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....
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.
Stochastic evolutionary dynamics of direct reciprocity.
Imhof, Lorens A; Nowak, Martin A
2010-02-01
Evolutionary game theory is the study of frequency-dependent selection. The success of an individual depends on the frequencies of strategies that are used in the population. We propose a new model for studying evolutionary dynamics in games with a continuous strategy space. The population size is finite. All members of the population use the same strategy. A mutant strategy is chosen from some distribution over the strategy space. The fixation probability of the mutant strategy in the resident population is calculated. The new mutant takes over the population with this probability. In this case, the mutant becomes the new resident. Otherwise, the existing resident remains. Then, another mutant is generated. These dynamics lead to a stationary distribution over the entire strategy space. Our new approach generalizes classical adaptive dynamics in three ways: (i) the population size is finite; (ii) mutants can be drawn non-locally and (iii) the dynamics are stochastic. We explore reactive strategies in the repeated Prisoner's Dilemma. We perform 'knock-out experiments' to study how various strategies affect the evolution of cooperation. We find that 'tit-for-tat' is a weak catalyst for the emergence of cooperation, while 'always cooperate' is a strong catalyst for the emergence of defection. Our analysis leads to a new understanding of the optimal level of forgiveness that is needed for the evolution of cooperation under direct reciprocity.
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
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...
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 (...
Evolutionary dynamics of complex communications networks
Karyotis, Vasileios; Papavassiliou, Symeon
2013-01-01
Until recently, most network design techniques employed a bottom-up approach with lower protocol layer mechanisms affecting the development of higher ones. This approach, however, has not yielded fascinating results in the case of wireless distributed networks. Addressing the emerging aspects of modern network analysis and design, Evolutionary Dynamics of Complex Communications Networks introduces and develops a top-bottom approach where elements of the higher layer can be exploited in modifying the lowest physical topology-closing the network design loop in an evolutionary fashion similar to
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.
The Evolutionary Dynamics of Biofuel Value Chains
DEFF Research Database (Denmark)
Ponte, Stefano
2014-01-01
and multipolarity. Empirically, I do so by examining the evolutionary dynamics of governance in biofuel value chains, with specific focus on the key regulatory and institutional features that facilitated their emergence and expansion. First, I examine the formation, evolution, and governance of three national....../regional value chains (in Brazil, the US, and the EU); then, I provide evidence to support a trend towards the increasing but still partial formation of a global biofuel value chain and examine its governance traits....
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
Institute of Scientific and Technical Information of China (English)
LI; Jin-hai
2012-01-01
<正>The DTL is very important accelerator structure, and it is necessary for the proton linac accelerator. We did the dynamics simulation for the 20 MeV DTL, and obtained the physical and mechanical parameters. The input energy of the DTL is 3 MeV, and the pulsed beam current is 50 mA.
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
Informations in Models of Evolutionary Dynamics
Rivoire, Olivier
2016-03-01
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of evolutionary dynamics and show how explicit results are obtained for a solvable subclass of these models. In several limits, the results coincide with those obtained in studies of information processing for communication, gambling or thermodynamics. In the most general case, however, information processing by biological populations shows unique features that motivate the analysis of specific models.
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 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.
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
Relaxation of Evolutionary Dynamics on the Bethe Lattice
Institute of Scientific and Technical Information of China (English)
TIAN Liang; LIN Min
2012-01-01
Realistic evolutionary systems are generally structured and are in infinite dimensions.We study the relaxation behavior of evolutionary dynamics on a Bethe lattice,which concerns the invasion of mutants into a population of wild-type individuals.Since the boundary effect plays a significant role in a finite system,with proper approximation we propose an effective method to characterize the evolutionary dynamics.The relaxation behavior of the invasion process is analytically investigated,which is confirmed by extensive simulations.This work is the first systematical investigation on evolutionary dynamics in an infinitely dimensional lattice.
Quasiclassical Calculations in Beam Dynamics
Fedorova, A N; Fedorova, Antonina N.; Zeitlin, Michael G.
2000-01-01
We present some applications of general harmonic/wavelet analysis approach (generalized coherent states, wavelet packets) to numerical/analytical calculations in (nonlinear) quasiclassical/quantum beam dynamics problems. (Naive) deformation quantization, multiresolution representations and Wigner transform are the key points.
Quantifying the evolutionary dynamics of language.
Lieberman, Erez; Michel, Jean-Baptiste; Jackson, Joe; Tang, Tina; Nowak, Martin A
2007-10-11
Human language is based on grammatical rules. Cultural evolution allows these rules to change over time. Rules compete with each other: as new rules rise to prominence, old ones die away. To quantify the dynamics of language evolution, we studied the regularization of English verbs over the past 1,200 years. Although an elaborate system of productive conjugations existed in English's proto-Germanic ancestor, Modern English uses the dental suffix, '-ed', to signify past tense. Here we describe the emergence of this linguistic rule amidst the evolutionary decay of its exceptions, known to us as irregular verbs. We have generated a data set of verbs whose conjugations have been evolving for more than a millennium, tracking inflectional changes to 177 Old-English irregular verbs. Of these irregular verbs, 145 remained irregular in Middle English and 98 are still irregular today. We study how the rate of regularization depends on the frequency of word usage. The half-life of an irregular verb scales as the square root of its usage frequency: a verb that is 100 times less frequent regularizes 10 times as fast. Our study provides a quantitative analysis of the regularization process by which ancestral forms gradually yield to an emerging linguistic rule.
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...
Bridging developmental systems theory and evolutionary psychology using dynamic optimization.
Frankenhuis, Willem E; Panchanathan, Karthik; Clark Barrett, H
2013-07-01
Interactions between evolutionary psychologists and developmental systems theorists have been largely antagonistic. This is unfortunate because potential synergies between the two approaches remain unexplored. This article presents a method that may help to bridge the divide, and that has proven fruitful in biology: dynamic optimization. Dynamic optimization integrates developmental systems theorists' focus on dynamics and contingency with the 'design stance' of evolutionary psychology. It provides a theoretical framework as well as a set of tools for exploring the properties of developmental systems that natural selection might favor, given particular evolutionary ecologies. We also discuss limitations of the approach.
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.
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.
A New Dynamical Evolutionary Algorithm Based on Statistical Mechanics
Institute of Scientific and Technical Information of China (English)
LI YuanXiang(李元香); ZOU XiuFen(邹秀芬); KANG LiShan(康立山); Zbigniew Michalewicz
2003-01-01
In this paper, a new dynamical evolutionary algorithm (DEA) is presented basedon the theory of statistical mechanics. The novelty of this kind of dynamical evolutionary algorithmis that all individuals in a population (called particles in a dynamical system) are running andsearching with their population evolving driven by a nev selecting mechanism. This mechanismsimulates the principle of molecular dynamics, which is easy to design and implement. A basictheoretical analysis for the dynamical evolutionary algorithm is given and as a consequence twostopping criteria of the algorithm are derived from the principle of energy minimization and the lawof entropy increasing. In order to verify the effectiveness of the scheme, DEA is applied to solvingsome typical numerical function minimization problems which are poorly solved by traditionalevolutionary algorithms. The experimental results show that DEA is fast and reliable.
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
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...
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.
Finding Global Minima with a New Dynamical Evolutionary Algorithm
Institute of Scientific and Technical Information of China (English)
无
2002-01-01
A new dynamical evolutionary algorithm (DEA) based on the theory of statistical mechanics is presented. This algorithm is very different from the traditional evolutionary algorithm and the two novel fe-atures are the unique of selecting strategy and the determination of individuals that are selected to crossover and mutate. We use DEA to solve a lot of global optimization problems that are nonlinear, multimodal and multidimensional and obtain satisfactory results.
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...
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...
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
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.
Evolutionary dynamics of altruism and cheating among social amoebas.
Brännström, A; Dieckmann, U
2005-08-01
Dictyostelium discoideum is a eukaryotic amoeba, which, when starvation is imminent, aggregates to form fruiting bodies consisting of a stalk of reproductively dead cells that supports spores. Because different clones may be involved in such aggregations, cheater strategies may emerge that allocate a smaller fraction of cells to stalk formation, thus gaining a reproductive advantage. In this paper, we model the evolutionary dynamics of allocation strategies in Dictyostelium under the realistic assumption that the number of clones involved in aggregations follows a random distribution. By determining the full course of evolutionary dynamics, we show that evolutionary branching in allocation strategies may occur, resulting in dimorphic populations that produce stalkless and stalked fruiting bodies. We also demonstrate that such dimorphisms are more likely to emerge when the variation in the number of clones involved in aggregations is large.
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
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.
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
Strategy selection in evolutionary game dynamics on group interaction networks.
Tan, Shaolin; Feng, Shasha; Wang, Pei; Chen, Yao
2014-11-01
Evolutionary game theory provides an appropriate tool for investigating the competition and diffusion of behavioral traits in biological or social populations. A core challenge in evolutionary game theory is the strategy selection problem: Given two strategies, which one is favored by the population? Recent studies suggest that the answer depends not only on the payoff functions of strategies but also on the interaction structure of the population. Group interactions are one of the fundamental interactive modes within populations. This work aims to investigate the strategy selection problem in evolutionary game dynamics on group interaction networks. In detail, the strategy selection conditions are obtained for some typical networks with group interactions. Furthermore, the obtained conditions are applied to investigate selection between cooperation and defection in populations. The conditions for evolution of cooperation are derived for both the public goods game and volunteer's dilemma game. Numerical experiments validate the above analytical results.
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 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.
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.
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
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.
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.
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 programming for goal-driven dynamic planning
Vaccaro, James M.; Guest, Clark C.; Ross, David O.
2002-03-01
one step closer to solving more difficult real-world AI problems. Using a hybrid approach that includes adaptation via evolutionary computation for the intelligent planning of a Risk player's turn provides better dynamic intelligent planning than more uniform approaches.
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.
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...
Evolutionary dynamics of fluctuating populations with strong mutualism
Chotibut, Thiparat; Nelson, David
2013-03-01
Evolutionary game theory with finite interacting populations is receiving increased attention, including subtle phenomena associated with number fluctuations, i.e., ``genetic drift.'' Models of cooperation and competition often utilize a simplified Moran model, with a strictly fixed total population size. We explore a more general evolutionary model with independent fluctuations in the numbers of two distinct species, in a regime characterized by ``strong mutualism.'' The model has two absorbing states, each corresponding to fixation of one of the two species, and allows exploration of the interplay between growth, competition, and mutualism. When mutualism is favored, number fluctuations eventually drive the system away from a stable fixed point, characterized by cooperation, to one of the absorbing states. Well-mixed populations will thus be taken over by a single species in a finite time, despite the bias towards cooperation. We calculate both the fixation probability and the mean fixation time as a function of the initial conditions and carrying capacities in the strong mutualism regime, using the method of matched asymptotic expansions. Our results are compared to computer simulations.
Evolutionary dynamics of bacteria in a human host environment
DEFF Research Database (Denmark)
Yang, Lei; Jelsbak, Lars; Marvig, Rasmus Lykke;
2011-01-01
the evolutionary dynamics of a lineage of a clinically important opportunistic bacterial pathogen, Pseudomonas aeruginosa, as it adapts to the airways of several individual cystic fibrosis patients over 200,000 bacterial generations, and provide estimates of mutation rates of bacteria in a natural environment...... with pleiotropic effects, followed by a period of genetic drift with limited phenotypic change and a genomic signature of negative selection, suggesting that the evolving lineage has reached a major adaptive peak in the fitness landscape. This contrasts with previous findings of continued positive selection from...... long-term in vitro evolution experiments. The evolved phenotype of the infecting bacteria further suggests that the opportunistic pathogen has transitioned to become a primary pathogen for cystic fibrosis patients....
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.
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 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...
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 ...
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).
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 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.
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.
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.
Nash equilibrium and evolutionary dynamics in semifinalists' dilemma
Baek, Seung Ki; Son, Seung-Woo; Jeong, Hyeong-Chai
2015-04-01
We consider a tournament among four equally strong semifinalists. The players have to decide how much stamina to use in the semifinals, provided that the rest is available in the final and the third-place playoff. We investigate optimal strategies for allocating stamina to the successive matches when players' prizes (payoffs) are given according to the tournament results. From the basic assumption that the probability to win a match follows a nondecreasing function of stamina difference, we present symmetric Nash equilibria for general payoff structures. We find three different phases of the Nash equilibria in the payoff space. First, when the champion wins a much bigger payoff than the others, any pure strategy can constitute a Nash equilibrium as long as all four players adopt it in common. Second, when the first two places are much more valuable than the other two, the only Nash equilibrium is such that everyone uses a pure strategy investing all stamina in the semifinal. Third, when the payoff for last place is much smaller than the others, a Nash equilibrium is formed when every player adopts a mixed strategy of using all or none of its stamina in the semifinals. In a limiting case that only last place pays the penalty, this mixed-strategy profile can be proved to be a unique symmetric Nash equilibrium, at least when the winning probability follows a Heaviside step function. Moreover, by using this Heaviside step function, we study the tournament by using evolutionary replicator dynamics to obtain analytic solutions, which reproduces the corresponding Nash equilibria on the population level and gives information on dynamic aspects.
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.
The Impact of Mutation Rate on the Computation Time of Evolutionary Dynamic Optimization
Chen, Tianshi; Tang, Ke; Chen, Guoliang; Yao, Xin
2011-01-01
Mutation has traditionally been regarded as an important operator in evolutionary algorithms. In particular, there have been many experimental studies which showed the effectiveness of adapting mutation rates for various static optimization problems. Given the perceived effectiveness of adaptive and self-adaptive mutation for static optimization problems, there have been speculations that adaptive and self-adaptive mutation can benefit dynamic optimization problems even more since adaptation and self-adaptation are capable of following a dynamic environment. However, few theoretical results are available in analyzing rigorously evolutionary algorithms for dynamic optimization problems. It is unclear when adaptive and self-adaptive mutation rates are likely to be useful for evolutionary algorithms in solving dynamic optimization problems. This paper provides the first rigorous analysis of adaptive mutation and its impact on the computation times of evolutionary algorithms in solving certain dynamic optimizatio...
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...
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...
Directory of Open Access Journals (Sweden)
C Brandon Ogbunugafor
2016-01-01
Full Text Available The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with
Ogbunugafor, C Brandon; Wylie, C Scott; Diakite, Ibrahim; Weinreich, Daniel M; Hartl, Daniel L
2016-01-01
The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions-drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors-pyrimethamine and cycloguanil-across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary "forks in the road" that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with regards to their
Ogbunugafor, C. Brandon; Wylie, C. Scott; Diakite, Ibrahim; Weinreich, Daniel M.; Hartl, Daniel L.
2016-01-01
The adaptive landscape analogy has found practical use in recent years, as many have explored how their understanding can inform therapeutic strategies that subvert the evolution of drug resistance. A major barrier to applications of these concepts is a lack of detail concerning how the environment affects adaptive landscape topography, and consequently, the outcome of drug treatment. Here we combine empirical data, evolutionary theory, and computer simulations towards dissecting adaptive landscape by environment interactions for the evolution of drug resistance in two dimensions—drug concentration and drug type. We do so by studying the resistance mediated by Plasmodium falciparum dihydrofolate reductase (DHFR) to two related inhibitors—pyrimethamine and cycloguanil—across a breadth of drug concentrations. We first examine whether the adaptive landscapes for the two drugs are consistent with common definitions of cross-resistance. We then reconstruct all accessible pathways across the landscape, observing how their structure changes with drug environment. We offer a mechanism for non-linearity in the topography of accessible pathways by calculating of the interaction between mutation effects and drug environment, which reveals rampant patterns of epistasis. We then simulate evolution in several different drug environments to observe how these individual mutation effects (and patterns of epistasis) influence paths taken at evolutionary “forks in the road” that dictate adaptive dynamics in silico. In doing so, we reveal how classic metrics like the IC50 and minimal inhibitory concentration (MIC) are dubious proxies for understanding how evolution will occur across drug environments. We also consider how the findings reveal ambiguities in the cross-resistance concept, as subtle differences in adaptive landscape topography between otherwise equivalent drugs can drive drastically different evolutionary outcomes. Summarizing, we discuss the results with
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
Iyer, Swami; Killingback, Timothy
2014-10-01
The traveler's dilemma game and the minimum-effort coordination game are social dilemmas that have received significant attention resulting from the fact that the predictions of classical game theory are inconsistent with the results found when the games are studied experimentally. Moreover, both the traveler's dilemma and the minimum-effort coordination games have potentially important applications in evolutionary biology. Interestingly, standard deterministic evolutionary game theory, as represented by the replicator dynamics in a well-mixed population, is also inadequate to account for the behavior observed in these games. Here we study the evolutionary dynamics of both these games in populations with interaction patterns described by a variety of complex network topologies. We investigate the evolutionary dynamics of these games through agent-based simulations on both model and empirical networks. In particular, we study the effects of network clustering and assortativity on the evolutionary dynamics of both games. In general, we show that the evolutionary behavior of the traveler's dilemma and minimum-effort coordination games on complex networks is in good agreement with that observed experimentally. Thus, formulating the traveler's dilemma and the minimum-effort coordination games on complex networks neatly resolves the paradoxical aspects of these games.
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.)
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...
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...
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...
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.
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.
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.
Quantifying evolutionary dynamics from variant-frequency time series.
Khatri, Bhavin S
2016-01-01
From Kimura's neutral theory of protein evolution to Hubbell's neutral theory of biodiversity, quantifying the relative importance of neutrality versus selection has long been a basic question in evolutionary biology and ecology. With deep sequencing technologies, this question is taking on a new form: given a time-series of the frequency of different variants in a population, what is the likelihood that the observation has arisen due to selection or neutrality? To tackle the 2-variant case, we exploit Fisher's angular transformation, which despite being discovered by Ronald Fisher a century ago, has remained an intellectual curiosity. We show together with a heuristic approach it provides a simple solution for the transition probability density at short times, including drift, selection and mutation. Our results show under that under strong selection and sufficiently frequent sampling these evolutionary parameters can be accurately determined from simulation data and so they provide a theoretical basis for techniques to detect selection from variant or polymorphism frequency time-series. PMID:27616332
Dynamics Calculation of CH-DTL
Institute of Scientific and Technical Information of China (English)
无
2011-01-01
CH-DTL is a new development of accelerator structure, which has high shunt impedance and simple structure. The beam dynamics of CH-DTL is based on KONUS method, whose characteristic is that the longitudinal focus is small or none,
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
Wang, Jun; Tao, Feng; Marowsky, Nicholas C.; Fan, Chuanzhu
2016-01-01
Gene duplication is a primary means to generate genomic novelties, playing an essential role in speciation and adaptation. Particularly in plants, a high abundance of duplicate genes has been maintained for significantly long periods of evolutionary time. To address the manner in which young duplicate genes were derived primarily from small-scale gene duplication and preserved in plant genomes and to determine the underlying driving mechanisms, we generated transcriptomes to produce the expression profiles of five tissues in Arabidopsis thaliana and the closely related species Arabidopsis lyrata and Capsella rubella. Based on the quantitative analysis metrics, we investigated the evolutionary processes of young duplicate genes in Arabidopsis. We determined that conservation, neofunctionalization, and specialization are three main evolutionary processes for Arabidopsis young duplicate genes. We explicitly demonstrated the dynamic functionalization of duplicate genes along the evolutionary time scale. Upon origination, duplicates tend to maintain their ancestral functions; but as they survive longer, they might be likely to develop distinct and novel functions. The temporal evolutionary processes and functionalization of plant duplicate genes are associated with their ancestral functions, dynamic DNA methylation levels, and histone modification abundances. Furthermore, duplicate genes tend to be initially expressed in pollen and then to gain more interaction partners over time. Altogether, our study provides novel insights into the dynamic retention processes of young duplicate genes in plant genomes. PMID:27485883
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.
Environmental fluctuations restrict eco-evolutionary dynamics in predator-prey system.
Hiltunen, Teppo; Ayan, Gökçe B; Becks, Lutz
2015-06-01
Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria-ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.
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.
Evolutionary dynamics of sporophytic self-incompatibility alleles in plants
DEFF Research Database (Denmark)
Schierup, M H; Vekemans, X; Christiansen, F B
1997-01-01
The stationary frequency distribution and allelic dynamics in finite populations are analyzed through stochastic simulations in three models of single-locus, multi-allelic sporophytic self-incompatibility. The models differ in the dominance relationships among alleles. In one model, alleles act c...
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 ...
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...
Research on Duplication Dynamics and Evolutionary Stable of Reverse Supply Chain
Huizhong, Dong; Hongli, Song
An evolutionary game model of Reverse Supply Chain(RSC) is established based on duplication dynamics function and evolutionary stable strategy. Using the model framework, this paper provides insights into a deeper understanding on how each supplier make strategic decision independently in reverse supply chain to determine their performance. The main conclusion is as follow: Under the market mechanism, not unless the extra income derived from the implementation of RSC exceeds zero point would the suppliers implement RSC strategy. When those suppliers are passive to RSC, the effective solution is that the government takes macro-control measures, for example, to force those suppliers implement RSC through punishment mechanism.
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
An evolutionary computational approach for the dynamic Stackelberg competition problems
Directory of Open Access Journals (Sweden)
Lorena Arboleda-Castro
2016-06-01
Full Text Available Stackelberg competition models are an important family of economical decision problems from game theory, in which the main goal is to find optimal strategies between two competitors taking into account their hierarchy relationship. Although these models have been widely studied in the past, it is important to note that very few works deal with uncertainty scenarios, especially those that vary over time. In this regard, the present research studies this topic and proposes a computational method for solving efficiently dynamic Stackelberg competition models. The computational experiments suggest that the proposed approach is effective for problems of this nature.
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. This work is supported by the Cyprus Research Promo-tion Foundation grant TΠE/ΠΛHPO/0609(BE)/05, NSF grants CCF-0937829,...
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
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...
The Tangled Nature Model of evolutionary dynamics reconsidered
DEFF Research Database (Denmark)
Andersen, Christian Walther; Sibani, Paolo
2016-01-01
The Tangled Nature Model of biological and cultural evolution features interacting agents which compete for limited resources and reproduce in an error prone fashion and at a rate depending on the `tangle' of interactions they maintain with others. The set of interactions linking a TNM individual...... all the interactions, while increasing $K$ up to the length of the genome ensures an increasing level of trait inheritance. We show that the distribution of the interactions generated by our rule is nearly independent of the value of $K$. Changing $K$ strengthens the core structure of the ecology....../t_{\\rm w}$, similarity to the pure aging behaviour approximately describing glassy systems of physical origin. Increasing the value of $K$ decreases the numerical value of the decay exponent of the power law, which is a clear quantitative dynamical effect of trait inheritance....
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
A New Definition and Calculation Model for Evolutionary Multi-Objective Optimization
Institute of Scientific and Technical Information of China (English)
Zhou Ai-min; Kang Li-shan; Chen Yu-ping; Huang Yu-zhen
2003-01-01
We present a new definition (Evolving Solutions) for Multi objective Optimization Problem (MOP) to answer the basic question (what's multi-objective optimal solution?) and advance an asynchronous evolutionary model (MINT Model) to solve MOPs. The new theory is based on our understanding of the natural evolution and the analysis of the difference between natural evolution and MOP, thus it is not only different from the Converting Optimization but also different from Pareto Optimization.Some tests prove that our new theory may conquer disadvantages of the upper two methods to some extent.
Eco-evolutionary dynamics of plant-herbivore communities: incorporating plant phenotypic plasticity.
Ohgushi, Takayuki
2016-04-01
The interplay between evolution and ecological communities is critical for the integration of different levels of biological organization. Recent work has begun to unveil the importance of plant phenotypic plasticity and plant-herbivore (co)evolution to link plant evolution and associated insect communities. Specifically, herbivore-induced plant traits (i.e., plastic phenotypes) have significant effects on the structure and diversity of herbivore communities, which can in turn promote the evolution of not only the focal plant but also insect community members. Here, I will provide a conceptual framework on the eco-evolutionary dynamics of plant-herbivore communities to understand how biological organizations are integrated in plant-insect interactions. Research on eco-evolutionary dynamics of plant-herbivore communities will undoubtedly enrich understanding of a wide range of plant-insect interactions. PMID:27436645
Evolutionary Game Dynamics in a Fitness-Dependent Wrlght-Fisher Process with Noise
Institute of Scientific and Technical Information of China (English)
全吉; 王先甲
2011-01-01
Evolutionary game dynamics in finite size populations can be described by a fitness-dependent Wright- Fisher process. We consider symmetric 2×2 games in a well-mixed population. In our model, two parameters to describe the level of player＇s rationality and noise intensity in environment are introduced. In contrast with the fixation probability method that used in a noiseless case, the introducing of the noise intensity parameter makes the process an ergodic Markov process and based on the limit distribution of the process, we can analysis the evolutionary stable strategy （ESS） of the games. We illustrate the effects of the two parameters on the ESS of games using the Prisoner＇s dilemma games （PDG） and the snowdrift games （SG）. We also compare the ESS of our model with that of the replicator dynamics in infinite size populations. The results are determined by simulation experiments.
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...
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...
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...
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...
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...
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.
CALCULATION AND IMPROVEMENT OF DYNAMIC CHARACTERISTICS OF CENTRIFUGE
Institute of Scientific and Technical Information of China (English)
无
2001-01-01
The modeling of the rotor-support system of a typical centrifuge is discussed. The impedance matching method, cooperating with Riccati transfer matrix method and modal analysis method are adopted to calculate its dynamic characteristics. The influences of the main parts to the critical speeds are analyzed. Based on the analysis, a critical speed in the operating speed range is tuned successfully, and thus the dynamic characteristics of the centrifuge are much improved.
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...
Gravitational field calculations on a dynamic lattice by distributed computing.
Mähönen, P.; Punkka, V.
A new method of calculating numerically time evolution of a gravitational field in general relativity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
Gravitation Field Calculations on a Dynamic Lattice by Distributed Computing
Mähönen, Petri; Punkka, Veikko
A new method of calculating numerically time evolution of a gravitational field in General Relatity is introduced. Vierbein (tetrad) formalism, dynamic lattice and massively parallelized computation are suggested as they are expected to speed up the calculations considerably and facilitate the solution of problems previously considered too hard to be solved, such as the time evolution of a system consisting of two or more black holes or the structure of worm holes.
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
Quasiclassical Calculations of Wigner Functions in Nonlinear Beam Dynamics
Fedorova, A N; Fedorova, Antonina N.; Zeitlin, Michael G.
2001-01-01
We present the application of variational-wavelet analysis to numerical/analytical calculations of Wigner functions in (nonlinear) quasiclassical beam dynamics problems. (Naive) deformation quantization and multiresolution representations are the key points. We construct the representation via multiscale expansions in generalized coherent states or high-localized nonlinear eigenmodes in the base of compactly supported wavelets and wavelet packets.
Evolutionary Design of Both Topologies and Parameters of a Hybrid Dynamical System
DEFF Research Database (Denmark)
Dupuis, Jean-Francois; Fan, Zhun; Goodman, Erik
2012-01-01
This paper investigates the issue of evolutionary design of open-ended plants for hybrid dynamical systems--i.e. both their topologies and parameters. Hybrid bond graphs are used to represent dynamical systems involving both continuous and discrete system dynamics. Genetic programming, with some...... special mechanisms incorporated, is used as a search tool to explore the open-ended design space of hybrid bond graphs. Combination of these two tools--i.e., hybrid bond graphs (HGBs) and genetic programming (GP)--leads to an approach called HBGGP that can automatically generate viable design candidates...... of hybrid dynamical systems that fulfill predefined design specifications. A comprehensive investigation of a case study of DC-DC converter design demonstrates the feasibility and effectiveness of the HBGGP approach. Important characteristics of the approach are also discussed, with some future research...
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.......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......-consistent procedure gives the same results as the more complicated procedure based on average over Voronoi cells. Graphs of the dynamic resistivity versus frequency are given for fiber densities and diameters typical for acoustic fiber materials....
A large scale molecular dynamics calculation of a lipid bilayer
Energy Technology Data Exchange (ETDEWEB)
Okazaki, Susumu [Tokyo Inst. of Tech. (Japan)
1998-03-01
Long time molecular dynamics simulations for the dipalmitoylphosphatidylcholine lipid bilayer in the liquid crystal phase could successfully be performed in the isothermal-isobaric ensemble using the Nose-Parrinello-Rahman extended system method. Three independent 2 ns calculations show excellent convergence to the same equilibrium state of the system in about 0.5 ns. Various structural properties such a atomic distribution, order parameter, gauche fraction in the alkyl chains, and bent structure of the head group and sn-2 chain were satisfactorily reproduced. Dynamic quantities such as trans-gauche transition were qualitatively in good correspondence the experiment. The calculations presented a microscopic picture of the whole molecular conformations, including the finding that there is not a collective tilt in bilayer. Some interesting dynamical observations concerning large structural fluctuations and pendulum motion of the alkyl chains were also made. (author)
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
Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments.
Jerison, Elizabeth R; Desai, Michael M
2015-12-01
Microbial evolution experiments enable us to watch adaptation in real time, and to quantify the repeatability and predictability of evolution by comparing identical replicate populations. Further, we can resurrect ancestral types to examine changes over evolutionary time. Until recently, experimental evolution has been limited to measuring phenotypic changes, or to tracking a few genetic markers over time. However, recent advances in sequencing technology now make it possible to extensively sequence clones or whole-population samples from microbial evolution experiments. Here, we review recent work exploiting these techniques to understand the genomic basis of evolutionary change in experimental systems. We first focus on studies that analyze the dynamics of genome evolution in microbial systems. We then survey work that uses observations of sequence evolution to infer aspects of the underlying fitness landscape, concentrating on the epistatic interactions between mutations and the constraints these interactions impose on adaptation.
Jousimo, Jussi; Tack, Ayco J M; Ovaskainen, Otso; Mononen, Tommi; Susi, Hanna; Tollenaere, Charlotte; Laine, Anna-Liisa
2014-06-13
Ecological theory predicts that disease incidence increases with increasing density of host networks, yet evolutionary theory suggests that host resistance increases accordingly. To test the combined effects of ecological and evolutionary forces on host-pathogen systems, we analyzed the spatiotemporal dynamics of a plant (Plantago lanceolata)-fungal pathogen (Podosphaera plantaginis)relationship for 12 years in over 4000 host populations. Disease prevalence at the metapopulation level was low, with high annual pathogen extinction rates balanced by frequent (re-)colonizations. Highly connected host populations experienced less pathogen colonization and higher pathogen extinction rates than expected; a laboratory assay confirmed that this phenomenon was caused by higher levels of disease resistance in highly connected host populations.
Against matching theory: predictions of an evolutionary theory of behavior dynamics.
McDowell, J J; Calvin, Nicholas T
2015-05-01
A selectionist theory of adaptive behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of resource acquisition or threat escape or avoidance. The theory is implemented by a computer program that creates an artificial organism and animates it with a population of potential behaviors. The population undergoes selection, recombination, and mutation across generations, or ticks of time, which produces a continuous stream of behavior that can be studied as if it were the behavior of a live organism. Novel predictions of the evolutionary theory can be compared to predictions of matching theory in a critical experiment that arranges concurrent schedules with reinforcer magnitudes that vary across conditions in one component of the schedules but not the other. Matching theory and the evolutionary theory make conflicting predictions about the outcome of this critical experiment, such that the results must disconfirm at least one of the theories. PMID:25680328
Against matching theory: predictions of an evolutionary theory of behavior dynamics.
McDowell, J J; Calvin, Nicholas T
2015-05-01
A selectionist theory of adaptive behavior dynamics instantiates the idea that behavior evolves in response to selection pressure from the environment in the form of resource acquisition or threat escape or avoidance. The theory is implemented by a computer program that creates an artificial organism and animates it with a population of potential behaviors. The population undergoes selection, recombination, and mutation across generations, or ticks of time, which produces a continuous stream of behavior that can be studied as if it were the behavior of a live organism. Novel predictions of the evolutionary theory can be compared to predictions of matching theory in a critical experiment that arranges concurrent schedules with reinforcer magnitudes that vary across conditions in one component of the schedules but not the other. Matching theory and the evolutionary theory make conflicting predictions about the outcome of this critical experiment, such that the results must disconfirm at least one of the theories.
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
Liao, David; Tlsty, Thea D
2014-08-01
Failure to understand evolutionary dynamics has been hypothesized as limiting our ability to control biological systems. An increasing awareness of similarities between macroscopic ecosystems and cellular tissues has inspired optimism that game theory will provide insights into the progression and control of cancer. To realize this potential, the ability to compare game theoretic models and experimental measurements of population dynamics should be broadly disseminated. In this tutorial, we present an analysis method that can be used to train parameters in game theoretic dynamics equations, used to validate the resulting equations, and used to make predictions to challenge these equations and to design treatment strategies. The data analysis techniques in this tutorial are adapted from the analysis of reaction kinetics using the method of initial rates taught in undergraduate general chemistry courses. Reliance on computer programming is avoided to encourage the adoption of these methods as routine bench activities.
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.
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.
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.
Stochastic win-stay-lose-shift strategy with dynamic aspirations in evolutionary social dilemmas
Amaral, Marco A.; Wardil, Lucas; Perc, Matjaž; da Silva, Jafferson K. L.
2016-09-01
In times of plenty expectations rise, just as in times of crisis they fall. This can be mathematically described as a win-stay-lose-shift strategy with dynamic aspiration levels, where individuals aspire to be as wealthy as their average neighbor. Here we investigate this model in the realm of evolutionary social dilemmas on the square lattice and scale-free networks. By using the master equation and Monte Carlo simulations, we find that cooperators coexist with defectors in the whole phase diagram, even at high temptations to defect. We study the microscopic mechanism that is responsible for the striking persistence of cooperative behavior and find that cooperation spreads through second-order neighbors, rather than by means of network reciprocity that dominates in imitation-based models. For the square lattice the master equation can be solved analytically in the large temperature limit of the Fermi function, while for other cases the resulting differential equations must be solved numerically. Either way, we find good qualitative agreement with the Monte Carlo simulation results. Our analysis also reveals that the evolutionary outcomes are to a large degree independent of the network topology, including the number of neighbors that are considered for payoff determination on lattices, which further corroborates the local character of the microscopic dynamics. Unlike large-scale spatial patterns that typically emerge due to network reciprocity, here local checkerboard-like patterns remain virtually unaffected by differences in the macroscopic properties of the interaction network.
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.
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.
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.
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
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
Effects of dynamical grouping on cooperation in N-person evolutionary snowdrift game
Ji, M.; Xu, C.; Hui, P. M.
2011-09-01
A population typically consists of agents that continually distribute themselves into different groups at different times. This dynamic grouping has recently been shown to be essential in explaining many features observed in human activities including social, economic, and military activities. We study the effects of dynamic grouping on the level of cooperation in a modified evolutionary N-person snowdrift game. Due to the formation of dynamical groups, the competition takes place in groups of different sizes at different times and players of different strategies are mixed by the grouping dynamics. It is found that the level of cooperation is greatly enhanced by the dynamic grouping of agents, when compared with a static population of the same size. As a parameter β, which characterizes the relative importance of the reward and cost, increases, the fraction of cooperative players fC increases and it is possible to achieve a fully cooperative state. Analytically, we present a dynamical equation that incorporates the effects of the competing game and group size distribution. The distribution of cooperators in different groups is assumed to be a binomial distribution, which is confirmed by simulations. Results from the analytic equation are in good agreement with numerical results from simulations. We also present detailed simulation results of fC over the parameter space spanned by the probabilities of group coalescence νm and group fragmentation νp in the grouping dynamics. A high νm and low νp promotes cooperation, and a favorable reward characterized by a high β would lead to a fully cooperative state.
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.
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.
Molecular evolutionary dynamics of Ross River virus and implications for vaccine efficacy.
Jones, Anita; Lowry, Kym; Aaskov, John; Holmes, Edward C; Kitchen, Andrew
2010-01-01
Ross River virus (RRV) is a mosquito-borne member of the genus Alphavirus that causes epidemic polyarthritis in humans, costing the Australian health system at least US$10 million annually. Recent progress in RRV vaccine development requires accurate assessment of RRV genetic diversity and evolution, particularly as they may affect the utility of future vaccination. In this study, we provide novel RRV genome sequences and investigate the evolutionary dynamics of RRV from time-structured E2 gene datasets. Our analysis indicates that, although RRV evolves at a similar rate to other alphaviruses (mean evolutionary rate of approx. 8x10(-4) nucleotide substitutions per site year(-1)), the relative genetic diversity of RRV has been continuously low through time, possibly as a result of purifying selection imposed by replication in a wide range of natural host and vector species. Together, these findings suggest that vaccination against RRV is unlikely to result in the rapid antigenic evolution that could compromise the future efficacy of current RRV vaccines.
Lemey, Philippe; Farci, Patrizia; Pybus, Oliver G.
2016-01-01
The treatment of HCV infection has seen significant progress, particularly since the approval of new direct-acting antiviral drugs. However these clinical achievements have been made despite an incomplete understanding of HCV replication and within-host evolution, especially compared with HIV-1. Here, we undertake a comprehensive analysis of HCV within-host evolution during chronic infection by investigating over 4000 viral sequences sampled longitudinally from 15 HCV-infected patients. We compare our HCV results to those from a well-studied HIV-1 cohort, revealing key differences in the evolutionary behaviour of these two chronic-infecting pathogens. Notably, we find an exceptional level of heterogeneity in the molecular evolution of HCV, both within and among infected individuals. Furthermore, these patterns are associated with the long-term maintenance of viral lineages within patients, which fluctuate in relative frequency in peripheral blood. Together, our findings demonstrate that HCV replication behavior is complex and likely comprises multiple viral subpopulations with distinct evolutionary dynamics. The presence of a structured viral population can explain apparent paradoxes in chronic HCV infection, such as rapid fluctuations in viral diversity and the reappearance of viral strains years after their initial detection. PMID:27631086
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.
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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.
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
Evolutionary decision-makings for the dynamic weapon-target assignment problem
Institute of Scientific and Technical Information of China (English)
CHEN Jie; XIN Bin; PENG ZhiHong; DOU LiHua; ZHANG Juan
2009-01-01
The dynamic weapon-target assignment (DWTA) problem is an important issue In the field of military command and control.An asset-based DWTA optimization model was proposed with four kinds of constraints considered,including capability constraints,strategy constraints,resource constraints and engagement feasibility constraints.A general "virtual"representation of decisions was presented to facilitate the generation of feasible decisions.The representation is in essence the permutation of all assignment pairs.A construction procedure converts the permutations into real feasible decisions.In order to solve this problem,three evolutionary decision-making algorithms,Including a genetic algorithm and two memeitc algorithms,were developed.Experimental results show that the memetic algorithm based on greedy local search can generate obviously better DWTA decisions,especially for large-scale problems,than the genetic algorithm and the memetic algorithm based on steepest local search.
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...
Van Zee, L; Skillman, E D; Zee, Liese van; Salzer, John J.; Skillman, Evan D.
2001-01-01
We present the results of high spatial resolution HI synthesis observations of six blue compact dwarf (BCD) galaxies. Optically, the selected galaxies have smooth, symmetric isophotes, and thus are the most likely of the BCD class to fade into an object morphologically similar to a dwarf elliptical when the current starburst ends. The neutral gas in all six galaxies appears to be rotationally supported, however, indicating that true morphological transformation from a BCD to a dE will require significant loss of angular momentum. Based on the observed neutral gas dynamics of these and other BCDs, it is unlikely that present-day BCDs will evolve directly into dwarf ellipticals after a starburst phase. We discuss alternative evolutionary scenarios for BCDs and place them within the larger context of galaxy formation and evolution models.
Evolutionary dynamics and genetic diversity from three genes of Anguillid rhabdovirus
DEFF Research Database (Denmark)
Bellec, Laure; Cabon, Joelle; Bergmann, Sven;
2014-01-01
play a role in this decline, even if their real contribution is still unclear. In this study, we investigate the evolutionary dynamics and genetic diversity of anguiillid rhabdoviruses by analysing sequences from the glycoprotein, nucleoprotein and phosphoprotein (P) genes of 57 viral strains collected......Wild freshwater eel populations have dramatically declined in recent past decades in Europe and America, partially through the impact of several factors including the wide spread of infectious diseases. The anguillid rhabdoviruses eel virus European X (EVEX) and eel virus American (EVA) potentially...... that the P gene is expected to evolve most rapidly. The nucleotide diversity observed is low (2-3 %) for the three genes, with a significantly higher variability within the P gene, which encodes multiple proteins from a single genomic RNA sequence, particularly a small C protein. This putative C protein...
Stochastic Win-Stay-Lose-Shift with dynamic aspirations in evolutionary social dilemmas
Amaral, Marco A; Perc, Matjaz; da Silva, Jafferson K L
2016-01-01
In times of plenty expectations rise, just as in times of crisis they fall. This can be mathematically described as a Win-Stay-Lose-Shift strategy with dynamic aspiration levels, where individuals aspire to be as wealthy as their average neighbor. Here we investigate this model in the realm of evolutionary social dilemmas on the square lattice and scale-free networks. By using the master equation and Monte Carlo simulations, we find that cooperators coexist with defectors in the whole phase diagram, even at high temptations to defect. We study the microscopic mechanism that is responsible for the striking persistence of cooperative behavior and find that cooperation spreads through second-order neighbors, rather than by means of network reciprocity that dominates in imitation-based models. For the square lattice the master equation can be solved analytically in the large temperature limit of the Fermi function, while for other cases the resulting differential equations must be solved numerically. Either way, ...
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.
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.
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.
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.
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...
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.
Ma, Jingjing; Liu, Jie; Ma, Wenping; Gong, Maoguo; Jiao, Licheng
2014-01-01
Community structure is one of the most important properties in social networks. In dynamic networks, there are two conflicting criteria that need to be considered. One is the snapshot quality, which evaluates the quality of the community partitions at the current time step. The other is the temporal cost, which evaluates the difference between communities at different time steps. In this paper, we propose a decomposition-based multiobjective community detection algorithm to simultaneously optimize these two objectives to reveal community structure and its evolution in dynamic networks. It employs the framework of multiobjective evolutionary algorithm based on decomposition to simultaneously optimize the modularity and normalized mutual information, which quantitatively measure the quality of the community partitions and temporal cost, respectively. A local search strategy dealing with the problem-specific knowledge is incorporated to improve the effectiveness of the new algorithm. Experiments on computer-generated and real-world networks demonstrate that the proposed algorithm can not only find community structure and capture community evolution more accurately, but also be steadier than the two compared algorithms.
Co-evolutionary dynamics of collective action with signaling for a quorum.
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Jorge M Pacheco
2015-02-01
Full Text Available Collective signaling for a quorum is found in a wide range of organisms that face collective action problems whose successful solution requires the participation of some quorum of the individuals present. These range from humans, to social insects, to bacteria. The mechanisms involved, the quorum required, and the size of the group may vary. Here we address the general question of the evolution of collective signaling at a high level of abstraction. We investigate the evolutionary dynamics of a population engaging in a signaling N-person game theoretic model. Parameter settings allow for loners and cheaters, and for costly or costless signals. We find a rich dynamics, showing how natural selection, operating on a population of individuals endowed with the simplest strategies, is able to evolve a costly signaling system that allows individuals to respond appropriately to different states of Nature. Signaling robustly promotes cooperative collective action, in particular when coordinated action is most needed and difficult to achieve. Two different signaling systems may emerge depending on Nature's most prevalent states.
Helbing, Dirk; Johansson, Anders
2010-01-01
Evolutionary game theory has been successfully used to investigate the dynamics of systems, in which many entities have competitive interactions. From a physics point of view, it is interesting to study conditions under which a coordination or cooperation of interacting entities will occur, be it spins, particles, bacteria, animals, or humans. Here, we analyze the case, where the entities are heterogeneous, particularly the case of two populations with conflicting interactions and two possible states. For such systems, explicit mathematical formulas will be determined for the stationary solutions and the associated eigenvalues, which determine their stability. In this way, four different types of system dynamics can be classified and the various kinds of phase transitions between them will be discussed. While these results are interesting from a physics point of view, they are also relevant for social, economic, and biological systems, as they allow one to understand conditions for (1) the breakdown of cooperation, (2) the coexistence of different behaviors (“subcultures”), (3) the evolution of commonly shared behaviors (“norms”), and (4) the occurrence of polarization or conflict. We point out that norms have a similar function in social systems that forces have in physics.
Harmon, Luke J.; Blank, Carrine E.
2016-01-01
Cyanobacteria have exerted a profound influence on the progressive oxygenation of Earth. As a complementary approach to examining the geologic record—phylogenomic and trait evolutionary analyses of extant species can lead to new insights. We constructed new phylogenomic trees and analyzed phenotypic trait data using novel phylogenetic comparative methods. We elucidated the dynamics of trait evolution in Cyanobacteria over billion-year timescales, and provide evidence that major geologic events in early Earth’s history have shaped—and been shaped by—evolution in Cyanobacteria. We identify a robust core cyanobacterial phylogeny and a smaller set of taxa that exhibit long-branch attraction artifacts. We estimated the age of nodes and reconstruct the ancestral character states of 43 phenotypic characters. We find high levels of phylogenetic signal for nearly all traits, indicating the phylogeny carries substantial predictive power. The earliest cyanobacterial lineages likely lived in freshwater habitats, had small cell diameters, were benthic or sessile, and possibly epilithic/endolithic with a sheath. We jointly analyzed a subset of 25 binary traits to determine whether rates of trait evolution have shifted over time in conjunction with major geologic events. Phylogenetic comparative analysis reveal an overriding signal of decreasing rates of trait evolution through time. Furthermore, the data suggest two major rate shifts in trait evolution associated with bursts of evolutionary innovation. The first rate shift occurs in the aftermath of the Great Oxidation Event and “Snowball Earth” glaciations and is associated with decrease in the evolutionary rates around 1.8–1.6 Ga. This rate shift seems to indicate the end of a major diversification of cyanobacterial phenotypes–particularly related to traits associated with filamentous morphology, heterocysts and motility in freshwater ecosystems. Another burst appears around the time of the Neoproterozoic
Tennessen, Jacob A; Govindarajulu, Rajanikanth; Ashman, Tia-Lynn; Liston, Aaron
2014-12-04
Whole-genome duplications are radical evolutionary events that have driven speciation and adaptation in many taxa. Higher-order polyploids have complex histories often including interspecific hybridization and dynamic genomic changes. This chromosomal reshuffling is poorly understood for most polyploid species, despite their evolutionary and agricultural importance, due to the challenge of distinguishing homologous sequences from each other. Here, we use dense linkage maps generated with targeted sequence capture to improve the diploid strawberry (Fragaria vesca) reference genome and to disentangle the subgenomes of the wild octoploid progenitors of cultivated strawberry, Fragaria virginiana and Fragaria chiloensis. Our novel approach, POLiMAPS (Phylogenetics Of Linkage-Map-Anchored Polyploid Subgenomes), leverages sequence reads to associate informative interhomeolog phylogenetic markers with linkage groups and reference genome positions. In contrast to a widely accepted model, we find that one of the four subgenomes originates with the diploid cytoplasm donor F. vesca, one with the diploid Fragaria iinumae, and two with an unknown ancestor close to F. iinumae. Extensive unidirectional introgression has converted F. iinumae-like subgenomes to be more F. vesca-like, but never the reverse, due either to homoploid hybridization in the F. iinumae-like diploid ancestors or else strong selection spreading F. vesca-like sequence among subgenomes through homeologous exchange. In addition, divergence between homeologous chromosomes has been substantially augmented by interchromosomal rearrangements. Our phylogenetic approach reveals novel aspects of the complicated web of genetic exchanges that occur during polyploid evolution and suggests a path forward for unraveling other agriculturally and ecologically important polyploid genomes.
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
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 ...
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.
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.
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.
Sorokin, Valery A; Gelfand, Mikhail S; Artamonova, Irena I
2010-04-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, CRISPR-forming events and reconstructed the likely evolutionary history of cassettes that had common spacers. Metagenomic collections allow for relatively unbiased analysis of phage-host interactions and CRISPR evolution. The results of this study demonstrate that CRISPR cassettes retain the memory of the local virus population at a particular ocean location. CRISPR evolution may be described using a limited vocabulary of elementary events that have a natural biological interpretation.
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
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\\...
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
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
Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe
2014-04-01
Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially
Directory of Open Access Journals (Sweden)
Bram Vrancken
2014-04-01
Full Text Available Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1 evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected
Vrancken, Bram; Rambaut, Andrew; Suchard, Marc A; Drummond, Alexei; Baele, Guy; Derdelinckx, Inge; Van Wijngaerden, Eric; Vandamme, Anne-Mieke; Van Laethem, Kristel; Lemey, Philippe
2014-04-01
Transmission lies at the interface of human immunodeficiency virus type 1 (HIV-1) evolution within and among hosts and separates distinct selective pressures that impose differences in both the mode of diversification and the tempo of evolution. In the absence of comprehensive direct comparative analyses of the evolutionary processes at different biological scales, our understanding of how fast within-host HIV-1 evolutionary rates translate to lower rates at the between host level remains incomplete. Here, we address this by analyzing pol and env data from a large HIV-1 subtype C transmission chain for which both the timing and the direction is known for most transmission events. To this purpose, we develop a new transmission model in a Bayesian genealogical inference framework and demonstrate how to constrain the viral evolutionary history to be compatible with the transmission history while simultaneously inferring the within-host evolutionary and population dynamics. We show that accommodating a transmission bottleneck affords the best fit our data, but the sparse within-host HIV-1 sampling prevents accurate quantification of the concomitant loss in genetic diversity. We draw inference under the transmission model to estimate HIV-1 evolutionary rates among epidemiologically-related patients and demonstrate that they lie in between fast intra-host rates and lower rates among epidemiologically unrelated individuals infected with HIV subtype C. Using a new molecular clock approach, we quantify and find support for a lower evolutionary rate along branches that accommodate a transmission event or branches that represent the entire backbone of transmitted lineages in our transmission history. Finally, we recover the rate differences at the different biological scales for both synonymous and non-synonymous substitution rates, which is only compatible with the 'store and retrieve' hypothesis positing that viruses stored early in latently infected cells preferentially
DEFF Research Database (Denmark)
Hansen, Sara Krogh; Vestergaard, Mikkel; Thøgersen, Lea;
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...
Evolutionary dynamics of the Ty3/gypsy LTR retrotransposons in the genome of Anopheles gambiae.
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Jose Manuel C Tubio
Full Text Available Ty3/gypsy elements represent one of the most abundant and diverse LTR-retrotransposon (LTRr groups in the Anopheles gambiae genome, but their evolutionary dynamics have not been explored in detail. Here, we conduct an in silico analysis of the distribution and abundance of the full complement of 1045 copies in the updated AgamP3 assembly. Chromosomal distribution of Ty3/gypsy elements is inversely related to arm length, with densities being greatest on the X, and greater on the short versus long arms of both autosomes. Taking into account the different heterochromatic and euchromatic compartments of the genome, our data suggest that the relative abundance of Ty3/gypsy LTRrs along each chromosome arm is determined mainly by the different proportions of heterochromatin, particularly pericentric heterochromatin, relative to total arm length. Additionally, the breakpoint regions of chromosomal inversion 2La appears to be a haven for LTRrs. These elements are underrepresented more than 7-fold in euchromatin, where 33% of the Ty3/gypsy copies are associated with genes. The euchromatin on chromosome 3R shows a faster turnover rate of Ty3/gypsy elements, characterized by a deficit of proviral sequences and the lowest average sequence divergence of any autosomal region analyzed in this study. This probably reflects a principal role of purifying selection against insertion for the preservation of longer conserved syntenyc blocks with adaptive importance located in 3R. Although some Ty3/gypsy LTRrs show evidence of recent activity, an important fraction are inactive remnants of relatively ancient insertions apparently subject to genetic drift. Consistent with these computational predictions, an analysis of the occupancy rate of putatively older insertions in natural populations suggested that the degenerate copies have been fixed across the species range in this mosquito, and also are shared with the sibling species Anopheles arabiensis.
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
Epidemiological and Evolutionary Dynamics of Influenza B Viruses in Malaysia, 2012-2014.
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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
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.
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.
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.
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.
Dynamic simulation of flash drums using rigorous physical property calculations
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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.
Calculated pKa Variations Expose Dynamic Allosteric Communication Networks.
Lang, Eric J M; Heyes, Logan C; Jameson, Geoffrey B; Parker, Emily J
2016-02-17
Allosteric regulation of protein function, the process by which binding of an effector molecule provokes a functional response from a distal site, is critical for metabolic pathways. Yet, the way the allosteric signal is communicated remains elusive, especially in dynamic, entropically driven regulation mechanisms for which no major conformational changes are observed. To identify these dynamic allosteric communication networks, we have developed an approach that monitors the pKa variations of ionizable residues over the course of molecular dynamics simulations performed in the presence and absence of an allosteric regulator. As the pKa of ionizable residues depends on their environment, it represents a simple metric to monitor changes in several complex factors induced by binding an allosteric effector. These factors include Coulombic interactions, hydrogen bonding, and solvation, as well as backbone motions and side chain fluctuations. The predictions that can be made with this method concerning the roles of ionizable residues for allosteric communication can then be easily tested experimentally by changing the working pH of the protein or performing single point mutations. To demonstrate the method's validity, we have applied this approach to the subtle dynamic regulation mechanism observed for Neisseria meningitidis 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase, the first enzyme of aromatic biosynthesis. We were able to identify key communication pathways linking the allosteric binding site to the active site of the enzyme and to validate these findings experimentally by reestablishing the catalytic activity of allosterically inhibited enzyme via modulation of the working pH, without compromising the binding affinity of the allosteric regulator.
DYNAMICS FOR VORTICES OF AN EVOLUTIONARY GINZBURG-LANDAU EQUATIONS IN 3 DIMENSIONS
Institute of Scientific and Technical Information of China (English)
刘祖汉
2002-01-01
This paper studies the asymptotic behavior of solutions to an evolutionary Ginzburg-Landau equation in 3 dimensions. It is shown that the motion of the Ginzburg-Landau vortex curves is the flow by its curvature. Away from the vortices, the author uses some measure theoretic arguments used by F. H. Lin in [16] to show the strong convergence of solutions.
Measuring telomere length and telomere dynamics in evolutionary biology and ecology
Nussey, Daniel H.; Baird, Duncan; Barrett, Emma; Boner, Winnie; Fairlie, Jennifer; Gemmell, Neil; Hartmann, Nils; Horn, Thorsten; Haussmann, Mark; Olsson, Mats; Turbill, Chris; Verhulst, Simon; Zahn, Sandrine; Monaghan, Pat
2014-01-01
Telomeres play a fundamental role in the protection of chromosomal DNA and in the regulation of cellular senescence. Recent work in human epidemiology and evolutionary ecology suggests adult telomere length (TL) may reflect past physiological stress and predict subsequent morbidity and mortality, in
Hydraulic calculation and dynamic analysis of columnar reversing gate
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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.
Calculations of the dynamic dipole polarizabilities for the Li+ ion
Zhang, Yong-Hui; Tang, Li-Yan; Zhang, Xian-Zhou; Shi, Ting-Yun
2016-10-01
The B-spline configuration-interaction method is applied to the investigations of dynamic dipole polarizabilities for the four lowest triplet states (2 3S, 33S, 23P, and 33P) of the Li+ ion. The accurate energies for the triplet states of n 3S, n 3P, and n 3D, the dipole oscillator strengths for 23S(33S) → n 3P, 23P(33P) → n 3S, and 23P(33P) → n 3D transitions, with the main quantum number n up to 10 are tabulated for references. The dynamic dipole polarizabilities for the four triplet states under a wide range of photon energy are also listed, which provide input data for analyzing the Stark shift of the Li+ ion. Furthermore, the tune-out wavelengths in the range from 100 nm to 1.2 μm for the four triplet states, and the magic wavelengths in the range from 100 nm to 600 nm for the 23S → 33S, 23S → 23P, and 23S → 33P transitions are determined accurately for the experimental design of the Li+ ion. Project supported by the National Basic Research Program of China (Grant No. 2012CB821305) and the National Natural Science Foundation of China (Grant Nos. 11474319, 11274348, and 91536102).
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
Molecular-dynamics calculation of the vacancy heat of transport
Energy Technology Data Exchange (ETDEWEB)
Schelling, Patrick K.; Ernotte, Jacques; Shokeen, Lalit; Tucker, William C. [Advanced Material Processing and Analysis Center and Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 (United States); Woods Halley, J. [Department of Physics, University of Minnesota, 116 Church Street SE, Minneapolis, Minnesota 555455 (United States)
2014-07-14
We apply the recently developed constrained-dynamics method to elucidate the thermodiffusion of vacancies in a single-component material. The derivation and assumptions used in the method are clearly explained. Next, the method is applied to compute the reduced heat of transport Q{sub v}{sup *}−h{sub fv} for vacancies in a single-component material. Results from simulations using three different Morse potentials, with one providing an approximate description of Au, and an embedded-atom model potential for Ni are presented. It is found that the reduced heat of transport Q{sub v}{sup *}−h{sub fv} may take either positive or negative values depending on the potential parameters and exhibits some dependence on temperature. It is also found that Q{sub v}{sup *}−h{sub fv} may be correlated with the activation entropy. The results are discussed in comparison with experimental and previous simulation results.
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
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
C.H. Hommes; M.I. Ochea
2010-01-01
This paper investigates, by means of simple, three and four strategy games, the occurrence of periodic and chaotic behaviour in a smooth version of the Best Response Dynamics, the Logit Dynamics. The main finding is that, unlike Replicator Dynamics, generic Hopf bifurcation and thus, stable limit cy
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
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....
An, Gary C
2010-01-01
The greatest challenge facing the biomedical research community is the effective translation of basic mechanistic knowledge into clinically effective therapeutics. This challenge is most evident in attempts to understand and modulate "systems" processes/disorders, such as sepsis, cancer, and wound healing. Formulating an investigatory strategy for these issues requires the recognition that these are dynamic processes. Representation of the dynamic behavior of biological systems can aid in the investigation of complex pathophysiological processes by augmenting existing discovery procedures by integrating disparate information sources and knowledge. This approach is termed Translational Systems Biology. Focusing on the development of computational models capturing the behavior of mechanistic hypotheses provides a tool that bridges gaps in the understanding of a disease process by visualizing "thought experiments" to fill those gaps. Agent-based modeling is a computational method particularly well suited to the translation of mechanistic knowledge into a computational framework. Utilizing agent-based models as a means of dynamic hypothesis representation will be a vital means of describing, communicating, and integrating community-wide knowledge. The transparent representation of hypotheses in this dynamic fashion can form the basis of "knowledge ecologies," where selection between competing hypotheses will apply an evolutionary paradigm to the development of community knowledge.
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.
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
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...
Multi-Loop Calculations of Anomalous Exponents in the Models of Critical Dynamics
Directory of Open Access Journals (Sweden)
Adzhemyan L. Ts.
2016-01-01
Full Text Available The Renormalization group method (RG is applied to the investigation of the E model of critical dynamics, which describes the transition from the normal to the superfluid phase in He4. The technique “Sector decomposition” with R’ operation is used for the calculation of the Feynman diagrams. The RG functions, critical exponents and critical dynamical exponent z, which determines the growth of the relaxation time near the critical point, have been calculated in the two-loop approximation in the framework of ε-expansion. The relevance of a fixed point for helium, where the dynamic scaling is weakly violated, is briefly discussed.
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.
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.
Analysis of Ant Colony Optimization and Population-Based Evolutionary Algorithms on Dynamic Problems
DEFF Research Database (Denmark)
Lissovoi, Andrei
This thesis presents new running time analyses of nature-inspired algorithms on various dynamic problems. It aims to identify and analyse the features of algorithms and problem classes which allow efficient optimization to occur in the presence of dynamic behaviour. We consider the following...
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-...
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.
Dynamics of cancer progression and suppression: A novel evolutionary game theory based approach.
Banerjee, Jeet; Ranjan, Tanvi; Layek, Ritwik Kumar
2015-01-01
In this paper, a novel mathematical approach is proposed for the dynamics of progression and suppression of cancer. We define mutant cell density, ρ(μ) (μ × ρ), as a primary factor in cancer dynamics, and use logistic growth model and replicator equation for defining the dynamics of total cell density (ρ) and mutant fraction (μ), respectively. Furthermore, in the proposed model, we introduce an analytical expression for a control parameter D (drug), to suppress the proliferation of mutants with extra fitness level σ. Lastly, we present a comparison of the proposed model with some existing models of tumour growth.
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.
Multiannual forecasting of seasonal influenza dynamics reveals climatic and evolutionary drivers
Axelsen, Jacob Bock; Yaari, Rami; Grenfell, Bryan T.; Stone, Lewi
2014-01-01
Seasonality in disease incidence is ubiquitous among infectious diseases. Seasonal drivers include weather variables, such as temperature and humidity, and social factors (e.g., contact patterns). Attempts to make long-term predictions of infectious diseases are hampered by the inability to understand the complex interplay of these factors. Here, we model the dynamics of seasonal influenza based on a high-quality 12-year Israeli dataset. The dynamics are completely explainable by the time evo...
Directory of Open Access Journals (Sweden)
Mi-Jeong Yoo
2014-01-01
Full Text Available The single-celled cotton (Gossypium hirsutum fiber provides an excellent model to investigate how human selection affects phenotypic evolution. To gain insight into the evolutionary genomics of cotton domestication, we conducted comparative transcriptome profiling of developing cotton fibers using RNA-Seq. Analysis of single-celled fiber transcriptomes from four wild and five domesticated accessions from two developmental time points revealed that at least one-third and likely one-half of the genes in the genome are expressed at any one stage during cotton fiber development. Among these, ~5,000 genes are differentially expressed during primary and secondary cell wall synthesis between wild and domesticated cottons, with a biased distribution among chromosomes. Transcriptome data implicate a number of biological processes affected by human selection, and suggest that the domestication process has prolonged the duration of fiber elongation in modern cultivated forms. Functional analysis suggested that wild cottons allocate greater resources to stress response pathways, while domestication led to reprogrammed resource allocation toward increased fiber growth, possibly through modulating stress-response networks. This first global transcriptomic analysis using multiple accessions of wild and domesticated cottons is an important step toward a more comprehensive systems perspective on cotton fiber evolution. The understanding that human selection over the past 5,000+ years has dramatically re-wired the cotton fiber transcriptome sets the stage for a deeper understanding of the genetic architecture underlying cotton fiber synthesis and phenotypic evolution.
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.
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.
The architecture of river networks can drive the evolutionary dynamics of aquatic populations.
Thomaz, Andréa T; Christie, Mark R; Knowles, L Lacey
2016-03-01
It is widely recognized that physical landscapes can shape genetic variation within and between populations. However, it is not well understood how riverscapes, with their complex architectures, affect patterns of neutral genetic diversity. Using a spatially explicit agent-based modeling (ABM) approach, we evaluate the genetic consequences of dendritic river shapes on local population structure. We disentangle the relative contribution of specific river properties to observed patterns of genetic variation by evaluating how different branching architectures and downstream flow regimes affect the genetic structure of populations situated within river networks. Irrespective of the river length, our results illustrate that the extent of river branching, confluence position, and levels of asymmetric downstream migration dictate patterns of genetic variation in riverine populations. Comparisons between simple and highly branched rivers show a 20-fold increase in the overall genetic diversity and a sevenfold increase in the genetic differentiation between local populations. Given that most rivers have complex architectures, these results highlight the importance of incorporating riverscape information into evolutionary models of aquatic species and could help explain why riverine fishes represent a disproportionately large amount of global vertebrate diversity per unit of habitable area.
Geuverink, E; Beukeboom, L W
2014-01-01
Sex determination in insects is characterized by a gene cascade that is conserved at the bottom but contains diverse primary signals at the top. The bottom master switch gene doublesex is found in all insects. Its upstream regulator transformer is present in the orders Hymenoptera, Coleoptera and Diptera, but has thus far not been found in Lepidoptera and in the basal lineages of Diptera. transformer is presumed to be ancestral to the holometabolous insects based on its shared domains and conserved features of autoregulation and sex-specific splicing. We interpret that its absence in basal lineages of Diptera and its order-specific conserved domains indicate multiple independent losses or recruitments into the sex determination cascade. Duplications of transformer are found in derived families within the Hymenoptera, characterized by their complementary sex determination mechanism. As duplications are not found in any other insect order, they appear linked to the haplodiploid reproduction of the Hymenoptera. Further phylogenetic analyses combined with functional studies are needed to understand the evolutionary history of the transformer gene among insects.
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.
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.
Mathematical Models For Calculating The Value Of Dynamic Viscosity Of A Liquid
Directory of Open Access Journals (Sweden)
Ślęzak M.
2015-06-01
Full Text Available The objective of this article is to review models for calculating the value of liquid dynamic viscosity. Issues of viscosity and rheological properties of liquid ferrous solutions are important from the perspective of modelling, along with the control of actual production processes related to the manufacturing of metals, including iron and steel. Conducted analysis within literature indicates that there are many theoretical considerations concerning the effect of viscosity of liquid metals solutions. The vast majority of models constitute a group of theoretical or semi-empirical equations, where thermodynamic parameters of solutions, or some parameters determined by experimental methods, are used for calculations of the dynamic viscosity coefficient.
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.…
A New Parallel Algorithm in Power Flow Calculation: Dynamic Asynchronous Parallel Algorithm
Institute of Scientific and Technical Information of China (English)
无
2000-01-01
Based on the general methods in power flow calculation of power system and onconceptions and classifications of parallel algorithm, a new approach named DynamicAsynchronous Parallel Algorithm that applies to the online analysis and real-time dispatching and controlling of large-scale power network was put forward in this paper. Its performances of high speed and dynamic following have been verified on IEEE-14 bus system.
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
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
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.
Evolutionary constraints on visual cortex architecture from the dynamics of hallucinations.
Butler, Thomas Charles; Benayoun, Marc; Wallace, Edward; van Drongelen, Wim; Goldenfeld, Nigel; Cowan, Jack
2012-01-10
In the cat or primate primary visual cortex (V1), normal vision corresponds to a state where neural excitation patterns are driven by external visual stimuli. A spectacular failure mode of V1 occurs when such patterns are overwhelmed by spontaneously generated spatially self-organized patterns of neural excitation. These are experienced as geometric visual hallucinations. The problem of identifying the mechanisms by which V1 avoids this failure is made acute by recent advances in the statistical mechanics of pattern formation, which suggest that the hallucinatory state should be very robust. Here, we report how incorporating physiologically realistic long-range connections between inhibitory neurons changes the behavior of a model of V1. We find that the sparsity of long-range inhibition in V1 plays a previously unrecognized but key functional role in preserving the normal vision state. Surprisingly, it also contributes to the observed regularity of geometric visual hallucinations. Our results provide an explanation for the observed sparsity of long-range inhibition in V1--this generic architectural feature is an evolutionary adaptation that tunes V1 to the normal vision state. In addition, it has been shown that exactly the same long-range connections play a key role in the development of orientation preference maps. Thus V1's most striking long-range features--patchy excitatory connections and sparse inhibitory connections--are strongly constrained by two requirements: the need for the visual state to be robust and the developmental requirements of the orientational preference map.
Cardoso, Rodrigo T N; da Cruz, André R; Wanner, Elizabeth F; Takahashi, Ricardo H C
2009-08-01
The biological pest control in agriculture, an environment-friendly practice, maintains the density of pests below an economic injury level by releasing a suitable quantity of their natural enemies. This work proposes a multi-objective numerical solution to biological pest control for soybean crops, considering both the cost of application of the control action and the cost of economic damages. The system model is nonlinear with impulsive control dynamics, in order to cope more effectively with the actual control action to be applied, which should be performed in a finite number of discrete time instants. The dynamic optimization problem is solved using the NSGA-II, a fast and trustworthy multi-objective genetic algorithm. The results suggest a dual pest control policy, in which the relative price of control action versus the associated additional harvest yield determines the usage of either a low control action strategy or a higher one.
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
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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.
An Evolutionary Algorithm Approach to Link Prediction in Dynamic Social Networks
Bliss, Catherine A.; Frank, Morgan R.; Danforth, Christopher M.; Dodds, Peter Sheridan
2013-01-01
Many real world, complex phenomena have underlying structures of evolving networks where nodes and links are added and removed over time. A central scientific challenge is the description and explanation of network dynamics, with a key test being the prediction of short and long term changes. For the problem of short-term link prediction, existing methods attempt to determine neighborhood metrics that correlate with the appearance of a link in the next observation period. Recent work has sugg...
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
Nonadiabatic quantum dynamics calculations for the N + NH --> N(2) + H reaction.
Yang, Huan; Hankel, M; Varandas, Antonio; Han, Keli
2010-09-01
Nonadiabatic quantum dynamics calculations on the two coupled potential energy surfaces (PESs) (1(2)A' and 2(2)A') and also adiabatic quantum calculations on the lowest adiabatic PES are reported for the title reaction. Reaction probabilities for total angular momenta, J, varying from 0 to 160, are calculated to obtain the integral cross section (ICS) for collision energies ranging from 0.05 to 1.0 eV. Calculations using both the close coupling and the Centrifugal Sudden (CS) approximation are carried out to evaluate the role of Coriolis coupling effects for this reaction. The results of the nonadiabatic calculations show that the nonadiabatic effects in the title reaction for the initial state of NH (v = 0, j = 0) could be neglected, at least in the collision energy range considered in this study.
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
Comparison of computer codes for calculating dynamic loads in wind turbines
Spera, D. A.
1978-01-01
The development of computer codes for calculating dynamic loads in horizontal axis wind turbines was examined, and a brief overview of each code was given. The performance of individual codes was compared against two sets of test data measured on a 100 KW Mod-0 wind turbine. All codes are aeroelastic and include loads which are gravitational, inertial and aerodynamic in origin.
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.
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.
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
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
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.
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
Kim, Kiyeon; Omori, Ryosuke; Ueno, Keisuke; Iida, Sayaka; Ito, Kimihito
2016-01-01
Understanding the evolutionary dynamics of influenza viruses is essential to control both avian and human influenza. Here, we analyze host-specific and segment-specific Tajima's D trends of influenza A virus through a systematic review using viral sequences registered in the National Center for Biotechnology Information. To avoid bias from viral population subdivision, viral sequences were stratified according to their sampling locations and sampling years. As a result, we obtained a total of 580 datasets each of which consists of nucleotide sequences of influenza A viruses isolated from a single population of hosts at a single sampling site within a single year. By analyzing nucleotide sequences in the datasets, we found that Tajima's D values of viral sequences were different depending on hosts and gene segments. Tajima's D values of viruses isolated from chicken and human samples showed negative, suggesting purifying selection or a rapid population growth of the viruses. The negative Tajima's D values in rapidly growing viral population were also observed in computer simulations. Tajima's D values of PB2, PB1, PA, NP, and M genes of the viruses circulating in wild mallards were close to zero, suggesting that these genes have undergone neutral selection in constant-sized population. On the other hand, Tajima's D values of HA and NA genes of these viruses were positive, indicating HA and NA have undergone balancing selection in wild mallards. Taken together, these results indicated the existence of unknown factors that maintain viral subtypes in wild mallards.
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.
Institute of Scientific and Technical Information of China (English)
Yuan Xiaoming; Sun Jing; Sun Rui
2006-01-01
An error analysis of the dynamic shear modulus of stiff specimens from tests performed by a new resonant column device developed by the Institute of Engineering Mechanics, China was conducted. A modified approach for calculating the dynamic shear modulus of the stiff specimens is presented. The error formula of the tests was deduced and parameters that impact the accuracy of the test were identified. Using six steel specimens with known standard stiffness as a base, a revised dynamic shear modulus calculation for stiff specimens was formulated by comparing three of the models.The maximum error between the test results and the calculated results shown by curves from both the free-vibration and the resonant-vibration tests is less than 6%. The free-vibration and resonant-vibration tests for three types of stiff samples with a known modulus indicate that the maximum deviation between the actual and the tested value using the modified approach were less than 10%. As a result, the modified approach presented here is shown to be reliable and the new device can be used for testing dynamic shear modulus of any stiff materials at low shear strain levels
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
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.
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.
Compensatory Drift and the Evolutionary Dynamics of Dosage-Sensitive Duplicate Genes.
Thompson, Ammon; Zakon, Harold H; Kirkpatrick, Mark
2016-02-01
Dosage-balance selection preserves functionally redundant duplicates (paralogs) at the optimum for their combined expression. Here we present a model of the dynamics of duplicate genes coevolving under dosage-balance selection. We call this the compensatory drift model. Results show that even when strong dosage-balance selection constrains total expression to the optimum, expression of each duplicate can diverge by drift from its original level. The rate of divergence slows as the strength of stabilizing selection, the size of the mutation effect, and/or the size of the population increases. We show that dosage-balance selection impedes neofunctionalization early after duplication but can later facilitate it. We fit this model to data from sodium channel duplicates in 10 families of teleost fish; these include two convergent lineages of electric fish in which one of the duplicates neofunctionalized. Using the model, we estimated the strength of dosage-balance selection for these genes. The results indicate that functionally redundant paralogs still may undergo radical functional changes after a prolonged period of compensatory drift.
基于SD的环境污染多人演化博弈问题研究%Multi-person evolutionary game of environmentpollution based on system dynamics
Institute of Scientific and Technical Information of China (English)
蔡玲如
2011-01-01
主要对政府与竞争关系条件下两企业之间的监督博弈演化过程进行动态性分析,利用系统动力学建立一个环境监管部门与两个竞争关系企业的多人演化博弈模型,分析不同惩罚策略对博弈均衡和过程的影响.结果表明:罚款额度的惩罚系数k的大小与博弈过程的动态性密切相关；一般惩罚策略能有效抑制环境污染,而动态惩罚策略则在博弈过程波动性控制方面具有明显效果.%This paper considered the competitive relationships between the polluting firms. The dynamic procedure of multi-person asymmetric evolutionary game model was developed based on system dynamics. Simulation results show that the penalty factor k, which indicated the limit of fine, was closely related with the volatility of the dynamic evolutionary procedure. And the static penalty strategy has a better effect on the restrain of environmental pollution, while the dynamic one can stabilize the fluctuation during the evolutionary game procedure.
Knowles, R.
1982-07-01
A general theory of moments for electrodynamic magnetic levitation systems has been developed using double Fourier series and dynamic circuit principles. Both employ Parseval's theorem using either wave constant derivatives or the polar waveconstant principle of the Fourier-Bessel/double Fourier series equivalence. A method for calculating angular derivatives of moments and forces is explained, and for all of these methods comparisons are made with experimental results obtained for single and split rail configurations. Extensions of dynamic circuit theory for tilted nonflat and circular magnets are also explained.
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)
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
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.
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...
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...
Lattice dynamics and spin-phonon interactions in multiferroic RMn2O5: Shell model calculations
Litvinchuk, A. P.
2009-08-01
The results of the shell model lattice dynamics calculations of multiferroic RMn2O5 materials (space group Pbam) are reported. Theoretical even-parity eigenmode frequencies are compared with those obtained experimentally in polarized Raman scattering experiments for R=Ho,Dy. Analysis of displacement patterns allows to identify vibrational modes which facilitate spin-phonon coupling by modulating the Mn-Mn exchange interaction and provides explanation of the observed anomalous temperature behavior of phonons.
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...
Dynamical calculation of third-harmonic generation in a semiconductor quantum well
Guazzotti, Stefano; Pusch, Andreas; Reiter, Doris E.; Hess, Ortwin
2016-09-01
Nonlinear phenomena in optically excited semiconductor structures are of high interest. Here we develop a model capable of studying the dynamics of the photoexcited carriers, including Coulomb interaction on a Hartree-Fock level, on the same footing as the dynamics of the light field impinging on an arbitrary photonic structure. Applying this method to calculate the third-harmonic generation in a semiconductor quantum well embedded in a Bragg mirror structure, we find that the power-law exponent of the intensity dependence of the third-harmonic generation depends on the frequency of the exciting pulse. Off-resonant pulses follow the expected cubic dependence, while the exponent is smaller for resonant pulses due to saturation effects in the induced carrier density. Our study provides a detailed understanding of the carrier and light field dynamics during nonlinear processes.
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.
Molecular dynamics (MD) calculation of the real zeta potential of neutral surfaces
Liu, Hongyi
2013-01-01
Molecular dynamics (MD) simulations of the zeta potential are so poor that it has become common to term their predictions "apparent". Here we demonstrate how MD methods can predict zeta potentials accurate enough they can be termed "real". The critical new aspects of our method are: (1) integrating the net average charge in surface-parallel layers from the midpoint of the fluid layer (where the electrostatic potential is zero) to and then into two solid caps, (2) determining the position of slipping plane with separate Couette flow models, and (3) calculating the charge distribution and electrostatic potential under static conditions. The solids are charge neutral surfaces composed of atoms with zero charge or charge balanced monovalent or divalent ions. The zeta potentials calculated are within a few millivolts of measured values, and the measured values fall within the simulation error bars. The zeta potentials calculated with the Helmholtz and Smoluchowski equation following current practice are 10's of mi...
A method of moments for calculating dynamic responses beyond linear response theory
Institute of Scientific and Technical Information of China (English)
Kang Yan-Mei; Xu Jian-Xue; Xie Yong
2005-01-01
A method of moments for calculating the dynamic response of periodically driven overdamped nonlinear stochastic systems in the general response sense is proposed, which is a modification of the method of moments confined within linear response theory. The calculating experience suggests that the proposed technique is simple and efficient in implementation, and the comparison with stochastic simulation shows that the first three orders of susceptibilities calculated by the proposed technique have high accuracy. The dependence of the spectral amplification parameters at the first three harmonics on the noise intensity is also investigated, and another observed phenomenon of stochastic resonance in the systems induced by the location of a single periodic orbit is disclosed and explained.
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.
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.
The effect of molecular dynamics sampling on the calculated observable gas-phase structures.
Tikhonov, Denis S; Otlyotov, Arseniy A; Rybkin, Vladimir V
2016-07-21
In this study, we compare the performance of various ab initio molecular dynamics (MD) sampling methods for the calculation of the observable vibrationally-averaged gas-phase structures of benzene, naphthalene and anthracene molecules. Nose-Hoover (NH), canonical and quantum generalized-Langevin-equation (GLE) thermostats as well as the a posteriori quantum correction to the classical trajectories have been tested and compared to the accurate path-integral molecular dynamics (PIMD), static anharmonic vibrational calculations as well as to the experimental gas electron diffraction data. Classical sampling methods neglecting quantum effects (NH and canonical GLE thermostats) dramatically underestimate vibrational amplitudes for the bonded atom pairs, both C-H and C-C, the resulting radial distribution functions exhibit nonphysically narrow peaks. This deficiency is almost completely removed by taking the quantum effects on the nuclei into account. The quantum GLE thermostat and a posteriori correction to the canonical GLE and NH thermostatted trajectories capture most vibrational quantum effects and closely reproduce computationally expensive PIMD and experimental radial distribution functions. These methods are both computationally feasible and accurate and are therefore recommended for calculations of the observable gas-phase structures. A good performance of the quantum GLE thermostat for the gas-phase calculations is encouraging since its parameters have been originally fitted for the condensed-phase calculations. Very accurate molecular structures can be predicted by combining the equilibrium geometry obtained at a high level of electronic structure theory with vibrational amplitudes and corrections calculated using MD driven by a lower level of electronic structure theory. PMID:27331660
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)
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
Calculation of the neutron electric dipole moment with two dynamical flavors of domain wall fermions
Berruto, F; Orginos, K; Soni, A
2005-01-01
We present a study of the neutron electric dipole moment ($\\vec d_N$) within the framework of lattice QCD with two flavors of dynamical lig ht quarks. The dipole moment is sensitive to the topological structure of the gaug e fields, and accuracy can only be achieved by using dynamical, or sea quark, calc ulations. However, the topological charge evolves slowly in these calculations, le ading to a relatively large uncertainty in $\\vec d_N$. It is shown, using quenched configurations, that a better sampling of the charge d istribution reduces this problem, but because the CP even part of the fermion determinant is absent, both the topological charge dis tribution and $\\vec d_N$ are pathological in the chiral limit. We discuss the statistical and systematic uncertainties arising from the topological charge distr ibution and unphysical size of the quark mass in our calculations and prospects fo r eliminating them. Our calculations employ the RBC collaboration two flavor domain wall fermion and DBW2 gauge action l...
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.
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
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...
Calculation technique for simulation of wave and fracture dynamics in a reinforced sheet
Ayzenberg-Stepanenko, M; Osharovich, G
2011-01-01
Mathematical models and computer algorithms are developed to calculate dynamic stress concentration and fracture wave propagation in a reinforced composite sheet. The composite consists of a regular system alternating extensible fibers and pliable adhesive layers. In computer simulations, we derive difference algorithms preventing or minimizing the parasite distortions caused by the mesh dispersion and obtain precise numerical solutions in the plane fracture problem of a pre-stretched sheet along the fibers. Interactive effects of microscale dynamic deformation and multiple damage in fibers and adhesive are studied. Two engineering models of the composite are considered: the first assumes that adhesive can be represented by inertionless bonds of constant stiffness, while in the second one an adhesive is described by inertial medium perceived shear stresses. Comparison of results allows the evaluation of facilities of models in wave and fracture patterns analysis.
Beardmore, K M; Beardmore, Keith M.; Gronbech-Jensen, Niels
1998-01-01
We present a highly efficient molecular dynamics scheme for calculating the concentration depth profile of dopants in ion irradiated materials. The scheme incorporates several methods for reducing the computational overhead, plus a rare event algorithm that allows statistically reliable results to be obtained over a range of several orders of magnitude in the dopant concentration. We give examples of using this scheme for calculating concentration profiles of dopants in crystalline silicon. Here we can predict the experimental profile over five orders of magnitude for both channeling and non-channeling implants at energies up to 100s of keV. The scheme has advantages over binary collision approximation (BCA) simulations, in that it does not rely on a large set of empirically fitted parameters. Although our scheme has a greater computational overhead than the BCA, it is far superior in the low ion energy regime, where the BCA scheme becomes invalid.
Dynamical analysis of tRNA Gln-GlnRS complex using normal mode calculation
Nakamura, Shugo; Ikeguchi, Mitsunori; Shimizu, Kentaro
2003-04-01
We applied normal mode calculation in internal coordinates to a complex of glutamine transfer RNA (tRNA Gln) and glutaminyl-tRNA synthetase (GlnRS). Calculated deviations of atoms agreed well with those obtained from X-ray data. The differences of motions corresponding to low mode frequencies between the free state and the complex state were analyzed. For GlnRS, many motions in the free state were conserved in the complex state, while the dynamics of tRNA Gln was largely affected by the complex formation. Superimposed images of the conserved and non-conserved motions of tRNA Gln clearly indicated the restricted direction of motions in the complex.
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.
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.
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.
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.
Dynamic mathematical model and numerical calculation method on spontaneous combustion of loose coal
Institute of Scientific and Technical Information of China (English)
WEN Hu(文虎)
2003-01-01
Through the experiment of coal spontaneous combustion and relationship particle size with oxidation character of loose coal, some calculation formula of characteristic parameters is got in the process of coal spontaneous combustion. According to these theories of porous medium hydrodynamics, mass transfer and heat transfer, mathematical models of air leak field, oxygen concentration field and temperature field are set up. Through experimental and theoretical analysis, 3-D dynamic mathematical model of coal spontaneous combustion is set up. The method of ascertaining boundary condition of model is analyzed, and finite difference method is adopted to solve 2-D mathematical model.
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)
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
Carretero-Paulet, Lorenzo; Albert, Victor A
2016-01-01
Molecular evolutionary analysis of gene families commonly involves a sequence of steps including multiple sequence alignment (MSA) and reconstructing phylogenetic trees, using any of the multiple algorithms available. SeaView is a multiplatform program that integrates different methods for performing the above tasks, and others, within a friendly and simple-to-use graphical user interface (Gouy et al. Mol Biol Evol 27(2):221-224, 2010). By using SeaView, we will investigate the evolutionary relationships among SAE1 genes in Brassicaceae species by means of two alternative methods of phylogenetic reconstruction: Maximum Likelihood (ML) and Neighbor-Joining (NJ). Prior to ML phylogenetic analysis (Guindon and Gascuel. Syst Biol 52(5):696-704, 2003), we will use ProtTest to select the best-fit evolutionary model of amino acid substitution for the MSA of SAE1 proteins (Abascal et al. Bioinformatics 21(9):2104-2105, 2005). PMID:27424762
DEFF Research Database (Denmark)
Levitis, Daniel
2015-01-01
of biological and cultural evolution. Demographic variation within and among human populations is influenced by our biology, and therefore by natural selection and our evolutionary background. Demographic methods are necessary for studying populations of other species, and for quantifying evolutionary fitness...
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.
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 similar footwear, relatively large inter-individual variations were found in the joint moment patterns during the stance phase. The differences between individuals were present in both the 2D and 3D analysis. For the entire sample of subjects the overall time course pattern of the ankle, knee and hip...
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.
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.
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
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 ...
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.)
Directory of Open Access Journals (Sweden)
V.I. Milykh
2015-12-01
Full Text Available Attention is paid to the popular FEMM (Finite Element Method Magnetics program which is effective in the numerical calculations of the magnetic fields of electrical machines. The principles of the automated calculations providing the analysis of the dynamics of electromagnetic processes in turbo-generators are presented. This is realized in the form of a script on the algorithmic language Lua integrated with FEMM. The temporal functions of electromagnetic quantities are obtained by multi-position calculations of the magnetic field with ensuring its rotation together with the turbo-generator rotor. The developed program is universal in terms of the geometry and dimensions of turbo-generators, as well as the modes of their work with a minimum of input data in numerical form. This paper shows "extraction" of discrete temporal functions: the magnetic flux linkage of the phase stator winding; forces acting on the current-carrying and ferromagnetic elements of the structure; the magnetic induction at the fixed points; electromagnetic moment. This list can be expanded as part of the created program, as well as the use of the program can be extended to other types of electrical machines. The obtaining of a change period of any functions is provided by rotating the rotor to 60°.
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.
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
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...
Quantitative calculation of reaction performance in sonochemical reactor by bubble dynamics
Xu, Zheng; Yasuda, Keiji; Liu, Xiao-Jun
2015-10-01
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. Project supported by the National Natural Science Foundation of China (Grant Nos. 11404245, 11204129, and 11211140039).
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.
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.
Lattice dynamics calculations for ferropericlase with internally consistent LDA+U method
Fukui, Hiroshi; Tsuchiya, Taku; Baron, Alfred Q. R.
2012-12-01
Vibrational densities of states and phonon dispersion relations for Mg0.875Fe0.125O ferropericlase in the high- and low-spin (HS and LS) states were calculated from first principles lattice dynamics using the internally consistent LDA+Utechnique. Finite-temperature thermodynamic properties were determined based on the quasi-harmonic approximation including the HS and LS mixing entropy and the magnetic entropy effects, which gave pressure and temperature variations of the low-spin fraction. Our results suggest that for thermodynamic modeling of the earth's interior, the effect of the mixed spin state cannot be ignored in the lower mantle, especially the lowermost part. The anomaly in the seismic wave velocity due to the spin crossover transition of ferropericlase, if it exists, is difficult to detect because of the wide pressure range of the transition, which is broadened by the temperature effect and the damping of the amplitude of the slow seismic wave.
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...
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 walking...
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
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)
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 (ext-link ext-link-type="uri" xlink.href="www.scilab.org">www.scilab.orgext-link>) which is an open source software.
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.
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.
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)
Cheng Changjun; Fan Xiaojun
2000-01-01
The relation between the Lyapunov exponent spectrun of a periodically excited non-autono mous dynamical system and the Lyapunov exponent spectrum of the corresponding autonomous system is given and the validity of the relation is verified theoretically and computationally. A direct method for calculating the Lyapunov exponent spectrum of non-autonomous dynamical systems is suggested in this paper, which makes it more convenient to calculate the Lyapunov exponent spectrum of the dynamical system periodically excited. Following the defi nition of the Lyapunov dimension D(LA) of the autonomous system, the definition of the Lyapunov dimension Dl of the non-autonomous dynamical system is also given, and the difference be- tween them is the integer 1, namely, D(A)L - DL = 1. For a quasi-poriodically excited dynamical system, similar conclusions are formed.
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 correlated among people who share environments because these individuals satisfice within their cognitive bounds by using cues in order of validity, as opposed to using cues arbitrarily. Any difference in expectations thereby arise from differences in cognitive ability, because two individuals with identical...... 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...
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
Energy Technology Data Exchange (ETDEWEB)
Furnish, M.D.; Boslough, M.B. [Sandia National Labs., Albuquerque, NM (United States); Gray, G.T. III [Los Alamos National Lab., NM (United States); Remo, J.L. [Quantametrics, Inc., St. James, NY (United States)
1994-07-01
We describe methods for measuring dynamical properties for two material categories of interest in understanding large-scale extraterrestrial impacts: iron-nickel and underdense materials (e.g. snow). Particular material properties measured by the present methods include Hugoniot release paths and constitutive properties (stress vs. strain). The iron-nickel materials lend themselves well to conventional shock and quasi-static experiments. As examples, a suite of experiments is described including six impact tests (wave profile compression/release) over the stress range 2--20 GPa, metallography, quasi-static and split Hopkinson pressure bar (SHPB) mechanical testing, and ultrasonic mapping and sound velocity measurements. Temperature sensitivity of the dynamic behavior was measured at high and low strain rates. Among the iron-nickel materials tested, an octahedrite was found to have behavior close to that of Armco iron under shock and quasi-static conditions, while an ataxite exhibited a significantly larger quasi-static yield strength than did the octahedrite or a hexahedrite. The underdense materials pose three primary experimental difficulties. First, the samples are friable; they can melt or sublimate during storage, preparation and testing. Second, they are brittle and crushable; they cannot withstand such treatment as traditional machining or launch in a gun system. Third, with increasing porosity the calculated Hugoniot density becomes rapidly more sensitive to errors in wave time-of-arrival measurements. Carefully chosen simulants eliminate preservation (friability) difficulties, but the other difficulties remain. A family of 36 impact tests was conducted on snow and snow simulants at Sandia, yielding reliable Hugoniot and reshock states, but limited release property information. Other methods for characterizing these materials are discussed.
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.
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 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)
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.)
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.
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
Energy Technology Data Exchange (ETDEWEB)
Ajloo, Davood; Ghadamgahi, Maryam; Shaheri, Freshte; Zarei, Kobra [Damghan Univ., Damghan (Iran, Islamic Republic of)
2014-05-15
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.
Sarangapani, Radhakrishnan; Reddy, Sreekantha T; Sikder, Arun K
2015-04-01
Molecular dynamics simulations studies are carried out on hydroxyl terminated polyethers that are useful in energetic polymeric binder applications. Energetic polymers derived from oxetanes with heterocyclic side chains with different energetic substituents are designed and simulated under the ensembles of constant particle number, pressure, temperature (NPT) and constant particle number, volume, temperature (NVT). Specific volume of different amorphous polymeric models is predicted using NPT-MD simulations as a function of temperature. Plots of specific volume versus temperature exhibited a characteristic change in slope when amorphous systems change from glassy to rubbery state. Several material properties such as Young's, shear, and bulk modulus, Poisson's ratio, etc. are predicted from equilibrated structures and established the structure-property relations among designed polymers. Energetic performance parameters of these polymers are calculated and results reveal that the performance of the designed polymers is comparable to the benchmark energetic polymers like polyNIMMO, polyAMMO and polyBAMO. Overall, it is worthy remark that this molecular simulations study on novel energetic polyethers provides a good guidance on mastering the design principles and allows us to design novel polymers of tailored properties.
Swynghedauw, B
2004-04-01
Nothing in biology makes sense except in the light of evolution. Evolutionary, or darwinian, medicine takes the view that contemporary diseases result from incompatibility between the conditions under which the evolutionary pressure had modified our genetic endowment and the lifestyle and dietary habits in which we are currently living, including the enhanced lifespan, the changes in dietary habits and the lack of physical activity. An evolutionary trait express a genetic polymorphism which finally improve fitness, it needs million years to become functional. A limited genetic diversity is a necessary prerequisite for evolutionary medicine. Nevertheless, search for a genetic endowment would become nearly impossible if the human races were genetically different. From a genetic point of view, homo sapiens, is homogeneous, and the so-called human races have only a socio-economic definition. Historically, Heart Failure, HF, had an infectious origin and resulted from mechanical overload which triggered mechanoconversion by using phylogenically ancient pleiotropic pathways. Adaptation was mainly caused by negative inotropism. Recently, HF was caused by a complex remodelling caused by the trophic effects of mechanics, ischemia, senescence, diabetes and, neurohormones. The generally admitted hypothesis is that cancers were largely caused by a combination of modern reproductive and dietary lifestyles mismatched with genotypic traits, plus the longer time available for a confrontation. Such a concept is illustrated for skin and breast cancers, and also for the link between cancer risk and dietary habits.
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...
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.
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
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
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.
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
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.
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
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.
Favarato, Ramon Marin; Silva, Maelin da; Oliveira, Renildo Ribeiro de; Artoni, Roberto Ferreira; Feldberg, Eliana; Matoso, Daniele Aparecida
2016-04-01
The Ancistrus genus differs from other Ancistrini due to its wide karyotypic diversity, varied diploid numbers, differences in sex chromosomes, and large number of species, as well as its tendency to form small populations with low vagility. This study investigated the role of 5S and 18S rDNA and telomeric repetitive sequences in the evolution of the karyotypic macrostructure of seven species of the genus Ancistrus from the Central Amazon. The results indicate a strong correlation between the location of ribosomal sites and fragile sites in the genome, particularly of 5S rDNA sequences, which are associated, in some species, with telomeric sequences at the sites of chromosomal healing. Moreover, the occurrence of two lineages was observed with regard to the synteny of ribosomal genes. The species of the genus Ancistrus showed high chromosomal lability associated with breakpoints, which was characterized by the presence of repetitive DNA sequences and this process is suggested to be an evolutionary model for the rapid fixation of structural rearrangements.
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.
Pan, Zhao; Whitehead, Jared; Thomson, Scott; Truscott, Tadd
2016-08-01
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.
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...
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.
Liao, David; Tlsty, Thea D
2014-08-01
The use of mathematical equations to analyse population dynamics measurements is being increasingly applied to elucidate complex dynamic processes in biological systems, including cancer. Purely 'empirical' equations may provide sufficient accuracy to support predictions and therapy design. Nevertheless, interpretation of fitting equations in terms of physical and biological propositions can provide additional insights that can be used both to refine models that prove inconsistent with data and to understand the scope of applicability of models that validate. The purpose of this tutorial is to assist readers in mathematically associating interpretations with equations and to provide guidance in choosing interpretations and experimental systems to investigate based on currently available biological knowledge, techniques in mathematical and computational analysis and methods for in vitro and in vivo experiments.
Modern Dynamical Coupled-Channels Calculations for Extracting and Understanding the Nucleon Spectrum
Kamano, Hiroyuki
2016-01-01
We give an overview of recent progress in the spectroscopic study of nucleon resonances within the dynamical coupled-channels analysis of meson-production reactions. The important role of multichannel reaction dynamics in understanding various properties of nucleon resonances is emphasized.
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...
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 ...
SU-E-T-465: Dose Calculation Method for Dynamic Tumor Tracking Using a Gimbal-Mounted Linac
Energy Technology Data Exchange (ETDEWEB)
Sugimoto, S; Inoue, T; Kurokawa, C; Usui, K; Sasai, K [Juntendo University, Bunkyo, Tokyo, JP (Japan); Utsunomiya, S [Niigata University, Niigata, Nigata, JP (Japan); Ebe, K [Joetsu General Hospital, Joetsu, Niigata, JP (Japan)
2014-06-01
Purpose: Dynamic tumor tracking using the gimbal-mounted linac (Vero4DRT, Mitsubishi Heavy Industries, Ltd., Japan) has been available when respiratory motion is significant. The irradiation accuracy of the dynamic tumor tracking has been reported to be excellent. In addition to the irradiation accuracy, a fast and accurate dose calculation algorithm is needed to validate the dose distribution in the presence of respiratory motion because the multiple phases of it have to be considered. A modification of dose calculation algorithm is necessary for the gimbal-mounted linac due to the degrees of freedom of gimbal swing. The dose calculation algorithm for the gimbal motion was implemented using the linear transformation between coordinate systems. Methods: The linear transformation matrices between the coordinate systems with and without gimbal swings were constructed using the combination of translation and rotation matrices. The coordinate system where the radiation source is at the origin and the beam axis along the z axis was adopted. The transformation can be divided into the translation from the radiation source to the gimbal rotation center, the two rotations around the center relating to the gimbal swings, and the translation from the gimbal center to the radiation source. After operating the transformation matrix to the phantom or patient image, the dose calculation can be performed as the no gimbal swing. The algorithm was implemented in the treatment planning system, PlanUNC (University of North Carolina, NC). The convolution/superposition algorithm was used. The dose calculations with and without gimbal swings were performed for the 3 × 3 cm{sup 2} field with the grid size of 5 mm. Results: The calculation time was about 3 minutes per beam. No significant additional time due to the gimbal swing was observed. Conclusions: The dose calculation algorithm for the finite gimbal swing was implemented. The calculation time was moderate.
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.
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...
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
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
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.
交互变邻域微分进化群搜索优化算法%Interactive Dynamic Neighborhood Differential Evolutionary Group Search Optimizer
Institute of Scientific and Technical Information of China (English)
贺国华; 崔志华; 谭瑛
2012-01-01
Group Search Optimizer! GSO) has the advantage of the design from a biological view, while animal scanning mechanisms are employed metaphorically to design optimum searching strategies for solving continuous optimization problems. Compared with some existing group intelligence algorithms, it has a better effect in the high dimensional problems. But from the individual foraging strategies it choose and the entire animal groups information sharing network topology, global optimal possibly missed and information exchange model is simple. Inspiration from the Newman and Watts model, Interactive Dynamic Neighborhood GSO( DXJSO) is proposed based on dynamic sampling. Adopting uniform designand the linear regression method on the parameter selection, 4 benchmark functions demonstrate the effectiveness of toe algorithm.%群搜索优化算法(Group Search Optimizer,GSO)具有广泛的生物学背景,特别是引入动物的视觉搜索机制,并且同一些已有的群智能算法相比较,在高维多峰问题上有更好的效果.但算法在个体觅食策略的选择上以及整个动物群体间信息共享的网络拓扑结构来看,存在错过最优值和信息交流模式过于简单的缺陷.受NW模型的启发,同时采用动态采样的方式提出了交互变邻域微分进化群搜索优化算法(Interactive Dynamic Neighborhood Differential Evolutionary GSO,IDGSO),并采用均匀设计和线性回归方法对参数进行选择,4个标准测试函数表明了IDGSO的有效性.
Energy Technology Data Exchange (ETDEWEB)
Koski, J.A.; Wix, S.D.; Cole, J.K.
1997-09-01
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.
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
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.
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.
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.
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.
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)
俞乐; 周洪涛; 曾伟
2015-01-01
针对政府重大工程项目合谋腐败现象频频发生，对政府利益和工程质量造成严重危害的问题，为了有效抑制监理方和承包商合谋现象发生，对政府工程项目下政府、监理公司和施工承包商三方演化博弈过程进行了研究。首先在有限理性的条件下引入前进理论建立博弈模型，得到Nash均衡，然后利用演化博弈理论求得不同监理风险态度状况下的演化稳定状态，最后，利用系统动力学软件对演化博弈过程进行仿真，验证稳定策略，并通过仿真得到抑制合谋的主要因素及打击方法，分析并给出了有限理性下打击合谋的监管策略，为打击政府重大工程项目合谋提供参考。%Corruption or collusion has frequently occurred in the major government investment projects , which has already brought great harm to the interest of the government and the quality of the projects .In order to effectively restrain collusion which formed by the supervision and the contractor , an evolutionary game model was structured to analyze the collusion in bounded ra-tionality.Firstly, through the model , the Nash equilibrium and the evolutionary equilibrium in different supervision ’ s risk atti-tudes were figured out based on combining prospect theory and evolutionary game theory .Then, a system dynamics model ( SD) was built to prove equilibrium results .The stability analysis and simulation illustrate the ways to control the collusion and prove that SD model and evolutionary game theory can work in controlling collusion for the government use .
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。
Structure and lattice dynamics of rare-earth ferroborate crystals: Ab initio calculation
Chernyshev, V. A.; Nikiforov, A. E.; Petrov, V. P.; Serdtsev, A. V.; Kashchenko, M. A.; Klimin, S. A.
2016-08-01
The ab initio calculation of the crystal structure and the phonon spectrum of crystals RFe3(BO3)4 ( R = Pr, Nd, Sm) has been performed in the framework of the density functional theory. The ion coordinates in the unit cell, the lattice parameters, the frequencies and the types of fundamental vibrations, and also the intensities of lines in the Raman spectrum and infrared reflection spectra have been found. The elastic constants of the crystals have been calculated. For low-frequency A 2 mode in PrFe3(BO3)4, a "seed" vibration frequency that strongly interacts with the electronic excitation on a praseodymium ion was found. The calculation results satisfactory agree with the experimental data.
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.
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.
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
Vincenzi, Simone
2014-08-01
One of the most dramatic consequences of climate change will be the intensification and increased frequency of extreme events. I used numerical simulations to understand and predict the consequences of directional trend (i.e. mean state) and increased variability of a climate variable (e.g. temperature), increased probability of occurrence of point extreme events (e.g. floods), selection pressure and effect size of mutations on a quantitative trait determining individual fitness, as well as the their effects on the population and genetic dynamics of a population of moderate size. The interaction among climate trend, variability and probability of point extremes had a minor effect on risk of extinction, time to extinction and distribution of the trait after accounting for their independent effects. The survival chances of a population strongly and linearly decreased with increasing strength of selection, as well as with increasing climate trend and variability. Mutation amplitude had no effects on extinction risk, time to extinction or genetic adaptation to the new climate. Climate trend and strength of selection largely determined the shift of the mean phenotype in the population. The extinction or persistence of the populations in an 'extinction window' of 10 years was well predicted by a simple model including mean population size and mean genetic variance over a 10-year time frame preceding the 'extinction window', although genetic variance had a smaller role than population size in predicting contemporary risk of extinction.
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
Tepper, H.L.; Scheinhardt-Engels, S.M.; Briels, W.J.
2003-01-01
A method is presented to design order parameters that can be used as discriminator in two-phase crystal-liquid molecular dynamics simulations. The proposed methodology is an extension to molecular crystal structures of a previously introduced discriminator for the atomic fcc environment [Phys. Rev.
On a class of TVD schemes for gas dynamic calculations. [Total Variation Diminishing
Yee, H. C.; Warming, R. F.; Harten, A.
1985-01-01
The purpose of this paper is to review a class of explicit and implicit second-order accurate Total Variation Diminishing (TVD) schemes and to show by numerical experiments, the performance of these schemes to the Euler equations of gas dynamics. The method of constructing these second-order accurate TVD schemes is sometimes known as the modified flux approach.
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
DEFF Research Database (Denmark)
Altin, Müfit; Göksu, Ömer; Sørensen, Poul Ejnar;
2016-01-01
the simulation convergence without adding complexity to the generic models, a first order filtering approach is proposed as a phase angle calculation algorithm in the grid synchronization of the rms type 4 wind turbine models. The proposed approach provides robustness for the simulation of large scale power...
移动商务信任的演化博弈及动态仿真①%Evolutionary Game and Dynamic Simulation of Trust in Mobile Commerce
Institute of Scientific and Technical Information of China (English)
郭零兵; 罗新星; 朱名勋
2013-01-01
用户信任是影响移动商务成功的关键因素之一，其形成与发展是一个动态演化的过程。运用演化博弈理论，研究用户信任的演化均衡状态，并应用Netlogo进行仿真。研究显示，建立潜在用户的信任，移动商家应采取主动发出可信信号；对于老用户，应致力于提升用户满意度；监管机制应随着移动商务的发展来调整其具体政策，在严格管理的同时营造适当宽松的发展环境，对受损用户的补偿和对失信商家的惩处，在初期应较大，随着监管机构提高其发现商家失信行为的概率，额度可以逐步减小。%Customer’s trust is one of the critical success factors of mobile commerce. Its formation and development is a dynamic evolutionary process. Using evolutionary game theory to study the evolution of customer trust equilibrium, and simulation application Netlogo. Studies have shown that to establish the confidence of potential users, m-merchants should take the initiative to issue a credible signal;For old users, should be committed to enhance customer satisfaction;regulatory mechanisms should adjust its policy with the development of m-commerce in the strict management create appropriate and comfortable environment for development, compensation to customers and punishment to dishonesty m-merchants should be larger at an early stage, with the regulatory authorities to improve the probability of its discovery merchants acts of dishonesty, the amount can be gradually reduced.
Borg, Michael; Melchior Hansen, Anders; Bredmose, Henrik
2016-09-01
Designing floating substructures for the next generation of 10MW and larger wind turbines has introduced new challenges in capturing relevant physical effects in dynamic simulation tools. In achieving technically and economically optimal floating substructures, structural flexibility may increase to the extent that it becomes relevant to include in addition to the standard rigid body substructure modes which are typically described through linear radiation-diffraction theory. This paper describes a method for the inclusion of substructural flexibility in aero-hydro-servo-elastic dynamic simulations for large-volume substructures, including wave-structure interactions, to form the basis of deriving sectional loads and stresses within the substructure. The method is applied to a case study to illustrate the implementation and relevance. It is found that the flexible mode is significantly excited in an extreme event, indicating an increase in predicted substructure internal loads.
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
Should Thermostatted Ring Polymer Molecular Dynamics be used to calculate reaction rates?
Hele, Timothy J H
2015-01-01
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 (TST) 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+H$_2$, D+MuH and F+H$_2$, and the prototypical polyatomic reaction H+CH$_4$. 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 less accurate than Ring Polymer Molecular Dynamics (RPMD) for symmetric reactions, and in certain asymmetric systems closer to the q...
Cancès, Eric; Castella, François; Chartier, Philippe; Faou, Erwan; Le Bris, Claude; Legoll, Frédéric; Turinici, Gabriel
2004-12-01
We introduce high-order formulas for the computation of statistical averages based on the long-time simulation of molecular dynamics trajectories. In some cases, this allows us to significantly improve the convergence rate of time averages toward ensemble averages. We provide some numerical examples that show the efficiency of our scheme. When trajectories are approximated using symplectic integration schemes (such as velocity Verlet), we give some error bounds that allow one to fix the parameters of the computation in order to reach a given desired accuracy in the most efficient manner.
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).
Babailov, S P; Purtov, P A; Fomin, E S
2016-08-01
An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.
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.
Implicit Total Variation Diminishing (TVD) schemes for steady-state calculations. [in gas dynamics
Yee, H. C.; Warming, R. F.; Harten, A.
1985-01-01
The novel implicit and unconditionally stable, high resolution Total Variation Diminishing (TVD) scheme whose application to steady state calculations is presently examined is a member of a one-parameter family of implicit, second-order accurate systems developed by Harten (1983) for the computation of weak solutions for one-dimensional hyperbolic conservation laws. The scheme will not generate spurious oscillations for a nonlinear scalar equation and a constant coefficient system. Numerical experiments for a quasi-one-dimensional nozzle problem show that the experimentally determined stability limit correlates exactly with the theoretical stability limit for the nonlinear scalar hyberbolic conservation laws.
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.
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.
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.)
Institute of Scientific and Technical Information of China (English)
Long Wang; Jiachun Li; Jifu Zhou
2009-01-01
The calculation of settling speed of coarse parti-cles is firstly addressed, with accelerated Stokesian dynamics without adjustable parameters, in which far field force act-ing on the particle instead of particle velocity is chosen as dependent variables to consider inter-particle hydrodynamic interactions. The sedimentation of a simple cubic array of spherical particles is simulated and compared to the results available to verify and validate the numerical code and computational scheme. The improved method keeps the same computational cost of the order O(Nlog N) as usual accelerated Stokesian dynamics does. Then, more realistic random suspension sedimentation is investigated with the help of Mont Carlo method. The computational results agree well with experimental fitting. Finally, the sedimentation of finer cohesive particle, which is often observed in estuary environment, is presented as a further application in coastal engineering.
Born Oppenheimer Molecular Dynamics calculation of the νO-H IR spectra for acetic acid cyclic dimers
El Amine Benmalti, Mohamed; Krallafa, Abdelghani; Gaigeot, Marie-Pierre
2015-01-01
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.].
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.
Malček, Michal; Bučinský, Lukáš; Valko, Marián; Biskupič, Stanislav
2015-09-01
The presented paper is focused on the calculation of hyperfine coupling constants (HFCC) of Cu (2+) ion in water environment. To simulate the conditions of the electron paramagnetic resonance (EPR) experiment in aqueous phase, molecular dynamics using the density functional theory (DFT) was employed. In total three different functionals (BLYP, B3LYP, M06) were employed for studying their suitability in describing coordination of Cu (2+) by water molecules. The system of our interest was composed of one Cu (2+) cation surrounded by a selected number (between thirty and fifty) of water molecules. Besides the non-relativistic HFCCs (Fermi contact terms) of Cu (2+) also the four-component relativistic HFCC calculations are presented. The importance of the proper evaluation of HFCCs, the inclusion of spin-orbit term, for Cu (2+) containing systems (Neese, J. Chem. Phys. 118, 3939 2003; Almeida et al., Chem. Phys. 332, 176 2007) is confirmed at the relativistic four-component level of theory.
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.
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.
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.
Dong, Lingli; Huo, Naxin; Wang, Yi; Deal, Karin; Wang, Daowen; Hu, Tiezhu; Dvorak, Jan; Anderson, Olin D; Luo, Ming-Cheng; Gu, Yong Q
2016-09-01
Prolamin and resistance gene families are important in wheat food use and in defense against pathogen attacks, respectively. To better understand the evolution of these multi-gene families, the DNA sequence of a 2.8-Mb genomic region, representing an 8.8 cM genetic interval and harboring multiple prolamin and resistance-like gene families, was analyzed in the diploid grass Aegilops tauschii, the D-genome donor of bread wheat. Comparison with orthologous regions from rice, Brachypodium, and sorghum showed that the Ae. tauschii region has undergone dramatic changes; it has acquired more than 80 non-syntenic genes and only 13 ancestral genes are shared among these grass species. These non-syntenic genes, including prolamin and resistance-like genes, originated from various genomic regions and likely moved to their present locations via sequence evolution processes involving gene duplication and translocation. Local duplication of non-syntenic genes contributed significantly to the expansion of gene families. Our analysis indicates that the insertion of prolamin-related genes occurred prior to the separation of the Brachypodieae and Triticeae lineages. Unlike in Brachypodium, inserted prolamin genes have rapidly evolved and expanded to encode different classes of major seed storage proteins in Triticeae species. Phylogenetic analyses also showed that the multiple insertions of resistance-like genes and subsequent differential expansion of each R gene family. The high frequency of non-syntenic genes and rapid local gene evolution correlate with the high recombination rate in the 2.8-Mb region with nine-fold higher than the genome-wide average. Our results demonstrate complex evolutionary dynamics in this agronomically important region of Triticeae species.
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.
A dynamic method for charging-up calculations: the case of GEM
Correia, P M M; Azevedo, C D R; Silva, A L M; Veenhof, R; Nemallapudi, Mythra Varun; Veloso, J F C A
2014-01-01
The simulation of Micro Pattern Gaseous Detectors (MPGDs) signal response is an important and powerful tool for the design and optimization of such detectors. However, several attempts to simulate exactly the effective charge gain have not been completely successful. Namely, the gain stability over time has not been fully understood. Charging-up of the insulator surfaces have been pointed as one of the responsible for the difference between experimental and Monte Carlo results. This work describes two iterative methods to simulate the charging-up in one MPGD device, the Gas Electron Multiplier (GEM). The first method uses a constant step for avalanches time evolution, very detailed, but slower to compute. The second method uses a dynamic step that improves the computing time. Good agreement between both methods was reached. Despite of comparison with experimental results shows that charging-up plays an important role in detectors operation, should not be the only responsible for the difference between simulat...
Liu, Zhen; Zhang, Yizheng
2009-12-01
Galanthus nivalis agglutinin (GNA), a mannose-specific lectin from snowdrop bulbs, is a member of the monocot mannose-specific lectin family and exhibits antiviral activity toward HIV. In the present study, molecular dynamics (MD) simulations were performed to study the interaction between GNA and its carbohydrate ligand over a specific time span. By analysis of the secondary structures, it was observed that the GNA conformation maintains rather stable along the trajectories and the high fluctuations were only centered on the carbohydrate recognition domains. Our MD simulations also reproduced most of the hydrogen bonds observed in the x-ray crystal structure. Furthermore, the obtained MD trajectories were used to estimate the binding free energy of the complex using the molecular mechanics/Poisson Boltzmann surface area (MM-PBSA) method. It was revealed by the inspection of the binding free energy components that the major contributions to the complex stability arose from electrostatic interactions.
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).
Institute of Scientific and Technical Information of China (English)
郭峰; 张红; 胡海泉; 程新路; 张利燕
2015-01-01
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.
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
Weisz, K; Shafer, R H; Egan, W; James, T L
1994-01-11
The solution structure of the DNA decamer d(CATTTGCATC)-d(GATGCAAATG), comprising the octamer motif of immunoglobulin genes, is determined by restrained molecular dynamics (rMD) simulations. The restraint data set includes interproton distances and torsion angles for the deoxyribose sugar ring which were previously obtained by a complete relaxation matrix analysis of the two-dimensional nuclear Overhauser enhancement (2D NOE) intensities and by the quantitative simulation of cross-peaks in double-quantum-filtered correlated (2QF-COSY) spectra. The influence of torsion angles and the number of experimental distance restraints on the structural refinement has been systematically examined. Omitting part of the experimental NOE-derived distances results in reduced restraint violations and lower R factors but impairs structural convergence in the rMD refinement. Eight separate restrained molecular dynamics simulations were carried out for 20 ps each, starting from either energy-minimized A- or B-DNA. Mutual atomic root-mean-square (rms) differences among the refined structures are well below 1 A and comparable to the rms fluctuations of the atoms about their average position, indicating convergence to essentially identical structures. The average refined structure was subjected to an additional 100 ps of rMD simulations and analyzed in terms of average torsion angles and helical parameters. The B-type duplex exhibits clear sequence-dependent variations in its geometry with a narrow minor groove at the T3.A3 tract and a large positive roll at the subsequent TG.CA step. This is accompanied by a noticeable bend of the global helix axis into the major groove. There is also evidence of significant flexibility of the sugar-phosphate backbone with rapid interconversion among different conformers.
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.
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, ...
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.
Institute of Scientific and Technical Information of China (English)
Kohji Tashiro
2007-01-01
The crystalline phase transition of aliphatic nylon 10/10 has been investigated on the basis of the simultaneous measurement of wide-angle and small-angle X-ray scatterings, the infrared spectral measurement and the molecular dynamics calculation. An interpretation of infrared spectra taken for a series of nylon samples and the corresponding model compounds was successfully made, allowing us to assign the infrared bands of the planar-zigzag methylene segments reasonably. As a result the methylene segmental parts of molecular chains were found to experience an order-to-disorder transition in the Brill transition region, where the intermolecular hydrogen bonds are kept alive although the bond strength becomes weaker at higher temperature. The small-angle X-ray scattering data revealed a slight change in lamellar stacking mode in the transition region. The crystal structure has been found to change more remarkably in the temperature region immediately below the melting point, where the conformationally disordered chains experienced drastic rotational and translational motions without any constraints by hydrogen bonds, and the lamellar thickness increased largely along the chain axis. These experimental results were reasonably reproduced by the molecular dynamics calculation performed at the various temperatures.
Evolutionary dynamics of metabolic adaptation
van Hoek, M.J.A.
2008-01-01
In this thesis we study how organisms adapt their metabolism to a changing environment. Metabolic adaptation occurs at different timescales. Organisms adapt their metabolism via metabolic regulation, which happens in the order of minutes to hours and via evolution, which takes many generations. Here
Evolutionary Dynamics Of Service Provisioning
Directory of Open Access Journals (Sweden)
Harry Katzan, Jr.
2012-03-01
Full Text Available Business evolves according to market conditions, based on availability and choice. The purpose of this paper is to develop a model that describes how service provisioning evolves through a metaphor of selection, survival of the fittest, replication, and mutation. Clients are free to choose a service provider within a provider category, and the model describes and delineates that behavior. Equations and examples are given.
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.
Simulating the Dynamics of Earth's Core: Using NCCS Supercomputers Speeds Calculations
2002-01-01
If one wanted to study Earth's core directly, one would have to drill through about 1,800 miles of solid rock to reach liquid core-keeping the tunnel from collapsing under pressures that are more than 1 million atmospheres and then sink an instrument package to the bottom that could operate at 8,000 F with 10,000 tons of force crushing every square inch of its surface. Even then, several of these tunnels would probably be needed to obtain enough data. Faced with difficult or impossible tasks such as these, scientists use other available sources of information - such as seismology, mineralogy, geomagnetism, geodesy, and, above all, physical principles - to derive a model of the core and, study it by running computer simulations. One NASA researcher is doing just that on NCCS computers. Physicist and applied mathematician Weijia Kuang, of the Space Geodesy Branch, and his collaborators at Goddard have what he calls the,"second - ever" working, usable, self-consistent, fully dynamic, three-dimensional geodynamic model (see "The Geodynamic Theory"). Kuang runs his model simulations on the supercomputers at the NCCS. He and Jeremy Bloxham, of Harvard University, developed the original version, written in Fortran 77, in 1996.
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.
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.
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
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.
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.
Martins-Costa, Marilia T C; García-Prieto, Francisco F; Ruiz-López, Manuel F
2015-02-14
Understanding the influence of solute-solvent interactions on chemical reactivity has been a subject of intense research in the last few decades. Theoretical studies have focused on bulk solvation phenomena and a variety of models and methods have been developed that are now widely used by both theoreticians and experimentalists. Much less attention has been paid, however, to processes that occur at liquid interfaces despite the important role such interfaces play in chemistry and biology. In this study, we have carried out sequential molecular dynamics simulations and quantum mechanical calculations to analyse the influence of the air-water interface on the reactivity of formaldehyde, acetaldehyde and benzaldehyde, three simple aldehydes of atmospheric interest. The calculated free-energy profiles exhibit a minimum at the interface, where the average reactivity indices may display large solvation effects. The study emphasizes the role of solvation dynamics, which are responsible for large fluctuations of some molecular properties. We also show that the photolysis rate constant of benzaldehyde in the range 290-308 nm increases by one order of magnitude at the surface of a water droplet, from 2.7 × 10(-5) s(-1) in the gas phase to 2.8 × 10(-4) s(-1) at the air-water interface, and we discuss the potential impact of this result on the chemistry of the troposphere. Experimental data in this domain are still scarce and computer simulations like those presented in this work may provide some insights that can be useful to design new experiments.
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.
OCB液晶显示的动力学计算%Dynamic Calculations for OCB Cell Liquid-Crystal Display
Institute of Scientific and Technical Information of China (English)
孙玉宝; 范志新; 张志东
2001-01-01
以液晶动力学理论为基础，考虑引流效应后，计算在强锚定和弱锚定边界条件下的OCB型盒中的指向矢分布和流动速度分布，给出透射光相对强度随时间变化有预倾角情况下的透射光相对强度。计算结果表明，OCB盒较平行排列盒和HAN盒具有更快的响应速度。%The study is based upon the dynamics theory with theliquid-crystals. Concerning of the back-flow effect, the distributions of the direction and the velocity in OCB cell are calculated under strong anchoring and weak anchoring conditions, respectively. The time dependence of the relative intensity of the transmission light is given. The curves of the relative intensity of the transmission light are also given for the various pretilt angles. The numerical calculations show that the response rate in OCB cell is faster than those in Homogeneous cell and HAN cell.
Mozafari, E.; Shulumba, N.; Steneteg, P.; Alling, B.; Abrikosov, Igor A.
2016-08-01
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 of elastic properties using the recently introduced method: symmetry imposed force constant temperature-dependent effective potential (SIFC-TDEP). We have chosen cubic paramagnetic CrN as a model system. This is done due to its technological importance and its demonstrated strong coupling between magnetic and lattice degrees of freedom. We have studied the temperature-dependent single-crystal and polycrystalline elastic constants of paramagentic CrN up to 1200 K. The obtained results at T = 300 K agree well with the experimental values of polycrystalline elastic constants as well as the Poisson ratio at room temperature. We observe that the Young's modulus is strongly dependent on temperature, decreasing by ˜14 % from T = 300 K to 1200 K. In addition we have studied the elastic anisotropy of CrN as a function of temperature and we observe that CrN becomes substantially more isotropic as the temperature increases. We demonstrate that the use of Birch law may lead to substantial errors for calculations of temperature induced changes of elastic moduli. The proposed methodology can be used for accurate predictions of mechanical properties of magnetic materials at temperatures above their magnetic order-disorder phase transition.
Epa, V. C.; Thorson, W. R.
1990-09-01
This paper concludes a theoretical study of vibrational dynamics in the bifluoride ion FHF-, which exhibits strongly anharmonic and coupled motions. Two previous papers have described an extended model potential surface for the system, developed a scheme for analysis based on a zero-order adiabatic separation of the proton bending and stretching motions (ν2,ν3) from the slower F-F symmetric-stretch motion (ν1), and presented results of accurate calculations of the adiabatic protonic eigenstates. Here the ν1 motion has been treated, in adiabatic approximation and also including nonadiabatic couplings in close-coupled calculations with up to three protonic states (channels). States of the system involving more than one quantum of protonic excitation (e.g., 2ν2, 2ν3 σg states; 3ν2, ν2+2ν3 πu states; ν3+2ν2, 3ν3 σu states) exhibit strong mixing at avoided crossings of protonic levels, and these effects are discussed in detail. Dipole matrix elements and relative intensities for vibrational transitions have been computed with an electronic dipole moment function based on ab initio calculations for an extended range of geometries. Frequencies, relative IR intensities and other properties of interest are compared with high resolution spectroscopic data for the gas-phase free ion and with the IR absorption spectra of KHF2(s) and NaHF2(s). Errors in the ab initio potential surface yield fundamental frequencies ν2 and ν3 100-250 cm-1 higher than those observed in either the free ion or the crystalline solids, but these differences are consistent and an unambiguous assignment of essentially all transitions in the IR spectrum of KHF2 is made. Calculated relative intensities for stretching mode (ν3, σu symmetry) transitions agree well with those observed in both KHF2 [e.g., bands (ν3+nν1), (ν3+2ν2), (3ν3), etc.] and the free ion (ν3,ν3+ν1). Calculated intensities for bending mode (ν2, πu symmetry) transitions agree well with experiment for the ν2
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.
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 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...
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.
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.
Lu, Haiting; Huang, Xiaoqin; AbdulHameed, Mohamed Diwan M; Zhan, Chang-Guo
2014-04-01
Molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations have been performed 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 CYP2A6-inhibitor binding affinity are two crucial internuclear distances, that is, the distance between the heme iron atom of CYP2A6 and the coordinating atom of the inhibitor, and the hydrogen-bonding distance between the N297 side chain of CYP2A6 and the pyridine nitrogen of the inhibitor. The combined MD simulations and QM/MM-PBSA calculations have led to dynamic CYP2A6-inhibitor binding structures that are consistent with the observed dynamic behaviors and structural features of CYP2A6-inhibitor binding, and led to the binding free energies that are in good agreement with the experimentally-derived binding free energies. The agreement between the calculated binding free energies and the experimentally-derived binding free energies suggests that the combined MD and QM/MM-PBSA approach may be used as a valuable tool to accurately predict the CYP2A6-inhibitor binding affinities in future computational design of new, potent and selective CYP2A6 inhibitors. PMID:24631364
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.
Sandhu, Paramvir; Zong, Jing; Yang, Delian; Wang, Qiang
2013-05-01
To highlight the importance of quantitative and parameter-fitting-free comparisons among different models/methods, we revisited the comparisons made by Groot and Madden [J. Chem. Phys. 108, 8713 (1998), 10.1063/1.476300] and Chen et al. [J. Chem. Phys. 122, 104907 (2005), 10.1063/1.1860351] between their dissipative particle dynamics (DPD) simulations of the DPD model and the self-consistent field (SCF) calculations of the "standard" model done by Matsen and Bates [Macromolecules 29, 1091 (1996), 10.1021/ma951138i] for diblock copolymer (DBC) A-B melts. The small values of the invariant degree of polymerization used in the DPD simulations do not justify the use of the fluctuation theory of Fredrickson and Helfand [J. Chem. Phys. 87, 697 (1987), 10.1063/1.453566] by Groot and Madden, and their fitting between the DPD interaction parameters and the Flory-Huggins χ parameter in the "standard" model also has no rigorous basis. Even with their use of the fluctuation theory and the parameter-fitting, we do not find the "quantitative match" for the order-disorder transition of symmetric DBC claimed by Groot and Madden. For lamellar and cylindrical structures, we find that the system fluctuations/correlations decrease the bulk period and greatly suppress the large depletion of the total segmental density at the A-B interfaces as well as its oscillations in A- and B-domains predicted by our SCF calculations of the DPD model. At all values of the A-block volume fractions in the copolymer f (which are integer multiples of 0.1), our SCF calculations give the same sequence of phase transitions with varying χN as the "standard" model, where N denotes the number of segments on each DBC chain. All phase boundaries, however, are shifted to higher χN due to the finite interaction range in the DPD model, except at f = 0.1 (and 0.9), where χN at the transition between the disordered phase and the spheres arranged on a body-centered cubic lattice is lower due to N = 10 in the DPD
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...
Lee, Yeon Joo; Imamura, Takeshi; Maejima, Yasumitsu; Sugiyama, Ko-ichiro
The thick cloud layer of Venus reflects solar radiation effectively, resulting in a Bond albedo of 76% (Moroz et al., 1985). Most of the incoming solar flux is absorbed in the upper cloud layer at 60-70 km altitude. An unknown UV absorber is a major sink of the solar energy at the cloud top level. It produces about 40-60% of the total solar heating near the cloud tops, depending on its vertical structure (Crisp et al., 1986; Lee et al., in preparation). UV images of Venus show a clear difference in morphology between laminar flow shaped clouds on the morning side and convective-like cells on the afternoon side of the planet in the equatorial region (Titov et al., 2012). This difference is probably related to strong solar heating at the cloud tops at the sub-solar point, rather than the influence from deeper level convection in the low and middle cloud layers (Imamura et al., 2014). Also, small difference in cloud top structures may trigger horizontal convection at this altitude, because various cloud top structures can significantly alter the solar heating and thermal cooling rates at the cloud tops (Lee et al., in preparation). Performing radiative forcing calculations for various cloud top structures using a radiative transfer model (SHDOM), we investigate the effect of solar heating at the cloud tops on atmospheric dynamics. We use CReSS (Cloud Resolving Storm Simulator), and consider the altitude range from 35 km to 90 km, covering a full cloud deck.
Energy Technology Data Exchange (ETDEWEB)
Sofronov, I.D.; Voronin, B.L.; Butnev, O.I. [VNIIEF (Russian Federation)] [and others
1997-12-31
The aim of the work performed is to develop a 3D parallel program for numerical calculation of gas dynamics problem with heat conductivity on distributed memory computational systems (CS), satisfying the condition of numerical result independence from the number of processors involved. Two basically different approaches to the structure of massive parallel computations have been developed. The first approach uses the 3D data matrix decomposition reconstructed at temporal cycle and is a development of parallelization algorithms for multiprocessor CS with shareable memory. The second approach is based on using a 3D data matrix decomposition not reconstructed during a temporal cycle. The program was developed on 8-processor CS MP-3 made in VNIIEF and was adapted to a massive parallel CS Meiko-2 in LLNL by joint efforts of VNIIEF and LLNL staffs. A large number of numerical experiments has been carried out with different number of processors up to 256 and the efficiency of parallelization has been evaluated in dependence on processor number and their parameters.
International Nuclear Information System (INIS)
With HEPAFIL, LAF II provides a FORTRAN program for the calculation of various parameters associated with the fluid dynamics of high efficiency particulate air filter units. Most of the currently available commercial deep pleat designs have been taken into consideration, e.g., high strength nuclear grade units employing separators with inclined corrugations, units for clean room applications, as well as low and medium efficiency EU 6 and EU 8 types having very low pressure drops. The flow resistance curves obtained from HEPAFIL could be verified in extensive experimental test. A user-friendly PC version with the integrated program library HEPAGAS can serve as a useful tool to the researcher in filter development as well as to the filter manufacturer for cost reduction analyses. Knowledge of the distributions of airstream, pressures and velocities within the flow channels of the filter pack allows more precise investigations of failure mechanisms and filtration characteristics for a wide range of flow conditions. The newest scientific application involves fundamental investigations into the cleanability of HEPA filter units. HEPAFIL offers filter manufacturers the opportunity to improve and optimize filter performance with respect to pressure drop, burst strength, and material costs, with a minimum of prototype fabrication and testing. (orig.)
Partovi-Azar, Pouya
2015-01-01
We present a computational method to accurately calculate Raman spectra from first principles with an at least one order of magnitude higher efficiency. This scheme thus allows to routinely calculate finite-temperature Raman spectra "on-the-fly" by means of \\textit{ab-initio} molecular dynamics simulations. To demonstrate the predictive power of this approach we investigate the effect of hydrophobic and hydrophilic solutes in water solution on the infrared and Raman spectra.
Exponential Expansion in Evolutionary Economics
DEFF Research Database (Denmark)
Frederiksen, Peter; Jagtfelt, Tue
2013-01-01
concepts are described in detail. Taken together it provides the rudimentary aspects of an economic system within an analytical perspective. It is argued that the main dynamic processes of the evolutionary perspective can be reduced to these four concepts. The model and concepts are evaluated in the light......This article attempts to solve current problems of conceptual fragmentation within the field of evolutionary economics. One of the problems, as noted by a number of observers, is that the field suffers from an assemblage of fragmented and scattered concepts (Boschma and Martin 2010). A solution...... to this problem is proposed in the form of a model of exponential expansion. The model outlines the overall structure and function of the economy as exponential expansion. The pictographic model describes four axiomatic concepts and their exponential nature. The interactive, directional, emerging and expanding...
Directory of Open Access Journals (Sweden)
Miller Andrew D
2003-06-01
Full Text Available Abstract Background Charging of transfer-RNA with cognate amino acid is accomplished by the aminoacyl-tRNA synthetases, and proceeds through an aminoacyl adenylate intermediate. The lysyl-tRNA synthetase has evolved an active site that specifically binds lysine and ATP. Previous molecular dynamics simulations of the heat-inducible Escherichia coli lysyl-tRNA synthetase, LysU, have revealed differences in the binding of ATP and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme. The possibility that this asymmetry results in different binding affinities for the ligands is addressed here by a parallel computational and biochemical study. Results Biochemical experiments employing isothermal calorimetry, steady-state fluorescence and circular dichroism are used to determine the order and stoichiometries of the lysine and nucleotide binding events, and the associated thermodynamic parameters. An ordered mechanism of substrate addition is found, with lysine having to bind prior to the nucleotide in a magnesium dependent process. Two lysines are found to bind per dimer, and trigger a large conformational change. Subsequent nucleotide binding causes little structural rearrangement and crucially only occurs at a single catalytic site, in accord with the simulations. Molecular dynamics based free energy calculations of the ATP binding process are used to determine the binding affinities of each site. Significant differences in ATP binding affinities are observed, with only one active site capable of realizing the experimental binding free energy. Half-of-the-sites models in which the nucleotide is only present at one active site achieve their full binding potential irrespective of the subunit choice. This strongly suggests the involvement of an anti-cooperative mechanism. Pathways for relaying information between the two active sites are proposed. Conclusions The asymmetry uncovered here appears to be a common
Evolutionary Explanation of Psychopaths
Seungbae Park
2013-01-01
Psychopaths are brutal individuals, having no empathetic concern for others. Initially, the existence of psychopaths seems to be a mystery from an evolutionary point of view. On close examination, however, it can be accommodated by evolutionary theory. Brutal individuals excelled meek individuals in the desperate circumstances where they had to fight their competitors over natural resources for survival and reproduction. This evolutionary explanation of psychopaths receives support from Pinke...
Remembering the evolutionary Freud.
Young, Allan
2006-03-01
Throughout his career as a writer, Sigmund Freud maintained an interest in the evolutionary origins of the human mind and its neurotic and psychotic disorders. In common with many writers then and now, he believed that the evolutionary past is conserved in the mind and the brain. Today the "evolutionary Freud" is nearly forgotten. Even among Freudians, he is regarded to be a red herring, relevant only to the extent that he diverts attention from the enduring achievements of the authentic Freud. There are three ways to explain these attitudes. First, the evolutionary Freud's key work is the "Overview of the Transference Neurosis" (1915). But it was published at an inopportune moment, forty years after the author's death, during the so-called "Freud wars." Second, Freud eventually lost interest in the "Overview" and the prospect of a comprehensive evolutionary theory of psychopathology. The publication of The Ego and the Id (1923), introducing Freud's structural theory of the psyche, marked the point of no return. Finally, Freud's evolutionary theory is simply not credible. It is based on just-so stories and a thoroughly discredited evolutionary mechanism, Lamarckian use-inheritance. Explanations one and two are probably correct but also uninteresting. Explanation number three assumes that there is a fundamental difference between Freud's evolutionary narratives (not credible) and the evolutionary accounts of psychopathology that currently circulate in psychiatry and mainstream journals (credible). The assumption is mistaken but worth investigating.
Energy Technology Data Exchange (ETDEWEB)
McMahan, A K
2005-03-30
This paper reports calculations for compressed Ce (4f{sup 1}), Pr (4f{sup 2}), and Nd (4f{sup 3}) using a combination of the local-density approximation (LDA) and dynamical mean field theory (DMFT), or LDA+DMFT. The 4f moment, spectra, and the total energy among other properties are examined as functions of volume and atomic number for an assumed face-centered cubic (fcc) structure. These materials are seen to be strongly localized at ambient pressure and for compressions up through the experimentally observed fcc phases ({gamma} phase for Ce), in the sense of having fully formed Hund's rules moments and little 4f spectral weight at the Fermi level. Subsequent compression for all three lanthanides brings about significant deviation of the moments from their Hund's rules values, a growing Kondo resonance at the fermi level, an associated softening in the total energy, and quenching of the spin orbit since the Kondo resonance is of mixed spin-orbit character while the lower Hubbard band is predominantly j = 5/2. while the most dramatic changes for Ce occur within the two-phase region of the {gamma}-{alpha} volume collapse transition, as found in earlier work, those for Pr and Nd occur within the volume range of the experimentally observed distorted fcc (dfcc) phase, which is therefore seen here as transitional and not part of the localized trivalent lanthanide sequence. The experimentally observed collapse to the {alpha}-U structure in Pr occurs only on further compression, and no such collapse is found in Nd. These lanthanides start closer to the localized limit for increasing atomic number, and so the theoretical signatures noted above are also offset to smaller volume as well, which is possibly related to the measured systematics of the size of the volume collapse being 15%, 9%, and none for Ce, Pr, and Nd, respectively.
Directory of Open Access Journals (Sweden)
Ilenia Giangreco
Full Text Available Matrix metalloproteinases (MMP are well-known biological targets implicated in tumour progression, homeostatic regulation, innate immunity, impaired delivery of pro-apoptotic ligands, and the release and cleavage of cell-surface receptors. Hence, the development of potent and selective inhibitors targeting these enzymes continues to be eagerly sought. In this paper, a number of alloxan-based compounds, initially conceived to bias other therapeutically relevant enzymes, were rationally modified and successfully repurposed to inhibit MMP-2 (also named gelatinase A in the nanomolar range. Importantly, the alloxan core makes its debut as zinc binding group since it ensures a stable tetrahedral coordination of the catalytic zinc ion in concert with the three histidines of the HExxHxxGxxH metzincin signature motif, further stabilized by a hydrogen bond with the glutamate residue belonging to the same motif. The molecular decoration of the alloxan core with a biphenyl privileged structure allowed to sample the deep S(1' specificity pocket of MMP-2 and to relate the high affinity towards this enzyme with the chance of forming a hydrogen bond network with the backbone of Leu116 and Asn147 and the side chains of Tyr144, Thr145 and Arg149 at the bottom of the pocket. The effect of even slight structural changes in determining the interaction at the S(1' subsite of MMP-2 as well as the nature and strength of the binding is elucidated via molecular dynamics simulations and free energy calculations. Among the herein presented compounds, the highest affinity (pIC(50 = 7.06 is found for BAM, a compound exhibiting also selectivity (>20 towards MMP-2, as compared to MMP-9, the other member of the gelatinases.
Feng, Xuan-Kai; Shi, Siqi; Shen, Jian-Yun; Shang, Shun-Li; Yao, Mei-Yi; Liu, Zi-Kui
2016-10-01
Since Zr-Fe-Sn is one of the key ternary systems for cladding and structural materials in nuclear industry, it is of significant importance to understand physicochemical properties related to Zr-Fe-Sn system. In order to design the new Zr alloys with advanced performance by CALPHAD method, the thermodynamic model for the lower order systems is required. In the present work, first-principles calculations are employed to obtain phonon, thermodynamic and elastic properties of Zr6FeSn2 with C22 structure and the end-members (C22-Zr6FeFe2, C22-Zr6SnSn2 and C22-Zr6SnFe2) in the model of (Zr)6(Fe, Sn)2(Fe, Sn)1. It is found that the imaginary phonon modes are absent for C22-Zr6FeSn2 and C22-Zr6SnSn2, indicating they are dynamically stable, while the other two end-members are unstable. Gibbs energies of C22-Zr6FeSn2 and C22-Zr6SnSn2 are obtained from the quasiharmonic phonon approach and can be added in the thermodynamic database: Nuclearbase. The C22-Zr6FeSn2's single-crystal elasticity tensor components along with polycrystalline bulk, shear and Young's moduli are computed with a least-squares approach based upon the stress tensor computed from first-principles method. The results indicate that distortion is more difficult in the directions normal the c-axis than along to it.
Zhang, Gaigong; Hu, Wei; Yang, Chao; Pask, John E
2015-01-01
Recently, we have proposed the adaptive local basis set for electronic structure calculations based on Kohn-Sham density functional theory in a pseudopotential framework. The adaptive local basis set is efficient and systematically improvable for total energy calculations. In this paper, we present the calculation of atomic forces, which can be used for a range of applications such as geometry optimization and molecular dynamics simulation. We demonstrate that, under mild assumptions, the computation of atomic forces can scale nearly linearly with the number of atoms in the system using the adaptive local basis set. We quantify the accuracy of the Hellmann-Feynman forces for a range of physical systems, benchmarked against converged planewave calculations, and find that the adaptive local basis set is efficient for both force and energy calculations, requiring at most a few tens of basis functions per atom to attain accuracy required in practice. Since the adaptive local basis set has implicit dependence on a...
Emergence of evolutionary cycles in size-structured food webs.
Ritterskamp, Daniel; Bearup, Daniel; Blasius, Bernd
2016-11-01
The interplay of population dynamics and evolution within ecological communities has been of long-standing interest for ecologists and can give rise to evolutionary cycles, e.g. taxon cycles. Evolutionary cycling was intensely studied in small communities with asymmetric competition; the latter drives the evolutionary processes. Here we demonstrate that evolutionary cycling arises naturally in larger communities if trophic interactions are present, since these are intrinsically asymmetric. To investigate the evolutionary dynamics of a trophic community, we use an allometric food web model. We find that evolutionary cycles emerge naturally for a large parameter ranges. The origin of the evolutionary dynamics is an intrinsic asymmetry in the feeding kernel which creates an evolutionary ratchet, driving species towards larger bodysize. We reveal different kinds of cycles: single morph cycles, and coevolutionary and mixed cycling of complete food webs. The latter refers to the case where each trophic level can have different evolutionary dynamics. We discuss the generality of our findings and conclude that ongoing evolution in food webs may be more frequent than commonly believed.
International Nuclear Information System (INIS)
In the treatment of elastically embeded shells by finite element methods, a calculation of the rigid body deformations before each iteration essentially improves the convergence of the method. This is also the case when calculating with fictitions densities instead of the real material densities. Some evidence has been obtained for the choice of a damping factor by empirical evaluation of several model calculations. (GL)
How mutation affects evolutionary games on graphs.
Allen, Benjamin; Traulsen, Arne; Tarnita, Corina E; Nowak, Martin A
2012-04-21
Evolutionary dynamics are affected by population structure, mutation rates and update rules. Spatial or network structure facilitates the clustering of strategies, which represents a mechanism for the evolution of cooperation. Mutation dilutes this effect. Here we analyze how mutation influences evolutionary clustering on graphs. We introduce new mathematical methods to evolutionary game theory, specifically the analysis of coalescing random walks via generating functions. These techniques allow us to derive exact identity-by-descent (IBD) probabilities, which characterize spatial assortment on lattices and Cayley trees. From these IBD probabilities we obtain exact conditions for the evolution of cooperation and other game strategies, showing the dual effects of graph topology and mutation rate. High mutation rates diminish the clustering of cooperators, hindering their evolutionary success. Our model can represent either genetic evolution with mutation, or social imitation processes with random strategy exploration.
Directory of Open Access Journals (Sweden)
H.Y. Wang
2012-03-01
Full Text Available The density-functional theory (DFT and density-functional perturbation theory (DFPT are employed to study the pressure dependence of elastic and dynamical properties of zinc-blende ZnS and ZnSe. The calculated elastic constants and phonon spectra from 0 GPa to 15 GPa are compared with the available experimental data. Generally, our calculated values are overestimated with experimental data, but agree well with recent other theoretical values. The discrepancies with experimental data are due to the use of local density approximation (LDA and effect of temperature. In this work, in order to compare with experimental data, we calculated and discussed the pressure derivatives of elastic constants, the pressure dependence of dynamical effect charge, and mode Grüneisen parameter at Γ.
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.
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
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...
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.
Linard, Benjamin; Nguyen, Ngoc Hoan; Prosdocimi, Francisco; Poch, Olivier; Thompson, Julie D
2012-01-01
Evolutionary systems biology aims to uncover the general trends and principles governing the evolution of biological networks. An essential part of this process is the reconstruction and analysis of the evolutionary histories of these complex, dynamic networks. Unfortunately, the methodologies for representing and exploiting such complex evolutionary histories in large scale studies are currently limited. Here, we propose a new formalism, called EvoluCode (Evolutionary barCode), which allows the integration of different evolutionary parameters (eg, sequence conservation, orthology, synteny …) in a unifying format and facilitates the multilevel analysis and visualization of complex evolutionary histories at the genome scale. The advantages of the approach are demonstrated by constructing barcodes representing the evolution of the complete human proteome. Two large-scale studies are then described: (i) the mapping and visualization of the barcodes on the human chromosomes and (ii) automatic clustering of the barcodes to highlight protein subsets sharing similar evolutionary histories and their functional analysis. The methodologies developed here open the way to the efficient application of other data mining and knowledge extraction techniques in evolutionary systems biology studies. A database containing all EvoluCode data is available at: http://lbgi.igbmc.fr/barcodes.
Directory of Open Access Journals (Sweden)
Inseon Ryoo
Full Text Available PURPOSE: To evaluate the usefulness of dynamic susceptibility contrast (DSC enhanced perfusion MR imaging in predicting major genetic alterations in glioblastomas. MATERIALS AND METHODS: Twenty-five patients (M:F = 13∶12, mean age: 52.1±15.2 years with pathologically proven glioblastoma who underwent DSC MR imaging before surgery were included. On DSC MR imaging, the normalized relative tumor blood volume (nTBV of the enhancing solid portion of each tumor was calculated by using dedicated software (Nordic TumorEX, NordicNeuroLab, Bergen, Norway that enabled semi-automatic segmentation for each tumor. Five major glioblastoma genetic alterations (epidermal growth factor receptor (EGFR, phosphatase and tensin homologue (PTEN, Ki-67, O6-methylguanine-DNA methyltransferase (MGMT and p53 were confirmed by immunohistochemistry and analyzed for correlation with the nTBV of each tumor. Statistical analysis was performed using the unpaired Student t test, ROC (receiver operating characteristic curve analysis and Pearson correlation analysis. RESULTS: The nTBVs of the MGMT methylation-negative group (mean 9.5±7.5 were significantly higher than those of the MGMT methylation-positive group (mean 5.4±1.8 (p = .046. In the analysis of EGFR expression-positive group, the nTBVs of the subgroup with loss of PTEN gene expression (mean: 10.3±8.1 were also significantly higher than those of the subgroup without loss of PTEN gene expression (mean: 5.6±2.3 (p = .046. Ki-67 labeling index indicated significant positive correlation with the nTBV of the tumor (p = .01. CONCLUSION: We found that glioblastomas with aggressive genetic alterations tended to have a high nTBV in the present study. Thus, we believe that DSC-enhanced perfusion MR imaging could be helpful in predicting genetic alterations that are crucial in predicting the prognosis of and selecting tailored treatment for glioblastoma patients.
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.
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
Computational and evolutionary aspects of language
Nowak, Martin A.; Komarova, Natalia L.; Niyogi, Partha
2002-06-01
Language is our legacy. It is the main evolutionary contribution of humans, and perhaps the most interesting trait that has emerged in the past 500 million years. Understanding how darwinian evolution gives rise to human language requires the integration of formal language theory, learning theory and evolutionary dynamics. Formal language theory provides a mathematical description of language and grammar. Learning theory formalizes the task of language acquisition-it can be shown that no procedure can learn an unrestricted set of languages. Universal grammar specifies the restricted set of languages learnable by the human brain. Evolutionary dynamics can be formulated to describe the cultural evolution of language and the biological evolution of universal grammar.
Institute of Scientific and Technical Information of China (English)
彭星光; 徐德民; 高晓光
2011-01-01
In order to solve dynamic multi-objective optimization problem(DMOPs), a dynamic multi-objective evolutionary algorithm based on Pareto set linkage and prediction(LP-DMOEA) is proposed and a Pareto set linking method based on hyperboxis designed. In this scheme, several time sequences which present the trend of Pareto solutions can be dynamically maintained. Based on the prediction of these time sequences, the initial population is generated. The LP-DMOEA is applied to the NSGA2 algorithm to solve three benchmark problems. Computational results show the effectiveness of the LPDMOEA to solve DMOPs.%针对动态多目标优化问题,提出一种基于Pareto解集关联与预测的动态多目标进化算法(LP-DMOEA),设计了基于超块的Pareto解集关联方法.该方法能够动态维护若十描述Pareto解变化规律的时间序列,通过对新环境下的Pareto解集进行预测来生成初始种群.将LP-DMOEA应用于非劣分类遗传算法(NSGA2),并对3类标准测试函数进行了实验,所得结果表明该方法能够有效求解动态优化问题.
International Nuclear Information System (INIS)
A non-linear analysis has been performed to determine relative motions between tubes and tube support plates (TSP) during a steam line break (SLB) event for steam generators. The SLB event results in blowdown of steam and water out of the steam generator. The fluid blowdown generates pressure drops across the TSPS, resulting in out-of-plane motion. The SLB induced pressure loads are calculated with a computer program that uses a drift-flux modeling of the two-phase flow. In order to determine the relative tube/TSP motions, a nonlinear dynamic time-history analysis is performed using a structural model that considers all of the significant component members relative to the tube support system. The dynamic response of the structure to the pressure loads is calculated using a special purpose computer program. This program links the various substructures at common degrees of freedom into a combined mass and stiffness matrix. The program accounts for structural non-linearities, including potential tube and TSP interaction at any given tube position. The program also accounts for structural damping as part of the dynamic response. Incorporating all of the above effects, the equations of motion are solved to give TSP displacements at the reduced set of DOF. Using the displacement results from the dynamic analysis, plate stresses are then calculated using the detailed component models. Displacements form the dynamic analysis are imposed as boundary conditions at the DOF locations, and the finite element program then solves for the overall distorted geometry. Calculations are also performed to assure that assumptions regarding elastic response of the various structural members and support points are valid
Energy Technology Data Exchange (ETDEWEB)
Ciftci, Yasemin Oe. [Gazi Univ., Ankara (Turkey). Dept. of Physics; Coban, Cansu [Balikesir Univ. (Turkey). Dept. of Physics
2016-05-01
The structural, mechanical, electronic, dynamic, and optical properties of the ZrPdSn compound crystallising into the MgAgAs structure are investigated by the ab initio calculations based on the density functional theory. The lattice constant, bulk modulus, and first derivative of bulk modulus were obtained by fitting the calculated total energy-atomic volume results to the Murnaghan equation of state. These results were compared to the previous data. The band structure and corresponding density of states (DOS) were also calculated and discussed. The elastic properties were calculated by using the stress-strain method, which shows that the MgAgAs phase of this compound is mechanically stable. The presented phonon dispersion curves and one-phonon DOS confirms that this compound is dynamically stable. In addition, the heat capacity, entropy, and free energy of ZrPdSn were calculated by using the phonon frequencies. Finally, the optical properties, such as dielectric function, reflectivity function, extinction coefficient, refractive index, and energy loss spectrum, were obtained under different pressures.
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…
Energy Technology Data Exchange (ETDEWEB)
Noll, Daniel [Goethe Univ., Frankfurt (Germany); Stancari, Giulio [Fermi National Accelerator Lab. (FNAL), Batavia, IL (United States)
2015-11-17
An electron lens is planned for the Fermilab Integrable Optics Test Accelerator as a nonlinear element for integrable dynamics, as an electron cooler, and as an electron trap to study space-charge compensation in rings. We present the main design principles and constraints for nonlinear integrable optics. A magnetic configuration of the solenoids and of the toroidal section is laid out. Singleparticle tracking is used to optimize the electron path. Electron beam dynamics at high intensity is calculated with a particle-in-cell code to estimate current limits, profile distortions, and the effects on the circulating beam. In the conclusions, we summarize the main findings and list directions for further work.
Directory of Open Access Journals (Sweden)
Anita Ghansah
Full Text Available BACKGROUND: Haemoglobin S (HbS and C (HbC are variants of the HBB gene which both protect against malaria. It is not clear, however, how these two alleles have evolved in the West African countries where they co-exist at high frequencies. Here we use haplotypic signatures of selection to investigate the evolutionary history of the malaria-protective alleles HbS and HbC in the Kassena-Nankana District (KND of Ghana. METHODOLOGY/PRINCIPAL FINDINGS: The haplotypic structure of HbS and HbC alleles was investigated, by genotyping 56 SNPs around the HBB locus. We found that, in the KND population, both alleles reside on extended haplotypes (approximately 1.5 Mb for HbS and 650 Kb for HbC that are significantly less diverse than those of the ancestral HbA allele. The extended haplotypes span a recombination hotspot that is known to exist in this region of the genome SIGNIFICANCE: Our findings show strong support for recent positive selection of both the HbS and HbC alleles and provide insights into how these two alleles have both evolved in the population of northern Ghana.
Janssens, Steven B; Vandelook, Filip; De Langhe, Edmond; Verstraete, Brecht; Smets, Erik; Vandenhouwe, Ines; Swennen, Rony
2016-06-01
Tropical Southeast Asia, which harbors most of the Musaceae biodiversity, is one of the most species-rich regions in the world. Its high degree of endemism is shaped by the region's tectonic and climatic history, with large differences between northern Indo-Burma and the Malayan Archipelago. Here, we aim to find a link between the diversification and biogeography of Musaceae and geological history of the Southeast Asian subcontinent. The Musaceae family (including five Ensete, 45 Musa and one Musella species) was dated using a large phylogenetic framework encompassing 163 species from all Zingiberales families. Evolutionary patterns within Musaceae were inferred using ancestral area reconstruction and diversification rate analyses. All three Musaceae genera - Ensete, Musa and Musella - originated in northern Indo-Burma during the early Eocene. Musa species dispersed from 'northwest to southeast' into Southeast Asia with only few back-dispersals towards northern Indo-Burma. Musaceae colonization events of the Malayan Archipelago subcontinent are clearly linked to the geological and climatic history of the region. Musa species were only able to colonize the region east of Wallace's line after the availability of emergent land from the late Miocene onwards.
Eco-evolutionary feedbacks drive species interactions
Andrade-Domínguez, Andrés; Salazar, Emmanuel; del Carmen Vargas-Lagunas, María; Kolter, Roberto; Encarnación, Sergio
2013-01-01
In the biosphere, many species live in close proximity and can thus interact in many different ways. Such interactions are dynamic and fall along a continuum between antagonism and cooperation. Because interspecies interactions are the key to understanding biological communities, it is important to know how species interactions arise and evolve. Here, we show that the feedback between ecological and evolutionary processes has a fundamental role in the emergence and dynamics of species interac...
Evolutionary stable investment in stock markets
Evstigneev, Igor V.; Hens, Thorsten; Schenk-Hoppé, Klaus Reiner
2003-01-01
This paper studies the performance of portfolio rules in incomplete markets for long-lived assets with endogenous prices. The dynamics of wealth shares in the process of repeated reinvestment of wealth is modelled as a random dynamical systems. The performance of a portfolio rule is determined by the wealth share eventually conquered in competition with other rules. We derive necessary and sufficient conditions for the evolutionary stability of portfolio rules when dividends are Markov or, in...
Bridging the gap between Schumpeterian competition and evolutionary game theory
DEFF Research Database (Denmark)
Andersen, Esben Sloth
This paper suggests that the analysis of Schumpeterian competition within the Nelson-Winter model should be complemented with evolutionary game theory. This model and its limitations for density-dependent Schumpeterian strategies are presented in terms of the equations of evolutionary dynamics...... strategies is proved. This is an example of Schumpeterian competition within evolutionary game theory........ Formulated as evolutionary games, the set of strategies can easily be extended from innovators and imitators to routinists, complementors, and mixers. All strategies are presented in relation to a modified version of the Hawk-Dove Game. In this setting, the possibility of coexistence of several Schumpeterian...
Lin, Shiang-Tai; Blanco, Mario; Goddard, William A.
2003-01-01
We propose a general approach for determining the entropy and free energy of complex systems as a function of temperature and pressure. In this method the Fourier transform of the velocity autocorrelation function, obtained from a short (20 ps) molecular dynamics trajectory is used to obtain the vibrational density of states (DoS) which is then used to calculate the thermodynamic properties by applying quantum statistics assuming each mode is a harmonic oscillator. This approach is quite accu...
Matricon, Geoffrey
2015-01-01
Life-cycle assessment is being applied to an increasing number of building projects from one side while the usual dynamic thermal simulations are being conducted from the other side on the same projects. However, there are few observations in the literature linking these two types of calculations: embodied and operating energies are rarely directly compared. This paper compares those energies for some case studies. The challenge is to quantify to what extent chosen structural materials can ch...
When development matters: From evolutionary psychology to evolutionary developmental psychology
Hernández Blasi, Carlos; Bjorklund, David F.; Gardiner, Amy K.
2008-01-01
This article presents evolutionary developmental psychology (EDP) as an emerging field of evolutionary psychology (EP). In describing the core tenets of both approaches and the differences between them, we emphasize the important roles that evolution and development have in understanding human behaviour. We suggest that developmental psychologists should pay more attention to evolutionary issues and, conversely, evolutionary psychologists should take development seriously ...
Music and evolutionary computation
Reis, Cecília; Marques, Viriato M.; Machado, J. A. Tenreiro
2011-01-01
This paper presents a brief history of the western music: from its genesis to serialism and the Darmstadt school. Also some mathematical aspects of music are then presented and confronted with music as a form of art. The question is, are these two distinct aspects compatible? Can computers be of real help in automatic composition? The more appealing algorithmic approach is evolutionary computation as it offers creativity potential. Therefore, the Evolutionary Algorithms are then introduced an...