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Sample records for dynamics genetic complexity

  1. Transcription closed and open complex dynamics studies reveal balance between genetic determinants and co-factors.

    Science.gov (United States)

    Sala, Adrien; Shoaib, Muhammad; Anufrieva, Olga; Mutharasu, Gnanavel; Jahan Hoque, Rawnak; Yli-Harja, Olli; Kandhavelu, Meenakshisundaram

    2015-05-19

    In E. coli, promoter closed and open complexes are key steps in transcription initiation, where magnesium-dependent RNA polymerase catalyzes RNA synthesis. However, the exact mechanism of initiation remains to be fully elucidated. Here, using single mRNA detection and dual reporter studies, we show that increased intracellular magnesium concentration affects Plac initiation complex formation resulting in a highly dynamic process over the cell growth phases. Mg2+ regulates transcription transition, which modulates bimodality of mRNA distribution in the exponential phase. We reveal that Mg2+ regulates the size and frequency of the mRNA burst by changing the open complex duration. Moreover, increasing magnesium concentration leads to higher intrinsic and extrinsic noise in the exponential phase. RNAP-Mg2+ interaction simulation reveals critical movements creating a shorter contact distance between aspartic acid residues and Nucleotide Triphosphate residues and increasing electrostatic charges in the active site. Our findings provide unique biophysical insights into the balanced mechanism of genetic determinants and magnesium ion in transcription initiation regulation during cell growth.

  2. Complex dynamics

    CERN Document Server

    Carleson, Lennart

    1993-01-01

    Complex dynamics is today very much a focus of interest. Though several fine expository articles were available, by P. Blanchard and by M. Yu. Lyubich in particular, until recently there was no single source where students could find the material with proofs. For anyone in our position, gathering and organizing the material required a great deal of work going through preprints and papers and in some cases even finding a proof. We hope that the results of our efforts will be of help to others who plan to learn about complex dynamics and perhaps even lecture. Meanwhile books in the field a. re beginning to appear. The Stony Brook course notes of J. Milnor were particularly welcome and useful. Still we hope that our special emphasis on the analytic side will satisfy a need. This book is a revised and expanded version of notes based on lectures of the first author at UCLA over several \\Vinter Quarters, particularly 1986 and 1990. We owe Chris Bishop a great deal of gratitude for supervising the production of cour...

  3. Dynamic semiparametric Bayesian models for genetic mapping of complex trait with irregular longitudinal data.

    Science.gov (United States)

    Das, Kiranmoy; Li, Jiahan; Fu, Guifang; Wang, Zhong; Li, Runze; Wu, Rongling

    2013-02-10

    Many phenomena of fundamental importance to biology and biomedicine arise as a dynamic curve, such as organ growth and HIV dynamics. The genetic mapping of these traits is challenged by longitudinal variables measured at irregular and possibly subject-specific time points, in which case nonnegative definiteness of the estimated covariance matrix needs to be guaranteed. We present a semiparametric approach for genetic mapping within the mixture-model setting by jointly modeling mean and covariance structures for irregular longitudinal data. Penalized spline is used to model the mean functions of individual quantitative trait locus (QTL) genotypes as latent variables, whereas an extended generalized linear model is used to approximate the covariance matrix. The parameters for modeling the mean-covariances are estimated by MCMC, using the Gibbs sampler and the Metropolis-Hastings algorithm. We derive the full conditional distributions for the mean and covariance parameters and compute Bayes factors to test the hypothesis about the existence of significant QTLs. We used the model to screen the existence of specific QTLs for age-specific change of body mass index with a sparse longitudinal data set. The new model provides powerful means for broadening the application of genetic mapping to reveal the genetic control of dynamic traits.

  4. A Comprehensive Image-based Phenomic Analysis Reveals the Complex Genetic Architecture of Shoot Growth Dynamics in Rice (Oryza sativa).

    Science.gov (United States)

    Campbell, Malachy T; Du, Qian; Liu, Kan; Brien, Chris J; Berger, Bettina; Zhang, Chi; Walia, Harkamal

    2017-07-01

    Early vigor is an important trait for many rice ( L.)-growing environments. However, genetic characterization and improvement for early vigor is hindered by the temporal nature of the trait and strong genotype × environment effects. We explored the genetic architecture of shoot growth dynamics during the early and active tillering stages by applying a functional modeling and genomewide association (GWAS) mapping approach on a diversity panel of ∼360 rice accessions. Multiple loci with small effects on shoot growth trajectory were identified, indicating a complex polygenic architecture. Natural variation for shoot growth dynamics was assessed in a subset of 31 accessions using RNA sequencing and hormone quantification. These analyses yielded a gibberellic acid (GA) catabolic gene, , which could influence GA levels to regulate vigor in the early tillering stage. Given the complex genetic architecture of shoot growth dynamics, the potential of genomic selection (GS) for improving early vigor was explored using all 36,901 single-nucleotide polymorphisms (SNPs) as well as several subsets of the most significant SNPs from GWAS. Shoot growth trajectories could be predicted with reasonable accuracy using the 50 most significant SNPs from GWAS (0.37-0.53); however, the accuracy of prediction was improved by including more markers, which indicates that GS may be an effective strategy for improving shoot growth dynamics during the vegetative growth stage. This study provides insights into the complex genetic architecture and molecular mechanisms underlying early shoot growth dynamics and provides a foundation for improving this complex trait in rice. Copyright © 2017 Crop Science Society of America.

  5. Virtual mutagenesis of the yeast cyclins genetic network reveals complex dynamics of transcriptional control networks.

    Directory of Open Access Journals (Sweden)

    Eliska Vohradska

    Full Text Available Study of genetic networks has moved from qualitative description of interactions between regulators and regulated genes to the analysis of the interaction dynamics. This paper focuses on the analysis of dynamics of one particular network--the yeast cyclins network. Using a dedicated mathematical model of gene expression and a procedure for computation of the parameters of the model from experimental data, a complete numerical model of the dynamics of the cyclins genetic network was attained. The model allowed for performing virtual experiments on the network and observing their influence on the expression dynamics of the genes downstream in the regulatory cascade. Results show that when the network structure is more complicated, and the regulatory interactions are indirect, results of gene deletion are highly unpredictable. As a consequence of quantitative behavior of the genes and their connections within the network, causal relationship between a regulator and target gene may not be discovered by gene deletion. Without including the dynamics of the system into the network, its functional properties cannot be studied and interpreted correctly.

  6. From observational to dynamic genetics

    Directory of Open Access Journals (Sweden)

    Claire M. A. Haworth

    2014-01-01

    Full Text Available Twin and family studies have shown that most traits are at least moderately heritable. But what are the implications of finding genetic influence for the design of intervention and prevention programs? For complex traits, heritability does not mean immutability, and research has shown that genetic influences can change with age, context and in response to behavioural and drug interventions. The most significant implications for intervention will come when we move from observational genetics to investigating dynamic genetics, including genetically sensitive interventions. Future interventions should be designed to overcome genetic risk and draw upon genetic strengths by changing the environment.

  7. Genetics of complex diseases

    DEFF Research Database (Denmark)

    Mellerup, Erling; Møller, Gert Lykke; Koefoed, Pernille

    2012-01-01

    A complex disease with an inheritable component is polygenic, meaning that several different changes in DNA are the genetic basis for the disease. Such a disease may also be genetically heterogeneous, meaning that independent changes in DNA, i.e. various genotypes, can be the genetic basis...... for the disease. Each of these genotypes may be characterized by specific combinations of key genetic changes. It is suggested that even if all key changes are found in genes related to the biology of a certain disease, the number of combinations may be so large that the number of different genotypes may be close...

  8. Genetics of complex diseases.

    Science.gov (United States)

    Motulsky, Arno G

    2006-02-01

    Approaches to the study of the genetic basis of common complex diseases and their clinical applications are considered. Monogenic Mendelian inheritance in such conditions is infrequent but its elucidation may help to detect pathogenic mechanisms in the more common variety of complex diseases. Involvement by multiple genes in complex diseases usually occurs but the isolation and identification of specific genes so far has been exceptional. The role of common polymorphisms as indicators of disease risk in various studies is discussed.

  9. Complex spatial dynamics maintain northern leopard frog (Lithobates pipiens) genetic diversity in a temporally varying landscape

    Science.gov (United States)

    Mushet, David M.; Euliss, Ned H.; Chen, Yongjiu; Stockwell, Craig A.

    2013-01-01

    In contrast to most local amphibian populations, northeastern populations of the Northern Leopard Frog (Lithobates pipiens) have displayed uncharacteristically high levels of genetic diversity that have been attributed to large, stable populations. However, this widely distributed species also occurs in areas known for great climatic fluctuations that should be reflected in corresponding fluctuations in population sizes and reduced genetic diversity. To test our hypothesis that Northern Leopard Frog genetic diversity would be reduced in areas subjected to significant climate variability, we examined the genetic diversity of L. pipiens collected from 12 sites within the Prairie Pothole Region of North Dakota. Despite the region's fluctuating climate that includes periods of recurring drought and deluge, we found unexpectedly high levels of genetic diversity approaching that of northeastern populations. Further, genetic structure at a landscape scale was strikingly homogeneous; genetic differentiation estimates (Dest) averaged 0.10 (SD = 0.036) across the six microsatellite loci we studied, and two Bayesian assignment tests (STRUCTURE and BAPS) failed to reveal the development of significant population structure across the 68 km breadth of our study area. These results suggest that L. pipiens in the Prairie Pothole Region consists of a large, panmictic population capable of maintaining high genetic diversity in the face of marked climate variability.

  10. Complexity and Dynamical Depth

    Directory of Open Access Journals (Sweden)

    Terrence Deacon

    2014-07-01

    Full Text Available We argue that a critical difference distinguishing machines from organisms and computers from brains is not complexity in a structural sense, but a difference in dynamical organization that is not well accounted for by current complexity measures. We propose a measure of the complexity of a system that is largely orthogonal to computational, information theoretic, or thermodynamic conceptions of structural complexity. What we call a system’s dynamical depth is a separate dimension of system complexity that measures the degree to which it exhibits discrete levels of nonlinear dynamical organization in which successive levels are distinguished by local entropy reduction and constraint generation. A system with greater dynamical depth than another consists of a greater number of such nested dynamical levels. Thus, a mechanical or linear thermodynamic system has less dynamical depth than an inorganic self-organized system, which has less dynamical depth than a living system. Including an assessment of dynamical depth can provide a more precise and systematic account of the fundamental difference between inorganic systems (low dynamical depth and living systems (high dynamical depth, irrespective of the number of their parts and the causal relations between them.

  11. Nonlinear dynamics and complexity

    CERN Document Server

    Luo, Albert; Fu, Xilin

    2014-01-01

    This important collection presents recent advances in nonlinear dynamics including analytical solutions, chaos in Hamiltonian systems, time-delay, uncertainty, and bio-network dynamics. Nonlinear Dynamics and Complexity equips readers to appreciate this increasingly main-stream approach to understanding complex phenomena in nonlinear systems as they are examined in a broad array of disciplines. The book facilitates a better understanding of the mechanisms and phenomena in nonlinear dynamics and develops the corresponding mathematical theory to apply nonlinear design to practical engineering.

  12. Transformations, Dynamics and Complexity

    CERN Document Server

    Glazunov, Nikolaj

    2011-01-01

    We review and investigate some new problems and results in the field of dynamical systems generated by iteration of maps, {\\beta}-transformations, partitions, group actions, bundle dynamical systems, Hasse-Kloosterman maps, and some aspects of complexity of the systems.

  13. Report: Genetics of complex diseases

    Institute of Scientific and Technical Information of China (English)

    MOTULSKY Arno G.

    2006-01-01

    Approaches to the study of the genetic basis of common complex diseases and their clinical applications are considered. Monogenic Mendelian inheritance in such conditions is infrequent but its elucidation may help to detect pathogenic mechanisms in the more common variety of complex diseases. Involvement by multiple genes in complex diseases usually occurs but the isolation and identification of specific genes so far has been exceptional. The role of common polymorphisms as indicators of disease risk in various studies is discussed.

  14. Complexity in Dynamical Systems

    Science.gov (United States)

    Moore, Cristopher David

    The study of chaos has shown us that deterministic systems can have a kind of unpredictability, based on a limited knowledge of their initial conditions; after a finite time, the motion appears essentially random. This observation has inspired a general interest in the subject of unpredictability, and more generally, complexity; how can we characterize how "complex" a dynamical system is?. In this thesis, we attempt to answer this question with a paradigm of complexity that comes from computer science, we extract sets of symbol sequences, or languages, from a dynamical system using standard methods of symbolic dynamics; we then ask what kinds of grammars or automata are needed a generate these languages. This places them in the Chomsky heirarchy, which in turn tells us something about how subtle and complex the dynamical system's behavior is. This gives us insight into the question of unpredictability, since these automata can also be thought of as computers attempting to predict the system. In the culmination of the thesis, we find a class of smooth, two-dimensional maps which are equivalent to the highest class in the Chomsky heirarchy, the turning machine; they are capable of universal computation. Therefore, these systems possess a kind of unpredictability qualitatively different from the usual "chaos": even if the initial conditions are known exactly, questions about the system's long-term dynamics are undecidable. No algorithm exists to answer them. Although this kind of unpredictability has been discussed in the context of distributed, many-degree-of -freedom systems (for instance, cellular automata) we believe this is the first example of such phenomena in a smooth, finite-degree-of-freedom system.

  15. Complex and Fractional Dynamics

    Directory of Open Access Journals (Sweden)

    J. A. Tenreiro Machado

    2017-02-01

    Full Text Available Complex systems (CS are pervasive in many areas, namely financial markets; highway transportation; telecommunication networks; world and country economies; social networks; immunological systems; living organisms; computational systems; and electrical and mechanical structures. CS are often composed of a large number of interconnected and interacting entities exhibiting much richer global scale dynamics than could be inferred from the properties and behavior of individual elements. [...

  16. Complex dynamics in nanosystems.

    Science.gov (United States)

    Ni, Xuan; Ying, Lei; Lai, Ying-Cheng; Do, Younghae; Grebogi, Celso

    2013-05-01

    Complex dynamics associated with multistability have been studied extensively in the past but mostly for low-dimensional nonlinear dynamical systems. A question of fundamental interest is whether multistability can arise in high-dimensional physical systems. Motivated by the ever increasing widespread use of nanoscale systems, we investigate a prototypical class of nanoelectromechanical systems: electrostatically driven Si nanowires, mathematically described by a set of driven, nonlinear partial differential equations. We develop a computationally efficient algorithm to solve the equations. Our finding is that multistability and complicated structures of basins of attraction are common types of dynamics, and the latter can be attributed to extensive transient chaos. Implications of these phenomena to device operations are discussed.

  17. Complex Hamiltonian Dynamics

    CERN Document Server

    Bountis, Tassos

    2012-01-01

    This book introduces and explores modern developments in the well established field of Hamiltonian dynamical systems. It focuses on high degree-of-freedom systems and the transitional regimes between regular and chaotic motion. The role of nonlinear normal modes is highlighted and the importance of low-dimensional tori in the resolution of the famous FPU paradox is emphasized. Novel powerful numerical methods are used to study localization phenomena and distinguish order from strongly and weakly chaotic regimes. The emerging hierarchy of complex structures in such regimes gives rise to particularly long-lived patterns and phenomena called quasi-stationary states, which are explored in particular in the concrete setting of one-dimensional Hamiltonian lattices and physical applications in condensed matter systems.  The self-contained and pedagogical approach is blended with a unique balance between mathematical rigor, physics insights and concrete applications. End of chapter exercises and (more demanding) res...

  18. Wolbachia association with the tsetse fly, Glossina fuscipes fuscipes, reveals high levels of genetic diversity and complex evolutionary dynamics

    Directory of Open Access Journals (Sweden)

    Symula Rebecca E

    2013-02-01

    Full Text Available Abstract Background Wolbachia pipientis, a diverse group of α-proteobacteria, can alter arthropod host reproduction and confer a reproductive advantage to Wolbachia-infected females (cytoplasmic incompatibility (CI. This advantage can alter host population genetics because Wolbachia-infected females produce more offspring with their own mitochondrial DNA (mtDNA haplotypes than uninfected females. Thus, these host haplotypes become common or fixed (selective sweep. Although simulations suggest that for a CI-mediated sweep to occur, there must be a transient phase with repeated initial infections of multiple individual hosts by different Wolbachia strains, this has not been observed empirically. Wolbachia has been found in the tsetse fly, Glossina fuscipes fuscipes, but it is not limited to a single host haplotype, suggesting that CI did not impact its population structure. However, host population genetic differentiation could have been generated if multiple Wolbachia strains interacted in some populations. Here, we investigated Wolbachia genetic variation in G. f. fuscipes populations of known host genetic composition in Uganda. We tested for the presence of multiple Wolbachia strains using Multi-Locus Sequence Typing (MLST and for an association between geographic region and host mtDNA haplotype using Wolbachia DNA sequence from a variable locus, groEL (heat shock protein 60. Results MLST demonstrated that some G. f. fuscipes carry Wolbachia strains from two lineages. GroEL revealed high levels of sequence diversity within and between individuals (Haplotype diversity = 0.945. We found Wolbachia associated with 26 host mtDNA haplotypes, an unprecedented result. We observed a geographical association of one Wolbachia lineage with southern host mtDNA haplotypes, but it was non-significant (p = 0.16. Though most Wolbachia-infected host haplotypes were those found in the contact region between host mtDNA groups, this association was non

  19. Population Dynamics of Genetic Regulatory Networks

    Science.gov (United States)

    Braun, Erez

    2005-03-01

    Unlike common objects in physics, a biological cell processes information. The cell interprets its genome and transforms the genomic information content, through the action of genetic regulatory networks, into proteins which in turn dictate its metabolism, functionality and morphology. Understanding the dynamics of a population of biological cells presents a unique challenge. It requires to link the intracellular dynamics of gene regulation, through the mechanism of cell division, to the level of the population. We present experiments studying adaptive dynamics of populations of genetically homogeneous microorganisms (yeast), grown for long durations under steady conditions. We focus on population dynamics that do not involve random genetic mutations. Our experiments follow the long-term dynamics of the population distributions and allow to quantify the correlations among generations. We focus on three interconnected issues: adaptation of genetically homogeneous populations following environmental changes, selection processes on the population and population variability and expression distributions. We show that while the population exhibits specific short-term responses to environmental inputs, it eventually adapts to a robust steady-state, largely independent of external conditions. Cycles of medium-switch show that the adapted state is imprinted in the population and that this memory is maintained for many generations. To further study population adaptation, we utilize the process of gene recruitment whereby a gene naturally regulated by a specific promoter is placed under a different regulatory system. This naturally occurring process has been recognized as a major driving force in evolution. We have recruited an essential gene to a foreign regulatory network and followed the population long-term dynamics. Rewiring of the regulatory network allows us to expose their complex dynamics and phase space structure.

  20. SYNCHRONIZATION IN COMPLEX DYNAMICAL NETWORKS

    Institute of Scientific and Technical Information of China (English)

    WANG Xiaofan; CHEN Guanrong

    2003-01-01

    In the past few years, the discovery of small-world and scale-free properties of many natural and artificial complex networks has stimulated increasing interest in further studying the underlying organizing principles of various complex networks. This has led to significant advances in understanding the relationship between the topology and the dynamics of such complex networks. This paper reviews some recent research works on the synchronization phenomenon in various dynamical networks with small-world and scalefree connections.

  1. Dynamical genetic programming in XCSF.

    Science.gov (United States)

    Preen, Richard J; Bull, Larry

    2013-01-01

    A number of representation schemes have been presented for use within learning classifier systems, ranging from binary encodings to artificial neural networks. This paper presents results from an investigation into using a temporally dynamic symbolic representation within the XCSF learning classifier system. In particular, dynamical arithmetic networks are used to represent the traditional condition-action production system rules to solve continuous-valued reinforcement learning problems and to perform symbolic regression, finding competitive performance with traditional genetic programming on a number of composite polynomial tasks. In addition, the network outputs are later repeatedly sampled at varying temporal intervals to perform multistep-ahead predictions of a financial time series.

  2. Mobile robot dynamic path planning based on improved genetic algorithm

    Science.gov (United States)

    Wang, Yong; Zhou, Heng; Wang, Ying

    2017-08-01

    In dynamic unknown environment, the dynamic path planning of mobile robots is a difficult problem. In this paper, a dynamic path planning method based on genetic algorithm is proposed, and a reward value model is designed to estimate the probability of dynamic obstacles on the path, and the reward value function is applied to the genetic algorithm. Unique coding techniques reduce the computational complexity of the algorithm. The fitness function of the genetic algorithm fully considers three factors: the security of the path, the shortest distance of the path and the reward value of the path. The simulation results show that the proposed genetic algorithm is efficient in all kinds of complex dynamic environments.

  3. Managing Complex Dynamical Systems

    Science.gov (United States)

    Cox, John C.; Webster, Robert L.; Curry, Jeanie A.; Hammond, Kevin L.

    2011-01-01

    Management commonly engages in a variety of research designed to provide insight into the motivation and relationships of individuals, departments, organizations, etc. This paper demonstrates how the application of concepts associated with the analysis of complex systems applied to such data sets can yield enhanced insights for managerial action.

  4. Complexity, dynamic cellular network, and tumorigenesis.

    Science.gov (United States)

    Waliszewski, P

    1997-01-01

    A holistic approach to tumorigenesis is proposed. The main element of the model is the existence of dynamic cellular network. This network comprises a molecular and an energetistic structure of a cell connected through the multidirectional flow of information. The interactions within dynamic cellular network are complex, stochastic, nonlinear, and also involve quantum effects. From this non-reductionist perspective, neither tumorigenesis can be limited to the genetic aspect, nor the initial event must be of molecular nature, nor mutations and epigenetic factors are mutually exclusive, nor a link between cause and effect can be established. Due to complexity, an unstable stationary state of dynamic cellular network rather than a group of unrelated genes determines the phenotype of normal and transformed cells. This implies relativity of tumor suppressor genes and oncogenes. A bifurcation point is defined as an unstable state of dynamic cellular network leading to the other phenotype-stationary state. In particular, the bifurcation point may be determined by a change of expression of a single gene. Then, the gene is called bifurcation point gene. The unstable stationary state facilitates the chaotic dynamics. This may result in a fractal dimension of both normal and tumor tissues. The co-existence of chaotic dynamics and complexity is the essence of cellular processes and shapes differentiation, morphogenesis, and tumorigenesis. In consequence, tumorigenesis is a complex, unpredictable process driven by the interplay between self-organisation and selection.

  5. Genetic basis of a cognitive complexity metric.

    Directory of Open Access Journals (Sweden)

    Narelle K Hansell

    Full Text Available Relational complexity (RC is a metric reflecting capacity limitation in relational processing. It plays a crucial role in higher cognitive processes and is an endophenotype for several disorders. However, the genetic underpinnings of complex relational processing have not been investigated. Using the classical twin model, we estimated the heritability of RC and genetic overlap with intelligence (IQ, reasoning, and working memory in a twin and sibling sample aged 15-29 years (N = 787. Further, in an exploratory search for genetic loci contributing to RC, we examined associated genetic markers and genes in our Discovery sample and selected loci for replication in four independent samples (ALSPAC, LBC1936, NTR, NCNG, followed by meta-analysis (N>6500 at the single marker level. Twin modelling showed RC is highly heritable (67%, has considerable genetic overlap with IQ (59%, and is a major component of genetic covariation between reasoning and working memory (72%. At the molecular level, we found preliminary support for four single-marker loci (one in the gene DGKB, and at a gene-based level for the NPS gene, having influence on cognition. These results indicate that genetic sources influencing relational processing are a key component of the genetic architecture of broader cognitive abilities. Further, they suggest a genetic cascade, whereby genetic factors influencing capacity limitation in relational processing have a flow-on effect to more complex cognitive traits, including reasoning and working memory, and ultimately, IQ.

  6. Coarse-graining complex dynamics

    DEFF Research Database (Denmark)

    Sibani, Paolo

    2013-01-01

    Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat-tailed distribu......Continuous Time Random Walks (CTRW) are widely used to coarse-grain the evolution of systems jumping from a metastable sub-set of their configuration space, or trap, to another via rare intermittent events. The multi-scaled behavior typical of complex dynamics is provided by a fat......-law and logarithmic relaxation behaviors ubiquitous in complex dynamics, together with the sub-diffusive time dependence of the Mean Square Displacement characteristic of single particles moving in a complex environment....

  7. Permutation Complexity in Dynamical Systems

    CERN Document Server

    Amigo, Jose

    2010-01-01

    The study of permutation complexity can be envisioned as a new kind of symbolic dynamics whose basic blocks are ordinal patterns, that is, permutations defined by the order relations among points in the orbits of dynamical systems. Since its inception in 2002 the concept of permutation entropy has sparked a new branch of research in particular regarding the time series analysis of dynamical systems that capitalizes on the order structure of the state space. Indeed, on one hand ordinal patterns and periodic points are closely related, yet ordinal patterns are amenable to numerical methods, while periodicity is not. Another interesting feature is that since it can be shown that random (unconstrained) dynamics has no forbidden patterns with probability one, their existence can be used as a fingerprint to identify any deterministic origin of orbit generation. This book is primarily addressed to researchers working in the field of nonlinear dynamics and complex systems, yet will also be suitable for graduate stude...

  8. Routine Discovery of Complex Genetic Models using Genetic Algorithms.

    Science.gov (United States)

    Moore, Jason H; Hahn, Lance W; Ritchie, Marylyn D; Thornton, Tricia A; White, Bill C

    2004-02-01

    Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the effects of other genes (i.e. epistasis or gene-gene interaction). Despite this need, the development of complex genetic models that can be used to simulate data is not always intuitive. In fact, only a few such models have been published. We have previously developed a genetic algorithm approach to discovering complex genetic models in which two single nucleotide polymorphisms (SNPs) influence disease risk solely through nonlinear interactions. In this paper, we extend this approach for the discovery of high-order epistasis models involving three to five SNPs. We demonstrate that the genetic algorithm is capable of routinely discovering interesting high-order epistasis models in which each SNP influences risk of disease only through interactions with the other SNPs in the model. This study opens the door for routine simulation of complex gene-gene interactions among SNPs for the development and evaluation of new statistical and computational approaches for identifying common, complex multifactorial disease susceptibility genes.

  9. Genetics Home Reference: Carney complex

    Science.gov (United States)

    ... cortisol (hypercortisolism) can lead to the development of Cushing syndrome. This syndrome causes weight gain in the face ... Institute of Diabetes and Digestive and Kidney Diseases: Cushing's Syndrome Educational Resources (7 links) Disease InfoSearch: Carney Complex ...

  10. Epidemic dynamics on complex networks

    Institute of Scientific and Technical Information of China (English)

    ZHOU Tao; FU Zhongqian; WANG Binghong

    2006-01-01

    Recently, motivated by the pioneer work in revealing the small-world effect and scale-free property of various real-life networks, many scientists devote themselves to studying complex networks. One of the ultimate goals is to understand how the topological structures affect the dynamics upon networks. In this paper, we give a brief review on the studies of epidemic dynamics on complex networks, including the description of classical epidemic models, the epidemic spread on small-world and scale-free networks, and network immunization. Finally, perspectives and some interesting problems are proposed.

  11. Complex Dynamics in Communication Networks

    CERN Document Server

    Kocarev, Ljupco

    2005-01-01

    Computer and communication networks are among society's most important infrastructures. The internet, in particular, is a giant global network of networks without central control or administration. It is a paradigm of a complex system, where complexity may arise from different sources: topological structure, network evolution, connection and node diversity, or dynamical evolution. The present volume is the first book entirely devoted to the new and emerging field of nonlinear dynamics of TCP/IP networks. It addresses both scientists and engineers working in the general field of communication networks.

  12. ON COMPLEX DYNAMIC CONTROL SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    CHENG Daizhan

    2003-01-01

    This paper presents some recent works on the control of dynamic systems, which have certain complex properties caused by singularity of the nonlinear structures, structure-varyings, or evolution process etc. First, we consider the structure singularity of nonlinear control systems. It was revealed that the focus of researches on nonlinear control theory is shifting from regular systems to singular systems. The singularity of nonlinear systems causes certain complexity. Secondly, the switched systems are considered. For such systems the complexity is caused by the structure varying. We show that the switched systems have significant characteristics of complex systems. Finally, we investigate the evolution systems. The evolution structure makes complexity, and itself is a proper model for complex systems.

  13. Statistical methods for analysing complex genetic traits

    NARCIS (Netherlands)

    El Galta, Rachid

    2006-01-01

    Complex traits are caused by multiple genetic and environmental factors, and are therefore difficult to study compared with simple Mendelian diseases. The modes of inheritance of Mendelian diseases are often known. Methods to dissect such diseases are well described in literature. For complex geneti

  14. Predicting complex mineral structures using genetic algorithms.

    Science.gov (United States)

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  15. Distilling pathophysiology from complex disease genetics.

    Science.gov (United States)

    Chakravarti, Aravinda; Clark, Andrew G; Mootha, Vamsi K

    2013-09-26

    Technologies for genome-wide sequence interrogation have dramatically improved our ability to identify loci associated with complex human disease. However, a chasm remains between correlations and causality that stems, in part, from a limiting theoretical framework derived from Mendelian genetics and an incomplete understanding of disease physiology. Here we propose a set of criteria, akin to Koch's postulates for infectious disease, for assigning causality between genetic variants and human disease phenotypes. Copyright © 2013 Elsevier Inc. All rights reserved.

  16. [Complex diseases: the importance of genetics].

    Science.gov (United States)

    Libioulle, C; Bours, V

    2012-01-01

    Complex diseases usually harbour hereditary factors linked with multiple susceptibility genes. The additive effects of genetic and environmental factors are responsible for the pathology. The impact of heredity has been demonstrated through family studies, but also, and mostly, through the study of adopted people and twins. Recently, genome wide association studies (GWAS) allowed the identification of many susceptibility genes for most complex diseases. However, a large part of the heritability is still missing, probably because of insufficient exploration of rare genetic variants and/or epigenetic factors. The ultimate goal of these genetic studies is the definition of an individual risk leading to specific preventive measures (model "predict and prevent"), but this purpose remains very remote for the majority of complex diseases.

  17. Project Dynamics and Emergent Complexity

    CERN Document Server

    Schlick, Christopher M

    2011-01-01

    The present paper presents theoretical and empirical analyses of project dynamics and emergent complexity in new product development (NPD) projects. A model-driven approach was taken and a vector autoregression (VAR) model of cooperative task processing was formulated. The model is explained and validated based on an empirical study carried out in a industrial company. Furthermore, concepts and measures of complex systems science were reviewed and applied to project management. To evaluate emergent complexity in NPD projects, an information-theory quantity -termed "effective measure complexity" (EMC)- was selected, because it can be derived from first principles and therefore has high construct validity. Furthermore, EMC can be calculated efficiently from generative models of task processing or purely from historical data, without intervening models. EMC measures the mutual information between the infinite past and future histories of a stochastic process. According to this principle, it is particularly inter...

  18. Gate complexity using Dynamic Programming

    OpenAIRE

    Sridharan, Srinivas; Gu, Mile; James, Matthew R.

    2008-01-01

    The relationship between efficient quantum gate synthesis and control theory has been a topic of interest in the quantum control literature. Motivated by this work, we describe in the present article how the dynamic programming technique from optimal control may be used for the optimal synthesis of quantum circuits. We demonstrate simulation results on an example system on SU(2), to obtain plots related to the gate complexity and sample paths for different logic gates.

  19. Complex dynamics of epileptic EEG.

    Science.gov (United States)

    Kannathal, N; Puthusserypady, Sadasivan K; Choo Min, Lim

    2004-01-01

    Electroencephalogram (EEG) - the recorded representation of electrical activity of the brain contain useful information about the state of the brain. Recent studies indicate that nonlinear methods can extract valuable information from neuronal dynamics. We compare the dynamical properties of EEG signals of healthy subjects with epileptic subjects using nonlinear time series analysis techniques. Chaotic invariants like correlation dimension (D2) , largest Lyapunov exponent (lambda1), Hurst exponent (H) and Kolmogorov entropy (K) are used to characterize the signal. Our study showed clear differences in dynamical properties of brain electrical activity of the normal and epileptic subjects with a confidence level of more than 90%. Furthermore to support this claim fractal dimension (FD) analysis is performed. The results indicate reduction in value of FD for epileptic EEG indicating reduction in system complexity.

  20. Migraine genetics : from monogenic to complex forms

    NARCIS (Netherlands)

    Vanmolkot, Kaate Raymond Josepha

    2008-01-01

    Migraine has a strong genetic component, but the identification of these factors has proven difficult mainly because of the complex interaction of multiple loci and environmental factors. Unraveling its molecular basis and deciphering pathways leading to migraine attacks will help identifying novel

  1. Migraine genetics : from monogenic to complex forms

    NARCIS (Netherlands)

    Vanmolkot, Kaate Raymond Josepha

    2008-01-01

    Migraine has a strong genetic component, but the identification of these factors has proven difficult mainly because of the complex interaction of multiple loci and environmental factors. Unraveling its molecular basis and deciphering pathways leading to migraine attacks will help identifying novel

  2. Parental and hybrid Daphnia from the D. longispina complex: long-term dynamics in genetic structure and significance of overwintering modes.

    Science.gov (United States)

    Griebel, J; Gießler, S; Yin, M; Wolinska, J

    2016-04-01

    In recent decades, hybridization has become a focus of attention because of its role in evolutionary processes. However, little is known about changes in genetic structure within and between parental species and hybrids over time. Here, we studied processes of genetic change in parental species and hybrids from the Daphnia longispina complex (Crustacea, Cladocera) over a period of six years across ten habitats. These cyclical parthenogens respond to fluctuating environments by switching from asexual to sexual reproduction. Importantly, sexually produced diapausing eggs, which resist extreme conditions such as low temperatures and serve as dispersal stages, are produced to a lower extent by hybrids. Long-term microsatellite data revealed clear differences between hybrids and parental species. In hybrids, clonal diversity values were lower, whereas heterozygosity and linkage disequilibrium values were higher compared to parental species. Clonal diversity of hybrids responded to the strength of the winter, with cold winters resulting in few genotypes in the following spring. In time windows when only asexual hybrid females survive, priority effects will favour the establishment of the hybrid offspring before hatchlings from parental diapause eggs can enter the community. The constant high levels of heterozygosity maintained by clonal reproduction in hybrids might lead to their successful establishment over time, when they are able to escape competition from both parental species. Although we found evidence that hybrids diversity depends on fluctuating environments, a direct link between hybrid abundance and the strength of winter was missing. Because of reduced adaptability in clonally reproducing hybrids, multiple factors must contribute to promoting their long-term success in fluctuating environments.

  3. 解复杂连续函数优化问题的动态量子遗传算法%Complex Continuous Function Optimization Problem of Dynamic Quantum Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    黄山; 覃华; 苏一丹; 冯志新

    2016-01-01

    研究了一种解复杂连续函数优化的动态量子遗传算法(DQGA)。设计一种动态量子旋转角的更新策略及量子门调整策略,以加快算法收敛速度,同时为淘汰适应度差的个体,量子旋转策略表中动态地嵌入了变异算子。在算法进化后期引入灾变算子使算法及时跳出局部最优,避免早熟收敛。五个复杂连续函数的测试实验表明:所提算法对复杂连续函数优化问题的寻优能力较 QGA 更强,算法的稳定性更高,算法的迭代次数亦优于传统量子遗传算法。%A complex continuous function optimization of dynamic quantum genetic algorithm (DQGA ) is studied .A dynamic update strategy of quantum rotation angle and quantum gate adjust strategy is designed to speed up the algorithm convergence speed ,at the same time for the elimination of poor fitness individuals ,the mutation operator dynamically is em-bedded in the quantum rotation strategy table .Introducing the cataclysm operator in the late evolution algorithm makes the algorithm timely and jump out of local optimum ,premature convergence is avoid .Five complex continuous functions of the test results show that the proposed algorithm’s optimization ability for optimization of complex continuous function is stron-ger than QGA ,the stability of the algorithm is higher ,the iteration number of the algorithm is superior to traditional quan-tum genetic algorithm .

  4. An improved genetic algorithm with dynamic topology

    Science.gov (United States)

    Cai, Kai-Quan; Tang, Yan-Wu; Zhang, Xue-Jun; Guan, Xiang-Min

    2016-12-01

    The genetic algorithm (GA) is a nature-inspired evolutionary algorithm to find optima in search space via the interaction of individuals. Recently, researchers demonstrated that the interaction topology plays an important role in information exchange among individuals of evolutionary algorithm. In this paper, we investigate the effect of different network topologies adopted to represent the interaction structures. It is found that GA with a high-density topology ends up more likely with an unsatisfactory solution, contrarily, a low-density topology can impede convergence. Consequently, we propose an improved GA with dynamic topology, named DT-GA, in which the topology structure varies dynamically along with the fitness evolution. Several experiments executed with 15 well-known test functions have illustrated that DT-GA outperforms other test GAs for making a balance of convergence speed and optimum quality. Our work may have implications in the combination of complex networks and computational intelligence. Project supported by the National Natural Science Foundation for Young Scientists of China (Grant No. 61401011), the National Key Technologies R & D Program of China (Grant No. 2015BAG15B01), and the National Natural Science Foundation of China (Grant No. U1533119).

  5. Complex networks: Dynamics and security

    Indian Academy of Sciences (India)

    Ying-Cheng Lai; Adilson Motter; Takashi Nishikawa; Kwangho Park; Liang Zhao

    2005-04-01

    This paper presents a perspective in the study of complex networks by focusing on how dynamics may affect network security under attacks. In particular, we review two related problems: attack-induced cascading breakdown and range-based attacks on links. A cascade in a network means the failure of a substantial fraction of the entire network in a cascading manner, which can be induced by the failure of or attacks on only a few nodes. These have been reported for the internet and for the power grid (e.g., the August 10, 1996 failure of the western United States power grid). We study a mechanism for cascades in complex networks by constructing a model incorporating the flows of information and physical quantities in the network. Using this model we can also show that the cascading phenomenon can be understood as a phase transition in terms of the key parameter characterizing the node capacity. For a parameter value below the phase-transition point, cascading failures can cause the network to disintegrate almost entirely. We will show how to obtain a theoretical estimate for the phase-transition point. The second problem is motivated by the fact that most existing works on the security of complex networks consider attacks on nodes rather than on links. We address attacks on links. Our investigation leads to the finding that many scale-free networks are more sensitive to attacks on short-range than on long-range links. Considering that the small-world phenomenon in complex networks has been identified as being due to the presence of long-range links, i.e., links connecting nodes that would otherwise be separated by a long node-to-node distance, our result, besides its importance concerning network efficiency and security, has the striking implication that the small-world property of scale-free networks is mainly due to short-range links.

  6. Wealth dynamics on complex networks

    Science.gov (United States)

    Garlaschelli, Diego; Loffredo, Maria I.

    2004-07-01

    We study a model of wealth dynamics (Physica A 282 (2000) 536) which mimics transactions among economic agents. The outcomes of the model are shown to depend strongly on the topological properties of the underlying transaction network. The extreme cases of a fully connected and a fully disconnected network yield power-law and log-normal forms of the wealth distribution, respectively. We perform numerical simulations in order to test the model on more complex network topologies. We show that the mixed form of most empirical distributions (displaying a non-smooth transition from a log-normal to a power-law form) can be traced back to a heterogeneous topology with varying link density, which on the other hand is a recently observed property of real networks.

  7. Genome dynamics, genetic complexity and macroevolution Dinámica del genoma, complejidad genética y macroevolución

    Directory of Open Access Journals (Sweden)

    MILTON GALLARDO

    2003-12-01

    Full Text Available Genome data analysis indicates that the major evolutionary transitions have been driven by substantial increases in genomic complexity. These increases, accounting for novelty in evolution, have proceeded mainly by gene duplication. This idea, advanced by Ohno (1968, remains current in the study of several organisms whose genomes have been sequenced. Maize, yeast, and humans contain more paralogons than would be expected to occur by chance, and this supports the contention that gene families were not formed de novo, but by large-scale DNA duplications. Lineage hybridization emerges as an efficient and widespread mechanism to create evolutionary novelty by recruiting redundant genes to new roles. Lateral gene transfer indicates a chimeric composition of prokaryote genomes. This peculiar manner of inheritance blurs the edges of phylogenetic lineages and suggests that the anastomosing and dichotomization of branches play key roles in determining the shape of the tree of life. Adaptive mutations have also enlarged the genetic framework of evolutionary thought by incorporating a new mechanism of gene formation. Moreover, developmental biology has provided solid grounds for understanding organisms as consisting of onto- and epigenetically organized modules. Rapid and drastic changes brought about by the study of developmental genes have discredited the notions that adaptation is achieved exclusively by stepwise allele replacement within populations, and that macroevolutionary change is extrapolated microevolution. Apparently, a broadening, if not a remodeling of the genetic framework in which we understand phylogeny and the evolution of morphological complexity, is emerging through the study of comparative genomicsEl análisis genómico comparado indica que las principales transiciones evolutivas se deben a un aumento de la complejidad genómica. Estos incrementos que dan cuenta de las novedades evolutivas se han originado principalmente por

  8. Theoretical research progress in complexity of complex dynamical networks

    Institute of Scientific and Technical Information of China (English)

    Fang Jinqing

    2007-01-01

    This article reviews the main progress in dynamical complexity of theoretical models for nonlinear complex networks proposed by our Joint Complex Network Research Group (JCNRG). The topological and dynamical properties of these theoretical models are numerically and analytically studied. Several findings are useful for understanding and deeply studying complex networks from macroscopic to microscopic levels and have a potential of applications in real-world networks.

  9. Dynamic Route Guidance Using Improved Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    Zhanke Yu

    2013-01-01

    Full Text Available This paper presents an improved genetic algorithm (IGA for dynamic route guidance algorithm. The proposed IGA design a vicinity crossover technique and a greedy backward mutation technique to increase the population diversity and strengthen local search ability. The steady-state reproduction is introduced to protect the optimized genetic individuals. Furthermore the junction delay is introduced to the fitness function. The simulation results show the effectiveness of the proposed algorithm.

  10. Autism Spectrum Disorder - A Complex Genetic Disorder

    Directory of Open Access Journals (Sweden)

    Ivanov Hristo Y.

    2015-03-01

    Full Text Available Autism spectrum disorder is an entity that reflects a scientific consensus that several previously separated disorders are actually a single spectrum disorder with different levels of symptom severity in two core domains - deficits in social communication and interaction, and restricted repetitive behaviors. Autism spectrum disorder is diagnosed in all racial, ethnic and socioeconomic groups and because of its increased prevalence, reported worldwide through the last years, made it one of the most discussed child psychiatric disorders. In term of aetiology as several other complex diseases, Autism spectrum disorder is considered to have a strong genetic component.

  11. Complex networks for streamflow dynamics

    Directory of Open Access Journals (Sweden)

    B. Sivakumar

    2014-07-01

    Full Text Available Streamflow modeling is an enormously challenging problem, due to the complex and nonlinear interactions between climate inputs and landscape characteristics over a wide range of spatial and temporal scales. A basic idea in streamflow studies is to establish connections that generally exist, but attempts to identify such connections are largely dictated by the problem at hand and the system components in place. While numerous approaches have been proposed in the literature, our understanding of these connections remains far from adequate. The present study introduces the theory of networks, and in particular complex networks, to examine the connections in streamflow dynamics, with a particular focus on spatial connections. Monthly streamflow data observed over a period of 52 years from a large network of 639 monitoring stations in the contiguous United States are studied. The connections in this streamflow network are examined using the concept of clustering coefficient, which is a measure of local density and quantifies the network's tendency to cluster. The clustering coefficient analysis is performed with several different threshold levels, which are based on correlations in streamflow data between the stations. The clustering coefficient values of the 639 stations are used to obtain important information about the connections in the network and their extent, similarity and differences between stations/regions, and the influence of thresholds. The relationship of the clustering coefficient with the number of links/actual links in the network and the number of neighbors is also addressed. The results clearly indicate the usefulness of the network-based approach for examining connections in streamflow, with important implications for interpolation and extrapolation, classification of catchments, and predictions in ungaged basins.

  12. Cognitive dynamics: complexity and creativity

    Energy Technology Data Exchange (ETDEWEB)

    Arecchi, F Tito [Dipartimento di Fisica, Universita di Firenze (Italy); Istituto Nazionale di Ottica Applicata, Florence (Italy)

    2007-05-15

    A scientific problem described within a given code is mapped by a corresponding computational problem. We call (algorithmic) complexity the bit length of the shortest instruction which solves the problem. Deterministic chaos in general affects a dynamical system making the corresponding problem experimentally and computationally heavy, since one must reset the initial conditions at a rate higher than that of information loss (Kolmogorov entropy). One can control chaos by adding to the system new degrees of freedom (information swapping: information lost by chaos is replaced by that arising from the new degrees of freedom). This implies a change of code, or a new augmented model. Within a single code, changing hypotheses is equivalent to fixing different sets of control parameters, each with a different a-priori probability, to be then confirmed and transformed to an a-posteriori probability via Bayes theorem. Sequential application of Bayes rule is nothing else than the Darwinian strategy in evolutionary biology. The sequence is a steepest ascent algorithm, which stops once maximum probability has been reached. At this point the hypothesis exploration stops. By changing code (and hence the set of relevant variables) one can start again to formulate new classes of hypotheses. We call creativity the action of code changing, which is guided by hints not formalized within the previous code, whence not accessible to a computer. We call semantic complexity the number of different scientific codes, or models, that describe a situation. It is however a fuzzy concept, in so far as this number changes due to interaction of the operator with the context. These considerations are illustrated with reference to a cognitive task, starting from synchronization of neuron arrays in a perceptual area and tracing the putative path towards a model building. Since this is a report on work in progress, we skip technicalities in order to stress the gist of the question, and provide

  13. Complex Dynamics of Equatorial Scintillation

    Science.gov (United States)

    Piersanti, Mirko; Materassi, Massimo; Forte, Biagio; Cicone, Antonio

    2017-04-01

    Radio power scintillation, namely highly irregular fluctuations of the power of trans-ionospheric GNSS signals, is the effect of ionospheric plasma turbulence. The scintillation patterns on radio signals crossing the medium inherit the ionospheric turbulence characteristics of inter-scale coupling, local randomness and large time variability. On this basis, the remote sensing of local features of the turbulent plasma is feasible by studying radio scintillation induced by the ionosphere. The distinctive character of intermittent turbulent media depends on the fluctuations on the space- and time-scale statistical properties of the medium. Hence, assessing how the signal fluctuation properties vary under different Helio-Geophysical conditions will help to understand the corresponding dynamics of the turbulent medium crossed by the signal. Data analysis tools, provided by complex system science, appear to be best fitting to study the response of a turbulent medium, as the Earth's equatorial ionosphere, to the non-linear forcing exerted by the Solar Wind (SW). In particular we used the Adaptive Local Iterative Filtering, the Wavelet analysis and the Information theory data analysis tool. We have analysed the radio scintillation and ionospheric fluctuation data at low latitude focusing on the time and space multi-scale variability and on the causal relationship between forcing factors from the SW environment and the ionospheric response.

  14. Minimal model for complex dynamics in cellular processes.

    Science.gov (United States)

    Suguna, C; Chowdhury, K K; Sinha, S

    1999-11-01

    Cellular functions are controlled and coordinated by the complex circuitry of biochemical pathways regulated by genetic and metabolic feedback processes. This paper aims to show, with the help of a minimal model of a regulated biochemical pathway, that the common nonlinearities and control structures present in biomolecular interactions are capable of eliciting a variety of functional dynamics, such as homeostasis, periodic, complex, and chaotic oscillations, including transients, that are observed in various cellular processes.

  15. Complex dynamical invariants for two-dimensional complex potentials

    Indian Academy of Sciences (India)

    J S Virdi; F Chand; C N Kumar; S C Mishra

    2012-08-01

    Complex dynamical invariants are searched out for two-dimensional complex potentials using rationalization method within the framework of an extended complex phase space characterized by $x = x_{1} + ip_{3}. y = x_{2} + ip_{4}, p_{x} = p_{1} + ix_{3}, p_{y} = p_{2} + ix_{4}$. It is found that the cubic oscillator and shifted harmonic oscillator admit quadratic complex invariants. THe obtained invariants may be useful for studying non-Hermitian Hamiltonian systems.

  16. Complex genetic mechanisms in glaucoma: An overview

    Directory of Open Access Journals (Sweden)

    Rao Kollu

    2011-12-01

    Full Text Available Glaucomas comprise a group of hereditary optic neuropathies characterized by progressive and irreversible visual field loss and damage to the optic nerve head. It is a complex disease with multiple molecular mechanisms underlying its pathogenesis. Genetic heterogeneity is the hallmark of all glaucomas and multiple chromosomal loci have been linked to the disease, but only a few genes have been characterized, viz. myocilin (MYOC, optineurin (OPTN, WDR36 and neurotrophin-4 (NTF4 in primary open angle glaucoma (POAG and CYP1B1 and LTBP2 in congenital and developmental glaucomas. Case-control-based association studies on candidate genes involved in different stages of glaucoma pathophysiology have indicated a very limited involvement. The complex mechanisms leading to glaucoma pathogenesis indicate that it could be attributed to multiple genes with varying magnitudes of effect. In this review, we provide an appraisal of the various efforts in unraveling the molecular mystery in glaucoma and also some future directions based on the available scientific knowledge and technological developments.

  17. Complex genetic mechanisms in glaucoma: an overview.

    Science.gov (United States)

    Rao, Kollu N; Nagireddy, Srujana; Chakrabarti, Subhabrata

    2011-01-01

    Glaucomas comprise a group of hereditary optic neuropathies characterized by progressive and irreversible visual field loss and damage to the optic nerve head. It is a complex disease with multiple molecular mechanisms underlying its pathogenesis. Genetic heterogeneity is the hallmark of all glaucomas and multiple chromosomal loci have been linked to the disease, but only a few genes have been characterized, viz. myocilin (MYOC), optineurin (OPTN), WDR36 and neurotrophin-4 (NTF4) in primary open angle glaucoma (POAG) and CYP1B1 and LTBP2 in congenital and developmental glaucomas. Case-control-based association studies on candidate genes involved in different stages of glaucoma pathophysiology have indicated a very limited involvement. The complex mechanisms leading to glaucoma pathogenesis indicate that it could be attributed to multiple genes with varying magnitudes of effect. In this review, we provide an appraisal of the various efforts in unraveling the molecular mystery in glaucoma and also some future directions based on the available scientific knowledge and technological developments.

  18. Team dynamics in complex projects

    NARCIS (Netherlands)

    Oeij, P.; Vroome, E.E.M. de; Dhondt, S.; Gaspersz, J.B.R.

    2012-01-01

    Complexity of projects is hotly debated and a factor which affects innovativeness of team performance. Much attention in the past is paid to technical complexity and many issues are related to natural and physical sciences. A growing awareness of the importance of socioorganisational issues is annou

  19. Team dynamics in complex projects

    NARCIS (Netherlands)

    Oeij, P.; Vroome, E.E.M. de; Dhondt, S.; Gaspersz, J.B.R.

    2012-01-01

    Complexity of projects is hotly debated and a factor which affects innovativeness of team performance. Much attention in the past is paid to technical complexity and many issues are related to natural and physical sciences. A growing awareness of the importance of socioorganisational issues is

  20. Taming Dynamical Complexity and Managing High Technology

    Institute of Scientific and Technical Information of China (English)

    FANGJin-qing; CHENGuan-rong; ZHAOGeng

    2003-01-01

    Variability is one of the most important features of complexity m complex networks anu systems,which usually depends sensitively on small perturbations. Various possible competing behaviours in a system may provide great flexibility in regulating or taming dynamical complexity, through which the designer may be able to better select and manage a desired behaviour for a specific application. In many high-tech fields, how to regulate or manage complexity is a very important but challenge issue.

  1. Symbolic Dynamics and Grammatical Complexity

    Science.gov (United States)

    Hao, Bai-Lin; Zheng, Wei-Mou

    The following sections are included: * Formal Languages and Their Complexity * Formal Language * Chomsky Hierarchy of Grammatical Complexity * The L-System * Regular Language and Finite Automaton * Finite Automaton * Regular Language * Stefan Matrix as Transfer Function for Automaton * Beyond Regular Languages * Feigenbaum and Generalized Feigenbaum Limiting Sets * Even and Odd Fibonacci Sequences * Odd Maximal Primitive Prefixes and Kneading Map * Even Maximal Primitive Prefixes and Distinct Excluded Blocks * Summary of Results

  2. Adaptive learning and complex dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Gomes, Orlando [Escola Superior de Comunicacao Social, Instituto Politecnico de Lisboa, Unidade de Investigacao em Desenvolvimento Empresarial Economics Research Center - UNIDE/ISCTE - ERC, Campus de Benfica do IPL, 1549-014 Lisbon (Portugal)], E-mail: ogomes@escs.ipl.pt

    2009-10-30

    In this paper, we explore the dynamic properties of a group of simple deterministic difference equation systems in which the conventional perfect foresight assumption gives place to a mechanism of adaptive learning. These systems have a common feature: under perfect foresight (or rational expectations) they all possess a unique fixed point steady state. This long-term outcome is obtained also under learning if the quality underlying the learning process is high. Otherwise, when the degree of inefficiency of the learning process is relatively strong, nonlinear dynamics (periodic and a-periodic cycles) arise. The specific properties of each one of the proposed systems is explored both in terms of local and global dynamics. One macroeconomic model is used to illustrate how the formation of expectations through learning may eventually lead to awkward long-term outcomes.

  3. Pinning Synchronization of Switched Complex Dynamical Networks

    Directory of Open Access Journals (Sweden)

    Liming Du

    2015-01-01

    Full Text Available Network topology and node dynamics play a key role in forming synchronization of complex networks. Unfortunately there is no effective synchronization criterion for pinning synchronization of complex dynamical networks with switching topology. In this paper, pinning synchronization of complex dynamical networks with switching topology is studied. Two basic problems are considered: one is pinning synchronization of switched complex networks under arbitrary switching; the other is pinning synchronization of switched complex networks by design of switching when synchronization cannot achieved by using any individual connection topology alone. For the two problems, common Lyapunov function method and single Lyapunov function method are used respectively, some global synchronization criteria are proposed and the designed switching law is given. Finally, simulation results verify the validity of the results.

  4. Controlling edge dynamics in complex networks

    OpenAIRE

    Nepusz, Tamás; Vicsek, Tamás

    2012-01-01

    The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable advances in the description of their structural and dynamical properties. However, much less effort has been devoted to studying the controllability of the dynamics taking place on them. Here we introduce and evaluate a dynamical process defined on the edges ...

  5. Product development projects dynamics and emergent complexity

    CERN Document Server

    Schlick, Christopher

    2016-01-01

    This book primarily explores two topics: the representation of simultaneous, cooperative work processes in product development projects with the help of statistical models, and the assessment of their emergent complexity using a metric from theoretical physics (Effective Measure Complexity, EMC). It is intended to promote more effective management of development projects by shifting the focus from the structural complexity of the product being developed to the dynamic complexity of the development processes involved. The book is divided into four main parts, the first of which provides an introduction to vector autoregression models, periodic vector autoregression models and linear dynamical systems for modeling cooperative work in product development projects. The second part presents theoretical approaches for assessing complexity in the product development environment, while the third highlights and explains closed-form solutions for the complexity metric EMC for vector autoregression models and linear dyn...

  6. Dynamics of complex quantum systems

    CERN Document Server

    Akulin, Vladimir M

    2014-01-01

    This book gathers together a range of similar problems that can be encountered in different fields of modern quantum physics and that have common features with regard to multilevel quantum systems. The main motivation was to examine from a uniform standpoint various models and approaches that have been developed in atomic, molecular, condensed matter, chemical, laser and nuclear physics in various contexts. The book should help senior-level undergraduate, graduate students and researchers putting particular problems in these fields into a broader scientific context and thereby taking advantage of well-established techniques used in adjacent fields. This second edition has been expanded to include substantial new material (e.g. new sections on Dynamic Localization and on Euclidean Random Matrices and new chapters on Entanglement, Open Quantum Systems, and Coherence Protection). It is based on the author’s lectures at the Moscow Institute of Physics and Technology, at the CNRS Aimé Cotton Laboratory, and on ...

  7. Genetics Home Reference: mitochondrial complex III deficiency

    Science.gov (United States)

    ... assembly associated with BCS1L gene mutations in isolated mitochondrial encephalopathy. Hum Mol Genet. 2007 May 15;16(10): ... Munnich A, Rustin P, Rötig A. A mutant mitochondrial respiratory chain ... with tubulopathy, encephalopathy and liver failure. Nat Genet. 2001 Sep;29( ...

  8. Spreading dynamics in complex networks

    CERN Document Server

    Pei, Sen

    2013-01-01

    Searching for influential spreaders in complex networks is an issue of great significance for applications across various domains, ranging from the epidemic control, innovation diffusion, viral marketing, social movement to idea propagation. In this paper, we first display some of the most important theoretical models that describe spreading processes, and then discuss the problem of locating both the individual and multiple influential spreaders respectively. Recent approaches in these two topics are presented. For the identification of privileged single spreaders, we summarize several widely used centralities, such as degree, betweenness centrality, PageRank, k-shell, etc. We investigate the empirical diffusion data in a large scale online social community -- LiveJournal. With this extensive dataset, we find that various measures can convey very distinct information of nodes. Of all the users in LiveJournal social network, only a small fraction of them involve in spreading. For the spreading processes in Li...

  9. Competitive Dynamics on Complex Networks

    CERN Document Server

    Zhao, Jiuhua; Wang, Xiaofan

    2014-01-01

    We consider a dynamical network model in which two competitors have fixed and different states, and each normal agent adjusts its state according to a distributed consensus protocol. The state of each normal agent converges to a steady value which is a convex combination of the competitors' states, and is independent of the initial states of agents. This implies that the competition result is fully determined by the network structure and positions of competitors in the network. We compute an Influence Matrix (IM) in which each element characterizing the influence of an agent on another agent in the network. We use the IM to predict the bias of each normal agent and thus predict which competitor will win. Furthermore, we compare the IM criterion with seven node centrality measures to predict the winner. We find that the competitor with higher Katz Centrality in an undirected network or higher PageRank in a directed network is much more likely to be the winner. These findings may shed new light on the role of n...

  10. Spreading dynamics in complex networks

    Science.gov (United States)

    Pei, Sen; Makse, Hernán A.

    2013-12-01

    Searching for influential spreaders in complex networks is an issue of great significance for applications across various domains, ranging from epidemic control, innovation diffusion, viral marketing, and social movement to idea propagation. In this paper, we first display some of the most important theoretical models that describe spreading processes, and then discuss the problem of locating both the individual and multiple influential spreaders respectively. Recent approaches in these two topics are presented. For the identification of privileged single spreaders, we summarize several widely used centralities, such as degree, betweenness centrality, PageRank, k-shell, etc. We investigate the empirical diffusion data in a large scale online social community—LiveJournal. With this extensive dataset, we find that various measures can convey very distinct information of nodes. Of all the users in the LiveJournal social network, only a small fraction of them are involved in spreading. For the spreading processes in LiveJournal, while degree can locate nodes participating in information diffusion with higher probability, k-shell is more effective in finding nodes with a large influence. Our results should provide useful information for designing efficient spreading strategies in reality.

  11. Ontology of Earth's nonlinear dynamic complex systems

    Science.gov (United States)

    Babaie, Hassan; Davarpanah, Armita

    2017-04-01

    As a complex system, Earth and its major integrated and dynamically interacting subsystems (e.g., hydrosphere, atmosphere) display nonlinear behavior in response to internal and external influences. The Earth Nonlinear Dynamic Complex Systems (ENDCS) ontology formally represents the semantics of the knowledge about the nonlinear system element (agent) behavior, function, and structure, inter-agent and agent-environment feedback loops, and the emergent collective properties of the whole complex system as the result of interaction of the agents with other agents and their environment. It also models nonlinear concepts such as aperiodic, random chaotic behavior, sensitivity to initial conditions, bifurcation of dynamic processes, levels of organization, self-organization, aggregated and isolated functionality, and emergence of collective complex behavior at the system level. By incorporating several existing ontologies, the ENDCS ontology represents the dynamic system variables and the rules of transformation of their state, emergent state, and other features of complex systems such as the trajectories in state (phase) space (attractor and strange attractor), basins of attractions, basin divide (separatrix), fractal dimension, and system's interface to its environment. The ontology also defines different object properties that change the system behavior, function, and structure and trigger instability. ENDCS will help to integrate the data and knowledge related to the five complex subsystems of Earth by annotating common data types, unifying the semantics of shared terminology, and facilitating interoperability among different fields of Earth science.

  12. Synchronization of fractional order complex dynamical networks

    Science.gov (United States)

    Wang, Yu; Li, Tianzeng

    2015-06-01

    In this letter the synchronization of complex dynamical networks with fractional order chaotic nodes is studied. A fractional order controller for synchronization of complex network is presented. Some new sufficient synchronization criteria are proposed based on the Lyapunov stability theory and the LaSalle invariance principle. These synchronization criteria can apply to an arbitrary fractional order complex network in which the coupling-configuration matrix and the inner-coupling matrix are not assumed to be symmetric or irreducible. It means that this method is more general and effective. Numerical simulations of two fractional order complex networks demonstrate the universality and the effectiveness of the proposed method.

  13. Controlling Complex Systems and Developing Dynamic Technology

    Science.gov (United States)

    Avizienis, Audrius Victor

    In complex systems, control and understanding become intertwined. Following Ilya Prigogine, we define complex systems as having control parameters which mediate transitions between distinct modes of dynamical behavior. From this perspective, determining the nature of control parameters and demonstrating the associated dynamical phase transitions are practically equivalent and fundamental to engaging with complexity. In the first part of this work, a control parameter is determined for a non-equilibrium electrochemical system by studying a transition in the morphology of structures produced by an electroless deposition reaction. Specifically, changing the size of copper posts used as the substrate for growing metallic silver structures by the reduction of Ag+ from solution under diffusion-limited reaction conditions causes a dynamical phase transition in the crystal growth process. For Cu posts with edge lengths on the order of one micron, local forces promoting anisotropic growth predominate, and the reaction produces interconnected networks of Ag nanowires. As the post size is increased above 10 microns, the local interfacial growth reaction dynamics couple with the macroscopic diffusion field, leading to spatially propagating instabilities in the electrochemical potential which induce periodic branching during crystal growth, producing dendritic deposits. This result is interesting both as an example of control and understanding in a complex system, and as a useful combination of top-down lithography with bottom-up electrochemical self-assembly. The second part of this work focuses on the technological development of devices fabricated using this non-equilibrium electrochemical process, towards a goal of integrating a complex network as a dynamic functional component in a neuromorphic computing device. Self-assembled networks of silver nanowires were reacted with sulfur to produce interfacial "atomic switches": silver-silver sulfide junctions, which exhibit

  14. Controlling complex Langevin dynamics at finite density

    Energy Technology Data Exchange (ETDEWEB)

    Aarts, Gert; Bongiovanni, Lorenzo [Swansea University, Department of Physics, College of Science, Swansea (United Kingdom); Seiler, Erhard [Max-Planck-Institut fuer Physik (Werner-Heisenberg-Institut), Muenchen (Germany); Sexty, Denes [Universitaet Heidelberg, Institut fuer Theoretische Physik, Heidelberg (Germany); Stamatescu, Ion-Olimpiu [Universitaet Heidelberg, Institut fuer Theoretische Physik, Heidelberg (Germany); FEST, Heidelberg (Germany)

    2013-07-15

    At nonzero chemical potential the numerical sign problem in lattice field theory limits the use of standard algorithms based on importance sampling. Complex Langevin dynamics provides a possible solution, but it has to be applied with care. In this review, we first summarise our current understanding of the approach, combining analytical and numerical insight. In the second part we study SL(N,C) gauge cooling, which was introduced recently as a tool to control complex Langevin dynamics in nonabelian gauge theories. We present new results in Polyakov chain models and in QCD with heavy quarks and compare various adaptive cooling implementations. (orig.)

  15. Testing dynamic stabilisation in complex Langevin simulations

    CERN Document Server

    Attanasio, Felipe

    2016-01-01

    Complex Langevin methods have been successfully applied in theories that suffer from a sign problem such as QCD with a chemical potential. We present and illustrate a novel method (dynamic stabilisation) that ensures that Complex Langevin simulations stay close to the SU(3) manifold, which lead to correct and improved results in the framework of pure Yang-Mills simulations and QCD in the limit of heavy quarks.

  16. Analysis and control of complex dynamical systems robust bifurcation, dynamic attractors, and network complexity

    CERN Document Server

    Imura, Jun-ichi; Ueta, Tetsushi

    2015-01-01

    This book is the first to report on theoretical breakthroughs on control of complex dynamical systems developed by collaborative researchers in the two fields of dynamical systems theory and control theory. As well, its basic point of view is of three kinds of complexity: bifurcation phenomena subject to model uncertainty, complex behavior including periodic/quasi-periodic orbits as well as chaotic orbits, and network complexity emerging from dynamical interactions between subsystems. Analysis and Control of Complex Dynamical Systems offers a valuable resource for mathematicians, physicists, and biophysicists, as well as for researchers in nonlinear science and control engineering, allowing them to develop a better fundamental understanding of the analysis and control synthesis of such complex systems.

  17. Dynamic information routing in complex networks

    Science.gov (United States)

    Kirst, Christoph; Timme, Marc; Battaglia, Demian

    2016-01-01

    Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function. PMID:27067257

  18. Dynamic information routing in complex networks

    Science.gov (United States)

    Kirst, Christoph; Timme, Marc; Battaglia, Demian

    2016-04-01

    Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this mechanism specifically for oscillatory dynamics and analyse how individual unit properties, the network topology and external inputs co-act to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine nonlocal network-wide communication. These results help understanding and designing information routing patterns across systems where collective dynamics co-occurs with a communication function.

  19. The self as a complex dynamic system

    Directory of Open Access Journals (Sweden)

    Sarah Mercer

    2011-04-01

    Full Text Available This article explores the potential offered by complexity theories for understanding language learners’ sense of self and attempts to show how the self might usefully be conceived of as a complex dynamic system. Rather than presenting empirical findings, the article discusses existent research on the self and aims at outlining a conceptual perspective that may inform future studies into the self and possibly other individual learner differences. The article concludes by critically considering the merits of a complexity perspective but also reflecting on the challenges it poses for research.

  20. Controlling complexity : the clinical relevance of mouse complex genetics

    NARCIS (Netherlands)

    Schughart, Klaus; Libert, Claude; Kas, Martien J

    2013-01-01

    Experimental animal models are essential to obtain basic knowledge of the underlying biological mechanisms in human diseases. Here, we review major contributions to biomedical research and discoveries that were obtained in the mouse model by using forward genetics approaches and that provided key in

  1. Worms under stress: unravelling genetic complex traits through perturbation

    NARCIS (Netherlands)

    Rodriguez Sanchez, M.

    2014-01-01

    The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two p

  2. Worms under stress: unravelling genetic complex traits through perturbation

    NARCIS (Netherlands)

    Rodriguez Sanchez, M.

    2014-01-01

    The genetic architecture of an organism could be considered ‘the most amazing piece of engineering’ existing in nature. Looking from a certain distance, the genetic complexity of an organism could be described as an immense jigsaw puzzle. As in a real jigsaw, the connection between two p

  3. Major depression as a complex dynamic system

    NARCIS (Netherlands)

    Cramer, A.O.J.; van Borkulo, C.D.; Giltay, E.J.; van der Maas, H.L.J.; Kendler, K.S.; Scheffer, M.; Borsboom, D.

    2016-01-01

    In this paper, we characterize major depression (MD) as a complex dynamic system in which symptoms (e.g., insomnia and fatigue) are directly connected to one another in a network structure. We hypothesize that individuals can be characterized by their own network with unique architecture and resulti

  4. Improving the Complexity of the Lorenz Dynamics

    Directory of Open Access Journals (Sweden)

    María Pilar Mareca

    2017-01-01

    Full Text Available A new four-dimensional, hyperchaotic dynamic system, based on Lorenz dynamics, is presented. Besides, the most representative dynamics which may be found in this new system are located in the phase space and are analyzed here. The new system is especially designed to improve the complexity of Lorenz dynamics, which, despite being a paradigm to understand the chaotic dissipative flows, is a very simple example and shows great vulnerability when used in secure communications. Here, we demonstrate the vulnerability of the Lorenz system in a general way. The proposed 4D system increases the complexity of the Lorenz dynamics. The trajectories of the novel system include structures going from chaos to hyperchaos and chaotic-transient solutions. The symmetry and the stability of the proposed system are also studied. First return maps, Poincaré sections, and bifurcation diagrams allow characterizing the global system behavior and locating some coexisting structures. Numerical results about the first return maps, Poincaré cross sections, Lyapunov spectrum, and Kaplan-Yorke dimension demonstrate the complexity of the proposed equations.

  5. Optimized dynamical decoupling via genetic algorithms

    Science.gov (United States)

    Quiroz, Gregory; Lidar, Daniel A.

    2013-11-01

    We utilize genetic algorithms aided by simulated annealing to find optimal dynamical decoupling (DD) sequences for a single-qubit system subjected to a general decoherence model under a variety of control pulse conditions. We focus on the case of sequences with equal pulse intervals and perform the optimization with respect to pulse type and order. In this manner, we obtain robust DD sequences, first in the limit of ideal pulses, then when including pulse imperfections such as finite-pulse duration and qubit rotation (flip-angle) errors. Although our optimization is numerical, we identify a deterministic structure that underlies the top-performing sequences. We use this structure to devise DD sequences which outperform previously designed concatenated DD (CDD) and quadratic DD (QDD) sequences in the presence of pulse errors. We explain our findings using time-dependent perturbation theory and provide a detailed scaling analysis of the optimal sequences.

  6. Optimized Dynamical Decoupling via Genetic Algorithms

    CERN Document Server

    Quiroz, Gregory

    2013-01-01

    We utilize genetic algorithms to find optimal dynamical decoupling (DD) sequences for a single-qubit system subjected to a general decoherence model under a variety of control pulse conditions. We focus on the case of sequences with equal pulse-intervals and perform the optimization with respect to pulse type and order. In this manner we obtain robust DD sequences, first in the limit of ideal pulses, then when including pulse imperfections such as finite pulse duration and qubit rotation (flip-angle) errors. Although our optimization is numerical, we identify a deterministic structure underlies the top-performing sequences. We use this structure to devise DD sequences which outperform previously designed concatenated DD (CDD) and quadratic DD (QDD) sequences in the presence of pulse errors. We explain our findings using time-dependent perturbation theory and provide a detailed scaling analysis of the optimal sequences.

  7. Dynamical principles of two-component genetic oscillators.

    Directory of Open Access Journals (Sweden)

    Raúl Guantes

    2006-03-01

    Full Text Available Genetic oscillators based on the interaction of a small set of molecular components have been shown to be involved in the regulation of the cell cycle, the circadian rhythms, or the response of several signaling pathways. Uncovering the functional properties of such oscillators then becomes important for the understanding of these cellular processes and for the characterization of fundamental properties of more complex clocks. Here, we show how the dynamics of a minimal two-component oscillator is drastically affected by its genetic implementation. We consider a repressor and activator element combined in a simple logical motif. While activation is always exerted at the transcriptional level, repression is alternatively operating at the transcriptional (Design I or post-translational (Design II level. These designs display differences on basic oscillatory features and on their behavior with respect to molecular noise or entrainment by periodic signals. In particular, Design I induces oscillations with large activator amplitudes and arbitrarily small frequencies, and acts as an "integrator" of external stimuli, while Design II shows emergence of oscillations with finite, and less variable, frequencies and smaller amplitudes, and detects better frequency-encoded signals ("resonator". Similar types of stimulus response are observed in neurons, and thus this work enables us to connect very different biological contexts. These dynamical principles are relevant for the characterization of the physiological roles of simple oscillator motifs, the understanding of core machineries of complex clocks, and the bio-engineering of synthetic oscillatory circuits.

  8. Coherent Dynamics of Complex Quantum Systems

    CERN Document Server

    Akulin, Vladimir M

    2006-01-01

    A large number of modern problems in physics, chemistry, and quantum electronics require a consideration of population dynamics in complex multilevel quantum systems. The purpose of this book is to provide a systematic treatment of these questions and to present a number of exactly solvable problems. It considers the different dynamical problems frequently encountered in different areas of physics from the same perspective, based mainly on the fundamental ideas of group theory and on the idea of ensemble average. Also treated are concepts of complete quantum control and correction of decoherence induced errors that are complementary to the idea of ensemble average. "Coherent Dynamics of Complex Quantum Systems" is aimed at senior-level undergraduate students in the areas of Atomic, Molecular, and Laser Physics, Physical Chemistry, Quantum Optics and Quantum Informatics. It should help them put particular problems in these fields into a broader scientific context and thereby take advantage of the well-elabora...

  9. Complex and Adaptive Dynamical Systems A Primer

    CERN Document Server

    Gros, Claudius

    2011-01-01

    We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...

  10. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2007-01-01

    We are living in an ever more complex world, an epoch where human actions can accordingly acquire far-reaching potentialities. Complex and adaptive dynamical systems are ubiquitous in the world surrounding us and require us to adapt to new realities and the way of dealing with them. This primer has been developed with the aim of conveying a wide range of "commons-sense" knowledge in the field of quantitative complex system science at an introductory level, providing an entry point to this both fascinating and vitally important subject. The approach is modular and phenomenology driven. Examples of emerging phenomena of generic importance treated in this book are: -- The small world phenomenon in social and scale-free networks. -- Phase transitions and self-organized criticality in adaptive systems. -- Life at the edge of chaos and coevolutionary avalanches resulting from the unfolding of all living. -- The concept of living dynamical systems and emotional diffusive control within cognitive system theory. Techn...

  11. Design tools for complex dynamic security systems.

    Energy Technology Data Exchange (ETDEWEB)

    Byrne, Raymond Harry; Rigdon, James Brian; Rohrer, Brandon Robinson; Laguna, Glenn A.; Robinett, Rush D. III (.; ); Groom, Kenneth Neal; Wilson, David Gerald; Bickerstaff, Robert J.; Harrington, John J.

    2007-01-01

    The development of tools for complex dynamic security systems is not a straight forward engineering task but, rather, a scientific task where discovery of new scientific principles and math is necessary. For years, scientists have observed complex behavior but have had difficulty understanding it. Prominent examples include: insect colony organization, the stock market, molecular interactions, fractals, and emergent behavior. Engineering such systems will be an even greater challenge. This report explores four tools for engineered complex dynamic security systems: Partially Observable Markov Decision Process, Percolation Theory, Graph Theory, and Exergy/Entropy Theory. Additionally, enabling hardware technology for next generation security systems are described: a 100 node wireless sensor network, unmanned ground vehicle and unmanned aerial vehicle.

  12. Genetics Home Reference: tuberous sclerosis complex

    Science.gov (United States)

    ... for School Success (GEMSS) Massachusetts General Hospital Merck Manual Consumer Version My46 Trait Profile Orphanet: Tuberous sclerosis complex Patient Support and Advocacy Resources (4 links) National Organization for Rare Disorders (NORD) Resource List from the ...

  13. Dynamic information routing in complex networks

    CERN Document Server

    Kirst, Christoph; Battaglia, Demian

    2015-01-01

    Flexible information routing fundamentally underlies the function of many biological and artificial networks. Yet, how such systems may specifically communicate and dynamically route information is not well understood. Here we identify a generic mechanism to route information on top of collective dynamical reference states in complex networks. Switching between collective dynamics induces flexible reorganization of information sharing and routing patterns, as quantified by delayed mutual information and transfer entropy measures between activities of a network's units. We demonstrate the power of this generic mechanism specifically for oscillatory dynamics and analyze how individual unit properties, the network topology and external inputs coact to systematically organize information routing. For multi-scale, modular architectures, we resolve routing patterns at all levels. Interestingly, local interventions within one sub-network may remotely determine non-local network-wide communication. These results help...

  14. Controlling edge dynamics in complex networks

    CERN Document Server

    Nepusz, Tamás

    2011-01-01

    The interaction of distinct units in physical, social, biological and technological systems naturally gives rise to complex network structures. Networks have constantly been in the focus of research for the last decade, with considerable advances in the description of their structural and dynamical properties. However, much less effort has been devoted to studying the controllability of the dynamics taking place on them. Here we introduce and evaluate a dynamical process defined on the edges of a network, and demonstrate that the controllability properties of this process significantly differ from simple nodal dynamics. Evaluation of real-world networks indicates that most of them are more controllable than their randomized counterparts. We also find that transcriptional regulatory networks are particularly easy to control. Analytic calculations show that networks with scale-free degree distributions have better controllability properties than uncorrelated networks, and positively correlated in- and out-degre...

  15. Network medicine approaches to the genetics of complex diseases.

    Science.gov (United States)

    Silverman, Edwin K; Loscalzo, Joseph

    2012-08-01

    Complex diseases are caused by perturbations of biological networks. Genetic analysis approaches focused on individual genetic determinants are unlikely to characterize the network architecture of complex diseases comprehensively. Network medicine, which applies systems biology and network science to complex molecular networks underlying human disease, focuses on identifying the interacting genes and proteins which lead to disease pathogenesis. The long biological path between a genetic risk variant and development of a complex disease involves a range of biochemical intermediates, including coding and non-coding RNA, proteins, and metabolites. Transcriptomics, proteomics, metabolomics, and other -omics technologies have the potential to provide insights into complex disease pathogenesis, especially if they are applied within a network biology framework. Most previous efforts to relate genetics to -omics data have focused on a single -omics platform; the next generation of complex disease genetics studies will require integration of multiple types of -omics data sets in a network context. Network medicine may also provide insight into complex disease heterogeneity, serve as the basis for new disease classifications that reflect underlying disease pathogenesis, and guide rational therapeutic and preventive strategies.

  16. Dynamic airspace configuration by genetic algorithm

    Directory of Open Access Journals (Sweden)

    Marina Sergeeva

    2017-06-01

    Full Text Available With the continuous air traffic growth and limits of resources, there is a need for reducing the congestion of the airspace systems. Nowadays, several projects are launched, aimed at modernizing the global air transportation system and air traffic management. In recent years, special interest has been paid to the solution of the dynamic airspace configuration problem. Airspace sector configurations need to be dynamically adjusted to provide maximum efficiency and flexibility in response to changing weather and traffic conditions. The main objective of this work is to automatically adapt the airspace configurations according to the evolution of traffic. In order to reach this objective, the airspace is considered to be divided into predefined 3D airspace blocks which have to be grouped or ungrouped depending on the traffic situation. The airspace structure is represented as a graph and each airspace configuration is created using a graph partitioning technique. We optimize airspace configurations using a genetic algorithm. The developed algorithm generates a sequence of sector configurations for one day of operation with the minimized controller workload. The overall methodology is implemented and successfully tested with air traffic data taken for one day and for several different airspace control areas of Europe.

  17. Genetic diversity in the Paramecium aurelia species complex.

    Science.gov (United States)

    Catania, Francesco; Wurmser, François; Potekhin, Alexey A; Przybos, Ewa; Lynch, Michael

    2009-02-01

    Current understanding of the population genetics of free-living unicellular eukaryotes is limited, and the amount of genetic variability in these organisms is still a matter of debate. We characterized-reproductively and genetically-worldwide samples of multiple Paramecium species belonging to a cryptic species complex, Paramecium aurelia, whose species have been shown to be reproductively isolated. We found that levels of genetic diversity both in the nucleus and in the mitochondrion are substantial within groups of reproductively compatible P. aurelia strains but drop considerably when strains are partitioned according to their phylogenetic groupings. Our study reveals the existence of discrepancies between the mating behavior of a number of P. aurelia strains and their multilocus genetic profile, a controversial finding that has major consequences for both the current methods of species assignment and the species problem in the P. aurelia complex.

  18. Genetic architecture of quantitative traits and complex diseases.

    Science.gov (United States)

    Fu, Wenqing; O'Connor, Timothy D; Akey, Joshua M

    2013-12-01

    More than 150 years after Mendel discovered the laws of heredity, the genetic architecture of phenotypic variation remains elusive. Here, we discuss recent progress in deciphering how genotypes map onto phenotypes, sources of genetic complexity, and how model organisms are illuminating general principles about the relationship between genetic and phenotypic variation. Moreover, we highlight insights gleaned from large-scale sequencing studies in humans, and how this knowledge informs outstanding questions about the genetic architecture of quantitative traits and complex diseases. Finally, we articulate how the confluence of technologies enabling whole-genome sequencing, comprehensive phenotyping, and high-throughput functional assays of polymorphisms will facilitate a more principled and mechanistic understanding of the genetic architecture of phenotypic variation.

  19. Genetic Algorithms in Dynamical Systems Optimisation and Adaptation

    NARCIS (Netherlands)

    Reus, N.M. de; Visser, E.K.; Bruggeman, B.

    1998-01-01

    Both in the design of dynamical systems, ranging from control systems to state estimators as in the adaptation of these systems the use of genetic algorithms is worth studying. This paper presents some approaches for using genetic algorithms in dynamical systems. The layouts and specific uses are di

  20. Genetic code expansion for multiprotein complex engineering.

    Science.gov (United States)

    Koehler, Christine; Sauter, Paul F; Wawryszyn, Mirella; Girona, Gemma Estrada; Gupta, Kapil; Landry, Jonathan J M; Fritz, Markus Hsi-Yang; Radic, Ksenija; Hoffmann, Jan-Erik; Chen, Zhuo A; Zou, Juan; Tan, Piau Siong; Galik, Bence; Junttila, Sini; Stolt-Bergner, Peggy; Pruneri, Giancarlo; Gyenesei, Attila; Schultz, Carsten; Biskup, Moritz Bosse; Besir, Hueseyin; Benes, Vladimir; Rappsilber, Juri; Jechlinger, Martin; Korbel, Jan O; Berger, Imre; Braese, Stefan; Lemke, Edward A

    2016-12-01

    We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, 'MultiBacTAG', (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure-function studies of novel eukaryotic complexes using single-molecule Förster resonance energy transfer as well as site-specific crosslinking strategies.

  1. Dynamics of network motifs in genetic regulatory networks

    Institute of Scientific and Technical Information of China (English)

    Li Ying; Liu Zeng-Rong; Zhang Jian-Bao

    2007-01-01

    Network motifs hold a very important status in genetic regulatory networks. This paper aims to analyse the dynamical property of the network motifs in genetic regulatory networks. The main result we obtained is that the dynamical property of a single motif is very simple with only an asymptotically stable equilibrium point, but the combination of several motifs can make more complicated dynamical properties emerge such as limit cycles. The above-mentioned result shows that network motif is a stable substructure in genetic regulatory networks while their combinations make the genetic regulatory network more complicated.

  2. Genetic algorithms applied to nonlinear and complex domains

    Energy Technology Data Exchange (ETDEWEB)

    Barash, D; Woodin, A E

    1999-06-01

    The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a ''final'' result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means.

  3. Genetic algorithms applied to nonlinear and complex domains

    Energy Technology Data Exchange (ETDEWEB)

    Barash, D; Woodin, A E

    1999-06-01

    The dissertation, titled ''Genetic Algorithms Applied to Nonlinear and Complex Domains'', describes and then applies a new class of powerful search algorithms (GAS) to certain domains. GAS are capable of solving complex and nonlinear problems where many parameters interact to produce a final result such as the optimization of the laser pulse in the interaction of an atom with an intense laser field. GAS can very efficiently locate the global maximum by searching parameter space in problems which are unsuitable for a search using traditional methods. In particular, the dissertation contains new scientific findings in two areas. First, the dissertation examines the interaction of an ultra-intense short laser pulse with atoms. GAS are used to find the optimal frequency for stabilizing atoms in the ionization process. This leads to a new theoretical formulation, to explain what is happening during the ionization process and how the electron is responding to finite (real-life) laser pulse shapes. It is shown that the dynamics of the process can be very sensitive to the ramp of the pulse at high frequencies. The new theory which is formulated, also uses a novel concept (known as the (t,t') method) to numerically solve the time-dependent Schrodinger equation Second, the dissertation also examines the use of GAS in modeling decision making problems. It compares GAS with traditional techniques to solve a class of problems known as Markov Decision Processes. The conclusion of the dissertation should give a clear idea of where GAS are applicable, especially in the physical sciences, in problems which are nonlinear and complex, i.e. difficult to analyze by other means.

  4. Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease.

    Science.gov (United States)

    Moreno-Moral, Aida; Pesce, Francesco; Behmoaras, Jacques; Petretto, Enrico

    2017-01-01

    Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.

  5. Complex Human Dynamics From Mind to Societies

    CERN Document Server

    Winkowska-Nowak, Katarzyna; Brée, David

    2013-01-01

    This book, edited and authored by a closely collaborating network of social scientists and psychologists, recasts typical research topics in these fields into the language of nonlinear, dynamic and complex systems. The aim is to provide scientists with different backgrounds - physics, applied mathematics and computer sciences - with the opportunity to apply the tools of their trade to an altogether new range of possible applications. At the same time, this book will serve as a first reference for a new generation of social scientists and psychologists wishing to familiarize themselves with the new methodology and the "thinking in complexity".

  6. Advances in the genetically-complex autoinflammatory diseases

    Science.gov (United States)

    Ombrello, Michael J.

    2015-01-01

    Monogenic diseases usually demonstrate Mendelian inheritance and are caused by highly penetrant genetic variants of a single gene. In contrast, genetically-complex diseases arise from a combination of multiple genetic and environmental factors. The concept of autoinflammation originally emerged from the identification of individual, activating lesions of the innate immune system as the molecular basis of the hereditary periodic fever syndromes. In addition to these rare, monogenic forms of autoinflammation, genetically-complex autoinflammatory diseases like the periodic fever, aphthous stomatitis, pharyngitis, and cervical adenitis (PFAPA) syndrome, chronic recurrent multifocal osteomyelitis (CRMO), Behçet’s disease, and systemic arthritis also fulfill the definition of autoinflammatory diseases - namely the development of apparently unprovoked episodes of inflammation without identifiable exogenous triggers and in the absence of autoimmunity. Interestingly, investigations of these genetically-complex autoinflammatory diseases have implicated both innate and adaptive immune abnormalities, blurring the line between autoinflammation and autoimmunity. This reinforces the paradigm of concerted innate and adaptive immune dysfunction leading to genetically-complex autoinflammatory phenotypes. PMID:26077134

  7. Markovian Dynamics on Complex Reaction Networks

    CERN Document Server

    Goutsias, John

    2012-01-01

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underling population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions, the computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating...

  8. Nonlinear Dynamics, Chaotic and Complex Systems

    Science.gov (United States)

    Infeld, E.; Zelazny, R.; Galkowski, A.

    2011-04-01

    Part I. Dynamic Systems Bifurcation Theory and Chaos: 1. Chaos in random dynamical systems V. M. Gunldach; 2. Controlling chaos using embedded unstable periodic orbits: the problem of optimal periodic orbits B. R. Hunt and E. Ott; 3. Chaotic tracer dynamics in open hydrodynamical flows G. Karolyi, A. Pentek, T. Tel and Z. Toroczkai; 4. Homoclinic chaos L. P. Shilnikov; Part II. Spatially Extended Systems: 5. Hydrodynamics of relativistic probability flows I. Bialynicki-Birula; 6. Waves in ionic reaction-diffusion-migration systems P. Hasal, V. Nevoral, I. Schreiber, H. Sevcikova, D. Snita, and M. Marek; 7. Anomalous scaling in turbulence: a field theoretical approach V. Lvov and I. Procaccia; 8. Abelian sandpile cellular automata M. Markosova; 9. Transport in an incompletely chaotic magnetic field F. Spineanu; Part III. Dynamical Chaos Quantum Physics and Foundations Of Statistical Mechanics: 10. Non-equilibrium statistical mechanics and ergodic theory L. A. Bunimovich; 11. Pseudochaos in statistical physics B. Chirikov; 12. Foundations of non-equilibrium statistical mechanics J. P. Dougherty; 13. Thermomechanical particle simulations W. G. Hoover, H. A. Posch, C. H. Dellago, O. Kum, C. G. Hoover, A. J. De Groot and B. L. Holian; 14. Quantum dynamics on a Markov background and irreversibility B. Pavlov; 15. Time chaos and the laws of nature I. Prigogine and D. J. Driebe; 16. Evolutionary Q and cognitive systems: dynamic entropies and predictability of evolutionary processes W. Ebeling; 17. Spatiotemporal chaos information processing in neural networks H. Szu; 18. Phase transitions and learning in neural networks C. Van den Broeck; 19. Synthesis of chaos A. Vanecek and S. Celikovsky; 20. Computational complexity of continuous problems H. Wozniakowski; Part IV. Complex Systems As An Interface Between Natural Sciences and Environmental Social and Economic Sciences: 21. Stochastic differential geometry in finance studies V. G. Makhankov; Part V. Conference Banquet

  9. [The application of genetic risk score in genetic studies of complex human diseases].

    Science.gov (United States)

    Dayan, Niu; Weili, Yan

    2015-12-01

    Complex diseases such as cardiovascular disease, type 2 diabetes, essential hypertension, asthma, obesity and cancer have spread across the globe and become the predominant cause of death. There are growing concerns over the role of genetic susceptibility in pathogenesis of complex diseases. However, the related susceptibility genes and sequence variations are still unknown. To elucidate the genetic basis of complex diseases, researchers have identified a large number of genetic variants associated with complex diseases through genome-wide association studies (GWAS) and candidate gene studies recently. The identification of these causal and/or associated variants promotes the development of approaches for complex diseases prediction and prevention. Genetic risk score (GRS), an emerging method for exploring correlation between single nucleotide polymorphisms (SNPs) and clinical phenotypes of complex diseases, integrates weak effects of multiple SNPs and dramatically enhances predictability of complex diseases by gene polymorphisms. This method has been applied successfully in genetic studies of many complex diseases. Here we focus on the introduction of the computational methods and evaluation criteria of GRS, enumerate a series of achievements through GRS application, discuss some limitations during application, and finally prospect the future of GRS.

  10. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2013-01-01

    Complex system theory is rapidly developing and gaining importance, providing tools and concepts central to our modern understanding of emergent phenomena. This primer offers an introduction to this area together with detailed coverage of the mathematics involved. All calculations are presented step by step and are straightforward to follow. This new third edition comes with new material, figures and exercises. Network theory, dynamical systems and information theory, the core of modern complex system sciences, are developed in the first three chapters, covering basic concepts and phenomena like small-world networks, bifurcation theory and information entropy. Further chapters use a modular approach to address the most important concepts in complex system sciences, with the emergence and self-organization playing a central role. Prominent examples are self-organized criticality in adaptive systems, life at the edge of chaos, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase...

  11. Genetic Testing for Complex Diseases: a Simulation Study Perspective

    CERN Document Server

    Vinh, Nguyen Xuan

    2011-01-01

    It is widely recognized nowadays that complex diseases are caused by, amongst the others, multiple genetic factors. The recent advent of genome-wide association study (GWA) has triggered a wave of research aimed at discovering genetic factors underlying common complex diseases. While the number of reported susceptible genetic variants is increasing steadily, the application of such findings into diseases prognosis for the general population is still unclear, and there are doubts about whether the size of the contribution by such factors is significant. In this respect, some recent simulation-based studies have shed more light to the prospect of genetic tests. In this report, we discuss several aspects of simulation-based studies: their parameters, their assumptions, and the information they provide.

  12. Automated design of complex dynamic systems.

    Directory of Open Access Journals (Sweden)

    Michiel Hermans

    Full Text Available Several fields of study are concerned with uniting the concept of computation with that of the design of physical systems. For example, a recent trend in robotics is to design robots in such a way that they require a minimal control effort. Another example is found in the domain of photonics, where recent efforts try to benefit directly from the complex nonlinear dynamics to achieve more efficient signal processing. The underlying goal of these and similar research efforts is to internalize a large part of the necessary computations within the physical system itself by exploiting its inherent non-linear dynamics. This, however, often requires the optimization of large numbers of system parameters, related to both the system's structure as well as its material properties. In addition, many of these parameters are subject to fabrication variability or to variations through time. In this paper we apply a machine learning algorithm to optimize physical dynamic systems. We show that such algorithms, which are normally applied on abstract computational entities, can be extended to the field of differential equations and used to optimize an associated set of parameters which determine their behavior. We show that machine learning training methodologies are highly useful in designing robust systems, and we provide a set of both simple and complex examples using models of physical dynamical systems. Interestingly, the derived optimization method is intimately related to direct collocation a method known in the field of optimal control. Our work suggests that the application domains of both machine learning and optimal control have a largely unexplored overlapping area which envelopes a novel design methodology of smart and highly complex physical systems.

  13. Automated design of complex dynamic systems.

    Science.gov (United States)

    Hermans, Michiel; Schrauwen, Benjamin; Bienstman, Peter; Dambre, Joni

    2014-01-01

    Several fields of study are concerned with uniting the concept of computation with that of the design of physical systems. For example, a recent trend in robotics is to design robots in such a way that they require a minimal control effort. Another example is found in the domain of photonics, where recent efforts try to benefit directly from the complex nonlinear dynamics to achieve more efficient signal processing. The underlying goal of these and similar research efforts is to internalize a large part of the necessary computations within the physical system itself by exploiting its inherent non-linear dynamics. This, however, often requires the optimization of large numbers of system parameters, related to both the system's structure as well as its material properties. In addition, many of these parameters are subject to fabrication variability or to variations through time. In this paper we apply a machine learning algorithm to optimize physical dynamic systems. We show that such algorithms, which are normally applied on abstract computational entities, can be extended to the field of differential equations and used to optimize an associated set of parameters which determine their behavior. We show that machine learning training methodologies are highly useful in designing robust systems, and we provide a set of both simple and complex examples using models of physical dynamical systems. Interestingly, the derived optimization method is intimately related to direct collocation a method known in the field of optimal control. Our work suggests that the application domains of both machine learning and optimal control have a largely unexplored overlapping area which envelopes a novel design methodology of smart and highly complex physical systems.

  14. Genetics of human episodic memory: dealing with complexity.

    Science.gov (United States)

    Papassotiropoulos, Andreas; de Quervain, Dominique J-F

    2011-09-01

    Episodic memory is a polygenic behavioral trait with substantial heritability estimates. Despite its complexity, recent empirical evidence supports the notion that behavioral genetic studies of episodic memory might successfully identify trait-associated molecules and pathways. The development of high-throughput genotyping methods, of elaborated statistical analyses and of phenotypic assessment methods at the neural systems level will facilitate the reliable identification of novel memory-related genes. Importantly, a necessary crosstalk between behavioral genetic studies and investigation of causality by molecular genetic studies will ultimately pave the way towards the identification of biologically important, and hopefully druggable, genes and molecular pathways related to human episodic memory.

  15. The geography of malaria genetics in the Democratic Republic of Congo: A complex and fragmented landscape.

    Science.gov (United States)

    Carrel, Margaret; Patel, Jaymin; Taylor, Steve M; Janko, Mark; Mwandagalirwa, Melchior Kashamuka; Tshefu, Antoinette K; Escalante, Ananias A; McCollum, Andrea; Alam, Md Tauqeer; Udhayakumar, Venkatachalam; Meshnick, Steven; Emch, Michael

    2015-05-01

    Understanding how malaria parasites move between populations is important, particularly given the potential for malaria to be reintroduced into areas where it was previously eliminated. We examine the distribution of malaria genetics across seven sites within the Democratic Republic of Congo (DRC) and two nearby countries, Ghana and Kenya, in order to understand how the relatedness of malaria parasites varies across space, and whether there are barriers to the flow of malaria parasites within the DRC or across borders. Parasite DNA was retrieved from dried blood spots from 7 Demographic and Health Survey sample clusters in the DRC. Malaria genetic characteristics of parasites from Ghana and Kenya were also obtained. For each of 9 geographic sites (7 DRC, 1 Ghana and 1 Kenya), a pair-wise RST statistic was calculated, indicating the genetic distance between malaria parasites found in those locations. Mapping genetics across the spatial extent of the study area indicates a complex genetic landscape, where relatedness between two proximal sites may be relatively high (RST > 0.64) or low (RST < 0.05), and where distal sites also exhibit both high and low genetic similarity. Mantel's tests suggest that malaria genetics differ as geographic distances increase. Principal Coordinate Analysis suggests that genetically related samples are not co-located. Barrier analysis reveals no significant barriers to gene flow between locations. Malaria genetics in the DRC have a complex and fragmented landscape. Limited exchange of genes across space is reflected in greater genetic distance between malaria parasites isolated at greater geographic distances. There is, however, evidence for close genetic ties between distally located sample locations, indicating that movement of malaria parasites and flow of genes is being driven by factors other than distance decay. This research demonstrates the contributions that spatial disease ecology and landscape genetics can make to

  16. Study on Dynamic Information of Animal Genetic Resources in China

    Institute of Scientific and Technical Information of China (English)

    MA Yue-hui; XU Gui-fang; WANG Duan-yun; LIU Hai-liang; YANG Yan

    2003-01-01

    The dynamic information of 331 animal genetic resources in 17 important animal genetic re-source provinces (regions) was analyzed. According to the population inbreeding coefficient, combiningwith the information of population dynamic change trend and cross degree, these genetic resources forthreatened degrees were classified. The results indicated that the population size of 138 breeds had in-creased, 147 breeds had decreased, 3 breeds were constant, 7 breeds (or varieties) were extinct, 9 breeds(or varieties) were critically endangered and needed urgently conserve, 50 breeds (or varieties) were endan-gered and should be conserved. We put forward a conservation and utilization plan for animal genetic re-sources.

  17. Complexity and accountability: the witches' brew of psychiatric genetics.

    Science.gov (United States)

    Arribas-Ayllon, Michael; Bartlett, Andrew; Featherstone, Katie

    2010-08-01

    This paper examines the role of complexity in descriptions of the aetiology of common psychiatric disorders. While scientists attest to the discovery of an underlying reality of complex inheritance--the so-called 'witches' brew' of genetic and non-genetic factors--we argue that 'complexity' also performs rhetorical work. In our analysis of scientific review papers (1999-2008), we find a relatively stable genre of accountability in which descriptions of complexity appear to neutralize past failures by incorporating different and sometimes competing methodological perspectives. We identify two temporal strategies: retrospective accounting, which reconstructs a history of psychiatric genetics that deals with the recent failures, citing earlier twin studies as proof of the heritability of common psychiatric disorders; and prospective accounting, which engages in the careful reconstruction of expectations by balancing methodological limitations with moderated optimism. Together, these strategies produce a simple-to-complex narrative that belies the ambivalent nature of complexity. We show that the rhetorical construction of complexity in scientific review papers is oriented to bridging disciplinary boundaries, marshalling new resources and reconstructing expectations that justify delays in gene discovery and risk prediction.

  18. Markovian dynamics on complex reaction networks

    Energy Technology Data Exchange (ETDEWEB)

    Goutsias, J., E-mail: goutsias@jhu.edu; Jenkinson, G., E-mail: jenkinson@jhu.edu

    2013-08-10

    Complex networks, comprised of individual elements that interact with each other through reaction channels, are ubiquitous across many scientific and engineering disciplines. Examples include biochemical, pharmacokinetic, epidemiological, ecological, social, neural, and multi-agent networks. A common approach to modeling such networks is by a master equation that governs the dynamic evolution of the joint probability mass function of the underlying population process and naturally leads to Markovian dynamics for such process. Due however to the nonlinear nature of most reactions and the large size of the underlying state-spaces, computation and analysis of the resulting stochastic population dynamics is a difficult task. This review article provides a coherent and comprehensive coverage of recently developed approaches and methods to tackle this problem. After reviewing a general framework for modeling Markovian reaction networks and giving specific examples, the authors present numerical and computational techniques capable of evaluating or approximating the solution of the master equation, discuss a recently developed approach for studying the stationary behavior of Markovian reaction networks using a potential energy landscape perspective, and provide an introduction to the emerging theory of thermodynamic analysis of such networks. Three representative problems of opinion formation, transcription regulation, and neural network dynamics are used as illustrative examples.

  19. Functional Maps of Protein Complexes from Quantitative Genetic Interaction Data

    OpenAIRE

    Sourav Bandyopadhyay; Ryan Kelley; Krogan, Nevan J.; Trey Ideker

    2008-01-01

    Recently, a number of advanced screening technologies have allowed for the comprehensive quantification of aggravating and alleviating genetic interactions among gene pairs. In parallel, TAP-MS studies (tandem affinity purification followed by mass spectroscopy) have been successful at identifying physical protein interactions that can indicate proteins participating in the same molecular complex. Here, we propose a method for the joint learning of protein complexes and their functional relat...

  20. Complex and adaptive dynamical systems a primer

    CERN Document Server

    Gros, Claudius

    2015-01-01

    This primer offers readers an introduction to the central concepts that form our modern understanding of complex and emergent behavior, together with detailed coverage of accompanying mathematical methods. All calculations are presented step by step and are easy to follow. This new fourth edition has been fully reorganized and includes new chapters, figures and exercises. The core aspects of modern complex system sciences are presented in the first chapters, covering network theory, dynamical systems, bifurcation and catastrophe theory, chaos and adaptive processes, together with the principle of self-organization in reaction-diffusion systems and social animals. Modern information theoretical principles are treated in further chapters, together with the concept of self-organized criticality, gene regulation networks, hypercycles and coevolutionary avalanches, synchronization phenomena, absorbing phase transitions and the cognitive system approach to the brain. Technical course prerequisites are the standard ...

  1. Simulating the dynamics of complex plasmas

    CERN Document Server

    Schwabe, Mierk

    2014-01-01

    Complex plasmas are low-temperature plasmas that contain micrometer-size particles in addition to the neutral gas particles and the ions and electrons that make up the plasma. The microparticles interact strongly and display a wealth of collective effects. Here we report on linked numerical simulations that reproduce many of the experimental results of complex plasmas. We model a capacitively coupled plasma with a fluid code written for the commercial package comsol. The output of this model is used to calculate forces on microparticles. The microparticles are modeled using the molecular dynamics package lammps, which we extended to include the forces from the plasma. Using this method, we are able to reproduce void formation, the separation of particles of different sizes into layers, lane formation, vortex formation, and other effects.

  2. Complex Dynamics in Information Sharing Networks

    Science.gov (United States)

    Cronin, Bruce

    This study examines the roll-out of an electronic knowledge base in a medium-sized professional services firm over a six year period. The efficiency of such implementation is a key business problem in IT systems of this type. Data from usage logs provides the basis for analysis of the dynamic evolution of social networks around the depository during this time. The adoption pattern follows an "s-curve" and usage exhibits something of a power law distribution, both attributable to network effects, and network position is associated with organisational performance on a number of indicators. But periodicity in usage is evident and the usage distribution displays an exponential cut-off. Further analysis provides some evidence of mathematical complexity in the periodicity. Some implications of complex patterns in social network data for research and management are discussed. The study provides a case study demonstrating the utility of the broad methodological approach.

  3. Enabling complex genetic circuits to respond to extrinsic environmental signals.

    Science.gov (United States)

    Hoynes-O'Connor, Allison; Shopera, Tatenda; Hinman, Kristina; Creamer, John Philip; Moon, Tae Seok

    2017-03-06

    Genetic circuits have the potential to improve a broad range of metabolic engineering processes and address a variety of medical and environmental challenges. However, in order to engineer genetic circuits that can meet the needs of these real-world applications, genetic sensors that respond to relevant extrinsic and intrinsic signals must be implemented in complex genetic circuits. In this work, we construct the first AND and NAND gates that respond to temperature and pH, two signals that have relevance in a variety of real-world applications. A previously identified pH-responsive promoter and a temperature-responsive promoter were extracted from the E. coli genome, characterized, and modified to suit the needs of the genetic circuits. These promoters were combined with components of the type III secretion system in Salmonella typhimurium and used to construct a set of AND gates with up to 23-fold change. Next, an antisense RNA was integrated into the circuit architecture to invert the logic of the AND gate and generate a set of NAND gates with up to 1168-fold change. These circuits provide the first demonstration of complex pH- and temperature-responsive genetic circuits, and lay the groundwork for the use of similar circuits in real-world applications. Biotechnol. Bioeng. 2017;9999: 1-6. © 2017 Wiley Periodicals, Inc.

  4. Genetic and epidemiological aspect of Complex Regional Pain Syndrome

    NARCIS (Netherlands)

    Rooij, Annetje Monique de

    2010-01-01

    Complex Regional Pain Syndrome (CRPS) is a painful disorder affecting one or more extremities. CRPS is characterized by various combinations of sensory, autonomic and motor disturbances. Genetic factors are suggested to play a role in CRPS, but this has not been extensively studied. Therefore the ai

  5. Genetic variability for tuber yield, quality, and virus disease complex ...

    African Journals Online (AJOL)

    Genetic variability for tuber yield, quality, and virus disease complex traits in Uganda ... Silk and Sowola which showed high flowering ability failed to fertilise and set ... Up to five genes may be involved in â-carotene synthesis and probably in ...

  6. Genetic divergence and the genetic architecture of complex traits in chromosome substitution strains of mice

    Directory of Open Access Journals (Sweden)

    Spiezio Sabrina H

    2012-05-01

    Full Text Available Abstract Background The genetic architecture of complex traits strongly influences the consequences of inherited mutations, genetic engineering, environmental and genetic perturbations, and natural and artificial selection. But because most studies are under-powered, the picture of complex traits is often incomplete. Chromosome substitution strains (CSSs are a unique paradigm for these genome surveys because they enable statistically independent, powerful tests for the phenotypic effects of each chromosome on a uniform inbred genetic background. A previous CSS survey in mice and rats revealed many complex trait genes (QTLs, large phenotypic effects, extensive epistasis, as well as systems properties such as strongly directional phenotypic changes and genetically-determined limits on the range of phenotypic variation. However, the unusually close genetic relation between the CSS progenitor strains in that study raised questions about the impact of genetic divergence: would greater divergence between progenitor strains, with the corresponding changes in gene regulation and protein function, lead to significantly more distinctive phenotypic features, or alternatively would epistasis and systems constraints, which are pervasive in CSSs, limit the range of phenotypic variation regardless of the extent of DNA sequence variation? Results We analyzed results for an extensive survey of traits in two new panels of CSSs where the donor strains were derived from inbred strains with more distant origins and discovered a strong similarity in genetic and systems properties among the three CSS panels, regardless of divergence time. Conclusion Our results argue that DNA sequence differences between host and donor strains did not substantially affect the architecture of complex traits, and suggest instead that strong epistasis buffered the phenotypic effects of genetic divergence, thereby constraining the range of phenotypic variation.

  7. Effects of complex life cycles on genetic diversity: cyclical parthenogenesis.

    Science.gov (United States)

    Rouger, R; Reichel, K; Malrieu, F; Masson, J P; Stoeckel, S

    2016-11-01

    Neutral patterns of population genetic diversity in species with complex life cycles are difficult to anticipate. Cyclical parthenogenesis (CP), in which organisms undergo several rounds of clonal reproduction followed by a sexual event, is one such life cycle. Many species, including crop pests (aphids), human parasites (trematodes) or models used in evolutionary science (Daphnia), are cyclical parthenogens. It is therefore crucial to understand the impact of such a life cycle on neutral genetic diversity. In this paper, we describe distributions of genetic diversity under conditions of CP with various clonal phase lengths. Using a Markov chain model of CP for a single locus and individual-based simulations for two loci, our analysis first demonstrates that strong departures from full sexuality are observed after only a few generations of clonality. The convergence towards predictions made under conditions of full clonality during the clonal phase depends on the balance between mutations and genetic drift. Second, the sexual event of CP usually resets the genetic diversity at a single locus towards predictions made under full sexuality. However, this single recombination event is insufficient to reshuffle gametic phases towards full-sexuality predictions. Finally, for similar levels of clonality, CP and acyclic partial clonality (wherein a fixed proportion of individuals are clonally produced within each generation) differentially affect the distribution of genetic diversity. Overall, this work provides solid predictions of neutral genetic diversity that may serve as a null model in detecting the action of common evolutionary or demographic processes in cyclical parthenogens (for example, selection or bottlenecks).

  8. Complex networks repair strategies: Dynamic models

    Science.gov (United States)

    Fu, Chaoqi; Wang, Ying; Gao, Yangjun; Wang, Xiaoyang

    2017-09-01

    Network repair strategies are tactical methods that restore the efficiency of damaged networks; however, unreasonable repair strategies not only waste resources, they are also ineffective for network recovery. Most extant research on network repair focuses on static networks, but results and findings on static networks cannot be applied to evolutionary dynamic networks because, in dynamic models, complex network repair has completely different characteristics. For instance, repaired nodes face more severe challenges, and require strategic repair methods in order to have a significant effect. In this study, we propose the Shell Repair Strategy (SRS) to minimize the risk of secondary node failures due to the cascading effect. Our proposed method includes the identification of a set of vital nodes that have a significant impact on network repair and defense. Our identification of these vital nodes reduces the number of switching nodes that face the risk of secondary failures during the dynamic repair process. This is positively correlated with the size of the average degree and enhances network invulnerability.

  9. The heterogeneous dynamics of economic complexity.

    Directory of Open Access Journals (Sweden)

    Matthieu Cristelli

    Full Text Available What will be the growth of the Gross Domestic Product (GDP or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.

  10. The heterogeneous dynamics of economic complexity.

    Science.gov (United States)

    Cristelli, Matthieu; Tacchella, Andrea; Pietronero, Luciano

    2015-01-01

    What will be the growth of the Gross Domestic Product (GDP) or the competitiveness of China, United States, and Vietnam in the next 3, 5 or 10 years? Despite this kind of questions has a large societal impact and an extreme value for economic policy making, providing a scientific basis for economic predictability is still a very challenging problem. Recent results of a new branch--Economic Complexity--have set the basis for a framework to approach such a challenge and to provide new perspectives to cast economic prediction into the conceptual scheme of forecasting the evolution of a dynamical system as in the case of weather dynamics. We argue that a recently introduced non-monetary metrics for country competitiveness (fitness) allows for quantifying the hidden growth potential of countries by the means of the comparison of this measure for intangible assets with monetary figures, such as GDP per capita. This comparison defines the fitness-income plane where we observe that country dynamics presents strongly heterogeneous patterns of evolution. The flow in some zones is found to be laminar while in others a chaotic behavior is instead observed. These two regimes correspond to very different predictability features for the evolution of countries: in the former regime, we find strong predictable pattern while the latter scenario exhibits a very low predictability. In such a framework, regressions, the usual tool used in economics, are no more the appropriate strategy to deal with such a heterogeneous scenario and new concepts, borrowed from dynamical systems theory, are mandatory. We therefore propose a data-driven method--the selective predictability scheme--in which we adopt a strategy similar to the methods of analogues, firstly introduced by Lorenz, to assess future evolution of countries.

  11. Genetic complexity underlying hybrid male sterility in Drosophila.

    Science.gov (United States)

    Sawamura, Kyoichi; Roote, John; Wu, Chung-I; Yamamoto, Masa-Toshi

    2004-02-01

    Recent genetic analyses of closely related species of Drosophila have indicated that hybrid male sterility is the consequence of highly complex synergistic effects among multiple genes, both conspecific and heterospecific. On the contrary, much evidence suggests the presence of major genes causing hybrid female sterility and inviability in the less-related species, D. melanogaster and D. simulans. Does this contrast reflect the genetic distance between species? Or, generally, is the genetic basis of hybrid male sterility more complex than that of hybrid female sterility and inviability? To clarify this point, the D. simulans introgression of the cytological region 34D-36A to the D. melanogaster genome, which causes recessive male sterility, was dissected by recombination, deficiency, and complementation mapping. The 450-kb region between two genes, Suppressor of Hairless and snail, exhibited a strong effect on the sterility. Males are (semi-)sterile if this region of the introgression is made homozygous or hemizygous. But no genes in the region singly cause the sterility; this region has at least two genes, which in combination result in male sterility. Further, the males are less fertile when heterozygous with a larger introgression, which suggests that dominant modifiers enhance the effects of recessive genes of male sterility. Such an epistatic view, even in the less-related species, suggests that the genetic complexity is special to hybrid male sterility.

  12. Dynamics of swimming bacteria at complex interfaces

    CERN Document Server

    Lopez, Diego

    2014-01-01

    Flagellated bacteria exploiting helical propulsion are known to swim along circular trajectories near surfaces. Fluid dynamics predicts this circular motion to be clockwise (CW) above a rigid surface (when viewed from inside the fluid) and counter-clockwise (CCW) below a free surface. Recent experimental investigations showed that complex physicochemical processes at the nearby surface could lead to a change in the direction of rotation, both at solid surfaces absorbing slip-inducing polymers and interfaces covered with surfactants. Motivated by these results, we use a far-field hydrodynamic model to predict the kinematics of swimming near three types of interfaces: clean fluid-fluid interface, slipping rigid wall, and a fluid interface covered by incompressible surfactants. Representing the helical swimmer by a superposition of hydrodynamic singularities, we first show that in all cases the surfaces reorient the swimmer parallel to the surface and attract it, both of which are a consequence of the Stokes dip...

  13. Major depression as a complex dynamical system

    CERN Document Server

    Cramer, Angélique O J; Giltay, Erik J; van der Maas, Han L J; Kendler, Kenneth S; Scheffer, Marten; Borsboom, Denny

    2016-01-01

    In this paper, we characterize major depression (MD) as a complex dynamical system in which symptoms (e.g., insomnia and fatigue) are directly connected to one another in a network structure. We hypothesize that individuals can be characterized by their own network with unique architecture and resulting dynamics. With respect to architecture, we show that individuals vulnerable to developing MD are those with strong connections between symptoms: e.g., only one night of poor sleep suffices to make a particular person feel tired. Such vulnerable networks, when pushed by forces external to the system such as stress, are more likely to end up in a depressed state; whereas networks with weaker connections tend to remain in or return to a healthy state. We show this with a simulation in which we model the probability of a symptom becoming active as a logistic function of the activity of its neighboring symptoms. Additionally, we show that this model potentially explains some well-known empirical phenomena such as s...

  14. Forest microbiome: diversity, complexity and dynamics.

    Science.gov (United States)

    Baldrian, Petr

    2016-11-16

    Globally, forests represent highly productive ecosystems that act as carbon sinks where soil organic matter is formed from residuals after biomass decomposition as well as from rhizodeposited carbon. Forests exhibit a high level of spatial heterogeneity and the importance of trees, the dominant primary producers, for their structure and functioning. Fungi, bacteria and archaea inhabit various forest habitats: foliage, the wood of living trees, the bark surface, ground vegetation, roots and the rhizosphere, litter, soil, deadwood, rock surfaces, invertebrates, wetlands or the atmosphere, each of which has its own specific features, such as nutrient availability or temporal dynamicy and specific drivers that affect microbial abundance, the level of dominance of bacteria or fungi as well as the composition of their communities. However, several microorganisms, and in particular fungi, inhabit or even connect multiple habitats, and most ecosystem processes affect multiple habitats. Forests are dynamic on a broad temporal scale with processes ranging from short-term events over seasonal ecosystem dynamics to long-term stand development after disturbances such as fires or insect outbreaks. The understanding of these processes can be only achieved by the exploration of the complex 'ecosystem microbiome' and its functioning using focused, integrative microbiological and ecological research performed across multiple habitats.

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

    Institute of Scientific and Technical Information of China (English)

    Shengxiang Yang; Renato Tinós

    2007-01-01

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

  16. Genetically complex epilepsies, copy number variants and syndrome constellations.

    Science.gov (United States)

    Mefford, Heather C; Mulley, John C

    2010-10-05

    Epilepsy is one of the most common neurological disorders, with a prevalence of 1% and lifetime incidence of 3%. There are numerous epilepsy syndromes, most of which are considered to be genetic epilepsies. Despite the discovery of more than 20 genes for epilepsy to date, much of the genetic contribution to epilepsy is not yet known. Copy number variants have been established as an important source of mutation in other complex brain disorders, including intellectual disability, autism and schizophrenia. Recent advances in technology now facilitate genome-wide searches for copy number variants and are beginning to be applied to epilepsy. Here, we discuss what is currently known about the contribution of copy number variants to epilepsy, and how that knowledge is redefining classification of clinical and genetic syndromes.

  17. Systems genetics of complex diseases using RNA-sequencing methods

    DEFF Research Database (Denmark)

    Mazzoni, Gianluca; Kogelman, Lisette; Suravajhala, Prashanth

    2015-01-01

    Next generation sequencing technologies have enabled the generation of huge quantities of biological data, and nowadays extensive datasets at different ‘omics levels have been generated. Systems genetics is a powerful approach that allows to integrate different ‘omics level and understand...... non-coding RNAs (ncRNAs). The integration of transcriptomics data with genomic data in a systems genetics context represents a valuable possibility to go deep into the causal and regulatory mechanisms that generate complex traits and diseases. However RNA-Seq data have to be treated carefully...... principally on merits and demerits of tools for post mapping quality control, normalization, differential expression analysis, gene network analysis, and integration of different omics data in order to generate a comprehensive guideline to systems genetics analysis using RNA-Seq data....

  18. Dynamics of Complex Interconnected Systems: Networks and Bioprocesses

    CERN Document Server

    Skjeltorp, Arne T

    2006-01-01

    The book reviews the synergism between various fields of research that are confronted with networks, such as genetic and metabolic networks, social networks, the Internet and ecological systems. In many cases, the interacting networks manifest so-called emergent properties that are not possessed by any of the individual components. This means that the detailed knowledge of the components is insufficient to describe the whole system. Recent work has indicated that networks in nature have so-called scale-free characteristics, and the associated dynamic network modelling shows unexpected results such as an amazing robustness against accidental failures. Modelling the signal transduction networks in bioprocesses as in living cells is a challenging interdisciplinary research area. It is now realized that the many features of molecular interaction networks within a cell are shared to a large degree by the other complex systems mentioned above, such as the Internet, computer chips and society. Thus knowledge gained ...

  19. Genetic mapping of complex discrete human diseases by discriminant analysis

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    The objective of the present study is to propose and evaluate a novel multivariate approach for genetic mapping of complex categorical diseases. This approach results from an application of standard stepwise discriminant analysis to detect linkage based on the differential marker identity-by-descent (IBD) distributions among the different groups of sib pairs. Two major advantages of this method are that it allows for simultaneously testing all markers, together with other genetic and environmental factors in a single multivariate setting and it avoids explicitly modeling the complex relationship between the affection status of sib pairs and the underlying genetic determinants. The efficiency and properties of the method are demonstrated via simulations. The proposed multivariate approach has successfully located the true position(s) under various genetic scenarios. The more important finding is that using highly densely spaced markers (1~2 cM) leads to only a marginal loss of statistical efficiency of the proposed methods in terms of gene localization and statistical power. These results have well established its utility and advantages as a fine-mapping tool. A unique property of the proposed method is the ability to map multiple linked trait loci to their precise positions due to its sequential nature, as demonstrated via simulations.

  20. Behavioral Genetic Toolkits: Toward the Evolutionary Origins of Complex Phenotypes.

    Science.gov (United States)

    Rittschof, C C; Robinson, G E

    2016-01-01

    The discovery of toolkit genes, which are highly conserved genes that consistently regulate the development of similar morphological phenotypes across diverse species, is one of the most well-known observations in the field of evolutionary developmental biology. Surprisingly, this phenomenon is also relevant for a wide array of behavioral phenotypes, despite the fact that these phenotypes are highly complex and regulated by many genes operating in diverse tissues. In this chapter, we review the use of the toolkit concept in the context of behavior, noting the challenges of comparing behaviors and genes across diverse species, but emphasizing the successes in identifying genetic toolkits for behavior; these successes are largely attributable to the creative research approaches fueled by advances in behavioral genomics. We have two general goals: (1) to acknowledge the groundbreaking progress in this field, which offers new approaches to the difficult but exciting challenge of understanding the evolutionary genetic basis of behaviors, some of the most complex phenotypes known, and (2) to provide a theoretical framework that encompasses the scope of behavioral genetic toolkit studies in order to clearly articulate the research questions relevant to the toolkit concept. We emphasize areas for growth and highlight the emerging approaches that are being used to drive the field forward. Behavioral genetic toolkit research has elevated the use of integrative and comparative approaches in the study of behavior, with potentially broad implications for evolutionary biologists and behavioral ecologists alike.

  1. Intraspecific Genetic dynamics under Climate Change

    DEFF Research Database (Denmark)

    Florez Rodriguez, Alexander

    Climate change has a deep influence on the maintenance and generation of global biodiversity. Past contractions, expansions and shifts in species’ ranges drove to changes in species genetic diversity. Noteworthy, the interaction among: climate change, range, population size and extinction is ofte...

  2. Sex differences in genetic architecture of complex phenotypes?

    Directory of Open Access Journals (Sweden)

    Jacqueline M Vink

    Full Text Available We examined sex differences in familial resemblance for a broad range of behavioral, psychiatric and health related phenotypes (122 complex traits in children and adults. There is a renewed interest in the importance of genotype by sex interaction in, for example, genome-wide association (GWA studies of complex phenotypes. If different genes play a role across sex, GWA studies should consider the effect of genetic variants separately in men and women, which affects statistical power. Twin and family studies offer an opportunity to compare resemblance between opposite-sex family members to the resemblance between same-sex relatives, thereby presenting a test of quantitative and qualitative sex differences in the genetic architecture of complex traits. We analyzed data on lifestyle, personality, psychiatric disorder, health, growth, development and metabolic traits in dizygotic (DZ same-sex and opposite-sex twins, as these siblings are perfectly matched for age and prenatal exposures. Sample size varied from slightly over 300 subjects for measures of brain function such as EEG power to over 30,000 subjects for childhood psychopathology and birth weight. For most phenotypes, sample sizes were large, with an average sample size of 9027 individuals. By testing whether the resemblance in DZ opposite-sex pairs is the same as in DZ same-sex pairs, we obtain evidence for genetic qualitative sex-differences in the genetic architecture of complex traits for 4% of phenotypes. We conclude that for most traits that were examined, the current evidence is that same the genes are operating in men and women.

  3. Advances in dynamic network modeling in complex transportation systems

    CERN Document Server

    Ukkusuri, Satish V

    2013-01-01

    This book focuses on the latest in dynamic network modeling, including route guidance and traffic control in transportation systems and other complex infrastructure networks. Covers dynamic traffic assignment, flow modeling, mobile sensor deployment and more.

  4. The complex genetic basis of congenital hypogonadotropic hypogonadism.

    Science.gov (United States)

    Vezzoli, Valeria; Duminuco, Paolo; Bassi, Ivan; Guizzardi, Fabiana; Persani, Luca; Bonomi, Marco

    2016-06-01

    Congenital hypogonadotropic hypogonadism (CHH) is a rare disease characterized by delayed/absent puberty and infertility due to an inadequate secretion or action of gonadotrophin-releasing hormone (GnRH), with an otherwise structurally and functionally normal hypothalamic-pituitary-gonadal (HPG) axis. CHH is genetically heterogeneous but, due to the infertility of affected individuals, most frequently emerges in a sporadic form, though numerous familial cases have also been registered. In around 50-60% of cases, CHH is associated with a variety of non-reproductive abnormalities, most commonly anosmia/hyposmia, which defines Kallmann Syndrome (KS) by its presence. Broadly-speaking, genetic defects that directly impact on hypothalamic secretion, regulation, or action of GnRH result in a pure neuroendocrine phenotype, normosmic CHH (nCHH), whereas genetic defects that impact of embryonic migration of GnRH neurons to the hypothalamus most commonly result in KS, though nCHH can also arise. Hence, the description of several pedigrees, comprising subjects exhibiting KS and others with nCHH. Although more than 24 genes have been described to be involved in CHH, molecular variants of these do not presently explain more than 35-45% of reported cases. Therefore, numerous other unidentified genes (or conceivably, epigenetic mechanisms) remain to be described to fully understand the pathogenesis of CHH, explaining the emergent idea that CHH is a complex genetic disease characterized by variable expressivity and penetrance. This review summarizes the current state of knowledge on the complex genetic basis of congenital hypogonadotropic hypogonadism and aims to be accessible to both researchers and clinicians.

  5. Complex genetic predisposition in adult and juvenile rheumatoid arthritis

    Directory of Open Access Journals (Sweden)

    Oppermann Joachim

    2004-02-01

    Full Text Available Abstract Background Rheumatoid arthritis (RA and juvenile rheumatoid arthritis (JRA are complex multifactorial diseases caused by environmental influences and an unknown number of predisposing genes. The present study was undertaken in order to investigate association of polymorphisms in candidate genes with RA and JRA in German subjects. Results Up to 200 unrelated German RA and JRA patients each and 300–400 healthy controls have been genotyped for HLA-DRB1, TNFa, TNFA -238a/g, TNFA -308a/g, TNFA -857c/t, TNFR1 -609g/t, TNFR1 P12P, TNFR2 del 15bp, IKBL -332a/g, IKBL -132t/a, IKBL C224R, CTLA4 -318c/t, CTLA4 T17A, PTPRC P57P, MIF -173g/c, the MIF and IFNG microsatellites as well as for D17S795, D17S807, D17S1821 by polyacrylamide gel electrophoresis, single-strand conformation polymorphism analysis, restriction fragment length polymorphism analysis or allele specific hybridization. None of the investigated genetic markers is associated with both, RA and JRA, but there are some statistically significant differences between patients and controls that have to be discussed sensibly. Conclusions The difficulty in investigating the genetics of complex disorders like RA and JRA may arise from genetic heterogeneity in the clinically defined disease cohorts (and generally limited power of such studies. In addition, several to many genes appear to be involved in the genetic predisposition, each of which exerting only small effects. The number of investigated patients has to be increased to establish the possibility of subdivison of the patients according their clinical symptoms, severity of disease, HLA status and other genetic characteristics.

  6. Guiding locomotion in complex dynamic environments

    Directory of Open Access Journals (Sweden)

    Brett R Fajen

    2013-07-01

    Full Text Available Locomotion in complex dynamic environments is an integral part of many daily activities, including walking in crowded spaces, driving on busy roadways, and playing sports. Many of the tasks that humans perform in such environments involve interactions with moving objects -- that is, they require people to coordinate their own movement with the movements of other objects. A widely adopted framework for research on the detection, avoidance, and interception of moving objects is the bearing angle model, according to which observers move so as to keep the bearing angle of the object constant for interception and varying for obstacle avoidance. The bearing angle model offers a simple, parsimonious account of visual control but has several significant limitations and does not easily scale up to more complex tasks. In this paper, I introduce an alternative account of how humans choose actions and guide locomotion in the presence of moving objects. I show how the new approach addresses the limitations of the bearing angle model and accounts for a variety of behaviors involving moving objects, including (1 choosing whether to pass in front of or behind a moving obstacle, (2 perceiving whether a gap between a pair of moving obstacles is passable, (3 avoiding a collision while passing through single or multiple lanes of traffic, (4 coordinating speed and direction of locomotion during interception, (5 simultaneously intercepting a moving target while avoiding a stationary or moving obstacle, and (6 knowing whether to abandon the chase of a moving target. I also summarize data from recent studies that support the new approach.

  7. Impact of the mitochondrial genetic background in complex III deficiency.

    Directory of Open Access Journals (Sweden)

    Mari Carmen Gil Borlado

    Full Text Available BACKGROUND: In recent years clinical evidence has emphasized the importance of the mtDNA genetic background that hosts a primary pathogenic mutation in the clinical expression of mitochondrial disorders, but little experimental confirmation has been provided. We have analyzed the pathogenic role of a novel homoplasmic mutation (m.15533 A>G in the cytochrome b (MT-CYB gene in a patient presenting with lactic acidosis, seizures, mild mental delay, and behaviour abnormalities. METHODOLOGY: Spectrophotometric analyses of the respiratory chain enzyme activities were performed in different tissues, the whole muscle mitochondrial DNA of the patient was sequenced, and the novel mutation was confirmed by PCR-RFLP. Transmitochondrial cybrids were constructed to confirm the pathogenicity of the mutation, and assembly/stability studies were carried out in fibroblasts and cybrids by means of mitochondrial translation inhibition in combination with blue native gel electrophoresis. PRINCIPAL FINDINGS: Biochemical analyses revealed a decrease in respiratory chain complex III activity in patient's skeletal muscle, and a combined enzyme defect of complexes III and IV in fibroblasts. Mutant transmitochondrial cybrids restored normal enzyme activities and steady-state protein levels, the mutation was mildly conserved along evolution, and the proband's mother and maternal aunt, both clinically unaffected, also harboured the homoplasmic mutation. These data suggested a nuclear genetic origin of the disease. However, by forcing the de novo functioning of the OXPHOS system, a severe delay in the biogenesis of the respiratory chain complexes was observed in the mutants, which demonstrated a direct functional effect of the mitochondrial genetic background. CONCLUSIONS: Our results point to possible pitfalls in the detection of pathogenic mitochondrial mutations, and highlight the role of the genetic mtDNA background in the development of mitochondrial disorders.

  8. Complex chloroplast RNA metabolism: just debugging the genetic programme?

    Directory of Open Access Journals (Sweden)

    Schmitz-Linneweber Christian

    2008-08-01

    Full Text Available Abstract Background The gene expression system of chloroplasts is far more complex than that of their cyanobacterial progenitor. This gain in complexity affects in particular RNA metabolism, specifically the transcription and maturation of RNA. Mature chloroplast RNA is generated by a plethora of nuclear-encoded proteins acquired or recruited during plant evolution, comprising additional RNA polymerases and sigma factors, and sequence-specific RNA maturation factors promoting RNA splicing, editing, end formation and translatability. Despite years of intensive research, we still lack a comprehensive explanation for this complexity. Results We inspected the available literature and genome databases for information on components of RNA metabolism in land plant chloroplasts. In particular, new inventions of chloroplast-specific mechanisms and the expansion of some gene/protein families detected in land plants lead us to suggest that the primary function of the additional nuclear-encoded components found in chloroplasts is the transgenomic suppression of point mutations, fixation of which occurred due to an enhanced genetic drift exhibited by chloroplast genomes. We further speculate that a fast evolution of transgenomic suppressors occurred after the water-to-land transition of plants. Conclusion Our inspections indicate that several chloroplast-specific mechanisms evolved in land plants to remedy point mutations that occurred after the water-to-land transition. Thus, the complexity of chloroplast gene expression evolved to guarantee the functionality of chloroplast genetic information and may not, with some exceptions, be involved in regulatory functions.

  9. The Complex Dynamics of Sponsored Search Markets

    Science.gov (United States)

    Robu, Valentin; La Poutré, Han; Bohte, Sander

    This paper provides a comprehensive study of the structure and dynamics of online advertising markets, mostly based on techniques from the emergent discipline of complex systems analysis. First, we look at how the display rank of a URL link influences its click frequency, for both sponsored search and organic search. Second, we study the market structure that emerges from these queries, especially the market share distribution of different advertisers. We show that the sponsored search market is highly concentrated, with less than 5% of all advertisers receiving over 2/3 of the clicks in the market. Furthermore, we show that both the number of ad impressions and the number of clicks follow power law distributions of approximately the same coefficient. However, we find this result does not hold when studying the same distribution of clicks per rank position, which shows considerable variance, most likely due to the way advertisers divide their budget on different keywords. Finally, we turn our attention to how such sponsored search data could be used to provide decision support tools for bidding for combinations of keywords. We provide a method to visualize keywords of interest in graphical form, as well as a method to partition these graphs to obtain desirable subsets of search terms.

  10. Fractional dynamics of globally slow transcription and its impact on deterministic genetic oscillation.

    Science.gov (United States)

    Wei, Kun; Gao, Shilong; Zhong, Suchuan; Ma, Hong

    2012-01-01

    In dynamical systems theory, a system which can be described by differential equations is called a continuous dynamical system. In studies on genetic oscillation, most deterministic models at early stage are usually built on ordinary differential equations (ODE). Therefore, gene transcription which is a vital part in genetic oscillation is presupposed to be a continuous dynamical system by default. However, recent studies argued that discontinuous transcription might be more common than continuous transcription. In this paper, by appending the inserted silent interval lying between two neighboring transcriptional events to the end of the preceding event, we established that the running time for an intact transcriptional event increases and gene transcription thus shows slow dynamics. By globally replacing the original time increment for each state increment by a larger one, we introduced fractional differential equations (FDE) to describe such globally slow transcription. The impact of fractionization on genetic oscillation was then studied in two early stage models--the Goodwin oscillator and the Rössler oscillator. By constructing a "dual memory" oscillator--the fractional delay Goodwin oscillator, we suggested that four general requirements for generating genetic oscillation should be revised to be negative feedback, sufficient nonlinearity, sufficient memory and proper balancing of timescale. The numerical study of the fractional Rössler oscillator implied that the globally slow transcription tends to lower the chance of a coupled or more complex nonlinear genetic oscillatory system behaving chaotically.

  11. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Directory of Open Access Journals (Sweden)

    Daniel Garrido-Sanz

    Full Text Available The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as

  12. Genomic and Genetic Diversity within the Pseudomonas fluorescens Complex.

    Science.gov (United States)

    Garrido-Sanz, Daniel; Meier-Kolthoff, Jan P; Göker, Markus; Martín, Marta; Rivilla, Rafael; Redondo-Nieto, Miguel

    2016-01-01

    The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.

  13. Genetic programming approach to evaluate complexity of texture images

    Science.gov (United States)

    Ciocca, Gianluigi; Corchs, Silvia; Gasparini, Francesca

    2016-11-01

    We adopt genetic programming (GP) to define a measure that can predict complexity perception of texture images. We perform psychophysical experiments on three different datasets to collect data on the perceived complexity. The subjective data are used for training, validation, and test of the proposed measure. These data are also used to evaluate several possible candidate measures of texture complexity related to both low level and high level image features. We select four of them (namely roughness, number of regions, chroma variance, and memorability) to be combined in a GP framework. This approach allows a nonlinear combination of the measures and could give hints on how the related image features interact in complexity perception. The proposed complexity measure M exhibits Pearson correlation coefficients of 0.890 on the training set, 0.728 on the validation set, and 0.724 on the test set. M outperforms each of all the single measures considered. From the statistical analysis of different GP candidate solutions, we found that the roughness measure evaluated on the gray level image is the most dominant one, followed by the memorability, the number of regions, and finally the chroma variance.

  14. Study of the structure and dynamics of complex biological networks

    Science.gov (United States)

    Samal, Areejit

    2008-12-01

    In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large scale metabolic networks inside three organisms, Escherichia coli, Saccharomyces cerevisiae and Staphylococcus aureus. We also study the dynamics of the large scale genetic network controlling E. coli metabolism. We have tried to explain the observed system level dynamical properties of these networks in terms of their underlying structure. Our studies of the system level dynamics of these large scale biological networks provide a different perspective on their functioning compared to that obtained from purely structural studies. Our study also leads to some new insights on features such as robustness, fragility and modularity of these large scale biological networks. We also shed light on how different networks inside the cell such as metabolic networks and genetic networks are interrelated to each other.

  15. Dynamic genetic architecture of metabolic syndrome attributes in the rat.

    Science.gov (United States)

    Seda, Ondrej; Liska, Frantisek; Krenova, Drahomira; Kazdova, Ludmila; Sedova, Lucie; Zima, Tomas; Peng, Junzheng; Pelinkova, Kveta; Tremblay, Johanne; Hamet, Pavel; Kren, Vladimir

    2005-04-14

    The polydactylous rat strain (PD/Cub) is a highly inbred (F > 90) genetic model of metabolic syndrome. The aim of this study was to analyze the genetic architecture of the metabolic derangements found in the PD/Cub strain and to assess its dynamics in time and in response to diet and medication. We derived a PD/Cub x BN/Cub (Brown Norway) F2 intercross population of 149 male rats and performed metabolic profiling and genotyping and multiple levels of genetic linkage and statistical analyses at five different stages of ontogenesis and after high-sucrose diet feeding and dexamethasone administration challenges. The interval mapping analysis of 83 metabolic and morphometric traits revealed over 50 regions genomewide with significant or suggestive linkage to one or more of the traits in the segregating PD/Cub x BN/Cub population. The multiple interval mapping showed that, in addition to "single" quantitative train loci, there are more than 30 pairs of loci across the whole genome significantly influencing the variation of particular traits in an epistatic fashion. This study represents the first whole genome analysis of metabolic syndrome in the PD/Cub model and reveals several new loci previously not connected to the genetics of insulin resistance and dyslipidemia. In addition, it attempts to present the concept of "dynamic genetic architecture" of metabolic syndrome attributes, evidenced by shifts in the genetic determination of syndrome features during ontogenesis and during adaptation to the dietary and pharmacological influences.

  16. Double symbolic joint entropy in nonlinear dynamic complexity analysis

    Science.gov (United States)

    Yao, Wenpo; Wang, Jun

    2017-07-01

    Symbolizations, the base of symbolic dynamic analysis, are classified as global static and local dynamic approaches which are combined by joint entropy in our works for nonlinear dynamic complexity analysis. Two global static methods, symbolic transformations of Wessel N. symbolic entropy and base-scale entropy, and two local ones, namely symbolizations of permutation and differential entropy, constitute four double symbolic joint entropies that have accurate complexity detections in chaotic models, logistic and Henon map series. In nonlinear dynamical analysis of different kinds of heart rate variability, heartbeats of healthy young have higher complexity than those of the healthy elderly, and congestive heart failure (CHF) patients are lowest in heartbeats' joint entropy values. Each individual symbolic entropy is improved by double symbolic joint entropy among which the combination of base-scale and differential symbolizations have best complexity analysis. Test results prove that double symbolic joint entropy is feasible in nonlinear dynamic complexity analysis.

  17. Hamiltonian dynamics for complex food webs.

    Science.gov (United States)

    Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

    2016-03-01

    We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

  18. Universal structural estimator and dynamics approximator for complex networks

    CERN Document Server

    Chen, Yu-Zhong

    2016-01-01

    Revealing the structure and dynamics of complex networked systems from observed data is of fundamental importance to science, engineering, and society. Is it possible to develop a universal, completely data driven framework to decipher the network structure and different types of dynamical processes on complex networks, regardless of their details? We develop a Markov network based model, sparse dynamical Boltzmann machine (SDBM), as a universal network structural estimator and dynamics approximator. The SDBM attains its topology according to that of the original system and is capable of simulating the original dynamical process. We develop a fully automated method based on compressive sensing and machine learning to find the SDBM. We demonstrate, for a large variety of representative dynamical processes on model and real world complex networks, that the equivalent SDBM can recover the network structure of the original system and predicts its dynamical behavior with high precision.

  19. Complex genetic interactions in a quantitative trait locus.

    Directory of Open Access Journals (Sweden)

    Himanshu Sinha

    2006-02-01

    Full Text Available Whether in natural populations or between two unrelated members of a species, most phenotypic variation is quantitative. To analyze such quantitative traits, one must first map the underlying quantitative trait loci. Next, and far more difficult, one must identify the quantitative trait genes (QTGs, characterize QTG interactions, and identify the phenotypically relevant polymorphisms to determine how QTGs contribute to phenotype. In this work, we analyzed three Saccharomyces cerevisiae high-temperature growth (Htg QTGs (MKT1, END3, and RHO2. We observed a high level of genetic interactions among QTGs and strain background. Interestingly, while the MKT1 and END3 coding polymorphisms contribute to phenotype, it is the RHO2 3'UTR polymorphisms that are phenotypically relevant. Reciprocal hemizygosity analysis of the Htg QTGs in hybrids between S288c and ten unrelated S. cerevisiae strains reveals that the contributions of the Htg QTGs are not conserved in nine other hybrids, which has implications for QTG identification by marker-trait association. Our findings demonstrate the variety and complexity of QTG contributions to phenotype, the impact of genetic background, and the value of quantitative genetic studies in S. cerevisiae.

  20. Protein complexes predictions within protein interaction networks using genetic algorithms.

    Science.gov (United States)

    Ramadan, Emad; Naef, Ahmed; Ahmed, Moataz

    2016-07-25

    Protein-protein interaction networks are receiving increased attention due to their importance in understanding life at the cellular level. A major challenge in systems biology is to understand the modular structure of such biological networks. Although clustering techniques have been proposed for clustering protein-protein interaction networks, those techniques suffer from some drawbacks. The application of earlier clustering techniques to protein-protein interaction networks in order to predict protein complexes within the networks does not yield good results due to the small-world and power-law properties of these networks. In this paper, we construct a new clustering algorithm for predicting protein complexes through the use of genetic algorithms. We design an objective function for exclusive clustering and overlapping clustering. We assess the quality of our proposed clustering algorithm using two gold-standard data sets. Our algorithm can identify protein complexes that are significantly enriched in the gold-standard data sets. Furthermore, our method surpasses three competing methods: MCL, ClusterOne, and MCODE in terms of the quality of the predicted complexes. The source code and accompanying examples are freely available at http://faculty.kfupm.edu.sa/ics/eramadan/GACluster.zip .

  1. Contribution of large region joint associations to complex traits genetics.

    Science.gov (United States)

    Paré, Guillaume; Asma, Senay; Deng, Wei Q

    2015-04-01

    A polygenic model of inheritance, whereby hundreds or thousands of weakly associated variants contribute to a trait's heritability, has been proposed to underlie the genetic architecture of complex traits. However, relatively few genetic variants have been positively identified so far and they collectively explain only a small fraction of the predicted heritability. We hypothesized that joint association of multiple weakly associated variants over large chromosomal regions contributes to complex traits variance. Confirmation of such regional associations can help identify new loci and lead to a better understanding of known ones. To test this hypothesis, we first characterized the ability of commonly used genetic association models to identify large region joint associations. Through theoretical derivation and simulation, we showed that multivariate linear models where multiple SNPs are included as independent predictors have the most favorable association profile. Based on these results, we tested for large region association with height in 3,740 European participants from the Health and Retirement Study (HRS) study. Adjusting for SNPs with known association with height, we demonstrated clustering of weak associations (p = 2x10-4) in regions extending up to 433.0 Kb from known height loci. The contribution of regional associations to phenotypic variance was estimated at 0.172 (95% CI 0.063-0.279; p < 0.001), which compared favorably to 0.129 explained by known height variants. Conversely, we showed that suggestively associated regions are enriched for known height loci. To extend our findings to other traits, we also tested BMI, HDLc and CRP for large region associations, with consistent results for CRP. Our results demonstrate the presence of large region joint associations and suggest these can be used to pinpoint weakly associated SNPs.

  2. Imaging complex nutrient dynamics in mycelial networks.

    Science.gov (United States)

    Fricker, M D; Lee, J A; Bebber, D P; Tlalka, M; Hynes, J; Darrah, P R; Watkinson, S C; Boddy, L

    2008-08-01

    Transport networks are vital components of multi-cellular organisms, distributing nutrients and removing waste products. Animal cardiovascular and respiratory systems, and plant vasculature, are branching trees whose architecture is thought to determine universal scaling laws in these organisms. In contrast, the transport systems of many multi-cellular fungi do not fit into this conceptual framework, as they have evolved to explore a patchy environment in search of new resources, rather than ramify through a three-dimensional organism. These fungi grow as a foraging mycelium, formed by the branching and fusion of threadlike hyphae, that gives rise to a complex network. To function efficiently, the mycelial network must both transport nutrients between spatially separated source and sink regions and also maintain its integrity in the face of continuous attack by mycophagous insects or random damage. Here we review the development of novel imaging approaches and software tools that we have used to characterise nutrient transport and network formation in foraging mycelia over a range of spatial scales. On a millimetre scale, we have used a combination of time-lapse confocal imaging and fluorescence recovery after photobleaching to quantify the rate of diffusive transport through the unique vacuole system in individual hyphae. These data then form the basis of a simulation model to predict the impact of such diffusion-based movement on a scale of several millimetres. On a centimetre scale, we have used novel photon-counting scintillation imaging techniques to visualize radiolabel movement in small microcosms. This approach has revealed novel N-transport phenomena, including rapid, preferential N-resource allocation to C-rich sinks, induction of simultaneous bi-directional transport, abrupt switching between different pre-existing transport routes, and a strong pulsatile component to transport in some species. Analysis of the pulsatile transport component using Fourier

  3. Intertidal population genetic dynamics at a microgeographic seascape scale.

    Science.gov (United States)

    Hu, Zi-Min

    2013-06-01

    The intertidal community is among the most physically harsh niches on earth, with highly heterogeneous environmental and biological factors that impose strong habitat selection on population abundance, genetic connectivity and ecological adaptation of organisms in nature. However, most genetic studies to date have concentrated on the influence of basin-wide or regional marine environments (e.g. habitat discontinuities, oceanic currents and fronts, and geographic barriers) on spatiotemporal distribution and composition of intertidal invertebrates having planktonic stages or long-distance dispersal capability. Little is known about sessile marine organisms (e.g. seaweeds) in the context of topographic tidal gradients and reproductive traits at the microgeographic scale. In this issue of Molecular Ecology, Krueger-Hadfield et al. () implemented an elaborate sampling strategy with red seaweed (Chondrus crispus) from a 90-m transect stand near Roscoff and comprehensively detected genome-scale genetic differentiation and biases in ploidy level. This study not only revealed that tidal height resulted in genetic differentiation between high- and low-shore stands and restricted the genetic exchange within the high-shore habitat, but also demonstrated that intergametophytic nonrandom fertilization in C. crispus can cause significant deviation from Hardy-Weinberg equilibrium. Such new genetic insights highlight the importance of microgeographic genetic dynamics and life history characteristics for better understanding the evolutionary processes of speciation and diversification of intertidal marine organisms. © 2013 John Wiley & Sons Ltd.

  4. Spatiotemporal dynamics of distributed synthetic genetic circuits

    Science.gov (United States)

    Kanakov, Oleg; Laptyeva, Tetyana; Tsimring, Lev; Ivanchenko, Mikhail

    2016-04-01

    We propose and study models of two distributed synthetic gene circuits, toggle-switch and oscillator, each split between two cell strains and coupled via quorum-sensing signals. The distributed toggle switch relies on mutual repression of the two strains, and oscillator is comprised of two strains, one of which acts as an activator for another that in turn acts as a repressor. Distributed toggle switch can exhibit mobile fronts, switching the system from the weaker to the stronger spatially homogeneous state. The circuit can also act as a biosensor, with the switching front dynamics determined by the properties of an external signal. Distributed oscillator system displays another biosensor functionality: oscillations emerge once a small amount of one cell strain appears amid the other, present in abundance. Distribution of synthetic gene circuits among multiple strains allows one to reduce crosstalk among different parts of the overall system and also decrease the energetic burden of the synthetic circuit per cell, which may allow for enhanced functionality and viability of engineered cells.

  5. Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations.

    Science.gov (United States)

    Trotter, Meredith V; Weissman, Daniel B; Peterson, Grant I; Peck, Kayla M; Masel, Joanna

    2014-12-01

    The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations.

  6. Dynamical systems examples of complex behaviour

    CERN Document Server

    Jost, Jürgen

    2005-01-01

    Our aim is to introduce, explain, and discuss the fundamental problems, ideas, concepts, results, and methods of the theory of dynamical systems and to show how they can be used in speci?c examples. We do not intend to give a comprehensive overview of the present state of research in the theory of dynamical systems, nor a detailed historical account of its development. We try to explain the important results, often neglecting technical re?nements 1 and, usually, we do not provide proofs. One of the basic questions in studying dynamical systems, i.e. systems that evolve in time, is the construction of invariants that allow us to classify qualitative types of dynamical evolution, to distinguish between qualitatively di?erent dynamics, and to studytransitions between di?erent types. Itis also important to ?nd out when a certain dynamic behavior is stable under small perturbations, as well as to understand the various scenarios of instability. Finally, an essential aspect of a dynamic evolution is the transformat...

  7. Emergence of dynamical complexity related to human heart rate variability

    Science.gov (United States)

    Chang, Mei-Chu; Peng, C.-K.; Stanley, H. Eugene

    2014-12-01

    We apply the refined composite multiscale entropy (MSE) method to a one-dimensional directed small-world network composed of nodes whose states are binary and whose dynamics obey the majority rule. We find that the resulting fluctuating signal becomes dynamically complex. This dynamical complexity is caused (i) by the presence of both short-range connections and long-range shortcuts and (ii) by how well the system can adapt to the noisy environment. By tuning the adaptability of the environment and the long-range shortcuts we can increase or decrease the dynamical complexity, thereby modeling trends found in the MSE of a healthy human heart rate in different physiological states. When the shortcut and adaptability values increase, the complexity in the system dynamics becomes uncorrelated.

  8. Exponential rise of dynamical complexity in quantum computing through projections.

    Science.gov (United States)

    Burgarth, Daniel Klaus; Facchi, Paolo; Giovannetti, Vittorio; Nakazato, Hiromichi; Pascazio, Saverio; Yuasa, Kazuya

    2014-10-10

    The ability of quantum systems to host exponentially complex dynamics has the potential to revolutionize science and technology. Therefore, much effort has been devoted to developing of protocols for computation, communication and metrology, which exploit this scaling, despite formidable technical difficulties. Here we show that the mere frequent observation of a small part of a quantum system can turn its dynamics from a very simple one into an exponentially complex one, capable of universal quantum computation. After discussing examples, we go on to show that this effect is generally to be expected: almost any quantum dynamics becomes universal once 'observed' as outlined above. Conversely, we show that any complex quantum dynamics can be 'purified' into a simpler one in larger dimensions. We conclude by demonstrating that even local noise can lead to an exponentially complex dynamics.

  9. Dynamics in electron transfer protein complexes

    NARCIS (Netherlands)

    Bashir, Qamar

    2010-01-01

    Recent studies have provided experimental evidence for the existence of an encounter complex, a transient intermediate in the formation of protein complexes. We have used paramagnetic relaxation enhancement NMR spectroscopy in combination with Monte Carlo simulations to characterize and visualize th

  10. Tuberous sclerosis complex: genetic basis and management strategies

    Directory of Open Access Journals (Sweden)

    Tsai V

    2012-02-01

    Full Text Available Victoria Tsai, Peter B CrinoPENN Epilepsy Center, PENN Tuberous Sclerosis Clinic, Department of Neurology and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USAAbstract: Tuberous sclerosis complex (TSC is an autosomal dominant genetic disorder that results from mutations in the TSC1 or TSC2 genes. TSC is a multisystem hamartoma syndrome with manifestations in the brain, heart, lungs, kidney, skin, and eyes. Neurologically, TSC patients may exhibit severe epilepsy, cognitive disabilities, and autism spectrum disorders. Many TSC patients also present with renal angiomyolipomas, polycystic kidney disease, skin lesions, and lymphangiomyomatosis. TSC1 and TSC2 proteins form a heterodimeric complex that serves to inhibit mammalian target of rapamycin (mTOR signaling pathway through Ras homolog enriched in brain (Rheb. TSC1 and TSC2 receive activating or inhibitory signals from multiple inputs including growth factors, insulin signaling, energy and amino acid levels, and proinflammatory pathways, which are then integrated to regulate the activity of the mTOR pathway. mTOR signaling plays a critical role in regulating cell growth, transcription, translation, and autophagy. Animal models have shed light on certain features of TSC, but failed to recapitulate the disease completely and currently further research is under way to better understand this devastating disorder. Clinical trials with mTOR inhibitors have shown promising results for some features of TSC, but further research needs to be conducted to establish full indications for therapeutic treatment.Keywords: tuberous sclerosis complex, TSC, TSC1, TSC2

  11. Dynamic Change of Genetic Diversity in Conserved Populations with Different Initial Genetic Architectures

    Institute of Scientific and Technical Information of China (English)

    LU Yun-feng; LI Hong-wei; WU Ke-liang; WU Chang-xin

    2013-01-01

    Maintenance and management of genetic diversity of farm animal genetic resources (AnGR) is very important for biological, socioeconomical and cultural significance. The core concern of conservation for farm AnGR is the retention of genetic diversity of conserved populations in a long-term perspective. However, numerous factors may affect evolution of genetic diversity of a conserved population. Among those factors, the genetic architecture of conserved populations is little considered in current conservation strategies. In this study, we investigated the dynamic changes of genetic diversity of conserved populations with two scenarios on initial genetic architectures by computer simulation in which thirty polymorphic microsatellite loci were chosen to represent genetic architecture of the populations with observed heterozygosity (Ho) and expected heterozygosity (He), observed and mean effective number of alleles (Ao and Ae), number of polymorphic loci (NP) and the percentage of polymorphic loci (PP), number of rare alleles (RA) and number of non-rich polymorphic loci (NRP) as the estimates of genetic diversity. The two scenarios on genetic architecture were taken into account, namely, one conserved population with same allele frequency (AS) and another one with actual allele frequency (AA). The results showed that the magnitude of loss of genetic diversity is associated with genetic architecture of initial conserved population, the amplitude of genetic diversity decline in the context AS was more narrow extent than those in context AA, the ranges of decline of Ho and Ao were about 4 and 2 times in AA compared with that in AS, respectively, the occurrence of first monomorphic locus and the time of change of measure NP in scenario AA is 20 generations and 23 generations earlier than that in scenario AS, respectively. Additionally, we found that NRP, a novel measure proposed by our research group, was a proper estimate for monitoring the evolution of genetic diversity

  12. Genetic modifier screens reveal new components that interact with the Drosophila dystroglycan-dystrophin complex.

    Directory of Open Access Journals (Sweden)

    Mariya M Kucherenko

    Full Text Available The Dystroglycan-Dystrophin (Dg-Dys complex has a capacity to transmit information from the extracellular matrix to the cytoskeleton inside the cell. It is proposed that this interaction is under tight regulation; however the signaling/regulatory components of Dg-Dys complex remain elusive. Understanding the regulation of the complex is critical since defects in this complex cause muscular dystrophy in humans. To reveal new regulators of the Dg-Dys complex, we used a model organism Drosophila melanogaster and performed genetic interaction screens to identify modifiers of Dg and Dys mutants in Drosophila wing veins. These mutant screens revealed that the Dg-Dys complex interacts with genes involved in muscle function and components of Notch, TGF-beta and EGFR signaling pathways. In addition, components of pathways that are required for cellular and/or axonal migration through cytoskeletal regulation, such as Semaphorin-Plexin, Frazzled-Netrin and Slit-Robo pathways show interactions with Dys and/or Dg. These data suggest that the Dg-Dys complex and the other pathways regulating extracellular information transfer to the cytoskeletal dynamics are more intercalated than previously thought.

  13. Dynamical complexity changes during two forms of meditation

    Science.gov (United States)

    Li, Jin; Hu, Jing; Zhang, Yinhong; Zhang, Xiaofeng

    2011-06-01

    Detection of dynamical complexity changes in natural and man-made systems has deep scientific and practical meaning. We use the base-scale entropy method to analyze dynamical complexity changes for heart rate variability (HRV) series during specific traditional forms of Chinese Chi and Kundalini Yoga meditation techniques in healthy young adults. The results show that dynamical complexity decreases in meditation states for two forms of meditation. Meanwhile, we detected changes in probability distribution of m-words during meditation and explained this changes using probability distribution of sine function. The base-scale entropy method may be used on a wider range of physiologic signals.

  14. Chaos and complexity in a simple model of production dynamics

    Directory of Open Access Journals (Sweden)

    I. Katzorke

    2000-01-01

    Full Text Available We consider complex dynamical behavior in a simple model of production dynamics, based on the Wiendahl’s funnel approach. In the case of continuous order flow a model of three parallel funnels reduces to the one-dimensional Bernoulli-type map, and demonstrates strong chaotic properties. The optimization of production costs is possible with the OGY method of chaos control. The dynamics changes drastically in the case of discrete order flow. We discuss different dynamical behaviors, the complexity and the stability of this discrete system.

  15. Dynamics Control of the Complex Systems via Nondifferentiability

    Directory of Open Access Journals (Sweden)

    Carmen Nejneru

    2013-01-01

    Full Text Available A new topic in the analyses of complex systems dynamics, considering that the movements of complex system entities take place on continuum but nondifferentiable curves, is proposed. In this way, some properties of complex systems (barotropic-type behaviour, self-similarity behaviour, chaoticity through turbulence and stochasticization, etc. are controlled through nondifferentiability of motion curves. These behaviours can simulate the standard properties of the complex systems (emergence, self-organization, adaptability, etc..

  16. Dynamics Control of the Complex Systems via Nondifferentiability

    OpenAIRE

    Carmen Nejneru; Anca Nicuţă; Boris Constantin; Liliana Rozemarie Manea; Mirela Teodorescu; Maricel Agop

    2013-01-01

    A new topic in the analyses of complex systems dynamics, considering that the movements of complex system entities take place on continuum but nondifferentiable curves, is proposed. In this way, some properties of complex systems (barotropic-type behaviour, self-similarity behaviour, chaoticity through turbulence and stochasticization, etc.) are controlled through nondifferentiability of motion curves. These behaviours can simulate the standard properties of the complex systems (emergence, se...

  17. Complex phase dynamics in coupled bursters

    DEFF Research Database (Denmark)

    Postnov, D.E.; Sosnovtseva, Olga; Malova, S.Y.;

    2003-01-01

    The phenomenon of phase multistability in the synchronization of two coupled oscillatory systems typically arises when the systems individually display complex wave forms associated, for instance, with the presence of subharmonic components. Alternatively, phase multistability can be caused...

  18. Human copy number variation and complex genetic disease.

    Science.gov (United States)

    Girirajan, Santhosh; Campbell, Catarina D; Eichler, Evan E

    2011-01-01

    Copy number variants (CNVs) play an important role in human disease and population diversity. Advancements in technology have allowed for the analysis of CNVs in thousands of individuals with disease in addition to thousands of controls. These studies have identified rare CNVs associated with neuropsychiatric diseases such as autism, schizophrenia, and intellectual disability. In addition, copy number polymorphisms (CNPs) are present at higher frequencies in the population, show high diversity in copy number, sequence, and structure, and have been associated with multiple phenotypes, primarily related to immune or environmental response. However, the landscape of copy number variation still remains largely unexplored, especially for smaller CNVs and those embedded within complex regions of the human genome. An integrated approach including characterization of single nucleotide variants and CNVs in a large number of individuals with disease and normal genomes holds the promise of thoroughly elucidating the genetic basis of human disease and diversity.

  19. Complexity and dynamics of topological and community structure in complex networks

    Science.gov (United States)

    Berec, Vesna

    2017-07-01

    Complexity is highly susceptible to variations in the network dynamics, reflected on its underlying architecture where topological organization of cohesive subsets into clusters, system's modular structure and resulting hierarchical patterns, are cross-linked with functional dynamics of the system. Here we study connection between hierarchical topological scales of the simplicial complexes and the organization of functional clusters - communities in complex networks. The analysis reveals the full dynamics of different combinatorial structures of q-th-dimensional simplicial complexes and their Laplacian spectra, presenting spectral properties of resulting symmetric and positive semidefinite matrices. The emergence of system's collective behavior from inhomogeneous statistical distribution is induced by hierarchically ordered topological structure, which is mapped to simplicial complex where local interactions between the nodes clustered into subcomplexes generate flow of information that characterizes complexity and dynamics of the full system.

  20. Genetics of personalities: no simple answers for complex traits.

    Science.gov (United States)

    Tschirren, Barbara; Bensch, Staffan

    2010-02-01

    Identifying the genes that underlie phenotypic variation in natural populations, and assessing the consequences of polymorphisms at these loci for individual fitness are major objectives in evolutionary biology. Yet, with the exception of a few success stories, little progress has been made, and our understanding of the link between genotype and phenotype is still in its infancy. For example, although body length in humans is largely genetically determined, with heritability estimates greater than 0.8, massive genome-wide association studies (GWAS) have only been able to account for a very small proportion of this variation (Gudbjartsson et al. 2008). If it is so difficult to explain the genetics behind relatively 'simple' traits, can we envision that it will at all be possible to find genes underlying complex behavioural traits in wild non-model organisms? Some notable examples suggest that this can indeed be a worthwhile endeavour. Recently, the circadian rhythm gene Clock has been associated with timing of breeding in a wild blue tit population (Johnsen et al. 2007; Liedvogel et al. 2009) and the Pgi gene to variation in dispersal and flight endurance in Glanville fritillary butterflies (Niitepold et al. 2009). A promising candidate gene for influencing complex animal personality traits, also known as behavioural syndromes (Sih et al. 2004), is the dopamine receptor D4 (DRD4) gene. Within the last decade, polymorphisms in this gene have been associated with variation in novelty seeking and exploration behaviour in a range of species, from humans to great tits (Schinka et al. 2002; Fidler et al. 2007). In this issue, Korsten et al. (2010) attempt to replicate this previously observed association in wild-living birds, and test for the generality of the association between DRD4 and personality across a number of European great tit populations.

  1. The dynamics of hybrid metabolic-genetic oscillators

    Science.gov (United States)

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

    2013-03-01

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

  2. On Natural Genetic Engineering: Structural Dynamism in Random Boolean Networks

    CERN Document Server

    Bull, Larry

    2012-01-01

    This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include changes in node connectivity based upon the current cell state, e.g., via transposable elements. The underlying behaviour of the resulting dynamical networks is investigated before their evolvability is explored using a version of the NK model of fitness landscapes. Structural dynamism is found to be selected for in non-stationary environments and subsequently shown capable of providing a mechanism for evolutionary innovation when such reorganizations are inherited.

  3. Applications of Nonlinear Dynamics Model and Design of Complex Systems

    CERN Document Server

    In, Visarath; Palacios, Antonio

    2009-01-01

    This edited book is aimed at interdisciplinary, device-oriented, applications of nonlinear science theory and methods in complex systems. In particular, applications directed to nonlinear phenomena with space and time characteristics. Examples include: complex networks of magnetic sensor systems, coupled nano-mechanical oscillators, nano-detectors, microscale devices, stochastic resonance in multi-dimensional chaotic systems, biosensors, and stochastic signal quantization. "applications of nonlinear dynamics: model and design of complex systems" brings together the work of scientists and engineers that are applying ideas and methods from nonlinear dynamics to design and fabricate complex systems.

  4. Nonlinear Dynamics of the Perceived Pitch of Complex Sounds

    CERN Document Server

    Cartwright, J H E; Piro, O; Cartwright, Julyan H. E.; Gonzalez, Diego L.; Piro, Oreste

    1999-01-01

    We apply results from nonlinear dynamics to an old problem in acoustical physics: the mechanism of the perception of the pitch of sounds, especially the sounds known as complex tones that are important for music and speech intelligibility.

  5. Topology identification of complex dynamical networks

    Science.gov (United States)

    Zhao, Junchan; Li, Qin; Lu, Jun-An; Jiang, Zhong-Ping

    2010-06-01

    Recently, some researchers investigated the topology identification for complex networks via LaSalle's invariance principle. The principle cannot be directly applied to time-varying systems since the positive limit sets are generally not invariant. In this paper, we study the topology identification problem for a class of weighted complex networks with time-varying node systems. Adaptive identification laws are proposed to estimate the coupling parameters of the networks with and without communication delays. We prove that the asymptotic identification is ensured by a persistently exciting condition. Numerical simulations are given to demonstrate the effectiveness of the proposed approach.

  6. Using Genetic Algorithms for Navigation Planning in Dynamic Environments

    Directory of Open Access Journals (Sweden)

    Ferhat Uçan

    2012-01-01

    Full Text Available Navigation planning can be considered as a combination of searching and executing the most convenient flight path from an initial waypoint to a destination waypoint. Generally the aim is to follow the flight path, which provides minimum fuel consumption for the air vehicle. For dynamic environments, constraints change dynamically during flight. This is a special case of dynamic path planning. As the main concern of this paper is flight planning, the conditions and objectives that are most probable to be used in navigation problem are considered. In this paper, the genetic algorithm solution of the dynamic flight planning problem is explained. The evolutionary dynamic navigation planning algorithm is developed for compensating the existing deficiencies of the other approaches. The existing fully dynamic algorithms process unit changes to topology one modification at a time, but when there are several such operations occurring in the environment simultaneously, the algorithms are quite inefficient. The proposed algorithm may respond to the concurrent constraint updates in a shorter time for dynamic environment. The most secure navigation of the air vehicle is planned and executed so that the fuel consumption is minimum.

  7. Parameters in dynamic models of complex traits are containers of missing heritability.

    Directory of Open Access Journals (Sweden)

    Yunpeng Wang

    Full Text Available Polymorphisms identified in genome-wide association studies of human traits rarely explain more than a small proportion of the heritable variation, and improving this situation within the current paradigm appears daunting. Given a well-validated dynamic model of a complex physiological trait, a substantial part of the underlying genetic variation must manifest as variation in model parameters. These parameters are themselves phenotypic traits. By linking whole-cell phenotypic variation to genetic variation in a computational model of a single heart cell, incorporating genotype-to-parameter maps, we show that genome-wide association studies on parameters reveal much more genetic variation than when using higher-level cellular phenotypes. The results suggest that letting such studies be guided by computational physiology may facilitate a causal understanding of the genotype-to-phenotype map of complex traits, with strong implications for the development of phenomics technology.

  8. Genetics of tuberous sclerosis complex: implications for clinical practice

    Directory of Open Access Journals (Sweden)

    Caban C

    2016-12-01

    Full Text Available Carolina Caban,1,2 Nubaira Khan,1,2 Daphne M Hasbani,3 Peter B Crino1,2 1Department of Neurology, 2Shriners Hospitals Pediatric Research Center, Temple University School of Medicine, 3Department of Neurology, St. Christopher’s Hospital for Children, Drexel University College of Medicine, Philadelphia, PA, USA Abstract: Tuberous sclerosis complex (TSC is a multisystem disorder that results from heterozygous mutations in either TSC1 or TSC2. The primary organ systems that are affected include the brain, skin, lung, kidney, and heart, all with variable frequency, penetrance, and severity. Neurological features include epilepsy, autism, and intellectual disability. There are more than 1,500 known pathogenic variants for TSC1 and TSC2, including deletion, nonsense, and missense mutations, and all pathogenic mutations are inactivating, leading to loss of function effects on the encoded proteins TSC1 and TSC2. These proteins form a complex to constitutively inhibit mechanistic target of rapamycin (mTOR signaling cascade, and as a consequence, mTOR signaling is constitutively active within all TSC-associated lesions. The mTOR inhibitors rapamycin (sirolimus and everolimus have been shown to reduce the size of renal and brain lesions and improve pulmonary function in TSC, and these compounds may also decrease seizure frequency. The clinical application of mTOR inhibitors in TSC has provided one of the first examples of precision medicine in a neurodevelopmental disorder. Keywords: TSC, epilepsy, genetics, mTOR, rapamycin

  9. Critical dynamics in genetic regulatory networks: examples from four kingdoms.

    Science.gov (United States)

    Balleza, Enrique; Alvarez-Buylla, Elena R; Chaos, Alvaro; Kauffman, Stuart; Shmulevich, Ilya; Aldana, Maximino

    2008-06-18

    The coordinated expression of the different genes in an organism is essential to sustain functionality under the random external perturbations to which the organism might be subjected. To cope with such external variability, the global dynamics of the genetic network must possess two central properties. (a) It must be robust enough as to guarantee stability under a broad range of external conditions, and (b) it must be flexible enough to recognize and integrate specific external signals that may help the organism to change and adapt to different environments. This compromise between robustness and adaptability has been observed in dynamical systems operating at the brink of a phase transition between order and chaos. Such systems are termed critical. Thus, criticality, a precise, measurable, and well characterized property of dynamical systems, makes it possible for robustness and adaptability to coexist in living organisms. In this work we investigate the dynamical properties of the gene transcription networks reported for S. cerevisiae, E. coli, and B. subtilis, as well as the network of segment polarity genes of D. melanogaster, and the network of flower development of A. thaliana. We use hundreds of microarray experiments to infer the nature of the regulatory interactions among genes, and implement these data into the Boolean models of the genetic networks. Our results show that, to the best of the current experimental data available, the five networks under study indeed operate close to criticality. The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us.

  10. Complex systems and networks dynamics, controls and applications

    CERN Document Server

    Yu, Xinghuo; Chen, Guanrong; Yu, Wenwu

    2016-01-01

    This elementary book provides some state-of-the-art research results on broad disciplinary sciences on complex networks. It presents an in-depth study with detailed description of dynamics, controls and applications of complex networks. The contents of this book can be summarized as follows. First, the dynamics of complex networks, for example, the cluster dynamic analysis by using kernel spectral methods, community detection algorithms in bipartite networks, epidemiological modeling with demographics and epidemic spreading on multi-layer networks, are studied. Second, the controls of complex networks are investigated including topics like distributed finite-time cooperative control of multi-agent systems by applying homogenous-degree and Lyapunov methods, composite finite-time containment control for disturbed second-order multi-agent systems, fractional-order observer design of multi-agent systems, chaos control and anticontrol of complex systems via Parrondos game and many more. Third, the applications of ...

  11. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations

    Science.gov (United States)

    Montinaro, Francesco; Busby, George B. J.; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L.; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. PMID:27838627

  12. Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations.

    Science.gov (United States)

    Montinaro, Francesco; Busby, George B J; Gonzalez-Santos, Miguel; Oosthuitzen, Ockie; Oosthuitzen, Erika; Anagnostou, Paolo; Destro-Bisol, Giovanni; Pascali, Vincenzo L; Capelli, Cristian

    2017-01-01

    The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries. Copyright © 2017 Montinaro et al.

  13. Dynamics of Complex Fluid-Fluid Interfaces

    NARCIS (Netherlands)

    Sagis, L.M.C.

    2016-01-01

    This chapter presents an overview of recent progress in modelling the behaviour of complex fluid–fluid interfaces with non-equilibrium thermodynamics. We will limit ourselves to frameworks employing the Gibbs dividing surface model, and start with a general discussion of the surface excess variables

  14. Complex phase dynamics in coupled bursters

    DEFF Research Database (Denmark)

    Postnov, D E; Sosnovtseva, Olga; Malova, S Y

    2003-01-01

    The phenomenon of phase multistability in the synchronization of two coupled oscillatory systems typically arises when the systems individually display complex wave forms associated, for instance, with the presence of subharmonic components. Alternatively, phase multistability can be caused...... the number of spikes per train and the proximity of a neighboring equilibrium point can influence the formation of coexisting regimes....

  15. Complex dynamics in supervised work groups

    Science.gov (United States)

    Dal Forno, Arianna; Merlone, Ugo

    2013-07-01

    In supervised work groups many factors concur to determine productivity. Some of them may be economical and some psychological. According to the literature, the heterogeneity in terms of individual capacity seems to be one of the principal causes for chaotic dynamics in a work group. May sorting groups of people with same capacity for effort be a solution? In the organizational psychology literature an important factor is the engagement in the task, while expectations are central in the economics literature. Therefore, we propose a dynamical model which takes into account both engagement in the task and expectations. An important lesson emerges. The intolerance deriving from the exposure to inequity may not be only caused by differences in individual capacities, but also by these factors combined. Consequently, solutions have to be found in this new direction.

  16. Ferrofluids, complex particle dynamics and braid description

    Energy Technology Data Exchange (ETDEWEB)

    Skjeltorp, A.T. E-mail: arne.skjeltorp@ife.no; Clausen, Sigmund; Helgesen, Geir

    2001-05-01

    Finely divided magnetic matter is important in many areas of science and technology. A special sub-class of systems are made up of freely moving particles suspended in a carrier liquid where the magnetic interactions play an important role in the actual structure formation and dynamical behaviour. These include ferrofluids, which are colloids of magnetic particles dispersed in carrier fluids, magnetic micro-beads, which are micrometer sized plastic beads loaded with iron oxide, and nonmagnetic particles dispersed in ferrofluids, forming the so-called 'magnetic holes'. How, in a simple and forceful way, is it possible to characterise the dynamics of systems with several moving components like dispersed magnetic particles subjected to external magnetic fields? The methods based on the theory of braids may provide the answer. Braid theory is a sub-field of mathematics known as topology. It involves classifying different ways of tracing curves in space. The topological description of braids thus provides a simple and concise language for describing the dynamics of a system of moving particles as if they perform a complicated dance as they move about one another, and the braid encodes the choreography of this dance.

  17. Genetic and logic networks with the signal-inhibitor-activator structure are dynamically robust

    Institute of Scientific and Technical Information of China (English)

    LI Fangting; TAN Ning

    2006-01-01

    The proteins, DNA and RNA interaction networks govern various biological functions in living cells, these networks should be dynamically robust in the intracellular and environmental fluctuations. Here, we use Boolean network to study the robust structure of both genetic and logic networks. First, SOS network in bacteria E. coli, which regulates cell survival and repair after DNA damage, is shown to be dynamically robust. Comparing with cell cycle network in budding yeast and flagella network in E. coli, we find the signal-inhibitor-activator (SIA) structure in transcription regulatory networks. Second, under the dynamical rule that inhibition is much stronger than activation, we have searched 3-node non-self-loop logical networks that are dynamically robust, and that if the attractive basin of a final attractor is as large as seven, and the final attractor has only one active node, then the active node acts as inhibitor, and the SIA and signal-inhibitor (SI) structures are fundamental architectures of robust networks. SIA and SI networks with dynamic robustness against environment uncertainties may be selected and maintained over the course of evolution, rather than blind trial-error testing and be ing an accidental consequence of particular evolutionary history. SIA network can perform a more complex process than SI network, andSIA might be used to design robust artificial genetic network. Our results provide dynamical support for why the inhibitors and SIA/SI structures are frequently employed in cellular regulatory networks.

  18. Emergence of dynamical order synchronization phenomena in complex systems

    CERN Document Server

    Manrubia, Susanna C; Zanette, Damián H

    2004-01-01

    Synchronization processes bring about dynamical order and lead tospontaneous development of structural organization in complex systemsof various origins, from chemical oscillators and biological cells tohuman societies and the brain. This book provides a review and adetailed theoretical analysis of synchronization phenomena in complexsystems with different architectures, composed of elements withperiodic or chaotic individual dynamics. Special attention is paid tostatistical concepts, such as nonequilibrium phase transitions, orderparameters and dynamical glasses.

  19. Genetic structure of the polymorphic metrosideros (Myrtaceae complex in the Hwaiian islands using nuclear microsatellite data.

    Directory of Open Access Journals (Sweden)

    Danica T Harbaugh

    Full Text Available BACKGROUND: Five species of Metrosideros (Myrtaceae are recognized in the Hawaiian Islands, including the widespread M. polymorpha, and are characterized by a multitude of distinctive, yet overlapping, habit, ecological, and morphological forms. It remains unclear, despite several previous studies, whether the morphological variation within Hawaiian Metrosideros is due to hybridization, genetic polymorphism, phenotypic plasticity, or some combination of these processes. The Hawaiian Metrosideros complex has become a model system to study ecology and evolution; however this is the first study to use microsatellite data for addressing inter-island patterns of variation from across the Hawaiian Islands. METHODOLOGY/PRINCIPAL FINDINGS: Ten nuclear microsatellite loci were genotyped from 143 individuals of Metrosideros. We took advantage of the bi-parental inheritance and rapid mutation rate of these data to examine the validity of the current taxonomy and to investigate whether Metrosideros plants from the same island are more genetically similar than plants that are morphologically similar. The Bayesian algorithm of the program structure was used to define genetic groups within Hawaiian Metrosideros and the closely related taxon M. collina from the Marquesas and Austral Islands. Several standard and nested AMOVAs were conducted to test whether the genetic diversity is structured geographically or taxonomically. CONCLUSIONS/SIGNIFICANCE: The results suggest that Hawaiian Metrosideros have dynamic gene flow, with genetic and morphological diversity structured not simply by geography or taxonomy, but as a result of parallel evolution on islands following rampant island-island dispersal, in addition to ancient chloroplast capture. Results also suggest that the current taxonomy requires major revisions in order to reflect the genetic structure revealed in the microsatellite data.

  20. Kinetic modeling of exciton migration in photosynthetic systems. 3. Application of genetic algorithms to simulations of excitation dynamics in three-dimensional photosystem I core antenna/reaction center complexes.

    OpenAIRE

    Trinkunas, G.; Holzwarth, A R

    1996-01-01

    A procedure is described to generate and optimize the lattice models for spectrally inhomogeneous photosynthetic antenna/reaction center (RC) particles. It is based on the genetic algorithm search for the pigment spectral type distributions on the lattice by making use of steady-state and time-resolved spectroscopic input data. Upon a proper fitness definition, a family of excitation energy transfer models can be tested for their compatibility with the availability experimental data. For the ...

  1. Understanding Learner Agency as a Complex Dynamic System

    Science.gov (United States)

    Mercer, Sarah

    2011-01-01

    This paper attempts to contribute to a fuller understanding of the nature of language learner agency by considering it as a complex dynamic system. The purpose of the study was to explore detailed situated data to examine to what extent it is feasible to view learner agency through the lens of complexity theory. Data were generated through a…

  2. Universal properties of dynamically complex systems - The organization of chaos

    Science.gov (United States)

    Procaccia, Itamar

    1988-06-01

    The complex dynamic behavior of natural systems far from equilibrium is discussed. Progress that has been made in understanding universal aspects of the paths to such behavior, of the trajectories at the borderline of chaos, and of the nature of the complexity in the chaotic regime, is reviewed. The emerging grammar of chaos is examined.

  3. Complex, Dynamic Systems: A New Transdisciplinary Theme for Applied Linguistics?

    Science.gov (United States)

    Larsen-Freeman, Diane

    2012-01-01

    In this plenary address, I suggest that Complexity Theory has the potential to contribute a transdisciplinary theme to applied linguistics. Transdisciplinary themes supersede disciplines and spur new kinds of creative activity (Halliday 2001 [1990]). Investigating complex systems requires researchers to pay attention to system dynamics. Since…

  4. Complex, Dynamic Systems: A New Transdisciplinary Theme for Applied Linguistics?

    Science.gov (United States)

    Larsen-Freeman, Diane

    2012-01-01

    In this plenary address, I suggest that Complexity Theory has the potential to contribute a transdisciplinary theme to applied linguistics. Transdisciplinary themes supersede disciplines and spur new kinds of creative activity (Halliday 2001 [1990]). Investigating complex systems requires researchers to pay attention to system dynamics. Since…

  5. Parameter Estimation in Epidemiology: from Simple to Complex Dynamics

    Science.gov (United States)

    Aguiar, Maíra; Ballesteros, Sebastién; Boto, João Pedro; Kooi, Bob W.; Mateus, Luís; Stollenwerk, Nico

    2011-09-01

    We revisit the parameter estimation framework for population biological dynamical systems, and apply it to calibrate various models in epidemiology with empirical time series, namely influenza and dengue fever. When it comes to more complex models like multi-strain dynamics to describe the virus-host interaction in dengue fever, even most recently developed parameter estimation techniques, like maximum likelihood iterated filtering, come to their computational limits. However, the first results of parameter estimation with data on dengue fever from Thailand indicate a subtle interplay between stochasticity and deterministic skeleton. The deterministic system on its own already displays complex dynamics up to deterministic chaos and coexistence of multiple attractors.

  6. Ethical and legal issues arising from complex genetic disorders. DOE final report

    Energy Technology Data Exchange (ETDEWEB)

    Andrews, Lori

    2002-10-09

    The project analyzed the challenges raised by complex genetic disorders in genetic counselling, for clinical practice, for public health, for quality assurance, and for protection against discrimination. The research found that, in some settings, solutions created in the context of single gene disorders are more difficult to apply to complex disorders. In other settings, the single gene solutions actually backfired and created additional problems when applied to complex genetic disorders. The literature of five common, complex genetic disorders--Alzheimer's, asthma, coronary heart disease, diabetes, and psychiatric illnesses--was evaluated in depth.

  7. Path planning for complex terrain navigation via dynamic programming

    Energy Technology Data Exchange (ETDEWEB)

    Kwok, K.S.; Driessen, B.J.

    1998-12-31

    This work considers the problem of planning optimal paths for a mobile robot traversing complex terrain. In addition to the existing obstacles, locations in the terrain where the slope is too steep for the mobile robot to navigate safely without tipping over become mathematically equivalent to extra obstacles. To solve the optimal path problem, the authors use a dynamic programming approach. The dynamic programming approach utilized herein does not suffer the difficulties associated with spurious local minima that the artificial potential field approaches do. In fact, a globally optimal solution is guaranteed to be found if a feasible solution exists. The method is demonstrated on several complex examples including very complex terrains.

  8. Complex Langevin dynamics for chiral random matrix theory

    Science.gov (United States)

    Mollgaard, A.; Splittorff, K.

    2013-12-01

    We apply complex Langevin dynamics to chiral random matrix theory at nonzero chemical potential. At large quark mass, the simulations agree with the analytical results while incorrect convergence is found for small quark masses. The region of quark masses for which the complex Langevin dynamics converges incorrectly is identified as the region where the fermion determinant frequently traces out a path surrounding the origin of the complex plane during the Langevin flow. This links the incorrect convergence to an ambiguity in the Langevin force due to the presence of the logarithm of the fermion determinant in the action.

  9. Complex Langevin Dynamics for chiral Random Matrix Theory

    CERN Document Server

    Mollgaard, A

    2013-01-01

    We apply complex Langevin dynamics to chiral random matrix theory at nonzero chemical potential. At large quark mass the simulations agree with the analytical results while incorrect convergence is found for small quark masses. The region of quark masses for which the complex Langevin dynamics converges incorrectly is identified as the region where the fermion determinant frequently traces out a path surrounding the origin of the complex plane during the Langevin flow. This links the incorrect convergence to an ambiguity in the Langevin force due to the presence of the logarithm of the fermion determinant in the action.

  10. Complexity of software trustworthiness and its dynamical statistical analysis methods

    Institute of Scientific and Technical Information of China (English)

    ZHENG ZhiMing; MA ShiLong; LI Wei; JIANG Xin; WEI Wei; MA LiLi; TANG ShaoTing

    2009-01-01

    Developing trusted softwares has become an important trend and a natural choice in the development of software technology and applications.At present,the method of measurement and assessment of software trustworthiness cannot guarantee safe and reliable operations of software systems completely and effectively.Based on the dynamical system study,this paper interprets the characteristics of behaviors of software systems and the basic scientific problems of software trustworthiness complexity,analyzes the characteristics of complexity of software trustworthiness,and proposes to study the software trustworthiness measurement in terms of the complexity of software trustworthiness.Using the dynamical statistical analysis methods,the paper advances an invariant-measure based assessment method of software trustworthiness by statistical indices,and hereby provides a dynamical criterion for the untrustworthiness of software systems.By an example,the feasibility of the proposed dynamical statistical analysis method in software trustworthiness measurement is demonstrated using numerical simulations and theoretical analysis.

  11. Dynamics of DNA/intercalator complexes

    Science.gov (United States)

    Schurr, J. M.; Wu, Pengguang; Fujimoto, Bryant S.

    1990-05-01

    Complexes of linear and supercoiled DNAs with different intercalating dyes are studied by time-resolved fluorescence polarization anisotropy using intercalated ethidium as the probe. Existing theory is generalized to take account of excitation transfer between intercalated ethidiums, and Forster theory is shown to be valid in this context. The effects of intercalated ethidium, 9-aminoacridine, and proflavine on the torsional rigidity of linear and supercoiled DNAs are studied up to rather high binding ratios. Evidence is presented that metastable secondary structure persists in dye-relaxed supercoiled DNAs, which contradicts the standard model of supercoiled DNAs.

  12. Spatial price dynamics: From complex network perspective

    Science.gov (United States)

    Li, Y. L.; Bi, J. T.; Sun, H. J.

    2008-10-01

    The spatial price problem means that if the supply price plus the transportation cost is less than the demand price, there exists a trade. Thus, after an amount of exchange, the demand price will decrease. This process is continuous until an equilibrium state is obtained. However, how the trade network structure affects this process has received little attention. In this paper, we give a evolving model to describe the levels of spatial price on different complex network structures. The simulation results show that the network with shorter path length is sensitive to the variation of prices.

  13. Advances in dynamics, patterns, cognition challenges in complexity

    CERN Document Server

    Pikovsky, Arkady; Rulkov, Nikolai; Tsimring, Lev

    2017-01-01

    This book focuses on recent progress in complexity research based on the fundamental nonlinear dynamical and statistical theory of oscillations, waves, chaos, and structures far from equilibrium. Celebrating seminal contributions to the field by Prof. M. I. Rabinovich of the University of California at San Diego, this volume brings together perspectives on both the fundamental aspects of complexity studies, as well as in applications in different fields ranging from granular patterns to understanding of the cognitive brain and mind dynamics. The slate of world-class authors review recent achievements that together present a broad and coherent coverage of modern research in complexity greater than the sum of its parts. Presents the most up-to-date developments in the studies of complexity Combines basic and applied aspects Links background nonlinear theory of oscillations and waves with modern approaches Allows readers to recognize general dynamical principles across the applications fields.

  14. Structural and dynamical properties of complex networks

    Science.gov (United States)

    Ghoshal, Gourab

    Recent years have witnessed a substantial amount of interest within the physics community in the properties of networks. Techniques from statistical physics coupled with the widespread availability of computing resources have facilitated studies ranging from large scale empirical analysis of the worldwide web, social networks, biological systems, to the development of theoretical models and tools to explore the various properties of these systems. Following these developments, in this dissertation, we present and solve for a diverse set of new problems, investigating the structural and dynamical properties of both model and real world networks. We start by defining a new metric to measure the stability of network structure to disruptions, and then using a combination of theory and simulation study its properties in detail on artificially generated networks; we then compare our results to a selection of networks from the real world and find good agreement in most cases. In the following chapter, we propose a mathematical model that mimics the structure of popular file-sharing websites such as Flickr and CiteULike and demonstrate that many of its properties can solved exactly in the limit of large network size. The remaining part of the dissertation primarily focuses on the dynamical properties of networks. We first formulate a model of a network that evolves under the addition and deletion of vertices and edges, and solve for the equilibrium degree distribution for a variety of cases of interest. We then consider networks whose structure can be manipulated by adjusting the rules by which vertices enter and leave the network. We focus in particular on degree distributions and show that, with some mild constraints, it is possible by a suitable choice of rules to arrange for the network to have any degree distribution we desire. In addition we define a simple local algorithm by which appropriate rules can be implemented in practice. Finally, we conclude our

  15. Micro-Level Affect Dynamics in Psychopathology Viewed From Complex Dynamical System Theory

    NARCIS (Netherlands)

    Wichers, M.; Wigman, J. T. W.; Myin-Germeys, I.

    2015-01-01

    This article discusses the role of moment-to-moment affect dynamics in mental disorder and aims to integrate recent literature on this topic in the context of complex dynamical system theory. First, we will review the relevance of temporal and contextual aspects of affect dynamics in relation to psy

  16. Modeling and Analysis of Complex Equipment Maintenance Dynamics

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    An equipment maintenance system is naturally a complex dynamical system. The effective maintenance management must be based on the knowledge of the system's intrinsic dynamics. And the structure of the maintenance system determines its behavior. This paper analyzes the basic structures and elements of a maintenance system for complex multi-components equipment. The maintenance system is considered as a dynamic system whose behavior is influenced by its structure's feedback and interaction, and the system's available resources. Building the dynamical model with Simulink, we show some results about the maintenance system's nonlinear dynamics, which are never given by stochastic process methods. The model can be used for understanding and determining maintenance system behavior, towards which operational adjustments of maintenance infrastructure, precise prediction of maintenance requirements and timely supply of maintenance resources can be made in a more informed way.

  17. Untangling complex dynamical systems via derivative-variable correlations

    Science.gov (United States)

    Levnaji, Zoran; Pikovsky, Arkady

    2014-05-01

    Inferring the internal interaction patterns of a complex dynamical system is a challenging problem. Traditional methods often rely on examining the correlations among the dynamical units. However, in systems such as transcription networks, one unit's variable is also correlated with the rate of change of another unit's variable. Inspired by this, we introduce the concept of derivative-variable correlation, and use it to design a new method of reconstructing complex systems (networks) from dynamical time series. Using a tunable observable as a parameter, the reconstruction of any system with known interaction functions is formulated via a simple matrix equation. We suggest a procedure aimed at optimizing the reconstruction from the time series of length comparable to the characteristic dynamical time scale. Our method also provides a reliable precision estimate. We illustrate the method's implementation via elementary dynamical models, and demonstrate its robustness to both model error and observation error.

  18. Complex dynamics in learning complicated games

    CERN Document Server

    Galla, Tobias

    2011-01-01

    Game theory is the standard tool used to model strategic interactions in evolutionary biology and social science. Traditional game theory studies the equilibria of simple games. But is traditional game theory applicable if the game is complicated, and if not, what is? We investigate this question here, defining a complicated game as one with many possible moves, and therefore many possible payoffs conditional on those moves. We investigate two-person games in which the players learn based on experience. By generating games at random we show that under some circumstances the strategies of the two players converge to fixed points, but under others they follow limit cycles or chaotic attractors. The dimension of the chaotic attractors can be very high, implying that the dynamics of the strategies are effectively random. In the chaotic regime the payoffs fluctuate intermittently, showing bursts of rapid change punctuated by periods of quiescence, similar to what is observed in fluid turbulence and financial marke...

  19. Dynamics of ranking processes in complex systems.

    Science.gov (United States)

    Blumm, Nicholas; Ghoshal, Gourab; Forró, Zalán; Schich, Maximilian; Bianconi, Ginestra; Bouchaud, Jean-Philippe; Barabási, Albert-László

    2012-09-21

    The world is addicted to ranking: everything, from the reputation of scientists, journals, and universities to purchasing decisions is driven by measured or perceived differences between them. Here, we analyze empirical data capturing real time ranking in a number of systems, helping to identify the universal characteristics of ranking dynamics. We develop a continuum theory that not only predicts the stability of the ranking process, but shows that a noise-induced phase transition is at the heart of the observed differences in ranking regimes. The key parameters of the continuum theory can be explicitly measured from data, allowing us to predict and experimentally document the existence of three phases that govern ranking stability.

  20. Ab initio lattice dynamics of complex structures

    DEFF Research Database (Denmark)

    Voss, Johannes

    2008-01-01

    systems in particular. A more detailed analysis of the phonon spectrum has been performed for the compound Mg(BH4)2, where several crystal symmetries have been proposed theoretically and experimentally. By means of an analysis of the instabilities of these structures, a new, stable phase has been......In this thesis, density functional theory is applied in a study of thermodynamic properties of so-called complex metal hydrides, which are promising materials for hydrogen storage applications. Since the unit cells of these crystals can be relatively large with many symmetrically inequivalent...... determined. Aiming at finding scaling relationships between alloy stabilities and computationally inexpensive properties, the stabilities of cation-alloyed metal aluminum hexahydrides have been studied. The analysis shows that charge density symmetries are correlated to the stability. In addition...

  1. Nuclear and cytoplasmic genetic diversity in weed beet and sugar beet accessions compared to wild relatives: new insights into the genetic relationships within the Beta vulgaris complex species.

    Science.gov (United States)

    Fénart, Stéphane; Arnaud, Jean-François; De Cauwer, Isabelle; Cuguen, Joël

    2008-05-01

    Hybridization between cultivated species and their wild relatives is now widely considered to be common. In the Beta vulgaris complex, the sugar beet seed multiplication areas have been the scene of inadvertent pollination of sugar beet seed bearers by wild ruderal pollen donors, generating a weedy form of beet which infests sugar beet fields in European countries. Up to now, investigations of evolutionary dynamics of genetic diversity within the B. vulgaris complex were addressed using few genetical markers and few accessions. In this study, we tackled this issue using a panel of complementary markers: five nuclear microsatellite loci, four mitochondrial minisatellite loci and one chloroplastic PCR-RFLP marker. We sampled 1,640 individuals that illustrate the actual distribution of inland ruderal beets of South Western France, weed beets and wild sea beets of northern France as well as the diversity of 35 contemporary European diploid cultivars. Nuclear genetic diversity in weed beets appeared to be as high as those of ruderal beets and sea beets, whereas the narrowness of cultivar accessions was confirmed. This genetic bottleneck in cultivars is even more important in the cytoplasmic genome as only one haplotype was found among all sugar beet cultivars. The large majority of weed beet populations also presented this unique cytoplasmic haplotype, as expected owing to their maternal cultivated origin. Nonetheless, various cytoplasmic haplotypes were found within three populations of weed beets, implying wild-to-weed seed flows. Finally, our findings gave new insights into the genetical relationships between the components of the B. vulgaris complex: (1) we found a very strong genetic divergence between wild sea beet and other relatives, which was unexpected given the recent evolutionary history and the full cross-compatibility of all taxa and (2) we definitely confirmed that the classification into cultivated, wild, ruderal and weed forms according to their

  2. A dynamic fuzzy clustering method based on genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    ZHENG Yan; ZHOU Chunguang; LIANG Yanchun; GUO Dongwei

    2003-01-01

    A dynamic fuzzy clustering method is presented based on the genetic algorithm. By calculating the fuzzy dissimilarity between samples the essential associations among samples are modeled factually. The fuzzy dissimilarity between two samples is mapped into their Euclidean distance, that is, the high dimensional samples are mapped into the two-dimensional plane. The mapping is optimized globally by the genetic algorithm, which adjusts the coordinates of each sample, and thus the Euclidean distance, to approximate to the fuzzy dissimilarity between samples gradually. A key advantage of the proposed method is that the clustering is independent of the space distribution of input samples, which improves the flexibility and visualization. This method possesses characteristics of a faster convergence rate and more exact clustering than some typical clustering algorithms. Simulated experiments show the feasibility and availability of the proposed method.

  3. Dynamics of complex fluids in rotary atomization

    Science.gov (United States)

    Keshavarz, Bavand; McKinley, Gareth; MIT, Mechanical Engineering Department Team

    2016-11-01

    We study the dynamics of fragmentation for different Newtonian and viscoelastic liquids in rotary atomization. In this process, at the rim of a spinning cup, the centripetal acceleration destabilizes the formed liquid torus due to the Rayleigh-Taylor instability. The resulting ligaments leave the liquid torus with a remarkably repeatable spacing that scales linearly with the inverse of the rotation rate. Filaments then follow a well-defined geometrical path-line that is described by the involute of the circle. Knowing the geometry of this phenomenon we derive the detailed kinematics of this process and compare it with the experimental observations. We show that the ligaments elongate tangentially to the involute of the circle and thin radially as they separate from the cup. A theoretical form is derived for the spatial variation of the filament deformation rate. Once the ligaments are far from the cup they breakup into droplets since they are not stretched fast enough (compared to the critical rate of capillary thinning). We couple these derivations with the known properties of Newtonian and viscoelastic liquids to provide a physical analysis for this fragmentation process that is compared in detail with our experiments.

  4. Early days in complex dynamics a history of complex dynamics in one variable during 1906-1942

    CERN Document Server

    Alexander, Daniel S; Rosa, Alessandro

    2011-01-01

    The theory of complex dynamics, whose roots lie in 19th-century studies of the iteration of complex function conducted by Kœnigs, Schröder, and others, flourished remarkably during the first half of the 20th century, when many of the central ideas and techniques of the subject developed. This book by Alexander, Iavernaro, and Rosa paints a robust picture of the field of complex dynamics between 1906 and 1942 through detailed discussions of the work of Fatou, Julia, Siegel, and several others. A recurrent theme of the authors' treatment is the center problem in complex dynamics. They present its complete history during this period and, in so doing, bring out analogies between complex dynamics and the study of differential equations, in particular, the problem of stability in Hamiltonian systems. Among these analogies are the use of iteration and problems involving small divisors which the authors examine in the work of Poincaré and others, linking them to complex dynamics, principally via the work of Samuel...

  5. Genetics of mammalian meiosis: regulation, dynamics and impact on fertility.

    Science.gov (United States)

    Handel, Mary Ann; Schimenti, John C

    2010-02-01

    Meiosis is an essential stage in gamete formation in all sexually reproducing organisms. Studies of mutations in model organisms and of human haplotype patterns are leading to a clearer understanding of how meiosis has adapted from yeast to humans, the genes that control the dynamics of chromosomes during meiosis, and how meiosis is tied to gametic success. Genetic disruptions and meiotic errors have important roles in infertility and the aetiology of developmental defects, especially aneuploidy. An understanding of the regulation of meiosis, coupled with advances in genomics, may ultimately allow us to diagnose the causes of meiosis-based infertilities, more wisely apply assisted reproductive technologies, and derive functional germ cells.

  6. 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.

  7. Dynamics of nanoparticles in complex fluids

    Science.gov (United States)

    Omari, Rami A.

    Soft matter is a subfield of condensed matter including polymers, colloidal dispersions, surfactants, and liquid crystals. These materials are familiar from our everyday life- glues, paints, soaps, and plastics are examples of soft materials. Many phenomena in these systems have the same underlying physical mechanics. Moreover, it has been recognized that combinations of these systems, like for example polymers and colloids, exhibit new properties which are not found in each system separately. These mixed systems have a higher degree of complexity than the separate systems. In order to understand their behavior, knowledge from each subfields of soft matter has to be put together. One of these complex systems is the mixture of nanoparticles with macromolecules such as polymers, proteins, etc. Understanding the interactions in these systems is essential for solving various problems in technological and medical fields, such as developing high performance polymeric materials, chromatography, and drug delivery vehicles. The author of this dissertation investigates fundemental soft matter systems, including colloid dispersions in polymer solutions and binary mixture. The diffusion of gold nanoparticles in semidilute and entangled solutions of polystyrene (PS) in toluene were studied using fluorescence correlation spectroscopy (FCS). In our experiments, the particle radius (R ≈ 2.5 nm) was much smaller compared to the radius of gyration of the chain but comparable to the average mesh size of the fluctuating polymer network. The diffusion coefficient (D) of the particles decreased monotonically with polymer concentration and it can be fitted with a stretched exponential function. At high concentration of the polymer, a clear subdiffusive motion of the particles was observed. The results were compared with the diffusion of free dyes, which showed normal diffusive behavior for all concentrations. In another polymer solution, poly ethylene glycol (PEG) in water, the

  8. Inverse problem of HIV cell dynamics using Genetic Algorithms

    Science.gov (United States)

    González, J. A.; Guzmán, F. S.

    2017-01-01

    In order to describe the cell dynamics of T-cells in a patient infected with HIV, we use a flavour of Perelson's model. This is a non-linear system of Ordinary Differential Equations that describes the evolution of healthy, latently infected, infected T-cell concentrations and the free viral cells. Different parameters in the equations give different dynamics. Considering the concentration of these types of cells is known for a particular patient, the inverse problem consists in estimating the parameters in the model. We solve this inverse problem using a Genetic Algorithm (GA) that minimizes the error between the solutions of the model and the data from the patient. These errors depend on the parameters of the GA, like mutation rate and population, although a detailed analysis of this dependence will be described elsewhere.

  9. New Concept of Dynamic Complexity in Quantum Mechanics and Beyond

    CERN Document Server

    Kirilyuk, A P

    1996-01-01

    The qualitatively new concept of dynamic complexity in quantum mechanics is based on a new paradigm appearing within a nonperturbational analysis of the Schroedinger equation for a generic Hamiltonian system. The unreduced analysis explicitly provides the complete, consistent solution as a set of many incompatible components ('realisations') which should permanently and probabilistically replace one another, since each of them is 'complete' in the ordinary sense. This discovery leads to the universally applicable concept of dynamic complexity and self-consistent, realistic resolution of the stagnating problems of quantum chaos, quantum measurement, indeterminacy and wave reduction. The peculiar, 'mysterious' character of quantum behaviour itself is seen now as a result of a dynamically complex, intrinsically multivalued behaviour of interacting fields at the corresponding lowest levels of the (now completely causal) structure of reality. Incorporating the results of the canonical theories as an over-simplifie...

  10. Some remarks on Lefschetz thimbles and complex Langevin dynamics

    CERN Document Server

    Aarts, Gert; Seiler, Erhard; Sexty, Denes

    2014-01-01

    Lefschetz thimbles and complex Langevin dynamics both provide a means to tackle the numerical sign problem prevalent in theories with a complex weight in the partition function, e.g. due to nonzero chemical potential. Here we collect some findings for the quartic model, and for U(1) and SU(2) models in the presence of a determinant, which have some features not discussed before, due to a singular drift. We find evidence for a relation between classical runaways and stable thimbles, and give an example of a degenerate fixed point. We typically find that the distributions sampled in complex Langevin dynamics are related to the thimble(s), but with some important caveats, for instance due to the presence of unstable fixed points in the Langevin dynamics.

  11. Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems

    CERN Document Server

    Vázquez, Luis

    2013-01-01

    Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems explores how Newton's equation for the motion of one particle in classical mechanics combined with finite difference methods allows creation of a mechanical scenario to solve basic problems in linear algebra and programming. The authors present a novel, unified numerical and mechanical approach and an important analysis method of optimization. This book also: Presents mechanical method for determining matrix singularity or non-independence of dimension and complexity Illustrates novel mathematical applications of classical Newton’s law Offers a new approach and insight to basic, standard problems Includes numerous examples and applications Newtonian Nonlinear Dynamics for Complex Linear and Optimization Problems is an ideal book for undergraduate and graduate students as well as researchers interested in linear problems and optimization, and nonlinear dynamics.      

  12. The Impact of Evolutionary Driving Forces on Human Complex Diseases: A Population Genetics Approach

    Directory of Open Access Journals (Sweden)

    Amr T. M. Saeb

    2016-01-01

    Full Text Available Investigating the molecular evolution of human genome has paved the way to understand genetic adaptation of humans to the environmental changes and corresponding complex diseases. In this review, we discussed the historical origin of genetic diversity among human populations, the evolutionary driving forces that can affect genetic diversity among populations, and the effects of human movement into new environments and gene flow on population genetic diversity. Furthermore, we presented the role of natural selection on genetic diversity and complex diseases. Then we reviewed the disadvantageous consequences of historical selection events in modern time and their relation to the development of complex diseases. In addition, we discussed the effect of consanguinity on the incidence of complex diseases in human populations. Finally, we presented the latest information about the role of ancient genes acquired from interbreeding with ancient hominids in the development of complex diseases.

  13. The Dynamic Checking of Complex Real Time System

    Institute of Scientific and Technical Information of China (English)

    YU Chao; HUANG Benwen; WU Guoqing

    2006-01-01

    The paper presents an dynamic execution model of complex real-time software based on requirement description model RTRSM, and then propose a checking method based on configuration covering and its corresponding algorithm. This checking method can check the execution situations between parallel elements in a dynamic execution step of real-time software systems. It also can check all the states and transitions which assure the completeness of checking. In the end, related theorem is proofed.

  14. Coupled disease-behavior dynamics on complex networks: A review

    Science.gov (United States)

    Wang, Zhen; Andrews, Michael A.; Wu, Zhi-Xi; Wang, Lin; Bauch, Chris T.

    2015-12-01

    It is increasingly recognized that a key component of successful infection control efforts is understanding the complex, two-way interaction between disease dynamics and human behavioral and social dynamics. Human behavior such as contact precautions and social distancing clearly influence disease prevalence, but disease prevalence can in turn alter human behavior, forming a coupled, nonlinear system. Moreover, in many cases, the spatial structure of the population cannot be ignored, such that social and behavioral processes and/or transmission of infection must be represented with complex networks. Research on studying coupled disease-behavior dynamics in complex networks in particular is growing rapidly, and frequently makes use of analysis methods and concepts from statistical physics. Here, we review some of the growing literature in this area. We contrast network-based approaches to homogeneous-mixing approaches, point out how their predictions differ, and describe the rich and often surprising behavior of disease-behavior dynamics on complex networks, and compare them to processes in statistical physics. We discuss how these models can capture the dynamics that characterize many real-world scenarios, thereby suggesting ways that policy makers can better design effective prevention strategies. We also describe the growing sources of digital data that are facilitating research in this area. Finally, we suggest pitfalls which might be faced by researchers in the field, and we suggest several ways in which the field could move forward in the coming years.

  15. Stochastic synchronization for time-varying complex dynamical networks

    Institute of Scientific and Technical Information of China (English)

    Guo Xiao-Yong; Li Jun-Min

    2012-01-01

    This paper studies the stochastic synchronization problem for time-varying complex dynamical networks. This model is totally different from some existing network models. Based on the Lyapunov stability theory, inequality techniques, and the properties of the Weiner process, some controllers and adaptive laws are designed to ensure achieving stochastic synchronization of a complex dynamical network model. A sufficient synchronization condition is given to ensure that the proposed network model is mean-square stable. Theoretical analysis and numerical simulation fully verify the main results.

  16. Dynamic inclusion complexes of metal nanoparticles inside nanocups.

    Science.gov (United States)

    Alarcón-Correa, Mariana; Lee, Tung-Chun; Fischer, Peer

    2015-06-01

    Host-guest inclusion complexes are abundant in molecular systems and of fundamental importance in living organisms. Realizing a colloidal analogue of a molecular dynamic inclusion complex is challenging because inorganic nanoparticles (NPs) with a well-defined cavity and portal are difficult to synthesize in high yield and with good structural fidelity. Herein, a generic strategy towards the fabrication of dynamic 1:1 inclusion complexes of metal nanoparticles inside oxide nanocups with high yield (>70%) and regiospecificity (>90%) by means of a reactive double Janus nanoparticle intermediate is reported. Experimental evidence confirms that the inclusion complexes are formed by a kinetically controlled mechanism involving a delicate interplay between bipolar galvanic corrosion and alloying-dealloying oxidation. Release of the NP guest from the nanocups can be efficiently triggered by an external stimulus. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Reconstructing complex networks with binary-state dynamics

    CERN Document Server

    Li, Jingwen; Lai, Ying-Cheng; Grebogi, Celso

    2015-01-01

    The prerequisite for our understanding of many complex networked systems lies in the reconstruction of network structure from measurable data. Although binary-state dynamics occurring in a broad class of complex networked systems in nature and society and has been intensively investigated, a general framework for reconstructing complex networks from binary states, the inverse problem, is lacking. Here we offer a general solution to the reconstruction problem by developing a data-based linearization approach for binary-state dynamics with linear, nonlinear, discrete and stochastic switching functions. The linearization allows us to convert the network reconstruction problem into a sparse signal reconstruction problem that can be resolved efficiently and credibly by convex optimization based on compressed sensing. The completely data-based linearization method and the sparse signal reconstruction constitutes a general framework for reconstructing complex networks without any knowledge of the binary-state dynami...

  18. On the Organizational Dynamics of the Genetic Code

    KAUST Repository

    Zhang, Zhang

    2011-06-07

    The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides—adenine, thymine, guanine and cytosine—according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

  19. On the organizational dynamics of the genetic code.

    Science.gov (United States)

    Zhang, Zhang; Yu, Jun

    2011-04-01

    The organization of the canonical genetic code needs to be thoroughly illuminated. Here we reorder the four nucleotides-adenine, thymine, guanine and cytosine-according to their emergence in evolution, and apply the organizational rules to devising an algebraic representation for the canonical genetic code. Under a framework of the devised code, we quantify codon and amino acid usages from a large collection of 917 prokaryotic genome sequences, and associate the usages with its intrinsic structure and classification schemes as well as amino acid physicochemical properties. Our results show that the algebraic representation of the code is structurally equivalent to a content-centric organization of the code and that codon and amino acid usages under different classification schemes were correlated closely with GC content, implying a set of rules governing composition dynamics across a wide variety of prokaryotic genome sequences. These results also indicate that codons and amino acids are not randomly allocated in the code, where the six-fold degenerate codons and their amino acids have important balancing roles for error minimization. Therefore, the content-centric code is of great usefulness in deciphering its hitherto unknown regularities as well as the dynamics of nucleotide, codon, and amino acid compositions.

  20. Structure, dynamics, assembly, and evolution of protein complexes.

    Science.gov (United States)

    Marsh, Joseph A; Teichmann, Sarah A

    2015-01-01

    The assembly of individual proteins into functional complexes is fundamental to nearly all biological processes. In recent decades, many thousands of homomeric and heteromeric protein complex structures have been determined, greatly improving our understanding of the fundamental principles that control symmetric and asymmetric quaternary structure organization. Furthermore, our conception of protein complexes has moved beyond static representations to include dynamic aspects of quaternary structure, including conformational changes upon binding, multistep ordered assembly pathways, and structural fluctuations occurring within fully assembled complexes. Finally, major advances have been made in our understanding of protein complex evolution, both in reconstructing evolutionary histories of specific complexes and in elucidating general mechanisms that explain how quaternary structure tends to evolve. The evolution of quaternary structure occurs via changes in self-assembly state or through the gain or loss of protein subunits, and these processes can be driven by both adaptive and nonadaptive influences.

  1. Soliton-Complex Dynamics in Strongly Dispersive Medium

    CERN Document Server

    Bogdan, M M; Maugin, G A; Bogdan, Mikhail M.; Kosevich, Arnold M.; Maugin, Gerard A.

    1999-01-01

    The concept of soliton complex in a nonlinear dispersive medium is proposed. It is shown that strongly interacting identical topological solitons in the medium can form bound soliton complexes which move without radiation. This phenomenon is considered to be universal and applicable to various physical systems. The soliton complex and its "excited" states are described analytically and numerically as solutions of nonlinear dispersive equations with the fourth and higher spatial or mixed derivatives. The dispersive sine-Gordon, double and triple sine-Gordon, and piecewise-linear models are studied in detail. Mechanisms and conditions of the formation of soliton complexes, and peculiarities of their stationary dynamics are investigated. A phenomenological approach to the description of the complexes and the classification of all the possible complex states are proposed. Some examples of physical systems, where the phenomenon can be experimentally observed, are briefly discussed.

  2. IMAGING THE BRAIN AS SCHIZOPHRENIA DEVELOPS: DYNAMIC & GENETIC BRAIN MAPS.

    Science.gov (United States)

    Thompson, Paul; Rapoport, Judith L; Cannon, Tyrone D; Toga, Arthur W

    2002-01-01

    Schizophrenia is a chronic, debilitating psychiatric disorder that affects 0.2-2% of the population worldwide. Often striking without warning in the late teens or early twenties, its symptoms include auditory and visual hallucinations, psychotic outbreaks, bizarre or disordered thinking, depression and social withdrawal. To combat the disease, new antipsychotic drugs are emerging; these atypical neuroleptics target dopamine and serotonin pathways in the brain, offering increased therapeutic efficacy with fewer side effects. Despite their moderate success in controlling some patients' symptoms, little is known about the causes of schizophrenia, and what triggers the disease. Its peculiar age of onset raises key questions: What physical changes occur in the brain as a patient develops schizophrenia? Do these deficits spread in the brain, and can they be opposed? How do they relate to psychotic symptoms? As risk for the disease is genetically transmitted, do a patient's relatives exhibit similar brain changes? Recent advances in brain imaging and genetics provide exciting insight on these questions. Neuroimaging can now chart the emergence and progression of deficits in the brain, providing an exceptionally sharp scalpel to dissect the effects of genetic risk, environmental triggers, and susceptibility genes. Visualizing the dynamics of the disease, these techniques also offer new strategies to evaluate drugs that combat the unrelenting symptoms of schizophrenia.

  3. Complex Dynamics of Discrete SEIS Models with Simple Demography

    Directory of Open Access Journals (Sweden)

    Hui Cao

    2011-01-01

    Full Text Available We investigate bifurcations and dynamical behaviors of discrete SEIS models with exogenous reinfections and a variety of treatment strategies. Bifurcations identified from the models include period doubling, backward, forward-backward, and multiple backward bifurcations. Multiple attractors, such as bistability and tristability, are observed. We also estimate the ultimate boundary of the infected regardless of initial status. Our rigorously mathematical analysis together with numerical simulations show that epidemiological factors alone can generate complex dynamics, though demographic factors only support simple equilibrium dynamics. Our model analysis supports and urges to treat a fixed percentage of exposed individuals.

  4. Structure-based control of complex networks with nonlinear dynamics

    CERN Document Server

    Zañudo, Jorge G T; Albert, Réka

    2016-01-01

    Given the network of interactions underlying a complex system, what can we learn about controlling such a system solely from its structure? Over a century of research in control theory has given us tools to answer this question, which were widely applied in science and engineering. Yet the current tools do not always consider the inherently nonlinear dynamics of real systems and the naturally occurring system states in their definition of "control", a term whose interpretation varies across disciplines. Here we use a new mathematical framework for structure-based control of networks governed by a broad class of nonlinear dynamics that includes the major dynamic models of biological, technological, and social processes. This framework provides realizable node overrides that steer a system towards any of its natural long term dynamic behaviors and which are guaranteed to be effective regardless of the dynamic details and parameters of the underlying system. We use this framework on several real networks, compar...

  5. Kinetic modeling of exciton migration in photosynthetic systems. 3. Application of genetic algorithms to simulations of excitation dynamics in three-dimensional photosystem I core antenna/reaction center complexes.

    Science.gov (United States)

    Trinkunas, G; Holzwarth, A R

    1996-07-01

    A procedure is described to generate and optimize the lattice models for spectrally inhomogeneous photosynthetic antenna/reaction center (RC) particles. It is based on the genetic algorithm search for the pigment spectral type distributions on the lattice by making use of steady-state and time-resolved spectroscopic input data. Upon a proper fitness definition, a family of excitation energy transfer models can be tested for their compatibility with the availability experimental data. For the case of the photosystem I core antenna (99 chlorophyll + primary electron donor pigment (P700)), three spectrally inhomogeneous three-dimensional lattice models, differing in their excitation transfer conditions, were tested. The relevant fit parameters were the pigment distribution on the lattice, the average lattice spacing of the main pool pigments, the distance of P700 and of long wavelength-absorbing (LWA) pigments to their nearest-neighbor main pool pigments, and the rate constant of charge separation from P700. For cyanobacterial PS I antenna/RC particles containing a substantial amount of LWA pigments, it is shown that the currently available experimental fluorescence data are consistent both with more migration-limited, and with more trap-limited excitation energy transfer models. A final decision between these different models requires more detailed experimental data. From all search runs about 30 different relative arrangements of P700 and LWA pigments were found. Several general features of all these different models can be noticed: 1) The reddest LWA pigment never appears next to P700. 2) The LWA pigments in most cases are spread on the surface of the lattice not far away from P700, with a pronounced tendency toward clustering of the LWA pigments. 3) The rate constant kP700 of charge separation is substantially higher than 1.2 ps-1, i.e., it exceeds the corresponding rate constant of purple bacterial RCs by at least a factor of four. 4) The excitation transfer

  6. Complexity and dynamism from an urban health perspective: a rationale for a system dynamics approach.

    Science.gov (United States)

    Tozan, Yesim; Ompad, Danielle C

    2015-06-01

    In a variety of urban health frameworks, cities are conceptualized as complex and dynamic yet commonly used epidemiological methods have failed to address this complexity and dynamism head on due to their narrow problem definitions and linear analytical representations. Scholars from a variety of disciplines have also long conceptualized cities as systems, but few have modeled urban health issues as problems within a system. Systems thinking in general and system dynamics in particular are relatively new approaches in public health, but ones that hold immense promise as methodologies to model and analyze the complexity underlying urban processes to effectively inform policy actions in dynamic environments. This conceptual essay reviews the utility of applying the concepts, principles, and methods of systems thinking to the study of complex urban health phenomena as a complementary approach to standard epidemiological methods using specific examples and provides recommendations on how to better incorporate systems thinking methods in urban health research and practice.

  7. Synchronization in Complex Networks of Nonlinear Dynamical Systems

    CERN Document Server

    Wu, Chai Wah

    2007-01-01

    This book brings together two emerging research areas: synchronization in coupled nonlinear systems and complex networks, and study conditions under which a complex network of dynamical systems synchronizes. While there are many texts that study synchronization in chaotic systems or properties of complex networks, there are few texts that consider the intersection of these two very active and interdisciplinary research areas. The main theme of this book is that synchronization conditions can be related to graph theoretical properties of the underlying coupling topology. The book introduces ide

  8. Applications of dynamical complexity theory in traditional Chinese medicine.

    Science.gov (United States)

    Ma, Yan; Sun, Shuchen; Peng, Chung-Kang

    2014-09-01

    Traditional Chinese medicine (TCM) has been gradually accepted by the world. Despite its widespread use in clinical settings, a major challenge in TCM is to study it scientifically. This difficulty arises from the fact that TCM views human body as a complex dynamical system, and focuses on the balance of the human body, both internally and with its external environment. As a result, conventional tools that are based on reductionist approach are not adequate. Methods that can quantify the dynamics of complex integrative systems may bring new insights and utilities about the clinical practice and evaluation of efficacy of TCM. The dynamical complexity theory recently proposed and its computational algorithm, Multiscale Entropy (MSE) analysis, are consistent with TCM concepts. This new system level analysis has been successfully applied to many health and disease related topics in medicine. We believe that there could be many promising applications of this dynamical complexity concept in TCM. In this article, we propose some promising applications and research areas that TCM practitioners and researchers can pursue.

  9. Dynamics of lane formation in driven binary complex plasmas

    NARCIS (Netherlands)

    Sutterlin, K. R.; Wysocki, A.; Ivlev, A. V.; Rath, C.; Thomas, H. M.; Rubin-Zuzic, M.; W. J. Goedheer,; Fortov, V. E.; Lipaev, A. M.; Molotkov, V. I.; Petrov, O. F.; Morfill, G. E.; Lowen, H.

    2009-01-01

    The dynamical onset of lane formation is studied in experiments with binary complex plasmas under microgravity conditions. Small microparticles are driven and penetrate into a cloud of big particles, revealing a strong tendency towards lane formation. The observed time-resolved lane-formation proces

  10. New Approach to Cluster Synchronization in Complex Dynamical Networks

    Institute of Scientific and Technical Information of China (English)

    LU Xin-Biao; QIN Bu-Zhi; LU Xin-Yu

    2009-01-01

    In this paper, a distributed control strategy is proposed to make a complex dynamical network achieve cluster synchronization, which means that nodes in the same group achieve the same synchronization state, while nodes in different groups achieve different synchronization states. The local and global stability of the cluster synchronization state are analyzed. Moreover, simulation results verify the effectiveness of the new approach

  11. Stochastic simulation of HIV population dynamics through complex network modelling

    NARCIS (Netherlands)

    Sloot, P.M.A.; Ivanov, S.V.; Boukhanovsky, A.V.; van de Vijver, D.A.M.C.; Boucher, C.A.B.

    2008-01-01

    We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and

  12. Stochastic simulation of HIV population dynamics through complex network modelling

    NARCIS (Netherlands)

    Sloot, P. M. A.; Ivanov, S. V.; Boukhanovsky, A. V.; van de Vijver, D. A. M. C.; Boucher, C. A. B.

    We propose a new way to model HIV infection spreading through the use of dynamic complex networks. The heterogeneous population of HIV exposure groups is described through a unique network degree probability distribution. The time evolution of the network nodes is modelled by a Markov process and

  13. 2D pattern evolution constrained by complex network dynamics

    CERN Document Server

    Rocha, L E C; Costa, Luciano da Fontoura; Rocha, Luis Enrique Correa da

    2006-01-01

    Complex networks have established themselves along the last years as being particularly suitable and flexible for representing and modeling several complex natural and human-made systems. At the same time in which the structural intricacies of such networks are being revealed and understood, efforts have also been directed at investigating how such connectivity properties define and constrain the dynamics of systems unfolding on such structures. However, lesser attention has been focused on hybrid systems, \\textit{i.e.} involving more than one type of network and/or dynamics. Because several real systems present such an organization (\\textit{e.g.} the dynamics of a disease coexisting with the dynamics of the immune system), it becomes important to address such hybrid systems. The current paper investigates a specific system involving a diffusive (linear and non-linear) dynamics taking place in a regular network while interacting with a complex network of defensive agents following Erd\\"os-R\\'enyi and Barab\\'a...

  14. Nonlinear Dynamics of Complex Coevolutionary Systems in Historical Times

    Science.gov (United States)

    Perdigão, Rui A. P.

    2016-04-01

    A new theoretical paradigm for statistical-dynamical modeling of complex coevolutionary systems is introduced, with the aim to provide historical geoscientists with a practical tool to analyse historical data and its underlying phenomenology. Historical data is assumed to represent the history of dynamical processes of physical and socio-economic nature. If processes and their governing laws are well understood, they are often treated with traditional dynamical equations: deterministic approach. If the governing laws are unknown or impracticable, the process is often treated as if being random (even if it is not): statistical approach. Although single eventful details - such as the exact spatiotemporal structure of a particular hydro-meteorological incident - may often be elusive to a detailed analysis, the overall dynamics exhibit group properties summarized by a simple set of categories or dynamical regimes at multiple scales - from local short-lived convection patterns to large-scale hydro-climatic regimes. The overwhelming microscale complexity is thus conveniently wrapped into a manageable group entity, such as a statistical distribution. In a stationary setting whereby the distribution is assumed to be invariant, alternating regimes are approachable as dynamical intermittence. For instance, in the context of bimodal climatic oscillations such as NAO and ENSO, each mode corresponds to a dynamical regime or phase. However, given external forcings or longer-term internal variability and multiscale coevolution, the structural properties of the system may change. These changes in the dynamical structure bring about a new distribution and associated regimes. The modes of yesteryear may no longer exist as such in the new structural order of the system. In this context, aside from regime intermittence, the system exhibits structural regime change. New oscillations may emerge whilst others fade into the annals of history, e.g. particular climate fluctuations during

  15. Synchronization criteria based on a general complex dynamical network model

    Institute of Scientific and Technical Information of China (English)

    ZHANG Jian-lin; WANG Chang-jian; XU Cong-fu

    2008-01-01

    Many complex dynamical networks display synchronization phenomena. We introduce a general complex dynamical network model. The model is equivalent to a simple vector model of adopting the Kronecker product. Some synchronization criteria, including time-variant networks and time-varying networks, are deduced based on Lyapunov's stability theory, and they are proven on the condition of obtaining a certain synchronous solution of an isolated cell. In particular, the inner-coupling matrix directly determines the synchronization of the time-invariant network; while for a time-varying periodic dynamical network, the asymptotic stability of a synchronous solution is determined by a constant matrix which is related to the fundamental solution matrices of the linearization system. Finally, illustrative examples are given to validate the results.

  16. Dynamic properties of epidemic spreading on finite size complex networks

    Institute of Scientific and Technical Information of China (English)

    Li Ying; Liu Yang; Shan Xiu-Ming; Ren Yong; Jiao Jian; Qiu Ben

    2005-01-01

    The Internet presents a complex topological structure, on which computer viruses can easily spread. By using theoretical analysis and computer simulation methods, the dynamic process of disease spreading on finite size networks with complex topological structure is investigated. On the finite size networks, the spreading process of SIS (susceptibleinfected-susceptible) model is a finite Markov chain with an absorbing state. Two parameters, the survival probability and the conditional infecting probability, are introduced to describe the dynamic properties of disease spreading on finite size networks. Our results can help understanding computer virus epidemics and other spreading phenomena on communication and social networks. Also, knowledge about the dynamic character of virus spreading is helpful for adopting immunity policy.

  17. Decentralized adaptive synchronization of an uncertain complex delayed dynamical network

    Institute of Scientific and Technical Information of China (English)

    Weisong ZHONG; Jun ZHAO; Georgi M.DIMIROVSKI

    2009-01-01

    In this paper,we investigate the locally and globally adaptive synchronization problem for an uncertain complex dynamical network with time-varying coupling delays based on the decentralized control.The coupling terms here are bounded by high-order polynomials with known gains that are ubiquitous in a large class of complex dynamical networks.We generalize the usual technology of searching for an appropriate coordinates transformation to change the network dynamics into a series of decoupled lower-dimensional systems.Several adaptive synchronization criteria are derived by constructing the Lyapunov-Krasovskii functional and Barbalat lemma,and the proposed criteria are simple in form and convenient for the practical engineering design.Numerical simulations illustrated by a nearest-neighbor coupling network verify the effectiveness of the proposed synchronization scheme.

  18. Balance between noise and information flow maximizes set complexity of network dynamics.

    Directory of Open Access Journals (Sweden)

    Tuomo Mäki-Marttunen

    Full Text Available Boolean networks have been used as a discrete model for several biological systems, including metabolic and genetic regulatory networks. Due to their simplicity they offer a firm foundation for generic studies of physical systems. In this work we show, using a measure of context-dependent information, set complexity, that prior to reaching an attractor, random Boolean networks pass through a transient state characterized by high complexity. We justify this finding with a use of another measure of complexity, namely, the statistical complexity. We show that the networks can be tuned to the regime of maximal complexity by adding a suitable amount of noise to the deterministic Boolean dynamics. In fact, we show that for networks with Poisson degree distributions, all networks ranging from subcritical to slightly supercritical can be tuned with noise to reach maximal set complexity in their dynamics. For networks with a fixed number of inputs this is true for near-to-critical networks. This increase in complexity is obtained at the expense of disruption in information flow. For a large ensemble of networks showing maximal complexity, there exists a balance between noise and contracting dynamics in the state space. In networks that are close to critical the intrinsic noise required for the tuning is smaller and thus also has the smallest effect in terms of the information processing in the system. Our results suggest that the maximization of complexity near to the state transition might be a more general phenomenon in physical systems, and that noise present in a system may in fact be useful in retaining the system in a state with high information content.

  19. Complex systems dynamics in aging: new evidence, continuing questions.

    Science.gov (United States)

    Cohen, Alan A

    2016-02-01

    There have long been suggestions that aging is tightly linked to the complex dynamics of the physiological systems that maintain homeostasis, and in particular to dysregulation of regulatory networks of molecules. This review synthesizes recent work that is starting to provide evidence for the importance of such complex systems dynamics in aging. There is now clear evidence that physiological dysregulation--the gradual breakdown in the capacity of complex regulatory networks to maintain homeostasis--is an emergent property of these regulatory networks, and that it plays an important role in aging. It can be measured simply using small numbers of biomarkers. Additionally, there are indications of the importance during aging of emergent physiological processes, functional processes that cannot be easily understood through clear metabolic pathways, but can nonetheless be precisely quantified and studied. The overall role of such complex systems dynamics in aging remains an important open question, and to understand it future studies will need to distinguish and integrate related aspects of aging research, including multi-factorial theories of aging, systems biology, bioinformatics, network approaches, robustness, and loss of complexity.

  20. Robustness of pinning a general complex dynamical network

    Energy Technology Data Exchange (ETDEWEB)

    Wang Lei, E-mail: lwang@buaa.edu.c [Laboratory of Mathematics, Information and Behavior of the Ministry of Education, Department of Systems and Control, Beihang University, Beijing 100191 (China); Sun Youxian [State Key Laboratory of Industrial Control Technology, Institute of Industrial Process Control, Zhejiang University, Hangzhou 310027 (China)

    2010-04-05

    This Letter studies the robustness problem of pinning a general complex dynamical network toward an assigned synchronous evolution. Several synchronization criteria are presented to guarantee the convergence of the pinning process locally and globally by construction of Lyapunov functions. In particular, if a pinning strategy has been designed for synchronization of a given complex dynamical network, then no matter what uncertainties occur among the pinned nodes, synchronization can still be guaranteed through the pinning. The analytical results show that pinning control has a certain robustness against perturbations on network architecture: adding, deleting and changing the weights of edges. Numerical simulations illustrated by scale-free complex networks verify the theoretical results above-acquired.

  1. Complex Dynamics Caused by Torus Bifurcation in Power Systems

    Institute of Scientific and Technical Information of China (English)

    YU Xiaodan; JIA Hongjie; DONG Cun

    2006-01-01

    Torus bifurcation is a relatively complicated bifurcation caused by a pair of complex conjuployed to reveal the relationship between torus bifurcation and some complex dynamics.Based on theoretical analysis and simulation studies, it is found that torus bifurcation is a typical route to chaos in power system.Some complex dynamics usually occur after a torus bifurcation, such as self-organization, deep bifurcations, exquisite structure, coexistence of chaos and divergence.It is also found that chaos has close relationship with various instability scenarios of power systems.Studies of this paper are helpful to understand the mechanism of torus bifurcation in power system and relationship of chaos and power system instabilities.

  2. Localised distributions and criteria for correctness in complex Langevin dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Aarts, Gert, E-mail: g.aarts@swan.ac.uk [Department of Physics, College of Science, Swansea University, Swansea (United Kingdom); Giudice, Pietro, E-mail: p.giudice@uni-muenster.de [Department of Physics, College of Science, Swansea University, Swansea (United Kingdom); Seiler, Erhard, E-mail: ehs@mppmu.mpg.de [Max-Planck-Institut für Physik (Werner-Heisenberg-Institut), München (Germany)

    2013-10-15

    Complex Langevin dynamics can solve the sign problem appearing in numerical simulations of theories with a complex action. In order to justify the procedure, it is important to understand the properties of the real and positive distribution, which is effectively sampled during the stochastic process. In the context of a simple model, we study this distribution by solving the Fokker–Planck equation as well as by brute force and relate the results to the recently derived criteria for correctness. We demonstrate analytically that it is possible that the distribution has support in a strip in the complexified configuration space only, in which case correct results are expected. -- Highlights: •Characterisation of the equilibrium distribution sampled in complex Langevin dynamics. •Connection between criteria for correctness and breakdown. •Solution of the Fokker–Planck equation in the case of real noise. •Analytical determination of support in complexified space.

  3. Lyapunov exponents a tool to explore complex dynamics

    CERN Document Server

    Pikovsky, Arkady

    2016-01-01

    Lyapunov exponents lie at the heart of chaos theory, and are widely used in studies of complex dynamics. Utilising a pragmatic, physical approach, this self-contained book provides a comprehensive description of the concept. Beginning with the basic properties and numerical methods, it then guides readers through to the most recent advances in applications to complex systems. Practical algorithms are thoroughly reviewed and their performance is discussed, while a broad set of examples illustrate the wide range of potential applications. The description of various numerical and analytical techniques for the computation of Lyapunov exponents offers an extensive array of tools for the characterization of phenomena such as synchronization, weak and global chaos in low and high-dimensional set-ups, and localization. This text equips readers with all the investigative expertise needed to fully explore the dynamical properties of complex systems, making it ideal for both graduate students and experienced researchers...

  4. Entropy and enthalpy of polyelectrolyte complexation: Langevin dynamics simulations.

    Science.gov (United States)

    Ou, Zhaoyang; Muthukumar, M

    2006-04-21

    We report a systematic study by Langevin dynamics simulation on the energetics of complexation between two oppositely charged polyelectrolytes of same charge density in dilute solutions of a good solvent with counterions and salt ions explicitly included. The enthalpy of polyelectrolyte complexation is quantified by comparisons of the Coulomb energy before and after complexation. The entropy of polyelectrolyte complexation is determined directly from simulations and compared with that from a mean-field lattice model explicitly accounting for counterion adsorption. At weak Coulomb interaction strengths, e.g., in solvents of high dielectric constant or with weakly charged polyelectrolytes, complexation is driven by a negative enthalpy due to electrostatic attraction between two oppositely charged chains, with counterion release entropy playing only a subsidiary role. In the strong interaction regime, complexation is driven by a large counterion release entropy and opposed by a positive enthalpy change. The addition of salt reduces the enthalpy of polyelectrolyte complexation by screening electrostatic interaction at all Coulomb interaction strengths. The counterion release entropy also decreases in the presence of salt, but the reduction only becomes significant at higher Coulomb interaction strengths. More significantly, in the range of Coulomb interaction strengths appropriate for highly charged polymers in aqueous solutions, complexation enthalpy depends weakly on salt concentration and counterion release entropy exhibits a large variation as a function of salt concentration. Our study quantitatively establishes that polyelectrolyte complexation in highly charged Coulomb systems is of entropic origin.

  5. Universality classes of fluctuation dynamics in hierarchical complex systems

    Science.gov (United States)

    Macêdo, A. M. S.; González, Iván R. Roa; Salazar, D. S. P.; Vasconcelos, G. L.

    2017-03-01

    A unified approach is proposed to describe the statistics of the short-time dynamics of multiscale complex systems. The probability density function of the relevant time series (signal) is represented as a statistical superposition of a large time-scale distribution weighted by the distribution of certain internal variables that characterize the slowly changing background. The dynamics of the background is formulated as a hierarchical stochastic model whose form is derived from simple physical constraints, which in turn restrict the dynamics to only two possible classes. The probability distributions of both the signal and the background have simple representations in terms of Meijer G functions. The two universality classes for the background dynamics manifest themselves in the signal distribution as two types of tails: power law and stretched exponential, respectively. A detailed analysis of empirical data from classical turbulence and financial markets shows excellent agreement with the theory.

  6. Rhythm dynamics of complex neuronal networks with mixed bursting neurons

    Institute of Scientific and Technical Information of China (English)

    Lü Yong-Bing; Shi Xia; Zheng Yan-Hong

    2013-01-01

    The spatiotemporal order and rhythm dynamics of a complex neuronal network with mixed bursting neurons are studied in this paper.A quantitative characteristic,the width factor,is introduced to describe the rhythm dynamics of an individual neuron,and the average width factor is used to characterize the rhythm dynamics of a neuronal network.An r parameter is introduced to denote the ratio of the short bursting neurons in the network.Then we investigate the effect of the ratio on the rhythm dynamics of the neuronal network.The critical value of r is derived,and the neurons in the network always remain short bursting when the r ratio is larger than the critical value.

  7. Genetic variability and relationships for populations of Cerastoderma edule and of the C. Glaucum complex

    Science.gov (United States)

    Hummel, H.; Wolowicz, M.; Bogaards, R. H.

    Genetic variability and relationships of populations of the cockles Cerastoderma edule and of the C. glaucum complex in Europe were determined by means of isoenzyme electrophoresis. Distinct isoenzyme markers allowed a clear distinction between these two taxa. C edule showed a higher genetic intra-population variability than the other cockle species. The imbalance of the genotypes within popuulation and the inter-population differentiation of the C. glaucum complex are stronger than in C. edule. The genetic variability is related to the different habitats of the species, the members of the C. glaucum complex living in more isolated areas and having more limited gene flow.

  8. Automated Guide Vehicles Dynamic Scheduling Based on Annealing Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Zou Gan

    2013-05-01

    Full Text Available Dispatching automated guided vehicles (AGVs is the common approach for AGVs scheduling in practice, the information about load arrivals in advance was not used to optimize the performance of the automated guided vehicles system (AGVsS. According to the characteristics of the AGVsS, the mathematical model of AGVs scheduling was established. A heuristic algorithm called Annealing Genetic Algorithm (AGA was presented to deal with the AGVs scheduling problem,and applied the algorithm dynamically by using it repeatedly under a combined rolling optimization strategy. the performance of the proposed approach for AGVs scheduling was compared with the dispatching rules by simulation. Results showed that the approach performs significantly better than the dispatching rules and proved that it is really effective for AGVsS.

  9. Reversible circuit synthesis by genetic programming using dynamic gate libraries

    Science.gov (United States)

    Abubakar, Mustapha Y.; Jung, Low Tang; Zakaria, Nordin; Younes, Ahmed; Abdel-Aty, Abdel-Haleem

    2017-06-01

    We have defined a new method for automatic construction of reversible logic circuits by using the genetic programming approach. The choice of the gate library is 100% dynamic. The algorithm is capable of accepting all possible combinations of the following gate types: NOT TOFFOLI, NOT PERES, NOT CNOT TOFFOLI, NOT CNOT SWAP FREDKIN, NOT CNOT TOFFOLI SWAP FREDKIN, NOT CNOT PERES, NOT CNOT SWAP FREDKIN PERES, NOT CNOT TOFFOLI PERES and NOT CNOT TOFFOLI SWAP FREDKIN PERES. Our method produced near optimum circuits in some cases when a particular subset of gate types was used in the library. Meanwhile, in some cases, optimal circuits were produced due to the heuristic nature of the algorithm. We compared the outcomes of our method with several existing synthesis methods, and it was shown that our algorithm performed relatively well compared to the previous synthesis methods in terms of the output efficiency of the algorithm and execution time as well.

  10. Parallel Genetic Algorithms with Dynamic Topology using Cluster Computing

    Directory of Open Access Journals (Sweden)

    ADAR, N.

    2016-08-01

    Full Text Available A parallel genetic algorithm (PGA conducts a distributed meta-heuristic search by employing genetic algorithms on more than one subpopulation simultaneously. PGAs migrate a number of individuals between subpopulations over generations. The layout that facilitates the interactions of the subpopulations is called the topology. Static migration topologies have been widely incorporated into PGAs. In this article, a PGA with a dynamic migration topology (D-PGA is proposed. D-PGA generates a new migration topology in every epoch based on the average fitness values of the subpopulations. The D-PGA has been tested against ring and fully connected migration topologies in a Beowulf Cluster. The D-PGA has outperformed the ring migration topology with comparable communication cost and has provided competitive or better results than a fully connected migration topology with significantly lower communication cost. PGA convergence behaviors have been analyzed in terms of the diversities within and between subpopulations. Conventional diversity can be considered as the diversity within a subpopulation. A new concept of permeability has been introduced to measure the diversity between subpopulations. It is shown that the success of the proposed D-PGA can be attributed to maintaining a high level of permeability while preserving diversity within subpopulations.

  11. Fine-scale spatial genetic dynamics over the life cycle of the tropical tree Prunus africana.

    Science.gov (United States)

    Berens, D G; Braun, C; González-Martínez, S C; Griebeler, E M; Nathan, R; Böhning-Gaese, K

    2014-11-01

    Studying fine-scale spatial genetic patterns across life stages is a powerful approach to identify ecological processes acting within tree populations. We investigated spatial genetic dynamics across five life stages in the insect-pollinated and vertebrate-dispersed tropical tree Prunus africana in Kakamega Forest, Kenya. Using six highly polymorphic microsatellite loci, we assessed genetic diversity and spatial genetic structure (SGS) from seed rain and seedlings, and different sapling stages to adult trees. We found significant SGS in all stages, potentially caused by limited seed dispersal and high recruitment rates in areas with high light availability. SGS decreased from seed and early seedling stages to older juvenile stages. Interestingly, SGS was stronger in adults than in late juveniles. The initial decrease in SGS was probably driven by both random and non-random thinning of offspring clusters during recruitment. Intergenerational variation in SGS could have been driven by variation in gene flow processes, overlapping generations in the adult stage or local selection. Our study shows that complex sequential processes during recruitment contribute to SGS of tree populations.

  12. On the complexity of Nash dynamics and Sink Equilibria

    CERN Document Server

    Mirrokni, Vahab

    2009-01-01

    Studying Nash dynamics is an important approach for analyzing the outcome of games with repeated selfish behavior of self-interested agents. Sink equilibria has been introduced by Goemans, Mirrokni, and Vetta for studying social cost on Nash dynamics over pure strategies in games. However, they do not address the complexity of sink equilibria in these games. Recently, Fabrikant and Papadimitriou initiated the study of the complexity of Nash dynamics in two classes of games. In order to completely understand the complexity of Nash dynamics in a variety of games, we study the following three questions for various games: (i) given a state in game, can we verify if this state is in a sink equilibrium or not? (ii) given an instance of a game, can we verify if there exists any sink equilibrium other than pure Nash equilibria? and (iii) given an instance of a game, can we verify if there exists a pure Nash equilibrium (i.e, a sink equilibrium with one state)? In this paper, we almost answer all of the above question...

  13. Green turtle (Chelonia mydas) genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil

    Science.gov (United States)

    Jordão, Juliana Costa; Bondioli, Ana Cristina Vigliar; Guebert, Flavia Maria; de Thoisy, Benoit; Toledo, Lurdes Foresti de Almeida

    2015-01-01

    Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs), where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas) at the Paranaguá Estuarine Complex (PEC), Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60), and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20–25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations. PMID:26500439

  14. Green turtle (Chelonia mydas) genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil.

    Science.gov (United States)

    Jordão, Juliana Costa; Bondioli, Ana Cristina Vigliar; Guebert, Flavia Maria; de Thoisy, Benoit; Toledo, Lurdes Foresti de Almeida

    2015-01-01

    Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs), where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas) at the Paranaguá Estuarine Complex (PEC), Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60), and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20-25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.

  15. Green turtle (Chelonia mydas genetic diversity at Paranaguá Estuarine Complex feeding grounds in Brazil

    Directory of Open Access Journals (Sweden)

    Juliana Costa Jordão

    2015-09-01

    Full Text Available Sea turtles are marine reptiles that undertake long migrations through their life, with limited information regarding juvenile stages. Feeding grounds (FGs, where they spend most of their lives, are composed by individuals from different natal origins, known as mixed stock populations. The aim of this study was to assess genetic composition, natal origins and demographic history of juvenile green turtles (Chelonia mydas at the Paranaguá Estuarine Complex (PEC, Brazil, considered a Natural World Heritage site. Tissue samples of stranded animals were collected (n = 60, and 700 bp mitochondrial DNA sequences were generated and compared to shorter sequences from previously published studies. Global exact tests of differentiation revealed significant differences among PEC and the other FGs, except those at the South Atlantic Ocean. Green turtles at PEC present genetic signatures similar to those of nesting females from Ascension Island, Guinea Bissau and Aves Island/Surinam. Population expansion was evidenced to have occurred 20–25 kYA, reinforcing the hypothesis of recovery from Southern Atlantic refugia after the last Glacial Maximum. These results contribute to a better understanding of the dynamics of green turtle populations at a protected area by providing knowledge on the dispersion patterns and reinforcing the importance of the interconnectivity between nesting and foraging populations.

  16. On Complex Langevin Dynamics and the Evaluation of Observables

    CERN Document Server

    Durakovic, Amel; Tranberg, Anders

    2014-01-01

    In stochastic quantisation, quantum mechanical expectation values are computed as averages over the time history of a stochastic process described by a Langevin equation. Complex stochastic quantisation, though theoretically not rigorously established, extends this idea to cases where the action is complex-valued by complexifying the basic degrees of freedom, all observables and allowing the stochastic process to probe the complexified configuration space. We review the method for a previously studied one-dimensional toy model, the U(1) one link model. We confirm that complex Langevin dynamics only works for a certain range of parameters, misestimating observables otherwise. A curious effect is observed where all moments of the basic stochastic variable are misestimated, although these misestimated moments may be used to construct, by a Taylor series, other observables that are reproduced correctly. This suggests a subtle but not completely resolved relationship between the original complex integration measur...

  17. Control of Complex Systems Using Bayesian Networks and Genetic Algorithm

    CERN Document Server

    Marwala, Tshilidzi

    2007-01-01

    A method based on Bayesian neural networks and genetic algorithm is proposed to control the fermentation process. The relationship between input and output variables is modelled using Bayesian neural network that is trained using hybrid Monte Carlo method. A feedback loop based on genetic algorithm is used to change input variables so that the output variables are as close to the desired target as possible without the loss of confidence level on the prediction that the neural network gives. The proposed procedure is found to reduce the distance between the desired target and measured outputs significantly.

  18. Complex Granular Flow Dynamics in Fruit Powder Production Lines

    OpenAIRE

    Bakhshinejad, Ali, 1984-

    2013-01-01

    One of the most important parts in every industry, is packaging which is located at the last part of the product line. In fruit powder product line lots of studies applied to study the complex dynamics of the powders in response to the vertical vibration. In this study cyclone collector condition was simulate with a rectangular throw out bin and the dynamics of the powders in response to the horizontal vibration studied. An ADXL345 accelerometer does employed in order to observe the accel...

  19. Active Control of Complex Systems via Dynamic (Recurrent) Neural Networks

    Science.gov (United States)

    1992-05-30

    individuals ( genetic , same diet, etc.). 35 I z= o + Xe xi + Xe, x xj + Oijk Xi X Xk + 3:4 i ij ijk Since it has been shown that the KG multinomial can model...AI Fiur 48:Dynamic PNNUsdithSyemInifcio Fit ACTIJ3.1 ACTD3.2 ACTD3.3 ACTD3.4 FtD . 14 1.615314 ACTD3.2 1.42 1.54 1.54 1.423 ACTD3.3 1.40 1.56 1.52

  20. Structural Dynamics of the MecA-ClpC Complex

    Science.gov (United States)

    Liu, Jing; Mei, Ziqing; Li, Ningning; Qi, Yutao; Xu, Yanji; Shi, Yigong; Wang, Feng; Lei, Jianlin; Gao, Ning

    2013-01-01

    The MecA-ClpC complex is a bacterial type II AAA+ molecular machine responsible for regulated unfolding of substrates, such as transcription factors ComK and ComS, and targeting them to ClpP for degradation. The six subunits of the MecA-ClpC complex form a closed barrel-like structure, featured with three stacked rings and a hollow passage, where substrates are threaded and translocated through successive pores. Although the general concepts of how polypeptides are unfolded and translocated by internal pore loops of AAA+ proteins have long been conceived, the detailed mechanistic model remains elusive. With cryoelectron microscopy, we captured four different structures of the MecA-ClpC complexes. These complexes differ in the nucleotide binding states of the two AAA+ rings and therefore might presumably reflect distinctive, representative snapshots from a dynamic unfolding cycle of this hexameric complex. Structural analysis reveals that nucleotide binding and hydrolysis modulate the hexameric complex in a number of ways, including the opening of the N-terminal ring, the axial and radial positions of pore loops, the compactness of the C-terminal ring, as well as the relative rotation between the two nucleotide-binding domain rings. More importantly, our structural and biochemical data indicate there is an active allosteric communication between the two AAA+ rings and suggest that concerted actions of the two AAA+ rings are required for the efficiency of the substrate unfolding and translocation. These findings provide important mechanistic insights into the dynamic cycle of the MecA-ClpC unfoldase and especially lay a foundation toward the complete understanding of the structural dynamics of the general type II AAA+ hexamers. PMID:23595989

  1. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.

    2011-01-01

    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  2. Improved time complexity analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2015-01-01

    A runtime analysis of the Simple Genetic Algorithm (SGA) for the OneMax problem has recently been presented proving that the algorithm with population size μ≤n1/8−ε requires exponential time with overwhelming probability. This paper presents an improved analysis which overcomes some limitations...

  3. Architectural DNA: A genetic exploration of complex structures

    NARCIS (Netherlands)

    Van Embden Andres, M.V.; Turrin, M.; Von Buelow, P.

    2011-01-01

    The approach demonstrated in this paper uses Evolutionary Computation (EC) to enhance and modify structural form based on biological micro structures.The forms are modified to conform to new boundary conditions associated with architectural structures.The process is based on a Genetic Algorithm (GA)

  4. Evolutionary genetics: inheritance of a complex pollination syndrome.

    Science.gov (United States)

    Wright, Kevin M; Bomblies, Kirsten

    2013-06-17

    How adaptive traits that are controlled by multiple genes evolve is an intriguing question in evolutionary genetics. A recent study shows that tight linkage allows genes that contribute to a multitrait pollination syndrome to be inherited together as a unit. Copyright © 2013 Elsevier Ltd. All rights reserved.

  5. Genetic Networks of Complex Disorders: from a Novel Search Engine for PubMed Article Database

    National Research Council Canada - National Science Library

    Jung, Jae-Yoon; Wall, Dennis Paul

    2013-01-01

    Finding genetic risk factors of complex disorders may involve reviewing hundreds of genes or thousands of research articles iteratively, but few tools have been available to facilitate this procedure...

  6. Life as Complex Systems Viewpoint from Intra-Inter Dynamics

    CERN Document Server

    Kaneko, K

    1998-01-01

    Basic problems in complex systems are surveyed in connection with Life. As a key issue for complex systems, complementarity between syntax/rule/parts and semantics/behavior/whole is stressed. To address the issue, a constructive approach for a biological system is proposed. As a construction in a computer, intra-inter dynamics is presented for cell biology, where the following five general features are drawn from our model experiments; intrinsic diversification, recursive type formation, rule generation, formation of internal representation, and macroscopic robustness. Significance of the constructed logic to the biology of existing organisms is also discussed.

  7. Linking extinction-colonization dynamics to genetic structure in a salamander metapopulation.

    Science.gov (United States)

    Cosentino, Bradley J; Phillips, Christopher A; Schooley, Robert L; Lowe, Winsor H; Douglas, Marlis R

    2012-04-22

    Theory predicts that founder effects have a primary role in determining metapopulation genetic structure. However, ecological factors that affect extinction-colonization dynamics may also create spatial variation in the strength of genetic drift and migration. We tested the hypothesis that ecological factors underlying extinction-colonization dynamics influenced the genetic structure of a tiger salamander (Ambystoma tigrinum) metapopulation. We used empirical data on metapopulation dynamics to make a priori predictions about the effects of population age and ecological factors on genetic diversity and divergence among 41 populations. Metapopulation dynamics of A. tigrinum depended on wetland area, connectivity and presence of predatory fish. We found that newly colonized populations were more genetically differentiated than established populations, suggesting that founder effects influenced genetic structure. However, ecological drivers of metapopulation dynamics were more important than age in predicting genetic structure. Consistent with demographic predictions from metapopulation theory, genetic diversity and divergence depended on wetland area and connectivity. Divergence was greatest in small, isolated wetlands where genetic diversity was low. Our results show that ecological factors underlying metapopulation dynamics can be key determinants of spatial genetic structure, and that habitat area and isolation may mediate the contributions of drift and migration to divergence and evolution in local populations.

  8. Genome evolution predicts genetic interactions in protein complexes and reveals cancer drug targets

    NARCIS (Netherlands)

    Lu, X.; Kensche, P.R.; Huynen, M.A.; Notebaart, R.A.

    2013-01-01

    Genetic interactions reveal insights into cellular function and can be used to identify drug targets. Here we construct a new model to predict negative genetic interactions in protein complexes by exploiting the evolutionary history of genes in parallel converging pathways in metabolism. We evaluate

  9. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    NARCIS (Netherlands)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F.; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We i

  10. Genome-wide association data reveal a global map of genetic interactions among protein complexes.

    Directory of Open Access Journals (Sweden)

    Gregory Hannum

    2009-12-01

    Full Text Available This work demonstrates how gene association studies can be analyzed to map a global landscape of genetic interactions among protein complexes and pathways. Despite the immense potential of gene association studies, they have been challenging to analyze because most traits are complex, involving the combined effect of mutations at many different genes. Due to lack of statistical power, only the strongest single markers are typically identified. Here, we present an integrative approach that greatly increases power through marker clustering and projection of marker interactions within and across protein complexes. Applied to a recent gene association study in yeast, this approach identifies 2,023 genetic interactions which map to 208 functional interactions among protein complexes. We show that such interactions are analogous to interactions derived through reverse genetic screens and that they provide coverage in areas not yet tested by reverse genetic analysis. This work has the potential to transform gene association studies, by elevating the analysis from the level of individual markers to global maps of genetic interactions. As proof of principle, we use synthetic genetic screens to confirm numerous novel genetic interactions for the INO80 chromatin remodeling complex.

  11. Complex chaos in the conditional dynamics of qubits

    CERN Document Server

    Kiss, T; Jex, I; Vymetal, S

    2005-01-01

    We analyse the consequences of measurement induced non-linearity for the dynamical behaviour of qubits. We present a one-qubit scheme where the equation governing the time evolution is a complex nonlinear map with one complex parameter. The map is a rational function of degree two leading to chaotic dynamics of the quantum state, in contrast to the usual notion of quantum chaos. The set of initial values with irregular behavior, the Julia set, has a nontrivial structure depending crucially on the parameter of the map. The family of maps labeled by the parameter can be characterized by the attractive fixed points. Each map with a fixed parameter can have at most two attractive cycles. This type of instability is also present in purification protocols based on conditional non-linear transformations of qubits.

  12. A dynamic epidemic control model on uncorrelated complex networks

    Institute of Scientific and Technical Information of China (English)

    Pei Wei-Dong; Chen Zeng-Qiang; Yuan Zhu-Zhi

    2008-01-01

    In this paper,a dynamic epidemic control model on the uncorrelated complex networks is proposed.By means of theoretical analysis,we found that the new model has a similar epidemic threshold as that of the susceptible-infectedrecovered (SIR) model on the above networks,but it can reduce the prevalence of the infected individuals remarkably.This result may help us understand epidemic spreading phenomena on real networks and design appropriate strategies to control infections.

  13. Coupled dark energy: a dynamical analysis with complex scalar field

    Energy Technology Data Exchange (ETDEWEB)

    Landim, Ricardo C.G. [Universidade de Sao Paulo, Instituto de Fisica, Caixa Postal 66318, Sao Paulo, SP (Brazil)

    2016-01-15

    The dynamical analysis for coupled dark energy with dark matter is presented, where a complex scalar field is taken into account and it is considered in the presence of a barothropic fluid. We consider three dark-energy candidates: quintessence, phantom, and tachyon. The critical points are found and their stabilities analyzed, leading to the three cosmological eras (radiation, matter, and dark energy), for a generic potential. The results presented here extend the previous analyses found in the literature. (orig.)

  14. Structure and dynamics of small van der Waals complexes

    Energy Technology Data Exchange (ETDEWEB)

    Loreau, J. [Service de Chimie Quantique et Photophysique, Université Libre de Bruxelles (ULB) CP 160/09, 1050 Brussels (Belgium)

    2014-10-06

    We illustrate computational aspects of the calculation of the potential energy surfaces of small (up to five atoms) van der Waals complexes with high-level quantum chemistry techniques such as the CCSD(T) method with extended basis sets. We discuss the compromise between the required accuracy and the computational time. Further, we show how these potential energy surfaces can be fitted and used in dynamical calculations such as non-reactive inelastic scattering.

  15. Quantum Sensing of Noisy and Complex Systems under Dynamical Control

    Directory of Open Access Journals (Sweden)

    Gershon Kurizki

    2016-12-01

    Full Text Available We review our unified optimized approach to the dynamical control of quantum-probe interactions with noisy and complex systems viewed as thermal baths. We show that this control, in conjunction with tools of quantum estimation theory, may be used for inferring the spectral and spatial characteristics of such baths with high precision. This approach constitutes a new avenue in quantum sensing, dubbed quantum noise spectroscopy.

  16. Dynamic Coherence in Excitonic Molecular Complexes under Various Excitation Conditions

    CERN Document Server

    Chenu, Aurélia; Mancal, Tomáš

    2013-01-01

    In this paper, we investigate the relevance of dynamic electronic coherence under conditions natural to light-harvesting systems. We formulate the results of a quantum mechanical treatment of a weak light-matter interaction in terms of experimental observable, such as the incident light spectrum and the absorption spectrum of the material, and we derive the description of the incoherent F\\"orster type energy transfer fully from the wave function formalism. We demonstrate that excitation of a coherent superposition of electronic eigenstates of natural light-harvesting complexes by sunlight or by excitation transfer from a neighboring antenna is unlikely and that dynamical coherence therefore cannot play any significant role in natural photosynthesis, regardless of their life time. Dynamical coherence as a transient phenomenon must be strictly distinguished from the effect of excited state delocalization (also termed quantum coherence in the literature) which is established by interaction between the pigments a...

  17. Dynamical complexity in the C.elegans neural network

    Science.gov (United States)

    Antonopoulos, C. G.; Fokas, A. S.; Bountis, T. C.

    2016-09-01

    We model the neuronal circuit of the C.elegans soil worm in terms of a Hindmarsh-Rose system of ordinary differential equations, dividing its circuit into six communities which are determined via the Walktrap and Louvain methods. Using the numerical solution of these equations, we analyze important measures of dynamical complexity, namely synchronicity, the largest Lyapunov exponent, and the ΦAR auto-regressive integrated information theory measure. We show that ΦAR provides a useful measure of the information contained in the C.elegans brain dynamic network. Our analysis reveals that the C.elegans brain dynamic network generates more information than the sum of its constituent parts, and that attains higher levels of integrated information for couplings for which either all its communities are highly synchronized, or there is a mixed state of highly synchronized and desynchronized communities.

  18. Topics in Complexity: Dynamical Patterns in the Cyberworld

    Science.gov (United States)

    Qi, Hong

    Quantitative understanding of mechanism in complex systems is a common "difficult" problem across many fields such as physical, biological, social and economic sciences. Investigation on underlying dynamics of complex systems and building individual-based models have recently been fueled by big data resulted from advancing information technology. This thesis investigates complex systems in social science, focusing on civil unrests on streets and relevant activities online. Investigation consists of collecting data of unrests from open digital source, featuring dynamical patterns underlying, making predictions and constructing models. A simple law governing the progress of two-sided confrontations is proposed with data of activities at micro-level. Unraveling the connections between activity of organizing online and outburst of unrests on streets gives rise to a further meso-level pattern of human behavior, through which adversarial groups evolve online and hyper-escalate ahead of real-world uprisings. Based on the patterns found, noticeable improvement of prediction of civil unrests is achieved. Meanwhile, novel model created from combination of mobility dynamics in the cyberworld and a traditional contagion model can better capture the characteristics of modern civil unrests and other contagion-like phenomena than the original one.

  19. Molecular dynamics simulations of a membrane protein/amphipol complex.

    Science.gov (United States)

    Perlmutter, Jason D; Popot, Jean-Luc; Sachs, Jonathan N

    2014-10-01

    Amphipathic polymers known as "amphipols" provide a highly stabilizing environment for handling membrane proteins in aqueous solutions. A8-35, an amphipol with a polyacrylate backbone and hydrophobic grafts, has been extensively characterized and widely employed for structural and functional studies of membrane proteins using biochemical and biophysical approaches. Given the sensitivity of membrane proteins to their environment, it is important to examine what effects amphipols may have on the structure and dynamics of the proteins they complex. Here we present the first molecular dynamics study of an amphipol-stabilized membrane protein, using Escherichia coli OmpX as a model. We begin by describing the structure of the complexes formed by supplementing OmpX with increasing amounts of A8-35, in order to determine how the amphipol interacts with the transmembrane and extramembrane surfaces of the protein. We then compare the dynamics of the protein in either A8-35, a detergent, or a lipid bilayer. We find that protein dynamics on all accessible length scales is restrained by A8-35, which provides a basis to understanding some of the stabilizing and functional effects of amphipols that have been experimentally observed.

  20. A new conceptual framework for investigating complex genetic disease

    Science.gov (United States)

    Hussain, Shobbir

    2015-01-01

    Some common diseases are known to have an inherited component, however, their population- and familial-incidence patterns do not conform to any known monogenic Mendelian pattern of inheritance and instead they are currently much better explained if an underlying polygenic architecture is posited. Studies that have attempted to identify the causative genetic factors have been designed on this polygenic framework, but so far the yield has been largely unsatisfactory. Based on accumulating recent observations concerning the roles of somatic mosaicism in disease, in this article a second framework which posits a single gene-two hit model which can be modulated by a mutator/anti-mutator genetic background is suggested. I discuss whether such a model can be considered a viable alternative based on current knowledge, its advantages over the current polygenic framework, and describe practical routes via which the new framework can be investigated. PMID:26583033

  1. Complex genetic origin of Indian populations and its implications

    Indian Academy of Sciences (India)

    Rakesh Tamang; Lalji Singh; Kumarasamy Thangaraj

    2012-11-01

    Indian populations are classified into various caste, tribe and religious groups, which altogether makes them very unique compared to rest of the world. The long-term firm socio-religious boundaries and the strict endogamy practices along with the evolutionary forces have further supplemented the existing high-level diversity. As a result, drawing definite conclusions on its overall origin, affinity, health and disease conditions become even more sophisticated than was thought earlier. In spite of these challenges, researchers have undertaken tireless and extensive investigations using various genetic markers to estimate genetic variation and its implication in health and diseases. We have demonstrated that the Indian populations are the descendents of the very first modern humans, who ventured the journey of out-of-Africa about 65,000 years ago. The recent gene flow from east and west Eurasia is also evident. Thus, this review attempts to summarize the unique genetic variation among Indian populations as evident from our extensive study among approximately 20,000 samples across India.

  2. Morphological evolution and genetic differentiation in Daphnia species complexes

    NARCIS (Netherlands)

    Gießer, S.; Mader, E.; Schwenk, K.

    1999-01-01

    Despite many ecological and evolutionary studies, the history of several species complexes within the freshwater crustacean genus Daphnia (Branchiopoda, Anomopoda) is poorly understood. In particular, the Daphnia longispina group, comprising several large-lake species, is characterized by pronounced

  3. Genetic Networks of Complex Disorders: from a Novel Search Engine for PubMed Article Database.

    Science.gov (United States)

    Jung, Jae-Yoon; Wall, Dennis Paul

    2013-01-01

    Finding genetic risk factors of complex disorders may involve reviewing hundreds of genes or thousands of research articles iteratively, but few tools have been available to facilitate this procedure. In this work, we built a novel publication search engine that can identify target-disorder specific, genetics-oriented research articles and extract the genes with significant results. Preliminary test results showed that the output of this engine has better coverage in terms of genes or publications, than other existing applications. We consider it as an essential tool for understanding genetic networks of complex disorders.

  4. An introduction to complex systems society, ecology, and nonlinear dynamics

    CERN Document Server

    Fieguth, Paul

    2017-01-01

    This undergraduate text explores a variety of large-scale phenomena - global warming, ice ages, water, poverty - and uses these case studies as a motivation to explore nonlinear dynamics, power-law statistics, and complex systems. Although the detailed mathematical descriptions of these topics can be challenging, the consequences of a system being nonlinear, power-law, or complex are in fact quite accessible. This book blends a tutorial approach to the mathematical aspects of complex systems together with a complementary narrative on the global/ecological/societal implications of such systems. Nearly all engineering undergraduate courses focus on mathematics and systems which are small scale, linear, and Gaussian. Unfortunately there is not a single large-scale ecological or social phenomenon that is scalar, linear, and Gaussian. This book offers students insights to better understand the large-scale problems facing the world and to realize that these cannot be solved by a single, narrow academic field or per...

  5. Universality of flux-fluctuation law in complex dynamical systems

    Science.gov (United States)

    Zhou, Zhao; Huang, Zi-Gang; Huang, Liang; Lai, Ying-Cheng; Yang, Lei; Xue, De-Sheng

    2013-01-01

    Recent work has revealed a law governing flux fluctuation and the average flux in complex dynamical systems. We establish the universality of this flux-fluctuation law through the following steps: (i) We derive the law in a more general setting, showing that it depends on a single parameter characterizing the external driving; (ii) we conduct extensive numerical computations using distinct external driving, different network topologies, and multiple traffic routing strategies; and (iii) we analyze data from an actual vehicle traffic system in a major city in China to lend more credence to the universality of the flux-fluctuation law. Additional factors considered include flux fluctuation on links, window size effect, and hidden topological structures such as nodal degree correlation. Besides its fundamental importance in complex systems, the flux-fluctuation law can be used to infer certain intrinsic property of the system for potential applications such as control of complex systems for improved performance.

  6. Modularity and the spread of perturbations in complex dynamical systems

    Science.gov (United States)

    Kolchinsky, Artemy; Gates, Alexander J.; Rocha, Luis M.

    2015-12-01

    We propose a method to decompose dynamical systems based on the idea that modules constrain the spread of perturbations. We find partitions of system variables that maximize "perturbation modularity," defined as the autocovariance of coarse-grained perturbed trajectories. The measure effectively separates the fast intramodular from the slow intermodular dynamics of perturbation spreading (in this respect, it is a generalization of the "Markov stability" method of network community detection). Our approach captures variation of modular organization across different system states, time scales, and in response to different kinds of perturbations: aspects of modularity which are all relevant to real-world dynamical systems. It offers a principled alternative to detecting communities in networks of statistical dependencies between system variables (e.g., "relevance networks" or "functional networks"). Using coupled logistic maps, we demonstrate that the method uncovers hierarchical modular organization planted in a system's coupling matrix. Additionally, in homogeneously coupled map lattices, it identifies the presence of self-organized modularity that depends on the initial state, dynamical parameters, and type of perturbations. Our approach offers a powerful tool for exploring the modular organization of complex dynamical systems.

  7. Retrospective analysis of main and interaction effects in genetic association studies of human complex traits

    DEFF Research Database (Denmark)

    Tan, Qihua; Christiansen, Lene; Brasch-Andersen, Charlotte;

    2007-01-01

    BACKGROUND: The etiology of multifactorial human diseases involves complex interactions between numerous environmental factors and alleles of many genes. Efficient statistical tools are demanded in identifying the genetic and environmental variants that affect the risk of disease development....... This paper introduces a retrospective polytomous logistic regression model to measure both the main and interaction effects in genetic association studies of human discrete and continuous complex traits. In this model, combinations of genotypes at two interacting loci or of environmental exposure...... regression model can be used as a convenient tool for assessing both main and interaction effects in genetic association studies of human multifactorial diseases involving genetic and non-genetic factors as well as categorical or continuous traits....

  8. Systems genetics view of endometriosis: a common complex disorder.

    Science.gov (United States)

    Baranov, Vladislav S; Ivaschenko, Tatyana E; Liehr, Thomas; Yarmolinskaya, Maria I

    2015-02-01

    Endometriosis is a condition in which cells derived from the endometrium grow outside the uterus, e.g. in the peritoneum (external genital endometriosis). As these cells are under the influence of female hormones, major symptoms of endometriosis are pain, especially during the cycle, and infertility. Numerous hypotheses for the formation of endometriosis can be found in the literature, but there is growing evidence of serious genetic contributions to endometriosis susceptibility. The involvement of genes, steroid hormone metabolism, immunological reactions, receptor formation, inflammation, proliferation, apoptosis, intercellular adhesion, cell invasion and angiogenesis as well as genes regulating the activity of aforementioned enzymes have been suggested. Some more recently suggested candidate genes picked up in genome-wide association studies are involved in oncogenesis, metaplasia of endometrium cells and pathways of embryonic development of the female reproductive system. However, gene mutations proven to be causative for endometriosis have not been identified so far, even though the abnormal expression of candidate genes for endometriosis could be provoked by different epigenetic modifications including DNA methylation, heterochromatization or introduction of regulatory miRNA. We hypothesize that endometriosis is induced by a combination of abnormal genetic and/or epigenetic mutations: the latter pave the way for pathological changes which become irreversible, and according to the "epigenetic landscape" theory, this proceeds to the typical clinical manifestations. Two stages in the endometriosis pathway are suggested: (1) induction of primary endometrial cells toward endometriosis, and (2) implantation and progression of these cells into endometriosis lesions. The model favors endometriosis as an outgrowth of primary cells different in their origin, canalization of pathological processes, manifestation diversity provoked by unique genetic background and

  9. Improved time complexity analysis of the Simple Genetic Algorithm

    DEFF Research Database (Denmark)

    Oliveto, Pietro S.; Witt, Carsten

    2015-01-01

    A runtime analysis of the Simple Genetic Algorithm (SGA) for the OneMax problem has recently been presented proving that the algorithm with population size μ≤n1/8−ε requires exponential time with overwhelming probability. This paper presents an improved analysis which overcomes some limitations...... this is a major improvement towards the reusability of the techniques in future systematic analyses of GAs. Finally, we consider the more natural SGA using selection with replacement rather than without replacement although the results hold for both algorithmic versions. Experiments are presented to explore...

  10. Studies of Transition Metal Complexes Using Dynamic NMR Techniques.

    Science.gov (United States)

    Coston, Timothy Peter John

    Available from UMI in association with The British Library. This Thesis is primarily concerned with the quantitative study of fluxional processes in, predominantly platinum(IV) complexes, with the ligands 1,1,2,2-tetrakis(methylthio)ethane (MeS)_2CHCH(SMe)_2 , and 1,1,2,2-tetrakis(methylthio)ethene (MeS) _2C=C(SMe)_2. Quantitative information relating to the energetics of these processes has been obtained by a combination of one- and two-dimensional NMR techniques. Chapter One provides an introduction to the background of fluxional processes in transition metal complexes together with data concerning the energetics of the processes that have already been studied by NMR techniques. Chapter Two provides a thorough grounding in NMR techniques, in particular those concerned with the quantitative measurement of rates involved in chemical exchange processes. A description of the use of 2D EXSY NMR spectroscopy in obtaining rate data is given. The properties of the magnetic isotope of platinum are given in Chapter Three. A general survey is also given of some additional compounds that have already been studied by platinum-195 spectroscopy. Chapter Four is concerned with the quantitative study of low temperature (complexes (PtXMe_3 (MeS)_2CHCH(SMe) _2) (X = Cl, Br, I). These complexes were studied by dynamic nuclear magnetic resonance and the information regarding the rates of sulphur inversion was obtained by complete band-shape analysis. Chapter Five is concerned with high temperature (>333 K) fluxionality, of the previous complexes, as studied by a combination of one- and two -dimensional NMR techniques. Aside from obtaining thermodynamic parameters for all the processes, a new novel mechanism is proposed. Chapter Six is primarily concerned with the NMR investigation of the new dinuclear complexes ((PtXMe _3)_2(MeS) _2CHCH(SMe)_2) (X = Cl, Br, I). The solution properties have been established and thermo-dynamic parameters obtained for low and high temperature

  11. Thinking in complexity the complex dynamics of matter, mind, and mankind

    CERN Document Server

    Mainzer, Klaus

    1994-01-01

    The theory of nonlinear complex systems has become a successful and widely used problem-solving approach in the natural sciences - from laser physics, quantum chaos and meteorology to molecular modeling in chemistry and computer simulations of cell growth in biology In recent times it has been recognized that many of the social, ecological and political problems of mankind are also of a global, complex and nonlinear nature And one of the most exciting topics of present scientific and public interest is the idea that even the human mind is governed largely by the nonlinear dynamics of complex systems In this wide-ranging but concise treatment Prof Mainzer discusses, in nontechnical language, the common framework behind these endeavours Special emphasis is given to the evolution of new structures in natural and cultural systems and it is seen clearly how the new integrative approach of complexity theory can give new insights that were not available using traditional reductionistic methods

  12. The dynamic relationship between polyandry and selfish genetic elements.

    Science.gov (United States)

    Wedell, Nina

    2013-03-05

    Selfish genetic elements (SGEs) are ubiquitous in eukaryotes and bacteria, and make up a large part of the genome. They frequently target sperm to increase their transmission success, but these manipulations are often associated with reduced male fertility. Low fertility of SGE-carrying males is suggested to promote polyandry as a female strategy to bias paternity against male carriers. Support for this hypothesis is found in several taxa, where SGE-carrying males have reduced sperm competitive ability. In contrast, when SGEs give rise to reproductive incompatibilities between SGE-carrying males and females, polyandry is not necessarily favoured, irrespective of the detrimental impact on male fertility. This is due to the frequency-dependent nature of these incompatibilities, because they will decrease in the population as the frequency of SGEs increases. However, reduced fertility of SGE-carrying males can prevent the successful population invasion of SGEs. In addition, SGEs can directly influence male and female mating behaviour, mating rates and reproductive traits (e.g. female reproductive tract length and male sperm). This reveals a potent and dynamic interaction between SGEs and polyandry highlighting the potential to generate sexual selection and conflict, but also indicates that polyandry can promote harmony within the genome by undermining the spread of SGEs.

  13. HDL and atherosclerotic cardiovascular disease: genetic insights into complex biology.

    Science.gov (United States)

    Rosenson, Robert S; Brewer, H Bryan; Barter, Philip J; Björkegren, Johan L M; Chapman, M John; Gaudet, Daniel; Kim, Daniel Seung; Niesor, Eric; Rye, Kerry-Anne; Sacks, Frank M; Tardif, Jean-Claude; Hegele, Robert A

    2017-08-10

    Plasma levels of HDL cholesterol (HDL-C) predict the risk of cardiovascular disease at the epidemiological level, but a direct causal role for HDL in cardiovascular disease remains controversial. Studies in animal models and humans with rare monogenic disorders link only particular HDL-associated mechanisms with causality, including those mechanisms related to particle functionality rather than cholesterol content. Mendelian randomization studies indicate that most genetic variants that affect a range of pathways that increase plasma HDL-C levels are not usually associated with reduced risk of cardiovascular disease, with some exceptions, such as cholesteryl ester transfer protein variants. Furthermore, only a fraction of HDL-C variation has been explained by known loci from genome-wide association studies (GWAS), suggesting the existence of additional pathways and targets. Systems genetics can enhance our understanding of the spectrum of HDL pathways, particularly those pathways that involve new and non-obvious GWAS loci. Bioinformatic approaches can also define new molecular interactions inferred from both large-scale genotypic data and RNA sequencing data to reveal biologically meaningful gene modules and networks governing HDL metabolism with direct relevance to disease end points. Targeting these newly recognized causal networks might inform the development of novel therapeutic strategies to reduce the risk of cardiovascular disease.

  14. Outlier-resilient complexity analysis of heartbeat dynamics

    Science.gov (United States)

    Lo, Men-Tzung; Chang, Yi-Chung; Lin, Chen; Young, Hsu-Wen Vincent; Lin, Yen-Hung; Ho, Yi-Lwun; Peng, Chung-Kang; Hu, Kun

    2015-03-01

    Complexity in physiological outputs is believed to be a hallmark of healthy physiological control. How to accurately quantify the degree of complexity in physiological signals with outliers remains a major barrier for translating this novel concept of nonlinear dynamic theory to clinical practice. Here we propose a new approach to estimate the complexity in a signal by analyzing the irregularity of the sign time series of its coarse-grained time series at different time scales. Using surrogate data, we show that the method can reliably assess the complexity in noisy data while being highly resilient to outliers. We further apply this method to the analysis of human heartbeat recordings. Without removing any outliers due to ectopic beats, the method is able to detect a degradation of cardiac control in patients with congestive heart failure and a more degradation in critically ill patients whose life continuation relies on extracorporeal membrane oxygenator (ECMO). Moreover, the derived complexity measures can predict the mortality of ECMO patients. These results indicate that the proposed method may serve as a promising tool for monitoring cardiac function of patients in clinical settings.

  15. Precise regulation of gene expression dynamics favors complex promoter architectures.

    Directory of Open Access Journals (Sweden)

    Dirk Müller

    2009-01-01

    Full Text Available Promoters process signals through recruitment of transcription factors and RNA polymerase, and dynamic changes in promoter activity constitute a major noise source in gene expression. However, it is barely understood how complex promoter architectures determine key features of promoter dynamics. Here, we employ prototypical promoters of yeast ribosomal protein genes as well as simplified versions thereof to analyze the relations among promoter design, complexity, and function. These promoters combine the action of a general regulatory factor with that of specific transcription factors, a common motif of many eukaryotic promoters. By comprehensively analyzing stationary and dynamic promoter properties, this model-based approach enables us to pinpoint the structural characteristics underlying the observed behavior. Functional tradeoffs impose constraints on the promoter architecture of ribosomal protein genes. We find that a stable scaffold in the natural design results in low transcriptional noise and strong co-regulation of target genes in the presence of gene silencing. This configuration also exhibits superior shut-off properties, and it can serve as a tunable switch in living cells. Model validation with independent experimental data suggests that the models are sufficiently realistic. When combined, our results offer a mechanistic explanation for why specific factors are associated with low protein noise in vivo. Many of these findings hold for a broad range of model parameters and likely apply to other eukaryotic promoters of similar structure.

  16. Clustering determines the dynamics of complex contagions in multiplex networks

    Science.gov (United States)

    Zhuang, Yong; Arenas, Alex; Yaǧan, Osman

    2017-01-01

    We present the mathematical analysis of generalized complex contagions in a class of clustered multiplex networks. The model is intended to understand spread of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is especially useful in problems related to spreading and percolation. The results present nontrivial dependencies between the clustering coefficient of the networks and its average degree. In particular, several phase transitions are shown to occur depending on these descriptors. Generally speaking, our findings reveal that increasing clustering decreases the probability of having global cascades and their size, however, this tendency changes with the average degree. There exists a certain average degree from which on clustering favors the probability and size of the contagion. By comparing the dynamics of complex contagions over multiplex networks and their monoplex projections, we demonstrate that ignoring link types and aggregating network layers may lead to inaccurate conclusions about contagion dynamics, particularly when the correlation of degrees between layers is high.

  17. Vibrational energy transfer dynamics in ruthenium polypyridine transition metal complexes.

    Science.gov (United States)

    Fedoseeva, Marina; Delor, Milan; Parker, Simon C; Sazanovich, Igor V; Towrie, Michael; Parker, Anthony W; Weinstein, Julia A

    2015-01-21

    Understanding the dynamics of the initial stages of vibrational energy transfer in transition metal complexes is a challenging fundamental question which is also of crucial importance for many applications, such as improving the performance of solar devices or photocatalysis. The present study investigates vibrational energy transport in the ground and the electronic excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2, a close relative of the efficient "N3" dye used in dye-sensitized solar cells. Using the emerging technique of ultrafast two-dimensional infrared spectroscopy, we show that, similarly to other transition-metal complexes, the central Ru heavy atom acts as a "bottleneck" making the energy transfer from small ligands with high energy vibrational stretching frequencies less favorable and thereby affecting the efficiency of vibrational energy flow in the complex. Comparison of the vibrational relaxation times in the electronic ground and excited state of Ru(4,4'-(COOEt)2-2,2-bpy)2(NCS)2 shows that it is dramatically faster in the latter. We propose to explain this observation by the intramolecular electrostatic interactions between the thiocyanate group and partially oxidised Ru metal center, which increase the degree of vibrational coupling between CN and Ru-N modes in the excited state thus reducing structural and thermodynamic barriers that slow down vibrational relaxation and energy transport in the electronic ground state. As a very similar behavior was earlier observed in another transition-metal complex, Re(4,4'-(COOEt)2-2,2'-bpy)(CO)3Cl, we suggest that this effect in vibrational energy dynamics might be common for transition-metal complexes with heavy central atoms.

  18. The Dynamics of Coalition Formation on Complex Networks

    Science.gov (United States)

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

    2015-08-01

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

  19. Young Children's Knowledge About the Moon: A Complex Dynamic System

    Science.gov (United States)

    Venville, Grady J.; Louisell, Robert D.; Wilhelm, Jennifer A.

    2012-08-01

    The purpose of this research was to use a multidimensional theoretical framework to examine young children's knowledge about the Moon. The research was conducted in the interpretive paradigm and the design was a multiple case study of ten children between the ages of three and eight from the USA and Australia. A detailed, semi-structured interview was conducted with each child. In addition, each child's parents were interviewed to determine possible social and cultural influences on the child's knowledge. We sought evidence about how the social and cultural experiences of the children might have influenced the development of their ideas. From a cognitive perspective we were interested in whether the children's ideas were constructed in a theory like form or whether the knowledge was the result of gradual accumulation of fragments of isolated cultural information. Findings reflected the strong and complex relationship between individual children, their social and cultural milieu, and the way they construct ideas about the Moon and astronomy. Findings are presented around four themes including ontology, creatures and artefacts, animism, and permanence. The findings support a complex dynamic system view of students' knowledge that integrates the framework theory perspective and the knowledge in fragments perspective. An initial model of a complex dynamic system of young children's knowledge about the Moon is presented.

  20. Entropy Rate Maps of Complex Excitable Dynamics in Cardiac Monolayers

    Directory of Open Access Journals (Sweden)

    Alexander Schlemmer

    2015-02-01

    Full Text Available The characterization of spatiotemporal complexity remains a challenging task. This holds in particular for the analysis of data from fluorescence imaging (optical mapping, which allows for the measurement of membrane potential and intracellular calcium at high spatial and temporal resolutions and, therefore, allows for an investigation of cardiac dynamics. Dominant frequency maps and the analysis of phase singularities are frequently used for this type of excitable media. These methods address some important aspects of cardiac dynamics; however, they only consider very specific properties of excitable media. To extend the scope of the analysis, we present a measure based on entropy rates for determining spatiotemporal complexity patterns of excitable media. Simulated data generated by the Aliev–Panfilov model and the cubic Barkley model are used to validate this method. Then, we apply it to optical mapping data from monolayers of cardiac cells from chicken embryos and compare our findings with dominant frequency maps and the analysis of phase singularities. The studies indicate that entropy rate maps provide additional information about local complexity, the origins of wave breakup and the development of patterns governing unstable wave propagation.

  1. Large scale molecular dynamics study of polymer-surfactant complex

    Science.gov (United States)

    Goswami, Monojoy; Sumpter, Bobby

    2012-02-01

    In this work, we study the self-assembly of cationic polyelectrolytes mediated by anionic surfactants in dilute or semi-dilute and gel states. The understanding of the dilute system is a requirement for the understanding of gel states. The importance of polyelectrolyte with oppositely charged colloidal particles can be found in biological systems, such as immobilization of enzymes in polyelectrolyte complexes or nonspecific association of DNA with protein. With the same understanding, interaction of surfactants with polyelectrolytes shows intriguing phenomena that are important for both in academic research as well as industrial applications. Many useful properties of PE surfactant complexes come from the highly ordered structures of surfactant self-assembly inside the PE aggregate. We do large scale molecular dynamics simulation using LAMMPS to understand the structure and dynamics of PE-surfactant systems. Our investigation shows highly ordered ring-string structures that have been observed experimentally in biological systems. We will investigate many different properties of PE-surfactant complexation which will be helpful for pharmaceutical, engineering and biological applications.

  2. Precision genetics for complex objectives in animal agriculture.

    Science.gov (United States)

    Fahrenkrug, S C; Blake, A; Carlson, D F; Doran, T; Van Eenennaam, A; Faber, D; Galli, C; Gao, Q; Hackett, P B; Li, N; Maga, E A; Muir, W M; Murray, J D; Shi, D; Stotish, R; Sullivan, E; Taylor, J F; Walton, M; Wheeler, M; Whitelaw, B; Glenn, B P

    2010-07-01

    Indirect modification of animal genomes by interspecific hybridization, cross-breeding, and selection has produced an enormous spectrum of phenotypic diversity over more than 10,000 yr of animal domestication. Using these established technologies, the farming community has successfully increased the yield and efficiency of production in most agricultural species while utilizing land resources that are often unsuitable for other agricultural purposes. Moving forward, animal well-being and agricultural sustainability are moral and economic priorities of consumers and producers alike. Therefore, these considerations will be included in any strategy designed to meet the challenges produced by global climate change and an expanding world population. Improvements in the efficiency and precision of genetic technologies will enable a timely response to meet the multifaceted food requirements of a rapidly increasing world population.

  3. Non-equilibrium dynamics of language games on complex networks

    CERN Document Server

    Dall'Asta, L; Barrat, A; Loreto, V; Asta, Luca Dall'; Baronchelli, Andrea; Barrat, Alain; Loreto, Vittorio

    2006-01-01

    The Naming Game is a model of non-equilibrium dynamics for the self-organized emergence of a linguistic convention or a communication system in a population of agents with pairwise local interactions. We present an extensive study of its dynamics on complex networks, that can be considered as the most natural topological embedding for agents involved in language games and opinion dynamics. Except for some community structured networks on which metastable phases can be observed, agents playing the Naming Game always manage to reach a global consensus. This convergence is obtained after a time generically scaling with the population's size $N$ as $t\\_{conv} \\sim N^{1.4 \\pm 0.1}$, i.e. much faster than for agents embedded on regular lattices. Moreover, the memory capacity required by the system scales only linearly with its size. Particular attention is given to heterogenous networks, in which the dynamical activity pattern of a node depends on its degree. High degree nodes have a fundamental role, but require l...

  4. Ultrafast Charge Recombination Dynamics in Ternary Electron Donor-Acceptor Complexes: (Benzene)2-Tetracyanoethylene Complexes.

    Science.gov (United States)

    Chiu, Chih-Chung; Hung, Chih-Chang; Cheng, Po-Yuan

    2016-12-08

    The charge-transfer (CT) state relaxation dynamics of the binary (1:1) and ternary (2:1) benzene/tetracyanoethylene (BZ/TCNE) complexes are reported. Steady-state and ultrafast time-resolved broadband fluorescence (TRFL) spectra of TCNE dissolved in a series of BZ/CCl4 mixed solvents are measured to elucidate the spectroscopic properties of the BZ/TCNE complexes and their CT-state relaxation dynamics. Both steady-state and TRFL spectra exhibit marked BZ concentration dependences, which can be attributed to the formation of two types of 2:1 complexes in the ground and excited states. By combining with the density functional theory (DFT) calculations, it was concluded that the BZ concentration dependence of the absorption spectra is mainly due to the formation and excitation of the sandwich-type 2:1 ternary complexes, whereas the changes in fluorescence spectra at high BZ concentrations are due to the formation of the asymmetric-type 2:1 ternary complex CT1 state. A unified mechanism involving both direct excitation and secondary formation of the 2:1 complexes CT states are proposed to account for the observations. The equilibrium charge recombination (CR) time constant of the 1:1 CT1 state is determined to be ∼150 ps in CCl4, whereas that of the 2:1 DDA-type CT1 state becomes ∼70 ps in 10% BZ/CCl4 and ∼34 ps in pure BZ. The CR rates and the CT1-S0 energy gap of these complexes in different solvents exhibit a correlation conforming to the Marcus inverted region. It is concluded that partial charge resonance occurring between the two adjacent BZs in the asymmetric-type 2:1 CT1-state reduces the CR reaction exothermicity and increases the CR rate.

  5. Without bounds a scientific canvas of nonlinearity and complex dynamics

    CERN Document Server

    Ryazantsev, Yuri; Starov, Victor; Huang, Guo-Xiang; Chetverikov, Alexander; Arena, Paolo; Nepomnyashchy, Alex; Ferrus, Alberto; Morozov, Eugene

    2013-01-01

    Bringing together over fifty contributions on all aspects of nonlinear and complex dynamics, this impressive topical collection is both a scientific and personal tribute, on the occasion of his 70th birthday, by many outstanding colleagues in the broad fields of research pursued by Prof. Manuel G Velarde. The topics selected reflect the research areas covered by the famous Instituto Pluridisciplinar at the Universidad Complutense of Madrid, which he co-founded over two decades ago, and include: fluid physics and related nonlinear phenomena at interfaces and in other geometries, wetting and spreading dynamics, geophysical and astrophysical flows, and novel aspects of electronic transport in anharmonic lattices, as well as topics in neurodynamics and robotics.

  6. Complex-Dynamical Approach to Cosmological Problem Solution

    CERN Document Server

    Kirilyuk, A P

    2005-01-01

    Universe structure emerges in the unreduced, complex-dynamic interaction process with the simplest initial configuration (two attracting homogeneous fields). The unreduced interaction analysis, avoiding any perturbative model, gives intrinsically creative cosmology describing the real, explicitly emerging world structure with dynamic randomness on each scale. Without imposing any postulates or additional entities, we obtain physically real, three-dimensional space, irreversibly flowing time, elementary particles with their detailed structure and intrinsic properties, causally complete and unified version of quantum and relativistic behaviour, the origin and number of naturally unified fundamental forces, classical behaviour emergence in a closed system, and true quantum chaos. Major problems of standard cosmology and astrophysics are consistently solved in this extended picture, including those of quantum cosmology and gravity, entropy growth and time arrow, "hierarchy" of elementary particles (Planckian unit...

  7. Slow dynamics of the contact process on complex networks

    Directory of Open Access Journals (Sweden)

    Ódor Géza

    2013-03-01

    Full Text Available The Contact Process has been studied on complex networks exhibiting different kinds of quenched disorder. Numerical evidence is found for Griffiths phases and other rare region effects, in Erdős Rényi networks, leading rather generically to anomalously slow (algebraic, logarithmic,… relaxation. More surprisingly, it turns out that Griffiths phases can also emerge in the absence of quenched disorder, as a consequence of sole topological heterogeneity in networks with finite topological dimension. In case of scalefree networks, exhibiting infinite topological dimension, slow dynamics can be observed on tree-like structures and a superimposed weight pattern. In the infinite size limit the correlated subspaces of vertices seem to cause a smeared phase transition. These results have a broad spectrum of implications for propagation phenomena and other dynamical process on networks and are relevant for the analysis of both models and empirical data.

  8. Dynamics of Dust Aggregates in a Complex Plasma

    Science.gov (United States)

    Davis, Allen; Carmona Reyes, Jorge; Matthews, Lorin; Hyde, Truell

    2012-10-01

    Charged dust aggregates play an important role in many astrophysical phenomena, such as early stages of protostellar and protoplanetary growth, the dynamics of planetary rings and cometary tails, and the formation of noctilucent clouds in earth's upper atmosphere. Dust is also expected to be an unwanted byproduct in the operation of plasma fusion devices, such as ITER. In all of these environments, direct study of the dust aggregates in their in situ environment is extremely difficult, if not impossible. As a model for these complex plasma environments, dust aggregates are formed in a laboratory plasma as monodisperse spheres are accelerated in a self-excited dust density wave. Individual dust particles are perturbed using a diode pumped solid state laser (Coherent VERDI) with their motions recorded by a high-speed camera at 1000 fps. Analysis of the particle motion allows determination of the aggregate characteristics which determine the grain dynamics, such as charge, mass, and gas drag.

  9. Hash function construction using weighted complex dynamical networks

    Institute of Scientific and Technical Information of China (English)

    Song Yu-Rong; Jiang Guo-Ping

    2013-01-01

    A novel scheme to construct a hash function based on a weighted complex dynamical network (WCDN) generated from an original message is proposed in this paper.First,the original message is divided into blocks.Then,each block is divided into components,and the nodes and weighted edges are well defined from these components and their relations.Namely,the WCDN closely related to the original message is established.Furthermore,the node dynamics of the WCDN are chosen as a chaotic map.After chaotic iterations,quantization and exclusive-or operations,the fixed-length hash value is obtained.This scheme has the property that any tiny change in message can be diffused rapidly through the WCDN,leading to very different hash values.Analysis and simulation show that the scheme possesses good statistical properties,excellent confusion and diffusion,strong collision resistance and high efficiency.

  10. Clustering determines the dynamics of complex contagions in multiplex networks

    CERN Document Server

    Zhuang, Yong; Yağan, Osman

    2016-01-01

    We present the mathematical analysis of generalized complex contagions in clustered multiplex networks for susceptible-infected-recovered (SIR)-like dynamics. The model is intended to understand diffusion of influence, or any other spreading process implying a threshold dynamics, in setups of interconnected networks with significant clustering. The contagion is assumed to be general enough to account for a content-dependent linear threshold model, where each link type has a different weight (for spreading influence) that may depend on the content (e.g., product, rumor, political view) that is being spread. Using the generating functions formalism, we determine the conditions, probability, and expected size of the emergent global cascades. This analysis provides a generalization of previous approaches and is specially useful in problems related to spreading and percolation. The results present non trivial dependencies between the clustering coefficient of the networks and its average degree. In particular, sev...

  11. Dynamical influence: how to measure individual contributions to collective dynamics in complex networks

    CERN Document Server

    Klemm, Konstantin; Eguiluz, Victor M; Miguel, Maxi San

    2010-01-01

    Identifying key players in complex networks remains a challenge affecting a great variety of research fields, from the efficient dissemination of ideas to drug target discovery in biomedical problems. The difficulty lies at several levels: how to single out the role of individual elements in such intermingled systems, or which is the best way to quantify their importance. Centrality measures aim at capturing the influence of a node from its position in a network. The key issue obviated is that the contribution of a node to the collective behaviour is not uniquely determined by the structure of the system but a result of both dynamics and network structure. Here we define dynamical influence as an explicit measure of how strongly a node's dynamical state affects collective behavior. Influence is derived analytically for dissipative processes in complex networks, directed or undirected. We show that it quantifies precisely how efficiently real systems may be driven by manipulating the state of single nodes. It ...

  12. Dynamic behavior and complexity of modulated optical micro ring resonator

    Institute of Scientific and Technical Information of China (English)

    Lei Yang; Wei Pan; Bin Luo; ShuiYing Xiang; Ning Jiang

    2011-01-01

    @@ The dynamic behavior of an optical micro ring resonator (OMRR) with an amplitude modulator positioned in the micro ring is investigated quantitatively by adopting a recently introduced quantifier, the permutation entropy (PE).The effects of modulation depth are focused on, and the roles of input power are considered.The two-dimensional (2D) maps of PE showing dependence on both modulation depth and input power are presented as well.PE values nearly increase with modulation depth.On the other hand, the optimal value of input power is achieved when the PE reaches its maximum.Thus, PE can successfully quantify the dynamics of modulated OMRR.Selecting the parameters in the region with high PE values would contribute to the complexity-enhanced OMRR-based chaotic communication systems.%The dynamic behavior of an optical micro ring resonator (OMRR) with an amplitude modulator positioned in the micro ring is investigated quantitatively by adopting a recently introduced quantifier, the permutation entropy (PE). The effects of modulation depth are focused on, and the roles of input power are considered. The two-dimensional (2D) maps of PE showing dependence on both modulation depth and input power are presented as well. PE values nearly increase with modulation depth. On the other hand, the optimal value of input power is achieved when the PE reaches its maximum. Thus, PE can successfully quantify the dynamics of modulated OMRR. Selecting the parameters in the region with high PE values would contribute to the complexity-enhanced OMRR-based chaotic communication systems.

  13. WATERWAVES: wave particles dynamics on a complex triatomic potential

    Science.gov (United States)

    Taioli, Simone; Tennyson, Jonathan

    2006-07-01

    The WATERWAVES program suite performs complex scattering calculations by propagating a wave packet in a complex, full-dimensional potential for non-rotating ( J=0) but vibrating triatomic molecules. Potential energy and decay probability surfaces must be provided. Expectation values of geometric quantities can be calculated, which are useful for following the wave packet motion. The programs use a local complex potential approximation (LCP) for the Hamiltonian and Jacobi coordinates. The bottleneck of the calculation is the application of each term of the Hamiltonian to the wave packet. To solve this problem the programs use a different representation for each term: normalized associated Legendre polynomials PjK(x) as a functional basis for the angular kinetic term and an evenly spaced grid for the radial kinetic term yielding a fully point-wise representation of the wave functions. The potential term is treated using an efficient Discrete Variable Representation (DVR) being diagonal in the coordinate representation. The radial kinetic term uses a fast Fourier transform (FFT) to obtain an operator which is diagonal in the momentum space. To avoid artificial reflection at the boundaries of the grid a complex absorbing potential is included for calculating continuum quantities. Asymptotic analysis is performed to obtain scattering observables such as cross sections and other dynamical properties. Program summaryProgram title: WATERWAVES Catalogue identifier:ADXT_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADXT_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: Freely available from CPC Programming language: Fortran 77 Computer(s) for which the program has been designed: PC Operating system(s) for which the program has been designed: Linux RAM required to execute with typical data: case dependent: test run requires 976 024 kB No. of bytes in distributed program, including test data, etc.:11

  14. Dynamic analysis of biochemical network using complex network method

    Directory of Open Access Journals (Sweden)

    Wang Shuqiang

    2015-01-01

    Full Text Available In this study, the stochastic biochemical reaction model is proposed based on the law of mass action and complex network theory. The dynamics of biochemical reaction system is presented as a set of non-linear differential equations and analyzed at the molecular-scale. Given the initial state and the evolution rules of the biochemical reaction system, the system can achieve homeostasis. Compared with random graph, the biochemical reaction network has larger information capacity and is more efficient in information transmission. This is consistent with theory of evolution.

  15. Universal nonexponential relaxation: Complex dynamics in simple liquids.

    Science.gov (United States)

    Turton, David A; Wynne, Klaas

    2009-11-28

    The dynamics of the noble-gas liquids underlies that of all liquids making them an important prototypical model system. Using optical Kerr-effect spectroscopy we show that for argon, krypton, and xenon, both the librational and diffusional contributions to the spectrum are surprisingly complex. The diffusional relaxation appears as a stretched-exponential, such as widely found in studies of structured (e.g., glass-forming) liquids and as predicted by mode-coupling theory. We show that this behavior is remarkably similar to that measured in water and suggest that it is a fundamental or universal property.

  16. Synchronization and Bifurcation of General Complex Dynamical Networks

    Institute of Scientific and Technical Information of China (English)

    SUN Wei-Gang; XU Cong-Xiang; LI Chang-Pin; FANG Jin-Qing

    2007-01-01

    In the present paper, synchronization and bifurcation of general complex dynamical networks are investigated. We mainly focus on networks with a somewhat general coupling matrix, i.e., the sum of each row equals a nonzero constant u. We derive a result that the networks can reach a new synchronous state, which is not the asymptotic limit set determined by the node equation. At the synchronous state, the networks appear bifurcation if we regard the constant u as a bifurcation parameter. Numerical examples are given to illustrate our derived conclusions.

  17. Complex Dynamics of an Adnascent-Type Game Model

    Directory of Open Access Journals (Sweden)

    Baogui Xin

    2008-01-01

    Full Text Available The paper presents a nonlinear discrete game model for two oligopolistic firms whose products are adnascent. (In biology, the term adnascent has only one sense, “growing to or on something else,” e.g., “moss is an adnascent plant.” See Webster's Revised Unabridged Dictionary published in 1913 by C. & G. Merriam Co., edited by Noah Porter. The bifurcation of its Nash equilibrium is analyzed with Schwarzian derivative and normal form theory. Its complex dynamics is demonstrated by means of the largest Lyapunov exponents, fractal dimensions, bifurcation diagrams, and phase portraits. At last, bifurcation and chaos anticontrol of this system are studied.

  18. Pinning control of a generalized complex dynamical network model

    Institute of Scientific and Technical Information of China (English)

    Huizhong YANG; Li SHENG

    2009-01-01

    This paper investigates the local and global synchronization of a generalized complex dynamical network model with constant and delayed coupling.Without assuming symmetry of the couplings,we proved that a single controller can pin the generalized complex network to a homogenous solution.Some previous synchronization results are generalized.In this paper,we first discuss how to pin an array of delayed neural networks to the synchronous solution by adding only one controller.Next,by using the Lyapunov functional method,some sufficient conditions are derived for the local and global synchronization of the coupled systems.The obtained results are expressed in terms of LMIs,which can be efficiently checked by the Matlab LMI toolbox.Finally,an example is given to illustrate the theoretical results.

  19. Dynamic of astrophysical jets in the complex octonion space

    CERN Document Server

    Weng, Zi-Hua

    2015-01-01

    The paper aims to consider the strength gradient force as the dynamic of astrophysical jets, explaining the movement phenomena of astrophysical jets. J. C. Maxwell applied the quaternion analysis to describe the electromagnetic theory. This encourages others to adopt the complex quaternion and octonion to depict the electromagnetic and gravitational theories. In the complex octonion space, it is capable of deducing the field potential, field strength, field source, angular momentum, torque, force and so forth. As one component of the force, the strength gradient force relates to the gradient of the norm of field strength only, and is independent of not only the direction of field strength but also the mass and electric charge for the test particle. When the strength gradient force is considered as the thrust of the astrophysical jets, one can deduce some movement features of astrophysical jets, including the bipolarity, matter ingredient, precession, symmetric distribution, emitting, collimation, stability, c...

  20. Control of complex dynamics and chaos in distributed parameter systems

    Energy Technology Data Exchange (ETDEWEB)

    Chakravarti, S.; Marek, M.; Ray, W.H. [Univ. of Wisconsin, Madison, WI (United States)

    1995-12-31

    This paper discusses a methodology for controlling complex dynamics and chaos in distributed parameter systems. The reaction-diffusion system with Brusselator kinetics, where the torus-doubling or quasi-periodic (two characteristic incommensurate frequencies) route to chaos exists in a defined range of parameter values, is used as an example. Poincare maps are used for characterization of quasi-periodic and chaotic attractors. The dominant modes or topos, which are inherent properties of the system, are identified by means of the Singular Value Decomposition. Tested modal feedback control schemas based on identified dominant spatial modes confirm the possibility of stabilization of simple quasi-periodic trajectories in the complex quasi-periodic or chaotic spatiotemporal patterns.

  1. Dynamic analysis of the human brain with complex cerebral sulci.

    Science.gov (United States)

    Tseng, Jung-Ge; Huang, Bo-Wun; Ou, Yi-Wen; Yen, Ke-Tien; Wu, Yi-Te

    2016-07-03

    The brain is one of the most vulnerable organs inside the human body. Head accidents often appear in daily life and are easy to cause different level of brain damage inside the skull. Once the brain suffered intense locomotive impact, external injuries, falls, or other accidents, it will result in different degrees of concussion. This study employs finite element analysis to compare the dynamic characteristics between the geometric models of an assumed simple brain tissue and a brain tissue with complex cerebral sulci. It is aimed to understand the free vibration of the internal brain tissue and then to protect the brain from injury caused by external influences. Reverse engineering method is used for a Classic 5-Part Brain (C18) model produced by 3B Scientific Corporation. 3D optical scanner is employed to scan the human brain structure model with complex cerebral sulci and imported into 3D graphics software to construct a solid brain model to simulate the real complex brain tissue. Obtaining the normal mode analysis by inputting the material properties of the true human brain into finite element analysis software, and then to compare the simplified and the complex of brain models.

  2. Computational complexity of ecological and evolutionary spatial dynamics.

    Science.gov (United States)

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

    2015-12-22

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

  3. Thresholds and Complex Dynamics of Interdependent Cascading Infrastructure Systems

    Science.gov (United States)

    Carreras, B. A.; Newman, D. E.; Dobson, I.; Lynch, V. E.; Gradney, Paul

    Critical infrastructures have a number of the characteristic properties of complex systems. Among these are infrequent large failures through cascading events. These events, though infrequent, often obey a power law distribution in their probability versus size which suggests that conventional risk analysis does not apply to these systems. Real infrastructure systems typically have an additional layer of complexity, namely the heterogeneous coupling to other infrastructure systems that can allow a failure in one system to propagate to the other system. Here, we model the infrastructure systems through a network with complex system dynamics. We use both mean field theory to get analytic results and a numerical complex systems model, Demon, for computational results. An isolated system has bifurcated fixed points and a cascading threshold which is the same as the bifurcation point. When systems are coupled, this is no longer true and the cascading threshold is different from the bifurcation point of the fixed point solutions. This change in the cascading threshold caused by the interdependence of the system can have an impact on the "safe operation" of interdependent infrastructure systems by changing the critical point and even the power law exponent.

  4. Mathematical and computer tools of discrete dynamic modeling and analysis of complex systems in control loop

    CERN Document Server

    Bagdasaryan, Armen

    2008-01-01

    We present a method of discrete modeling and analysis of multilevel dynamics of complex large-scale hierarchical dynamic systems subject to external dynamic control mechanism. Architectural model of information system supporting simulation and analysis of dynamic processes and development scenarios (strategies) of complex large-scale hierarchical systems is also proposed.

  5. Genetic diversity and population genetic structure analysis of Echinococcus granulosus sensu stricto complex based on mitochondrial DNA signature.

    Directory of Open Access Journals (Sweden)

    Monika Sharma

    Full Text Available The genetic diversity and population genetics of the Echinococcus granulosus sensu stricto complex were investigated based on sequencing of mitochondrial DNA (mtDNA. Total 81 isolates of hydatid cyst collected from ungulate animals from different geographical areas of North India were identified by sequencing of cytochrome c oxidase subunit1 (coxi gene. Three genotypes belonging to E. granulosus sensu stricto complex were identified (G1, G2 and G3 genotypes. Further the nucleotide sequences (retrieved from GenBank for the coxi gene from seven populations of E. granulosus sensu stricto complex covering 6 continents, were compared with sequences of isolates analysed in this study. Molecular diversity indices represent overall high mitochondrial DNA diversity for these populations, but low nucleotide diversity between haplotypes. The neutrality tests were used to analyze signatures of historical demographic events. The Tajima's D test and Fu's FS test showed negative value, indicating deviations from neutrality and both suggested recent population expansion for the populations. Pairwise fixation index was significant for pairwise comparison of different populations (except between South America and East Asia, Middle East and Europe, South America and Europe, Africa and Australia, indicating genetic differentiation among populations. Based on the findings of the present study and those from earlier studies, we hypothesize that demographic expansion occurred in E. granulosus after the introduction of founder haplotype particular by anthropogenic movements.

  6. Did genetic drift drive increases in genome complexity?

    Directory of Open Access Journals (Sweden)

    Kenneth D Whitney

    2010-08-01

    Full Text Available Mechanisms underlying the dramatic patterns of genome size variation across the tree of life remain mysterious. Effective population size (N(e has been proposed as a major driver of genome size: selection is expected to efficiently weed out deleterious mutations increasing genome size in lineages with large (but not small N(e. Strong support for this model was claimed from a comparative analysis of N(eu and genome size for ≈30 phylogenetically diverse species ranging from bacteria to vertebrates, but analyses at that scale have so far failed to account for phylogenetic nonindependence of species. In our reanalysis, accounting for phylogenetic history substantially altered the perceived strength of the relationship between N(eu and genomic attributes: there were no statistically significant associations between N(eu and gene number, intron size, intron number, the half-life of gene duplicates, transposon number, transposons as a fraction of the genome, or overall genome size. We conclude that current datasets do not support the hypothesis of a mechanistic connection between N(e and these genomic attributes, and we suggest that further progress requires larger datasets, phylogenetic comparative methods, more robust estimators of genetic drift, and a multivariate approach that accounts for correlations between putative explanatory variables.

  7. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats

    Science.gov (United States)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W.; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D.; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H.; Koller, Daniel L.; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A.; Worley, Kim C.; Muzny, Donna M.; Gibbs, Richard A.; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J.; Keane, Thomas; Atanur, Santosh S.; Aitman, Tim J.; Flicek, Paul; Malinauskas, Tomas; Jones, E. Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-01-01

    Genetic mapping on fully sequenced individuals is transforming our understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating novel genes in models of anxiety, heart disease and multiple sclerosis. The relation between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show the extent and spatial pattern of variation in inbred rats differ significantly from those of inbred mice, and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species. PMID:23708188

  8. Combined sequence-based and genetic mapping analysis of complex traits in outbred rats.

    Science.gov (United States)

    Baud, Amelie; Hermsen, Roel; Guryev, Victor; Stridh, Pernilla; Graham, Delyth; McBride, Martin W; Foroud, Tatiana; Calderari, Sophie; Diez, Margarita; Ockinger, Johan; Beyeen, Amennai D; Gillett, Alan; Abdelmagid, Nada; Guerreiro-Cacais, Andre Ortlieb; Jagodic, Maja; Tuncel, Jonatan; Norin, Ulrika; Beattie, Elisabeth; Huynh, Ngan; Miller, William H; Koller, Daniel L; Alam, Imranul; Falak, Samreen; Osborne-Pellegrin, Mary; Martinez-Membrives, Esther; Canete, Toni; Blazquez, Gloria; Vicens-Costa, Elia; Mont-Cardona, Carme; Diaz-Moran, Sira; Tobena, Adolf; Hummel, Oliver; Zelenika, Diana; Saar, Kathrin; Patone, Giannino; Bauerfeind, Anja; Bihoreau, Marie-Therese; Heinig, Matthias; Lee, Young-Ae; Rintisch, Carola; Schulz, Herbert; Wheeler, David A; Worley, Kim C; Muzny, Donna M; Gibbs, Richard A; Lathrop, Mark; Lansu, Nico; Toonen, Pim; Ruzius, Frans Paul; de Bruijn, Ewart; Hauser, Heidi; Adams, David J; Keane, Thomas; Atanur, Santosh S; Aitman, Tim J; Flicek, Paul; Malinauskas, Tomas; Jones, E Yvonne; Ekman, Diana; Lopez-Aumatell, Regina; Dominiczak, Anna F; Johannesson, Martina; Holmdahl, Rikard; Olsson, Tomas; Gauguier, Dominique; Hubner, Norbert; Fernandez-Teruel, Alberto; Cuppen, Edwin; Mott, Richard; Flint, Jonathan

    2013-07-01

    Genetic mapping on fully sequenced individuals is transforming understanding of the relationship between molecular variation and variation in complex traits. Here we report a combined sequence and genetic mapping analysis in outbred rats that maps 355 quantitative trait loci for 122 phenotypes. We identify 35 causal genes involved in 31 phenotypes, implicating new genes in models of anxiety, heart disease and multiple sclerosis. The relationship between sequence and genetic variation is unexpectedly complex: at approximately 40% of quantitative trait loci, a single sequence variant cannot account for the phenotypic effect. Using comparable sequence and mapping data from mice, we show that the extent and spatial pattern of variation in inbred rats differ substantially from those of inbred mice and that the genetic variants in orthologous genes rarely contribute to the same phenotype in both species.

  9. Genetics of tuberous sclerosis complex: implications for clinical practice

    Science.gov (United States)

    Caban, Carolina; Khan, Nubaira; Hasbani, Daphne M; Crino, Peter B

    2017-01-01

    Tuberous sclerosis complex (TSC) is a multisystem disorder that results from heterozygous mutations in either TSC1 or TSC2. The primary organ systems that are affected include the brain, skin, lung, kidney, and heart, all with variable frequency, penetrance, and severity. Neurological features include epilepsy, autism, and intellectual disability. There are more than 1,500 known pathogenic variants for TSC1 and TSC2, including deletion, nonsense, and missense mutations, and all pathogenic mutations are inactivating, leading to loss of function effects on the encoded proteins TSC1 and TSC2. These proteins form a complex to constitutively inhibit mechanistic target of rapamycin (mTOR) signaling cascade, and as a consequence, mTOR signaling is constitutively active within all TSC-associated lesions. The mTOR inhibitors rapamycin (sirolimus) and everolimus have been shown to reduce the size of renal and brain lesions and improve pulmonary function in TSC, and these compounds may also decrease seizure frequency. The clinical application of mTOR inhibitors in TSC has provided one of the first examples of precision medicine in a neurodevelopmental disorder. PMID:28053551

  10. A Bayesian Algorithm for Functional Mapping of Dynamic Complex Traits

    Directory of Open Access Journals (Sweden)

    Rongling Wu

    2009-04-01

    Full Text Available Functional mapping of dynamic traits measured in a longitudinal study was originally derived within the maximum likelihood (ML context and implemented with the EM algorithm. Although ML-based functional mapping possesses many favorable statistical properties in parameter estimation, it may be computationally intractable for analyzing longitudinal data with high dimensions and high measurement errors. In this article, we derive a general functional mapping framework for quantitative trait locus mapping of dynamic traits within the Bayesian paradigm. Markov chain Monte Carlo techniques were implemented for functional mapping to estimate biologically and statistically sensible parameters that model the structures of time-dependent genetic effects and covariance matrix. The Bayesian approach is useful to handle difficulties in constructing confidence intervals as well as the identifiability problem, enhancing the statistical inference of functional mapping. We have undertaken simulation studies to investigate the statistical behavior of Bayesian-based functional mapping and used a real example with F2 mice to validate the utilization and usefulness of the model.

  11. Statistical power to detect genetic (covariance of complex traits using SNP data in unrelated samples.

    Directory of Open Access Journals (Sweden)

    Peter M Visscher

    2014-04-01

    Full Text Available We have recently developed analysis methods (GREML to estimate the genetic variance of a complex trait/disease and the genetic correlation between two complex traits/diseases using genome-wide single nucleotide polymorphism (SNP data in unrelated individuals. Here we use analytical derivations and simulations to quantify the sampling variance of the estimate of the proportion of phenotypic variance captured by all SNPs for quantitative traits and case-control studies. We also derive the approximate sampling variance of the estimate of a genetic correlation in a bivariate analysis, when two complex traits are either measured on the same or different individuals. We show that the sampling variance is inversely proportional to the number of pairwise contrasts in the analysis and to the variance in SNP-derived genetic relationships. For bivariate analysis, the sampling variance of the genetic correlation additionally depends on the harmonic mean of the proportion of variance explained by the SNPs for the two traits and the genetic correlation between the traits, and depends on the phenotypic correlation when the traits are measured on the same individuals. We provide an online tool for calculating the power of detecting genetic (covariation using genome-wide SNP data. The new theory and online tool will be helpful to plan experimental designs to estimate the missing heritability that has not yet been fully revealed through genome-wide association studies, and to estimate the genetic overlap between complex traits (diseases in particular when the traits (diseases are not measured on the same samples.

  12. Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

    DEFF Research Database (Denmark)

    Nielsen, Henrik Bjørn; Almeida, Mathieu; Juncker, Agnieszka

    2014-01-01

    , such as particular bacterial strains or viruses, remains a largely unsolved problem. Here we present a method, based on binning co-abundant genes across a series of metagenomic samples, that enables comprehensive discovery of new microbial organisms, viruses and co-inherited genetic entities and aids assembly...... affiliations between MGS and hundreds of viruses or genetic entities. Our method provides the means for comprehensive profiling of the diversity within complex metagenomic samples....

  13. Complex processes from dynamical architectures with time-scale hierarchy.

    Directory of Open Access Journals (Sweden)

    Dionysios Perdikis

    Full Text Available The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes.

  14. Complex processes from dynamical architectures with time-scale hierarchy.

    Science.gov (United States)

    Perdikis, Dionysios; Huys, Raoul; Jirsa, Viktor

    2011-02-10

    The idea that complex motor, perceptual, and cognitive behaviors are composed of smaller units, which are somehow brought into a meaningful relation, permeates the biological and life sciences. However, no principled framework defining the constituent elementary processes has been developed to this date. Consequently, functional configurations (or architectures) relating elementary processes and external influences are mostly piecemeal formulations suitable to particular instances only. Here, we develop a general dynamical framework for distinct functional architectures characterized by the time-scale separation of their constituents and evaluate their efficiency. Thereto, we build on the (phase) flow of a system, which prescribes the temporal evolution of its state variables. The phase flow topology allows for the unambiguous classification of qualitatively distinct processes, which we consider to represent the functional units or modes within the dynamical architecture. Using the example of a composite movement we illustrate how different architectures can be characterized by their degree of time scale separation between the internal elements of the architecture (i.e. the functional modes) and external interventions. We reveal a tradeoff of the interactions between internal and external influences, which offers a theoretical justification for the efficient composition of complex processes out of non-trivial elementary processes or functional modes.

  15. Tear Film Dynamics: the roles of complex structure and rheology

    Science.gov (United States)

    Dey, Mohar; Feng, James; Vivek, Atul S.; Dixit, Harish N.; Richhariya, Ashutosh

    2016-11-01

    Ocular surface infections such as microbial and fungal keratitis are among leading causes of blindness in the world. A thorough understanding of the pre-corneal tear film dynamics is essential to comprehend the role of various tear layer components in the escalation of such ocular infections. The pre-corneal tear film comprises of three layers of complex fluids, viz. the innermost mucin layer, a hydrophilic protective cover over the sensitive corneal epithelium, the intermediate aqueous layer that forms the bulk of the tear film and is often embedded with large number of bio-polymers either in the form of soluble mucins or pathogens, and finally the outermost lipid layer that stabilizes the film by decreasing the air/tear film interfacial tension. We have developed a comprehensive mathematical model to describe such a film by incorporating the effects of the non-uniform mucin distribution along with the complex rheology of the aqueous layer with/without pathogens, Marangoni effects from the lipid layer and the slip effects at the base of the tear film. A detailed linear stability analysis and a fully non-linear solution determine the break up time (BUT) of such a tear film. We also probe the role of the various components of the pre-corneal tear film in the dynamics of rupture.

  16. Identifying Changes of Complex Flood Dynamics with Recurrence Analysis

    Science.gov (United States)

    Wendi, D.; Merz, B.; Marwan, N.

    2016-12-01

    Temporal changes in flood hazard system are known to be difficult to detect and attribute due to multiple drivers that include complex processes that are non-stationary and highly variable. These drivers, such as human-induced climate change, natural climate variability, implementation of flood defense, river training, or land use change, could impact variably on space-time scales and influence or mask each other. Flood time series may show complex behavior that vary at a range of time scales and may cluster in time. Moreover hydrological time series (i.e. discharge) are often subject to measurement errors, such as rating curve error especially in the case of extremes where observation are actually derived through extrapolation. This study focuses on the application of recurrence based data analysis techniques (recurrence plot) for understanding and quantifying spatio-temporal changes in flood hazard in Germany. The recurrence plot is known as an effective tool to visualize the dynamics of phase space trajectories i.e. constructed from a time series by using an embedding dimension and a time delay, and it is known to be effective in analyzing non-stationary and non-linear time series. Sensitivity of the common measurement errors and noise on recurrence analysis will also be analyzed and evaluated against conventional methods. The emphasis will be on the identification of characteristic recurrence properties that could associate typical dynamic to certain flood events.

  17. Complexity, Sustainability, Justice, and Meaning: Chronological Versus Dynamical Time

    Directory of Open Access Journals (Sweden)

    Horacio Velasco

    2009-11-01

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    When nonlinear dynamics came to be complemented with semiotic modulation through the implement of symbol-mediated language (a complementation subsequently termed semantic closure as first instantiated through the communicating (as opposed  to merely dynamically interacting molecular complexes of the cell, what can be termed semiotic hysteresis was born. The paper attempts to show that indefinitely evolving complexity, sustainability, justice, and meaning are indissolubly bound with chronological time in the sense of semiotic hysteresis (as afforded initially by non-cognitive semantic closure and subsequently, at least one hopes, by cognitive semantic closure: This semiotic hysteresis yields the indefinite evolutionary time of the living condition—including culture.

     

  18. Population isolates in South Tyrol and their value for genetic dissection of complex diseases.

    Science.gov (United States)

    Marroni, F; Pichler, I; De Grandi, A; Volpato, C Beu; Vogl, F D; Pinggera, G K; Bailey-Wilson, J E; Pramstaller, P P

    2006-11-01

    The study of genetic isolates is a promising approach for the study of complex genetic traits. The small and constant population size, lack of migration, and multiple relationships between individuals in the isolate population could reduce the genetic diversity, and lead to increased levels of linkage disequilibrium (LD). We studied the extent of LD on Xq13 in six population isolates from South Tyrol in the Eastern Italian Alps. We found different levels of LD in our study samples, probably reflecting their degrees of isolation and their demographic histories. The highest values were obtained in Val Gardena (ranking among the highest levels of LD in Europe) and in Stelvio, which qualified as a microisolate according to historical information, and biodemographic and genealogical criteria. Phylogenetic analysis revealed that the two Ladin-speaking populations are genetically distant from each other, and from their German-speaking neighbours, and are characterized by a smaller effective population size than the neighbouring valleys. These peculiar characteristics suggest that South Tyrol could be a unique resource for the study of complex diseases, showing all the characteristics of isolated populations with the advantage of including, in a fairly homogeneous environment, two genetically differentiated sub-populations. This could allow investigators to gain an insight into the contribution of genetic heterogeneity in complex diseases.

  19. Functional Loop Dynamics of the Streptavidin-Biotin Complex

    Science.gov (United States)

    Song, Jianing; Li, Yongle; Ji, Changge; Zhang, John Z. H.

    2015-01-01

    Accelerated molecular dynamics (aMD) simulation is employed to study the functional dynamics of the flexible loop3-4 in the strong-binding streptavidin-biotin complex system. Conventional molecular (cMD) simulation is also performed for comparison. The present study reveals the following important properties of the loop dynamics: (1) The transition of loop3-4 from open to closed state is observed in 200 ns aMD simulation. (2) In the absence of biotin binding, the open-state streptavidin is more stable, which is consistent with experimental evidences. The free energy (ΔG) difference is about 5 kcal/mol between two states. But with biotin binding, the closed state is more stable due to electrostatic and hydrophobic interactions between the loop3-4 and biotin. (3) The closure of loop3-4 is concerted to the stable binding of biotin to streptavidin. When the loop3-4 is in its open-state, biotin moves out of the binding pocket, indicating that the interactions between the loop3-4 and biotin are essential in trapping biotin in the binding pocket. (4) In the tetrameric streptavidin system, the conformational change of the loop3-4 in each monomer is independent of each other. That is, there is no cooperative binding for biotin bound to the four subunits of the tetramer.

  20. The Nonrandom Brain: Efficiency, Economy, and Complex Dynamics

    Directory of Open Access Journals (Sweden)

    Olaf eSporns

    2011-02-01

    Full Text Available Modern anatomical tracing and imaging techniques are beginning to reveal the structural anatomy of neural circuits at small and large scales in unprecedented detail. When examined with analytic tools from graph theory and network science, neural connectivity exhibits highly nonrandom features, including high clustering and short path length, as well as modules and highly central hub nodes. These characteristic topological features of neural connections shape nonrandom dynamic interactions that occur during spontaneous activity or in response to external stimulation. Disturbances of connectivity and thus of neural dynamics are thought to underlie a number of disease states of the brain, and some evidence suggests that degraded functional performance of brain networks may be the outcome of a process of randomization affecting their nodes and edges. This article provides a survey of the nonrandom structure of neural connectivity, primarily at the large-scale of regions and pathways in the mammalian cerebral cortex. In addition, we will discuss how nonrandom connections can give rise to differentiated and complex patterns of dynamics and information flow. Finally, we will explore the idea that at least some disorders of the nervous system are associated with increased randomness of neural connections.

  1. Triplet repeat DNA structures and human genetic disease: dynamic mutations from dynamic DNA

    Indian Academy of Sciences (India)

    Richard R Sinden; Vladimir N Potaman; Elena A Oussatcheva; Christopher E Pearson; Yuri L Lyubchenko; Luda S Shlyakhtenko

    2002-02-01

    Fourteen genetic neurodegenerative diseases and three fragile sites have been associated with the expansion of (CTG)n•(CAG)n, (CGG)n•(CCG)n, or (GAA)n•(TTC)n repeat tracts. Different models have been proposed for the expansion of triplet repeats, most of which presume the formation of alternative DNA structures in repeat tracts. One of the most likely structures, slipped strand DNA, may stably and reproducibly form within triplet repeat sequences. The propensity to form slipped strand DNA is proportional to the length and homogeneity of the repeat tract. The remarkable stability of slipped strand DNA may, in part, be due to loop-loop interactions facilitated by the sequence complementarity of the loops and the dynamic structure of three-way junctions formed at the loop-outs.

  2. Pheochromocytoma and paraganglioma: understanding the complexities of the genetic background.

    Science.gov (United States)

    Fishbein, Lauren; Nathanson, Katherine L

    2012-01-01

    Pheochromocytomas and paragangliomas (PCC/PGL) are tumors derived from the adrenal medulla or extra-adrenal ganglia, respectively. They are rare and often benign tumors that are associated with high morbidity and mortality due to mass effect and high circulating catecholamines. Although most PCCs and PGLs are thought to be sporadic, over one third are associated with 10 known susceptibility genes. Mutations in three genes causing well characterized tumor syndromes are associated with an increased risk of developing PCCs and PGLs, including VHL (von Hippel-Lindau disease), NF1 (Neurofibromatosis Type 1), and RET (Multiple Endocrine Neoplasia Type 2). Mutations in any of the succinate dehydrogenase (SDH) complex subunit genes (SDHA, SDHB, SDHC, SDHD) can lead to PCCs and PGLs with variable penetrance, as can mutations in the subunit cofactor, SDHAF2. Recently, two additional genes have been identified, TMEM127 and MAX. Although these tumors are rare in the general population, occurring in two to eight per million people, they are more commonly associated with an inherited mutation than any other cancer type. This review summarizes the known germline and somatic mutations leading to the development of PCC and PGL, as well as biochemical profiling for PCCs/PGLs and screening of mutation carriers.

  3. Multiple-node basin stability in complex dynamical networks

    Science.gov (United States)

    Mitra, Chiranjit; Choudhary, Anshul; Sinha, Sudeshna; Kurths, Jürgen; Donner, Reik V.

    2017-03-01

    Dynamical entities interacting with each other on complex networks often exhibit multistability. The stability of a desired steady regime (e.g., a synchronized state) to large perturbations is critical in the operation of many real-world networked dynamical systems such as ecosystems, power grids, the human brain, etc. This necessitates the development of appropriate quantifiers of stability of multiple stable states of such systems. Motivated by the concept of basin stability (BS) [P. J. Menck et al., Nat. Phys. 9, 89 (2013), 10.1038/nphys2516], we propose here the general framework of multiple-node basin stability for gauging the global stability and robustness of networked dynamical systems in response to nonlocal perturbations simultaneously affecting multiple nodes of a system. The framework of multiple-node BS provides an estimate of the critical number of nodes that, when simultaneously perturbed, significantly reduce the capacity of the system to return to the desired stable state. Further, this methodology can be applied to estimate the minimum number of nodes of the network to be controlled or safeguarded from external perturbations to ensure proper operation of the system. Multiple-node BS can also be utilized for probing the influence of spatially localized perturbations or targeted attacks to specific parts of a network. We demonstrate the potential of multiple-node BS in assessing the stability of the synchronized state in a deterministic scale-free network of Rössler oscillators and a conceptual model of the power grid of the United Kingdom with second-order Kuramoto-type nodal dynamics.

  4. Soil water dynamics during precipitation in genetic horizons of Retisol

    Science.gov (United States)

    Zaleski, Tomasz; Klimek, Mariusz; Kajdas, Bartłomiej

    2017-04-01

    Retisols derived from silty deposits dominate in the soil cover of the Carpathian Foothills. The hydrophysical properties of these are determined by the grain-size distribution of the parent material and the soil's "primary" properties shaped in the deposition process. The other contributing factors are the soil-forming processes, such as lessivage (leaching of clay particles), and the morphogenetic processes that presently shape the relief. These factors are responsible for the "secondary" differentiation of hydrophysical properties across the soil profile. Both the primary and secondary hydrophysical properties of soils (the rates of water retention, filtration and infiltration, and the moisture distribution over the soil profile) determine their ability to take in rainfall, the amount of rainwater taken in, and the ways of its redistribution. The aims of the study, carried out during 2015, were to investigate the dynamics of soil moisture in genetic horizons of Retisol derived from silty deposits and to recognize how fast and how deep water from precipitation gets into soil horizons. Data of soil moisture were measured using 5TM moisture and temperature sensor and collected by logger Em50 (Decagon Devices USA). Data were captured every 10 minutes from 6 sensors at depths: - 10 cm, 20 cm, 40 cm, 60 cm and 80 cm. Precipitation data come from meteorological station situated 50 m away from the soil profile. Two zones differing in the type of water regime were distinguished in Retisol: an upper zone comprising humic and eluvial horizons, and a lower zone consisting of illuvial and parent material horizons. The upper zone shows smaller retention of water available for plants, and relatively wide fluctuations in moisture content, compared to the lower zone. The lower zone has stable moisture content during the vegetation season, with values around the water field capacity. Large changes in soil moisture were observed while rainfall. These changes depend on the volume

  5. Genetic algorithms with memory- and elitism-based immigrants in dynamic environments.

    Science.gov (United States)

    Yang, Shengxiang

    2008-01-01

    In recent years the genetic algorithm community has shown a growing interest in studying dynamic optimization problems. Several approaches have been devised. The random immigrants and memory schemes are two major ones. The random immigrants scheme addresses dynamic environments by maintaining the population diversity while the memory scheme aims to adapt genetic algorithms quickly to new environments by reusing historical information. This paper investigates a hybrid memory and random immigrants scheme, called memory-based immigrants, and a hybrid elitism and random immigrants scheme, called elitism-based immigrants, for genetic algorithms in dynamic environments. In these schemes, the best individual from memory or the elite from the previous generation is retrieved as the base to create immigrants into the population by mutation. This way, not only can diversity be maintained but it is done more efficiently to adapt genetic algorithms to the current environment. Based on a series of systematically constructed dynamic problems, experiments are carried out to compare genetic algorithms with the memory-based and elitism-based immigrants schemes against genetic algorithms with traditional memory and random immigrants schemes and a hybrid memory and multi-population scheme. The sensitivity analysis regarding some key parameters is also carried out. Experimental results show that the memory-based and elitism-based immigrants schemes efficiently improve the performance of genetic algorithms in dynamic environments.

  6. Collaborative Research. Damage and Burst Dynamics in Failure of Complex Geomaterials. A Statistical Physics Approach to Understanding the Complex Emergent Dynamics in Near Mean-Field Geological Materials

    Energy Technology Data Exchange (ETDEWEB)

    Rundle, John B. [Univ. of California, Davis, CA (United States); Klein, William [Boston Univ., MA (United States)

    2015-09-29

    We have carried out research to determine the dynamics of failure in complex geomaterials, specifically focusing on the role of defects, damage and asperities in the catastrophic failure processes (now popularly termed “Black Swan events”). We have examined fracture branching and flow processes using models for invasion percolation, focusing particularly on the dynamics of bursts in the branching process. We have achieved a fundamental understanding of the dynamics of nucleation in complex geomaterials, specifically in the presence of inhomogeneous structures.

  7. Ecological dynamics and complex interactions of Agrobacterium megaplasmids

    Directory of Open Access Journals (Sweden)

    Thomas Gene Platt

    2014-11-01

    Full Text Available As with many pathogenic bacteria, agrobacterial plant pathogens carry most of their virulence functions on a horizontally transmissible genetic element. The tumor-inducing (Ti plasmid encodes the majority of virulence functions for the crown gall agent Agrobacterium tumefaciens. This includes the vir genes which drive genetic transformation of host cells and the catabolic genes needed to utilize the opines produced by infected plants. The Ti plasmid also encodes, an opine-dependent quorum sensing system that tightly regulates Ti plasmid copy number and its conjugal transfer to other agrobacteria. Many natural agrobacteria are avirulent, lacking the Ti plasmid. The burden of harboring the Ti plasmid depends on the environmental context. Away from diseased hosts, plasmid costs are low but the benefit of the plasmid is also absent. Consequently, plasmidless genotypes are favored. On infected plants the costs of the Ti plasmid can be very high, but balanced by the opine benefits, locally favoring plasmid bearing cells. Cheating derivatives which do not incur virulence costs but can benefit from opines are favored on infected plants and in most other environments, and these are frequently isolated from nature. Many agrobacteria also harbor an At plasmid which can stably coexist with a Ti plasmid. At plasmid genes are less well characterized but in general facilitate metabolic activities in the rhizosphere and bulk soil, such as the ability to breakdown plant exudates. Examination of A. tumefaciens C58, revealed that harboring it’s At plasmid is much more costly than harboring it’s Ti plasmid, but conversely the At plasmid is extremely difficult to cure. The interactions between these co-resident plasmids are complex, and depend on environmental context. However, the presence of a Ti plasmid appears to mitigate At plasmid costs, consistent with the high frequency with which they are found together.

  8. Computational complexity of symbolic dynamics at the onset of chaos

    Science.gov (United States)

    Lakdawala, Porus

    1996-05-01

    In a variety of studies of dynamical systems, the edge of order and chaos has been singled out as a region of complexity. It was suggested by Wolfram, on the basis of qualitative behavior of cellular automata, that the computational basis for modeling this region is the universal Turing machine. In this paper, following a suggestion of Crutchfield, we try to show that the Turing machine model may often be too powerful as a computational model to describe the boundary of order and chaos. In particular we study the region of the first accumulation of period doubling in unimodal and bimodal maps of the interval, from the point of view of language theory. We show that in relation to the ``extended'' Chomsky hierarchy, the relevant computational model in the unimodal case is the nested stack automaton or the related indexed languages, while the bimodal case is modeled by the linear bounded automaton or the related context-sensitive languages.

  9. Complex dynamical behaviors of daily data series in stock exchange

    Science.gov (United States)

    Wang, Hongchun; Chen, Guanrong; Lü, Jinhu

    2004-12-01

    It is well known that many economic data series show chaotic behaviors. In this Letter, we further investigate the complex dynamical behaviors of the daily data series, including opening quotation, closing quotation, maximum price, minimum price, and total exchange quantum, in Shenzhen stock exchange and Shanghai stock exchange, which are two representative stock exchanges in mainland China. The maximum Lyapunov exponents, correlation dimensions, and frequency spectra are calculated for these time series. Our results indicate that some daily data series of stock exchanges display low-dimensional chaotic behaviors, and some other daily data series do not show any chaotic behavior. Moreover, we introduce a weighted one-rank local-region approach for predicting short-term daily data series of stock exchange.

  10. Complex Ion Dynamics in Carbonate Lithium-Ion Battery Electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Ong, Mitchell T.; Bhatia, Harsh; Gyulassy, Attila G.; Draeger, Erik W.; Pascucci, Valerio; Bremer, Peer-Timo; Lordi, Vincenzo; Pask, John E.

    2017-03-16

    Li-ion battery performance is strongly influenced by ionic conductivity, which depends on the mobility of the Li ions in solution, and is related to their solvation structure. In this work, we have performed first-principles molecular dynamics (FPMD) simulations of a LiPF6 salt solvated in different Li-ion battery organic electrolytes. We employ an analytical method using relative angles from successive time intervals to characterize complex ionic motion in multiple dimensions from our FPMD simulations. We find different characteristics of ionic motion on different time scales. We find that the Li ion exhibits a strong caging effect due to its strong solvation structure, while the counterion, PF6– undergoes more Brownian-like motion. Our results show that ionic motion can be far from purely diffusive and provide a quantitative characterization of the microscopic motion of ions over different time scales.

  11. Reduced complexity turbo equalization using a dynamic Bayesian network

    Science.gov (United States)

    Myburgh, Hermanus C.; Olivier, Jan C.; van Zyl, Augustinus J.

    2012-12-01

    It is proposed that a dynamic Bayesian network (DBN) is used to perform turbo equalization in a system transmitting information over a Rayleigh fading multipath channel. The DBN turbo equalizer (DBN-TE) is modeled on a single directed acyclic graph by relaxing the Markov assumption and allowing weak connections to past and future states. Its complexity is exponential in encoder constraint length and approximately linear in the channel memory length. Results show that the performance of the DBN-TE closely matches that of a traditional turbo equalizer that uses a maximum a posteriori equalizer and decoder pair. The DBN-TE achieves full convergence and near-optimal performance after small number of iterations.

  12. Complex Dynamic Flows in Solar Flare Sheet Structures

    Science.gov (United States)

    McKenzie, David E.; Reeves, Katharine K.; Savage, Sabrina

    2012-01-01

    Observations of high-energy emission from solar flares often reveal the presence of large sheet-like structures, sometimes extending over a space comparable to the Sun's radius. Given that these structures are found between a departing coronal mass ejection and the post-eruption flare arcade, it is natural to associate the structure with a current sheet; though the relationship is unclear. Moreover, recent high-resolution observations have begun to reveal that the motions in this region are highly complex, including reconnection outflows, oscillations, and apparent wakes and eddies. We present a detailed first look at the complicated dynamics within this supra-arcade plasma, and consider implications for the interrelationship between the plasma and its embedded magnetic field.

  13. Dynamics of competing ideas in complex social systems

    CERN Document Server

    Wang, Yubo; Liu, Jian

    2011-01-01

    Individuals accepting an idea may intentionally or unintentionally impose influences in a certain neighborhood area, making other individuals within the area less likely or even impossible to accept other competing ideas. Depending on whether such influences strictly prohibit neighborhood individuals from accepting other ideas or not, we classify them into exclusive and non-exclusive influences, respectively. Our study reveals for the first time the rich and complex dynamics of two competing ideas with neighborhood influences in scale-free social networks: depending on whether they have exclusive or non-exclusive influences, the final state varies from multiple coexistence to founder control to exclusion, with different sizes of population accepting each of the ideas respectively. Such results provide insights helpful for better understanding the spread (and the control of spread) of ideas in human society.

  14. Self-Avoiding Random Dynamics on Integer Complex Systems

    CERN Document Server

    Hamze, Firas; de Freitas, Nando

    2011-01-01

    This paper introduces a new specialized algorithm for equilibrium Monte Carlo sampling of binary-valued systems, which allows for large moves in the state space. This is achieved by constructing self-avoiding walks (SAWs) in the state space. As a consequence, many bits are flipped in a single MCMC step. We name the algorithm SARDONICS, an acronym for Self-Avoiding Random Dynamics on Integer Complex Systems. The algorithm has several free parameters, but we show that Bayesian optimization can be used to automatically tune them. SARDONICS performs remarkably well in a broad number of sampling tasks: toroidal ferromagnetic and frustrated Ising models, 3D Ising models, restricted Boltzmann machines and chimera graphs arising in the design of quantum computers.

  15. Universal relation between skewness and kurtosis in complex dynamics.

    Science.gov (United States)

    Cristelli, Matthieu; Zaccaria, Andrea; Pietronero, Luciano

    2012-06-01

    We identify an important correlation between skewness and kurtosis for a broad class of complex dynamic systems and present a specific analysis of earthquake and financial time series. Two regimes of non-Gaussianity can be identified: a parabolic one, which is common in various fields of physics, and a power law one, with exponent 4/3, which at the moment appears to be specific of earthquakes and financial markets. For this property we propose a model and an interpretation in terms of very rare events dominating the statistics independently on the nature of the events considered. The predicted scaling relation between skewness and kurtosis matches very well the experimental pattern of the second regime. Regarding price fluctuations, this situation characterizes a universal stylized fact.

  16. Nonlinear problems of complex natural systems: Sun and climate dynamics.

    Science.gov (United States)

    Bershadskii, A

    2013-01-13

    The universal role of the nonlinear one-third subharmonic resonance mechanism in generation of strong fluctuations in complex natural dynamical systems related to global climate is discussed using wavelet regression detrended data. The role of the oceanic Rossby waves in the year-scale global temperature fluctuations and the nonlinear resonance contribution to the El Niño phenomenon have been discussed in detail. The large fluctuations in the reconstructed temperature on millennial time scales (Antarctic ice core data for the past 400,000 years) are also shown to be dominated by the one-third subharmonic resonance, presumably related to the Earth's precession effect on the energy that the intertropical regions receive from the Sun. The effects of galactic turbulence on the temperature fluctuations are also discussed.

  17. Genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River (upper Mekong).

    Science.gov (United States)

    Chen, Weitao; Shen, Yanjun; Gan, Xiaoni; Wang, Xuzhen; He, Shunping

    2016-09-01

    The genus Schizothorax (Cyprinidae), one of the most diverse genera of ichthyofauna of the Qinghai-Tibetan Plateau (QTP), is a good candidate for investigating patterns of genetic variation and evolutionary mechanisms. In this study, sequences from the mitochondrial control region, the cytochrome b gene, and two nuclear genes were used to re-examine the genetic diversity and investigate the evolutionary history of the Schizothorax species complex inhabiting the Lancang River. Three maternal clades were detected in the Schizothorax species complex, but frequent nuclear allele sharing also occurred among the three maternal clades. A discrepancy between topologies of mitochondrial and nuclear loci might result from introgression or/and incomplete lineage sorting. The divergence of the clades of the Schizothorax species complex was closely related to the Late Pliocene and Early Pleistocene orogenesis of the QTP and Southwest Mountains of China. Demographic analyses indicated that the species complex subsequently persisted in situ with stable populations during Pleistocene glacial cycling, which suggested that Pleistocene climate changes did not exert a remarkable influence on the species complex. Our study provides a comprehensive analysis of the genetic diversity and evolutionary history of the Schizothorax species complex in the Lancang River.

  18. PM Synchronous Motor Dynamic Modeling with Genetic Algorithm ...

    African Journals Online (AJOL)

    Adel

    intelligence like neural network, genetic algorithm, etc (El Shahat and El Shewy, ..... maximum power factor has the most powerful effect on all various machine .... Artificial Intelligence, Renewable Energy, Power System, Control Systems, PV ...

  19. Bayesian state space models for dynamic genetic network construction across multiple tissues.

    Science.gov (United States)

    Liang, Yulan; Kelemen, Arpad

    2016-08-01

    Construction of gene-gene interaction networks and potential pathways is a challenging and important problem in genomic research for complex diseases while estimating the dynamic changes of the temporal correlations and non-stationarity are the keys in this process. In this paper, we develop dynamic state space models with hierarchical Bayesian settings to tackle this challenge for inferring the dynamic profiles and genetic networks associated with disease treatments. We treat both the stochastic transition matrix and the observation matrix time-variant and include temporal correlation structures in the covariance matrix estimations in the multivariate Bayesian state space models. The unevenly spaced short time courses with unseen time points are treated as hidden state variables. Hierarchical Bayesian approaches with various prior and hyper-prior models with Monte Carlo Markov Chain and Gibbs sampling algorithms are used to estimate the model parameters and the hidden state variables. We apply the proposed Hierarchical Bayesian state space models to multiple tissues (liver, skeletal muscle, and kidney) Affymetrix time course data sets following corticosteroid (CS) drug administration. Both simulation and real data analysis results show that the genomic changes over time and gene-gene interaction in response to CS treatment can be well captured by the proposed models. The proposed dynamic Hierarchical Bayesian state space modeling approaches could be expanded and applied to other large scale genomic data, such as next generation sequence (NGS) combined with real time and time varying electronic health record (EHR) for more comprehensive and robust systematic and network based analysis in order to transform big biomedical data into predictions and diagnostics for precision medicine and personalized healthcare with better decision making and patient outcomes.

  20. PREFACE: Complex dynamics of fluids in disordered and crowded environments Complex dynamics of fluids in disordered and crowded environments

    Science.gov (United States)

    Coslovich, Daniele; Kahl, Gerhard; Krakoviack, Vincent

    2011-06-01

    Over the past two decades, the dynamics of fluids under nanoscale confinement has attracted much attention. Motivation for this rapidly increasing interest is based on both practical and fundamental reasons. On the practical and rather applied side, problems in a wide range of scientific topics, such as polymer and colloidal sciences, rheology, geology, or biophysics, benefit from a profound understanding of the dynamical behaviour of confined fluids. Further, effects similar to those observed in confinement are expected in fluids whose constituents have strong size or mass asymmetry, and in biological systems where crowding and obstruction phenomena in the cytosol are responsible for clear separations of time scales for macromolecular transport in the cell. In fundamental research, on the other hand, the interest focuses on the complex interplay between confinement and structural relaxation, which is responsible for the emergence of new phenomena in the dynamics of the system: in confinement, geometric constraints associated with the pore shape are imposed to the adsorbed fluids and an additional characteristic length scale, i.e. the pore size, comes into play. For many years, the topic has been mostly experimentally driven. Indeed, a broad spectrum of systems has been investigated by sophisticated experimental techniques, while theoretical and simulation studies were rather scarce due to conceptual and computational issues. In the past few years, however, theory and simulations could largely catch up with experiments. On one side, new theories have been put forward that duly take into account the porosity, the connectivity, and the randomness of the confinement. On the other side, the ever increasing available computational power now allows investigations that were far out of reach a few years ago. Nowadays, instead of isolated state points, systematic investigations on the dynamics of confined fluids, covering a wide range of system parameters, can be realized

  1. Dynamical complexity in the perception-based network formation model

    Science.gov (United States)

    Jo, Hang-Hyun; Moon, Eunyoung

    2016-12-01

    Many link formation mechanisms for the evolution of social networks have been successful to reproduce various empirical findings in social networks. However, they have largely ignored the fact that individuals make decisions on whether to create links to other individuals based on cost and benefit of linking, and the fact that individuals may use perception of the network in their decision making. In this paper, we study the evolution of social networks in terms of perception-based strategic link formation. Here each individual has her own perception of the actual network, and uses it to decide whether to create a link to another individual. An individual with the least perception accuracy can benefit from updating her perception using that of the most accurate individual via a new link. This benefit is compared to the cost of linking in decision making. Once a new link is created, it affects the accuracies of other individuals' perceptions, leading to a further evolution of the actual network. As for initial actual networks, we consider both homogeneous and heterogeneous cases. The homogeneous initial actual network is modeled by Erdős-Rényi (ER) random networks, while we take a star network for the heterogeneous case. In any cases, individual perceptions of the actual network are modeled by ER random networks with controllable linking probability. Then the stable link density of the actual network is found to show discontinuous transitions or jumps according to the cost of linking. As the number of jumps is the consequence of the dynamical complexity, we discuss the effect of initial conditions on the number of jumps to find that the dynamical complexity strongly depends on how much individuals initially overestimate or underestimate the link density of the actual network. For the heterogeneous case, the role of the highly connected individual as an information spreader is also discussed.

  2. The Collaborative Cross, a community resource for the genetic analysis of complex traits

    NARCIS (Netherlands)

    Churchill, Gary A.; Jansen, Ritsert C.; Airey, D.C.; Allayee, H.; Angel, J.M.; Attie, A.D.; Beatty, J.; Beavis, W.D.; Belknap, J.K.; Bennett, B.; Berrettini, W.; Bleich, A.; Bogue, M.; Broman, K.W.; Buck, K.J.; Buckler, E.; Burmeister, M.; Chesler, E.J.; Cheverud, J.M.; Clapcote, S.; Cook, M.N.; Cox, R.D.; Crabbe, J.C.; Crusio, W.E.; Darvasi, A.; Deschnepper, C.F.; Doerge, R.W.; Farber, C.R.; Forejt, J.; Gaile, D.; Garlow, S.J.; Geiger, H.; Gershenfeld, H.; Gordon, T.; Gu, J.; Gu, W.K.; de Haan, G; Hayes, N.L.; Heller, C.; Himmelbauer, H.; Hitzemann, R.; Hunter, K.; Hsu, H.C.; Iraqi, F.A.; Ivandic, B.; Jacob, H.J.; Jjepsen, K.J.; Johnson, D.K.; Johnson, T.E.; Kempermann, G.; Kendziorski, C.; Kotb, M.; Kooy, R.F; Llamas, B.; Lammert, F.; Lassalle, J.M.; Lowenstein, P.R.; Lu, L.; Lusiss, A.; Manly, K.F.; Marcucio, R.; Matthews, D.; Medrano, J.F.; Miller, D.R.; Mittleman, G.; Mock, B.A.; Mogil, J.S.; Montagutelli, X.; Morahan, G.; Morris, D.G.; Mott, R; Nadeau, J.H.; Nagase, H.; Nowakowski, R.S.; O'Hara, B.F.; Osadchuk, A.V.; Page, G.P.; Paigen, B.; Paigen, K.; Palmer, Abraham A.; Pan, H.J.; Peltonen-Palotie, L.; Pomp, D.; Peirce, J.; Pravenec, M.; Prows, D.R.; Qi, Z.H.; Reeves, R.H.; Roder, J.; Rosen, G.D.; Schadt, E.E.; Schalkwyk, L.C.; Seltzer, Z.; Shimomura, K.; Shou, S.M.; Sillanpaa, M.J.; Siracusa, L.D.; Snoeck, H.W.; Spearow, J.L.; Deschepper, Christian F.; Jepsen, Karl J.; Lusis, Aldons; O’Hara, Bruce F.; Sillanpää, Mikko J.; Tarantino, Lisa M.; Svenson, Karen; Threadgill, David; Toth, Linda A.; Valdar, William; Pardo-Manuel de Villena, Fernando; Warden, Craig; Whatley, Steve; Williams, Robert W.; Wiltshire, Tim; Yi, Nengjun; Zhang, Dabao; Zhang, Min; Zou, Fei; Montagutelli, X.; Tarantino, LM; Toth, LA; de Villena, FPM; Yi, NJ; Zhang, DB; Williams, O.

    2004-01-01

    The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are

  3. The variation game: Cracking complex genetic disorders with NGS and omics data.

    Science.gov (United States)

    Cui, Hongzhu; Dhroso, Andi; Johnson, Nathan; Korkin, Dmitry

    2015-06-01

    Tremendous advances in Next Generation Sequencing (NGS) and high-throughput omics methods have brought us one step closer towards mechanistic understanding of the complex disease at the molecular level. In this review, we discuss four basic regulatory mechanisms implicated in complex genetic diseases, such as cancer, neurological disorders, heart disease, diabetes, and many others. The mechanisms, including genetic variations, copy-number variations, posttranscriptional variations, and epigenetic variations, can be detected using a variety of NGS methods. We propose that malfunctions detected in these mechanisms are not necessarily independent, since these malfunctions are often found associated with the same disease and targeting the same gene, group of genes, or functional pathway. As an example, we discuss possible rewiring effects of the cancer-associated genetic, structural, and posttranscriptional variations on the protein-protein interaction (PPI) network centered around P53 protein. The review highlights multi-layered complexity of common genetic disorders and suggests that integration of NGS and omics data is a critical step in developing new computational methods capable of deciphering this complexity.

  4. The genetics of complex human behaviour: Cannabis use, personality, sexuality and mating

    NARCIS (Netherlands)

    Verweij, K.J.H.

    2012-01-01

    I investigated the genetic and environmental etiology of individual differences in a variety of complex human behaviours, broadly captured within three domains - 1) cannabis use, 2) personality, and 3) sexuality and mating. Research questions and hypotheses are addressed with large community-based,

  5. The genetics of complex human behaviour: Cannabis use, personality, sexuality and mating

    NARCIS (Netherlands)

    Verweij, K.J.H.

    2012-01-01

    I investigated the genetic and environmental etiology of individual differences in a variety of complex human behaviours, broadly captured within three domains - 1) cannabis use, 2) personality, and 3) sexuality and mating. Research questions and hypotheses are addressed with large community-based,

  6. The Collaborative Cross, a community resource for the genetic analysis of complex traits

    NARCIS (Netherlands)

    Churchill, Gary A.; Jansen, Ritsert C.; Airey, D.C.; Allayee, H.; Angel, J.M.; Attie, A.D.; Beatty, J.; Beavis, W.D.; Belknap, J.K.; Bennett, B.; Berrettini, W.; Bleich, A.; Bogue, M.; Broman, K.W.; Buck, K.J.; Buckler, E.; Burmeister, M.; Chesler, E.J.; Cheverud, J.M.; Clapcote, S.; Cook, M.N.; Cox, R.D.; Crabbe, J.C.; Crusio, W.E.; Darvasi, A.; Deschnepper, C.F.; Doerge, R.W.; Farber, C.R.; Forejt, J.; Gaile, D.; Garlow, S.J.; Geiger, H.; Gershenfeld, H.; Gordon, T.; Gu, J.; Gu, W.K.; de Haan, G; Hayes, N.L.; Heller, C.; Himmelbauer, H.; Hitzemann, R.; Hunter, K.; Hsu, H.C.; Iraqi, F.A.; Ivandic, B.; Jacob, H.J.; Jjepsen, K.J.; Johnson, D.K.; Johnson, T.E.; Kempermann, G.; Kendziorski, C.; Kotb, M.; Kooy, R.F; Llamas, B.; Lammert, F.; Lassalle, J.M.; Lowenstein, P.R.; Lu, L.; Lusiss, A.; Manly, K.F.; Marcucio, R.; Matthews, D.; Medrano, J.F.; Miller, D.R.; Mittleman, G.; Mock, B.A.; Mogil, J.S.; Montagutelli, X.; Morahan, G.; Morris, D.G.; Mott, R; Nadeau, J.H.; Nagase, H.; Nowakowski, R.S.; O'Hara, B.F.; Osadchuk, A.V.; Page, G.P.; Paigen, B.; Paigen, K.; Palmer, Abraham A.; Pan, H.J.; Peltonen-Palotie, L.; Pomp, D.; Peirce, J.; Pravenec, M.; Prows, D.R.; Qi, Z.H.; Reeves, R.H.; Roder, J.; Rosen, G.D.; Schadt, E.E.; Schalkwyk, L.C.; Seltzer, Z.; Shimomura, K.; Shou, S.M.; Sillanpaa, M.J.; Siracusa, L.D.; Snoeck, H.W.; Spearow, J.L.; Deschepper, Christian F.; Jepsen, Karl J.; Lusis, Aldons; O’Hara, Bruce F.; Sillanpää, Mikko J.; Tarantino, Lisa M.; Svenson, Karen; Threadgill, David; Toth, Linda A.; Valdar, William; Pardo-Manuel de Villena, Fernando; Warden, Craig; Whatley, Steve; Williams, Robert W.; Wiltshire, Tim; Yi, Nengjun; Zhang, Dabao; Zhang, Min; Zou, Fei; Montagutelli, X.; Tarantino, LM; Toth, LA; de Villena, FPM; Yi, NJ; Zhang, DB; Williams, O.

    2004-01-01

    The goal of the Complex Trait Consortium is to promote the development of resources that can be used to understand, treat and ultimately prevent pervasive human diseases. Existing and proposed mouse resources that are optimized to study the actions of isolated genetic loci on a fixed background are

  7. Copper dynamics in doped metal-bis(histidine) complexes.

    Science.gov (United States)

    Colaneri, Michael J; Vitali, Jacqueline

    2014-07-03

    Electron paramagnetic resonance (EPR) temperature-dependent measurements were undertaken on three Cu(II)-doped metal-histidine complexes to assess copper site dynamic behavior. Previous single-crystal EPR analysis on two of these, zinc d,l-histidine pentahydrate (ZnDLH) and bis(l-histidinato)cadmium dihydrate (CdLH), found that doped Cu(2+) can be modeled as hopping between two neighboring conformational states, with a temperature-dependent rate becoming large enough at room temperature to produce an "averaged" spectrum. By comparing spectra from their powdered form, we show that Cu(2+) doped into a third system, Cd(2+)-d,l-histidine (CdDLH), also exhibits temperature-dependent EPR with features indicating a similar motional-averaging process. In addition, the change of g and copper hyperfine parameters from low to high temperature for CdDLH resembles that in ZnDLH, whereas the change in these parameters for CdLH is like that found in a fourth copper-doped system, zinc l-histidine dihydrate (ZnLH). Taken together, these results suggest that averaging motion between neighboring copper sites is common in metal-bis(histidine) compounds. More detailed studies on biological models are thus warranted, especially because they reveal unique relationships between structure, dynamic processes, and stability and can lead to a better understanding of the role played by site flexibility in copper proteins.

  8. Early signatures of regime shifts in complex dynamical systems

    Indian Academy of Sciences (India)

    Indrani Bose; Mainak Pal

    2015-02-01

    A large number of studies have recently been carried out on the early signatures of regime shifts in a number of dynamical systems, e.g., ecosystems, the climate, fish and wildlife populations, financial markets, complex diseases and gene circuits. The underlying model in most cases is that of the fold-bifurcation in which a sudden regime shift occurs at a bifurcation point. The shift involves a discontinuous jump from one type of stable steady state to another. The dynamics of natural systems have both deterministic and stochastic components. The early signatures of abrupt regime shifts include the critical slowing down as a transition point is approached, rising variance and the lag-1 autocorrelation function, increased skewness of the steady-state probability distribution and the ratio of two mean first passage times for the exits from the stable steady states as the bifurcation point is approached. Noise-induced regime shifts are also possible for which the vicinity of the bifurcation point is not essential. In this paper, we review examples of regime shifts in natural systems and the associated early signatures. We further discuss how such approaches provide useful insights on a cell biological process involving the fold-bifurcation.

  9. Dynamic hysteresis in the rheology of complex fluids.

    Science.gov (United States)

    Puisto, Antti; Mohtaschemi, Mikael; Alava, Mikko J; Illa, Xavier

    2015-04-01

    Recently, rheological hysteresis has been studied systematically in a wide range of complex fluids combining global rheology and time-resolved velocimetry. In this paper we present an analysis of the roles of the three most fundamental mechanisms in simple-yield-stress fluids: structure dynamics, viscoelastic response, and spatial flow heterogeneities, i.e., time-dependent shear bands. Dynamical hysteresis simulations are done analogously to rheological ramp-up and -down experiments on a coupled model which incorporates viscoelasticity and time-dependent structure evolution. Based on experimental data, a coupling between hysteresis measured from the local velocity profiles and that measured from the global flow curve has been suggested. According to the present model, even if transient shear banding appears during the shear ramps, in typical narrow-gap devices, only a small part of the hysteretic response can be attributed to heterogeneous flow. This results in decoupling of the hysteresis measured from the local velocity profiles and the global flow curve, demonstrating that for an arbitrary time-dependent rheological response this proposed coupling can be very weak.

  10. Proceedings of "Optical Probes of Dynamics in Complex Environments"

    Energy Technology Data Exchange (ETDEWEB)

    Sension, R; Tokmakoff, A

    2008-04-01

    This document contains the proceedings from the symposium on Optical Probes of Dynamics in Complex Environments, which organized as part of the 235th National Meeting of the American Chemical Society in New Orleans, LA from April 6 to 10, 2008. The study of molecular dynamics in chemical reaction and biological processes using time ƒresolved spectroscopy plays an important role in our understanding of energy conversion, storage, and utilization problems. Fundamental studies of chemical reactivity, molecular rearrangements, and charge transport are broadly supported by the DOE Office of Science because of their role in the development of alternative energy sources, the understanding of biological energy conversion processes, the efficient utilization of existing energy resources, and the mitigation of reactive intermediates in radiation chemistry. In addition, time resolved spectroscopy is central to all of DOEs grand challenges for fundamental energy science. This symposium brought together leaders in the field of ultrafast spectroscopy, including experimentalists, theoretical chemists, and simulators, to discuss the most recent scientific and technological advances. DOE support for this conference was used to help young US and international scientists travel to the meeting. The latest technology in ultrafast infrared, optical, and xray spectroscopy and the scientific advances that these methods enable were covered. Particular emphasis was placed on new experimental methods used to probe molecular dynamics in liquids, solids, interfaces, nanostructured materials, and biomolecules.

  11. Dynamics of Crowd Behaviors: From Complex Plane to Quantum Random Fields

    Science.gov (United States)

    Ivancevic, Vladimir G.; Reid, Darryn J.

    2015-11-01

    The following sections are included: * Complex Plane Dynamics of Crowds and Groups * Introduction * Complex-Valued Dynamics of Crowd and Group Behaviors * Kähler Geometry of Crowd and Group Dynamics * Computer Simulations of Crowds and Croups Dynamics * Braids of Agents' Behaviors in the Complex Plane * Hilbert-Space Control of Crowds and Groups Dynamics * Quantum Random Fields: A Unique Framework for Simulation, Optimization, Control and Learning * Introduction * Adaptive Quantum Oscillator * Optimization and Learning on Banach and Hilbert Spaces * Appendix * Complex-Valued Image Processing * Linear Integral Equations * Riemann-Liouville Fractional Calculus * Rigorous Geometric Quantization * Supervised Machine-Learning Methods * First-Order Logic and Quantum Random Fields

  12. Translating inter-individual genetic variation to biological function in complex phenotypes

    DEFF Research Database (Denmark)

    Yadav, Rachita

    . The project work discussed in chapter 6 is aimed towards understanding the various underlying differences in obesity responses in fat cells from different white adipose tissue depots under diet-induced and genetic obesity by decoding the global epigenetic modifications. The fourth section of this thesis work...... examines epigenetic, genetic, transcriptomic and proteomic variations within different multifactorial diseases and this pivotal information is then annotated and associated to its corresponding phenotype. Childhood asthma and obesity are the two main phenotypic themes in this thesis. In the first section...... artificial neural network (ANN) based methodology of selecting genetic and clinical features with predictive power for childhood asthma. The goal of these studies is to understand the complex genetics of childhood asthma. The third part of this thesis (chapters 5 and 6) focuses on various mechanisms involved...

  13. Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways.

    Science.gov (United States)

    Sun, Changhui; Chen, Dan; Fang, Jun; Wang, Pingrong; Deng, Xiaojian; Chu, Chengcai

    2014-12-01

    Although the molecular basis of flowering time control is well dissected in the long day (LD) plant Arabidopsis, it is still largely unknown in the short day (SD) plant rice. Rice flowering time (heading date) is an important agronomic trait for season adaption and grain yield, which is affected by both genetic and environmental factors. During the last decade, as the nature of florigen was identified, notable progress has been made on exploration how florigen gene expression is genetically controlled. In Arabidopsis expression of certain key flowering integrators such as FLOWERING LOCUS C (FLC) and FLOWERING LOCUS T (FT) are also epigenetically regulated by various chromatin modifications, however, very little is known in rice on this aspect until very recently. This review summarized the advances of both genetic networks and chromatin modifications in rice flowering time control, attempting to give a complete view of the genetic and epigenetic architecture in complex network of rice flowering pathways.

  14. Characterizing cosmochemical materials with genetic affinities to the Earth: Genetic and chronological diversity within the IAB iron meteorite complex

    Science.gov (United States)

    Worsham, Emily A.; Bermingham, Katherine R.; Walker, Richard J.

    2017-06-01

    The IAB iron meteorite complex consists of a main group (MG) and five chemical subgroups (sLL, sLM, sLH, sHL, and sHH). Here, mass-independent Mo and radiogenic 182W isotope compositions are reported for IAB complex meteorites to evaluate the genetics and chronology, respectively, of the MG and subgroups. Osmium isotopes are used to correct for cosmic ray exposure effects on isotopes of Mo and W. The MG and three subgroups (i.e., sLL, sLM, and sLH), characterized by low Au abundances, have the same Mo isotopic compositions within analytical uncertainty, consistent with a common genetic origin. These meteorites, together with winonaites, are the only cosmochemical materials yet identified with Mo isotopic compositions that are identical to Earth. The Mo isotopic compositions of two subgroups characterized by higher Au abundances (sHL and sHH) are identical to one another within uncertainty, but differ from the low Au subgroups, indicating derivation from genetically distinct materials. The MG has a 182W, post calcium-aluminum inclusion (CAI) formation model age of 3.4 ± 0.7 Ma. One of the low Au subgroups (sLM) is ∼1.7 Ma younger, whereas the high Au subgroups are ∼1.5-3 Ma older. The new Mo-W data, coupled with chemical data, indicate that the MG and the low Au subgroups formed in different impact-generated melts, some of which evidently formed on a chemically disparate, but genetically identical parent body. The high Au subgroups likely formed via core-formation processes on separate, internally-heated parent bodies from other IAB subgroups. The IAB complex meteorites fall on a linear trend defined by 94Mo/96Mo vs. 95Mo/96Mo, along with most other iron meteorite groups. Variation along this line was caused by mixing between at least two nebular components. One component was likely a pure s-process enriched nucleosynthetic carrier, and the other a homogenized nebular component. Sombrerete, currently classified as an sHL iron, has a Mo isotopic composition that

  15. Swarm satellite mission scheduling & planning using Hybrid Dynamic Mutation Genetic Algorithm

    Science.gov (United States)

    Zheng, Zixuan; Guo, Jian; Gill, Eberhard

    2017-08-01

    Space missions have traditionally been controlled by operators from a mission control center. Given the increasing number of satellites for some space missions, generating a command list for multiple satellites can be time-consuming and inefficient. Developing multi-satellite, onboard mission scheduling & planning techniques is, therefore, a key research field for future space mission operations. In this paper, an improved Genetic Algorithm (GA) using a new mutation strategy is proposed as a mission scheduling algorithm. This new mutation strategy, called Hybrid Dynamic Mutation (HDM), combines the advantages of both dynamic mutation strategy and adaptive mutation strategy, overcoming weaknesses such as early convergence and long computing time, which helps standard GA to be more efficient and accurate in dealing with complex missions. HDM-GA shows excellent performance in solving both unconstrained and constrained test functions. The experiments of using HDM-GA to simulate a multi-satellite, mission scheduling problem demonstrates that both the computation time and success rate mission requirements can be met. The results of a comparative test between HDM-GA and three other mutation strategies also show that HDM has outstanding performance in terms of speed and reliability.

  16. Dissecting the genetics of complex inheritance: linkage disequilibrium mapping provides insight into Crohn disease.

    Science.gov (United States)

    Elding, Heather; Lau, Winston; Swallow, Dallas M; Maniatis, Nikolas

    2011-12-09

    Family studies for Crohn disease (CD) report extensive linkage on chromosome 16q and pinpoint NOD2 as a possible causative locus. However, linkage is also observed in families that do not bear the most frequent NOD2 causative mutations, but no other signals on 16q have been found so far in published genome-wide association studies. Our aim is to identify this missing genetic contribution. We apply a powerful genetic mapping approach to the Wellcome Trust Case-Control Consortium and the National Institute of Diabetes and Digestive and Kidney Diseases genome-wide association data on CD. This method takes into account the underlying structure of linkage disequilibrium (LD) by using genetic distances from LD maps and provides a location for the causal agent. We find genetic heterogeneity within the NOD2 locus and also show an independent and unsuspected involvement of the neighboring gene, CYLD. We find associations with the IRF8 region and the region containing CDH1 and CDH3, as well as substantial phenotypic and genetic heterogeneity for CD itself. The genes are known to be involved in inflammation and immune dysregulation. These findings provide insight into the genetics of CD and suggest promising directions for understanding disease heterogeneity. The application of this method thus paves the way for understanding complex inheritance in general, leading to the dissection of different pathways and ultimately, personalized treatment. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  17. Statistical inference on genetic data reveals the complex demographic history of human populations in central Asia.

    Science.gov (United States)

    Palstra, Friso P; Heyer, Evelyne; Austerlitz, Frédéric

    2015-06-01

    The demographic history of modern humans constitutes a combination of expansions, colonizations, contractions, and remigrations. The advent of large scale genetic data combined with statistically refined methods facilitates inference of this complex history. Here we study the demographic history of two genetically admixed ethnic groups in Central Asia, an area characterized by high levels of genetic diversity and a history of recurrent immigration. Using Approximate Bayesian Computation, we infer that the timing of admixture markedly differs between the two groups. Admixture in the traditionally agricultural Tajiks could be dated back to the onset of the Neolithic transition in the region, whereas admixture in Kyrgyz is more recent, and may have involved the westward movement of Turkic peoples. These results are confirmed by a coalescent method that fits an isolation-with-migration model to the genetic data, with both Central Asian groups having received gene flow from the extremities of Eurasia. Interestingly, our analyses also uncover signatures of gene flow from Eastern to Western Eurasia during Paleolithic times. In conclusion, the high genetic diversity currently observed in these two Central Asian peoples most likely reflects the effects of recurrent immigration that likely started before historical times. Conversely, conquests during historical times may have had a relatively limited genetic impact. These results emphasize the need for a better understanding of the genetic consequences of transmission of culture and technological innovations, as well as those of invasions and conquests.

  18. Adult plant development in triticale (× triticosecale wittmack) is controlled by dynamic genetic patterns of regulation.

    Science.gov (United States)

    Würschum, Tobias; Liu, Wenxin; Alheit, Katharina V; Tucker, Matthew R; Gowda, Manje; Weissmann, Elmar A; Hahn, Volker; Maurer, Hans Peter

    2014-09-18

    Many biologically and agronomically important traits are dynamic and show temporal variation. In this study, we used triticale (× Triticosecale Wittmack) as a model crop to assess the genetic dynamics underlying phenotypic plasticity of adult plant development. To this end, a large mapping population with 647 doubled haploid lines derived from four partially connected families from crosses among six parents was scored for developmental stage at three different time points. Using genome-wide association mapping, we identified main effect and epistatic quantitative trait loci (QTL) at all three time points. Interestingly, some of these QTL were identified at all time points, whereas others appear to only contribute to the genetic architecture at certain developmental stages. Our results illustrate the temporal contribution of QTL to the genetic control of adult plant development and more generally, the temporal genetic patterns of regulation that underlie dynamic traits.

  19. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement

    Science.gov (United States)

    Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida

    2009-06-01

    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.

  20. Extreme genetic code optimality from a molecular dynamics calculation of amino acid polar requirement.

    Science.gov (United States)

    Butler, Thomas; Goldenfeld, Nigel; Mathew, Damien; Luthey-Schulten, Zaida

    2009-06-01

    A molecular dynamics calculation of the amino acid polar requirement is used to score the canonical genetic code. Monte Carlo simulation shows that this computational polar requirement has been optimized by the canonical genetic code, an order of magnitude more than any previously known measure, effectively ruling out a vertical evolution dynamics. The sensitivity of the optimization to the precise metric used in code scoring is consistent with code evolution having proceeded through the communal dynamics of statistical proteins using horizontal gene transfer, as recently proposed. The extreme optimization of the genetic code therefore strongly supports the idea that the genetic code evolved from a communal state of life prior to the last universal common ancestor.

  1. The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation

    Institute of Scientific and Technical Information of China (English)

    Markus J. Buehler; Alexander Hartmaier; Mark A. Duchaineau; Farid F. Abraham; Huajian Gao

    2005-01-01

    We analyze a large-scale molecular dynamics simulation of work hardening in a model system of a ductile solid.With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening in this ductile material. These are (1) dislocation cutting processes, jog formation and generation of trails of point defects; (2) activation of secondary slip systems by Frank-Read and cross-slip mechanisms; and (3) formation of sessile dislocations such as Lomer-Cottrell locks.We report the discovery of a new class of point defects referred to as trail of partial point defects, which could play an important role in situations when partial dislocations dominate plasticity. Another important result of the present work is the rediscovery of the Fleischer-mechanism of cross-slip of partial dislocations that was theoretically proposed more than 50 years ago, and is now, for the first time, confirmed by atomistic simulation. On the typical time scale of molecular dynamics simulations, the dislocations self-organize into a complex sessile defect topology. Our analysis illustrates numerous mechanisms formerly only conjectured in textbooks and observed indirectly in experiments. It is the first time that such a rich set of fundamental phenomena have been revealed in a single computer simulation, and its dynamical evolution has been studied. The present study exemplifies the simulation and analysis of the complex nonlinear dynamics of a many-particle system during failure using ultra-large scale computing.

  2. Studying microstructural dynamics of complex fluids with particle tracking microrheology

    Science.gov (United States)

    Breedveld, Victor

    2004-11-01

    Over the last decade, particle tracking microrheology has matured as a new tool for complex fluids research. The main advantages of microrheology over traditional macroscopic rheometry are: the required sample size is extremely small ( ˜ 1 microliter); local viscoelastic properties in a sample can be probed with high spatial resolution ( ˜1-10 micrometer); and the sample is not disturbed by moving rheometer parts. I will present two examples of recent work in my group that highlight how these characteristics can be exploited to acquire unique information about the microstructure of complex fluids. First, we have studied protein unfolding. Traditionally, protein unfolding is studied with spectroscopic techniques (circular dichroism, NMR, fluorescence). Although viscosity has been listed in textbooks as a suitable technique, few -if any- quantitative rheological studies of unfolding have been reported, mainly due to technical difficulties. With microrheology, we have been able to quantify the size of the folded and unfolded protein, as well as the Gibbs free energy of unfolding, for aqueous bovine serum albumine solutions upon addition of urea as a denaturant. The results are in excellent agreement with literature data. Secondly, we have developed new technology for studying the microstructural dynamics of solvent-responsive complex fluids. In macroscopic rheometry it is virtually impossible to change solvent composition and measure the rheological response of a sample. By integrating microfluidics and microrheology we have been able to overcome this barrier: due to the micrometer lengthscales in microfluidiv devices, diffusive timescales in a dialysis set-up become short enough to achieve rapid and reversible changes in sample composition, without affecting the concentration of macromolecular components. Our dialysis cell for microrheology is a unique tool for studying the dynamics of structural and rheological changes induced by solvent composition. I will

  3. A complex-valued neural dynamical optimization approach and its stability analysis.

    Science.gov (United States)

    Zhang, Songchuan; Xia, Youshen; Zheng, Weixing

    2015-01-01

    In this paper, we propose a complex-valued neural dynamical method for solving a complex-valued nonlinear convex programming problem. Theoretically, we prove that the proposed complex-valued neural dynamical approach is globally stable and convergent to the optimal solution. The proposed neural dynamical approach significantly generalizes the real-valued nonlinear Lagrange network completely in the complex domain. Compared with existing real-valued neural networks and numerical optimization methods for solving complex-valued quadratic convex programming problems, the proposed complex-valued neural dynamical approach can avoid redundant computation in a double real-valued space and thus has a low model complexity and storage capacity. Numerical simulations are presented to show the effectiveness of the proposed complex-valued neural dynamical approach.

  4. Construction of exact complex dynamical invariant of a two-dimensional classical system

    Indian Academy of Sciences (India)

    Fakir Chand; S C Mishra

    2006-12-01

    We present the construction of exact complex dynamical invariant of a two-dimensional classical dynamical system on an extended complex space utilizing Lie algebraic approach. These invariants are expected to play a vital role in understanding the complex trajectories of both classical and quantum systems.

  5. Complex systems approach to fire dynamics and climate change impacts

    Science.gov (United States)

    Pueyo, S.

    2012-04-01

    I present some recent advances in complex systems theory as a contribution to understanding fire regimes and forecasting their response to a changing climate, qualitatively and quantitatively. In many regions of the world, fire sizes have been found to follow, approximately, a power-law frequency distribution. As noted by several authors, this distribution also arises in the "forest fire" model used by physicists to study mechanisms that give rise to scale invariance (the power law is a scale-invariant distribution). However, this model does not give and does not pretend to give a realistic description of fire dynamics. For example, it gives no role to weather and climate. Pueyo (2007) developed a variant of the "forest fire" model that is also simple but attempts to be more realistic. It also results into a power law, but the parameters of this distribution change through time as a function of weather and climate. Pueyo (2007) observed similar patterns of response to weather in data from boreal forest fires, and used the fitted response functions to forecast fire size distributions in a possible climate change scenario, including the upper extreme of the distribution. For some parameter values, the model in Pueyo (2007) displays a qualitatively different behavior, consisting of simple percolation. In this case, fire is virtually absent, but megafires sweep through the ecosystem a soon as environmental forcings exceed a critical threshold. Evidence gathered by Pueyo et al. (2010) suggests that this is realistic for tropical rainforests (specifically, well-conserved upland rainforests). Some climate models suggest that major tropical rainforest regions are going to become hotter and drier if climate change goes ahead unchecked, which could cause such abrupt shifts. Not all fire regimes are well described by this model. Using data from a tropical savanna region, Pueyo et al. (2010) found that the dynamics in this area do not match its assumptions, even though fire

  6. The spectrum of mutations controlling complex traits and the genetics of fitness in plants.

    Science.gov (United States)

    Falke, K Christin; Glander, Shirin; He, Fei; Hu, Jinyong; de Meaux, Juliette; Schmitz, Gregor

    2013-12-01

    Elucidating the molecular basis of natural variation in complex traits is the key for their effective management in crops or natural systems. This review focuses on plant variation. It will first, show that genetic modifications causing major alterations in polygenic phenotypes often hit targets within an array of 'candidate genes', second, present new methods that include mutations of all effect sizes, and help exhaustively describe the molecular systems underlying complex traits, and third, discuss recent findings regarding the role of epigenetic variants, which in plants are often maintained through both mitosis and meiosis. Exploring the whole spectrum of mutations controlling complex traits is made possible by the combination of genetic, genomic and epigenomic approaches.

  7. Conserved Genetic Interactions between Ciliopathy Complexes Cooperatively Support Ciliogenesis and Ciliary Signaling.

    Directory of Open Access Journals (Sweden)

    Laura E Yee

    2015-11-01

    Full Text Available Mutations in genes encoding cilia proteins cause human ciliopathies, diverse disorders affecting many tissues. Individual genes can be linked to ciliopathies with dramatically different phenotypes, suggesting that genetic modifiers may participate in their pathogenesis. The ciliary transition zone contains two protein complexes affected in the ciliopathies Meckel syndrome (MKS and nephronophthisis (NPHP. The BBSome is a third protein complex, affected in the ciliopathy Bardet-Biedl syndrome (BBS. We tested whether mutations in MKS, NPHP and BBS complex genes modify the phenotypic consequences of one another in both C. elegans and mice. To this end, we identified TCTN-1, the C. elegans ortholog of vertebrate MKS complex components called Tectonics, as an evolutionarily conserved transition zone protein. Neither disruption of TCTN-1 alone or together with MKS complex components abrogated ciliary structure in C. elegans. In contrast, disruption of TCTN-1 together with either of two NPHP complex components, NPHP-1 or NPHP-4, compromised ciliary structure. Similarly, disruption of an NPHP complex component and the BBS complex component BBS-5 individually did not compromise ciliary structure, but together did. As in nematodes, disrupting two components of the mouse MKS complex did not cause additive phenotypes compared to single mutants. However, disrupting both Tctn1 and either Nphp1 or Nphp4 exacerbated defects in ciliogenesis and cilia-associated developmental signaling, as did disrupting both Tctn1 and the BBSome component Bbs1. Thus, we demonstrate that ciliary complexes act in parallel to support ciliary function and suggest that human ciliopathy phenotypes are altered by genetic interactions between different ciliary biochemical complexes.

  8. Estimation of instantaneous complex dynamics through Lyapunov exponents: a study on heartbeat dynamics.

    Science.gov (United States)

    Valenza, Gaetano; Citi, Luca; Barbieri, Riccardo

    2014-01-01

    Measures of nonlinearity and complexity, and in particular the study of Lyapunov exponents, have been increasingly used to characterize dynamical properties of a wide range of biological nonlinear systems, including cardiovascular control. In this work, we present a novel methodology able to effectively estimate the Lyapunov spectrum of a series of stochastic events in an instantaneous fashion. The paradigm relies on a novel point-process high-order nonlinear model of the event series dynamics. The long-term information is taken into account by expanding the linear, quadratic, and cubic Wiener-Volterra kernels with the orthonormal Laguerre basis functions. Applications to synthetic data such as the Hénon map and Rössler attractor, as well as two experimental heartbeat interval datasets (i.e., healthy subjects undergoing postural changes and patients with severe cardiac heart failure), focus on estimation and tracking of the Instantaneous Dominant Lyapunov Exponent (IDLE). The novel cardiovascular assessment demonstrates that our method is able to effectively and instantaneously track the nonlinear autonomic control dynamics, allowing for complexity variability estimations.

  9. Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

    Science.gov (United States)

    Kwac, Kijeong; Lee, Chewook; Jung, Yousung; Han, Jaebeom; Kwak, Kyungwon; Zheng, Junrong; Fayer, M D; Cho, Minhaeng

    2006-12-28

    Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

  10. Wake Dynamics in the Atmospheric Boundary Layer Over Complex Terrain

    Science.gov (United States)

    Markfort, Corey D.

    The goal of this research is to advance our understanding of atmospheric boundary layer processes over heterogeneous landscapes and complex terrain. The atmospheric boundary layer (ABL) is a relatively thin (˜ 1 km) turbulent layer of air near the earth's surface, in which most human activities and engineered systems are concentrated. Its dynamics are crucially important for biosphere-atmosphere couplings and for global atmospheric dynamics, with significant implications on our ability to predict and mitigate adverse impacts of land use and climate change. In models of the ABL, land surface heterogeneity is typically represented, in the context of Monin-Obukhov similarity theory, as changes in aerodynamic roughness length and surface heat and moisture fluxes. However, many real landscapes are more complex, often leading to massive boundary layer separation and wake turbulence, for which standard models fail. Trees, building clusters, and steep topography produce extensive wake regions currently not accounted for in models of the ABL. Wind turbines and wind farms also generate wakes that combine in complex ways to modify the ABL. Wind farms are covering an increasingly significant area of the globe and the effects of large wind farms must be included in regional and global scale models. Research presented in this thesis demonstrates that wakes caused by landscape heterogeneity must be included in flux parameterizations for momentum, heat, and mass (water vapor and trace gases, e.g. CO2 and CH4) in ABL simulation and prediction models in order to accurately represent land-atmosphere interactions. Accurate representation of these processes is crucial for the predictions of weather, air quality, lake processes, and ecosystems response to climate change. Objectives of the research reported in this thesis are: 1) to investigate turbulent boundary layer adjustment, turbulent transport and scalar flux in wind farms of varying configurations and develop an improved

  11. Quantum Dynamical Behaviour in Complex Systems - A Semiclassical Approach

    Energy Technology Data Exchange (ETDEWEB)

    Ananth, Nandini [Univ. of California, Berkeley, CA (United States)

    2008-01-01

    One of the biggest challenges in Chemical Dynamics is describing the behavior of complex systems accurately. Classical MD simulations have evolved to a point where calculations involving thousands of atoms are routinely carried out. Capturing coherence, tunneling and other such quantum effects for these systems, however, has proven considerably harder. Semiclassical methods such as the Initial Value Representation (SC-IVR) provide a practical way to include quantum effects while still utilizing only classical trajectory information. For smaller systems, this method has been proven to be most effective, encouraging the hope that it can be extended to deal with a large number of degrees of freedom. Several variations upon the original idea of the SCIVR have been developed to help make these larger calculations more tractable; these range from the simplest, classical limit form, the Linearized IVR (LSC-IVR) to the quantum limit form, the Exact Forward-Backward version (EFB-IVR). In this thesis a method to tune between these limits is described which allows us to choose exactly which degrees of freedom we wish to treat in a more quantum mechanical fashion and to what extent. This formulation is called the Tuning IVR (TIVR). We further describe methodology being developed to evaluate the prefactor term that appears in the IVR formalism. The regular prefactor is composed of the Monodromy matrices (jacobians of the transformation from initial to finial coordinates and momenta) which are time evolved using the Hessian. Standard MD simulations require the potential surfaces and their gradients, but very rarely is there any information on the second derivative. We would like to be able to carry out the SC-IVR calculation without this information too. With this in mind a finite difference scheme to obtain the Hessian on-the-fly is proposed. Wealso apply the IVR formalism to a few problems of current interest. A method to obtain energy eigenvalues accurately for complex

  12. No evidence for a genetic blueprint: The case of the "complex" mammalian photoreceptor

    Directory of Open Access Journals (Sweden)

    G Kumaramanickavel

    2015-01-01

    Full Text Available Despite the intensity of the search for genes causing inherited retinal degenerations over the past 3 decades, of the approximately 200 disease genes identified to date, all appear to be ordinary housekeeping genes specifying proteins playing basic structural and functional roles in the mature photoreceptor cells. No genes or genetic elements have been identified which can be construed as having a specific morphogenic role, directing the development of the cytoarchitecture of any particular retinal cell. The evidence suggests that the cytoarchitecture of the retinal photoreceptors, although enormously complex, arises from the self-organization of the cells constituents without any regulation or direction from an external genetic blueprint.

  13. Dynamics of Symmetric Conserved Mass Aggregation Model on Complex Networks

    Institute of Scientific and Technical Information of China (English)

    HUA Da-Yin

    2009-01-01

    We investigate the dynamical behaviour of the aggregation process in the symmetric conserved mass aggregation model under three different topological structures. The dispersion σ(t, L) = (∑i(mi - ρ0)2/L)1/2 is defined to describe the dynamical behaviour where ρ0 is the density of particle and mi is the particle number on a site. It is found numerically that for a regular lattice and a scale-free network, σ(t, L) follows a power-law scaling σ(t, L) ~ tδ1 and σ(t, L) ~ tδ4 from a random initial condition to the stationary states, respectively. However, for a small-world network, there are two power-law scaling regimes, σ(t, L) ~ tδ2 when t<T and a(t, L) ~ tδ3 when tT. Moreover, it is found numerically that δ2 is near to δ1 for small rewiring probability q, and δ3 hardly changes with varying q and it is almost the same as δ4. We speculate that the aggregation of the connection degree accelerates the mass aggregation in the initial relaxation stage and the existence of the long-distance interactions in the complex networks results in the acceleration of the mass aggregation when tT for the small-world networks. We also show that the relaxation time T follows a power-law scaling τ Lz and σ(t, L) in the stationary state follows a power-law σs(L) ~ Lσ for three different structures.

  14. Obesity and genomics: role of technology in unraveling the complex genetic architecture of obesity.

    Science.gov (United States)

    Apalasamy, Yamunah Devi; Mohamed, Zahurin

    2015-04-01

    Obesity is a complex and multifactorial disease that occurs as a result of the interaction between "obesogenic" environmental factors and genetic components. Although the genetic component of obesity is clear from the heritability studies, the genetic basis remains largely elusive. Successes have been achieved in identifying the causal genes for monogenic obesity using animal models and linkage studies, but these approaches are not fruitful for polygenic obesity. The developments of genome-wide association approach have brought breakthrough discovery of genetic variants for polygenic obesity where tens of new susceptibility loci were identified. However, the common SNPs only accounted for a proportion of heritability. The arrival of NGS technologies and completion of 1000 Genomes Project have brought other new methods to dissect the genetic architecture of obesity, for example, the use of exome genotyping arrays and deep sequencing of candidate loci identified from GWAS to study rare variants. In this review, we summarize and discuss the developments of these genetic approaches in human obesity.

  15. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Directory of Open Access Journals (Sweden)

    Beata Szefler

    2016-10-01

    Full Text Available Glucose oxidase (GOx is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2. GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI. The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD study of the PEI ligand (C14N8_07_B22 and the GOx enzyme (3QVR was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1 of −5.8 kcal/mol and (LIG2 of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1 and on its surface (LIG2 were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

  16. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase

    Science.gov (United States)

    Szefler, Beata; Diudea, Mircea V.; Putz, Mihai V.; Grudzinski, Ireneusz P.

    2016-01-01

    Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H2O2). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of −5.8 kcal/mol and (LIG2) of −4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase. PMID:27801788

  17. Molecular Dynamic Studies of the Complex Polyethylenimine and Glucose Oxidase.

    Science.gov (United States)

    Szefler, Beata; Diudea, Mircea V; Putz, Mihai V; Grudzinski, Ireneusz P

    2016-10-27

    Glucose oxidase (GOx) is an enzyme produced by Aspergillus, Penicillium and other fungi species. It catalyzes the oxidation of β-d-glucose (by the molecular oxygen or other molecules, like quinones, in a higher oxidation state) to form d-glucono-1,5-lactone, which hydrolyses spontaneously to produce gluconic acid. A coproduct of this enzymatic reaction is hydrogen peroxide (H₂O₂). GOx has found several commercial applications in chemical and pharmaceutical industries including novel biosensors that use the immobilized enzyme on different nanomaterials and/or polymers such as polyethylenimine (PEI). The problem of GOx immobilization on PEI is retaining the enzyme native activity despite its immobilization onto the polymer surface. Therefore, the molecular dynamic (MD) study of the PEI ligand (C14N8_07_B22) and the GOx enzyme (3QVR) was performed to examine the final complex PEI-GOx stabilization and the affinity of the PEI ligand to the docking sites of the GOx enzyme. The docking procedure showed two places/regions of major interaction of the protein with the polymer PEI: (LIG1) of -5.8 kcal/mol and (LIG2) of -4.5 kcal/mol located inside the enzyme and on its surface, respectively. The values of enthalpy for the PEI-enzyme complex, located inside of the protein (LIG1) and on its surface (LIG2) were computed. Docking also discovered domains of the GOx protein that exhibit no interactions with the ligand or have even repulsive characteristics. The structural data clearly indicate some differences in the ligand PEI behavior bound at the two places/regions of glucose oxidase.

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

    Science.gov (United States)

    Cortez, Michael H

    2016-09-01

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

  19. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies.

    Directory of Open Access Journals (Sweden)

    Masakazu Kohda

    2016-01-01

    Full Text Available Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4 as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3 and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21 as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder.

  20. A Comprehensive Genomic Analysis Reveals the Genetic Landscape of Mitochondrial Respiratory Chain Complex Deficiencies

    Science.gov (United States)

    Nyuzuki, Hiromi; Moriyama, Yohsuke; Mizuno, Yosuke; Hirata, Tomoko; Yatsuka, Yukiko; Yamashita-Sugahara, Yzumi; Nakachi, Yutaka; Kato, Hidemasa; Okuda, Akihiko; Tamaru, Shunsuke; Borna, Nurun Nahar; Banshoya, Kengo; Aigaki, Toshiro; Sato-Miyata, Yukiko; Ohnuma, Kohei; Suzuki, Tsutomu; Nagao, Asuteka; Maehata, Hazuki; Matsuda, Fumihiko; Higasa, Koichiro; Nagasaki, Masao; Yasuda, Jun; Yamamoto, Masayuki; Fushimi, Takuya; Shimura, Masaru; Kaiho-Ichimoto, Keiko; Harashima, Hiroko; Yamazaki, Taro; Mori, Masato; Murayama, Kei; Ohtake, Akira; Okazaki, Yasushi

    2016-01-01

    Mitochondrial disorders have the highest incidence among congenital metabolic disorders characterized by biochemical respiratory chain complex deficiencies. It occurs at a rate of 1 in 5,000 births, and has phenotypic and genetic heterogeneity. Mutations in about 1,500 nuclear encoded mitochondrial proteins may cause mitochondrial dysfunction of energy production and mitochondrial disorders. More than 250 genes that cause mitochondrial disorders have been reported to date. However exact genetic diagnosis for patients still remained largely unknown. To reveal this heterogeneity, we performed comprehensive genomic analyses for 142 patients with childhood-onset mitochondrial respiratory chain complex deficiencies. The approach includes whole mtDNA and exome analyses using high-throughput sequencing, and chromosomal aberration analyses using high-density oligonucleotide arrays. We identified 37 novel mutations in known mitochondrial disease genes and 3 mitochondria-related genes (MRPS23, QRSL1, and PNPLA4) as novel causative genes. We also identified 2 genes known to cause monogenic diseases (MECP2 and TNNI3) and 3 chromosomal aberrations (6q24.3-q25.1, 17p12, and 22q11.21) as causes in this cohort. Our approaches enhance the ability to identify pathogenic gene mutations in patients with biochemically defined mitochondrial respiratory chain complex deficiencies in clinical settings. They also underscore clinical and genetic heterogeneity and will improve patient care of this complex disorder. PMID:26741492

  1. Contributions of the complexity paradigm to the understanding of Cerrado's organization and dynamics

    National Research Council Canada - National Science Library

    MATTOS, SÉRGIO H.V.L. DE; VICENTE, LUIZ E; PEREZ FILHO, ARCHIMEDES; PIQUEIRA, JOSÉ R.C

    2016-01-01

    .... The contributions of the complexity paradigm in this context are still less exploited, despite its great potential for explanations and predictions presented in previous diverse dynamic systems...

  2. A genetic algorithm for dynamic parameters reverse deduction of integrated anchorage system

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In the analysis of the system of anchoring bar and wall rock in small strain and longitudinal vibration dynamic response, the influence of the cement grouting as well as the rock layer on the anchor bar can be evaluated as the two kinds of parameters: the dynamic stiffness and the damp, which are the vital reference of the anchorage quality. Based on the analytic solution to the dynamic equation of the integrated anchor bar, the new approach which combines genetic algorithm and the toolbox of Matlab is applied to solve the problem of multi-parameters reverse deduction for integrated anchorage system in dynamic testing. Using the traits of the self-organizing, self-adapting and the fast convergence speed of the genetic algorithm, the optimum of all possible solutions to dynamic parameters is obtained by calculating the project instances. Examples show that the method presented in this paper is effective and reliable.

  3. Molecular dynamic simulation of complex NS2B-NS3 DENV2 ...

    African Journals Online (AJOL)

    Usman Sumo Friend Tambunan, Irwan Kurniawan, Arli Aditya Parikesit ... The results provide conformational changes of enzyme-inhibitor complex ... These results show that dynamic behavior of the complex occurs in the presence of solvent.

  4. Proofreading of Peptide-MHC Complexes through Dynamic Multivalent Interactions.

    Science.gov (United States)

    Thomas, Christoph; Tampé, Robert

    2017-01-01

    The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein-protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that

  5. Proofreading of Peptide—MHC Complexes through Dynamic Multivalent Interactions

    Science.gov (United States)

    Thomas, Christoph; Tampé, Robert

    2017-01-01

    The adaptive immune system is able to detect and destroy cells that are malignantly transformed or infected by intracellular pathogens. Specific immune responses against these cells are elicited by antigenic peptides that are presented on major histocompatibility complex class I (MHC I) molecules and recognized by cytotoxic T lymphocytes at the cell surface. Since these MHC I-presented peptides are generated in the cytosol by proteasomal protein degradation, they can be metaphorically described as a window providing immune cells with insights into the state of the cellular proteome. A crucial element of MHC I antigen presentation is the peptide-loading complex (PLC), a multisubunit machinery, which contains as key constituents the transporter associated with antigen processing (TAP) and the MHC I-specific chaperone tapasin (Tsn). While TAP recognizes and shuttles the cytosolic antigenic peptides into the endoplasmic reticulum (ER), Tsn samples peptides in the ER for their ability to form stable complexes with MHC I, a process called peptide proofreading or peptide editing. Through its selection of peptides that improve MHC I stability, Tsn contributes to the hierarchy of immunodominant peptide epitopes. Despite the fact that it concerns a key event in adaptive immunity, insights into the catalytic mechanism of peptide proofreading carried out by Tsn have only lately been gained via biochemical, biophysical, and structural studies. Furthermore, a Tsn homolog called TAP-binding protein-related (TAPBPR) has only recently been demonstrated to function as a second MHC I-specific chaperone and peptide proofreader. Although TAPBPR is PLC-independent and has a distinct allomorph specificity, it is likely to share a common catalytic mechanism with Tsn. This review focuses on the current knowledge of the multivalent protein–protein interactions and the concomitant dynamic molecular processes underlying peptide-proofreading catalysis. We do not only derive a model that

  6. Molecular genetics of the swine major histocompatibility complex, the SLA complex.

    Science.gov (United States)

    Lunney, Joan K; Ho, Chak-Sum; Wysocki, Michal; Smith, Douglas M

    2009-03-01

    The swine major histocompatibility complex (MHC) or swine leukocyte antigen (SLA) complex is one of the most gene-dense regions in the swine genome. It consists of three major gene clusters, the SLA class I, class III and class II regions, that span approximately 1.1, 0.7 and 0.5Mb, respectively, making the swine MHC the smallest among mammalian MHC so far examined and the only one known to span the centromere. This review summarizes recent updates to the Immuno Polymorphism Database-MHC (IPD-MHC) website (http://www.ebi.ac.uk/ipd/mhc/sla/) which serves as the repository for maintaining a list of all SLA recognized genes and their allelic sequences. It reviews the expression of SLA proteins on cell subsets and their role in antigen presentation and regulating immune responses. It concludes by discussing the role of SLA genes in swine models of transplantation, xenotransplantation, cancer and allergy and in swine production traits and responses to infectious disease and vaccines.

  7. Nonlinear problems of complex natural systems: Sun and climate dynamics

    CERN Document Server

    Bershadskii, A

    2012-01-01

    Universal role of the nonlinear one-third subharmonic resonance mechanism in generation of the strong fluctuations in such complex natural dynamical systems as global climate and global solar activity is discussed using wavelet regression detrended data. Role of the oceanic Rossby waves in the year-scale global temperature fluctuations and the nonlinear resonance contribution to the El Nino phenomenon have been discussed in detail. The large fluctuations of the reconstructed temperature on the millennial time-scales (Antarctic ice cores data for the past 400,000 years) are also shown to be dominated by the one-third subharmonic resonance, presumably related to Earth precession effect on the energy that the intertropical regions receive from the Sun. Effects of Galactic turbulence on the temperature fluctuations are discussed in this content. It is also shown that the one-third subharmonic resonance can be considered as a background for the 11-years solar cycle, and again the global (solar) rotation and chaoti...

  8. Stochastic dynamics of complex systems: from glasses to evolution (series on complexity science)

    CERN Document Server

    Sibani, Paolo

    2013-01-01

    Dynamical evolution over long time scales is a prominent feature of all the systems we intuitively think of as complex - for example, ecosystems, the brain or the economy. In physics, the term ageing is used for this type of slow change, occurring over time scales much longer than the patience, or indeed the lifetime, of the observer. The main focus of this book is on the stochastic processes which cause ageing, and the surprising fact that the ageing dynamics of systems which are very different at the microscopic level can be treated in similar ways. The first part of this book provides the necessary mathematical and computational tools and the second part describes the intuition needed to deal with these systems. Some of the first few chapters have been covered in several other books, but the emphasis and selection of the topics reflect both the authors' interests and the overall theme of the book. The second part contains an introduction to the scientific literature and deals in some detail with the desc...

  9. Consistent Cosmology, Dynamic Relativity and Causal Quantum Mechanics as Unified Manifestations of the Symmetry of Complexity

    CERN Document Server

    Kirilyuk, A P

    2006-01-01

    The universal symmetry, or conservation, of complexity underlies any law or principle of system dynamics and describes the unceasing transformation of dynamic information into dynamic entropy as the unique way to conserve their sum, the total dynamic complexity. Here we describe the real world structure emergence and dynamics as manifestation of the universal symmetry of complexity of initially homogeneous interaction between two protofields. It provides the unified complex-dynamic, causally complete origin of physically real, 3D space, time, elementary particles, their properties (mass, charge, spin, etc.), quantum, relativistic, and classical behaviour, as well as fundamental interaction forces, including naturally quantized gravitation. The old and new cosmological problems (including "dark" mass and energy) are basically solved for this explicitly emerging, self-tuning world structure characterised by strictly positive (and large) energy-complexity. A general relation is obtained between the numbers of wo...

  10. Genetic evidence of peripheral isolation and low diversity in marginal populations of the Acropora hyacinthus complex

    Science.gov (United States)

    Suzuki, Go; Keshavmurthy, Shashank; Hayashibara, Takeshi; Wallace, Carden C.; Shirayama, Yoshihisa; Chen, Chaolun Allen; Fukami, Hironobu

    2016-12-01

    Zooxanthellate corals are found throughout the tropics, but also extend into subtropical and marginal locations due to the presence of warm ocean currents. The population history of corals in marginal locations is of great interest in relation to changing global climatic conditions, as species edge zones might play an important role in evolutionary innovation. Here, we examine the genetic structure of a widely distributed coral species complex, Acropora hyacinthus, from tropical to high subtropical regions along the Kuroshio Current in Taiwan and Japan. Population genetic analysis of 307 specimens from 18 locations (7 reefal and 11 marginal) identified at least four genetic lineages within the A. hyacinthus complex: HyaA, HyaB, HyaC (dominating reefal locations) and HyaD dominating marginal locations in mainland Japan and Taiwan, except the upper Penghu Islands, which were dominated by HyaC. Crossing experiments suggested semi-incompatibility and hybridization between HyaC and D from reefal locations, implying that the existence of hybridization partners enhances diversification and genetic diversity. An incomplete barrier between the HyaC and HyaD dominations was found along the two straits in the Ryukyu Islands, where Kuroshio Current flows constantly. Despite geographical distance, the genetic composition of populations in mainland Japan was comparable to that in mainland Taiwan, which may reflect a region-specific connectivity around the northern limit of A. hyacinthus in the Pacific. In contrast, populations in the Ryukyu Islands were not significantly different from those of Palau and the Great Barrier Reef. While the precise taxonomic nature of the lineages found around the Kuroshio Current remains to be elucidated, these results indicate that, despite the presence of four lineages in the Kuroshio triangle, low genetic diversity populations of the two main lines might be isolating and differentiating in the marginal region.

  11. Synthetic multicellular oscillatory systems: controlling protein dynamics with genetic circuits

    Energy Technology Data Exchange (ETDEWEB)

    Koseska, Aneta [Interdisciplinary Center for Dynamics of Complex Systems, University of Potsdam, D-14469 Potsdam (Germany); Volkov, Evgenii [Department of Theoretical Physics, Lebedev Physical Institute, Leninskii 53, Moscow (Russian Federation); Kurths, Juergen, E-mail: akoseska@uni-potsdam.de [Institute of Physics, Humboldt University Berlin, D-10099 Berlin (Germany)

    2011-10-15

    Synthetic biology is a relatively new research discipline that combines standard biology approaches with the constructive nature of engineering. Thus, recent efforts in the field of synthetic biology have given a perspective to consider cells as 'programmable matter'. Here, we address the possibility of using synthetic circuits to control protein dynamics. In particular, we show how intercellular communication and stochasticity can be used to manipulate the dynamical behavior of a population of coupled synthetic units and, in this manner, finely tune the expression of specific proteins of interest, e.g. in large bioreactors.

  12. Inferring genetic architecture of complex traits using Bayesian integrative analysis of genome and transcriptiome data

    DEFF Research Database (Denmark)

    Ehsani, Alireza; Sørensen, Peter; Pomp, Daniel;

    2012-01-01

    Background To understand the genetic architecture of complex traits and bridge the genotype-phenotype gap, it is useful to study intermediate -omics data, e.g. the transcriptome. The present study introduces a method for simultaneous quantification of the contributions from single nucleotide...... polymorphisms (SNPs) and transcript abundances in explaining phenotypic variance, using Bayesian whole-omics models. Bayesian mixed models and variable selection models were used and, based on parameter samples from the model posterior distributions, explained variances were further partitioned at the level......-modal distribution of genomic values collapses, when gene expressions are added to the model Conclusions With increased availability of various -omics data, integrative approaches are promising tools for understanding the genetic architecture of complex traits. Partitioning of explained variances at the chromosome...

  13. Symposium on Short-Term Genetic Bioassays in the Evaluation of Complex Environmental Mixtures

    CERN Document Server

    Sandhu, Shahbeg; Lewtas, Joellen; Claxton, Larry; Strauss, Gary; Nesnow, Stephen

    1985-01-01

    With this proceedings of the fourth symposium on complex mixtures, we continue to revise and extend our knowledge of genetic methods for the evaluation of chemical mixtures in the environment. The early chapters of this volume are devoted to new bioassay techniques that are directly applicable to the monitoring of environments contaminated with genotoxic chemicals. Microbiological methods have been further refined to meet the special needs of atmospheric monitoring so that very small samples may now be efficiently tested. New in situ methods utilizing green plants actually avoid many of the usual difficulties of sample collection and preparation and offer special advantages in monitoring wastewater, sludges, and hazardous wastes. Insects also are being employed very effectively in the evaluation of gaseous air pollutants in controlled laboratory investigations. Increased emphasis has been placed on a comprehensive assessment of the potential of complex mixtures t9 cause various kinds of genetic damage. New as...

  14. The stabilizing effects of genetic diversity on predator-prey dynamics.

    Science.gov (United States)

    Steiner, Christopher F; Masse, Jordan

    2013-01-01

    Heterogeneity among prey in their susceptibility to predation is a potentially important stabilizer of predator-prey interactions, reducing the magnitude of population oscillations and enhancing total prey population abundance. When microevolutionary responses of prey populations occur at time scales comparable to population dynamics, adaptive responses in prey defense can, in theory, stabilize predator-prey dynamics and reduce top-down effects on prey abundance. While experiments have tested these predictions, less explored are the consequences of the evolution of prey phenotypes that can persist in both vulnerable and invulnerable classes. We tested this experimentally using a laboratory aquatic system composed of the rotifer Brachionus calyciflorus as a predator and the prey Synura petersenii, a colony-forming alga that exhibits genetic variation in its propensity to form colonies and colony size (larger colonies are a defense against predators). Prey populations of either low initial genetic diversity and low adaptive capacity or high initial genetic diversity and high adaptive capacity were crossed with predator presence and absence. Dynamics measured over the last 127 days of the 167-day experiment revealed no effects of initial prey genetic diversity on the average abundance or temporal variability of predator populations. However, genetic diversity and predator presence/absence interactively affected prey population abundance and stability; diversity of prey had no effects in the absence of predators but stabilized dynamics and increased total prey abundance in the presence of predators. The size structure of the genetically diverse prey populations diverged from single strain populations in the presence of predators, showing increases in colony size and in the relative abundance of cells found in colonies. Our work sheds light on the adaptive value of colony formation and supports the general view that genetic diversity and intraspecific trait variation of

  15. Dynamics and genetic structure of Argentine ant supercolonies in their native range

    DEFF Research Database (Denmark)

    Vogel, Valérie; Pedersen, Jes S; d'Ettorre, Patrizia

    2009-01-01

    units. Genetic and chemical distances between supercolonies were positively correlated, but there were no other significant associations between geographic, genetic, chemical, and behavioral distances. A comparison of supercolonies sampled in 1999 and 2005 revealed a very high turnover, with about one......-third of the supercolonies being replaced yearly. This dynamic is likely to involve strong competition between supercolonies and thus act as a potent selective force maintaining unicoloniality over evolutionary time....

  16. Presence of voltage-gated potassium channel complex antibody in a case of genetic prion disease.

    Science.gov (United States)

    Jammoul, Adham; Lederman, Richard J; Tavee, Jinny; Li, Yuebing

    2014-06-05

    Voltage-gated potassium channel (VGKC) complex antibody-mediated encephalitis is a recently recognised entity which has been reported to mimic the clinical presentation of Creutzfeldt-Jakob disease (CJD). Testing for the presence of this neuronal surface autoantibody in patients presenting with subacute encephalopathy is therefore crucial as it may both revoke the bleak diagnosis of prion disease and allow institution of potentially life-saving immunotherapy. Tempering this optimistic view is the rare instance when a positive VGKC complex antibody titre occurs in a definite case of prion disease. We present a pathologically and genetically confirmed case of CJD with elevated serum VGKC complex antibody titres. This case highlights the importance of interpreting the result of a positive VGKC complex antibody with caution and in the context of the overall clinical manifestation.

  17. Genetic Differentiation of Different Geographical Populations of Bemisia tabaci (Gennadius) Complex

    Institute of Scientific and Technical Information of China (English)

    CHU Dong; LIU Guo-xia; FAN Zhong-xue; TAO Yun-li; ZHANG You-jun

    2007-01-01

    Bemisia tabaci (Gennadius) is a species complex, which includes different geographical populations with genetic differentiation. The recent progress on the genetic differentiation of various geographical populations of B. tabaci complex was introduced. The genetic differentiation was further analyzed on the basis of the sequences of mtDNA COI and rDNA ITSl recorded in the world's GenBank. Five groups are defined on the basis of mtDNA COI and rDNA ITS1, including the Asia group, America group, Africa group, Australia group, and Biotype B/Mediterranean/Middle East/ Northern Africa/Biotype Ms group. There are several ungrouped geographical classifications, such as the Uganda population, Ivory Coast population, and Taiwan population. Geographical isolation may be the most important factor that contributed to the genetic differentiation of various geographical populations of B. tabaci. Many populations with biological advantages invaded new regions and caused severe economic losses within human activity. It is necessary to strengthen the research of B. tabaci biotype to prevent the spread of invaded populations and the invasion of potentially dangerous populations.

  18. Regulation and controlled synchronization for complex dynamical systems

    NARCIS (Netherlands)

    Huijberts, H.J.C.; Nijmeijer, Henk; Willems, R.M.A.

    2000-01-01

    In this paper we investigate the problem of controlled synchronization as a regulator problem. In controlled synchronization one is given autonomous transmitter dynamics and controlled receiver dynamics. The question is to find a (output) feedback controller that achieves matching between

  19. The socio-genetics of a complex society: female gelada relatedness patterns mirror association patterns in a multilevel society.

    Science.gov (United States)

    Snyder-Mackler, Noah; Alberts, Susan C; Bergman, Thore J

    2014-12-01

    Multilevel societies with fission-fusion dynamics--arguably the most complex animal societies--are defined by two or more nested levels of organization. The core of these societies are modular social units that regularly fission and fuse with one another. Despite convergent evolution in disparate taxa, we know strikingly little about how such societies form and how fitness benefits operate. Understanding the kinship structure of complex societies could inform us about the origins of the social structure as well as about the potential for individuals in these societies to accrue indirect fitness benefits. Here, we combined genetic and behavioural data on geladas (Theropithecus gelada), an Old World Monkey, to complete the most comprehensive socio-genetic analysis of a multilevel society to date. In geladas, individuals in the core social 'units', associate at different frequencies to form 'teams', 'bands' and, the largest aggregations, 'communities'. Units were composed of closely related females, and females remained with their close kin during permanent fissions of units. Interestingly, female-female relatedness also significantly predicted between-unit, between-team and between-band association patterns, while male-male relatedness did not. Thus, it is likely that the socio-genetic structure of gelada society results from females maintaining associations with their female relatives during successive unit fissions--possibly in an attempt to balance the direct and indirect fitness benefits of group living. Overall, the persistence of associations among related females across generations appears to drive the formation of higher levels of gelada society, suggesting that females seek kin for inclusive fitness benefits at multiple levels of gelada society.

  20. DREAM4: Combining genetic and dynamic information to identify biological networks and dynamical models.

    Directory of Open Access Journals (Sweden)

    Alex Greenfield

    Full Text Available BACKGROUND: Current technologies have lead to the availability of multiple genomic data types in sufficient quantity and quality to serve as a basis for automatic global network inference. Accordingly, there are currently a large variety of network inference methods that learn regulatory networks to varying degrees of detail. These methods have different strengths and weaknesses and thus can be complementary. However, combining different methods in a mutually reinforcing manner remains a challenge. METHODOLOGY: We investigate how three scalable methods can be combined into a useful network inference pipeline. The first is a novel t-test-based method that relies on a comprehensive steady-state knock-out dataset to rank regulatory interactions. The remaining two are previously published mutual information and ordinary differential equation based methods (tlCLR and Inferelator 1.0, respectively that use both time-series and steady-state data to rank regulatory interactions; the latter has the added advantage of also inferring dynamic models of gene regulation which can be used to predict the system's response to new perturbations. CONCLUSION/SIGNIFICANCE: Our t-test based method proved powerful at ranking regulatory interactions, tying for first out of methods in the DREAM4 100-gene in-silico network inference challenge. We demonstrate complementarity between this method and the two methods that take advantage of time-series data by combining the three into a pipeline whose ability to rank regulatory interactions is markedly improved compared to either method alone. Moreover, the pipeline is able to accurately predict the response of the system to new conditions (in this case new double knock-out genetic perturbations. Our evaluation of the performance of multiple methods for network inference suggests avenues for future methods development and provides simple considerations for genomic experimental design. Our code is publicly available at http://err.bio.nyu.edu/inferelator/.

  1. Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex.

    Science.gov (United States)

    Reboul, Cyril F; Meyer, Grischa R; Porebski, Benjamin T; Borg, Natalie A; Buckle, Ashley M

    2012-01-01

    The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent 'snapshots' and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP) yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156) located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into 'scanning' mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.

  2. Epitope flexibility and dynamic footprint revealed by molecular dynamics of a pMHC-TCR complex.

    Directory of Open Access Journals (Sweden)

    Cyril F Reboul

    Full Text Available The crystal structures of unliganded and liganded pMHC molecules provide a structural basis for TCR recognition yet they represent 'snapshots' and offer limited insight into dynamics that may be important for interaction and T cell activation. MHC molecules HLA-B*3501 and HLA-B*3508 both bind a 13 mer viral peptide (LPEP yet only HLA-B*3508-LPEP induces a CTL response characterised by the dominant TCR clonetype SB27. HLA-B*3508-LPEP forms a tight and long-lived complex with SB27, but the relatively weak interaction between HLA-B*3501-LPEP and SB27 fails to trigger an immune response. HLA-B*3501 and HLA-B*3508 differ by only one amino acid (L/R156 located on α2-helix, but this does not alter the MHC or peptide structure nor does this polymorphic residue interact with the peptide or SB27. In the absence of a structural rationalisation for the differences in TCR engagement we performed a molecular dynamics study of both pMHC complexes and HLA-B*3508-LPEP in complex with SB27. This reveals that the high flexibility of the peptide in HLA-B*3501 compared to HLA-B*3508, which was not apparent in the crystal structure alone, may have an under-appreciated role in SB27 recognition. The TCR pivots atop peptide residues 6-9 and makes transient MHC contacts that extend those observed in the crystal structure. Thus MD offers an insight into 'scanning' mechanism of SB27 that extends the role of the germline encoded CDR2α and CDR2β loops. Our data are consistent with the vast body of experimental observations for the pMHC-LPEP-SB27 interaction and provide additional insights not accessible using crystallography.

  3. Understanding the complex etiologies of developmental disorders: behavioral and molecular genetic approaches.

    Science.gov (United States)

    Willcutt, Erik G; Pennington, Bruce F; Duncan, Laramie; Smith, Shelley D; Keenan, Janice M; Wadsworth, Sally; Defries, John C; Olson, Richard K

    2010-09-01

    This article has 2 primary goals. First, a brief tutorial on behavioral and molecular genetic methods is provided for readers without extensive training in these areas. To illustrate the application of these approaches to developmental disorders, etiologically informative studies of reading disability (RD), math disability (MD), and attention-deficit hyperactivity disorder (ADHD) are then reviewed. Implications of the results for these specific disorders and for developmental disabilities as a whole are discussed, and novel directions for future research are highlighted. Previous family and twin studies of RD, MD, and ADHD are reviewed systematically, and the extensive molecular genetic literatures on each disorder are summarized. To illustrate 4 novel extensions of these etiologically informative approaches, new data are presented from the Colorado Learning Disabilities Research Center, an ongoing twin study of the etiology of RD, ADHD, MD, and related disorders. RD, MD, and ADHD are familial and heritable, and co-occur more frequently than expected by chance. Molecular genetic studies suggest that all 3 disorders have complex etiologies, with multiple genetic and environmental risk factors each contributing to overall risk for each disorder. Neuropsychological analyses indicate that the 3 disorders are each associated with multiple neuropsychological weaknesses, and initial evidence suggests that comorbidity between the 3 disorders is due to common genetic risk factors that lead to slow processing speed.

  4. The genetic dynamics of the rapid and recent colonization of Denmark by Arion lusitanicus (Mollusca, Pulmonata, Arionidae).

    Science.gov (United States)

    Engelke, S; Kömpf, J; Jordaens, K; Tomiuk, J; Parker, E D

    2011-06-01

    We describe the genetic dynamics of the recent establishment of the 'Iberian slug', Arion lusitanicus J. Mabille 1868, in Denmark and compare its population structure to two other members of the 'large Arion complex', Arion ater ater, native to Denmark, and Arion ater rufus, introduced into Denmark in the early 1900s. Assaying allozyme polymorphism at seven enzyme loci, we found that: (1) None of the three taxa reproduce primarily by self-fertilization. Differences among loci and colonies in the pattern of deviation from Hardy-Weinberg equilibrium are most consistent with isolate mixing and perhaps with low amounts of selfing. (2) For both A. lusitanicus and A. a. rufus, gene diversity is lower in Danish colonies than in southern German colonies, implying population bottlenecks in the establishment of Danish colonies. (3) Significant linkage disequilibrium values usually involve the same three loci, viz. PGI, MDH-1 and MDH-2, suggesting physical linkage among these loci. (4) For both A. a. rufus and A. lusitanicus, the overall gene frequencies from Denmark and southern Germany are homogeneous, while variation among colonies within these regions ranges from around 15 to 28% for the three taxa. This indicates strong, local population genetic subdivision but with little restriction to gene flow from possible source areas. The heterogeneity in measures of diversity and differentiation indicates that population structure for all three taxa is dominated by ongoing founder effects, local extinction/colonisation dynamics, and genetic drift processes.

  5. Nonlinear dynamics optimization with particle swarm and genetic algorithms for SPEAR3 emittance upgrade

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Xiaobiao; Safranek, James

    2014-09-01

    Nonlinear dynamics optimization is carried out for a low emittance upgrade lattice of SPEAR3 in order to improve its dynamic aperture and Touschek lifetime. Two multi-objective optimization algorithms, a genetic algorithm and a particle swarm algorithm, are used for this study. The performance of the two algorithms are compared. The result shows that the particle swarm algorithm converges significantly faster to similar or better solutions than the genetic algorithm and it does not require seeding of good solutions in the initial population. These advantages of the particle swarm algorithm may make it more suitable for many accelerator optimization applications.

  6. Classification of time series patterns from complex dynamic systems

    Energy Technology Data Exchange (ETDEWEB)

    Schryver, J.C.; Rao, N.

    1998-07-01

    An increasing availability of high-performance computing and data storage media at decreasing cost is making possible the proliferation of large-scale numerical databases and data warehouses. Numeric warehousing enterprises on the order of hundreds of gigabytes to terabytes are a reality in many fields such as finance, retail sales, process systems monitoring, biomedical monitoring, surveillance and transportation. Large-scale databases are becoming more accessible to larger user communities through the internet, web-based applications and database connectivity. Consequently, most researchers now have access to a variety of massive datasets. This trend will probably only continue to grow over the next several years. Unfortunately, the availability of integrated tools to explore, analyze and understand the data warehoused in these archives is lagging far behind the ability to gain access to the same data. In particular, locating and identifying patterns of interest in numerical time series data is an increasingly important problem for which there are few available techniques. Temporal pattern recognition poses many interesting problems in classification, segmentation, prediction, diagnosis and anomaly detection. This research focuses on the problem of classification or characterization of numerical time series data. Highway vehicles and their drivers are examples of complex dynamic systems (CDS) which are being used by transportation agencies for field testing to generate large-scale time series datasets. Tools for effective analysis of numerical time series in databases generated by highway vehicle systems are not yet available, or have not been adapted to the target problem domain. However, analysis tools from similar domains may be adapted to the problem of classification of numerical time series data.

  7. Investigation of Plasmas Having Complex, Dynamic Evolving Morphology

    Energy Technology Data Exchange (ETDEWEB)

    Bellan, Paul M. [California Inst. of Technology (CalTech), Pasadena, CA (United States)

    2017-01-03

    Three different types of plasmas have been investigated using both experimental and theoretical methods. The first type of plasma is dense, highly ionized, governed by magnetohydrodynamics, and highly dynamic. This plasma is relevant to solar coronal loops, astrophysical jets, and other situations where strong magnetic forces act on the plasma. A well-diagnosed laboratory experiment creates a magnetohydrodynamically driven highly collimated plasma jet. This jet undergoes a kink instability such that it rapidly develops a corkscrew shape. The kink causes lateral acceleration of the jet, and this lateral acceleration drives a Rayleigh-Taylor instability that in turn chokes the current flowing in the jet and causes a magnetic reconnection. The magnetic reconnection causes electron and ion heating as well as emission of whistler waves. This entire sequence of events has been observed, measured in detail, and related to theoretical models. The second type of plasma is a transient rf-produced plasma used as a seed plasma for the magnetohydrodynamic experiments described above. Detailed atomic physics ionization processes have been investigated and modeled. The third type of plasma that has been studied is a dusty plasma where the dust particles are spontaneously growing ice grains. The rapid growth of the ice grains to large size and their highly ordered alignment has been investigated as well as collective motion of the ice grains, including well-defined flows on the surface of nested toroids. In addition to the experimental work described above, several related theoretical models have been developed, most notably a model showing how a complex interaction between gravity and magnetic fields on extremely weakly ionized plasma in an accretion disk provides an electric power source that can drive astrophysical jets associated with the accretion disk. Eighteen papers reporting this work have been published in a wide variety of journals.

  8. The Hybrid Dynamic Prototype Construction and Parameter Optimization with Genetic Algorithm for Support Vector Machine

    Directory of Open Access Journals (Sweden)

    Chun-Liang Lu

    2015-10-01

    Full Text Available The optimized hybrid artificial intelligence model is a potential tool to deal with construction engineering and management problems. Support vector machine (SVM has achieved excellent performance in a wide variety of applications. Nevertheless, how to effectively reduce the training complexity for SVM is still a serious challenge. In this paper, a novel order-independent approach for instance selection, called the dynamic condensed nearest neighbor (DCNN rule, is proposed to adaptively construct prototypes in the training dataset and to reduce the redundant or noisy instances in a classification process for the SVM. Furthermore, a hybrid model based on the genetic algorithm (GA is proposed to simultaneously optimize the prototype construction and the SVM kernel parameters setting to enhance the classification accuracy. Several UCI benchmark datasets are considered to compare the proposed hybrid GA-DCNN-SVM approach with the previously published GA-based method. The experimental results illustrate that the proposed hybrid model outperforms the existing method and effectively improves the classification performance for the SVM.

  9. Unraveling the genetic complexity of Drosophila stardust during photoreceptor morphogenesis and prevention of light-induced degeneration.

    Science.gov (United States)

    Berger, Sandra; Bulgakova, Natalia A; Grawe, Ferdi; Johnson, Kevin; Knust, Elisabeth

    2007-08-01

    Drosophila Stardust, a membrane-associated guanylate kinase (MAGUK), recruits the transmembrane protein Crumbs and the cytoplasmic proteins DPATJ and DLin-7 into an apically localized protein scaffold. This evolutionarily conserved complex is required for epithelial cell polarity in Drosophila embryos and mammalian cells in culture. In addition, mutations in Drosophila crumbs and DPATJ impair morphogenesis of photoreceptor cells (PRCs) and result in light-dependent retinal degeneration. Here we show that stardust is a genetically complex locus. While all alleles tested perturb epithelial cell polarity in the embryo, only a subset of them affects morphogenesis of PRCs or induces light-dependent retinal degeneration. Alleles retaining particular postembryonic functions still express some Stardust protein in pupal and/or adult eyes. The phenotypic complexity is reflected by the expression of distinct splice variants at different developmental stages. All proteins expressed in the retina contain the PSD95, Discs Large, ZO-1 (PDZ), Src homology 3 (SH3), and guanylate kinase (GUK) domain, but lack a large region in the N terminus encoded by one exon. These results suggest that Stardust-based protein scaffolds are dynamic, which is not only mediated by multiple interaction partners, but in addition by various forms of the Stardust protein itself.

  10. Chronic imaging of cortical sensory map dynamics using a genetically encoded calcium indicator

    OpenAIRE

    Minderer, M; Liu, W.; Sumanovski, L. T.; Kügler, S; Helmchen, F; Margolis, D. J.

    2012-01-01

    Abstract  In vivo optical imaging can reveal the dynamics of large-scale cortical activity, but methods for chronic recording are limited. Here we present a technique for long-term investigation of cortical map dynamics using wide-field ratiometric fluorescence imaging of the genetically encoded calcium indicator (GECI) Yellow Cameleon 3.60. We find that wide-field GECI signals report sensory-evoked activity in anaesthetized mouse somatosensory cortex with high sensitivity and spatiotemporal ...

  11. Extracting quantum dynamics from genetic learning algorithms through principal component analysis

    CERN Document Server

    White, J L; Bucksbaum, P H

    2004-01-01

    Genetic learning algorithms are widely used to control ultrafast optical pulse shapes for photo-induced quantum control of atoms and molecules. An outstanding issue is how to use the solutions found by these algorithms to learn about the system's quantum dynamics. We propose a simple method based on principal component analysis of the control space, which can reveal the degrees of freedom responsible for control, and aid in the construction of an effective Hamiltonian for the dynamics.

  12. GeneLink: a database to facilitate genetic studies of complex traits

    Directory of Open Access Journals (Sweden)

    Wolfsberg Tyra G

    2004-10-01

    Full Text Available Abstract Background In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data management systems are often critical to the success of these projects. To minimize the difficulties inherent in complex trait studies, we have developed GeneLink, a Web-accessible, password-protected Sybase database. Results GeneLink is a powerful tool for complex trait mapping, enabling genotypic data to be easily merged with pedigree and extensive phenotypic data. Specifically designed to facilitate large-scale (multi-center genetic linkage or association studies, GeneLink securely and efficiently handles large amounts of data and provides additional features to facilitate data analysis by existing software packages and quality control. These include the ability to download chromosome-specific data files containing marker data in map order in various formats appropriate for downstream analyses (e.g., GAS and LINKAGE. Furthermore, an unlimited number of phenotypes (either qualitative or quantitative can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. Conclusions GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC. GeneLink is freely available at http://research.nhgri.nih.gov/genelink.

  13. Theoretical Studies on Docking Dynamics and Electronic Structure in Metalloprotein Complexes

    Science.gov (United States)

    Sugiyama, Ayumu; Nishikawa, Keigo; Yamamoto, Tetsunori; Purqon, Acep; Nishikawa, Kiyoshi; Nagao, Hidemi

    2007-12-01

    An investigating of docking structure and dynamics between metalloprotein is interested from the viewpoint of searching the function of protein. We investigate the cytochrome c551 and azurin complexes by three computational methods, quantum mechanical calculation, docking searching algorism and molecular dynamics simulation. At first we present the docking structure of the cytochrome c551-azurin complexes expected by ZDOCK searching algorism. Quantum chemical calculation is tools to estimate the charge distrubution around the active site for each protein and force field parameters. From these parameters, we reproduce the protein docking dynamics by molecular dynamics simulation. We analyze some physical properties of complex system such as binding free energy, dynamical cross correlation map, and so on. We discuss the docking stability and dynamical effect of the cytochrome c551-azurin complexes.

  14. Understanding the complexity of temperature dynamics in Xinjiang, China, from multitemporal scale and spatial perspectives.

    Science.gov (United States)

    Xu, Jianhua; Chen, Yaning; Li, Weihong; Liu, Zuhan; Wei, Chunmeng; Tang, Jie

    2013-01-01

    Based on the observed data from 51 meteorological stations during the period from 1958 to 2012 in Xinjiang, China, we investigated the complexity of temperature dynamics from the temporal and spatial perspectives by using a comprehensive approach including the correlation dimension (CD), classical statistics, and geostatistics. The main conclusions are as follows (1) The integer CD values indicate that the temperature dynamics are a complex and chaotic system, which is sensitive to the initial conditions. (2) The complexity of temperature dynamics decreases along with the increase of temporal scale. To describe the temperature dynamics, at least 3 independent variables are needed at daily scale, whereas at least 2 independent variables are needed at monthly, seasonal, and annual scales. (3) The spatial patterns of CD values at different temporal scales indicate that the complex temperature dynamics are derived from the complex landform.

  15. Understanding the Complexity of Temperature Dynamics in Xinjiang, China, from Multitemporal Scale and Spatial Perspectives

    Directory of Open Access Journals (Sweden)

    Jianhua Xu

    2013-01-01

    Full Text Available Based on the observed data from 51 meteorological stations during the period from 1958 to 2012 in Xinjiang, China, we investigated the complexity of temperature dynamics from the temporal and spatial perspectives by using a comprehensive approach including the correlation dimension (CD, classical statistics, and geostatistics. The main conclusions are as follows (1 The integer CD values indicate that the temperature dynamics are a complex and chaotic system, which is sensitive to the initial conditions. (2 The complexity of temperature dynamics decreases along with the increase of temporal scale. To describe the temperature dynamics, at least 3 independent variables are needed at daily scale, whereas at least 2 independent variables are needed at monthly, seasonal, and annual scales. (3 The spatial patterns of CD values at different temporal scales indicate that the complex temperature dynamics are derived from the complex landform.

  16. Agent-oriented modeling of the dynamics of complex biological processes I: single agent models

    NARCIS (Netherlands)

    Jonker, C.M.; Treur, J.

    2008-01-01

    In the pair of papers of which this is Part I, the agent-oriented modeling perspective to cope with biological complexity is discussed. Three levels of dynamics are distinguished and related to each other: dynamics of externally observable agent behavior, dynamics of internal agent processes, and dy

  17. Population genetic dynamics of an invasion reconstructed from the sediment egg bank.

    Science.gov (United States)

    Möst, Markus; Oexle, Sarah; Marková, Silvia; Aidukaite, Dalia; Baumgartner, Livia; Stich, Hans-Bernd; Wessels, Martin; Martin-Creuzburg, Dominik; Spaak, Piet

    2015-08-01

    Biological invasions are a global issue with far-reaching consequences for single species, communities and whole ecosystems. Our understanding of modes and mechanisms of biological invasions requires knowledge of the genetic processes associated with successful invasions. In many instances, this information is particularly difficult to obtain as the initial phases of the invasion process often pass unnoticed and we rely on inferences from contemporary population genetic data. Here, we combined historic information with the genetic analysis of resting eggs to reconstruct the invasion of Daphnia pulicaria into Lower Lake Constance (LLC) in the 1970s from the resting egg bank in the sediments. We identified the invader as 'European D. pulicaria' originating from meso- and eutrophic lowland lakes and ponds in Central Europe. The founding population was characterized by extremely low genetic variation in the resting egg bank that increased considerably over time. Furthermore, strong evidence for selfing and/or biparental inbreeding was found during the initial phase of the invasion, followed by a drop of selfing rate to low levels in subsequent decades. Moreover, the increase in genetic variation was most pronounced during early stages of the invasion, suggesting additional introductions during this period. Our study highlights that genetic data covering the entire invasion process from its beginning can be crucial to accurately reconstruct the invasion history of a species. We show that propagule banks can preserve such information enabling the study of population genetic dynamics and sources of genetic variation in successful invasive populations. © 2015 John Wiley & Sons Ltd.

  18. Decreased neuroautonomic complexity in men during an acute major depressive episode: analysis of heart rate dynamics

    OpenAIRE

    Leistedt, S J-J; Linkowski, P.; Lanquart, J-P; Mietus, J E; Davis, Roger B.; Goldberger, Ary Louis; Costa, Madalena Damasio

    2011-01-01

    Major depression affects multiple physiologic systems. Therefore, analysis of signals that reflect integrated function may be useful in probing dynamical changes in this syndrome. Increasing evidence supports the conceptual framework that complex variability is a marker of healthy, adaptive control mechanisms and that dynamical complexity decreases with aging and disease. We tested the hypothesis that heart rate (HR) dynamics in non-medicated, young to middle-aged males during an acute major ...

  19. Genetics of inflammatory bowel disease: The role of the HLA complex

    Institute of Scientific and Technical Information of China (English)

    Tariq Ahmad; Sara E Marshall; Derek Jewell

    2006-01-01

    The human leucocyte antigen (HLA) complex on chromosome 6p21.3 is the most extensively studied genetic region in Inflammatory bowel disease (IBD).Consistent evidence of linkage to IBD3 (6p21.1-23), an area which encompasses the HLA complex, has been demonstrated for both Crohn's disease and ulcerative colitis, and a number of replicated associations with disease susceptibility and phenotype have recently emerged. However, despite these efforts the HLA susceptibility gene (s) for IBD remain elusive, a consequence of strong linkage disequilibrium, extensive polymorphism and high gene density across this region.This article reviews current knowledge of the role of HLA complex genes in IBD susceptibility and phenotype, and discusses the factors currently limiting the translation of this knowledge to clinical practice.

  20. A Low-Complexity PTS Based on Greedy and Genetic Algorithm for OFDM Systems

    Institute of Scientific and Technical Information of China (English)

    LUO Renze; ZHANG Chengsen; NIU Na; LI Rui

    2015-01-01

    Partial transmit sequence (PTS) is one of eff ective technique to reduce high Peak-to-average power ratio (PAPR) in Orthogonal frequency division multiplex-ing (OFDM) system. However, the complexity of Original PTS (O-PTS) increases exponentially with the number of sub-blocks. To reduce the computational complexity while still off ering a lower PAPR, a new PTS method is pro-posed to search for suboptimal rotating vectors in this pa-per. In the proposed method, the candidate rotation vec-tors are generated based on greedy and genetic algorithm. We also combine the proposed method and the superim-posed training sequence method to get a further PAPR reduction. The theory and simulations results show that the proposed method can achieve better PAPR reduction and significantly reduce the computational complexity.

  1. Complex phylogenetic distribution of a non-canonical genetic code in green algae

    Directory of Open Access Journals (Sweden)

    Keeling Patrick J

    2010-10-01

    Full Text Available Abstract Background A non-canonical nuclear genetic code, in which TAG and TAA have been reassigned from stop codons to glutamine, has evolved independently in several eukaryotic lineages, including the ulvophycean green algal orders Dasycladales and Cladophorales. To study the phylogenetic distribution of the standard and non-canonical genetic codes, we generated sequence data of a representative set of ulvophycean green algae and used a robust green algal phylogeny to evaluate different evolutionary scenarios that may account for the origin of the non-canonical code. Results This study demonstrates that the Dasycladales and Cladophorales share this alternative genetic code with the related order Trentepohliales and the genus Blastophysa, but not with the Bryopsidales, which is sister to the Dasycladales. This complex phylogenetic distribution whereby all but one representative of a single natural lineage possesses an identical deviant genetic code is unique. Conclusions We compare different evolutionary scenarios for the complex phylogenetic distribution of this non-canonical genetic code. A single transition to the non-canonical code followed by a reversal to the canonical code in the Bryopsidales is highly improbable due to the profound genetic changes that coincide with codon reassignment. Multiple independent gains of the non-canonical code, as hypothesized for ciliates, are also unlikely because the same deviant code has evolved in all lineages. Instead we favor a stepwise acquisition model, congruent with the ambiguous intermediate model, whereby the non-canonical code observed in these green algal orders has a single origin. We suggest that the final steps from an ambiguous intermediate situation to a non-canonical code have been completed in the Trentepohliales, Dasycladales, Cladophorales and Blastophysa but not in the Bryopsidales. We hypothesize that in the latter lineage an initial stage characterized by translational ambiguity was

  2. On Impact Dynamics under Complex or Extreme Conditions

    KAUST Repository

    Kouraytem, Nadia

    2016-11-01

    The impact of a spherical object onto a surface of a liquid, solid or granular material, is a configuration which occurs in numerous industrial and natural phenomena. The resulting dynamics can produce complex outcomes and often occur on very short time-scales. Their study thereby requires high-speed video imaging, as is done herein. This three-part dissertation investigates widely disparate but kindred impact configurations, where the impacting object is a solid steel sphere, or a molten metal droplet. The substrate, on the other hand, is either granular material, a liquid, or solid ice. Therefore both fluid mechanics and thermodynamics play a key role in some of these dynamics. Part I, investigates the penetration depth of a steel sphere which impacts onto a granular bed containing a mixture of grains of two different sizes. The addition of smaller grains within a bed of larger grains can promote a “lubrication” effect and deeper penetration of the sphere. However, there needs to be enough mass fraction of the smaller grains so that they get lodged between the larger grains and are not simply like isolated rattlers inside the voids between the larger grains. This lubrication occurs even though the addition of the small grains increases the overall packing fraction of the bed. We compare the enhanced penetration for the mixtures to a simple interpolative model based on the results for monodispersed media of the constitutive sizes. The strongest lubrication is observed for large irregular shaped Ottawa sand grains, which are seeded with small spherical glass beads. Part II, tackles the topic of a molten metal drop impacting onto a pool of water. When the drop temperature is far above the boiling temperature of water, a continuous vapor layer can form at the interface between the metal and water, in what is called the Leidenfrost phenomenon. This vapor layer can become unstable forming what is called a vapor explosion, which can break up the molten metal drop

  3. Kernel Approach for Modeling Interaction Effects in Genetic Association Studies of Complex Quantitative Traits.

    Science.gov (United States)

    Broadaway, K Alaine; Duncan, Richard; Conneely, Karen N; Almli, Lynn M; Bradley, Bekh; Ressler, Kerry J; Epstein, Michael P

    2015-07-01

    The etiology of complex traits likely involves the effects of genetic and environmental factors, along with complicated interaction effects between them. Consequently, there has been interest in applying genetic association tests of complex traits that account for potential modification of the genetic effect in the presence of an environmental factor. One can perform such an analysis using a joint test of gene and gene-environment interaction. An optimal joint test would be one that remains powerful under a variety of models ranging from those of strong gene-environment interaction effect to those of little or no gene-environment interaction effect. To fill this demand, we have extended a kernel machine based approach for association mapping of multiple SNPs to consider joint tests of gene and gene-environment interaction. The kernel-based approach for joint testing is promising, because it incorporates linkage disequilibrium information from multiple SNPs simultaneously in analysis and permits flexible modeling of interaction effects. Using simulated data, we show that our kernel machine approach typically outperforms the traditional joint test under strong gene-environment interaction models and further outperforms the traditional main-effect association test under models of weak or no gene-environment interaction effects. We illustrate our test using genome-wide association data from the Grady Trauma Project, a cohort of highly traumatized, at-risk individuals, which has previously been investigated for interaction effects. © 2015 WILEY PERIODICALS, INC.

  4. Dynamic and Static Assessment of Phonological Awareness in Preschool: A Behavior-Genetic Study

    Science.gov (United States)

    Coventry, William L.; Byrne, Brian; Olson, Richard K.; Corley, Robin; Samuelsson, Stefan

    2011-01-01

    The genetic and environmental overlap between static and dynamic measures of preschool phonological awareness (PA) and their relation to preschool letter knowledge (LK) and kindergarten reading were examined using monozygotic and dizygotic twin children (maximum N = 1,988). The static tests were those typically used to assess a child's current…

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

    Science.gov (United States)

    Hendry, A P

    2013-12-01

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

  6. Antitumor Cell-Complex Vaccines Employing Genetically Modified Tumor Cells and Fibroblasts

    Directory of Open Access Journals (Sweden)

    Antonio Miguel

    2014-02-01

    Full Text Available The present study evaluates the immune response mediated by vaccination with cell complexes composed of irradiated B16 tumor cells and mouse fibroblasts genetically modified to produce GM-CSF. The animals were vaccinated with free B16 cells or cell complexes. We employed two gene plasmid constructions: one high producer (pMok and a low producer (p2F. Tumor transplant was performed by injection of B16 tumor cells. Plasma levels of total IgG and its subtypes were measured by ELISA. Tumor volumes were measured and survival curves were obtained. The study resulted in a cell complex vaccine able to stimulate the immune system to produce specific anti-tumor membrane proteins (TMP IgG. In the groups vaccinated with cells transfected with the low producer plasmid, IgG production was higher when we used free B16 cell rather than cell complexes. Nonspecific autoimmune response caused by cell complex was not greater than that induced by the tumor cells alone. Groups vaccinated with B16 transfected with low producer plasmid reached a tumor growth delay of 92% (p ≤ 0.01. When vaccinated with cell complex, the best group was that transfected with high producer plasmid, reaching a tumor growth inhibition of 56% (p ≤ 0.05. Significant survival (40% was only observed in the groups vaccinated with free transfected B16 cells.

  7. Complex dynamics in diatomic molecules. Part II: Quantum trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Yang, C.-D. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: cdyang@mail.ncku.edu.tw; Weng, H.-J. [Department of Aeronautics and Astronautics, National Cheng Kung University, Tainan 701, Taiwan (China)], E-mail: principlex@yahoo.com.tw

    2008-10-15

    The second part of this paper deals with quantum trajectories in diatomic molecules, which has not been considered before in the literature. Morse potential serves as a more accurate function than a simple harmonic oscillator for illustrating a realistic picture about the vibration of diatomic molecules. However, if we determine molecular dynamics by integrating the classical force equations derived from a Morse potential, we will find that the resulting trajectories do not consist with the probabilistic prediction of quantum mechanics. On the other hand, the quantum trajectory determined by Bohmian mechanics [Bohm D. A suggested interpretation of the quantum theory in terms of hidden variable. Phys. Rev. 1952;85:166-179] leads to the conclusion that a diatomic molecule is motionless in all its vibrational eigen-states, which also contradicts probabilistic prediction of quantum mechanics. In this paper, we point out that the quantum trajectory of a diatomic molecule completely consistent with quantum mechanics does exist and can be solved from the quantum Hamilton equations of motion derived in Part I, which is based on a complex-space formulation of fractal spacetime [El Naschie MS. A review of E-Infinity theory and the mass spectrum of high energy particle physics. Chaos, Solitons and Fractals 2004;19:209-36; El Naschie MS. E-Infinity theory - some recent results and new interpretations. Chaos, Solitons and Fractals 2006;29:845-853; El Naschie MS. The concepts of E-infinity. An elementary introduction to the cantorian-fractal theory of quantum physics. Chaos, Solitons and Fractals 2004;22:495-511; El Naschie MS. SU(5) grand unification in a transfinite form. Chaos, Solitons and Fractals 2007;32:370-374; Nottale L. Fractal space-time and microphysics: towards a theory of scale relativity. Singapore: World Scientific; 1993; Ord G. Fractal space time and the statistical mechanics of random works. Chaos, Soiltons and Fractals 1996;7:821-843] approach to quantum

  8. Complex dynamics in planar two-electron quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Schroeter, Sebastian Josef Arthur

    2013-06-25

    Quantum dots play an important role in a wide range of recent experimental and technological developments. In particular they are promising candidates for realisations of quantum bits and further applications in quantum information theory. The harmonically confined Hooke's atom model is experimentally verified and separates in centre-of-mass and relative coordinates. Findings that are contradictory to this separability call for an extension of the model, in particular changing the confinement potential. In order to study effects of an anharmonic confinement potential on spectral properties of planar two-electron quantum dots a sophisticated numerical approach is developed. Comparison between the Helium atom, Hooke's atom and an anharmonic potential model are undertaken in order to improve the description of quantum dots. Classical and quantum features of complexity and chaos are investigated and used to characterise the dynamics of the system to be mixed regular-chaotic. Influence of decoherence can be described by quantum fidelity, which measures the effect of a perturbation on the time evolution. The quantum fidelity of eigenstates of the system depends strongly on the properties of the perturbation. Several methods for solving the time-dependent Schrödinger equation are implemented and a high level of accuracy for long time evolutions is achieved. The concept of offset entanglement, the entanglement of harmonic models in the noninteracting limit, is introduced. This concept explains different questions raised in the literature for harmonic quantum dot models, recently. It shows that only in the groundstate the electrons are not entangled in the fermionic sense. The applicability, validity, and origin of Hund's first rule in general quantum dot models is further addressed. In fact Hund's first rule is only applicable, and in this case also valid, for one pair of singlet and triplet states in Hooke's atom. For more realistic models of two

  9. General Intelligence (g): Overview of a Complex Construct and Its Implications for Genetics Research.

    Science.gov (United States)

    Plucker, Jonathan A; Shelton, Amy L

    2015-01-01

    Current technology has dramatically increased the prevalence of studies to establish the genetic correlates of a wide variety of human characteristics, including not only the physical attributes that determine what we look like and the risk of physiological disease but also the psychological and cognitive characteristics that often define who we are as individuals. Perhaps one of the most deeply personal and often controversial characteristics is the concept of general intelligence, known in the psychological literature as "g." As with the genetic study of any complex trait, the first step in studying the genetics of g is to carefully define the characteristic of interest. For g, this entails establishing what intelligence means and providing a clear operational definition for how it will be measured. In this paper, we provide a brief historical and theoretical overview of the construct of general intelligence, describe its relationship to the contemporary measurement of intelligence, and discuss these concepts in light of the challenges associated with defining g as a characteristic in the study of genetics.

  10. The complex genetics of gait speed: genome-wide meta-analysis approach

    Science.gov (United States)

    Lunetta, Kathryn L.; Smith, Jennifer A.; Eicher, John D.; Vered, Rotem; Deelen, Joris; Arnold, Alice M.; Buchman, Aron S.; Tanaka, Toshiko; Faul, Jessica D.; Nethander, Maria; Fornage, Myriam; Adams, Hieab H.; Matteini, Amy M.; Callisaya, Michele L.; Smith, Albert V.; Yu, Lei; De Jager, Philip L.; Evans, Denis A.; Gudnason, Vilmundur; Hofman, Albert; Pattie, Alison; Corley, Janie; Launer, Lenore J.; Knopman, Davis S.; Parimi, Neeta; Turner, Stephen T.; Bandinelli, Stefania; Beekman, Marian; Gutman, Danielle; Sharvit, Lital; Mooijaart, Simon P.; Liewald, David C.; Houwing-Duistermaat, Jeanine J.; Ohlsson, Claes; Moed, Matthijs; Verlinden, Vincent J.; Mellström, Dan; van der Geest, Jos N.; Karlsson, Magnus; Hernandez, Dena; McWhirter, Rebekah; Liu, Yongmei; Thomson, Russell; Tranah, Gregory J.; Uitterlinden, Andre G.; Weir, David R.; Zhao, Wei; Starr, John M.; Johnson, Andrew D.; Ikram, M. Arfan; Bennett, David A.; Cummings, Steven R.; Deary, Ian J.; Harris, Tamara B.; Kardia, Sharon L. R.; Mosley, Thomas H.; Srikanth, Velandai K.; Windham, Beverly G.; Newman, Ann B.; Walston, Jeremy D.; Davies, Gail; Evans, Daniel S.; Slagboom, Eline P.; Ferrucci, Luigi; Kiel, Douglas P.; Murabito, Joanne M.; Atzmon, Gil

    2017-01-01

    Emerging evidence suggests that the basis for variation in late-life mobility is attributable, in part, to genetic factors, which may become increasingly important with age. Our objective was to systematically assess the contribution of genetic variation to gait speed in older individuals. We conducted a meta-analysis of gait speed GWASs in 31,478 older adults from 17 cohorts of the CHARGE consortium, and validated our results in 2,588 older adults from 4 independent studies. We followed our initial discoveries with network and eQTL analysis of candidate signals in tissues. The meta-analysis resulted in a list of 536 suggestive genome wide significant SNPs in or near 69 genes. Further interrogation with Pathway Analysis placed gait speed as a polygenic complex trait in five major networks. Subsequent eQTL analysis revealed several SNPs significantly associated with the expression of PRSS16, WDSUB1 and PTPRT, which in addition to the meta-analysis and pathway suggested that genetic effects on gait speed may occur through synaptic function and neuronal development pathways. No genome-wide significant signals for gait speed were identified from this moderately large sample of older adults, suggesting that more refined physical function phenotypes will be needed to identify the genetic basis of gait speed in aging. PMID:28077804

  11. Architecture and dynamics of proteins and aqueous solvation complexes

    NARCIS (Netherlands)

    Lotze, S.M.

    2015-01-01

    For this thesis, the molecular dynamics of water and biological (model) systems have been studied with advanced nonlinear optical techniques. In chapters 4-5, the technique of femtosecond mid-infrared pump probe spectroscopy has been used to study the energy transfer and the reorientational dynamics

  12. Complexities of Organization Dynamics and Development: Leaders and Managers

    Science.gov (United States)

    Nderu-Boddington, Eulalee

    2008-01-01

    This article shows the theoretical framework for understanding organizational dynamics and development - the change theory and subordinate relationships within contemporary organizations. The emphasis is on power strategies and the relationship to organizational dynamics and development. The integrative process broadens the understanding of…

  13. Modularity and the Spread of Perturbations in Complex Dynamical Systems

    CERN Document Server

    Kolchinsky, Artemy; Rocha, Luis M

    2015-01-01

    We propose a method to decompose a multivariate dynamical system into weakly-coupled modules based on the idea that module boundaries constrain the spread of perturbations. Using a novel quality function called 'perturbation modularity', we find system coarse-grainings that optimally separate the dynamics of perturbation spreading into fast intra-modular and slow inter-modular components. Our method is defined directly in terms of system dynamics, unlike approaches that find communities in networks (whether in structural networks or 'functional networks' of statistical dependencies) or that impose arbitrary dynamics onto graphs. Due to this, we are able to capture the variation of modular organization across states, timescales, and in response to different perturbations, aspects of modularity which are all relevant to real-world dynamical systems. However, in certain cases, mappings exist between perturbation modularity and community detection methods of `Markov stability' and Newman's modularity. Our approac...

  14. Self-organization of complex networks as a dynamical system

    Science.gov (United States)

    Aoki, Takaaki; Yawata, Koichiro; Aoyagi, Toshio

    2015-01-01

    To understand the dynamics of real-world networks, we investigate a mathematical model of the interplay between the dynamics of random walkers on a weighted network and the link weights driven by a resource carried by the walkers. Our numerical studies reveal that, under suitable conditions, the co-evolving dynamics lead to the emergence of stationary power-law distributions of the resource and link weights, while the resource quantity at each node ceaselessly changes with time. We analyze the network organization as a deterministic dynamical system and find that the system exhibits multistability, with numerous fixed points, limit cycles, and chaotic states. The chaotic behavior of the system leads to the continual changes in the microscopic network dynamics in the absence of any external random noises. We conclude that the intrinsic interplay between the states of the nodes and network reformation constitutes a major factor in the vicissitudes of real-world networks.

  15. Some additional considerations in modelling the dynamic traits and genome-wide association studies. Comments on "Mapping complex traits as a dynamic system" by L. Sun and R. Wu

    Science.gov (United States)

    Das, Kiranmoy

    2015-06-01

    The revolution in the genetic research in our time is mainly due to (i) the successful completion of human genome project (2003) and its derivative hapmap project (2005), (ii) advanced statistical methodologies for analyzing ultrahigh dimensional data and (iii) the availability of statistical softwares (R, SAS etc.) to analyze large datasets. When complex traits are to be modeled as dynamic systems, the statistical issues regarding the complexity in the model, predictive power of the model, computational cost etc. are to be addressed adequately for powerful inferences. I will mention two additional considerations (statistical) which make dynamic models more meaningful and the results from GWAS more reliable.

  16. Type 2 diabetes: genetic data sharing to advance complex disease research.

    Science.gov (United States)

    Flannick, Jason; Florez, Jose C

    2016-09-01

    As with other complex diseases, unbiased association studies followed by physiological and experimental characterization have for years formed a paradigm for identifying genes or processes of relevance to type 2 diabetes mellitus (T2D). Recent large-scale common and rare variant genome-wide association studies (GWAS) suggest that substantially larger association studies are needed to identify most T2D loci in the population. To hasten clinical translation of genetic discoveries, new paradigms are also required to aid specialized investigation of nascent hypotheses. We argue for an integrated T2D knowledgebase, designed for a worldwide community to access aggregated large-scale genetic data sets, as one paradigm to catalyse convergence of these efforts.

  17. Complex Dynamical Network Control for Trajectory Tracking Using Delayed Recurrent Neural Networks

    Directory of Open Access Journals (Sweden)

    Jose P. Perez

    2014-01-01

    Full Text Available In this paper, the problem of trajectory tracking is studied. Based on the V-stability and Lyapunov theory, a control law that achieves the global asymptotic stability of the tracking error between a delayed recurrent neural network and a complex dynamical network is obtained. To illustrate the analytic results, we present a tracking simulation of a dynamical network with each node being just one Lorenz’s dynamical system and three identical Chen’s dynamical systems.

  18. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Silgado, Julio C. Cardona; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniete; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L.; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Gruenblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M. J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Restrepo, Sandra C. Mesa; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlo N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosario, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Duarte, Ana V. Valencia; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Routeau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson B.; Stewart, Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2015-01-01

    Objective: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The autho

  19. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    2015-01-01

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The autho

  20. Cross-disorder genome-wide analyses suggest a complex genetic relationship between Tourette's syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Cusi, Daniele; Delorme, Richard; Denys, D.; Dion, Yves; Eapen, Valsama; Heutink, Peter; Cox, Nancy J; Pauls, David L

    2015-01-01

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The autho

  1. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H|info:eu-repo/dai/nl/113700644; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C|info:eu-repo/dai/nl/194111423; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  2. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Silgado, Julio C. Cardona; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniete; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L.; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Gruenblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M. J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Restrepo, Sandra C. Mesa; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlo N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosario, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Duarte, Ana V. Valencia; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Routeau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson B.; Stewart, Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    Objective: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The

  3. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A; Scharf, Jeremiah M; Neale, Benjamin M; Davis, Lea K; Gamazon, Eric R; Derks, Eske M; Evans, Patrick; Edlund, Christopher K; Crane, Jacquelyn; Fagerness, Jesen A; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L; Bellodi, Laura; Benarroch, Fortu; Berrió, Gabriel Bedoya; Bienvenu, O Joseph; Black, Donald W; Bloch, Michael H; Brentani, Helena; Bruun, Ruth D; Budman, Cathy L; Camarena, Beatriz; Campbell, Desmond D; Cappi, Carolina; Silgado, Julio C Cardona; Cavallini, Maria C; Chavira, Denise A; Chouinard, Sylvain; Cook, Edwin H; Cookson, M R; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniele; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L; Girard, Simon L; Grabe, Hans J; Grados, Marco A; Greenberg, Benjamin D; Gross-Tsur, Varda; Grünblatt, Edna; Hardy, John; Heiman, Gary A; Hemmings, Sian M J; Herrera, Luis D; Hezel, Dianne M; Hoekstra, Pieter J; Jankovic, Joseph; Kennedy, James L; King, Robert A; Konkashbaev, Anuar I; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T; Mesa Restrepo, Sandra C; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L; Naarden, Allan L; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A; Pakstis, Andrew J; Pato, Michele T; Pato, Carlos N; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L; Renner, Tobias; Reus, Victor I; Richter, Margaret A; Riddle, Mark A; Robertson, Mary M; Romero, Roxana; Rosário, Maria C; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S; Samuels, Jack; Sandor, Paul; Service, Susan K; Sheppard, Brooke; Singer, Harvey S; Smit, Jan H|info:eu-repo/dai/nl/113700644; Stein, Dan J; Strengman, Eric; Tischfield, Jay A; Turiel, Maurizio; Valencia Duarte, Ana V; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R; Westenberg, Herman G M; Shugart, Yin Yao; Hounie, Ana G; Miguel, Euripedes C; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C|info:eu-repo/dai/nl/194111423; McMahon, William; Posthuma, Danielle; Oostra, Ben A; Nestadt, Gerald; Rouleau, Guy A; Purcell, Shaun; Jenike, Michael A; Heutink, Peter; Hanna, Gregory L; Conti, David V; Arnold, Paul D; Freimer, Nelson B; Stewart, S Evelyn; Knowles, James A; Cox, Nancy J; Pauls, David L

    2015-01-01

    OBJECTIVE: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The autho

  4. Cross-Disorder Genome-Wide Analyses Suggest a Complex Genetic Relationship Between Tourette's Syndrome and OCD

    NARCIS (Netherlands)

    Yu, Dongmei; Mathews, Carol A.; Scharf, Jeremiah M.; Neale, Benjamin M.; Davis, Lea K.; Gamazon, Eric R.; Derks, Eske M.; Evans, Patrick; Edlund, Christopher K.; Crane, Jacquelyn; Osiecki, Lisa; Gallagher, Patience; Gerber, Gloria; Haddad, Stephen; Illmann, Cornelia; McGrath, Lauren M.; Mayerfeld, Catherine; Arepalli, Sampath; Barlassina, Cristina; Barr, Cathy L.; Bellodi, Laura; Benarroch, Fortu; Berrio, Gabriel Bedoya; Bienvenu, O. Joseph; Black, Donald W.; Bloch, Michael H.; Brentani, Helena; Bruun, Ruth D.; Budman, Cathy L.; Camarena, Beatriz; Campbell, Desmond D.; Cappi, Carolina; Silgado, Julio C. Cardona; Cavallini, Maria C.; Chavira, Denise A.; Chouinard, Sylvain; Cook, Edwin H.; Cookson, M. R.; Coric, Vladimir; Cullen, Bernadette; Cusi, Daniete; Delorme, Richard; Denys, Damiaan; Dion, Yves; Eapen, Valsama; Egberts, Karin; Falkai, Peter; Fernandez, Thomas; Fournier, Eduardo; Garrido, Helena; Geller, Daniel; Gilbert, Donald L.; Girard, Simon L.; Grabe, Hans J.; Grados, Marco A.; Greenberg, Benjamin D.; Gross-Tsur, Varda; Gruenblatt, Edna; Hardy, John; Heiman, Gary A.; Hemmings, Sian M. J.; Herrera, Luis D.; Hezel, Dianne M.; Hoekstra, Pieter J.; Jankovic, Joseph; Kennedy, James L.; King, Robert A.; Konkashbaev, Anuar I.; Kremeyer, Barbara; Kurlan, Roger; Lanzagorta, Nuria; Leboyer, Marion; Leckman, James F.; Lennertz, Leonhard; Liu, Chunyu; Lochner, Christine; Lowe, Thomas L.; Lupoli, Sara; Macciardi, Fabio; Maier, Wolfgang; Manunta, Paolo; Marconi, Maurizio; McCracken, James T.; Restrepo, Sandra C. Mesa; Moessner, Rainald; Moorjani, Priya; Morgan, Jubel; Muller, Heike; Murphy, Dennis L.; Naarden, Allan L.; Nurmi, Erika; Ochoa, William Cornejo; Ophoff, Roel A.; Pakstis, Andrew J.; Pato, Michele T.; Pato, Carlo N.; Piacentini, John; Pittenger, Christopher; Pollak, Yehuda; Rauch, Scott L.; Renner, Tobias; Reus, Victor I.; Richter, Margaret A.; Riddle, Mark A.; Robertson, Mary M.; Romero, Roxana; Rosario, Maria C.; Rosenberg, David; Ruhrmann, Stephan; Sabatti, Chiara; Salvi, Erika; Sampaio, Aline S.; Samuels, Jack; Sandor, Paul; Service, Susan K.; Sheppard, Brooke; Singer, Harvey S.; Smit, Jan H.; Stein, Dan J.; Strengman, Eric; Tischfield, Jay A.; Turiel, Maurizio; Duarte, Ana V. Valencia; Vallada, Homero; Veenstra-VanderWeele, Jeremy; Walitza, Susanne; Wang, Ying; Weale, Mike; Weiss, Robert; Wendland, Jens R.; Westenberg, Herman G. M.; Shugart, Yin Yao; Hounie, Ana G.; Miguel, Euripedes C.; Nicolini, Humberto; Wagner, Michael; Ruiz-Linares, Andres; Cath, Danielle C.; McMahon, William; Posthuma, Danielle; Oostra, Ben A.; Nestadt, Gerald; Routeau, Guy A.; Purcell, Shaun; Jenike, Michael A.; Heutink, Peter; Hanna, Gregory L.; Conti, David V.; Arnold, Paul D.; Freimer, Nelson B.; Stewart, Evelyn; Knowles, James A.; Cox, Nancy J.; Pauls, David L.

    2015-01-01

    Objective: Obsessive-compulsive disorder (OCD) and Tourette's syndrome are highly heritable neurodevelopmental disorders that are thought to share genetic risk factors. However, the identification of definitive susceptibility genes for these etiologically complex disorders remains elusive. The autho

  5. Allele-specific methylation occurs at genetic variants associated with complex disease.

    Directory of Open Access Journals (Sweden)

    John N Hutchinson

    Full Text Available We hypothesize that the phenomenon of allele-specific methylation (ASM may underlie the phenotypic effects of multiple variants identified by Genome-Wide Association studies (GWAS. We evaluate ASM in a human population and document its genome-wide patterns in an initial screen at up to 380,678 sites within the genome, or up to 5% of the total genomic CpGs. We show that while substantial inter-individual variation exists, 5% of assessed sites show evidence of ASM in at least six samples; the majority of these events (81% are under genetic influence. Many of these cis-regulated ASM variants are also eQTLs in peripheral blood mononuclear cells and monocytes and/or in high linkage-disequilibrium with variants linked to complex disease. Finally, focusing on autoimmune phenotypes, we extend this initial screen to confirm the association of cis-regulated ASM with multiple complex disease-associated variants in an independent population using next-generation bisulfite sequencing. These four variants are implicated in complex phenotypes such as ulcerative colitis and AIDS progression disease (rs10491434, Celiac disease (rs2762051, Crohn's disease, IgA nephropathy and early-onset inflammatory bowel disease (rs713875 and height (rs6569648. Our results suggest cis-regulated ASM may provide a mechanistic link between the non-coding genetic changes and phenotypic variation observed in these diseases and further suggests a route to integrating DNA methylation status with GWAS results.

  6. Dynamic Bandwidth Allocation Technique in ATM Networks Based on Fuzzy Neural Networks and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    ZhangLiangjie; LiYanda; 等

    1997-01-01

    In this paper,a dynamic bandwidth allocation technique based on fuzz neural networks(FNNs) and genetic algorithm(GA)is proposed for preventive congestion control in ATM network.The traffic model based on FNN does not need the descriptive traffic parameters in detail,which greatly depend on the user's terminal.Genetic algorithm is used to predict the equivalent bandwidth of the accepted traffic in real-time.Thus,the proposed scheme can estimate the dynamic bandwidth of the network in the time scale from the call arrival to the call admission/rejection due to the fuzzy-tech and GA hardware implementation.Simulation results show that the scheme can perform accurate dynamic bandwidth allocation to DN/OFF bursty traffic in accordance with the required quality of service(QOS),and the bandwidth utilization is improved from the overall point of view.

  7. Stochastic dynamic simulation modeling including multitrait genetics to estimate genetic, technical, and financial consequences of dairy farm reproduction and selection strategies

    Science.gov (United States)

    The objective of this study was to develop a daily stochastic dynamic dairy simulation model which included multi-trait genetics, and to evaluate the effects of various reproduction and selection strategies on the genetic, technical and financial performance of a dairy herd. The 12 correlated geneti...

  8. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  9. Complex-Dynamical Solution to Many-Body Interaction Problem and Its Applications in Fundamental Physics

    CERN Document Server

    Kirilyuk, Andrei P

    2012-01-01

    We review the recently proposed unreduced, complex-dynamical solution to many-body problem with arbitrary interaction and its application to unified solution of fundamental problems, including foundations of causally complete quantum mechanics, relativity, particle properties and cosmology. We first analyse the universal properties of many-body problem solution without any perturbative reduction and show that the emerging new quality of fundamental dynamic multivaluedness (or redundance) of resulting system configuration leads to universal concept of dynamic complexity, chaoticity and fractality of any real system behaviour. We then consider unified features of this complex dynamics. Applications of that universal description to systems at various complexity levels have been performed and in this paper we review those at the lowest, fundamental complexity levels leading to causal understanding of unified origins of quantum mechanics, relativity (special and general), elementary particles, their intrinsic prop...

  10. Dynamic Programming and Genetic Algorithm for Business Processes Optimisation

    Directory of Open Access Journals (Sweden)

    Mateusz Wibig

    2012-12-01

    Full Text Available There are many business process modelling techniques, which allow to capture features of those processes, but graphical, diagrammatic models seems to be used most in companies and organizations. Although the modelling notations are more and more mature and can be used not only to visualise the process idea but also to implement it in the workflow solution and although modern software allows us to gather a lot of data for analysis purposes, there is still not much commercial used business process optimisation methods. In this paper the scheduling / optimisation method for automatic task scheduling in business processes models is described. The Petri Net model is used, but it can be easily applied to any other modelling notation, where the process is presented as a set of tasks, i.e. BPMN (Business Process Modelling Notation. The method uses Petri Nets’, business processes’ scalability and dynamic programming concept to reduce the necessary computations, by revising only those parts of the model, to which the change was applied.

  11. Enhanced dynamic complexity in the human EEG during creative thinking.

    Science.gov (United States)

    Mölle, M; Marshall, L; Lutzenberger, W; Pietrowsky, R; Fehm, H L; Born, J

    1996-04-12

    This study shows that divergent thinking, considered the general process underlying creative production, can be distinguished from convergent, analytical thought based on the dimensional complexity of ongoing electroencephalographic (EEG) activity. EEG complexity over the central and posterior cortex was higher while subjects solved tasks of divergent than convergent thinking, and also higher than during mental relaxation. Over the frontal cortex, EEG complexity was comparable during divergent thinking and mental relaxation, but reduced during convergent thinking. Results indicate that the basic process underlying the generation of novel ideas expresses itself in a strong increase in the EEG's complexity, reflecting higher degrees of freedom in the competitive interactions among cortical neuron assemblies. Frontocortical EEG complexity being comparable with that during mental relaxation, speaks for a loosened attentional control during creative thinking.

  12. A Constraint Embedding Approach for Complex Vehicle Suspension Dynamics

    Science.gov (United States)

    2015-04-24

    2015, Barcelona, Catalonia , Spain same number of degrees of freedom as the number of independent degrees of freedom for the loops they replace...13. SUPPLEMENTARY NOTES ECCOMAS Thematic Conference on Multibody Dynamics 2015, June 29-July 2, 2015, Barcelona, Catalonia , Spain 14. ABSTRACT See...Z39-18 ECCOMAS Thematic Conference on Multibody Dynamics June 29 - July 2, 2015, Barcelona, Catalonia , Spain A Constraint Embedding Approach for

  13. Discovering link communities in complex networks by an integer programming model and a genetic algorithm.

    Science.gov (United States)

    Li, Zhenping; Zhang, Xiang-Sun; Wang, Rui-Sheng; Liu, Hongwei; Zhang, Shihua

    2013-01-01

    Identification of communities in complex networks is an important topic and issue in many fields such as sociology, biology, and computer science. Communities are often defined as groups of related nodes or links that correspond to functional subunits in the corresponding complex systems. While most conventional approaches have focused on discovering communities of nodes, some recent studies start partitioning links to find overlapping communities straightforwardly. In this paper, we propose a new quantity function for link community identification in complex networks. Based on this quantity function we formulate the link community partition problem into an integer programming model which allows us to partition a complex network into overlapping communities. We further propose a genetic algorithm for link community detection which can partition a network into overlapping communities without knowing the number of communities. We test our model and algorithm on both artificial networks and real-world networks. The results demonstrate that the model and algorithm are efficient in detecting overlapping community structure in complex networks.

  14. Metal speciation dynamics and bioavailability: Inert and labile complexes

    Energy Technology Data Exchange (ETDEWEB)

    Van Leeuwen, H.P.

    1999-11-01

    The free-ion activity model for the biouptake of metals from complex media is limited to cases where mass transfer is not flux-determining. This paper considers the simultaneous effects of bioconversion kinetics and metal transport in the medium coupled with metal complex dissociation kinetics. For the two kinetically limiting situations of inert and fully labile complexes, the bioavailabilities of bioinactive metal complexes are analyzed under conditions where (i) the actual biouptake follows a Michaelis-Menten type of steady-state flux and (ii) the supply of free metal is governed by diffusion of free metal or coupled diffusion of the different labile metal species. The resulting steady-site fluxes are given in terms of two fundamental quantities, i.e., the relative bioaffinity parameter (a) and the ratio between the limiting uptake flux and the limiting transport flux (b). For labile complexes, these variables are differentiated by a complexation parameter defined by the ration between the free metal on activity and the total labile metal activity. Limits of the uptake flux for extreme values of the bioaffinity parameter a and the limiting flux ratio b are easily derived from the general flux expression. The analysis precisely shows under what conditions labile complex species contribute to the biouptake process or, equivalently, under what conditions the free-ion activity model is not obeyed.

  15. Complex molecular genetic abnormalities involving three or more genetic mutations are important prognostic factors for acute myeloid leukemia.

    Science.gov (United States)

    Wakita, S; Yamaguchi, H; Ueki, T; Usuki, K; Kurosawa, S; Kobayashi, Y; Kawata, E; Tajika, K; Gomi, S; Koizumi, M; Fujiwara, Y; Yui, S; Fukunaga, K; Ryotokuji, T; Hirakawa, T; Arai, K; Kitano, T; Kosaka, F; Tamai, H; Nakayama, K; Fukuda, T; Inokuchi, K

    2016-03-01

    We conducted a comprehensive analysis of 28 recurrently mutated genes in acute myeloid leukemia (AML) in 271 patients with de novo AML. Co-mutations were frequently detected in the intermediate cytogenetic risk group, at an average of 2.76 co-mutations per patient. When assessing the prognostic impact of these co-mutations in the intermediate cytogenetic risk group, overall survival (OS) was found to be significantly shorter (P=0.0006) and cumulative incidence of relapse (CIR) significantly higher (P=0.0052) in patients with complex molecular genetic abnormalities (CMGAs) involving three or more mutations. This trend was marked even among patients aged ⩽65 years who were also FLT3-ITD (FMS-like tyrosine kinase 3 internal tandem duplications)-negative (OS: P=0.0010; CIR: P=0.1800). Moreover, the multivariate analysis revealed that CMGA positivity was an independent prognostic factor associated with OS (P=0.0007). In stratification based on FLT3-ITD and CEBPA status and 'simplified analysis of co-mutations' using seven genes that featured frequently in CMGAs, CMGA positivity retained its prognostic value in transplantation-aged patients of the intermediate cytogenetic risk group (OS: P=0.0002. CIR: Pmutation analysis to have clinical usefulness and applicability.

  16. Foundations of Complex Systems Nonlinear Dynamics, Statistical Physics, and Prediction

    CERN Document Server

    Nicolis, Gregoire

    2007-01-01

    Complexity is emerging as a post-Newtonian paradigm for approaching a large body of phenomena of concern at the crossroads of physical, engineering, environmental, life and human sciences from a unifying point of view. This book outlines the foundations of modern complexity research as it arose from the cross-fertilization of ideas and tools from nonlinear science, statistical physics and numerical simulation. It is shown how these developments lead to an understanding, both qualitative and quantitative, of the complex systems encountered in nature and in everyday experience and, conversely, h

  17. Determination of Scaling Parameter and Dynamical Resonances in Complex-Rotated Hamiltonian Ⅱ: Numerical Analysis

    Institute of Scientific and Technical Information of China (English)

    LIU Zong-Liang; ZHAO Fang; LI Shao-Hua; ZHAO Mei-Shan; CHEN Chang-Yong

    2008-01-01

    This paper is concerned with the determination of a unique scaling parameter in complex scaling analysis and with accurate calculation of dynamics resonances. In the preceding paper we have presented a theoretical analysis and provided a formalism for dynamical resonance calculations. In this paper we present accurate numerical results for two non-trivial dynamical processes, namely, models of diatomie molecular predissoeiation and of barrier potential scattering for resonances. The results presented in this paper confirm our theoretical analysis, remove a theoretical ambiguity on determination of the complex scaling parameter, and provide an improved understanding for dynamical resonance calculations in rigged Hilbert space.

  18. The Influence of Information Acquisition on the Complex Dynamics of Market Competition

    Science.gov (United States)

    Guo, Zhanbing; Ma, Junhai

    In this paper, we build a dynamical game model with three bounded rational players (firms) to study the influence of information on the complex dynamics of market competition, where useful information is about rival’s real decision. In this dynamical game model, one information-sharing team is composed of two firms, they acquire and share the information about their common competitor, however, they make their own decisions separately, where the amount of information acquired by this information-sharing team will determine the estimation accuracy about the rival’s real decision. Based on this dynamical game model and some creative 3D diagrams, the influence of the amount of information on the complex dynamics of market competition such as local dynamics, global dynamics and profits is studied. These results have significant theoretical and practical values to realize the influence of information.

  19. Rate-prediction structure complexity analysis for multi-view video coding using hybrid genetic algorithms

    Science.gov (United States)

    Liu, Yebin; Dai, Qionghai; You, Zhixiang; Xu, Wenli

    2007-01-01

    Efficient exploitation of the temporal and inter-view correlation is critical to multi-view video coding (MVC), and the key to it relies on the design of prediction chain structure according to the various pattern of correlations. In this paper, we propose a novel prediction structure model to design optimal MVC coding schemes along with tradeoff analysis in depth between compression efficiency and prediction structure complexity for certain standard functionalities. Focusing on the representation of the entire set of possible chain structures rather than certain typical ones, the proposed model can given efficient MVC schemes that adaptively vary with the requirements of structure complexity and video source characteristics (the number of views, the degrees of temporal and interview correlations). To handle large scale problem in model optimization, we deploy a hybrid genetic algorithm which yields satisfactory results shown in the simulations.

  20. Bayesian model selection in complex linear systems, as illustrated in genetic association studies.

    Science.gov (United States)

    Wen, Xiaoquan

    2014-03-01

    Motivated by examples from genetic association studies, this article considers the model selection problem in a general complex linear model system and in a Bayesian framework. We discuss formulating model selection problems and incorporating context-dependent a priori information through different levels of prior specifications. We also derive analytic Bayes factors and their approximations to facilitate model selection and discuss their theoretical and computational properties. We demonstrate our Bayesian approach based on an implemented Markov Chain Monte Carlo (MCMC) algorithm in simulations and a real data application of mapping tissue-specific eQTLs. Our novel results on Bayes factors provide a general framework to perform efficient model comparisons in complex linear model systems.