. An amplification of CHEK2 was detected in African great apes and the highest CHEK2 copy number of all analysed species was observed in the human genome. Furthermore, we detected variation in CHEK2 copy numbers within the analysed set of human samples. Conclusion Our detailed analysis revealed the highly dynamic nature of CHEK2 duplication during anthropoid evolution. We determined a burst of CHEK2 duplication after the radiation of orangutan and African great apes and identified the highest CHEK2 copy number
DEVELOPMENT OF CALCULATING MODEL APPLICABLE FOR CYLINDER WALL DYNAMIC HEAT TRANSFER
Institute of Scientific and Technical Information of China (English)
ZHONG Minjun; SHI Tielin
2007-01-01
In the calculation of submarine air conditioning load of the early stage, the obtained heat is regarded as cooling load. The confusion of the two words causing the cooling load figured out is abnormally high, and the change of air conditioning cooling load can not be indicated. In accordance with submarine structure and heat transfer characteristics of its inner components, Laplace transformation to heat conduction differential equation of cylinder wall is carried out. The dynamic calculation of submarine conditioning load based on this model is also conducted, and the results of calculation are compared with those of static cooling load calculation. It is concluded that the dynamic cooling load calculation methods can illustrate the change of submarine air conditioning cooling load more accurate than the static one.
Hao, Yajiang; Inhester, Ludger; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-07-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging. PMID:26798806
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Hao, Yajiang; Hanasaki, Kota; Son, Sang-Kil; Santra, Robin
2015-01-01
We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL) pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
Efficient electronic structure calculation for molecular ionization dynamics at high x-ray intensity
Directory of Open Access Journals (Sweden)
Yajiang Hao
2015-07-01
Full Text Available We present the implementation of an electronic-structure approach dedicated to ionization dynamics of molecules interacting with x-ray free-electron laser (XFEL pulses. In our scheme, molecular orbitals for molecular core-hole states are represented by linear combination of numerical atomic orbitals that are solutions of corresponding atomic core-hole states. We demonstrate that our scheme efficiently calculates all possible multiple-hole configurations of molecules formed during XFEL pulses. The present method is suitable to investigate x-ray multiphoton multiple ionization dynamics and accompanying nuclear dynamics, providing essential information on the chemical dynamics relevant for high-intensity x-ray imaging.
ALUNNO-BRUSCIA, Marianne; van der Veer, Henk W.; Kooijman, Sebastiaan A. L. M.
2009-01-01
The European Research Project AquaDEB (20072011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main sci...
International Nuclear Information System (INIS)
We study exchange of stability in the dynamics of solitary wave solutions under changes in the nonlinear balance in a 1+1 evolutionary partial differential equation related both to shallow water waves and to turbulence. We find that solutions of the equation mt+umx+buxm=νmxx with m=u-α2uxx for fluid velocity u(x,t) change their behavior at the special values b=0,±1,±2,±3
DEFF Research Database (Denmark)
Nash, Ulrik William
2014-01-01
The concept of evolutionary expectations descends from cue learning psychology, synthesizing ideas on rational expectations with ideas on bounded rationality, to provide support for these ideas simultaneously. Evolutionary expectations are rational, but within cognitive bounds. Moreover, they are...... cognitive bounds will perceive business opportunities identically. In addition, because cues provide information about latent causal structures of the environment, changes in causality must be accompanied by changes in cognitive representations if adaptation is to be maintained. The concept of evolutionary...
Eiben, Aguston; Schoenauer, Marc
2002-01-01
Evolutionary computing (EC) is an exciting development in Computer Science. It amounts to building, applying and studying algorithms based on the Darwinian principles of natural selection. In this paper we briefly introduce the main concepts behind evolutionary computing. We present the main components all evolutionary algorithms (EA), sketch the differences between different types of EAs and survey application areas ranging from optimization, modeling and simulation to entertainment.
The effect of dynamical quark mass on the calculation of a strange quark star's structure
Institute of Scientific and Technical Information of China (English)
Gholam Hossein Bordbar; Babak Ziaei
2012-01-01
We discuss the dynamical behavior of strange quark matter components,in particular the effects of density dependent quark mass on the equation of state of strange quark matter.The dynamical masses of quarks are computed within the Nambu-Jona-Lasinio model,then we perform strange quark matter calculations employing the MIT bag model with these dynamical masses.For the sake of comparing dynamical mass interaction with QCD quark-quark interaction,we consider the one-gluon-exchange term as the effective interaction between quarks for the MIT bag model.Our dynamical approach illustrates an improvement in the obtained equation of state values.We also investigate the structure of the strange quark star using TolmanOppenheimer-Volkoff equations for all applied models.Our results show that dynamical mass interaction leads to lower values for gravitational mass.
Kim, Kiyeon
2016-01-13
Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima’s D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima’s D values of viral sequences were different depending on hosts and gene segments. Tajima’s D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima’s D values in rapidly growing viral population were also observed in computer simulations. Tajima’s D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima’s D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
Calculations of Bose-Einstein correlations from Relativistic Quantum Molecular Dynamics
International Nuclear Information System (INIS)
Bose-Einstein correlation functions which are in good agreement with pion data can be calculated from an event generator. Here pion and (preliminary) kaon data from CERN experiment NA44 are compared to the calculations. The dynamics of 200 GeV/nucleon 32S + Pb collisions are calculated, without correlations due to interference patterns of a many-body wavefunction for identical particles, using the Relativistic Quantum Molecular Dynamics model (RQMD). The model is used to generate the phase-space coordinates of the emitted hadrons at the time they suffer their last strong interaction (freeze-out). Using the freeze-out position and momentum of pairs of randomly selected identical particles, a two-particle symmetrized wave-function is calculated and used to add two-body correlations. Details of the technique have been described previously. The method is similar to that used in the Spacer program
Calculation of the coefficient and dynamics of water diffusion in graphite joints
Institute of Scientific and Technical Information of China (English)
WANG Jun; LIU Wen-bin
2006-01-01
The coefficient and dynamics of water diffusion in adhesive-graphite joints were calculated insitu with energy dispersive X-ray (EDX) analysis, a method that is significantly simpler than elemental analysis. Water diffusion coefficient and dynamics of adhesive-graphite joints treated by different surface treatment methods were also investigated. Calculation results indicated that the water diffusion rate in adhesive-graphite joints treated by sandpaper was higher than that treated by chemical oxidation or by silane couple agent. Also the durability of graphite joints treated by coupling agent is superior to that treated by chemical oxidation or sandpaper burnishing.
Using Selectively Applied Accelerated Molecular Dynamics to Enhance Free Energy Calculations
Wereszczynski, Jeff; McCammon, J. Andrew
2010-01-01
Accelerated molecular dynamics (aMD) has been shown to enhance conformational space sampling relative to classical molecular dynamics; however, the exponential reweighting of aMD trajectories, which is necessary for the calculation of free energies relating to the classical system, is oftentimes problematic, especially for systems larger than small poly peptides. Here, we propose a method of accelerating only the degrees of freedom most pertinent to sampling, thereby reducing the total accele...
Beam optics and dynamics, calculations and measurements at the Saclay superconducting Booster
International Nuclear Information System (INIS)
To improve the optics and dynamics calculations along the booster lines, emittances in the longitudinal and radial phase space have been measured just before injection in the booster linac. We report here the main results of these measurements which are used to set the initial conditions in our ray tracing and transport programs. A first order calculation has also been performed from which we deduce the matrix equivalent to a resonator in the radial phase space
Sirer, Irmak
2006-01-01
Dielectric properties of an aqueous lysozyme solution were calculated from 2 ns long MD simulations in the temperature range of 150-300 K and an 4 ns long simulation at 300 K. Static and frequency dependent dielectric constants of the system were calculated from auto- and cross-correlations of its three components (protein, water, ions). Cole-Cole plots for protein, water and the total solution were obtained. Emergence of an intense protein-water interaction above the dynamical transition bet...
Calculating Conductance of Ion Channels – Linking Molecular Dynamics and Electrophysiology
International Nuclear Information System (INIS)
Molecular dynamics computer simulations were combined with an electrodiffusion model to compute conduction of simple ion channels. The main assumptions of the model, and the consistency, efficiency and accuracy of the ion current calculations were tested and found satisfactory. The calculated current-voltage dependence for a synthetic peptide channel is in agreement with experiments and correctly captures the asymmetry of current with respect to applied field
Fan, Zheyong; Siro, Topi; harju, Ari
2012-01-01
In this paper, we develop a highly efficient molecular dynamics code fully implemented on graphics processing units for thermal conductivity calculations using the Green-Kubo formula. We compare two different schemes for force evaluation, a previously used thread-scheme where a single thread is used for one particle and each thread calculates the total force for the corresponding particle, and a new block-scheme where a whole block is used for one particle and each thread in the block calcula...
Shaughnessy, M C; Jones, R E
2016-02-01
We develop and demonstrate a method to efficiently use density functional calculations to drive classical dynamics of complex atomic and molecular systems. The method has the potential to scale to systems and time scales unreachable with current ab initio molecular dynamics schemes. It relies on an adapting dataset of independently computed Hellmann-Feynman forces for atomic configurations endowed with a distance metric. The metric on configurations enables fast database lookup and robust interpolation of the stored forces. We discuss mechanisms for the database to adapt to the needs of the evolving dynamics, while maintaining accuracy, and other extensions of the basic algorithm. PMID:26669825
The Variable Size Memory-based Evolutionary Algorithm in Dynamic Environments%动态环境下基于可变记忆的进化算法
Institute of Scientific and Technical Information of China (English)
关守平; 尹晓峰
2011-01-01
常规基于记忆的进化算法在动态环境中往往达不到期望的效果,这主要是由于记忆体大小的限制.为此提出了动态环境下基于可变记忆的进化算法(IMEEA),其核心思想是算法中拥有两个种群,即搜索种群和记忆种群,同时采用过度变异策略来增加种群的多样性.算法中的两个种群有最小和最大的允许长度,并且种群的大小根据进化过程的进行而不断变化.仿真结果表明,在动态环境中IMEEA算法的跟踪误差要小于常规的记忆提高进化算法(MEEA),从而证明了所提算法的有效性.%Traditional memory-based evolutionary algorithms often may not achieve the desired performances in dynamic environments, which is mainly due to the fixed memory size. A variable size memory-based evolutionary algorithm is proposed. The improved memory enhanced evolutionary algorithm (IMEEA), which combines memory population and search population,and hyper-mutation is used to promote and maintain diversity. The two populations have minimum and maximum sizes allowed that change according to the stage of the evolutionary process. Simulation results show that the tracking error of the IMEEA is less than the memory enhanced evolutionary algorithm (MEEA), and then prove the effectiveness of this new algorithm.
Červinka, Ctirad; Pádua, Agilio A H; Fulem, Michal
2016-03-10
This work presents a molecular dynamics simulation study concerning the thermodynamic data of ionic liquids (ILs) including phase change enthalpies, liquid phase densities, radial and spatial distribution functions, and diffusive properties. Three homologous series of ILs were selected for this study, namely, 1-alkyl-3-methylimidazolium tetrafluoroborates, hexafluorophosphates, and 1,1,2,2-tetrafluoroethanesulfonates, so that properties of 36 ILs are calculated in total. The trends of calculated properties are compared to available experimental data and thoroughly discussed in context of the homologous series. The calculated trends of the vaporization enthalpies within the series are supported by analyzing the structural properties of the ILs. An excellent agreement of calculated structural properties (liquid phase density) with the experimental counterparts is reached. The calculated enthalpic properties are overestimated considerably; thus, further development of the force fields for ILs is required. PMID:26848831
Seethaler, Pamela M.; Fuchs, Lynn S.; Fuchs, Douglas; Compton, Donald L.
2012-01-01
The purpose of this study was to assess the value of dynamic assessment (DA; degree of scaffolding required to learn unfamiliar mathematics content) for predicting 1st-grade calculations (CAs) and word problems (WPs) development, while controlling for the role of traditional assessments. Among 184 1st graders, predictors (DA, Quantity…
Three-dimensional dynamic calculation in the low energy region of an electron linac
International Nuclear Information System (INIS)
The model of charge discs with variable radius and the model of charge rings are used in the three-dimensional dynamic calculation at the low energy region of an electron linac. The charged particles displacement, rate of displacement and trajectories are computed. The RMS emittance and pictures of beam emittance on different phase planes are also given
Tao, Wei; Shen, Zheng-Kang; Zhang, Yong
2016-04-01
The Longmen Shan, located in the conjunction of the eastern margin the Tibet plateau and Sichuan basin, is a typical area for studying the deformation pattern of the Tibet plateau. Following the 2008 Mw 7.9 Wenchuan earthquake (WE) rupturing the Longmen Shan Fault (LSF), a great deal of observations and studies on geology, geophysics, and geodesy have been carried out for this region, with results published successively in recent years. Using the 2D viscoelastic finite element model, introducing the rate-state friction law to the fault, this thesis makes modeling of the earthquake recurrence process and the dynamic evolutionary processes in an earthquake cycle of 10 thousand years. By analyzing the displacement, velocity, stresses, strain energy and strain energy increment fields, this work obtains the following conclusions: (1) The maximum coseismic displacement on the fault is on the surface, and the damage on the hanging wall is much more serious than that on the foot wall of the fault. If the detachment layer is absent, the coseismic displacement would be smaller and the relative displacement between the hanging wall and foot wall would also be smaller. (2) In every stage of the earthquake cycle, the velocities (especially the vertical velocities) on the hanging wall of the fault are larger than that on the food wall, and the values and the distribution patterns of the velocity fields are similar. While in the locking stage prior to the earthquake, the velocities in crust and the relative velocities between hanging wall and foot wall decrease. For the model without the detachment layer, the velocities in crust in the post-seismic stage is much larger than those in other stages. (3) The maximum principle stress and the maximum shear stress concentrate around the joint of the fault and detachment layer, therefore the earthquake would nucleate and start here. (4) The strain density distribution patterns in stages of the earthquake cycle are similar. There are two
Dračínský, Martin; Bouř, Petr; Hodgkinson, Paul
2016-03-01
The influence of temperature on NMR chemical shifts and quadrupolar couplings in model molecular organic solids is explored using path integral molecular dynamics (PIMD) and density functional theory (DFT) calculations of shielding and electric field gradient (EFG) tensors. An approach based on convoluting calculated shielding or EFG tensor components with probability distributions of selected bond distances and valence angles obtained from DFT-PIMD simulations at several temperatures is used to calculate the temperature effects. The probability distributions obtained from the quantum PIMD simulations, which includes nuclear quantum effects, are significantly broader and less temperature dependent than those obtained with conventional DFT molecular dynamics or with 1D scans through the potential energy surface. Predicted NMR observables for the model systems were in excellent agreement with experimental data. PMID:26857802
Cao, Jun; Xie, Zhi-Zhong; Yu, Xiaodong
2016-08-01
In the present work, the combined electronic structure calculations and surface hopping simulations have been performed to investigate the excited-state decay of the parent oxazole in the gas phase. Our calculations show that the S2 state decay of oxazole is an ultrafast process characterized by the ring-opening and ring-closure of the five-membered oxazole ring, in which the triplet contribution is minor. The ring-opening involves the Osbnd C bond cleavage affording the nitrile ylide and airine intermediates, while the ring-closure gives rise to a bicyclic species through a 2sbnd 5 bond formation. The azirine and bicyclic intermediates in the S0 state are very likely involved in the phototranspositions of oxazoles. This is different from the previous mechanism in which these intermediates in the T1 state have been proposed for these phototranspositions.
The Pi-ta gene in rice has been used to control rice blast pathogen, Magnaporthe oryza, in rice growing areas worldwide for decades. To understand the evolutionary process and natural selection of Pi-ta during rice domestication, we first examined sequences of the genomic region of Pi-ta in geograph...
Schilthuizen, M.
2011-01-01
The karst formations of southeast Asia are a wonderful evolutionary and ecological experiment, and a sad example of observable extinction (Clements et al., 2006). In this paper, I shall focus on those in Malaysia and, in particular, on the land snail faunas that they support.
Dopfer, Kurt
2006-01-01
The paper provides an overview of major recent contributions in evolutionary economics. It starts of demonstrating that the pioneers of this approach such as Veblen, Schumpeter, Marshall and Hayek saw the economy as continuously changing and that this kind of "realism of perception" guides essentially also contemporary evolutionary economics. The economy is viewed as an evolving system of structured knowledge governing economic operations. Theoretically, a micro-meso-macro architecture is pro...
Szöllösi, Tomáš
2012-01-01
The first part of this work deals with the optimization and evolutionary algorithms which are used as a tool to solve complex optimization problems. The discussed algorithms are Differential Evolution, Genetic Algorithm, Simulated Annealing and deterministic non-evolutionary algorithm Taboo Search.. Consequently the discussion is held on the issue of testing the optimization algorithms through the use of the test function gallery and comparison solution all algorithms on Travelling salesman p...
Eremeev, Anton V.
2015-01-01
This manuscript contains an outline of lectures course "Evolutionary Algorithms" read by the author in Omsk State University n.a. F.M.Dostoevsky. The course covers Canonic Genetic Algorithm and various other genetic algorithms as well as evolutioanry algorithms in general. Some facts, such as the Rotation Property of crossover, the Schemata Theorem, GA performance as a local search and "almost surely" convergence of evolutionary algorithms are given with complete proofs. The text is in Russian.
Chiara, Matteo; Caruso, Marta; D'Erchia, Anna Maria; Manzari, Caterina; Fraccalvieri, Rosa; Goffredo, Elisa; Latorre, Laura; Miccolupo, Angela; Padalino, Iolanda; Santagada, Gianfranco; Chiocco, Doriano; Pesole, Graziano; Horner, David S; Parisi, Antonio
2015-08-01
Historically, genome-wide and molecular characterization of the genus Listeria has concentrated on the important human pathogen Listeria monocytogenes and a small number of closely related species, together termed Listeria sensu strictu. More recently, a number of genome sequences for more basal, and nonpathogenic, members of the Listeria genus have become available, facilitating a wider perspective on the evolution of pathogenicity and genome level evolutionary dynamics within the entire genus (termed Listeria sensu lato). Here, we have sequenced the genomes of additional Listeria fleischmannii and Listeria newyorkensis isolates and explored the dynamics of genome evolution in Listeria sensu lato. Our analyses suggest that acquisition of genetic material through gene duplication and divergence as well as through lateral gene transfer (mostly from outside Listeria) is widespread throughout the genus. Novel genetic material is apparently subject to rapid turnover. Multiple lines of evidence point to significant differences in evolutionary dynamics between the most basal Listeria subclade and all other congeners, including both sensu strictu and other sensu lato isolates. Strikingly, these differences are likely attributable to stochastic, population-level processes and contribute to observed variation in genome size across the genus. Notably, our analyses indicate that the common ancestor of Listeria sensu lato lacked flagella, which were acquired by lateral gene transfer by a common ancestor of Listeria grayi and Listeria sensu strictu, whereas a recently functionally characterized pathogenicity island, responsible for the capacity to produce cobalamin and utilize ethanolamine/propane-2-diol, was acquired in an ancestor of Listeria sensu strictu. PMID:26185097
International Nuclear Information System (INIS)
Kinetic parameters for dynamic study of two different configurations, 8 and 9, both with standard fuel, 20% enrichment and Flip (Fuel Life Improvement Program with 70% enrichment) fuel, for TRIGA Mark-III reactor from Mexico Nuclear Center, are obtained. A calculation method using both WIMS-D4 and DTF-IV and DAC1 was established, to decide which of those two configurations has the best safety and operational conditions. Validation of this methodology is done by calculate those parameters for a reactor core with new standard fuel. Configuration 9 is recommended to be use. (Author)
International Nuclear Information System (INIS)
The generalized geometrical optics model for the detonation shock dynamics (DSD) has been incorporated into the two dimensional hydro-code WSU to form a combination code ADW for numerical simulation of explosive acceleration of metals. An analytical treatment of the coupling conditions at the nodes just behind the detonation front is proposed. The experiments on two kinds of explosive-flyer assemblies with different length/diameter ratio were carried out to verify the ADW calculations, where the tested explosive was HMX or TATB based. It is found that the combination of DSD and hydro-code can improve the calculation precision, and has advantages in larger meshes and less CPU time
Institute of Scientific and Technical Information of China (English)
王岩国; 刘红荣; 杨奇斌; 张泽
2003-01-01
Off-axis electron holography in a field emission gun transmission-electron microscope and electron dynamic calculation are used to determine the absorption coefficient and inelastic mean free path (IMFP) of copper.Dependence of the phase shift of the exit electron wave on the specimen thickness is established by electron dynamic simulation. The established relationship makes it possible to determine the specimen thickness with the calculated phase shift by match of the phase shift measured in the reconstructed phase image. Based on the measured amplitudes in reconstructed exit electron wave and reference wave in the vacuum, the examined IMFP of electron with energy of 200kV in Cu is obtained to be 96nm.
Seethaler, Pamela M.; Fuchs, Lynn S.; Fuchs, Douglas; Compton, Donald L.
2012-01-01
The purpose of this study was to assess the value of dynamic assessment (DA; degree of scaffolding required to learn unfamiliar mathematics content) for predicting 1st-grade calculations (CA) and word problems (WP) development, while controlling for the role of traditional assessments. Among 184 1st graders, predictors (DA, Quantity Discrimination, Test of Mathematics Ability, language, and reasoning) were assessed near the start of 1st grade. CA and WP were assessed near the end of 1st grade...
Kellens, W.; Neutens, T.; Deckers, P.; Reyns, J.; P. De Maeyer
2012-01-01
Since coastal tourism is one of the fastest growing sectors of tourism industry, coastal areas have become increasingly vulnerable in the case of flooding. While in recent years a number of different methods have been put forward to map coastal flood risks, the implications of tourism dynamics for the assessment of human casualties has remained largely overlooked in these models. This chapter examines to what extent the ignorance of ( residential) coastal tourism may bias the calculations of ...
Comparison of inverse dynamics calculated by two- and three-dimensional models during walking
DEFF Research Database (Denmark)
Alkjaer, T; Simonsen, E B; Dyhre-Poulsen, P
2001-01-01
The purpose of the study was to compare joint moments calculated by a two- (2D) and a three-dimensional (3D) inverse dynamics model to examine how the different approaches influenced the joint moment profiles. Fifteen healthy male subjects participated in the study. A five-camera video system...... recorded the subjects as they walked across two force plates. The subjects were invited to approach a walking speed of 4.5 km/h. The ankle, knee and hip joint moments in the sagittal plane were calculated by 2D and 3D inverse dynamics analysis and compared. Despite the uniform walking speed (4.53 km/h) and...... magnitude of the joint moments calculated by 2D and 3D inverse dynamics but the inter-individual variation was not affected by the different models. The simpler 2D model seems therefore appropriate for human gait analysis. However, comparisons of gait data from different studies are problematic if the...
The fifth Atomic Energy Research dynamic benchmark calculation with HEXTRAN-SMABRE
International Nuclear Information System (INIS)
The fifth Atomic Energy Research dynamic benchmark is the first Atomic Energy Research benchmark for coupling of the thermohydraulic codes and three-dimensional reactor dynamic core models. In VTT HEXTRAN 2.7 is used for the core dynamics and SMABRE 4.6 as a thermohydraulic model for the primary and secondary loops. The plant model for SMABRE is based mainly on two input models. the Loviisa model and standard WWER-440/213 plant model. The primary circuit includes six separate loops, totally 505 nodes and 652 junctions. The reactor pressure vessel is divided into six parallel channels. In HEXTRAN calculation 176 symmetry is used in the core. In the sequence of main steam header break at the hot standby state, the liquid temperature is decreased symmetrically in the core inlet which leads to return to power. In the benchmark, no isolations of the steam generators are assumed and the maximum core power is about 38 % of the nominal power at four minutes after the break opening in the HEXTRAN-SMABRE calculation. Due to boric acid in the high pressure safety injection water, the power finally starts to decrease. The break flow is pure steam in the HEXTRAN-SMABRE calculation during the whole transient even in the swell levels in the steam generators are very high due to flashing. Because of sudden peaks in the preliminary results of the steam generator heat transfer, the SMABRE drift-flux model was modified. The new model is a simplified version of the EPRI correlation based on test data. The modified correlation behaves smoothly. In the calculations nuclear data is based on the ENDF/B-IV library and it has been evaluated with the CASMO-HEX code. The importance of the nuclear data was illustrated by repeating the benchmark calculation with using three different data sets. Optimal extensive data valid from hot to cold conditions were not available for all types of fuel enrichments needed in this benchmark.(Author)
Poulicard, Nils; Pacios, Luis Fernández; Gallois, Jean-Luc; Piñero, Daniel; García-Arenal, Fernando
2016-01-01
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 p...
Belkacem, Ali; Slaughter, Daniel
2015-05-01
Understanding electron-driven chemical reactions is important for improving a variety of technological applications such as materials processing and the important role they play in the radiation damage in bulk matter. Furthermore, dissociative electron attachment often exhibits site-selective bond cleavage, which holds promise for prediction and precise control of electron-driven chemical reactions. Recent dynamical studies of these reactions have demonstrated that an understanding of anion dissociation dynamics beyond simple one-dimensional models is crucial in interpreting the measured fragment angular distributions. We combine ion fragment momentum imaging experiments with electron attachment entrance amplitude calculations to interrogate the non-Born-Oppenheimer dynamics of dissociative electron attachment in polyatomic molecules. We will report recent experimental developments in molecules of technological interest including methanol, methane and uracil. Work supported by Chemical Sciences, Geosciences and Biosciences division of BES/DOE.
Methods of Electro-Dynamic Stability Calculation of Flexible Bus-bars in High Voltage Switch Gears
I. I. Sergey; Y. G. Panamarenka; A. S. Mikhalyov
2010-01-01
The improved vector-parametrical and simplified methods for calculation of electro-dynamic stability parameters of flexible busbars in high voltage switch gears have been presented in the paper. The developed methods and their software can be taken as a basis of methodological instructions on calculation of short-circuit current electro-dynamic action on flexible conductors of switching gears.
Gorelik, Gregory; Shackelford, Todd K
2014-01-01
In this article, we advance the concept of "evolutionary awareness," a metacognitive framework that examines human thought and emotion from a naturalistic, evolutionary perspective. We begin by discussing the evolution and current functioning of the moral foundations on which our framework rests. Next, we discuss the possible applications of such an evolutionarily-informed ethical framework to several domains of human behavior, namely: sexual maturation, mate attraction, intrasexual competition, culture, and the separation between various academic disciplines. Finally, we discuss ways in which an evolutionary awareness can inform our cross-generational activities-which we refer to as "intergenerational extended phenotypes"-by helping us to construct a better future for ourselves, for other sentient beings, and for our environment. PMID:25300054
Directory of Open Access Journals (Sweden)
V.O. Kharchenko
2015-06-01
Full Text Available Within this paper we have the studied structural and electronic properties of zirconium crystal with vacancies from the first principles. We have defined the optimal values for the lattice constants. The corresponding densities of states and energetic spectrum were calculated. These results gave a possibility to define the Fermi structure of the zirconium crystal with vacancies. In the framework of the molecular dynamics simulations we have studied the dynamics of the ensemble of periodically located vacancies in the zirconium crystal with an increase in temperature. We have analyzed the reconstruction of atomic structure and change in the total volume of the crystal with the temperature growth. The dependencies of the volume expansion coefficient for the pure zirconium without vacancies end zirconium crystal with different vacancies concentration on the temperature were studied.
Cheluvaraja, Srinath; Meirovitch, Hagai
2006-07-14
Hypothetical scanning (HS) is a method for calculating the absolute entropy S and free energy F from a sample generated by any simulation technique. With this approach each sample configuration is reconstructed with the help of transition probabilities (TPs) and their product leads to the configuration's probability, hence to the entropy. Recently a new way for calculating the TPs by Monte Carlo (MC) simulations has been suggested, where all system interactions are taken into account. Therefore, this method--called HSMC--is in principle exact where the only approximation is due to insufficient sampling. HSMC has been applied very successfully to liquid argon, TIP3P water, self-avoiding walks on a lattice, and peptides. Because molecular dynamics (MD) is considered to be significantly more efficient than MC for a compact polymer chain, in this paper HSMC is extended to MD simulations as applied to peptides. Like before, we study decaglycine in vacuum but for the first time also a peptide with side chains, (Val)(2)(Gly)(6)(Val)(2). The transition from MC to MD requires implementing essential changes in the reconstruction process of HSMD. Results are calculated for three microstates, helix, extended, and hairpin. HSMD leads to very stable differences in entropy TDeltaS between these microstates with small errors of 0.1-0.2 kcal/mol (T=100 K) for a wide range of calculation parameters with extremely high efficiency. Various aspects of HSMD and plans for future work are discussed. PMID:16848609
Calculating gravitationally self-consistent sea level changes driven by dynamic topography
Austermann, J.; Mitrovica, J. X.
2015-12-01
We present a generalized formalism for computing gravitationally self-consistent sea level changes driven by the combined effects of dynamic topography, geoid perturbations due to mantle convection, ice mass fluctuations and sediment redistribution on a deforming Earth. Our mathematical treatment conserves mass of the surface (ice plus ocean) load and the solid Earth. Moreover, it takes precise account of shoreline migration and the associated ocean loading. The new formalism avoids a variety of approximations adopted in previous models of sea level change driven by dynamic topography, including the assumption that a spatially fixed isostatic amplification of `air-loaded' dynamic topography accurately accounts for ocean loading effects. While our approach is valid for Earth models of arbitrary complexity, we present numerical results for a set of simple cases in which a pattern of dynamic topography is imposed, the response to surface mass loading assumes that Earth structure varies only with depth and that isostatic equilibrium is maintained at all times. These calculations, involving fluid Love number theory, indicate that the largest errors in previous predictions of sea level change driven by dynamic topography occur in regions of shoreline migration, and thus in the vicinity of most geological markers of ancient sea level. We conclude that a gravitationally self-consistent treatment of long-term sea level change is necessary in any effort to use such geological markers to estimate ancient ice volumes.
International Nuclear Information System (INIS)
Purpose: Brachytherapy is a standard option of care for prostate cancer patients but may be improved by dynamic dose calculation based on localized seed positions. The American Brachytherapy Society states that the major current limitation of intraoperative treatment planning is the inability to localize the seeds in relation to the prostate. An image-guidance system was therefore developed to localize seeds for dynamic dose calculation. Methods: The proposed system is based on transrectal ultrasound (TRUS) and mobile C-arm fluoroscopy, while using a simple fiducial with seed-like markers to compute pose from the nonencoded C-arm. Three or more fluoroscopic images and an ultrasound volume are acquired and processed by a pipeline of algorithms: (1) seed segmentation, (2) fiducial detection with pose estimation, (3) seed matching with reconstruction, and (4) fluoroscopy-to-TRUS registration. Results: The system was evaluated on ten phantom cases, resulting in an overall mean error of 1.3 mm. The system was also tested on 37 patients and each algorithm was evaluated. Seed segmentation resulted in a 1% false negative rate and 2% false positive rate. Fiducial detection with pose estimation resulted in a 98% detection rate. Seed matching with reconstruction had a mean error of 0.4 mm. Fluoroscopy-to-TRUS registration had a mean error of 1.3 mm. Moreover, a comparison of dose calculations between the authors’ intraoperative method and an independent postoperative method shows a small difference of 7% and 2% forD90 and V100, respectively. Finally, the system demonstrated the ability to detect cold spots and required a total processing time of approximately 1 min. Conclusions: The proposed image-guidance system is the first practical approach to dynamic dose calculation, outperforming earlier solutions in terms of robustness, ease of use, and functional completeness
International Nuclear Information System (INIS)
After an accidental release of radionuclides to the inhabited environment the external gamma irradiation from deposited radioactivity contributes significantly to the radiation exposure of the population for extended periods. For evaluating this exposure pathway, three main model requirements are needed: (i) to calculate the air kerma value per photon emitted per unit source area, based on Monte Carlo (MC) simulations; (ii) to describe the distribution and dynamics of radionuclides on the diverse urban surfaces; and (iii) to combine all these elements in a relevant urban model to calculate the resulting doses according to the actual scenario. This paper provides an overview about the different approaches to calculate photon transport in urban areas and about several dose calculation codes published. Two types of Monte Carlo simulations are presented using the global and the local approaches of photon transport. Moreover, two different philosophies of the dose calculation, the 'location factor method' and a combination of relative contamination of surfaces with air kerma values are described. The main features of six codes (ECOSYS, EDEM2M, EXPURT, PARATI, TEMAS, URGENT) are highlighted together with a short model-model features intercomparison
Alunno-Bruscia, Marianne; van der Veer, Henk W.; Kooijman, Sebastiaan A. L. M.
2009-08-01
The European Research Project AquaDEB (2007-2011, http://www.ifremer.fr/aquadeb/) is joining skills and expertise of some French and Dutch research institutes and universities to analyse the physiological flexibility of aquatic organisms and to link it to ecological and evolutionary processes within a common theoretical framework for quantitative bioenergetics [Kooijman, S.A.L.M., 2000. Dynamic energy and mass budgets in biological systems. Cambridge University Press, Cambridge]. The main scientific objectives in AquaDEB are i) to study and compare the sensitivity of aquatic species (mainly molluscs and fish) to environmental variability of natural or human origin, and ii) to evaluate the related consequences at different biological levels (individual, population, ecosystem) and temporal scales (life cycle, population dynamics, evolution). At mid-term life, the AquaDEB collaboration has already yielded interesting results by quantifying bio-energetic processes of various aquatic species (e.g. molluscs, fish, crustaceans, algae) with a single mathematical framework. It has also allowed to federate scientists with different backgrounds, e.g. mathematics, microbiology, ecology, chemistry, and working in different fields, e.g. aquaculture, fisheries, ecology, agronomy, ecotoxicology, climate change. For the two coming years, the focus of the AquaDEB collaboration will be in priority: (i) to compare energetic and physiological strategies among species through the DEB parameter values and to identify the factors responsible for any differences in bioenergetics and physiology; and to compare dynamic (DEB) versus static (SEB) energy models to study the physiological performance of aquatic species; (ii) to consider different scenarios of environmental disruption (excess of nutrients, diffuse or massive pollution, exploitation by man, climate change) to forecast effects on growth, reproduction and survival of key species; (iii) to scale up the models for a few species from
International Nuclear Information System (INIS)
Surgery has contributed to unveil a tumor behavior that is difficult to reconcile with the models of tumorigenesis based on gradualism. The postsurgical patterns of progression include unexpected features such as distant interactions and variable rhythms. The underlying evidence can be summarized as follows: (1) the resection of the primary tumor is able to accelerate the evolution of micrometastasis in early stages, and (2) the outcome is transiently opposed in advanced tumors. The objective of this paper is to give some insight into tumorigenesis and surgery-related effects, by applying the concepts of the evolutionary theory in those tumor behaviors that gompertzian and tissular-centered models are unable to explain. According to this view, tumors are the consequence of natural selection operating at the somatic level, which is the basic mechanism of tumorigenesis, notwithstanding the complementary role of the intrinsic constrictions of complex networks. A tumor is a complicated phenomenon that entails growth, evolution and development simultaneously. So, an evo-devo perspective can explain how and why tumor subclones are able to translate competition from a metabolic level into neoangiogenesis and the immune response. The paper proposes that distant interactions are an extension of the ecological events at the local level. This notion explains the evolutionary basis for tumor dormancy, and warns against the teleological view of tumorigenesis as a process directed towards the maximization of a concrete trait such as aggressiveness
Hopkins, Melanie J.; Smith, Andrew B.
2015-03-01
How ecological and morphological diversity accrues over geological time has been much debated by paleobiologists. Evidence from the fossil record suggests that many clades reach maximal diversity early in their evolutionary history, followed by a decline in evolutionary rates as ecological space fills or due to internal constraints. Here, we apply recently developed methods for estimating rates of morphological evolution during the post-Paleozoic history of a major invertebrate clade, the Echinoidea. Contrary to expectation, rates of evolution were lowest during the initial phase of diversification following the Permo-Triassic mass extinction and increased over time. Furthermore, although several subclades show high initial rates and net decreases in rates of evolution, consistent with "early bursts" of morphological diversification, at more inclusive taxonomic levels, these bursts appear as episodic peaks. Peak rates coincided with major shifts in ecological morphology, primarily associated with innovations in feeding strategies. Despite having similar numbers of species in today's oceans, regular echinoids have accrued far less morphological diversity than irregular echinoids due to lower intrinsic rates of morphological evolution and less morphological innovation, the latter indicative of constrained or bounded evolution. These results indicate that rates of evolution are extremely heterogenous through time and their interpretation depends on the temporal and taxonomic scale of analysis.
Energy Technology Data Exchange (ETDEWEB)
Bayonas, Alberto Carmona [Department of Hematology and Medical Oncology, Hospital Morales Meseguer, Murcia (Spain)
2011-03-02
Surgery has contributed to unveil a tumor behavior that is difficult to reconcile with the models of tumorigenesis based on gradualism. The postsurgical patterns of progression include unexpected features such as distant interactions and variable rhythms. The underlying evidence can be summarized as follows: (1) the resection of the primary tumor is able to accelerate the evolution of micrometastasis in early stages, and (2) the outcome is transiently opposed in advanced tumors. The objective of this paper is to give some insight into tumorigenesis and surgery-related effects, by applying the concepts of the evolutionary theory in those tumor behaviors that gompertzian and tissular-centered models are unable to explain. According to this view, tumors are the consequence of natural selection operating at the somatic level, which is the basic mechanism of tumorigenesis, notwithstanding the complementary role of the intrinsic constrictions of complex networks. A tumor is a complicated phenomenon that entails growth, evolution and development simultaneously. So, an evo-devo perspective can explain how and why tumor subclones are able to translate competition from a metabolic level into neoangiogenesis and the immune response. The paper proposes that distant interactions are an extension of the ecological events at the local level. This notion explains the evolutionary basis for tumor dormancy, and warns against the teleological view of tumorigenesis as a process directed towards the maximization of a concrete trait such as aggressiveness.
Directory of Open Access Journals (Sweden)
Alberto Carmona Bayonas
2011-03-01
Full Text Available Surgery has contributed to unveil a tumor behavior that is difficult to reconcile with the models of tumorigenesis based on gradualism. The postsurgical patterns of progression include unexpected features such as distant interactions and variable rhythms. The underlying evidence can be summarized as follows: (1 the resection of the primary tumor is able to accelerate the evolution of micrometastasis in early stages, and (2 the outcome is transiently opposed in advanced tumors. The objective of this paper is to give some insight into tumorigenesis and surgery-related effects, by applying the concepts of the evolutionary theory in those tumor behaviors that gompertzian and tissular-centered models are unable to explain. According to this view, tumors are the consequence of natural selection operating at the somatic level, which is the basic mechanism of tumorigenesis, notwithstanding the complementary role of the intrinsic constrictions of complex networks. A tumor is a complicated phenomenon that entails growth, evolution and development simultaneously. So, an evo-devo perspective can explain how and why tumor subclones are able to translate competition from a metabolic level into neoangiogenesis and the immune response. The paper proposes that distant interactions are an extension of the ecological events at the local level. This notion explains the evolutionary basis for tumor dormancy, and warns against the teleological view of tumorigenesis as a process directed towards the maximization of a concrete trait such as aggressiveness.
Cartoixà, Xavier; Dettori, Riccardo; Melis, Claudio; Colombo, Luciano; Rurali, Riccardo
2016-07-01
We study thermal transport in porous Si nanowires (SiNWs) by means of approach-to-equilibrium molecular dynamics simulations. We show that the presence of pores greatly reduces the thermal conductivity, κ, of the SiNWs as long mean free path phonons are suppressed. We address explicitly the dependence of κ on different features of the pore topology—such as the porosity and the pore diameter—and on the nanowire (NW) geometry—diameter and length. We use the results of the molecular dynamics calculations to tune an effective model, which is capable of capturing the dependence of κ on porosity and NW diameter. The model illustrates the failure of Matthiessen's rule to describe the coupling between boundary and pore scattering, which we account for by the inclusion of an additional empirical term.
Wei, Xing
2016-01-01
For understanding magnetic effects on dynamical tides, we study the rotating magneto-hydrodynamic (MHD) flow driven by harmonic forcing. The linear responses are analytically derived in a periodic box under the local WKB approximation. Both the kinetic and Ohmic dissipations at the resonant frequencies are calculated and the various parameters are investigated. Although magnetic pressure may be negligible compared to thermal pressure, magnetic field can be important for the first-order perturbation, e.g. dynamical tides. It is found that magnetic field splits the resonant frequency, namely the rotating hydrodynamic flow has only one resonant frequency but the rotating MHD flow has two, one positive and the other negative. In the weak field regime the dissipations are asymmetric around the two resonant frequencies and this asymmetry is more striking with a weaker magnetic field. It is also found that both the kinetic and Ohmic dissipations at the resonant frequencies are inversely proportional to the Ekman num...
Energy Technology Data Exchange (ETDEWEB)
Belyaev, Andrey K., E-mail: belyaev@herzen.spb.ru [Department of Theoretical Physics, Herzen University, St. Petersburg 191186 (Russian Federation); Domcke, Wolfgang, E-mail: wolfgang.domcke@ch.tum.de [Department Chemie, Technische Universität München, D-85747 Garching (Germany); Lasser, Caroline, E-mail: classer@ma.tum.de; Trigila, Giulio, E-mail: trigila@ma.tum.de [Zentrum Mathematik, Technische Universität München, D-85747 Garching (Germany)
2015-03-14
The Landau–Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs a recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Three different time scales are detected for the nuclear dynamics: Ultrafast Jahn–Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; and relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs. Beyond 100 fs, the adiabatic electronic populations are nearly constant due to a dynamic equilibrium between the three states. The ultrafast nonradiative decay of the excited-state populations provides a qualitative explanation of the experimental evidence that the ammonia cation is nonfluorescent.
Tests and calculations of reinforced concrete beams subject to dynamic reversed loads
International Nuclear Information System (INIS)
This study presents the tests of a reinforced concrete beam conducted by the Department of Mechanical and Thermal Studies at the Centre d'Etudes Nucleaires, Saclay, France. The actual behavior of nuclear power plant buildings submitted to seismic loads is generally non linear even for moderate seismic levels. The non linearity is specially important for reinforced concrete beams type buildings. To estimate the safety factors when the building is designed by standard methods, accurate non linear calculations are necessary. For such calculations one of the most difficult point is to define a correct model for the behavior of a reinforced beam subject to reversed loads. For that purpose, static and dynamic experimental tests on a shaking table have been carried out and a model reasonably accurate has been established and checked on the tests results
Fast plane wave density functional theory molecular dynamics calculations on multi-GPU machines
International Nuclear Information System (INIS)
Plane wave pseudopotential (PWP) density functional theory (DFT) calculation is the most widely used method for material simulations, but its absolute speed stagnated due to the inability to use large scale CPU based computers. By a drastic redesign of the algorithm, and moving all the major computation parts into GPU, we have reached a speed of 12 s per molecular dynamics (MD) step for a 512 atom system using 256 GPU cards. This is about 20 times faster than the CPU version of the code regardless of the number of CPU cores used. Our tests and analysis on different GPU platforms and configurations shed lights on the optimal GPU deployments for PWP-DFT calculations. An 1800 step MD simulation is used to study the liquid phase properties of GaInP
Cis/trans Coordination in olefin metathesis by static and molecular dynamic DFT calculations
Poater, Albert
2014-05-25
In regard to [(N-heterocyclic carbene)Ru]-based catalysts, it is still a matter of debate if the substrate binding is preferentially cis or trans to the N-heterocyclic carbene ligand. By means of static and molecular dynamic DFT calculations, a simple olefin, like ethylene, is shown to be prone to the trans binding. Bearing in mind the higher reactivity of trans isomers in olefin metathesis, this insight helps to construct small alkene substrates with increased reactivity. © 2014 Springer Science+Business Media New York.
First-Principles Molecular Dynamics Calculations of the Equation of State for Tantalum
Directory of Open Access Journals (Sweden)
Shigeaki Ono
2009-10-01
Full Text Available The equation of state of tantalum (Ta has been investigated to 100 GPa and 3,000 K using the first-principles molecular dynamics method. A large volume dependence of the thermal pressure of Ta was revealed from the analysis of our data. A significant temperature dependence of the calculated effective Grüneisen parameters was confirmed at high pressures. This indicates that the conventional approach to analyze thermal properties using the Mie-Grüneisen approximation is likely to have a significant uncertainty in determining the equation of state for Ta, and that an intrinsic anharmonicity should be considered to analyze the equation of state.
Thermal Transport between Graphene Sheets and SiC Substrate by Molecular-Dynamical Calculation
Zan Wang; Kedong Bi; Huawei Guan; Jiong Wang
2014-01-01
Using nonequilibrium molecular dynamics, we investigate the mechanisms of thermal transport across SiC/graphene sheets. In simulations, 3C-, 4H-, and 6H-SiC are considered separately. Interfacial thermal resistances between Bernal stacking graphene sheets and SiC (Si- or C-terminated) are calculated at the ranges of 100 K~700 K. The results indicate, whether Si-terminated or C-terminated interface, the interfacial thermal resistances of 4H- and 6H-SiC have similar trends over temperatures. Si...
Energy Technology Data Exchange (ETDEWEB)
Kimminau, G; Nagler, B; Higginbotham, A; Murphy, W; Park, N; Hawreliak, J; Kadau, K; Germann, T C; Bringa, E M; Kalantar, D; Lorenzana, H; Remington, B; Wark, J
2008-06-19
Calculations of the x-ray diffraction patterns from shocked crystals derived from the results of Non-Equilibrium-Molecular-Dynamics (NEMD) simulations are presented. The atomic coordinates predicted by the NEMD simulations combined with atomic form factors are used to generate a discrete distribution of electron density. A Fast-Fourier-Transform (FFT) of this distribution provides an image of the crystal in reciprocal space, which can be further processed to produce quantitative simulated data for direct comparison with experiments that employ picosecond x-ray diffraction from laser-irradiated crystalline targets.
Compressive Loads on the Lumbar Spine During Lifting: 4D WATBAK versus Inverse Dynamics Calculations
Directory of Open Access Journals (Sweden)
M. H. Cole
2005-01-01
Full Text Available Numerous two- and three-dimensional biomechanical models exist for the purpose of assessing the stresses placed on the lumbar spine during the performance of a manual material handling task. More recently, researchers have utilised their knowledge to develop specific computer-based models that can be applied in an occupational setting; an example of which is 4D WATBAK. The model used by 4D WATBAK bases its predications on static calculations and it is assumed that these static loads reasonably depict the actual dynamic loads acting on the lumbar spine. Consequently, it was the purpose of this research to assess the agreement between the static predictions made by 4D WATBAK and those from a comparable dynamic model. Six individuals were asked to perform a series of five lifting tasks, which ranged from lifting 2.5 kg to 22.5 kg and were designed to replicate the lifting component of the Work Capacity Assessment Test used within Australia. A single perpendicularly placed video camera was used to film each performance in the sagittal plane. The resultant two-dimensional kinematic data were input into the 4D WATBAK software and a dynamic biomechanical model to quantify the compression forces acting at the L4/L5 intervertebral joint. Results of this study indicated that as the mass of the load increased from 2.5 kg to 22.5 kg, the static compression forces calculated by 4D WATBAK became increasingly less than those calculated using the dynamic model (mean difference ranged from 22.0% for 2.5 kg to 42.9% for 22.5 kg. This study suggested that, for research purposes, a validated three-dimensional dynamic model should be employed when a task becomes complex and when a more accurate indication of spinal compression or shear force is required. Additionally, although it is clear that 4D WATBAK is particularly suited to industrial applications, it is suggested that the limitations of such modelling tools be carefully considered when task-risk and employee
出行行为决策动力系统的演化分析%Evolutionary Analysis of Dynamical Systems of Travel Behavioral Decision-Making
Institute of Scientific and Technical Information of China (English)
李卓君
2013-01-01
The road traffic flow evolutionary patterns of metropolitan areas evolve slowly through a complex multi-dimensional travel decision-making behavior (including travel mode, departure time and route choice joint decision-making). Aims at the general travel behavioral decision-making process, proposes a novel dynamical systems formulation of the traffic assignment problem using evolutionary game theory. The assumptions on drivers ’ behavior in multi-dimensional travel choice are supposed to be fairly general and reasonable. And the stable properties of this dy-namical system on its equilibrium points are investigated using Lyapunov method in a general network. It shows that the evolutionary dynamical system exist only one solution on the condi-tion that the traveler population satisfies some hypotheses which individual ’s trip payoff satisfy some constraint conditions. These mean that there maybe exist inherent motive power which drive the traffic flow evolve to some stable patterns from long run view point. It can improve our understandings to urban traffic flow evolution process and provide significant reference for rele-vant management section.%城市道路流量通过一个复杂的多维出行决策行为（同时包含出行模式、出发时间和路径）缓慢地进行演化。针对一般的出行行为决策过程，使用演化博弈理论，提出一个新的交通分配问题的动力系统模型，对驾驶者的多维出行选择进行相当一般和合理的假设，使用李雅普洛夫方法在一般网络上考察均衡点的稳定性，结果表明，当个体出行收益满足一些约束条件的时候，演化动力系统存在唯一的均衡解。这意味着从长远观点来看，交通系统可能存在着内在的驱动力，使得它的流量朝着稳定的模式发展。这些结果可以提高对于城市交通流演化的理解，并且为相关的管理部分提供有价值的参考。
International Nuclear Information System (INIS)
The aim of this work is to calculate, directly from projection data, concise images characterizing the spatial and temporal distribution of labelled compounds from dynamic PET data. Conventionally, image reconstruction and the calculation of parametric images are performed sequentially. By combining the two processes, low-noise parametric images are obtained, using a computationally feasible parametric iterative reconstruction (Pir) algorithm. Pir is performed by restricting the pixel time - activity curves to a positive linear sum of predefined time characteristics. The weights in this sum are then calculated directly from the PET projection data, using an iterative algorithm based on a maximum-likelihood iterative algorithm commonly used for tomographic reconstruction. The ability of the algorithm to extract known kinetic components from the raw data is assessed, using data from both a phantom experiment and clinical studies. The calculated parametric images indicate differential kinetic behaviour and have been used to aid in the identification of tissues which exhibit differences in the handling of labelled compounds. These parametric images should be helpful in defining regions of interest with similar functional behaviour, and with Fag Pakatal analysis. (author)
Heylighen, Francis
2011-01-01
Evolutionary psychology (EP) is an approach to the study of the mind that is founded on Darwin’s theory of evolution by natural selection. It assumes that our mental abilities, emotions and preferences are adapted specifically for solving problems of survival and reproduction in humanity’s ancestral environment, and derives testable predictions from this assumption. This has important implications for our understanding of the conditions for human well-being.
Reactor physics simulations with coupled Monte Carlo calculation and computational fluid dynamics
International Nuclear Information System (INIS)
A computational code system based on coupling the Monte Carlo code MCNP5 and the Computational Fluid Dynamics (CFD) code STAR-CD was developed as an audit tool for lower order nuclear reactor calculations. This paper presents the methodology of the developed computer program 'McSTAR'. McSTAR is written in FORTRAN90 programming language and couples MCNP5 and the commercial CFD code STAR-CD. MCNP uses a continuous energy cross section library produced by the NJOY code system from the raw ENDF/B data. A major part of the work was to develop and implement methods to update the cross section library with the temperature distribution calculated by STARCD for every region. Three different methods were investigated and implemented in McSTAR. The user subroutines in STAR-CD are modified to read the power density data and assign them to the appropriate variables in the program and to write an output data file containing the temperature, density and indexing information to perform the mapping between MCNP and STAR-CD cells. Preliminary testing of the code was performed using a 3x3 PWR pin-cell problem. The preliminary results are compared with those obtained from a STAR-CD coupled calculation with the deterministic transport code DeCART. Good agreement in the keff and the power profile was observed. Increased computational capabilities and improvements in computational methods have accelerated interest in high fidelity modeling of nuclear reactor cores during the last several years. High-fidelity has been achieved by utilizing full core neutron transport solutions for the neutronics calculation and computational fluid dynamics solutions for the thermal-hydraulics calculation. Previous researchers have reported the coupling of 3D deterministic neutron transport method to CFD and their application to practical reactor analysis problems. One of the principal motivations of the work here was to utilize Monte Carlo methods to validate the coupled deterministic neutron transport
Reactor physics simulations with coupled Monte Carlo calculation and computational fluid dynamics.
Energy Technology Data Exchange (ETDEWEB)
Seker, V.; Thomas, J. W.; Downar, T. J.; Purdue Univ.
2007-01-01
A computational code system based on coupling the Monte Carlo code MCNP5 and the Computational Fluid Dynamics (CFD) code STAR-CD was developed as an audit tool for lower order nuclear reactor calculations. This paper presents the methodology of the developed computer program 'McSTAR'. McSTAR is written in FORTRAN90 programming language and couples MCNP5 and the commercial CFD code STAR-CD. MCNP uses a continuous energy cross section library produced by the NJOY code system from the raw ENDF/B data. A major part of the work was to develop and implement methods to update the cross section library with the temperature distribution calculated by STARCD for every region. Three different methods were investigated and implemented in McSTAR. The user subroutines in STAR-CD are modified to read the power density data and assign them to the appropriate variables in the program and to write an output data file containing the temperature, density and indexing information to perform the mapping between MCNP and STAR-CD cells. Preliminary testing of the code was performed using a 3x3 PWR pin-cell problem. The preliminary results are compared with those obtained from a STAR-CD coupled calculation with the deterministic transport code DeCART. Good agreement in the k{sub eff} and the power profile was observed. Increased computational capabilities and improvements in computational methods have accelerated interest in high fidelity modeling of nuclear reactor cores during the last several years. High-fidelity has been achieved by utilizing full core neutron transport solutions for the neutronics calculation and computational fluid dynamics solutions for the thermal-hydraulics calculation. Previous researchers have reported the coupling of 3D deterministic neutron transport method to CFD and their application to practical reactor analysis problems. One of the principal motivations of the work here was to utilize Monte Carlo methods to validate the coupled deterministic
Directory of Open Access Journals (Sweden)
Oliver Ratmann
2007-11-01
Full Text Available Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication-divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene
Chisholm, Rebecca H.; Lorenzi, Tommaso; Desvillettes, Laurent; Hughes, Barry D.
2016-08-01
Epigenetic mechanisms are increasingly recognised as integral to the adaptation of species that face environmental changes. In particular, empirical work has provided important insights into the contribution of epigenetic mechanisms to the persistence of clonal species, from which a number of verbal explanations have emerged that are suited to logical testing by proof-of-concept mathematical models. Here, we present a stochastic agent-based model and a related deterministic integrodifferential equation model for the evolution of a phenotype-structured population composed of asexually-reproducing and competing organisms which are exposed to novel environmental conditions. This setting has relevance to the study of biological systems where colonising asexual populations must survive and rapidly adapt to hostile environments, like pathogenesis, invasion and tumour metastasis. We explore how evolution might proceed when epigenetic variation in gene expression can change the reproductive capacity of individuals within the population in the new environment. Simulations and analyses of our models clarify the conditions under which certain evolutionary paths are possible and illustrate that while epigenetic mechanisms may facilitate adaptation in asexual species faced with environmental change, they can also lead to a type of "epigenetic load" and contribute to extinction. Moreover, our results offer a formal basis for the claim that constant environments favour individuals with low rates of stochastic phenotypic variation. Finally, our model provides a "proof of concept" of the verbal hypothesis that phenotypic stability is a key driver in rescuing the adaptive potential of an asexual lineage and supports the notion that intense selection pressure can, to an extent, offset the deleterious effects of high phenotypic instability and biased epimutations, and steer an asexual population back from the brink of an evolutionary dead end.
A dynamic economic model and calculation methods for conventional and nuclear power plant
International Nuclear Information System (INIS)
PLTCST is a dynamic economic analysis code for conventional and nuclear power plant. In the code a dynamic economic model and prediction method are used for calculating and comparing nuclear and coal-fired power generation costs and investment efficiency. Using a year by year revenue requirements' procedure together with leveling over the economic life of the plant, the code calculates base costs, fixed costs, constructed costs, power generation costs and average discounted costs of conventional and nuclear power plant in both constant and nominal dollars. According to rules of Energy Department, the indexes of financial and national economy are also considered. As the nuclear energy application is in the beginning in China, the resources collecting may have various forms, and equipment imported, technique transfer and joint venture are also possible. The code has the ability to deal with these conditions separately. So far, the code has been applied successfully to the investment estimation for Fujian province 2 x 600 MW, Qinshan 2 x 600 MW, Jiangsu province 2 x 450 MW nuclear power plants and Guangdong rare-earth plant, and economic analysis of Shenyang antibiotics plant and so on
Lattice dynamic calculated using a range of water potentials for ice Ih
International Nuclear Information System (INIS)
Complete text of publication follows. A series of lattice dynamic calculations have been carried out for the dispersion curves and phonon density of states of ice Ih using a range of pair-wise water potentials (such a MCY, TIP4P and etc) and a one-site polarisable potential developed by Dang et al [1]. It was found that the one-site polarisable potential gives the two-body intermolecular stretching interactions too strong and hence the translational frequencies produced are much high than measured ones. Contrarily, the MCY potential [2] is too weak, resulting that the translational frequency cut-off is much lower than observed. However the TIP4P potential [3] produces the correct bandwidth for both translational and librational frequencies although some details are still incorrectly reproduced. The results show that the lattice (or molecular) dynamic calculations of the vibrational frequencies provide a much sensitive way to test the water potentials developed than the traditional method by reproducing the structure factors of water from the potential functions [4]. (author)
Institute of Scientific and Technical Information of China (English)
无
2010-01-01
A dynamic calculation model of frame supporting structures with prestressed anchors for the slope stability is proposed. The frame and soil are closely contacted in the role of prestressed anchors and they cannot be separated along the whole slope. The lateral displacement of frame and soil is nearly in phase. The movement characteristic satisfies the theory of elastic foundation beam. The frame is treated with elastic foundation beam in this model. The influence of prestressed anchors is simplified as linear spring and damped system related with velocity. Under the condition of horizontal earthquake excitation, the equation of vibration response is established by using the model of dynamic Winkler beam and the analytical solutions are obtained for simple harmonic vibration. This method is applied to a case record for illustration of its capability, in order to verify the method, 3D nonlinear FEM (ADINA) is used to analyze the seismic performance of this case, the comparative results show that the design and the analysis are safe and credible by using the proposed method. The calculation model provides a new way for earthquake analysis and seismic design of slope stability supported by frame structure with prestressed anchors.
International Nuclear Information System (INIS)
The necessity of creating mesophysics is motivated on the basis of a general likeness of the description of many phenomena and processes in micro- and macroworld. For a general and detailed investigation of the former in modern high energy physics (HEP), the Absolute (arising from Minkovsky and irrespective of any reference system) universal approach is used. Its two conceptually new branches are non-linear system-dynamic and non-Euclidean evolutionary ones. They are complementary ones and completely adequate to an extreme complexity of directly unobservable HEP objects. Some primary problems of them are briefly made clear on the basis of synergetics principles and HEP's internal Lobachevsky-Euclidean geometry. They are noted as the primary content of the Lobachevsky-Poincare Programme (LPP) the idea of which has been proposed recently for their successive solution
International Nuclear Information System (INIS)
Highlights: • Defining a DG dynamic planning problem. • Applying a new evolutionary algorithm called “CMAES” in planning process. • Considering electricity price and fuel price variation stochastic conditions. • Scenario generation and reduction with MCS and backward reduction programs. • Considering approximately all of the costs of the distribution system. - Abstract: This paper presents a dynamic DG planning problem considering uncertainties related to the intermittent nature of the DG technologies such as wind turbines and solar units in addition to the stochastic economic conditions. The stochastic economic situation includes the uncertainties related to the fuel and electricity price of each year. The Monte Carlo simulation is used to generate the possible scenarios of uncertain situations and the produced scenarios are reduced through backward reduction program. The aim of this paper is to maximize the revenue of the distribution system through the benefit cost analysis alongside the encouraging and punishment functions. In order to close to reality, the different growth rates for the planning period are selected. In this paper the Covariance Matrix Adaptation Evolutionary Strategy is introduced and is used to find the best planning scheme of the DG units. The different DG types are considered in the planning problem. The main assumption of this paper is that the DISCO is the owner of the distribution system and the DG units. The proposed method is tested on a 9 bus test distribution system and the results are compared with the known genetic algorithm and PSO methods to show the applicability of the CMAES method in this problem
Austrian Carbon Calculator (ACC) - modelling soil carbon dynamics in Austrian soils
Sedy, Katrin; Freudenschuss, Alexandra; Zethner, Gehard; Spiegel, Heide; Franko, Uwe; Gründling, Ralf; Xaver Hölzl, Franz; Preinstorfer, Claudia; Haslmayr, Hans Peter; Formayer, Herbert
2014-05-01
Austrian Carbon Calculator (ACC) - modelling soil carbon dynamics in Austrian soils. The project funded by the Klima- und Energiefonds, Austrian Climate Research Programme, 4th call Authors: Katrin Sedy, Alexandra Freudenschuss, Gerhard Zethner (Environment Agency Austria), Heide Spiegel (Austrian Agency for Health and Food Safety), Uwe Franko, Ralf Gründling (Helmholtz Centre for Environmental Research) Climate change will affect plant productivity due to weather extremes. However, adverse effects could be diminished and satisfying production levels may be maintained with proper soil conditions. To sustain and optimize the potential of agricultural land for plant productivity it will be necessary to focus on preserving and increasing soil organic carbon (SOC). Carbon sequestration in agricultural soils is strongly influenced by management practice. The present management is affected by management practices that tend to speed up carbon loss. Crop rotation, soil cultivation and the management of crop residues are very important measures to influence carbon dynamics and soil fertility. For the future it will be crucial to focus on practical measures to optimize SOC and to improve soil structure. To predict SOC turnover the existing humus balance model the application of the "Carbon Candy Balance" was verified by results from Austrian long term field experiments and field data of selected farms. Thus the main aim of the project is to generate a carbon balancing tool box that can be applied in different agricultural production regions to assess humus dynamics due to agricultural management practices. The toolbox will allow the selection of specific regional input parameters for calculating the C-balance at field level. However farmers or other interested user can also apply their own field data to receive the result of C-dynamics under certain management practises within the next 100 years. At regional level the impact of predefined changes in agricultural management
Belyaev, Andrey K; Lasser, Caroline; Trigila, Giulio
2014-01-01
The Landau--Zener (LZ) type classical-trajectory surface-hopping algorithm is applied to the nonadiabatic nuclear dynamics of the ammonia cation after photoionization of the ground-state neutral molecule to the excited states of the cation. The algorithm employs the recently proposed formula for nonadiabatic LZ transition probabilities derived from the adiabatic potential energy surfaces. The evolution of the populations of the ground state and the two lowest excited adiabatic states is calculated up to 200 fs. The results agree well with quantum simulations available for the first 100 fs based on the same potential energy surfaces. Four different time scales are detected for the nuclear dynamics: Ultrafast Jahn--Teller dynamics between the excited states on a 5 fs time scale; fast transitions between the excited state and the ground state within a time scale of 20 fs; relatively slow partial conversion of a first-excited-state population to the ground state within a time scale of 100 fs; and nearly constant ...
How competition affects evolutionary rescue
Osmond, Matthew Miles; de Mazancourt, Claire
2013-01-01
Populations facing novel environments can persist by adapting. In nature, the ability to adapt and persist will depend on interactions between coexisting individuals. Here we use an adaptive dynamic model to assess how the potential for evolutionary rescue is affected by intra- and interspecific competition. Intraspecific competition (negative density-dependence) lowers abundance, which decreases the supply rate of beneficial mutations, hindering evolutionary rescue. On the other hand, inters...
Cattoli, Giovanni; Fusaro, Alice; Monne, Isabella; Coven, Fethiye; Joannis, Tony; El-Hamid, Hatem S Abd; Hussein, Aly Ahmed; Cornelius, Claire; Amarin, Nadim Mukhles; Mancin, Marzia; Holmes, Edward C; Capua, Ilaria
2011-11-21
Highly pathogenic avian influenza (HPAI) H5N1 (clade 2.2) was introduced into Egypt in early 2006. Despite the control measures taken, including mass vaccination of poultry, the virus rapidly spread among commercial and backyard flocks. Since the initial outbreaks, the virus in Egypt has evolved into a third order clade (clade 2.2.1) and diverged into antigenically and genetically distinct subclades. To better understand the dynamics of HPAI H5N1 evolution in countries that differ in vaccination policy, we undertook an in-depth analysis of those virus strains circulating in Egypt between 2006 and 2010, and compared countries where vaccination was adopted (Egypt and Indonesia) to those where it was not (Nigeria, Turkey and Thailand). This study incorporated 751 sequences (Egypt n=309, Indonesia n=149, Nigeria n=106, Turkey n=87, Thailand n=100) of the complete haemagglutinin (HA) open reading frame, the major antigenic determinant of influenza A virus. Our analysis revealed that two main Egyptian subclades (termed A and B) have co-circulated in domestic poultry since late 2007 and exhibit different profiles of positively selected codons and rates of nucleotide substitution. The mean evolutionary rate of subclade A H5N1 viruses was 4.07×10(-3) nucleotide substitutions per site, per year (HPD 95%, 3.23-4.91), whereas subclade B possessed a markedly higher substitution rate (8.87×10(-3); 95% HPD 7.0-10.72×10(-3)) and a stronger signature of positive selection. Although the direct association between H5N1 vaccination and virus evolution is difficult to establish, we found evidence for a difference in the evolutionary dynamics of H5N1 viruses among countries where vaccination was or was not adopted. In particular, both evolutionary rates and the number of positively selected sites were higher in virus populations circulating in countries applying avian influenza vaccination for H5N1, compared to viruses circulating in countries which had never used vaccination. We
Lattice dynamics and electron-phonon coupling calculations using nondiagonal supercells
Lloyd-Williams, Jonathan H.; Monserrat, Bartomeu
2015-11-01
We study the direct calculation of total energy derivatives for lattice dynamics and electron-phonon coupling calculations using supercell matrices with nonzero off-diagonal elements. We show that it is possible to determine the response of a periodic system to a perturbation characterized by a wave vector with reduced fractional coordinates (m1/n1,m2/n2,m3/n3) using a supercell containing a number of primitive cells equal to the least common multiple of n1,n2, and n3. If only diagonal supercell matrices are used, a supercell containing n1n2n3 primitive cells is required. We demonstrate that the use of nondiagonal supercells significantly reduces the computational cost of obtaining converged zero-point energies and phonon dispersions for diamond and graphite. We also perform electron-phonon coupling calculations using the direct method to sample the vibrational Brillouin zone with grids of unprecedented size, which enables us to investigate the convergence of the zero-point renormalization to the thermal and optical band gaps of diamond.
Accuracy of dynamic calculations using shell models under local impulse loading
International Nuclear Information System (INIS)
Depending on soil conditions and load cases in dynamic calculations of nuclear power plants today more exact mathematical models may be used. For axisymmetric structures like reactor buildings, steel containments, circular tanks or coolant towers mathematical idealisations are used which especially deal with axisymmetric shell models. The calculations for these structures mentioned above, in the last 10 years, were generally carried out by applying specialised and qualified FE-programs. In order to qualify the results obtained using axisymmetric shell models as well the approved computer program MESY (Schrader 1976, 1978) several comparisons between computation and measurements were performed. As an example for these comparisons, impulse loadings, such as aircraft impact, applied by means of a pendulum on the HDR reactor will be shown. The analytical results were obtained prior to the general tests based on a loading function measured in a preliminary test step. In these calculations 11 harmonics were considered in the frequency range up to 80 Hz. Typical results will be shown and discussed, particularly the distribution of the maximum acceleration in the meridional and circumferential direction of the building. The analytical results for the structural response obtained using axisymmetric shell models conform satisfactorily to test results, especially in the area of load introduction in both (meridian and circumferential) directions. (orig.)
Molecular dynamics calculation of rotational diffusion coefficient of a carbon nanotube in fluid
Cao, Bing-Yang; Dong, Ruo-Yu
2014-01-01
Rotational diffusion processes are correlated with nanoparticle visualization and manipulation techniques, widely used in nanocomposites, nanofluids, bioscience, and so on. However, a systematical methodology of deriving this diffusivity is still lacking. In the current work, three molecular dynamics (MD) schemes, including equilibrium (Green-Kubo formula and Einstein relation) and nonequilibrium (Einstein-Smoluchowski relation) methods, are developed to calculate the rotational diffusion coefficient, taking a single rigid carbon nanotube in fluid argon as a case. We can conclude that the three methods produce same results on the basis of plenty of data with variation of the calculation parameters (tube length, diameter, fluid temperature, density, and viscosity), indicative of the validity and accuracy of the MD simulations. However, these results have a non-negligible deviation from the theoretical predictions of Tirado et al. [J. Chem. Phys. 81, 2047 (1984)], which may come from several unrevealed factors of the theory. The three MD methods proposed in this paper can also be applied to other situations of calculating rotational diffusion coefficient.
Energy Technology Data Exchange (ETDEWEB)
Eisenbach, Markus [Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Perera, Meewanage Dilina N. [Univ. of Georgia, Athens, GA (United States). Center for Simulational Physics; Landau, David P [Univ. of Georgia, Athens, GA (United States). Center for Simulational Physics; Nicholson, Don M. [Univ. of North Carolina, Asheville, NC (United States). Dept. of Physics; Yin, Junqi [Univ. of Tennessee, Knoxville, TN (United States). National Inst. for Computational Sciences; Brown, Greg [Florida State Univ., Tallahassee, FL (United States). Dept. of Physics
2015-01-01
We present a unified approach to describe the combined behavior of the atomic and magnetic degrees of freedom in magnetic materials. Using Monte Carlo simulations directly combined with first principles the Curie temperature can be obtained ab initio in good agreement with experimental values. The large scale constrained first principles calculations have been used to construct effective potentials for both the atomic and magnetic degrees of freedom that allow the unified study of influence of phonon-magnon coupling on the thermodynamics and dynamics of magnetic systems. The MC calculations predict the specific heat of iron in near perfect agreement with experimental results from 300K to above Tc and allow the identification of the importance of the magnon-phonon interaction at the phase-transition. Further Molecular Dynamics and Spin Dynamics calculations elucidate the dynamics of this coupling and open the potential for quantitative and predictive descriptions of dynamic structure factors in magnetic materials using first principles-derived simulations.
Methods of Electro-Dynamic Stability Calculation of Flexible Bus-bars in High Voltage Switch Gears
Directory of Open Access Journals (Sweden)
I. I. Sergey
2010-01-01
Full Text Available The improved vector-parametrical and simplified methods for calculation of electro-dynamic stability parameters of flexible busbars in high voltage switch gears have been presented in the paper. The developed methods and their software can be taken as a basis of methodological instructions on calculation of short-circuit current electro-dynamic action on flexible conductors of switching gears.
Poulicard, Nils; Pacios, Luis Fernández; Gallois, Jean-Luc; Piñero, Daniel; García-Arenal, Fernando
2016-08-01
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the
Poulicard, Nils; Pacios, Luis Fernández; Gallois, Jean-Luc; Piñero, Daniel; García-Arenal, Fernando
2016-01-01
This work analyses the genetic variation and evolutionary patterns of recessive resistance loci involved in matching-allele (MA) host-pathogen interactions, focusing on the pvr2 resistance gene to potyviruses of the wild pepper Capsicum annuum glabriusculum (chiltepin). Chiltepin grows in a variety of wild habitats in Mexico, and its cultivation in home gardens started about 25 years ago. Potyvirus infection of Capsicum plants requires the physical interaction of the viral VPg with the pvr2 product, the translation initiation factor eIF4E1. Mutations impairing this interaction result in resistance, according to the MA model. The diversity of pvr2/eIF4E1 in wild and cultivated chiltepin populations from six biogeographical provinces in Mexico was analysed in 109 full-length coding sequences from 97 plants. Eleven alleles were found, and their interaction with potyvirus VPg in yeast-two-hybrid assays, plus infection assays of plants, identified six resistance alleles. Mapping resistance mutations on a pvr2/eIF4E1 model structure showed that most were around the cap-binding pocket and strongly altered its surface electrostatic potential, suggesting resistance-associated costs due to functional constraints. The pvr2/eIF4E1 phylogeny established that susceptibility was ancestral and resistance was derived. The spatial structure of pvr2/eIF4E1 diversity differed from that of neutral markers, but no evidence of selection for resistance was found in wild populations. In contrast, the resistance alleles were much more frequent, and positive selection stronger, in cultivated chiltepin populations, where diversification of pvr2/eIF4E1 was higher. This analysis of the genetic variation of a recessive resistance gene involved in MA host-pathogen interactions in populations of a wild plant show that evolutionary patterns differ according to the plant habitat, wild or cultivated. It also demonstrates that human management of the plant population has profound effects on the
Hunt, Tam
2015-01-01
Evolution as an idea has a lengthy history, even though the idea of evolution is generally associated with Darwin today. Rebecca Stott provides an engaging and thoughtful overview of this history of evolutionary thinking in her 2013 book, Darwin's Ghosts: The Secret History of Evolution. Since Darwin, the debate over evolution—both how it takes place and, in a long war of words with religiously-oriented thinkers, whether it takes place—has been sustained and heated. A growing share of this de...
Institute of Scientific and Technical Information of China (English)
Ordom Brian Huot; Punya Nachappa; Cecilia Tamborindeguy
2013-01-01
Plants have evolved and diversified to reduce the damages imposed by infectious pathogens and herbivorous insects.Living in a sedentary lifestyle,plants are constantly adapting to their environment.They employ various strategies to increase performance and fitness.Thus,plants developed cost-effective strategies to defend against specific insects and pathogens.Plant defense,however,imposes selective pressure on insects and pathogens.This selective pressure provides incentives for pathogens and insects to diversify and develop strategies to counter plant defense.This results in an evolutionary arms race among plants,pathogens and insects.The ever-changing adaptations and physiological alterations among these organisms make studying plant-vector-pathogen interactions a challenging and fascinating field.Studying plant defense and plant protection requires knowledge of the relationship among organisms and the adaptive strategies each organism utilize.Therefore,this review focuses on the integral parts of plant-vectorpathogen interactions in order to understand the factors that affect plant defense and disease development.The review addresses plant-vector-pathogen co-evolution,plant defense strategies,specificity of plant defenses and plant-vector-pathogen interactions.Improving the comprehension of these factors will provide a multi-dimensional perspective for the future research in pest and disease management.
CALCULATION OF THE UNIQUE HIGH-RISE BUILDING FOR EARTHQUAKES IN NONLINEAR DYNAMIC FORMULATION
Directory of Open Access Journals (Sweden)
Mkrtychev Oleg Vartanovich
2016-06-01
Full Text Available The article contains the calculation of a 80-storey high-rise building on 3-component accelerograms with different dominant frequencies. The “Akhmat Tower” belongs to the complex “Grozny-city 2” and is classified as a unique construction, its height is 400 m. During the construction unique high-rise buildings and high-rise buildings in seismic areas an additional computational studies are required, which should take into account the nonlinear nature of the design. For the case of linear instrumental-synthesized accelerograms, it is necessary to apply nonlinear dynamic methods. The studies were conducted using the software LS-DYNA, implementing the methods of direct integration of the equations of motion by the explicit scheme. The constructive scheme of the building frame is braced, the spatial stability is ensured by load-bearing interior walls, columns and hard disks, and frame metal coatings. The choice of the type and dimensions of the finite element and the step of integration is due to the ability to perform calculations in reasonable time, and to the required accuracy of calculation. For this aim the issues of convergence of the solutions on a number of settlement schemes were investigated with the terms of thickened mesh of finite elements: 0.5 m; 1 m; 2 m; 3 m. As a result of the research it was obtained that the best is to split into finite elements with a characteristic size of 2 m. The calculation of the building is made on rigid foundation. The authors used accelerograms normalized for earthquakes of 8 and 9 points on the MSK-64 scale. The destruction of the elements in the process of loading, and the interaction of the elements during their contact was taken into account, i.e. the calculation was made taking into account physical, geometrical and structural nonlinearities. The article analyzes the results of the calculation. The authors evaluated the seismic stability of the building. Possible ways to improve the seismic
Reactor physics simulations with coupled Monte Carlo calculation and computational fluid dynamics
International Nuclear Information System (INIS)
The interest in high fidelity modeling of nuclear reactor cores has increased over the last few years and has become computationally more feasible because of the dramatic improvements in processor speed and the availability of low cost parallel platforms. In the research here high fidelity, multi-physics analyses was performed by solving the neutron transport equation using Monte Carlo methods and by solving the thermal-hydraulics equations using computational fluid dynamics. A computation tool based on coupling the Monte Carlo code MCNP5 and the Computational Fluid Dynamics (CFD) code STAR-CD was developed as an audit tool for lower order nuclear reactor calculations. This paper presents the methodology of the developed computer program 'McSTAR' along with the verification and validation efforts. McSTAR is written in PERL programming language and couples MCNP5 and the commercial CFD code STAR-CD. MCNP uses a continuous energy cross section library produced by the NJOY code system from the raw ENDF/B data. A major part of the work was to develop and implement methods to update the cross section library with the temperature distribution calculated by STAR-CD for every region. Three different methods were investigated and two of them are implemented in McSTAR. The user subroutines in STAR-CD are modified to read the power density data and assign them to the appropriate variables in the program and to write an output data file containing the temperature, density and indexing information to perform the mapping between MCNP and STAR-CD cells. The necessary input file manipulation, data file generation, normalization and multi-processor calculation settings are all done through the program flow in McSTAR. Initial testing of the code was performed using a single pin cell and a 3X3 PWR pin-cell problem. The preliminary results of the single pin-cell problem are compared with those obtained from a STAR-CD coupled calculation with the deterministic transport code De
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
Institute of Scientific and Technical Information of China (English)
徐峥; 安田启司; 刘晓峻
2015-01-01
In order to design a sonochemical reactor with high reaction efficiency, it is important to clarify the size and intensity of the sonochemical reaction field. In this study, the reaction field in a sonochemical reactor is estimated from the distribution of pressure above the threshold for cavitation. The quantitation of hydroxide radical in a sonochemical reactor is obtained from the calculation of bubble dynamics and reaction equations. The distribution of the reaction field of the numerical simulation is consistent with that of the sonochemical luminescence. The sound absorption coefficient of liquid in the sonochemical reactor is much larger than that attributed to classical contributions which are heat conduction and shear viscosity. Under the dual irradiation, the reaction field becomes extensive and intensive because the acoustic pressure amplitude is intensified by the interference of two ultrasonic waves.
Bilayer Hubbard model for 3He: a cluster dynamical mean-field calculation
International Nuclear Information System (INIS)
Inspired by recent experiments on bilayer 3He, we consider a bilayer Hubbard model on a triangular lattice. For appropriate model parameters, we observe a band-selective Mott transition at a critical chemical potential, μc, corresponding to the solidification of the fermions in the first layer. The growth of the effective mass on the metallic side (μ c) is cut off by a first order transition in which the first layer fermions drop out of the Luttinger volume and their spin degrees of freedom become locked in a spin singlet state. These results are obtained from a cluster dynamical mean-field calculation on an eight-site cluster with a quantum Monte Carlo cluster solver.
Dynamic Response Calculation of Spatial Elastic Multibody Systems with High-Frequency Excitation
International Nuclear Information System (INIS)
The objective of this paper is to establish a computational scheme for dynamic response calculations of a three-dimensional multibody mechanical system with impulsive forces, which give rise to high-frequency excitations. The finite-element method is employed to represent the local deformations of three-dimensional beam-like elastic components by either a finite set of nodal coordinates or a truncated set of modal coordinates. A reduced-order model is obtained by invoking a modal transformation. Both planar and complex modal reduction schemes are established. The developed formulation is implemented into a multibody simulation program that assembles the equations of motion and proceeds with its solution. The computational scheme permits a change in the basis of the modal space in order to regulate the admittance of higher frequencies and to accommodate any change in the kinematic configuration. Numerical examples are presented to demonstrate the applicability of the developed computational scheme
Evolutionary constrained optimization
Deb, Kalyanmoy
2015-01-01
This book makes available a self-contained collection of modern research addressing the general constrained optimization problems using evolutionary algorithms. Broadly the topics covered include constraint handling for single and multi-objective optimizations; penalty function based methodology; multi-objective based methodology; new constraint handling mechanism; hybrid methodology; scaling issues in constrained optimization; design of scalable test problems; parameter adaptation in constrained optimization; handling of integer, discrete and mix variables in addition to continuous variables; application of constraint handling techniques to real-world problems; and constrained optimization in dynamic environment. There is also a separate chapter on hybrid optimization, which is gaining lots of popularity nowadays due to its capability of bridging the gap between evolutionary and classical optimization. The material in the book is useful to researchers, novice, and experts alike. The book will also be useful...
Evolutionary genetics of maternal effects.
Wolf, Jason B; Wade, Michael J
2016-04-01
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
Svrčková, Pavla; Pysanenko, Andriy; Lengyel, Jozef; Rubovič, Peter; Kočišek, Jaroslav; Poterya, Viktoriya; Slavíček, Petr; Fárník, Michal
2015-10-21
We investigate the solvent effects on photodissociation dynamics of the S-H bond in ethanethiol CH3CH2SH (EtSH). The H fragment images are recorded by velocity map imaging (VMI) at 243 nm in various expansion regimes ranging from isolated molecules to clusters of different sizes and compositions. The VMI experiment is accompanied by electron ionization mass spectrometry using a reflectron time-of-flight mass spectrometer (RTOFMS). The experimental data are interpreted using ab initio calculations. The direct S-H bond fission results in a peak of fast fragments at Ekin(H) ≈ 1.25 eV with a partly resolved structure corresponding to vibrational levels of the CH3CH2S cofragment. Clusters of different nature ranging from dimers to large (EtSH)N, N ≥ 10, clusters and to ethanethiol clusters embedded in larger argon "snowballs" are investigated. In the clusters a sharp peak of near-zero kinetic energy fragments occurs due to the caging. The dynamics of the fragment caging is pictured theoretically, using multi-reference ab initio theory for the ethanethiol dimer. The larger cluster character is revealed by the simultaneous analysis of the VMI and RTOFMS experiments; none of these tools alone can provide the complete picture. PMID:25743944
Insights inot the atomic many-particle dynamics of scattering processes by ab-initio calculations
International Nuclear Information System (INIS)
The present thesis gives a theoretical contribution to the understanding of the many-particle dynamics in inelastic ion-atom collisions. Many-electron dynamics in ion-helium collisions and proton-sodium collisions was theoretically studied. The description is based on the semiclassical approximation with the straight orbit for the projectile motion. The ion-atom collision problem is by this reduced to a time-dependent many-electron problem and in the non-relativistic approximation described by the time-dependent Schroedinger equation. The solution of the many-electron problem pursues in the framework of the time-dependent density functional theory. The time-dependent Schroedinger equation for the interacting many-electron problem is transformed to the system of the time-dependent Kohn-Sham equations and solved by the two-center-basis generator method. The unknown time-dependent exchange-correlation one-particle potential forces different approximation int he time-dependent Kohn-Shan scheme. In this thesis the model of the independent electrons was applied as basis model, in which the electron-electron correlation is consistently neglected in all parts and in all steps. Differential cross sections for different one- and two-electron processes were calculated in the so-called eikonal approximation for the collisional systems p-He, He2+-He, and Arq+-He (q=15-18)
International Nuclear Information System (INIS)
Molecular dynamics method is used for the properties prediction of new lanthanum-strontium cuprates La2-xSrxCuO4-δ based functional materials. The most interesting phases have been synthesized, and electrophysical and thermomechanical properties have been investigated for the verification of acquired calculated data. High values of oxygen diffusion constants is demonstrated to be occurred in solid solutions La2-xSrxCuO4-δ with fine degree of substitution Sr→La (to x=1). Values of lattice parameters, thermal expansion coefficients and oxygen diffusion constants are agree with experimental data. Observed anisotropy of anion transport for all studied compositions is responsible for peculiarities of crystal structure of complex oxides. Applied molecular dynamics method permits to reveal the contribution of separate kinds of oxygen ions (equatorial and apical) in ionic transport at microscopic level, as well as really prove that the oxygen diffusion happens in the ordinary jump mechanism, mainly in (CuO2)-layers
The effect of walking speed on local dynamic stability is sensitive to calculation methods
DEFF Research Database (Denmark)
Stenum, Jan; Bruijn, Sjoerd M; Jensen, Bente Rona
2014-01-01
Local dynamic stability has been assessed by the short-term local divergence exponent (λS), which quantifies the average rate of logarithmic divergence of infinitesimally close trajectories in state space. Both increased and decreased local dynamic stability at faster walking speeds have been......% and 140% of preferred walking speed) for 3min each, while upper body accelerations in three directions were sampled. From these time-series, λS was calculated by three different methods using: (a) a fixed time interval and expressed as logarithmic divergence per stride-time (λS-a), (b) a fixed number...... of strides and expressed as logarithmic divergence per time (λS-b) and (c) a fixed number of strides and expressed as logarithmic divergence per stride-time (λS-c). Mean preferred walking speed was 1.16±0.09m/s. There was only a minor effect of walking speed on λS-a. λS-b increased with increasing...
Palomeque, Teresa; Muñoz-López, Martín; Carrillo, José A; Lorite, Pedro
2005-01-01
The present study characterizes the complex satellite DNA from the specialized phytophagous beetle species Chrysolina carnifex. The satellite DNA is formed by six monomer types, partially homologous but having diverged enough to be separate on the phylogenetic trees, since each monomer type is located on a different branch, having statistically significant bootstrap values. Its analysis suggests a common evolutionary origin of all monomers from the same 211-bp sequence mainly by means of base-substitution mutations evolutionarily fixed to each monomer type and duplications and/or deletions of pre-existing segments in the 211-bp sequence. The analysis of the sequences and Southern hybridizations suggest that the monomers are organized in three types of repeats: monomers (211-bp) and higher-order repeats in the form of dimers (477-bp) or even trimers (633-bp). These repetitive units are not isolated from others, and do not present the pattern characteristic for the regular tandem arrangement of satellite DNA. In-situ hybridization with biotinylated probes corresponding to the three types of repeats showed the pericentromeric location of these sequences in all meiotic bivalents, coinciding with the heterochromatic blocks revealed by C-banding, indicating in addition that each type of repeat is neither isolated from others nor located in specific chromosomes but rather that they are intermixed in the heterochromatic regions. The presence of this repetitive DNA in C. haemoptera, C. bankii and C. americana was also tested by Southern analysis. The results show that this satellite DNA sequence is specific to the C. carnifex genome but has not been found in three other species of Chrysolina occupying similar or different host plants. PMID:16331411
Directory of Open Access Journals (Sweden)
Xiaohong Li
2011-02-01
Full Text Available Aside from primary prevention, early detection remains the most effective way to decrease mortality associated with the majority of solid cancers. Previous cancer screening models are largely based on classification of at-risk populations into three conceptually defined groups (normal, cancer without symptoms, and cancer with symptoms. Unfortunately, this approach has achieved limited successes in reducing cancer mortality. With advances in molecular biology and genomic technologies, many candidate somatic genetic and epigenetic "biomarkers" have been identified as potential predictors of cancer risk. However, none have yet been validated as robust predictors of progression to cancer or shown to reduce cancer mortality. In this Perspective, we first define the necessary and sufficient conditions for precise prediction of future cancer development and early cancer detection within a simple physical model framework. We then evaluate cancer risk prediction and early detection from a dynamic clonal evolution point of view, examining the implications of dynamic clonal evolution of biomarkers and the application of clonal evolution for cancer risk management in clinical practice. Finally, we propose a framework to guide future collaborative research between mathematical modelers and biomarker researchers to design studies to investigate and model dynamic clonal evolution. This approach will allow optimization of available resources for cancer control and intervention timing based on molecular biomarkers in predicting cancer among various risk subsets that dynamically evolve over time.
An algorithm for the calculation of dose distributions from dynamic wedges
International Nuclear Information System (INIS)
The Clinac 2100C of Varian has the option of a dynamic wedge. The control of the dynamic wedge is done by means of a segmentation table, which specifies a number of asymmetric fields with corresponding numbers of monitor units. Advantages of this dynamic wedge are the possibility to have more wedge angles and an increased flexibility of operation; a disadvantage is that the measurement of the data needed for a planning system may be time consuming. For the calculation of the dose distribution, we have developed an algorithm which eradicates this disadvantage because it only uses measured data from square fields of the open beam: central axis depth-doses, profiles and Peak Scatter Factors. It is based on a previously developed method which separates the dose into three factors: depth-dose, boundary distribution and envelope profile, and computes the dose of irregular field as well. Depth-dose and boundary distribution are computed by convolution of a field intensity with 'scatter' and 'boundary' pencil beam kernels respectively. For a rectangular field, the field intensity is computed by a weighted sum of intensity matrices, derived from the segmentation table. The matrix elements are equal to 1 within the asymmetric fields and equal to an effective transmission factor under the jaws. The weighting factors in the sum take into account the number of monitor units and the collimator scatter back to the monitor. For an irregular field, the blocked parts of the field are modified, taking into account the transmission through the blocks. This algorithm has been implemented in CADPLAN (Varian-Dosetek) and has been compared with measurements. The results are in good agreement with the international requirements on dose accuracy
On the Calculation of Solid-Fluid Contact Angles from Molecular Dynamics
Directory of Open Access Journals (Sweden)
Carmelo Herdes
2013-09-01
Full Text Available A methodology for the determination of the solid-fluid contact angle, to be employed within molecular dynamics (MD simulations, is developed and systematically applied. The calculation of the contact angle of a fluid drop on a given surface, averaged over an equilibrated MD trajectory, is divided in three main steps: (i the determination of the fluid molecules that constitute the interface, (ii the treatment of the interfacial molecules as a point cloud data set to define a geometric surface, using surface meshing techniques to compute the surface normals from the mesh, (iii the collection and averaging of the interface normals collected from the post-processing of the MD trajectory. The average vector thus found is used to calculate the Cassie contact angle (i.e., the arccosine of the averaged normal z-component. As an example we explore the effect of the size of a drop of water on the observed solid-fluid contact angle. A single coarse-grained bead representing two water molecules and parameterized using the SAFT-γ Mie equation of state (EoS is employed, meanwhile the solid surfaces are mimicked using integrated potentials. The contact angle is seen to be a strong function of the system size for small nano-droplets. The thermodynamic limit, corresponding to the infinite size (macroscopic drop is only truly recovered when using an excess of half a million water coarse-grained beads and/or a drop radius of over 26 nm.
Teo, Ivan; Mayne, Christopher G; Schulten, Klaus; Lelièvre, Tony
2016-06-14
Adaptive multilevel splitting (AMS) is a rare event sampling method that requires minimal parameter tuning and allows unbiased sampling of transition pathways of a given rare event. Previous simulation studies have verified the efficiency and accuracy of AMS in the calculation of transition times for simple systems in both Monte Carlo and molecular dynamics (MD) simulations. Now, AMS is applied for the first time to an MD simulation of protein-ligand dissociation, representing a leap in complexity from the previous test cases. Of interest is the dissociation rate, which is typically too low to be accessible to conventional MD. The present study joins other recent efforts to develop advanced sampling techniques in MD to calculate dissociation rates, which are gaining importance in the pharmaceutical field as indicators of drug efficacy. The system investigated here, benzamidine bound to trypsin, is an example common to many of these efforts. The AMS estimate of the dissociation rate was found to be (2.6 ± 2.4) × 10(2) s(-1), which compares well with the experimental value. PMID:27159059
International Nuclear Information System (INIS)
The paper gives a brief survey of the fifth three-dimensional dynamic Atomic Energy Research benchmark calculation results received with the code DYN3D/ATHLET at NRI Rez. This benchmark was defined at the seventh Atomic Energy Research Symposium (Hoernitz near Zittau, 1997). Its initiating event is a symmetrical break of the main steam header at the end of the first fuel cycle and hot shutdown conditions with one stuck out control rod group. The calculations were performed with the externally coupled codes ATHLET Mod.1.1 Cycle C and DYN3DH1.1/M3. The standard WWER-440/213 input deck of ATHLET code was adopted for benchmark purposes and for coupling with the code DYN3D. The first part of paper contains a brief characteristics of NPP input deck and reactor core model. The second part shows the time dependencies of important global and local parameters. In comparison with the results published at the eighth Atomic Energy Research Symposium (Bystrice nad Pernstejnem, 1998), the results published in this paper are based on improved ATHLET descriptions of control and safety systems. (Author)
Results of the fifth three-dimensional dynamic atomic energy research benchmark problem calculation
International Nuclear Information System (INIS)
The pare gives a brief survey of the fifth three-dimensional dynamic atomic energy research benchmark calculation results received with the code DYN3D/ATHLET at NRI Rez. This benchmark was defined at the seventh AER Symposium. Its initiating event is a symmetrical break of the main steam header at the end of the first fuel cycle and hot shutdown conditions with one stuck out control rot group. The calculations were performed with the externally coupled codes ATHLET Mod.1.1 Cycle C and DYN3DH1.1/M3. The Kasseta library was used for the generation of reactor core neutronic parameters. The standard WWER-440/213 input deck of ATHLET code was adopted for benchmark purposes and for coupling with the code DYN3D. The first part of paper contains a brief characteristics of NPP input deck and reactor core model. The second part shows the time dependencies of important global, fuel assembly and loops parameters.(Author)
Institute of Scientific and Technical Information of China (English)
WANGShidao; HUANGPeizhu
1995-01-01
Along with underground mining, movement and deformation of overburden gradually extends in all directions and up to the ground surface and finally forms a surface subsidence basin. The surface movement progressively stabilizes until coal mining is completed and forms a stable movement basin. Two types of basins, i.e. static and dynamic subsidence basins are distinguished in the paper, a classification of the basins and a description of their characteristics are presented. Based on the analysis of measured data by Yanzhou Coal Mining Bureau, during mining operation, the movement characteristics of surface point, subsidence equation, subsidence rate equation and the law of distribution of movement parameters of surface point relative to principal section of movement basin are addressed in this paper. Moreover the calculating formula of the movement parameters for an arbitrary surface point and the expression for calculating the maximum subsidence rate are also proposed. On the basis of the findings, the movement deformation formula for an arbitrary surface point in any directions during mining operation is highlighted.
Transmission Loss Calculation using A and B Loss Coefficients in Dynamic Economic Dispatch Problem
Jethmalani, C. H. Ram; Dumpa, Poornima; Simon, Sishaj P.; Sundareswaran, K.
2016-04-01
This paper analyzes the performance of A-loss coefficients while evaluating transmission losses in a Dynamic Economic Dispatch (DED) Problem. The performance analysis is carried out by comparing the losses computed using nominal A loss coefficients and nominal B loss coefficients in reference with load flow solution obtained by standard Newton-Raphson (NR) method. Density based clustering method based on connected regions with sufficiently high density (DBSCAN) is employed in identifying the best regions of A and B loss coefficients. Based on the results obtained through cluster analysis, a novel approach in improving the accuracy of network loss calculation is proposed. Here, based on the change in per unit load values between the load intervals, loss coefficients are updated for calculating the transmission losses. The proposed algorithm is tested and validated on IEEE 6 bus system, IEEE 14 bus, system IEEE 30 bus system and IEEE 118 bus system. All simulations are carried out using SCILAB 5.4 (www.scilab.org) which is an open source software.
Jing Chen; Rui-Min Wang; Lei Li; Zhi-Hong Zhang; Xiao-She Dong
2013-01-01
Due to high efficiency and good scalability, hierarchical hybrid P2P architecture has drawn more and more attention in P2P streaming research and application fields recently. The problem about super peer selection, which is the key problem in hybrid heterogeneous P2P architecture, is becoming highly challenging because super peers must be selected from a huge and dynamically changing network. A distributed super peer selection (SPS) algorithm for hybrid heterogeneous P2P streaming system base...
Baillie, Gregory J.; Galiano, Monica; Agapow, Paul-Michael; Myers, Richard; Chiam, Rachael; Gall, Astrid; Palser, Anne L.; Watson, Simon J.; Hedge, Jessica; Underwood, Anthony; Platt, Steven; McLean, Estelle; Pebody, Richard G.; Rambaut, Andrew; Green, Jonathan
2012-01-01
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of ...
Murase, Yohsuke
2010-06-01
Community assembly is studied using individual-based multispecies models. The models have stochastic population dynamics with mutation, migration, and extinction of species. Mutants appear as a result of mutation of the resident species, while migrants have no correlation with the resident species. It is found that the dynamics of community assembly with mutations are quite different from the case with migrations. In contrast to mutation models, which show intermittent dynamics of quasi-steady states interrupted by sudden reorganizations of the community, migration models show smooth and gradual renewal of the community. As a consequence, instead of the 1/f diversity fluctuations found for the mutation models, 1/f2, random-walk like fluctuations are observed for the migration models. In addition, a characteristic species-lifetime distribution is found: a power law that is cut off by a "skewed" distribution in the long-lifetime regime. The latter has a longer tail than a simple exponential function, which indicates an age-dependent species-mortality function. Since this characteristic profile has been observed, both in fossil data and in several other mathematical models, we conclude that it is a universal feature of macroevolution. © 2010 Elsevier Ltd.
Calculation model of non-linear dynamic deformation of composite multiphase rods
Directory of Open Access Journals (Sweden)
Mishchenko Andrey Viktorovich
2014-05-01
Full Text Available The method of formulating non-linear physical equations for multiphase rods is suggested in the article. Composite multiphase rods possess various structures, include shear, polar, radial and axial inhomogeneity. The Timoshenko’s hypothesis with the large rotation angles is used. The method is based on the approximation of longitudinal normal stress low by basic functions expansions regarding the linear viscosity low. The shear stresses are calculated with the equilibrium equation using the subsidiary function of the longitudinal shift force. The system of differential equations connecting the internal forces and temperature with abstract deformations are offered by the basic functions. The application of power functions with arbitrary index allows presenting the compact form equations. The functional coefficients in this system are the highest order rigidity characteristics. The whole multiphase cross-section rigidity characteristics are offered the sums of the rigidity characteristics of the same phases individually. The obtained system allows formulating the well-known particular cases. Among them: hard plasticity and linear elastic deformation, different module deformation and quadratic Gerstner’s low elastic deformation. The reform of differential equations system to the quasilinear is suggested. This system contains the secant variable rigidity characteristics depending on abstract deformations. This system includes the sum of the same uniform blocks of different order. The rods phases defined the various set of uniform blocks phase materials. The integration of dynamic, kinematic and physical equations taking into account initial and edge condition defines the full dynamical multiphase rods problem. The quasilinear physical equations allow getting the variable flexibility matrix of multiphase rod and rods system.
Calculation of the renal clearance by dynamic measurement of the excreted activity
International Nuclear Information System (INIS)
Aim: In this paper we present a new method to measure the renal slope-clearance of Tc-99m-MAG-3 in a single-shot model (Excretion-clearance). Method: A renal scintigraphy with Tc-99m-MAG-3 was performed in 22 patients. The excreted activity of the tracer in the kidneys and the bladder was dynamically measured using a double-head gamma-camera. Additionally, the total absorption over the kidneys and the bladder was determined. The Excretion-clearance was calculated in a differential and an integral variant. Simultaneously the 2-compartment-clearance (Sapirstein-clearance), the Oberhausen-clearance and the Bubeck-clearance were calculated. Results: The Sapirstein-clearance is considered as the 'goldstandard' in a single-shot modell. The correlation of the Bubeck-clearance and the Oberhausen-clearance ranged from r=0.96 to r=0.97, the Excretion-clearance (differential-method) correlated with r=0.90. The absolute difference of the clearance-values was lowest comparing the Bubeck-clearance with the Sapirstein-clearance with an average difference of 11%, whereas the Excretion-clearance revealed at least an average difference of 21% and the Oberhausen-clearance of 24%. Discussion: The Excretion-clearance requires a more complicated protocoll measuring the clearance in comparison to the Bubeck-clearance. The results of the excretion-clearance differ more from the Sapirstein-clearance with regard to the examined patient population than the Bubeck-clearance. Regarding the theoretical basis of the methods, we expect advantages of the Excretion-clearance compared with the Bubeck-clearance in patients with compartmental disproportion or with a low clearance. We are going to prove this in combination with the above mentioned methodical improvements in a further study. (orig.)
Evolutionary Information Theory
Mark Burgin
2013-01-01
Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we const...
International Nuclear Information System (INIS)
The two-plane HUBBARD model, which is a model for some electronic properties of undoped YBCO superconductors as well as displays a MOTT metal-to-insulator transition and a metal-to-band insulator transition, is studied within Dynamical Mean-Field Theory using HIRSCH-FYE Monte Carlo. In order to find the different transitions and distinguish the types of insulator, we calculate the single-particle spectral densities, the self-energies and the optical conductivities. We conclude that there is a continuous transition from MOTT to band insulator. In the second part, ground state properties of a diagonally disordered HUBBARD model is studied using a generalisation of Path Integral Renormalisation Group, a variational method which can also determine low-lying excitations. In particular, the distribution of antiferromagnetic properties is investigated. We conclude that antiferromagnetism breaks down in a percolation-type transition at a critical disorder, which is not changed appreciably by the inclusion of correlation effects, when compared to earlier studies. Electronic and excitation properties at the system sizes considered turn out to primarily depend on the geometry. (orig.)
Implicit finite-difference method for fluid-dynamics calculation in the primary coolant systems
International Nuclear Information System (INIS)
A multidimensional Eulerian finite-difference method for calculating fluid transients in the primary coolant systems of liquid metal fast breeder reactors is described. The full, time-dependent, nonlinear hydrodynamic equations employed in the formulation are approximated by finite-difference forms and solved numerically using the implicit treatment of the density and velocity of the ICE technique. For pressure loading in any range, the method offers a stable and accurate scheme. In the elbow region, a two-dimensional model is considered to approximate the flow in the radial and tangential directions. In the straight pipe or other piping components the flow is assumed to be axisymmetric. The external walls of the pipe and components can be considered either as rigid or deformable, while those of the elbow can only be rigid. In the deformable-wall analysis, a thin-shell model is provided to analyze the dynamic response of the component wall. Three examples are given, illustrating the analysis of pressure-pulse propagation in the fluid contained (1) in an elastic-plastic pipe, (2) in a pipe-elbow loop, and (3) in a simple valve system. (7 references) (U.S.)
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
Energy Technology Data Exchange (ETDEWEB)
Andoh, Y.; Yoshii, N.; Yamada, A.; Kojima, H.; Mizutani, K.; Okazaki, S., E-mail: okazaki@apchem.nagoya-u.ac.jp [Department of Applied Chemistry, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan); Fujimoto, K. [Department of Pharmacy, College of Pharmaceutical Sciences, Ritsumeikan University, Nojihigashi, Kusatsu, Shiga 525-8577 (Japan); Nakagawa, A. [Institute for Protein Research, Osaka University, Yamadaoka, Suita, Osaka 565-0871 (Japan); Nomoto, A. [Institute of Microbial Chemistry, Kamiosaki, Shinagawa-ku, Tokyo 141-0021 (Japan)
2014-10-28
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 10{sup 6} all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it.
International Nuclear Information System (INIS)
The principle of corresponding state on the fluctuation structure, which is the spatial distribution of various clusters of molecules caused by density fluctuations, in supercritical states around the critical points has been investigated. In this paper, we performed Molecular Dynamics (MD) simulation to extract the fluctuation structure around the critical points of 2-Center-Lennard-Jones (2CLJ) fluids, whose characteristics change by their molecular elongations. First, we indentified some critical points of 2CLJ fluids with comparatively shorter elongations applying Lotfi's function, which correctly describes the liquid-vapor coexistence line of Lennard-Jones (LJ) fluid, and successfully defined each critical point. Next, two methods were applied in the estimation of the fluctuation structure: one is the evaluation of the dispersion of the number of molecules at a certain domain, and the other is the calculation of static structure factor. As a result, in 2CLJ fluids which have shorter molecular elongations comparatively, the principle of corresponding state is satisfied because of the small differences in the fluctuation structures extracted in the present two methods. On the other hand, some results imply that the fluctuation may decrease in 2CLJ fluids which have the longer molecular elongations although more accurate evaluation of the critical points in those fluids is necessary for the further investigation. (author)
Energy Technology Data Exchange (ETDEWEB)
Heilmann, D.B.
2007-02-15
The two-plane HUBBARD model, which is a model for some electronic properties of undoped YBCO superconductors as well as displays a MOTT metal-to-insulator transition and a metal-to-band insulator transition, is studied within Dynamical Mean-Field Theory using HIRSCH-FYE Monte Carlo. In order to find the different transitions and distinguish the types of insulator, we calculate the single-particle spectral densities, the self-energies and the optical conductivities. We conclude that there is a continuous transition from MOTT to band insulator. In the second part, ground state properties of a diagonally disordered HUBBARD model is studied using a generalisation of Path Integral Renormalisation Group, a variational method which can also determine low-lying excitations. In particular, the distribution of antiferromagnetic properties is investigated. We conclude that antiferromagnetism breaks down in a percolation-type transition at a critical disorder, which is not changed appreciably by the inclusion of correlation effects, when compared to earlier studies. Electronic and excitation properties at the system sizes considered turn out to primarily depend on the geometry. (orig.)
International Nuclear Information System (INIS)
In this paper the authors study the on- momentum nonlinear equations of motion for the coupled transverse motion of a single charged particle in a storage ring. The authors seek for the maximum initial linear amplitudes in the two transverse directions x and y which lead to bounded particle motion as t tends to infinity. Although the authors restrict themselves to sextupole fields in this paper, the authors may easily extend the method to any order multipole. The aim of this work is to derive an analytic approximate expression for the dynamical aperture. The authors approach the solutions of x and y by use of a classical secular perturbation theory. Every coefficient of the perturbation series can be expressed as an analytic function of all the lower order coefficients. Although perturbation theory if it is evaluated to certain specific order leads only to an approximation in terms of bounded (trigonometric) functions the authors may derive information about the stability limit by considering the convergency radius of the general perturbation. This is done in the present paper by deriving an approximate analytic expression for the n-th order perturbation contribution of the whole series using only results up to second order. The actual calculations have been performed for the fully two dimensional case but for simplicity the authors shall explain only the one dimensional case of the pure horizontal motion
International Nuclear Information System (INIS)
Co(II)-tetrasulfonated phthalocyanine (CoTSP) is known to be aggregated to dimer at high concentration levels in water. A study on the aggregation of CoTSP using multivariate curve resolution analysis of the visible absorbance spectra over a concentration range of 30, 40 and 50 μM in the presence of dimethyl sulfoxide (DMSO), dimethyl formamide (DMF), acetonitrile (AN) and ethanol (EtOH) in the concentration range of 0 to 3.57 M is conducted. A hard modeling-based multivariate curve resolution method was applied to determine the dissociation constants of the CoTSP aggregates at various temperatures ranging from 25, 45 and 65 .deg. C and in the presence of various co-solvents. Dissociation constant for aggregation was increased and then decrease by temperature and concentration of phthalocyanine, respectively. Utilizing the vant Hoff relation, the enthalpy and entropy of the dissociation equilibriums were calculated. For the dissociation of both aggregates, the enthalpy and entropy changes were positive and negative, respectively. Molecular dynamics simulation of cosolvent effect on CoTSP aggregation was done to confirm spectroscopy results. Results of radial distribution function (RDF), root mean square deviation (RMSD) and distance curves confirmed more effect of polar solvent to decrease monomer formation
All-atom molecular dynamics calculation study of entire poliovirus empty capsids in solution
International Nuclear Information System (INIS)
Small viruses that belong, for example, to the Picornaviridae, such as poliovirus and foot-and-mouth disease virus, consist simply of capsid proteins and a single-stranded RNA (ssRNA) genome. The capsids are quite stable in solution to protect the genome from the environment. Here, based on long-time and large-scale 6.5 × 106 all-atom molecular dynamics calculations for the Mahoney strain of poliovirus, we show microscopic properties of the viral capsids at a molecular level. First, we found equilibrium rapid exchange of water molecules across the capsid. The exchange rate is so high that all water molecules inside the capsid (about 200 000) can leave the capsid and be replaced by water molecules from the outside in about 25 μs. This explains the capsid's tolerance to high pressures and deactivation by exsiccation. In contrast, the capsid did not exchange ions, at least within the present simulation time of 200 ns. This implies that the capsid can function, in principle, as a semipermeable membrane. We also found that, similar to the xylem of trees, the pressure of the solution inside the capsid without the genome was negative. This is caused by coulombic interaction of the solution inside the capsid with the capsid excess charges. The negative pressure may be compensated by positive osmotic pressure by the solution-soluble ssRNA and the counter ions introduced into it
Haskins, Justin; Kinaci, Alper; Sevik, Cem; Cagin, Tahir
2012-01-01
It is widely known that graphene and many of its derivative nanostructures have exceedingly high reported thermal conductivities (up to 4000 W/mK at 300 K). Such attractive thermal properties beg the use of these structures in practical devices; however, to implement these materials while preserving transport quality, the influence of structure on thermal conductivity should be thoroughly understood. For graphene nanostructures, having average phonon mean free paths on the order of one micron, a primary concern is how size influences the potential for heat conduction. To investigate this, we employ a novel technique to evaluate the lattice thermal conductivity from the Green-Kubo relations and equilibrium molecular dynamics in systems where phonon-boundary scattering dominates heat flow. Specifically, the thermal conductivities of graphene nanoribbons and carbon nanotubes are calculated in sizes up to 3 microns, and the relative influence of boundary scattering on thermal transport is determined to be dominant at sizes less than 1 micron, after which the thermal transport largely depends on the quality of the nanostructure interface. The method is also extended to carbon nanostructures (fullerenes) where phonon confinement, as opposed to boundary scattering, dominates, and general trends related to the influence of curvature on thermal transport in these materials are discussed.
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-01-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measur...
Geocomputation and Research on the Urban Evolutionary Dynamics%地学(理)计算与城市演化动力学研究
Institute of Scientific and Technical Information of China (English)
刘妙龙; 黄佩蓓
2001-01-01
This paper briefly introduces the historical development of Geocomputation, explores the technical bases and the supports of surveying and geoinformatics for the development of Geocomputation, analyses and discusses some results and problems resulting from research on the fractal city, which is one of the most popular and useful methods for research on the urban evolutionary dynamics. The aim of the paper is to put the Geocomputation forward from the view of surveying and geoinformatics.%简要介绍了地学(理)计算学的历史发展，在理论上对地学(理)计算的技术基础和测绘科学技术保证作了探讨，分析讨论了城市演化动力学研究方法之一的城市分形研究的一些结果与问题，旨在从测绘科学技术的角度推动地学(理)计算学的发展。
Directory of Open Access Journals (Sweden)
Cleather Daniel J
2010-11-01
Full Text Available Abstract Background A vast number of biomechanical studies have employed inverse dynamics methods to calculate inter-segmental moments during movement. Although all inverse dynamics methods are rooted in classical mechanics and thus theoretically the same, there exist a number of distinct computational methods. Recent research has demonstrated a key influence of the dynamics computation of the inverse dynamics method on the calculated moments, despite the theoretical equivalence of the methods. The purpose of this study was therefore to explore the influence of the choice of inverse dynamics on the calculation of inter-segmental moments. Methods An inverse dynamics analysis was performed to analyse vertical jumping and weightlifting movements using two distinct methods. The first method was the traditional inverse dynamics approach, in this study characterized as the 3 step method, where inter-segmental moments were calculated in the local coordinate system of each segment, thus requiring multiple coordinate system transformations. The second method (the 1 step method was the recently proposed approach based on wrench notation that allows all calculations to be performed in the global coordinate system. In order to best compare the effect of the inverse dynamics computation a number of the key assumptions and methods were harmonized, in particular unit quaternions were used to parameterize rotation in both methods in order to standardize the kinematics. Results Mean peak inter-segmental moments calculated by the two methods were found to agree to 2 decimal places in all cases and were not significantly different (p > 0.05. Equally the normalized dispersions of the two methods were small. Conclusions In contrast to previously documented research the difference between the two methods was found to be negligible. This study demonstrates that the 1 and 3 step method are computationally equivalent and can thus be used interchangeably in
Vegt, de, F.; Briels, Wim J.; Wessling, Matthias; Strathmann, Heiner
1996-01-01
The excess free energy of small molecules in the amorphous polymers poly(ethylene) and poly(dimethylsiloxane) was calculated, using the test-particle-insertion method. The method was applied to polymer configurations obtained from molecular dynamics simulations with differently prepared initial guess configurations. It was found that the calculated solubility coefficients strongly depend on the quality of the initial guess configuration. Slow compression of dilute systems, during which proces...
Wei, K; Lin, Y; Xie, D
2015-06-01
Southeast Asia has been the breeding ground for many emerging diseases in the past decade, and it is in this region that new genetic variants of HPAI H5N1 viruses have been emerging. Cross-border movement of animals accelerates the spread of H5N1, and the changing environmental conditions also exert strong selective pressure on the viruses. The transboundary zoonotic diseases caused by H5N1 pose a serious and continual threat to global economy and public health. Here, we divided the H5N1 viruses isolated in Southeast Asia during 2003-2009 into four groups according to their phylogenetic relationships among HA gene sequences. Molecular evolution analysis suggests populations in expansion rather than a positive selection for group 2 and group 3, yet group 4 is under strong positive selection. Site 193 was found to be a potential glycosylation site and located in receptor-binding domain. Note that site 193 tends to appear in avian isolates instead of human strains. Population dynamics analysis reveals that the effective population size of infections in Southeast Asia has undergone three obvious increases, and the results are consistent with the epidemiological analysis. Ecological and phylogeographical analyses show that agro-ecological environments, migratory birds, domestic waterfowl, especially free-ranging ducks, are crucial in the occurrence, maintenance and spread of H5N1 virus. The epidemiological links between Indonesia and Suphanburi observed suggest that viruses in Indonesia were originated from multiple introductions. PMID:23952973
Baillie, Gregory J.; Galiano, Monica; Agapow, Paul-Michael; Myers, Richard; Chiam, Rachael; Gall, Astrid; Palser, Anne L.; Watson, Simon J.; Hedge, Jessica; Underwood, Anthony; Platt, Steven; McLean, Estelle; Pebody, Richard G.; Rambaut, Andrew; Green, Jonathan; Daniels, Rod; Pybus, Oliver G.; Zambon, Maria
2012-01-01
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic. PMID:22013031
International Nuclear Information System (INIS)
Safety is one of the most important and desirable characteristics in a nuclear plant Natural circulation cooling systems are noted for providing passive safety. These systems can be used as mechanism for removing the residual heat from the reactor, or even as the main cooling system for heated sections, such as the core. In this work, a computational fluid dynamics (CFD) code called CFX is used to simulate the process of natural circulation in a research reactor pool after its shutdown. The physical model studied is similar to the Open Pool Australian Light water reactor (OPAL), and contains the core, cooling pool, reflecting tank, circulation pipes and chimney. For best computing performance, the core region was modeled as a porous medium, where the parameters were obtained from a separately detailed CFD analysis. This work also aims to study the viability of the implementation of Differential Evolution algorithm for optimization the physical and operational parameters that, obeying the laws of similarity, lead to a test section on a reduced scale of the reactor pool.
Baillie, Gregory J; Galiano, Monica; Agapow, Paul-Michael; Myers, Richard; Chiam, Rachael; Gall, Astrid; Palser, Anne L; Watson, Simon J; Hedge, Jessica; Underwood, Anthony; Platt, Steven; McLean, Estelle; Pebody, Richard G; Rambaut, Andrew; Green, Jonathan; Daniels, Rod; Pybus, Oliver G; Kellam, Paul; Zambon, Maria
2012-01-01
Virus gene sequencing and phylogenetics can be used to study the epidemiological dynamics of rapidly evolving viruses. With complete genome data, it becomes possible to identify and trace individual transmission chains of viruses such as influenza virus during the course of an epidemic. Here we sequenced 153 pandemic influenza H1N1/09 virus genomes from United Kingdom isolates from the first (127 isolates) and second (26 isolates) waves of the 2009 pandemic and used their sequences, dates of isolation, and geographical locations to infer the genetic epidemiology of the epidemic in the United Kingdom. We demonstrate that the epidemic in the United Kingdom was composed of many cocirculating lineages, among which at least 13 were exclusively or predominantly United Kingdom clusters. The estimated divergence times of two of the clusters predate the detection of pandemic H1N1/09 virus in the United Kingdom, suggesting that the pandemic H1N1/09 virus was already circulating in the United Kingdom before the first clinical case. Crucially, three clusters contain isolates from the second wave of infections in the United Kingdom, two of which represent chains of transmission that appear to have persisted within the United Kingdom between the first and second waves. This demonstrates that whole-genome analysis can track in fine detail the behavior of individual influenza virus lineages during the course of a single epidemic or pandemic. PMID:22013031
Photophysics of Auramine-O: electronic structure calculations and nonadiabatic dynamics simulations.
Xie, Bin-Bin; Xia, Shu-Hua; Chang, Xue-Ping; Cui, Ganglong
2016-01-01
Diphenylmethane dyes are very useful photoinduced molecular rotors; however, their photophysical mechanisms are still elusive until now. In this work, we adopted combined static electronic structure calculations (MS-CASPT2//CASSCF) and trajectory-based surface-hopping dynamics simulations (OM2/MRCI) to study the S1 excited-state relaxation mechanism of a representative diphenylmethane dye Auramine-O. On the basis of the optimized S1 minima and the computed emission bands, we have for the first time assigned experimentally proposed three transient states (i.e. S1-LE, S1-I1 or S1-I2, and S1-II). Mechanistically, upon irradiation to the S1 state, the system first relaxes to the locally excited S1 minimum (S1-LE). Starting from this point, there exist two kinds of relaxation paths to S1-II. In the sequential path, the system first evolves into S1-I1 or S1-I2 and then runs into S1-II; in the concerted one, the system, bypassing S1-I1 and S1-I2, directly runs into S1-II. In addition, the system can decay to the S0 state in the vicinity of three S1/S0 conical intersections i.e. S1S0-I1, S1S0-I2, and S1S0-II. In the S1 dynamic simulations, 54% trajectories decay to the S0 state via S1S0-II; the remaining trajectories are de-excited to the S0 state via S1S0-I1 (11%) and S1S0-I2 (35%). Our present theoretical investigation does not support the experimentally proposed S1 excited-state hypothesis that the intramolecular rotation of the two dimethyl groups around the C-N bond is responsible for the rapid decay of the emission band at about 500 nm; instead, it should be heavily interrelated with the rotation of the two dimethylanilino groups. Finally, this work provides important mechanistic insights into similar diphenylmethane dyes. PMID:26615798
Analytical formulas for calculating the blocking probability of a dynamic star network
Institute of Scientific and Technical Information of China (English)
Jiajia Chen; Xiang Lü; Sailing He
2005-01-01
For a dynamic routing and wavelength assignment (RWA) a star topology is shown to be more efficient in comparison with a ring topology. Analytical formulas for a dynamic RWA in a star network are presented and verified with virtual simulation.
Zhang, Yong; Otani, Akihito; Maginn, Edward J
2015-08-11
Equilibrium molecular dynamics is often used in conjunction with a Green-Kubo integral of the pressure tensor autocorrelation function to compute the shear viscosity of fluids. This approach is computationally expensive and is subject to a large amount of variability because the plateau region of the Green-Kubo integral is difficult to identify unambiguously. Here, we propose a time decomposition approach for computing the shear viscosity using the Green-Kubo formalism. Instead of one long trajectory, multiple independent trajectories are run and the Green-Kubo relation is applied to each trajectory. The averaged running integral as a function of time is fit to a double-exponential function with a weighting function derived from the standard deviation of the running integrals. Such a weighting function minimizes the uncertainty of the estimated shear viscosity and provides an objective means of estimating the viscosity. While the formal Green-Kubo integral requires an integration to infinite time, we suggest an integration cutoff time tcut, which can be determined by the relative values of the running integral and the corresponding standard deviation. This approach for computing the shear viscosity can be easily automated and used in computational screening studies where human judgment and intervention in the data analysis are impractical. The method has been applied to the calculation of the shear viscosity of a relatively low-viscosity liquid, ethanol, and relatively high-viscosity ionic liquid, 1-n-butyl-3-methylimidazolium bis(trifluoromethane-sulfonyl)imide ([BMIM][Tf2N]), over a range of temperatures. These test cases show that the method is robust and yields reproducible and reliable shear viscosity values. PMID:26574439
Czech Academy of Sciences Publication Activity Database
Straka, Michal; Lantto, P.; Vaara, J.
2008-01-01
Roč. 112, č. 12 (2008), s. 2658-2668. ISSN 1089-5639 Institutional research plan: CEZ:AV0Z40550506 Keywords : NMR * theoretical calculations * role of dynamics Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 2.871, year: 2008
International Nuclear Information System (INIS)
The Lawrence Livermore Laboratory is currently involved in a 1/5 scale testing program on the Mark I BWR pressure suppression system. A key element of the test setup is a pressure vessel that is a 900 sector of a torus. Proper performance of the 900 torus depends on its structural integrity and structural dynamic characteristics. It must sustain the internal pressurization of the planned tests, and its dynamic response to the transient test loads should be minimal. If the structural vibrations are too great, interpretation of important load cell and pressure transducer data will be difficult. The purpose of the report is to bring together under one cover calculations pertaining to the structural dynamic characteristics and structural integrity of 900 torus. The report is divided into the following sections: (1) system description in which the torus and associated hardware are briefly described; (2) structural dynamics in which calculations of natural frequency and dynamic response are presented; and (3) structural integrity in which stress calculations for design purposes are presented; and an appendix which contains an LLL internal report comparing the expected load cell response for a three and four-point supported torus
Pan, Zhao; Thomson, Scott; Truscott, Tadd
2016-01-01
Obtaining pressure field data from particle image velocimetry (PIV) is an attractive technique in fluid dynamics due to its noninvasive nature. The application of this technique generally involves integrating the pressure gradient or solving the pressure Poisson equation using a velocity field measured with PIV. However, very little research has been done to investigate the dynamics of error propagation from PIV-based velocity measurements to the pressure field calculation. Rather than measure the error through experiment, we investigate the dynamics of the error propagation by examining the Poisson equation directly. We analytically quantify the error bound in the pressure field, and are able to illustrate the mathematical roots of why and how the Poisson equation based pressure calculation propagates error from the PIV data. The results show that the error depends on the shape and type of boundary conditions, the dimensions of the flow domain, and the flow type.
Evolutionary Minority Games: the benefits of imitation
Metzler, Richard; Horn, Christian
2002-01-01
In the original Evolutionary Minority Game, a segregation into two populations with opposing preferences is observed under many circumstances. We show that this segregation becomes more pronounced and more robust if the dynamics are changed slightly, such that strategies with above-average fitness become more frequent. Similar effects occur also for a generalization of the EMG to more than two choices, and for evolutionary dynamics of a different stochastic strategy for the Minority Game.
Evolutionary Information Theory
Directory of Open Access Journals (Sweden)
Mark Burgin
2013-04-01
Full Text Available Evolutionary information theory is a constructive approach that studies information in the context of evolutionary processes, which are ubiquitous in nature and society. In this paper, we develop foundations of evolutionary information theory, building several measures of evolutionary information and obtaining their properties. These measures are based on mathematical models of evolutionary computations, machines and automata. To measure evolutionary information in an invariant form, we construct and study universal evolutionary machines and automata, which form the base for evolutionary information theory. The first class of measures introduced and studied in this paper is evolutionary information size of symbolic objects relative to classes of automata or machines. In particular, it is proved that there is an invariant and optimal evolutionary information size relative to different classes of evolutionary machines. As a rule, different classes of algorithms or automata determine different information size for the same object. The more powerful classes of algorithms or automata decrease the information size of an object in comparison with the information size of an object relative to weaker4 classes of algorithms or machines. The second class of measures for evolutionary information in symbolic objects is studied by introduction of the quantity of evolutionary information about symbolic objects relative to a class of automata or machines. To give an example of applications, we briefly describe a possibility of modeling physical evolution with evolutionary machines to demonstrate applicability of evolutionary information theory to all material processes. At the end of the paper, directions for future research are suggested.
Acceleration Schemes for Ab-Initio Molecular Dynamics and Electronic Structure Calculations
Tassone, Francesco; Mauri, Francesco; Car, Roberto
1994-01-01
We study the convergence and the stability of fictitious dynamical methods for electrons. First, we show that a particular damped second-order dynamics has a much faster rate of convergence to the ground-state than first-order steepest descent algorithms while retaining their numerical cost per time step. Our damped dynamics has efficiency comparable to that of conjugate gradient methods in typical electronic minimization problems. Then, we analyse the factors that limit the size of the integ...
Rationality of expectations: comparison of neoclassical and evolutionary approaches
Emilia Tomczyk
2006-01-01
Paper compares two major schools of economic thought – neoclassical and evolutionary – from the perspective of keystone assumption: rationality of economic agents. It discusses role of rationality assumption in neoclassical and evolutionary theories; importance of expectations; and perspectives for analyzing them within the framework of evolutionary game theory – namely, through replicator dynamics.
Lechner, Sarah; Ferretti, Luca; Schöning, Caspar; Kinuthia, Wanja; Willemsen, David; Hasselmann, Martin
2013-01-01
Deciphering the evolutionary processes driving nucleotide variation in multiallelic genes is limited by the number of genetic systems in which such genes occur. The complementary sex determiner (csd) gene in the honey bee Apis mellifera is an informative example for studying allelic diversity and the underlying evolutionary forces in a well-described model of balancing selection. Acting as the primary signal of sex determination, diploid individuals heterozygous for csd develop into females, ...
Structure and lattice dynamics of PrFe3(BO3)4: Ab initio calculation
Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.
2016-06-01
The crystal structure and phonon spectrum of PrFe3(BO3)4 are ab initio calculated in the context of the density functional theory. The ion coordinates in the unit cell of a crystal and the lattice parameters are evaluated from the calculations. The types and frequencies of the fundamental vibrations, as well as the line intensities of the IR spectrum, are determined. The elastic constants of the crystal are calculated. A "seed" frequency of the vibration strongly interacting with the electron excitation on the praseodymium ion is obtained for low-frequency A 2 mode. The calculated results are in agreement with the known experimental data.
Mueller, Roland Guenther
1987-06-01
In order to account for subcooled boiling in calculations of neutron physics and thermal hydraulics of light water reactors (where vapor bubbles strongly influence the nuclear chain reaction), a dynamic model is derived from the time-dependent conservation equations. It contains methods for the time-dependent determination of evaporation and condensation heat flow and for the heat transfer coefficient in subcooled boiling. It enables the complete two-phase flow region to be treated consistently. The calculation model was verified using measured data of experiments covering a wide range of thermodynamic boundary conditions. In all cases very good agreement is reached. The results from the coupling of the new calculation model with a neutron kinetics program proves its suitability for the steady-state and transient calculation of reactor cores.
Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M.; Zhan, Chang-Guo
2014-01-01
Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been perforemd to explore the dynamic behaviors of cytochrome P450 2A6 (CYP2A6) binding with nicotine analogs (that are typical inhibitors) and to calculate their binding free energies in combination with Poisson-Boltzmann surface area (PBSA) calculations. The combined MD simulations and QM/MM-PBSA calculations reveal that the most important structural parameters affecting the CYP2...
Directory of Open Access Journals (Sweden)
R. Fabík
2009-10-01
Full Text Available This paper presents a new model for calculation of critical strain for initialization of dynamic recrystallization. The new model reflects the history of forming in the deformation zone during rolling. In this region of restricted deformation, the strain rate curve for the surface of the strip exhibits two peaks. These are the two reasons why the onset of dynamic recrystallization DRX near the surface of the rolled part occurs later than in theory during strip rolling. The present model had been used in a program for simulation of forming processes with the aid of FEM and a comparison between the physical experiment and a mathematical model had been drawn.
Ab initio calculations of phonon dispersion and lattice dynamics in TlGaTe{sub 2}
Energy Technology Data Exchange (ETDEWEB)
Jafarova, Vusala; Orudzhev, Guseyn; Alekperov, Oktay; Mamedov, Nazim; Abdullayev, Nadir; Najafov, Arzu [Institute of Physics (Innovation Sector), 33 H. Javid ave, Baku 1143 (Azerbaijan); Paucar, Raul [Institute of Physics (Innovation Sector), 33 H. Javid ave, Baku 1143 (Azerbaijan); Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016 (Japan); Shim, YongGu [Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531 (Japan); Wakita, Kazuki [Chiba Institute of Technology, 2-17-1 Tsudanuma, Narashino, Chiba 275-0016 (Japan)
2015-06-15
This work reports the results of DFT-based calculations of phonon spectra of TlGaTe{sub 2}. The dispersion of phonon bands was calculated along the directions of Brillouin zone (BZ) that include symmetry points. The calculated phonon frequencies at the centre of BZ were compared with those obtained by Raman spectroscopy with the aid of a confocal laser microscopy system. A fairly good agreement between the calculated and experimental data was found. Complimentary, molar heat capacity at constant volume and Debye temperature were calculated in the range 5/500 K on the base of the obtained phonon density of states. The obtained temperature dependencies were compared with available experimental data.The results of comparison were satisfactory. (copyright 2015 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)
International Nuclear Information System (INIS)
We present converged quantum dynamics for the H + D2 reaction at a total energy high enough to produce HD in the v' = 3, j' = 7 vibrational-rotational state and for total angular momenta J = 0, 1, and 2. We compare state-to-state partial cross sections for H + D2 (v = 0-2, j = 0, J = 0-2) → HD (v' = 0-2, j') + H and H + D2 (v = 1, j = 6, J = 0-2) → HD (v' = 0-2, j') + H as calculated from classical trajectory calculations with quantized initial conditions, i.e., a quasiclassical trajectory (QCT) simulation, to the results of converged quantum dynamics calculations involving up to 654 coupled channels. Final states in the QCT calculations are assigned by the quadratic smooth sampling (QSS) method. Since the quasiclassical and quantal calculations are carried out with the same potential energy surface, the comparison provides a direct test of the accuracy of the quasiclassical simulations as a function of the initial vibrational-rotational state and the final vibrational-rotational state
Mozafari, Elham; Shulumba, Nina; Steneteg, Peter; Alling, Björn; Abrikosov, Igor A.
2016-01-01
We present a theoretical scheme to calculate the elastic constants of magnetic materials in the high-temperature paramagnetic state. Our approach is based on a combination of disordered local moments picture and ab initio molecular dynamics (DLM-MD). Moreover, we investigate a possibility to enhance the efficiency of the simulations using recently introduced method: symmetry imposed force constant temperature dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as ...
Kinetic inductance of Josephson-junction arrays: Dynamic and equilibrium calculations
International Nuclear Information System (INIS)
The low-frequency inverse kinetic inductance L-1 of an overdamped junction array at temperature T=0 is shown to equal that of an equivalent impedance network. The ijth bond of the network has an inverse inductance (2eEij/ℎ)cos(θi0-θj0-Aij), where Eij is the Josephson coupling energy of the ijth bond, θi0 is the ground-state phase of the grain i, and Aij is the usual magnetic phase factor. Using this theorem, we calculate L-1 for square lattices as large as 180x180. The calculated L-1 agrees well with the T=0 limit of the helicity modulus γ calculated by conventional Monte Carlo techniques. In triangular arrays, the Monte Carlo calculation of γ yields a series of peaks at frustrations f=1/2(1-1/N), where N is an integer ≥2, consistent with experiments
International Nuclear Information System (INIS)
Shipboard fires both in the same ship hold and in an adjacent hold aboard a break-bulk cargo ship are simulated with a commercial finite-volume computational fluid mechanics code. The fire models and modeling techniques are described and discussed. Temperatures and heat fluxes to a simulated materials package are calculated and compared to experimental values. The overall accuracy of the calculations is assessed
Directory of Open Access Journals (Sweden)
I.P.Omelyan
2005-01-01
Full Text Available The transverse momentum time autocorrelation functions and wavevector- and frequency-dependent shear viscosity are calculated for an interaction site model of water using a modified collective mode approach and molecular dynamics simulations. The modified mode approach is based on a formulation which consistently takes into account non-Markovian effects into the kinetic memory kernels. As is demonstrated by comparing the theory results with the molecular dynamics data, the entire frequency dependence of the shear viscosity can be reproduced quantitatively over the whole wavelength range in terms of six generalized collective modes employing the kinetic memory kernel in the non-Markovian approximation of the third order. It is also shown that the results corresponding to the exact atomic and abbreviated molecular descriptions may differ considerably. In the infinite wavevector regime the dynamic correlations are completely determined by a single free motion of the molecules.
Energy Technology Data Exchange (ETDEWEB)
Lewis, M.W.; Kashiwa, B.A.; Meier, R.W. [Los Alamos National Lab., NM (United States); Bishop, S. [US Army Night Vision and Electronic Sensors Directorate, Fort Belvoir, VA (United States)
1994-08-01
Two- and three-dimensional fluid-structure interaction computer programs for the simulation of nonlinear dynamics were developed and applied to a number of problems. The programs were created by coupling Arbitrary Lagrangian-Eulerian finite volume fluid dynamics programs with strictly Lagrangian finite element structural dynamics programs. The resulting coupled programs can use either fully explicit or implicit time integration. The implicit time integration is accomplished by iterations of the fluid dynamics pressure solver and the structural dynamics system solver. The coupled programs have been used to solve problems involving incompressible fluids, membrane and shell elements, compressible multiphase flows, explosions in both air and water, and large displacements. In this paper, we present the approach used for the coupling and describe test problems that verify the two-dimensional programs against an experiment and an analytical linear problem. The experiment involves an explosion underwater near an instrumented thin steel plate. The analytical linear problem is the vibration of an infinite cylinder surrounded by an incompressible fluid to a given radius.
Hybridization of evolutionary algorithms
Fister, Iztok; Mernik, Marjan; Brest, Janez
2012-01-01
Evolutionary algorithms are good general problem solver but suffer from a lack of domain specific knowledge. However, the problem specific knowledge can be added to evolutionary algorithms by hybridizing. Interestingly, all the elements of the evolutionary algorithms can be hybridized. In this chapter, the hybridization of the three elements of the evolutionary algorithms is discussed: the objective function, the survivor selection operator and the parameter settings. As an objective function...
Khare, Ankur; Himmetoglu, Burak; Johnson, Melissa; Norris, David J.; Cococcioni, Matteo; Aydil, Eray S.
2012-04-01
The electronic structure, lattice dynamics, and Raman spectra of the kesterite, stannite, and pre-mixed Cu-Au (PMCA) structures of Cu2ZnSnS4 (CZTS) and Cu2ZnSnSe4 (CZTSe) were calculated using density functional theory (DFT). Differences in longitudinal and transverse optical (LO-TO) splitting in kesterite, stannite, and PMCA structures can be used to differentiate them. The Γ-point phonon frequencies, which give rise to Raman scattering, exhibit small but measurable shifts, for these three structures. Experimentally measured Raman scattering from CZTS and CZTSe thin films were examined in light of DFT calculations and deconvoluted to explain subtle shifts and asymmetric line shapes often observed in CZTS and CZTSe Raman spectra. Raman spectroscopy in conjunction with ab initio calculations can be used to differentiate between kesterite, stannite, and PMCA structures of CZTS and CZTSe.
Institute of Scientific and Technical Information of China (English)
Z.J.YANG; A.J.DEEKS
2008-01-01
A frequency-domain approach based on the semi-analytical scaled boundary finite element method(SBFEM) was developed to calculate dynamic stress intensity factors(DSIFs) at bimaterial interface cracks subjected to transient loading.Be-cause the stress solutions of the SBFEM in the frequency domain are analytical in the radial direction,and the complex stress singularity at the bimaterial interface crack tip is explicitly represented in the stress solutions,the mixed-mode DSIFs were calculated directly by definition.The complex frequency-response functions of DSIFs were then used by the fast Fourier transform(FFT) and the inverse FFT to calculate time histories of DSIFs.A benchmark example was modelled.Good re-sults were obtained by modelling the example with a small number of degrees of freedom due to the semi-analytical nature of the SBFEM.
Institute of Scientific and Technical Information of China (English)
Z.J.YANG; A.J.DEEKS
2008-01-01
A frequency-domain approach based on the semi-analytical scaled boundary finite element method (SBFEM) was developed to calculate dynamic stress intensity factors (DSIFs) at bimaterial interface cracks subjected to transient loading. Be-cause the stress solutions of the SBFEM in the frequency domain are analytical in the radial direction, and the complex stress singularity at the bimaterial interface crack tip is explicitly represented in the stress solutions, the mixed-mode DSIFs were calculated directly by definition. The complex frequency-response functions of DSIFs were then used by the fast Fourier transform (FFT) and the inverse FFT to calculate time histories of DSIFs. A benchmark example was modelled. Good re-sults were obtained by modelling the example with a small number of degrees of freedom due to the semi-analytical nature of the SBFEM.
International Nuclear Information System (INIS)
We have performed first-principles calculations to investigate the behavior under hydrostatic pressure of the structural, elastic and lattice dynamics properties of aluminum phosphide crystal (AlP), in both zinc-blende (B3) and nickel arsenide (B8) phases. Our calculated structural and electronic properties are in good agreement with previous theoretical and experimental results. The elastic constants, bulk modulus (B), shear modulus (G), and Young's modulus (E), Born effective charge and static dielectric constant ε0, were calculated with the generalized gradient approximations and the density functional perturbation theory (DFPT). Our results in the pressure behavior of the elastic and dielectric properties of both phases are compared and contrasted with the common III–V materials. The Born effective charge ZB decreases linearly with pressure increasing, while the static dielectric constant decreases quadratically with the increase of pressure
Energy Technology Data Exchange (ETDEWEB)
Lakel, S., E-mail: s.lakel@yahoo.fr [Laboratory of physical materials - University of LAGHOUAT – BP 37G, Laghouat (Algeria); Laboratoire de Matériaux Semi Conducteurs et Métalliques «LMSM», Université de Biskra (Algeria); Okbi, F. [Laboratoire de Sciences Fondamentales, Université Amar Telidji de Laghouat, BP 37G, Laghouat 03000 (Algeria); Ibrir, M. [Laboratoire de Sciences Fondamentales, Université Amar Telidji de Laghouat, BP 37G, Laghouat 03000 (Algeria); Département de physique, Université de M' sila (Algeria); Almi, K. [Laboratoire de Matériaux Semi Conducteurs et Métalliques «LMSM», Université de Biskra (Algeria)
2015-03-30
We have performed first-principles calculations to investigate the behavior under hydrostatic pressure of the structural, elastic and lattice dynamics properties of aluminum phosphide crystal (AlP), in both zinc-blende (B3) and nickel arsenide (B8) phases. Our calculated structural and electronic properties are in good agreement with previous theoretical and experimental results. The elastic constants, bulk modulus (B), shear modulus (G), and Young's modulus (E), Born effective charge and static dielectric constant ε{sub 0}, were calculated with the generalized gradient approximations and the density functional perturbation theory (DFPT). Our results in the pressure behavior of the elastic and dielectric properties of both phases are compared and contrasted with the common III–V materials. The Born effective charge ZB decreases linearly with pressure increasing, while the static dielectric constant decreases quadratically with the increase of pressure.
Mebrouki, M.; Ouahrani, T.; Çiftci, Y. Öztekin
2016-07-01
Using a toolkit of theoretical techniques comprising ab initio density functional theory calculations and quasiharmonic approximation, we investigate temperature dependence of dynamical properties of BaVO_3 perovskite. This interest is triggered by the fact that, recently, it was possible to synthesize a BaVO_3 perovskite, in a cubic phase, at high pressure and temperature. First-principle calculations are achieved thanks to recent development in numerical facilities, especially phonon dispersion curves which are then fully obtained. Elastic constants of the compound are dependent on temperature due to the inevitable anharmonic effects in solids. We show that at low temperature, the full account of the thermal effects incorporating the phonon densities and Sommerfeld model is more appropriate to calculate the thermal properties of a metal.
The Citation Field of Evolutionary Economics
Dolfsma, Wilfred
2010-01-01
Evolutionary economics has developed into an academic field of its own, institutionalized around, amongst others, the Journal of Evolutionary Economics (JEE). This paper analyzes the way and extent to which evolutionary economics has become an interdisciplinary journal, as its aim was: a journal that is indispensable in the exchange of expert knowledge on topics and using approaches that relate naturally with it. Analyzing citation data for the relevant academic field for the Journal of Evolutionary Economics, we use insights from scientometrics and social network analysis to find that, indeed, the JEE is a central player in this interdisciplinary field aiming mostly at understanding technological and regional dynamics. It does not, however, link firmly with the natural sciences (including biology) nor to management sciences, entrepreneurship, and organization studies. Another journal that could be perceived to have evolutionary acumen, the Journal of Economic Issues, does relate to heterodox economics journa...
Evolutionary robotics – A review
Indian Academy of Sciences (India)
Dilip Kumar Pratihar
2003-12-01
In evolutionary robotics, a suitable robot control system is developed automatically through evolution due to the interactions between the robot and its environment. It is a complicated task, as the robot and the environment constitute a highly dynamical system. Several methods have been tried by various investigators to solve this problem. This paper provides a survey on some of these important studies carried out in the recent past.
Evolutionary biology and life histories
Brown, C R; Thomson, D. L.
2004-01-01
The demographic processes that drive the spread of populations through environments and in turn determine the abundance of organisms are the same demographic processes that drive the spread of genes through populations and in turn determine gene frequencies and fitness. Conceptually, marked similarities exist in the dynamic processes underlying population ecology and those underlying evolutionary biology. Central to an understanding of both disciplines is life history and its component demogr...
Dynamical basis sets for algebraic variational calculations in quantum-mechanical scattering theory
Sun, Yan; Kouri, Donald J.; Truhlar, Donald G.; Schwenke, David W.
1990-01-01
New basis sets are proposed for linear algebraic variational calculations of transition amplitudes in quantum-mechanical scattering problems. These basis sets are hybrids of those that yield the Kohn variational principle (KVP) and those that yield the generalized Newton variational principle (GNVP) when substituted in Schlessinger's stationary expression for the T operator. Trial calculations show that efficiencies almost as great as that of the GNVP and much greater than the KVP can be obtained, even for basis sets with the majority of the members independent of energy.
Calculations of the gas-dynamic parameters in the bottom part of a tornado
International Nuclear Information System (INIS)
Prof. Sergej P. Bautin proposed and justified a new scheme of the origin and functioning of natural upward flows such as swirling tornadoes and tropical cyclones. All gasdynamic parameters in the bottom parts of tornadoes with various intensities have been calculated in this work on the basis of this scheme using data from the Fujita scale
Calculations of power series development for solving problems of dynamic heat transfer
International Nuclear Information System (INIS)
For a given turbulent pipe flow, the transient heat occurs by convection as well as by thermal diffusity. In order to describe this process, a system of partial differential equations is given. The solution of this system will be possible with power series development. Therefore the calculation with power series will be shortly described and new methods will be developed. (author)
International Nuclear Information System (INIS)
Highlights: • Development of a neural network model to predict the requiered plutonium content. • The accuracy of this model is very good (0.37% of error). • Development of a neural network model to predict evolution of average cross sections. • Predictions allow calculating fuel depletion quickly and with a very good accuracy. • This approach has been applied to the PWR MOX case in a dynamic fuel cycle code. - Abstract: Dynamic fuel cycle simulation tools calculate nuclei inventories and mass flows evolution in an entire fuel cycle, from the mine to the final disposal. Usually, the fuel depletion in reactor is handled by a fuel loading model and a mean cross section predictor. In the case of a PWR–MOX, a fuel loading model provides from a plutonium stock the plutonium fraction in the fresh fuel needed to reach a specific burnup. A mean cross section predictor aims to assess isotopic cross sections required for building Bateman equations for any fresh fuel composition with a sufficient accuracy and a reasonable computing time. This paper presents a methodology based on neural networks for building a fuel loading model and a cross section predictor for a PWR reactor loaded with MOX fuel. The mean error of the plutonium content prediction from the fuel loading model is 0.37%. Furthermore, the mean cross section predictor allows completion of the fuel depletion calculation in less than one minute with excellent accuracy. A maximum deviation of 3% on main nuclei is obtained at the end of cycle between inventories calculated from neural networks and from the reference coupled neutron transport/fuel depletion calculation
Czech Academy of Sciences Publication Activity Database
Kessler, Jiří; Dračínský, Martin; Bouř, Petr
2013-01-01
Roč. 34, č. 5 (2013), s. 366-371. ISSN 0192-8651 R&D Projects: GA ČR GAP208/11/0105; GA MŠk(CZ) LH11033 Grant ostatní: GA MŠk(CZ) LM2010005 Institutional support: RVO:61388963 Keywords : molecular dynamics * clusters * density functional theory * Raman optical activity * NMR Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.601, year: 2013
Should thermostatted ring polymer molecular dynamics be used to calculate thermal reaction rates?
International Nuclear Information System (INIS)
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time transition-state theory limit is identical to rigorous quantum transition-state theory, and we find that its long-time limit is independent of the location of the dividing surface. TRPMD rate theory is then applied to one-dimensional model systems, the atom-diatom bimolecular reactions H + H2, D + MuH, and F + H2, and the prototypical polyatomic reaction H + CH4. Above the crossover temperature, the TRPMD rate is virtually invariant to the strength of the friction applied to the internal ring-polymer normal modes, and beneath the crossover temperature the TRPMD rate generally decreases with increasing friction, in agreement with the predictions of Kramers theory. We therefore find that TRPMD is approximately equal to, or less accurate than, ring polymer molecular dynamics for symmetric reactions, and for certain asymmetric systems and friction parameters closer to the quantum result, providing a basis for further assessment of the accuracy of this method
International Nuclear Information System (INIS)
The embedding of time series provides a valuable, and sometimes indispensable, tool in order to analyze the dynamical properties of a chaotic system. To this purpose, the choice of the embedding dimension and lag is decisive. The scientific literature describes several methods for selecting the most appropriate parameter pairs. Unfortunately, no conclusive criterion to decide which method – and thus which embedding pair – is the best has been so far devised. A widely employed quantity to compare different methods is the maximum Lyapunov exponent (MLE) because, for chaotic systems that have explicit analytic representations, MLE can be numerically evaluated independently of the embedding dimension and lag. Within this framework, we investigated the dependence on the calculated MLE on the embedding dimension and lag in the case of three dynamical systems that are also widespreadly used as reference systems, namely the Lorenz, Rössler and Mackey-Glass attractors. By also taking into account the statistical fluctuations of the calculated MLE, we propose a new method to assess which systems provide suitable test benches for the comparison of different embedding methods via MLE calculation. For example we found that, despite of its popularity in this scientific context, the Rössler attractor is not a reliable workbench to test the validity of an embedding method
Calculations of power series development for solving problems of dynamics heat transfer
International Nuclear Information System (INIS)
For a given turbulent pipe flow, the transient heat occurs by convection as well as by thermal diffusity. In order to describe this process, a system of differnetial equations is given. The solution of this system will be possible with power series development at unknown coefficients. Therefore the calculation with power series will be shortly described and completed at several points and the development of determinants with power series as elements will be pointed out. (auth.)
DYNAMICAL CALCULATIONS OF (K)over-bar AND MULTI-(K)over-bar NUCLEI
Czech Academy of Sciences Publication Activity Database
Gazda, D.; Mareš, Jiří; Friedman, E.; Gal, A.
2009-01-01
Roč. 24, 2-3 (2009), s. 438-441. ISSN 0217-751X. [Conference MESON 2008. Jagiellonian Univ, Cracow, 06.06.2008-10.06.2008] R&D Projects: GA AV ČR IAA100480617 Institutional research plan: CEZ:AV0Z10480505 Keywords : (K)over-bar-nuclear RMF calculations * (K)over-bar-nuclear bound states * kaon condensation Subject RIV: BE - Theoretical Physics Impact factor: 0.941, year: 2009
Evolutionary fingerprints in genome-scale networks
Schütte, Moritz
2012-01-01
Mathematical modeling of biological phenomena has experienced increasing interest since new high-throughput technologies give access to growing amounts of molecular data. These modeling approaches are especially able to test hypotheses which are not yet experimentally accessible or guide an experimental setup. One particular attempt investigates the evolutionary dynamics responsible for today's composition of organisms. Computer simulations either propose an evolutionary mechanism and thus re...
The Evolutionary Robustness of Forgiveness and Cooperation
Bó, Pedro Dal
2012-01-01
We study the evolutionary robustness of strategies in infinitely repeated prisoners' dilemma games in which players make mistakes with a small probability and are patient. The evolutionary process we consider is given by the replicator dynamics. We show that there are strategies with a uniformly large basin of attraction independently of the size of the population. Moreover, we show that those strategies forgive defections and, assuming that they are symmetric, they cooperate.
Evolutionary freezing in a competitive population
Johnson, N F; Leonard, D. J. T.; Hui, P. M.; T. S. Lo(Dept. of Chemical Physics, The Weizmann Institute of Science, Rehovot, Israel)
1999-01-01
We show that evolution in a population of adaptive agents, repeatedly competing for a limited resource, can come to an abrupt halt. This transition from evolutionary to non-evolutionary behavior arises as the global resource level is changed, and is reminiscent of a phase transition to a frozen state. Its origin lies in the inductive decision-making of the agents, the limited global information that they possess and the dynamical feedback inherent in the system.
Numerical calculations of a high power CW CO2 gas-dynamic laser
Al-Hawat, Sharif; Al-Mutaib, Kheir
2008-03-01
Numerical solution of gas-dynamic laser equations in a gas mixture CO2:N2:H2O was carried out, using five-temperature-model (one translational and four vibrational temperatures) by a computational program written in FORTRAN. The spatial distributions of population inversion, gain and temperatures of the gas flow, in addition to the laser intensity and power extraction were studied inside the cavity, for certain initial conditions like pressure (p0=20 atm), temperature (T0= 1500 K), ratio of gases in the laser mixture (CO2:N2:H2O ≡ 10:85:5).
DEFF Research Database (Denmark)
Bigoni, Daniele; Engsig-Karup, Allan Peter; True, Hans
2012-01-01
This paper describes the results of the application of Uncertainty Quantification methods to a railway vehicle dynamical example. Uncertainty Quantification methods take the probability distribution of the system parameters that stems from the parameter tolerances into account in the result. In...... this paper the methods are applied to a lowdimensional vehicle dynamical model composed by a two-axle bogie, which is connected to a car body by a lateral linear spring, a lateral damper and a torsional spring. Their characteristics are not deterministically defined, but they are defined by probability...... distributions. The model - but with deterministically defined parameters - was studied in [1], and this article will focus on the calculation of the critical speed of the model, when the distribution of the parameters is taken into account. Results of the application of the traditional Monte Carlo sampling...
Energy Technology Data Exchange (ETDEWEB)
Cenian, A.
1985-02-01
A theoretical model of population-inversion formation by means of rapid expansion of a previously heated mixture of CO2 and Ar is described. Various admissible radiative transitions between CO2 levels comprised in coupled v1 and v2 modes are considered without any assumption as to the form of the vibrational energy distribution. The resulting kinetic equations have been integrated together with gas-dynamic ones. The vibrational energy exchange and relaxation processes are treated according to SSH theory. The calculations presented have permitted the checking of the assumption that the vibrational energy remains frozen and can be neglected in the gas-dynamic equations that describe the flow in supersonic nozzles for the relative concentration of CO2, xi(CO2) less than about 0.1. 13 references.
Born Oppenheimer Molecular Dynamics calculation of the νO-H IR spectra for acetic acid cyclic dimers
International Nuclear Information System (INIS)
Both ab initio molecular dynamics simulations based on the Born-Oppenheimer approach calculations and a quantum theoretical model are used in order to study the IR spectrum of the acetic acid dimer in the gas phase. The theoretical model is taking into account the strong anharmonic coupling, Davydov coupling, multiple Fermi resonances between the first harmonics of some bending modes and the first excited state of the symmetric combination of the two vO-H modes and the quantum direct and indirect relaxation. The IR spectra obtained from DFT-based molecular dynamics is compared with our theoretical lineshape and with experiment. Note that in a previous work we have shown that our approach reproduces satisfactorily the main futures of the IR experimental lineshapes of the acetic acid dimer [Mohamed el Amine Benmalti, Paul Blaise, H. T. Flakus, Olivier Henri-Rousseau, Chem Phys, 320(2006) 267-274.
Cai, Yufei; Zhang, Jianhui; Zhu, Chunling; Huang, Jun; Jiang, Feng
2016-05-01
The atomizer with micro cone apertures has advantages of ultra-fine atomized droplets, low power consumption and low temperature rise. The current research of this kind of atomizer mainly focuses on the performance and its application while there is less research of the principle of the atomization. Under the analysis of the dispenser and its micro-tapered aperture's deformation, the volume changes during the deformation and vibration of the micro-tapered aperture on the dispenser are calculated by coordinate transformation. Based on the characters of the flow resistance in a cone aperture, it is found that the dynamic cone angle results from periodical changes of the volume of the micro-tapered aperture of the atomizer and this change drives one-way flows. Besides, an experimental atomization platform is established to measure the atomization rates with different resonance frequencies of the cone aperture atomizer. The atomization performances of cone aperture and straight aperture atomizers are also measured. The experimental results show the existence of the pumping effect of the dynamic tapered angle. This effect is usually observed in industries that require low dispersion and micro- and nanoscale grain sizes, such as during production of high-pressure nozzles and inhalation therapy. Strategies to minimize the pumping effect of the dynamic cone angle or improve future designs are important concerns. This research proposes that dynamic micro-tapered angle is an important cause of atomization of the atomizer with micro cone apertures.
Energy Technology Data Exchange (ETDEWEB)
Waegeneers, Nadia, E-mail: nadia.waegeneers@var.fgov.be; Ruttens, Ann; De Temmerman, Ludwig
2011-06-15
A chain model was developed to calculate the flow of cadmium from soil, drinking water and feed towards bovine tissues. The data used for model development were tissue Cd concentrations of 57 bovines and Cd concentrations in soil, feed and drinking water, sampled at the farms were the bovines were reared. Validation of the model occurred with a second set of measured tissue Cd concentrations of 93 bovines of which age and farm location were known. The exposure part of the chain model consists of two parts: (1) a soil-plant transfer model, deriving cadmium concentrations in feed from basic soil characteristics (pH and organic matter content) and soil Cd concentrations, and (2) bovine intake calculations, based on typical feed and water consumption patterns for cattle and Cd concentrations in feed and drinking water. The output of the exposure model is an animal-specific average daily Cd intake, which is then taken forward to a kinetic uptake model in which time-dependent Cd concentrations in bovine tissues are calculated. The chain model was able to account for 65%, 42% and 32% of the variation in observed kidney, liver and meat Cd concentrations in the validation study. - Research highlights: {yields} Cadmium transfer from soil, drinking water and feed to bovine tissues was modeled. {yields} The model was based on 57 bovines and corresponding feed and soil Cd concentrations. {yields} The model was validated with an independent data set of 93 bovines. {yields} The model explained 65% of variation in kidney Cd in the validation study.
International Nuclear Information System (INIS)
A chain model was developed to calculate the flow of cadmium from soil, drinking water and feed towards bovine tissues. The data used for model development were tissue Cd concentrations of 57 bovines and Cd concentrations in soil, feed and drinking water, sampled at the farms were the bovines were reared. Validation of the model occurred with a second set of measured tissue Cd concentrations of 93 bovines of which age and farm location were known. The exposure part of the chain model consists of two parts: (1) a soil-plant transfer model, deriving cadmium concentrations in feed from basic soil characteristics (pH and organic matter content) and soil Cd concentrations, and (2) bovine intake calculations, based on typical feed and water consumption patterns for cattle and Cd concentrations in feed and drinking water. The output of the exposure model is an animal-specific average daily Cd intake, which is then taken forward to a kinetic uptake model in which time-dependent Cd concentrations in bovine tissues are calculated. The chain model was able to account for 65%, 42% and 32% of the variation in observed kidney, liver and meat Cd concentrations in the validation study. - Research highlights: → Cadmium transfer from soil, drinking water and feed to bovine tissues was modeled. → The model was based on 57 bovines and corresponding feed and soil Cd concentrations. → The model was validated with an independent data set of 93 bovines. → The model explained 65% of variation in kidney Cd in the validation study.
Energy Technology Data Exchange (ETDEWEB)
Berizzi, A.; Silvestri, A.; Zaninelli, D. (Politecnico di Milano (Italy). Dipartimento di Elettrotecnica); Massucco, S. (Univ. di Pavia (Italy). Dipartimento di Ingegneria Elettrica)
An essential issue concerning short-circuit studies is about how precise should short-circuit calculations be. Simplified procedures have been proposed for many years by International Committees to provide reference methods for the manual computation and for the use of rated, rather than operating, equipment data. Recently, dynamic programs have been used to accurately simulate short-circuit currents. Two widely adopted international standards (ANSI/IEEE C37.010.1979 and IEC 909 Standards) are investigated in this paper for comparing and pointing out the most significant differences in methodologies, assumptions, computed currents, and results. An outline of the two standards is presented and a detailed comparison is carried on. The procedures of the two standards are applied to a test network proposed in the IEC 909 Standard. Results of calculations by the two standards are compared using the results of a transient study performed by the EMTP simulation program as a reference basis.
Quantum dynamics calculation of reaction probability for H+Cl2→HCl+Cl
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + Cl2 based on the GHNS potential energy surface with total angular momentum J = 0. The effects of the translational, vibrational and rotational excitation of Cl2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Quantum dynamics calculation of reaction probability for H+Cl2→HC1+Cl
Institute of Scientific and Technical Information of China (English)
王胜龙; 赵新生
2001-01-01
We present in this paper a time-dependent quantum wave packet calculation of the initial state selected reaction probability for H + CI2 based on the GHNS potential energy surface with total angular momentum J= 0. The effects of the translational, vibrational and rotational excitation of CI2 on the reaction probability have been investigated. In a broad region of the translational energy, the rotational excitation enhances the reaction probability while the vibrational excitation depresses the reaction probability. The theoretical results agree well with the fact that it is an early down-hill reaction.
Calculation of radionuclide dispersion in flowing waters with a dynamic model
International Nuclear Information System (INIS)
Knowledge of the dispersion behaviour of radionuclides in a flowing water is essential for estimating the effects on the general public of incidents and accidents in plants where radioactive substances are handled and releases into flowing waters can occur. A one-dimensional model is presented which was developed to calculate the distribution of radionuclides over the environmental sectors water, suspended matter, and sediment along a river. The model is based on three coupled differential equations, which are solved numerically. In the example given a Runge-Kutta-method of fourth order was used. There are still limitations on the validation of the model because corresponding measurements are not yet available. (orig.)
Real-time calculations of many-body dynamics in quantum systems
Nakatsukasa, Takashi
2012-01-01
Real-time computation of time-dependent quantum mechanical problems are presented for nuclear many-body problems. Quantum tunneling in nuclear fusion at low energy is described using a time-dependent wave packet. A real-time method of calculating strength functions using the time-dependent Schroedinger equation is utilized to properly treat the continuum boundary condition. To go beyond the few-body models,we resort to the density-functional theory. The nuclear mean-field models are briefly r...
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.
Institute of Scientific and Technical Information of China (English)
GAO Ning; LAI Wen-Sheng
2006-01-01
@@ The calculation of elastic constants of Ag/Pd superlattice thin films by molecular dynamics simulations with many-body potentials is presented. It reveals that the elastic constants C11 and C55 increase with decreasing modulation wavelength A of the films, which is consistent with experiments. However, the change of C11 and C55 with A is found to be around the values determined by a rule of mixture using bulk elastic constants of metals.No supermodulus effect is observed and it is due to cancellation between enhanced and reduced contributions to elastic constants from Ag and Pd layers subjected to compressive and tensile strains, respectively.
A DYNAMIC APPROACH TO CALCULATE SHADOW PRICES OF WATER RESOURCES FOR NINE MAJOR RIVERS IN CHINA
Institute of Scientific and Technical Information of China (English)
Jing HE; Xikang CHEN; Yong SHI
2006-01-01
China is experiencing from serious water issues. There are many differences among the Nine Major Rivers basins of China in the construction of dikes, reservoirs, floodgates, flood discharge projects, flood diversion projects, water ecological construction, water conservancy management, etc.The shadow prices of water resources for Nine Major Rivers can provide suggestions to the Chinese government. This article develops a dynamic shadow prices approach based on a multiperiod input-output optimizing model. Unlike previous approaches, the new model is based on the dynamic computable general equilibrium (DCGE) model to solve the problem of marginal long-term prices of water resources.First, definitions and algorithms of DCGE are elaborated. Second, the results of shadow prices of water resources for Nine Major Rivers in 1949-2050 in China using the National Water Conservancy input-holding-output table for Nine Major Rivers in 1999 are listed. A conclusion of this article is that the shadow prices of water resources for Nine Major Rivers are largely based on the extent of scarcity.Selling prices of water resources should be revised via the usage of parameters representing shadow prices.
Preliminary calculation of αs from Green functions with dynamical quarks
International Nuclear Information System (INIS)
We present preliminary results on the computation of the QCD running coupling constant in the MOM-tilde scheme and Landau gauge with two flavours of dynamical Wilson quarks. Gluon momenta range up to about 7 GeV (β 5.6, 5.8 and 6.0) with a constant dynamical-quark mass. This range already allows to exhibit some evidence for a sizable 1/μ2 correction to the asymptotic behaviour, as in the quenched approximation, although a fit without power corrections is still possible with a reasonable χ2. Following the conclusions of our quenched study, we take into account 1/μ2 correction to the asymptotic behaviour. We find Λ Nf=2/MS=264(27)MeVx[a-1(5.6,0.1560)/2.19 GeV], which leads to αs(MZ) 0.113(3)(4). The latter result h as to be taken as a preliminary indication rather than a real prediction in view of the systematic errors still to be controlled. Still, being two sigmas below the experimental result makes it very encouraging. (author)
International Nuclear Information System (INIS)
This work was focused on the investigation of early stage oxidation in order to understand the fundamental oxidation behavior of nickel by using first principle method and molecular dynamics. Also, ReaxFF reactive force field was modified potentials for Ni/O systems. Nickel based alloys are one of the most important structure materials in modern nuclear industry. Nickel based alloys have a good corrosion resistance and mechanical properties to tolerate harsh and extreme environments. However, the interaction of nickel and nickel based alloys with water and oxygen atom causes dissolution of metallic atom and diffusion of elements. After then, oxidation arises at the surface. Therefore, the formation of oxide layer is an unavoidable process in high temperature water environments. The oxidation process of nickel based alloys is at the origin of the initiation of stress corrosion cracking(SCC), Stress corrosion cracking is arisen from interaction of mechanical, metallurgical, and electrochemical factors. It can induce failure of structural materials. Hence, it is important to understand and solve stress corrosion cracking in nickel based alloys. Therefore, this study's objective is to understand processes of early stage oxidation through the first principles method and molecular dynamics simulation
A dynamic multi-scale model for transient radiative transfer calculations
International Nuclear Information System (INIS)
A dynamic multi-scale model which couples the transient radiative transfer equation (RTE) and the diffusion equation (DE) is proposed and validated. It is based on a domain decomposition method where the system is divided into a mesoscopic subdomain, where the RTE is solved, and a macroscopic subdomain where the DE is solved. A buffer zone is introduced between the mesoscopic and the macroscopic subdomains, as proposed by Degond and Jin (2005 [1]), where a coupled system of two equations, one at the mesoscopic and the other at the macroscopic scale, is solved. The DE and the RTE are coupled through the equations inside the buffer zone, instead of being coupled through a geometric interface like in standard domain decomposition methods. One main advantage is that no boundary or interface conditions are needed for the DE. The model is compared to Monte Carlo, finite volume and P1 solutions in one dimensional stationary and transient test cases, and presents promising results in terms of trade-off between accuracy and computational requirements. -- Highlights: ► A dynamic multi-scale model for transient radiative transfer is developed. ► The model couple the RTE and the diffusion equation in a very robust way. ► The model is validated in a 1D test case of short-pulse laser application. ► A good trade-off between accuracy and computational requirement is obtained.
Yang, Jerry Zhijian
2014-01-01
Irving and Kirkwood formulism (IK formulism) provides a way to compute continuum mechanics quantities at certain location in terms of molecular variables. To make the approach more practical in computer simulation, Hardy proposed to use a spacial kernel function that couples continuum quantities with atomistic information. To reduce irrational fluctuations, Murdoch proposed to use a temporal kernel function to smooth the physical quantities obtained in Hardy's approach. In this paper, we generalize the original IK formulism to systematically incorporate both spacial and temporal average. The Cauchy stress tensor is derived in this generalized IK formulism (g-IK formulism). Analysis is given to illuminate the connection and difference between g-IK formulism and traditional temporal post-process approach. The relationship between Cauchy stress and first Piola-Kirchhoff stress is restudied in the framework of g-IK formulism. Numerical experiments using molecular dynamics are conducted to examine the analysis res...
Dense fluid self-diffusion coefficient calculations using perturbation theory and molecular dynamics
Directory of Open Access Journals (Sweden)
COELHO L. A. F.
1999-01-01
Full Text Available A procedure to correlate self-diffusion coefficients in dense fluids by using the perturbation theory (WCA coupled with the smooth-hard-sphere theory is presented and tested against molecular simulations and experimental data. This simple algebraic expression correlates well the self-diffusion coefficients of carbon dioxide, ethane, propane, ethylene, and sulfur hexafluoride. We have also performed canonical ensemble molecular dynamics simulations by using the Hoover-Nosé thermostat and the mean-square displacement formula to compute self-diffusion coefficients for the reference WCA intermolecular potential. The good agreement obtained from both methods, when compared with experimental data, suggests that the smooth-effective-sphere theory is a useful procedure to correlate diffusivity of pure substances.
Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan
2015-11-01
We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).
Numerical fluid dynamics calculations of nonequilibrium steam-water flows with entrained droplets
International Nuclear Information System (INIS)
The present work has developed a computational fluid dynamics formulation that efficiently solves the conservation laws for a vapor field, a continuous liquid field, and two dispersed droplet fields. The thermal-hydraulic effects resulting from the exchange of mass, momentum and energy between the vapor and the dispersed droplet phases has been accurately modeled. This work is an advancement of the state-of-the-art for engineering analyses of nonequilibrium steam-water-droplet flows in heated channels. It is particularly applicable for boiling steam-water flows in which it is important to represent the effects of significant thermal nonequilibrium between the vapor and the liquid phases. This work was shown to be in good agreement with unique experimental measurements of significant thermal nonequilibrium between the vapor and dispersed droplets. The tests analyzed covered a range of mass fluxes and wall heating rates, and were all at low pressures where nonequilibrium effects are most pronounced
Lattice dynamics and chemical bonding in Sb2Te3 from first-principles calculations
International Nuclear Information System (INIS)
Pressure effects on the lattice dynamics and the chemical bonding of the three-dimensional topological insulator, Sb2Te3, have been studied from a first-principles perspective in its rhombohedral phase. Where it is possible to compare, theory agrees with most of the measured phonon dispersions. We find that the inclusion of relativistic effects, in terms of the spin-orbit interaction, affects the vibrational features to some extend and creates large fluctuations on phonon density of state in high frequency zone. By investigations of structure and electronic structure, we analyze in detail the semiconductor to metal transition at ∼2 GPa followed by an electronic topological transition at a pressure of ∼4.25 GPa
Calculating the dynamics of High Explosive Violent Response (HEVR) after ignition
Energy Technology Data Exchange (ETDEWEB)
Reaugh, J E
2008-10-15
. Such measures include damage to the confinement, the velocity and fragment size distributions from what was the confinement, and air blast. In the first phase (advisory) model described in [1], the surface to volume ratio and the ignition parameter are calibrated by comparison with experiments using the UK explosive. In order to achieve the second phase (interactive) model, and so calculate the pressure developed and the velocity imparted to the confinement, we need to calculate the spread of the ignition front, the subsequent burn behavior behind that front, and the response of unburned and partially burned explosive to pressurization. A preliminary model to do such calculations is described here.
Commercon, Benoit; Dullemond, Cornelis P; Henning, Thomas
2012-01-01
The low-mass star formation evolutionary sequence is relatively well-defined both from observations and theoretical considerations. The first hydrostatic core is the first protostellar equilibrium object that is formed during the star formation process. Using state-of-the-art radiation-magneto-hydrodynamic 3D adaptive mesh refinement calculations, we aim to provide predictions for the dust continuum emission from first hydrostatic cores. We investigate the collapse and the fragmentation of magnetized one solar mass prestellar dense cores and the formation and evolution of first hydrostatic cores using the RAMSES code. We use three different magnetization levels for the initial conditions, which cover a large variety of early evolutionary morphology, e.g., the formation of a disk or a pseudo-disk, outflow launching, and fragmentation. We post-process the dynamical calculations using the 3D radiative transfer code RADMC-3D. We compute spectral energy distributions and usual evolutionary stage indicators such as...
Zhou, Q.; Joseph, P. F.
2005-05-01
An approach combining finite element with boundary element methods is proposed to calculate the elastic vibration and acoustic field radiated from an underwater structure. The FEM software NASTRAN is employed for computation of the structural vibration. An uncoupled boundary element method, based on the potential decomposition technique, is described to determine the acoustic added mass and damping coefficients that result due to fluid loading effects. The acoustic matrices of added mass and damping coefficients are then added to the structural mass and damping matrices, respectively, by the DMAP modules of NASTRAN. Numerical results are shown to be in good agreement with experimental data. The complex eigenvalue analyses of underwater structure are obtained by NASTRAN solution sequence SOL107. Results obtained from this study suggest that the natural frequencies of underwater structures are only weakly dependent on the acoustic frequency if the acoustic wavelength is roughly twice as large as the maximum structural dimension.
Hehenkamp, Burkhard; Leininger, Wolfgang; Possajennikov, Alex
2001-01-01
Tullock’s analysis of rent-seeking is reconsidered from an evolutionary point of view. We show that evolutionarily stable behavior in a rent-seeking contest differs from efficient rent-seeking behavior in a Nash equilibrium. We explore that implications of evolutionary stability for rent-seeking behavior and relate them to the well examined Nash equilibrium behavior. A most interesting result is an overdissipation law, which holds in evolutionary equilibrium.
Overview: Evolutionary Algorithms
Bartz-Beielstein, Thomas (Dr.); Mersmann, Olaf
2014-01-01
Evolutionary algorithm (EA) is an umbrella term used to describe population-based stochastic direct search algorithms that in some sense mimic natural evolution. Prominent representatives of such algorithms are genetic algorithms, evolution strategies, evolutionary programming, and genetic programming. On the basis of the evolutionary cycle, similarities and differences between these algorithms are described. We briefly discuss how EAs can be adapted to work well in case of multiple objective...
Overview: Evolutionary Algorithms
Bartz-Beielstein, Thomas (Dr.); Branke, Jürgen; Mehnen, Jörn; Mersmann, Olaf
2015-01-01
Evolutionary algorithm (EA) is an umbrella term used to describe population-based stochastic direct search algorithms that in some sense mimic natural evolution. Prominent representatives of such algorithms are genetic algorithms, evolution strategies, evolutionary programming, and genetic programming. On the basis of the evolutionary cycle, similarities and differences between these algorithms are described. We briefly discuss how EAs can be adapted to work well in case of multiple objective...
Machalski, J; Jamrozy, M
2004-01-01
The time evolution of `fiducial' radio sources derived from fitting the dynamical model of Kaiser et al. (1997) is compared with the observational data for the `clan' sources found in the sample of giant and normal-size FRII-type sources published Paper I (Machalski et al. 2004). Each `clan' comprises 3, 4 or 5 sample sources having similar values of the two basic physical parameters: the jet power Q_{0} and central density of the galaxy nucleus rho_{0} (determined in Paper I) but different ages, radio luminosities and axial ratios. These sources are considered as the `same' source observed at different epochs of its lifetime and used to fit the evolutionary luminosity-size (P-D) and energy density-total energy (u_{c}-E_{tot}) tracks derived from the model for a `fiducial' source with Q0 and rho_{0} equal to the means of relevant values obtained for the `clan' members, as well as to constrain the evolutionary model of the source dynamics used. In the result we find that (i) The best fit is achieved when the K...
Cao, Jun; Xie, Zhi-Zhong
2016-03-01
The ab initio electronic structure calculations and CASSCF-based nonadiabatic dynamics simulations have been used to investigate the internal conversion and intersystem crossing process of both trans-acrolein and 2-cyclopentenone in the gas phase. Our calculation results show that relaxation from the Franck-Condon region to an S1 minimum is ultrafast and that the S1 state will dominantly undergo intersystem crossing to triplet states due to the existence of significant barriers to access the S1/S0 intersection points and of energetically close-lying triplet states. The S1/T2/T1 three-state intersection is observed in our dynamics simulations to play an important role in the population of the lowest triplet state, which is consistent with previous suggestions. Although the evolution into triplet states involves a similar path and gives rise to a similar triplet quantum yield for these two molecules, the intersystem crossing rate of 2-cyclopentenone is lower owing to the ring constraint that results in a smaller spin-orbital coupling in the singlet-triplet crossing region. The present theoretical study reproduces the experimental results and gives an explanation about the structural factors that govern the excited-state decay of some types of α,β-enones. PMID:26882275
Evolutionary Algorithm Definition
Directory of Open Access Journals (Sweden)
Nada M.A. AL-Salami
2009-01-01
Full Text Available Problem statement: Most resent evolutionary algorithms work under weak theoretical basis and thus, they are computationally expensive. Approach: This study discussed the use of new evolutionary algorithm for automatic programming, based on theoretical definitions of program behaviors. Evolutionary process adapted fixed and self-organized input-output specification of the problem, to evolve good finite state machine that efficiently satisfies these specifications. Results: The proposed algorithm enhanced evolutionary process by simultaneously solving multi-parts from the same problem. Conclusion: The probability that the algorithm will converge to the optimal solution was highly enhanced when decomposing the main problem into multi-part.
Results of calculation of the dynamic behaviour of pressure suppression system during blowdown
International Nuclear Information System (INIS)
The computational model is based on several simplifications: The concrete parts of the containment are assumed to be rigid under the applied loadings, so that only the spherical shell with its annular condensation chamber will be investigated. As there is a plane of symmetry in the structure and in the loadings (and hence in the response as well) only half of the structure must be analyzed. A useful method to compute the behaviour of such a complex shell structure is the Finite Elements Method. Here the programme STRUDL-DYNAL was used, which has a linear, triangular shallow shell element with 5 degrees of freedom and with lumped inertia properties. In order to determine the necessary refinement of the discretization, the dynamic behaviour of the most important parts of the containment structure was analyzed individually. The computations showed that the lowest eigenfrequency of a simple shell may have a rather complex mode shape, e.g. a high circumferential order of cylindrical or conical shells and that higher frequencies may have simpler mode shapes. This behaviour requires a relative fine grid for discretization, as there must be sufficient degrees of freedom for the correct representation of the complex low modes. With respect to these effects, the structure was discretized by a spatial grid of 230 joints and 420 triangular finite elements. The resulting problem has about 1,200 degrees of freedom. The computation of the first 30 eigenfrequencies between 10 and 50 cps and of the corresponding mode shapes took about 75 min at 2,000 K memory size. There are some modes where the whole structure is vibrating; so at 10 cps the containment is vibrating like a vertically clamped beam; at 29 cps the structure goes up and down; at 32 cps horizontal cross sections are deformed elliptically. In addition there is a great number of modes with only parts of the structure vibrating at large amplitudes, especially the cylindrical and conical shell parts of the containment while
Calculation and Experiment for Dynamic Response of Bridge in Deep Water Under Seismic Excitation
Institute of Scientific and Technical Information of China (English)
柳春光; 孙国帅
2014-01-01
The-fluid-structure-interaction-under-seismic-excitation-is-very-complicated,-and-thus-the-damage-identification-of-the-bridge-in-deep-water-is-the-key-technique-to-ensure-the-safe-service.-Based-on-nonlinear-Morison-equation-considering-the-added-mass-effect-and-the-fluid-structure-interaction-effect,-the-effect-of-hydrodynamic-pressure-on-the-structure-is-analyzed.-A-series-of-underwater-shaking-table-tests-are-conducted-in-the-air-and-in-water.-The-dynamic-characteristics-affected-by-hydrodynamic-pressure-are-discussed-and-the-distribution-of-hydrodynamic-pressure-is-also-analyzed.-In-addition,-the-damage-of-structure-is-distinguished-through-the-natural-frequency-and-the-difference-of-modal-curvature,-and-is-then-compared-with-the-test-results.-The-numerical-simulation-and-test-of-this-study-indicate-that-the-effect-of-hydrodynamic-pressure-on-the-structure-should-not-be-neglected.-It-is-also-found-that-the-presence-of-the-damage,-the-location-of-the-damage-and-the-degree-of-the-severity-can-be-judged-through-the-variation-of-structure-frequency-and-the-difference-of-modal-curvature.
Lattice Calculation of Heavy-Light Decay Constants with Two Flavors of Dynamical Quarks
Bernard, C; DeGrand, T A; DeTar, C E; Gottlieb, S; Heller, U M; McNeile, C; Orginos, K; Sugar, R; Toussaint, D; Gottlieb, Steven; Heller, Urs M.
2002-01-01
We present results for $f_B$, $f_{B_s}$, $f_D$, $f_{D_s}$ and their ratios in the presence of two flavors of light sea quarks ($N_f=2$). We use Wilson light valence quarks and Wilson and static heavy valence quarks; the sea quarks are simulated with staggered fermions. Additional quenched simulations with nonperturbatively improved clover fermions allow us to improve our control of the continuum extrapolation. For our central values the masses of the sea quarks are not extrapolated to the physical $u$, $d$ masses; that is, the central values are "partially quenched." We find, for example, $f_B = 190 (7) (^{+24}_{-17}) (^{+11}_{-2})$ MeV, $f_{B_s}/f_B = 1.16 (1) (2) (2)$, $f_{D_s} = 241 (5) (^{+27}_{-26}) (^{+9}_{-4})$ MeV, and $f_{B}/f_{D_s} = 0.79 (2) (^{+5}_{-4}) (3)$, where the errors are statistical, systematic (within the partially quenched $N_f=2$ approximation), and systematic (due to the missing strange sea quark and to partial quenching), respectively. A calculation using "fat-link clover" valence fe...
International Nuclear Information System (INIS)
The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics. (paper)
Sakko, Arto; Rossi, Tuomas P.; Nieminen, Risto M.
2014-08-01
The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na2 molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics. The nanoparticle dimer has a plasmon resonance in the visible part of the electromagnetic spectrum, and the Na2 molecule has an electron-hole excitation in the same energy range. Due to the dynamical interaction of the two subsystems the plasmon and the molecular excitations couple, creating a hybridized molecular-plasmon excited state. This state has unique properties that yield e.g. enhanced photoabsorption compared to the freestanding Na2 molecule. The computational approach used enables decoupling of the mutual plasmon-molecule interaction, and our analysis verifies that it is not legitimate to neglect the backcoupling effect when describing the dynamical interaction between plasmonic material and nearby molecules. Time-resolved analysis shows nearly instantaneous formation of the coupled state, and provides an intuitive picture of the underlying physics.
Jacchetti, Emanuela; Gabellieri, Edi; Cioni, Patrizia; Bizzarri, Ranieri; Nifosì, Riccardo
2016-05-14
By combining spectroscopic measurements under high pressure with molecular dynamics simulations and quantum mechanics calculations we investigate how sub-angstrom structural perturbations are able to tune protein function. We monitored the variations in fluorescence output of two green fluorescent protein mutants (termed Mut2 and Mut2Y, the latter containing the key T203Y mutation) subjected to pressures up to 600 MPa, at various temperatures in the 280-320 K range. By performing 150 ns molecular dynamics simulations of the protein structures at various pressures, we evidenced subtle changes in conformation and dynamics around the light-absorbing chromophore. Such changes explain the measured spectral tuning in the case of the sizable 120 cm(-1) red-shift observed for pressurized Mut2Y, but absent in Mut2. Previous work [Barstow et al., Proc. Natl. Acad. Sci. U. S. A., 2008, 105, 13362] on pressure effects on GFP also involved a T203Y mutant. On the basis of cryocooling X-ray crystallography, the pressure-induced fluorescence blue shift at low temperature (77 K) was attributed to key changes in relative conformation of the chromophore and Tyr203 phenol ring. At room temperature, however, a red shift was observed at high pressure, analogous to the one we observe in Mut2Y. Our investigation of structural variations in compressed Mut2Y also explains their result, bridging the gap between low-temperature and room-temperature high-pressure effects. PMID:27102429
Energy Technology Data Exchange (ETDEWEB)
Amaro, Rommie E [ORNL; Cheng, Xiaolin [ORNL; Ivanov, Ivaylo N [ORNL; Xu, Dong [ORNL; McCammon, Jonathan [ORNL
2009-01-01
The comparative dynamics and inhibitor binding free energies of group-1 and group-2 pathogenic influenza A subtype neuraminidase (NA) enzymes are of fundamental biological interest and relevant to structure-based drug design studies for antiviral compounds. In this work, we present seven generalized Born molecular dynamics simulations of avian (N1)- and human (N9)-type NAs in order to probe the comparative flexibility of the two subtypes, both with and without the inhibitor oseltamivir bound. The enhanced sampling obtained through the implicit solvent treatment suggests several provocative insights into the dynamics of the two subtypes, including that the group-2 enzymes may exhibit similar motion in the 430-binding site regions but different 150-loop motion. End-point free energy calculations elucidate the contributions to inhibitor binding free energies and suggest that entropic considerations cannot be neglected when comparing across the subtypes. We anticipate the findings presented here will have broad implications for the development of novel antiviral compounds against both seasonal and pandemic influenza strains.
International Nuclear Information System (INIS)
Background and purpose: In this study the possibilities for implementing 1D tissue-deficit compensation techniques by a dynamic single absorber were investigated. This research firstly involved a preliminary examination on the accuracy of a pencil beam-based algorithm, implemented for irregularly shaped photon beams in our 3D treatment planning system (TPS) (Cadplan 2.7, Varian-Dosetek Oy), in calculating dose distributions delivered in 1D non-uniform fields. Once the reliability of the pencil beam (PB) algorithm for dose calculations in non-uniform beams was verified, we proceeded to test the feasibility of tissue-deficit compensation using our single absorber modulator. As an example, we considered a mantle field technique. Materials and methods: To evaluate the accuracy of the method employed in calculating dose distributions delivered in 1D non-uniform fields, three different fluence profiles, which could be considered as a small sample representative of clinically relevant applications, were selected. The incident non-uniform fluences were simulated by the sum of simple blocked fields (i.e. with rectangular 'strip' blocks, one per beam) properly weighed by the 'modulation factors' Fi, defined in each interval of the subdivided profile as the ratio between the desired fluence and the open field fluence. Depth dose distributions in a cubic phantom were then calculated by the TPS and compared with the corresponding doses (at 5 and 10 cm acrylic depths) delivered by the single absorber modulation system. In the present application, the absorber speed profile able to compensate for the tissue deficit along the cranio-caudal direction and then homogenizing the dose distribution on a 'midline' isocentric plane with sufficient accuracy can be directly derived from anatomic data, such as the SSDs (source-skin distances) along the patient contour. The compensation can be verified through portal dosimetry techniques (using a traditional port film system). Results: The
Evolutionary humanoid robotics
Eaton, Malachy
2015-01-01
This book examines how two distinct strands of research on autonomous robots, evolutionary robotics and humanoid robot research, are converging. The book will be valuable for researchers and postgraduate students working in the areas of evolutionary robotics and bio-inspired computing.
Evolutionary Justification of Plagiarism
Karpov, Alexander
2016-01-01
This paper provides evolutionary game theoretic model of plagiarism. The paper finds the relationship between author effort, publication value, and the frequency of plagiarism. There are two types of equilibria. Plagiarist-free equilibria are neutrally stable. The only evolutionary stable state is characterized by a positive share of plagiarists.
Sharma, Pragati; Roy, Sudip; Karimi-Varzaneh, Hossein Ali
2016-02-25
Microsecond atomic-scale molecular dynamics simulation has been employed to calculate the glass-transition temperature (Tg) of cis- and trans-1,4-polybutadiene (PB) and 1,4-polyisoprene (PI). Both all-atomistic and united-atom models have been simulated using force fields, already available in literature. The accuracy of these decade old force fields has been tested by comparing calculated glass-transition temperatures to the corresponding experimental values. Tg depicts the phase transition in elastomers and substantially affects various physical properties of polymers, and hence the reproducibility of Tg becomes very crucial from a thermodynamic point of view. Such validation using Tg also evaluates the ability of these force fields to be used for advanced materials like rubber nanocomposites, where Tg is greatly affected by the presence of fillers. We have calculated Tg for a total of eight systems, featuring all-atom and united-atom models of cis- and trans-PI and -PB, which are the major constituents of natural and synthetic rubber. Tuning and refinement of the force fields has also been done using quantum-chemical calculations to obtain desirable density and Tg. Thus, a set of properly validated force fields, capable of reproducing various macroscopic properties of rubber, has been provided. A novel polymer equilibration protocol, involving potential energy convergence as the equilibration criterion, has been proposed. We demonstrate that not only macroscopic polymer properties like density, thermal expansion coefficient, and Tg but also local structural characteristics like end-to-end distance (R) and radius of gyration (Rg) and mechanical properties like bulk modulus have also been equilibrated using our strategy. Complete decay of end-to-end vector autocorrelation function with time also supports proper equilibration using our strategy. PMID:26836395
Polymorphic Evolutionary Games.
Fishman, Michael A
2016-06-01
In this paper, I present an analytical framework for polymorphic evolutionary games suitable for explicitly modeling evolutionary processes in diploid populations with sexual reproduction. The principal aspect of the proposed approach is adding diploid genetics cum sexual recombination to a traditional evolutionary game, and switching from phenotypes to haplotypes as the new game׳s pure strategies. Here, the relevant pure strategy׳s payoffs derived by summing the payoffs of all the phenotypes capable of producing gametes containing that particular haplotype weighted by the pertinent probabilities. The resulting game is structurally identical to the familiar Evolutionary Games with non-linear pure strategy payoffs (Hofbauer and Sigmund, 1998. Cambridge University Press), and can be analyzed in terms of an established analytical framework for such games. And these results can be translated into the terms of genotypic, and whence, phenotypic evolutionary stability pertinent to the original game. PMID:27016340
International Nuclear Information System (INIS)
Full text: To understand the plasma-wall interaction on divertor plates, we investigate the interaction of hydrogen atoms and carbon materials used in the high heat flux components by the use of the following simulations. Monte-Carlo (MC) method based on binary collision approximation can calculate the sputtering process of hydrogen atoms on the carbon material quickly. Classical molecular dynamics (MD) method employs multi-body potential models and can treat realistic structures of crystal and molecule. The ab-initio method can calculate electron energy in quantum mechanics, which is regarded as realistic potential for atoms. In the present paper, the interaction of the hydrogen and the carbon material is investigated using the multi-scale (MC, MD and ab-initio) methods. The bombardment of hydrogen atoms onto the carbon material is simulated by the ACAT-code of the MC method, which cannot represent the structure of crystal, and the MD method using modified reactive empirical bond order (REBO) potential, which treats single crystal graphite and amorphous carbon. Consequently, we clarify that the sputtering yield and the reflection rate calculated by the ACAT-code agree with those on the amorphous carbon calculated by the MD. Moreover, there are many kinds of REBO potential for the MD. Adsorption, reflection and penetration rates between a hydrogen atom and a graphene surface are calculated by the MD simulations using the two kinds of potential model. For the incident energy of less than 1 eV, the MD simulation using the modified REBO potential, which is based on Brenner's REBO potential in 2002, shows that reflection is dominant, while the most popular Brenner's REBO potential in 1990 shows that adsorption is dominant. This reflection of the low energy injection is caused by a small potential barrier for the hydrogen atom in the modified REBO potential. The small potential barrier is confirmed by the ab-initio calculations, which are hybrid DFT (B3LYP/cc-pVDZ), ab
The application of statistical physics to evolutionary biology
Sella, Guy; Hirsh, Aaron E
2005-01-01
A number of fundamental mathematical models of the evolutionary process exhibit dynamics that can be difficult to understand analytically. Here we show that a precise mathematical analogy can be drawn between certain evolutionary and thermodynamic systems, allowing application of the powerful machinery of statistical physics to analysis of a family of evolutionary models. Analytical results that follow directly from this approach include the steady-state distribution of fixed genotypes and th...
International Nuclear Information System (INIS)
Dust particles observed in universe as well as in laboratory and technological plasma devices are still under investigation. At low temperature, these particles are strongly negatively charged and are able to form a 2D or 3D coulomb crystal. In this work, our aim was to check the ideal gas law validity for a 2D single-layer dust crystal recently reported in the literature. For this purpose, we have simulated, using the molecular dynamics method, its thermodynamic properties for different values of dust particles number and confinement parameters. The obtained results have allowed us to invalidate the ideal gas behaviour and to propose an effective equation of state which assumes a near zero dust temperature. Furthermore, the value of the calculated sound velocity was found to be in a good agreement with experimental data published elsewhere
Seko, Atsuto; Togo, Atsushi; Hayashi, Hiroyuki; Tsuda, Koji; Chaput, Laurent; Tanaka, Isao
2015-11-01
Compounds of low lattice thermal conductivity (LTC) are essential for seeking thermoelectric materials with high conversion efficiency. Some strategies have been used to decrease LTC. However, such trials have yielded successes only within a limited exploration space. Here, we report the virtual screening of a library containing 54 779 compounds. Our strategy is to search the library through Bayesian optimization using for the initial data the LTC obtained from first-principles anharmonic lattice-dynamics calculations for a set of 101 compounds. We discovered 221 materials with very low LTC. Two of them even have an electronic band gap <1 eV , which makes them exceptional candidates for thermoelectric applications. In addition to those newly discovered thermoelectric materials, the present strategy is believed to be powerful for many other applications in which the chemistry of materials is required to be optimized.
Energy Technology Data Exchange (ETDEWEB)
Djouder, M., E-mail: djouder-madjid@ummto.dz; Kermoun, F.; Mitiche, M. D.; Lamrous, O. [Laboratoire de Physique et Chimie Quantique, Université Mouloud Mammeri Tizi-Ouzou, BP 17 RP, 15000 Tizi-Ouzou (Algeria)
2016-01-15
Dust particles observed in universe as well as in laboratory and technological plasma devices are still under investigation. At low temperature, these particles are strongly negatively charged and are able to form a 2D or 3D coulomb crystal. In this work, our aim was to check the ideal gas law validity for a 2D single-layer dust crystal recently reported in the literature. For this purpose, we have simulated, using the molecular dynamics method, its thermodynamic properties for different values of dust particles number and confinement parameters. The obtained results have allowed us to invalidate the ideal gas behaviour and to propose an effective equation of state which assumes a near zero dust temperature. Furthermore, the value of the calculated sound velocity was found to be in a good agreement with experimental data published elsewhere.
Brzozowski, K.; Stawikowski, M.; Ślusarz, R.; Sikorska, E.; Lesner, A.; Łęgowska, A.; Rolka, K.
2015-11-01
Trypsin inhibitor SFTI-1 is the smallest and the most potent among BBI inhibitors. It is also an interesting object for SAR studies since it is cyclic 14 amino acid molecule which additionally contains disulfide bridge. We showed that elimination of head-to-tail cycliztion did not influence its activity. Moreover peptoid monomers of Nlys and Nphe introduced in the substrate specificity P1 position of monocyclic SFTI-1 preserved trypsin and chymotripsin inhibitory activity respectively and made P1-P1‧ bond proteolytically stable. These findings motivated us to perform conformational analysis of [Nphe5]SFTI-1 by means of 2D NMR spectroscopy and molecular dynamics calculations. Obtained structure occurred to be in a good agreement with published structures for wild-type SFTI-1, its monocyclic analog with disulfide bridge only as well as one containing Nlys peptoid monomer in P1 position.
Barall, M.
2009-01-01
We present a new finite-element technique for calculating dynamic 3-D spontaneous rupture on an earthquake fault, which can reduce the required computational resources by a factor of six or more, without loss of accuracy. The grid-doubling technique employs small cells in a thin layer surrounding the fault. The remainder of the modelling volume is filled with larger cells, typically two or four times as large as the small cells. In the resulting non-conforming mesh, an interpolation method is used to join the thin layer of smaller cells to the volume of larger cells. Grid-doubling is effective because spontaneous rupture calculations typically require higher spatial resolution on and near the fault than elsewhere in the model volume. The technique can be applied to non-planar faults by morphing, or smoothly distorting, the entire mesh to produce the desired 3-D fault geometry. Using our FaultMod finite-element software, we have tested grid-doubling with both slip-weakening and rate-and-state friction laws, by running the SCEC/ USGS 3-D dynamic rupture benchmark problems. We have also applied it to a model of the Hayward fault, Northern California, which uses realistic fault geometry and rock properties. FaultMod implements fault slip using common nodes, which represent motion common to both sides of the fault, and differential nodes, which represent motion of one side of the fault relative to the other side. We describe how to modify the traction-at-split-nodes method to work with common and differential nodes, using an implicit time stepping algorithm. ?? Journal compilation ?? 2009 RAS.
Steps Towards an Evolutionary Physics
Tiezzi, E
2006-01-01
If thermodynamics is to physics as logic is to philosophy, recent theoretical advancements lend new coherence to the marvel and dynamism of life on Earth. Enzo Tiezzi's "Steps Towards an Evolutionary Physics" is a primer and guide, to those who would to stand on the shoulders of giants to attain this view: Heisenberg, Planck, Bateson, Varela, and Prigogine as well as notable contemporary scientists. The adventure of such a free and enquiring spirit thrives not so much on answers as on new questions. The book offers a new gestalt on the uncertainty principle and concept of probability. A wide r
Micro Evolutionary Processes and Adaptation
Institute of Scientific and Technical Information of China (English)
SHADMANOV R K; RUBAN I N; VOROPAEVA N L; SHADMANOVA A R
2008-01-01
@@ It would be well to note that in the absence of clear data about the formation of adaptation systems,or mechanisms of their occurrence,all that is recognized is the realization of the micro evolutionary processes.There is no well-defined connection between information exchange and formation of adaptation systems.Obviously,it occurs because mechanisms and systems reacting to any external actions are not considered from the point of view of "coexistence" of dynamic and static processes and structures.
Oliver, Mike; Staruch, Robert; Gladwish, Adam; Craig, Jeff; Chen, Jeff; Wong, Eugene
2008-05-01
Respiratory gating is emerging as a tool to limit the effect of motion for liver and lung tumors. In order to study the impact of target motion and gated intensity modulated radiation therapy (IMRT) delivery, a computer program was developed to simulate segmental IMRT delivery to a moving phantom. Two distinct plans were delivered to a rigid-motion phantom with a film insert in place under four conditions: static, sinusoidal motion, gated sinusoidal motion with a duty cycle of 25% and gated sinusoidal motion with duty cycle of 50% under motion conditions of a typical patient (A = 1 cm, T = 4 s). The MLC controller log files and gating log files were retained to perform a retrospective Monte Carlo dose calculation of the plans. Comparison of the 2D planar dose distributions between simulation and measurement demonstrated that our technique had at least 94% of the points passing gamma criteria of 3% for dose difference and 3 mm as the distance to agreement. This note demonstrates that the use of dynamic multi-leaf collimator and respiratory monitoring system log files together with a fast Monte Carlo dose calculation algorithm is an accurate and efficient way to study the dosimetric effect of motion for gated or non-gated IMRT delivery on a rigidly-moving body.
Li, Qiang; Yu, Guichang; Liu, Shulian; Zheng, Shuiying
2012-09-01
Journal bearings are important parts to keep the high dynamic performance of rotor machinery. Some methods have already been proposed to analysis the flow field of journal bearings, and in most of these methods simplified physical model and classic Reynolds equation are always applied. While the application of the general computational fluid dynamics (CFD)-fluid structure interaction (FSI) techniques is more beneficial for analysis of the fluid field in a journal bearing when more detailed solutions are needed. This paper deals with the quasi-coupling calculation of transient fluid dynamics of oil film in journal bearings and rotor dynamics with CFD-FSI techniques. The fluid dynamics of oil film is calculated by applying the so-called "dynamic mesh" technique. A new mesh movement approach is presented while the dynamic mesh models provided by FLUENT are not suitable for the transient oil flow in journal bearings. The proposed mesh movement approach is based on the structured mesh. When the journal moves, the movement distance of every grid in the flow field of bearing can be calculated, and then the update of the volume mesh can be handled automatically by user defined function (UDF). The journal displacement at each time step is obtained by solving the moving equations of the rotor-bearing system under the known oil film force condition. A case study is carried out to calculate the locus of the journal center and pressure distribution of the journal in order to prove the feasibility of this method. The calculating results indicate that the proposed method can predict the transient flow field of a journal bearing in a rotor-bearing system where more realistic models are involved. The presented calculation method provides a basis for studying the nonlinear dynamic behavior of a general rotor-bearing system.
Evolutionary tree reconstruction
Cheeseman, Peter; Kanefsky, Bob
1990-01-01
It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.
International Nuclear Information System (INIS)
The gantry for proton radiotherapy at the Paul Scherrer Institute (PSI) is designed specifically for the spot-scanning technique. Use of this technique to its full potential requires dose calculation algorithms which are capable of precisely simulating each scanned beam individually. Different specialized analytical dose calculations have been developed, which attempt to model the effects of density heterogeneities in the patient's body on the dose. Their accuracy has been evaluated by a comparison with Monte Carlo calculated dose distributions in the case of a simple geometrical density interface parallel to the beam and typical anatomical situations. A specialized ray casting model which takes range dilution effects (broadening of the spectrum of proton ranges) into account has been found to produce results of good accuracy. This algorithm can easily be implemented in the iterative optimization procedure used for the calculation of the optimal contribution of each individual scanned pencil beam. In most cases an elemental pencil beam dose calculation has been found to be most accurate. Due to the long computing time, this model is currently used only after the optimization procedure as an alternative method of calculating the dose. (author)
Ecological and Evolutionary Effects of Dispersal on Freshwater Zooplankton
Allen, Michael R.
2009-01-01
A recent focus on contemporary evolution and the connections between communities has sought to more closely integrate ecology with evolutionary biology. Studies of coevolutionary dynamics, life history evolution, and rapid local adaptation demonstrate that ecological circumstances can dictate evolutionary trajectories. Thus, variation in species…
Nagapetyan, Tigran
2011-01-01
In this work we widespread statistical physics (chemical kinetic stochastic) approach to the investigation of macrosystems, arise in economic, sociology and traffic flow theory. The main line is a definition of equilibrium of macrosystem as most probable macrostate of invariant measure of Markov dynamic (corresponds to the macrosystem). We demonstrate new dynamical interpretations for the well known static model of correspondence matrix calculation. Based on this model we propose a best response dynamics for the Beckmann's traffic flow distribution model. We prove that this "natural" dynamic under quite general conditions converges to the Nash-Wardrop's equilibrium. After that we consider two interesting demonstration examples.
Diversity-Based Adaptive Evolutionary Algorithms
Jr., Maury Meirelles Gouvêa; Araújo, Aluizio Fausto Ribeiro
2010-01-01
This paper presented a survey about diversity-based evolutionary algorithms. Two sets of models were presented, one to minimize the diversity loss and another to control the population diversity based on a desired diversity range or level. The problem of the inappropriate level of diversity with respect to the environment and its dynamic can be