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Sample records for chaos intrinsically disordered

  1. Ordered and Disordered Defect Chaos

    CERN Document Server

    Granzow, G D; Granzow, Glen D.; Riecke, Hermann

    1997-01-01

    Defect-chaos is studied numerically in coupled Ginzburg-Landau equations for parametrically driven waves. The motion of the defects is traced in detail yielding their life-times, annihilation partners, and distances traveled. In a regime in which in the one-dimensional case the chaotic dynamics is due to double phase slips, the two-dimensional system exhibits a strongly ordered stripe pattern. When the parity-breaking instability to traveling waves is approached this order vanishes and the correlation function decays rapidly. In the ordered regime the defects have a typical life-time, whereas in the disordered regime the life-time distribution is exponential. The probability of large defect loops is substantially larger in the disordered regime.

  2. Intrinsically disordered proteins and biomineralization.

    Science.gov (United States)

    Boskey, Adele L; Villarreal-Ramirez, Eduardo

    2016-01-01

    In vertebrates and invertebrates, biomineralization is controlled by the cell and the proteins they produce. A large number of these proteins are intrinsically disordered, gaining some secondary structure when they interact with their binding partners. These partners include the component ions of the mineral being deposited, the crystals themselves, the template on which the initial crystals form, and other intrinsically disordered proteins and peptides. This review speculates why intrinsically disordered proteins are so important for biomineralization, providing illustrations from the SIBLING (small integrin binding N-glycosylated) proteins and their peptides. It is concluded that the flexible structure, and the ability of the intrinsically disordered proteins to bind to a multitude of surfaces is crucial, but details on the precise-interactions, energetics and kinetics of binding remain to be determined. PMID:26807759

  3. Protein intrinsic disorder in plants

    Directory of Open Access Journals (Sweden)

    Florencio ePazos

    2013-09-01

    Full Text Available To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disordered proteins allows them to bind multiple partners in transient interactions of high specificity and low affinity. In concordance, in plants this type of proteins has been found in processes requiring these complex and versatile interaction networks. These include transcription factor networks, where disordered proteins act as integrators of different signals or link different transcription factor subnetworks due to their ability to interact (in many cases simultaneously with different partners. Similarly, they also serve as signal integrators in signalling cascades, such as those related to response to external stimuli. Disordered proteins have also been found in plants in many stress-response processes, acting as protein chaperones or protecting other cellular components and structures. In plants, it is especially important to have complex and versatile networks able to quickly and efficiently respond to changing environmental conditions since these organisms can not escape and have no other choice than adapting to them. Consequently, protein disorder can play an especially important role in plants, providing them with a fast mechanism to obtain complex, interconnected and versatile molecular networks.

  4. Transition to Quantum Chaos in Weakly Disordered Graphene Nanoflakes

    OpenAIRE

    Rycerz, Adam

    2011-01-01

    We analyze numerically ensembles of tight-binding Hamiltonians describing highly-symmetric graphene nanoflakes with weak diagonal disorder induced by random electrostatic potential landscapes. When increasing the disorder strength, statistical distribution of energy levels evolves from Poissonian to Wigner, indicating the transition to quantum chaos. Power laws with the universal exponent map the disorder strength in nanoflakes of different sizes, boundaries, and microscopic disorder types on...

  5. Protein intrinsic disorder in plants

    OpenAIRE

    Florencio ePazos; Natalia ePietrosemoli; García-Martín, Juan A.; Roberto eSolano

    2013-01-01

    To some extent contradicting the classical paradigm of the relationship between protein 3D structure and function, now it is clear that large portions of the proteomes, especially in higher organisms, lack a fixed structure and still perform very important functions. Proteins completely or partially unstructured in their native (functional) form are involved in key cellular processes underlain by complex networks of protein interactions. The intrinsic conformational flexibility of these disor...

  6. Genome-Wide Prediction of Intrinsic Disorder; Sequence Alignment of Intrinsically Disordered Proteins

    Science.gov (United States)

    Midic, Uros

    2012-01-01

    Intrinsic disorder (ID) is defined as a lack of stable tertiary and/or secondary structure under physiological conditions in vitro. Intrinsically disordered proteins (IDPs) are highly abundant in nature. IDPs possess a number of crucial biological functions, being involved in regulation, recognition, signaling and control, e.g. their functional…

  7. Disorder Chaos in the Spherical Mean-Field Model

    Science.gov (United States)

    Chen, Wei-Kuo; Hsieh, Hsi-Wei; Hwang, Chii-Ruey; Sheu, Yuan-Chung

    2015-07-01

    We study the problem of disorder chaos in the spherical mean-field model. It concerns the behavior of the overlap between two independently sampled spin configurations from two Gibbs measures with the same external parameters. The prediction states that if the disorders in the Hamiltonians are slightly decoupled, then the overlap will be concentrated near a constant value. Following Guerra's replica symmetry breaking scheme, we establish this at the levels of the free energy and the Gibbs measure.

  8. Order, disorder and chaos in crystal lattice

    International Nuclear Information System (INIS)

    The properties of two two-dimensional mappings corresponding to the solutions of spin models on a Cayley tree in infinite coordination limit are analised in detail. The models under consideration are related to some mechanisms which were proposed to explain the occurrence of modulated phases in magnetic crystals. The existence of devil's staircases characterized by fractal dimensionalities which increase with temperature is shown. Numerical evidences to support the existence of a strange attractor, of a fractal character, in the Ising model with competing interactions restricted to the branches of a Cayley tree are presented. The route to chaos agrees with the scenario of Feigenbaum. (Author)

  9. Predicting intrinsic disorder in proteins: an overview

    Institute of Scientific and Technical Information of China (English)

    Bo He; Kejun Wang; Yunlong Liu; Bin Xue; Vladimir N Uversky; A Keith Dunker

    2009-01-01

    The discovery of intrinsically disordered proteins IDP I.e., biologically active proteins that do not possess stable secondary and/or tertiary structures came as an unexpected surprise, as the existence of such proteins is in contradiction to the traditional "sequence---,structure--,function" paradigm. Accurate prediction of a protein's predisposition to be intrinsically disordered is a necessary prerequisite for the further understanding of principles and mechanisms of protein folding and function, and is a key for the elaboration of a new structural and functional hierarchy of proteins. Therefore, prediction of IDPs has attracted the attention of many researchers, and a number of prediction tools have been developed. Predictions of disorder, in turn, are playing major roles in directing labora-tory experiments that are leading to the discovery of ever more disordered proteins, and thereby leading to a positive feedback loop in the investigation of these proteins, in this review of algorithms for intrinsic disorder prediction, the basic concepts of various prediction methods for IDPs are summarized, the strengths and shortcomings of many of the methods are analyzed, and the difficulties and directions of future development of IDP prediction techniques are discussed.

  10. Disorder in milk proteins: caseins, intrinsically disordered colloids.

    Science.gov (United States)

    Redwan, Elrashdy M; Xue, Bin; Almehdar, Hussein A; Uversky, Vladimir N

    2015-01-01

    This article opens a series of reviews on the abundance and roles of intrinsic disorder in milk proteins. The focus of this introductory article on caseins is symbolic, since caseins were among the first recognized functional unfolded proteins and since they are definitely the most disordered, the most abundant, and the most studied of all milk proteins. In eutherian milks, the casein family includes at least three and usually four major members (αs1-, αs2-, β-, and κ-caseins) that are unrelated in sequence. However, in some species, two different αS2-casein genes are active, and therefore the total number of caseins can be as high as five. These proteins have found a number of uses in food industry. The functional repertoire of caseins ranges from nutritional function to involvement in the improving and/or maintaining cardiovascular health, to crucial contribution to the milk capacity to transport calcium phosphate, to serve as molecular chaperones, and to protect the mother's mammary gland against amyloidoses and ectopic calcification. An intricate feature of caseins is their ability to assemble to colloidal protein particles, casein micelles, serving to sequester and transport amorphous calcium phosphate. These and many other functions of caseins are obviously dependent on their intrinsically disordered nature and are controlled by various posttranslational modifications. Since various aspects of casein structure and function are rather well studied and since several recent reviews emphasized the functional roles of caseins' intrinsic disorder, the major goal of this article is to show how intrinsic disorder is encoded in the amino acid sequences of these proteins. PMID:25714333

  11. Complexity and Chaos Theories as Potential Paradigms for Understanding and Treating Dissociative Disorders.

    Science.gov (United States)

    Drinkard, Lynne Bradford

    1995-01-01

    Early systems theory was a precursor of complexity theory, a global theory that suggests that the universe is an open system interacting on many dimensions. Chaos theory, a subset of complexity theory, states that in seeming chaos there is an underlying order. Between chaos and order lies emergence, from which healthy growth and change occur. Twenty years ago, chaos theory did not have a name and dissociative disorders were largely written off as rare or more imaginative than real. After physicists and mathematicians explained chaos and complexity in language understood by those outside their fields, scientists and practitioners from disparate disciplines were struck by the potential for applying the theories to their respective fields. Complexity and chaos theory combine reductionistic and holistic approaches to explain phenomena. Many mental health practitioners have suggested that a systems framework based in complexity theory may lead to greater understanding of human nature and ultimately toward more effective treatment of different disorders. This paper proposes that complexity and chaos theories may offer insight into the efficacy of various treatments for dissociative disorders.

  12. Chaos

    OpenAIRE

    Kadelka, C.; D. Murrugarra; Laubenbacher, R.

    2013-01-01

    The global dynamics of gene regulatory networks are known to show robustness to perturbations in the form of intrinsic and extrinsic noise, as well as mutations of individual genes. One molecular mechanism underlying this robustness has been identified as the action of so-called microRNAs that operate via feedforward loops. We present results of a computational study, using the modeling framework of stochastic Boolean networks, which explores the role that such network motifs play in stabiliz...

  13. Molecular Recognition by Templated Folding of an Intrinsically Disordered Protein

    Science.gov (United States)

    Toto, Angelo; Camilloni, Carlo; Giri, Rajanish; Brunori, Maurizio; Vendruscolo, Michele; Gianni, Stefano

    2016-02-01

    Intrinsically disordered proteins often become structured upon interacting with their partners. The mechanism of this ‘folding upon binding’ process, however, has not been fully characterised yet. Here we present a study of the folding of the intrinsically disordered transactivation domain of c-Myb (c-Myb) upon binding its partner KIX. By determining the structure of the folding transition state for the binding of wild-type and three mutational variants of KIX, we found a remarkable plasticity of the folding pathway of c-Myb. To explain this phenomenon, we show that the folding of c-Myb is templated by the structure of KIX. This adaptive folding behaviour, which occurs by heterogeneous nucleation, differs from the robust homogeneous nucleation typically observed for globular proteins. We suggest that this templated folding mechanism may enable intrinsically disordered proteins to achieve specific and reliable binding with multiple partners while avoiding aberrant interactions.

  14. Abnormalities of Intrinsic Functional Connectivity in Autism Spectrum Disorders

    OpenAIRE

    Monk, Christopher S.; Peltier, Scott J.; Wiggins, Jillian Lee; Weng, Shih-Jen; Carrasco, Melisa; Risi, Susan; Lord, Catherine

    2009-01-01

    Autism spectrum disorders (ASD) impact social functioning and communication, and individuals with these disorders often have restrictive and repetitive behaviors. Accumulating data indicate that ASD is associated with alterations of neural circuitry. Functional MRI (FMRI) studies have focused on connectivity in the context of psychological tasks. However, even in the absence of a task, the brain exhibits a high degree of functional connectivity, known as intrinsic or resting connectivity. Not...

  15. Intrinsic Structural Disorder Confers Cellular Viability on Oncogenic Fusion Proteins

    OpenAIRE

    Hedi Hegyi; László Buday; Peter Tompa

    2009-01-01

    Chromosomal translocations, which often generate chimeric proteins by fusing segments of two distinct genes, represent the single major genetic aberration leading to cancer. We suggest that the unifying theme of these events is a high level of intrinsic structural disorder, enabling fusion proteins to evade cellular surveillance mechanisms that eliminate misfolded proteins. Predictions in 406 translocation-related human proteins show that they are significantly enriched in disorder (43.3% vs....

  16. Intrinsic disorders and annealing metamict zircon as wave-guides

    International Nuclear Information System (INIS)

    The study of intrinsic disorders in zircon showed that at certain temperature during an annealing process, both Schottky and interstitial disorders would dominate the zircon structure. This time would be the best time to implant relative ions by diffusion, or directly to use an accelerator to implant these ions, then anneal the metamict zircon to tailor the characteristics of the zircon as wave-guides

  17. DSS1/Sem1, a Multifunctional and Intrinsically Disordered Protein

    DEFF Research Database (Denmark)

    Kragelund, Birthe B; Schenstrøm, Signe M; Rebula, Caio A;

    2016-01-01

    DSS1/Sem1 is a versatile intrinsically disordered protein. Besides being a bona fide subunit of the 26S proteasome, DSS1 associates with other protein complexes, including BRCA2-RPA, involved in homologous recombination; the Csn12-Thp3 complex, involved in RNA splicing; the integrator, involved in...

  18. From chaos to disorder: Statistics of the eigenfunctions of microwave cavities

    Indian Academy of Sciences (India)

    Prabhakar Pradhan; S Sridhar

    2002-02-01

    We study the statistics of the experimental eigenfunctions of chaotic and disordered microwave billiards in terms of the moments of their spatial distributions, such as the inverse participation ratio (IPR) and density-density auto-correlation. A path from chaos to disorder is described in terms of increasing IPR. In the chaotic, ballistic limit, the data correspond well with universal results from random matrix theory. Deviations from universal distributions are observed due to disorder induced localization, and for the weakly disordered case the data are well-described by including finite conductance and mean free path contributions in the framework of nonlinear sigma models of supersymmetry.

  19. Intrinsic noise and two-dimensional maps: quasicycles, quasiperiodicity, and chaos.

    Science.gov (United States)

    Parra-Rojas, César; Challenger, Joseph D; Fanelli, Duccio; McKane, Alan J

    2014-09-01

    We develop a formalism to describe the discrete-time dynamics of systems containing an arbitrary number of interacting species. The individual-based model, which forms our starting point, is described by a Markov chain, which in the limit of large system sizes is shown to be very well-approximated by a Fokker-Planck-like equation, or equivalently by a set of stochastic difference equations. This formalism is applied to the specific case of two species: one predator species and its prey species. Quasicycles, stochastic cycles sustained and amplified by the demographic noise, previously found in continuous-time predator-prey models are shown to exist, and their behavior predicted from a linear noise analysis is shown to be in very good agreement with simulations. The effects of the noise on other attractors in the corresponding deterministic map, such as periodic cycles, quasiperiodicity, and chaos, are also investigated. PMID:25314423

  20. Spatial disorder and degradation kinetics in intrinsic biodegradation schemes

    Energy Technology Data Exchange (ETDEWEB)

    LaViolette, R.A.; Stoner, D.L. [Idaho National Engineering and Environmental Lab., Idaho Falls, ID (United States); Watwood, M.E. [Idaho State Univ., Pocatello, ID (United States). Dept. of Biological Sciences; Ginn, T.R. [Univ. of California, Davis, CA (United States). Dept. of Civil and Environmental Engineering

    1999-06-10

    The restoration of contaminated soils by intrinsic biodegradation employs microorganisms in the subsurface that degrade the contaminant substrate infiltrating the subsurface matrix. The outcome of intrinsic biodegradation has been difficult to predict. The authors examine a source of the difficulty with a computational model of diffusive-reactive transport that introduces spatial disorder in the arrangement of the degrading microorganisms. Spatial disorder alone, even on the small scales that characterize the distance between aggregates of microorganisms, is enough to induce a wide range of times to complete the degradation to an arbitrary limit. The mean time for the concentration to achieve the limit becomes twice that for the case of spatial order. Bounds on the range of the effective degradation kinetics can be obtained by computing the distribution of times to complete degradation.

  1. Functional correlations of respiratory syncytial virus proteins to intrinsic disorder.

    Science.gov (United States)

    Whelan, Jillian N; Reddy, Krishna D; Uversky, Vladimir N; Teng, Michael N

    2016-04-26

    Protein intrinsic disorder is an important characteristic demonstrated by the absence of higher order structure, and is commonly detected in multifunctional proteins encoded by RNA viruses. Intrinsically disordered regions (IDRs) of proteins exhibit high flexibility and solvent accessibility, which permit several distinct protein functions, including but not limited to binding of multiple partners and accessibility for post-translational modifications. IDR-containing viral proteins can therefore execute various functional roles to enable productive viral replication. Respiratory syncytial virus (RSV) is a globally circulating, non-segmented, negative sense (NNS) RNA virus that causes severe lower respiratory infections. In this study, we performed a comprehensive evaluation of predicted intrinsic disorder of the RSV proteome to better understand the functional role of RSV protein IDRs. We included 27 RSV strains to sample major RSV subtypes and genotypes, as well as geographic and temporal isolate differences. Several types of disorder predictions were applied to the RSV proteome, including per-residue (PONDR®-FIT and PONDR® VL-XT), binary (CH, CDF, CH-CDF), and disorder-based interactions (ANCHOR and MoRFpred). We classified RSV IDRs by size, frequency and function. Finally, we determined the functional implications of RSV IDRs by mapping predicted IDRs to known functional domains of each protein. Identification of RSV IDRs within functional domains improves our understanding of RSV pathogenesis in addition to providing potential therapeutic targets. Furthermore, this approach can be applied to other NNS viruses that encode essential multifunctional proteins for the elucidation of viral protein regions that can be manipulated for attenuation of viral replication. PMID:27062995

  2. Random coil chemical shift for intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Brander, Søren; Poulsen, Flemming Martin

    2011-01-01

    Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins. The quality of the secondary chemical shifts is dependent on an appropriate choice of random coil chemical shifts. We report random coil chemical....... Temperature has a non-negligible effect on the (13)C random coil chemical shifts, so temperature coefficients are reported for the random coil chemical shifts to allow extrapolation to other temperatures. The pH dependence of the histidine random coil chemical shifts is investigated in a titration series...

  3. Understanding Viral Transmission Behavior via Protein Intrinsic Disorder Prediction: Coronaviruses

    OpenAIRE

    Gerard Kian-Meng Goh; A. Keith Dunker; Vladimir N Uversky

    2012-01-01

    Besides being a common threat to farm animals and poultry, coronavirus (CoV) was responsible for the human severe acute respiratory syndrome (SARS) epidemic in 2002–4. However, many aspects of CoV behavior, including modes of its transmission, are yet to be fully understood. We show that the amount and the peculiarities of distribution of the protein intrinsic disorder in the viral shell can be used for the efficient analysis of the behavior and transmission modes of CoV. The proposed model a...

  4. The transcriptional repressor domain of Gli3 is intrinsically disordered.

    Directory of Open Access Journals (Sweden)

    Robert Tsanev

    Full Text Available The transcription factor Gli3 is acting mainly as a transcriptional repressor in the Sonic hedgehog signal transduction pathway. Gli3 contains a repressor domain in its N-terminus from residue G106 to E236. In this study we have characterized the intracellular structure of the Gli3 repressor domain using a combined bioinformatics and experimental approach. According to our findings the Gli3 repressor domain while being intrinsically disordered contains predicted anchor sites for partner interactions. The obvious interaction partners to test were Ski and DNA; however, with both of these the structure of Gli3 repressor domain remained disordered. To locate residues important for the repressor function we mutated several residues within the Gli3 repressor domain. Two of these, H141A and H157N, targeting predicted helical regions, significantly decreased transcriptional repression and thus identify important functional parts of the domain.

  5. Intrinsic structural disorder confers cellular viability on oncogenic fusion proteins.

    Directory of Open Access Journals (Sweden)

    Hedi Hegyi

    2009-10-01

    Full Text Available Chromosomal translocations, which often generate chimeric proteins by fusing segments of two distinct genes, represent the single major genetic aberration leading to cancer. We suggest that the unifying theme of these events is a high level of intrinsic structural disorder, enabling fusion proteins to evade cellular surveillance mechanisms that eliminate misfolded proteins. Predictions in 406 translocation-related human proteins show that they are significantly enriched in disorder (43.3% vs. 20.7% in all human proteins, they have fewer Pfam domains, and their translocation breakpoints tend to avoid domain splitting. The vicinity of the breakpoint is significantly more disordered than the rest of these already highly disordered fusion proteins. In the unlikely event of domain splitting in fusion it usually spares much of the domain or splits at locations where the newly exposed hydrophobic surface area approximates that of an intact domain. The mechanisms of action of fusion proteins suggest that in most cases their structural disorder is also essential to the acquired oncogenic function, enabling the long-range structural communication of remote binding and/or catalytic elements. In this respect, there are three major mechanisms that contribute to generating an oncogenic signal: (i a phosphorylation site and a tyrosine-kinase domain are fused, and structural disorder of the intervening region enables intramolecular phosphorylation (e.g., BCR-ABL; (ii a dimerisation domain fuses with a tyrosine kinase domain and disorder enables the two subunits within the homodimer to engage in permanent intermolecular phosphorylations (e.g., TFG-ALK; (iii the fusion of a DNA-binding element to a transactivator domain results in an aberrant transcription factor that causes severe misregulation of transcription (e.g. EWS-ATF. Our findings also suggest novel strategies of intervention against the ensuing neoplastic transformations.

  6. Intrinsic disorder of human Yin Yang 1 protein.

    Science.gov (United States)

    Górecki, Andrzej; Bonarek, Piotr; Górka, Adam Kazimierz; Figiel, Małgorzata; Wilamowski, Mateusz; Dziedzicka-Wasylewska, Marta

    2015-07-01

    YY1 (Yin Yang 1) is a zinc finger protein with an essential role in various biological functions via DNA- and protein-protein interactions with numerous partners. YY1 is involved in the regulation of a broad spectrum of cellular processes such as embryogenesis, proliferation, tumorigenesis, and snRNA transcription. The more than 100 reported targets of the YY1 protein suggest that it contains intrinsically disordered regions that are involved in such diverse interactions. Here, we present a study of the structural properties of human YY1 using several biochemical and biophysical techniques (fluorescence, circular dichroism, gel filtration chromatography, proteolytic susceptibility) together with various bioinformatics approaches. To facilitate our exploration of the YY1 structure, the full-length protein as well as an N-terminal fragment (residues 1-295) and the C-terminal DNA binding domain were used. We found the N-terminus to be a non-compact fragment of YY1 with little residual secondary structure and lacking a well-defined tertiary structure. The results of our study indicate that YY1 belongs to the family of intrinsically disordered proteins (IDPs), which exist natively in a partially unfolded conformation. Proteins 2015; 83:1284-1296. © 2015 Wiley Periodicals, Inc. PMID:25963536

  7. Identification of Inhibitors of Biological Interactions Involving Intrinsically Disordered Proteins

    Directory of Open Access Journals (Sweden)

    Daniela Marasco

    2015-04-01

    Full Text Available Protein–protein interactions involving disordered partners have unique features and represent prominent targets in drug discovery processes. Intrinsically Disordered Proteins (IDPs are involved in cellular regulation, signaling and control: they bind to multiple partners and these high-specificity/low-affinity interactions play crucial roles in many human diseases. Disordered regions, terminal tails and flexible linkers are particularly abundant in DNA-binding proteins and play crucial roles in the affinity and specificity of DNA recognizing processes. Protein complexes involving IDPs are short-lived and typically involve short amino acid stretches bearing few “hot spots”, thus the identification of molecules able to modulate them can produce important lead compounds: in this scenario peptides and/or peptidomimetics, deriving from structure-based, combinatorial or protein dissection approaches, can play a key role as hit compounds. Here, we propose a panoramic review of the structural features of IDPs and how they regulate molecular recognition mechanisms focusing attention on recently reported drug-design strategies in the field of IDPs.

  8. Conformational propensities of intrinsically disordered proteins from NMR chemical shifts

    International Nuclear Information System (INIS)

    The realization that a protein can be fully functional even in the absence of a stable three-dimensional structure has motivated a large number of studies describing the conformational behaviour of these proteins at atomic resolution. Here, we review recent advances in the determination of local structural propensities of intrinsically disordered proteins (IDPs) from experimental NMR chemical shifts. A mapping of the local structure in IDPs is of paramount importance in order to understand the molecular details of complex formation, in particular, for IDPs that fold upon binding or undergo structural transitions to pathological forms of the same protein. We discuss experimental strategies for the spectral assignment of IDPs, chemical shift prediction algorithms and the generation of representative structural ensembles of IDPs on the basis of chemical shifts. Additionally, we highlight the inherent degeneracies associated with the determination of IDP sub-state populations from NMR chemical shifts alone. (authors)

  9. Intrinsically Disordered Proteins in a Physics-Based World

    Directory of Open Access Journals (Sweden)

    Jianhan Chen

    2010-12-01

    Full Text Available Intrinsically disordered proteins (IDPs are a newly recognized class of functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play fundamental roles, and are extensively involved in human diseases. For signaling and regulation, IDPs often fold into stable structures upon binding to specific targets. The mechanisms of these coupled binding and folding processes are of significant importance because they underlie the organization of regulatory networks that dictate various aspects of cellular decision-making. This review first discusses the challenge in detailed experimental characterization of these heterogeneous and dynamics proteins and the unique and exciting opportunity for physics-based modeling to make crucial contributions, and then summarizes key lessons from recent de novo simulations of the structure and interactions of several regulatory IDPs.

  10. Mental-disorder detection using chaos and nonlinear dynamical analysis of photoplethysmographic signals

    International Nuclear Information System (INIS)

    Highlights: • Chaos and nonlinear dynamical analysis are applied for mental-disorder detection. • Experimental results show significant detection improvement with feature synergy. • Proposed approach is effective for analysis of photoplethysmographic signals. • Proposed approach is promising for developing automated mental-health systems. -- Abstract: Mental disorder can be defined as a psychological disturbance of thought or emotion. In particular, depression is a mental disease which can ultimately lead to death from suicide. If depression is identified, it can be treated with medication and psychotherapy. However, the diagnosis of depression is difficult and there are currently no any quick and reliable medical tests to detect if someone is depressed. This is because the exact cause of depression is still unknown given the belief that depression results in chemical brain changes, genetic disorder, stress, or the combination of these problems. Photoplethysmography has recently been realized as a non-invasive optical technique that can give new insights into the physiology and pathophysiology of the central and peripheral nervous systems. We present in this paper an automated mental-disorder detection approach in a general sense based on a novel synergy of chaos and nonlinear dynamical methods for the analysis of photoplethysmographic finger pulse waves of mental and control subjects. Such an approach can be applied for automated detection of depression as a special case. Because of the computational effectiveness of the studied methods and low cost of generation of the physiological signals, the proposed automated detection of mental illness is feasible for real-life applications including self-assessment, self-monitoring, and computerized health care

  11. Stochastic Chaos with Its Control and Synchronization

    Institute of Scientific and Technical Information of China (English)

    Zhang Ying; Xu Wei; Zhang Tianshu; Yang Xiaoli; Wu Cunli; Fang Tong

    2008-01-01

    The discovery of chaos in the sixties of last century was a breakthrough in concept,revealing the truth that some disorder behavior, called chaos, could happen even in a deterministic nonlinear system under barely deterministic disturbance. After a series of serious studies, people begin to acknowledge that chaos is a specific type of steady state motion other than the conventional periodic and quasi-periodic ones, featuring a sensitive dependence on initial conditions, resulting from the intrinsic randomness of a nonlinear system itself. In fact, chaos is a collective phenomenon consisting of massive individual chaotic responses, corresponding to different initial conditions in phase space. Any two adjacent individual chaotic responses repel each other, thus causing not only the sensitive dependence on initial conditions but also the existence of at least one positive top Lyapunov exponent (TLE) for chaos. Meanwhile, all the sample responses share one common invariant set on the Poincaré map, called chaotic attractor,which every sample response visits from time to time ergodically. So far, the existence of at least one positive TLE is a commonly acknowledged remarkable feature of chaos. We know that there are various forms of uncertainties in the real world. In theoretical studies, people often use stochastic models to describe these uncertainties, such as random variables or random processes.Systems with random variables as their parameters or with random processes as their excitations are often called stochastic systems. No doubt, chaotic phenomena also exist in stochastic systems, which we call stochastic chaos to distinguish it from deterministic chaos in the deterministic system. Stochastic chaos reflects not only the intrinsic randomness of the nonlinear system but also the external random effects of the random parameter or the random excitation.Hence, stochastic chaos is also a collective massive phenomenon, corresponding not only to different initial

  12. Conformational disorder in folded and intrinsically disordered proteins from nuclear magnetic resonance

    International Nuclear Information System (INIS)

    Biological macromolecules are, by essence, dynamical systems. While the importance of this flexibility is nowadays well established, the accurate characterization of the conformational disorder of these systems remains an important challenge. Nuclear magnetic resonance spectroscopy is a unique tool to probe these motions at atomic level, through the analysis of spin relaxation or residual dipolar couplings. The latter allows all motions occurring at timescales faster than the millisecond to be investigated, including physiologically important timescales. The information presents in those couplings is interpreted here using mainly analytical approaches in order to quantify the amounts of dynamics present in folded protein, to determine the direction of those motions and to obtain structural information within this conformational disorder. These analytical approaches are complemented by numerical methods, that allowed the observation of phenomena from a different point of view or the investigation of other systems such as intrinsically disordered proteins. All of these studies demonstrate an important complementarity between structural order and conformational disorder. (author)

  13. Disorder and defects are not intrinsic to boron carbide

    Science.gov (United States)

    Mondal, Swastik; Bykova, Elena; Dey, Somnath; Ali, Sk Imran; Dubrovinskaia, Natalia; Dubrovinsky, Leonid; Parakhonskiy, Gleb; van Smaalen, Sander

    2016-01-01

    A unique combination of useful properties in boron-carbide, such as extreme hardness, excellent fracture toughness, a low density, a high melting point, thermoelectricity, semi-conducting behavior, catalytic activity and a remarkably good chemical stability, makes it an ideal material for a wide range of technological applications. Explaining these properties in terms of chemical bonding has remained a major challenge in boron chemistry. Here we report the synthesis of fully ordered, stoichiometric boron-carbide B13C2 by high-pressure-high-temperature techniques. Our experimental electron-density study using high-resolution single-crystal synchrotron X-ray diffraction data conclusively demonstrates that disorder and defects are not intrinsic to boron carbide, contrary to what was hitherto supposed. A detailed analysis of the electron density distribution reveals charge transfer between structural units in B13C2 and a new type of electron-deficient bond with formally unpaired electrons on the C-B-C group in B13C2. Unprecedented bonding features contribute to the fundamental chemistry and materials science of boron compounds that is of great interest for understanding structure-property relationships and development of novel functional materials.

  14. Multiscale enhanced sampling of intrinsically disordered protein conformations.

    Science.gov (United States)

    Lee, Kuo Hao; Chen, Jianhan

    2016-03-01

    In a recently developed multiscale enhanced sampling (MSES) technique, topology-based coarse-grained (CG) models are coupled to atomistic force fields to enhance the sampling of atomistic protein conformations. Here, the MSES protocol is refined by designing more sophisticated Hamiltonian/temperature replica exchange schemes that involve additional parameters in the MSES coupling restraint potential, to more carefully control how conformations are coupled between the atomistic and CG models. A specific focus is to derive an optimal MSES protocol for simulating conformational ensembles of intrinsically disordered proteins (IDPs). The efficacy of the refined protocols, referred to as MSES-soft asymptote (SA), was evaluated using two model peptides with various levels of residual helicities. The results show that MSES-SA generates more reversible helix-coil transitions and leads to improved convergence on various ensemble conformational properties. This study further suggests that more detailed CG models are likely necessary for more effective sampling of local conformational transition of IDPs. © 2015 Wiley Periodicals, Inc. PMID:26052838

  15. Structural biology of intrinsically disordered proteins: Revisiting unsolved mysteries.

    Science.gov (United States)

    Sigalov, Alexander B

    2016-06-01

    The emergence of intrinsically disordered proteins (IDPs) has challenged the classical protein structure-function paradigm by introducing a new paradigm of "coupled binding and folding". This paradigm suggests that IDPs fold upon binding to their partners. Further studies, however, revealed a novel and previously unrecognized phenomenon of "uncoupled binding and folding" suggesting that IDPs do not necessarily fold upon interaction with their lipid and protein partners. The complex and often unusual biophysics of IDPs makes structural characterization of these proteins and their complexes not only challenging but often resulting in opposite conclusions. For this reason, some crucial questions in this field remain unsolved for well over a decade. Considering an important role of IDPs in cellular regulation, signaling and control in health and disease, more efforts are needed to solve these mysteries. Here, I focus on two long-standing contradictions in the literature concerning dimerization and membrane-binding activities of IDPs. Molecular explanation of these discrepancies is provided. I also demonstrate how resolution of these critical issues in the field of IDPs results in our expanded understanding of cell function and has multiple applications in biology and medicine. PMID:27004461

  16. Disorder and defects are not intrinsic to boron carbide.

    Science.gov (United States)

    Mondal, Swastik; Bykova, Elena; Dey, Somnath; Ali, Sk Imran; Dubrovinskaia, Natalia; Dubrovinsky, Leonid; Parakhonskiy, Gleb; van Smaalen, Sander

    2016-01-01

    A unique combination of useful properties in boron-carbide, such as extreme hardness, excellent fracture toughness, a low density, a high melting point, thermoelectricity, semi-conducting behavior, catalytic activity and a remarkably good chemical stability, makes it an ideal material for a wide range of technological applications. Explaining these properties in terms of chemical bonding has remained a major challenge in boron chemistry. Here we report the synthesis of fully ordered, stoichiometric boron-carbide B13C2 by high-pressure-high-temperature techniques. Our experimental electron-density study using high-resolution single-crystal synchrotron X-ray diffraction data conclusively demonstrates that disorder and defects are not intrinsic to boron carbide, contrary to what was hitherto supposed. A detailed analysis of the electron density distribution reveals charge transfer between structural units in B13C2 and a new type of electron-deficient bond with formally unpaired electrons on the C-B-C group in B13C2. Unprecedented bonding features contribute to the fundamental chemistry and materials science of boron compounds that is of great interest for understanding structure-property relationships and development of novel functional materials. PMID:26777140

  17. Intrinsically disordered cytoplasmic domains of two cytokine receptors mediate conserved interactions with membranes

    DEFF Research Database (Denmark)

    Haxholm, Gitte Wolfsberg; Nikolajsen, Louise Fletcher; Olsen, Johan Gotthardt;

    2015-01-01

    . This study presents the first comprehensive structural characterization of any cytokine receptor ICD and demonstrates that the human prolactin and growth hormone receptor ICDs are intrinsically disordered throughout their entire lengths. We show that they interact specifically with hallmark lipids...

  18. Physical white chaos generation

    CERN Document Server

    Wang, Anbang; Wang, Bingjie; Li, Lei; Zhang, Mingjiang; Zhang, Wendong

    2014-01-01

    Physical chaos is a fascinating prospect for high-speed data security by serving as a masking carrier or a key source, but suffers from a colored spectrum that divulges system's intrinsic oscillations and degrades randomness. Here, we demonstrate that physical chaos with a white spectrum can be achieved by the optical heterodyning of two delayed-feedback lasers. A white chaotic spectrum with 1-dB fluctuation in a band of 11 GHz is experimentally obtained. The white chaos also has a perfect delta-like autocorrelation function and a high dimensionality of greater than 10, which makes chaos reconstruction extremely difficult and thus improves security.

  19. Content of intrinsic disorder influences the outcome of cell-free protein synthesis

    OpenAIRE

    Tokmakov, Alexander A.; Kurotani, Atsushi; Ikeda, Mariko; Terazawa, Yumiko; Shirouzu, Mikako; Stefanov, Vasily; SAKURAI, Tetsuya; Yokoyama, Shigeyuki

    2015-01-01

    Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yield...

  20. Isolating Intrinsic Processing Disorders from Second Language Acquisition.

    Science.gov (United States)

    Lock, Robin H.; Layton, Carol A.

    2002-01-01

    Evaluation of the validity of the Learning Disabilities Diagnostic Inventory with limited-English-proficient (LEP) students in grades 2-7 found that nondisabled LEP students were over-identified as having intrinsic processing deficits. Examination of individual student protocols highlighted the need to train teacher-raters in language acquisition…

  1. Roles of Intrinsic Disorder in Protein-Nucleic Acid Interactions

    OpenAIRE

    Dyson, H. Jane

    2011-01-01

    Interactions between proteins and nucleic acids typify the role of disordered segments, linkers, tails and other entities in the function of complexes that must form with high affinity and specificity but which must be capable of dissociating when no longer needed. While much of the emphasis in the literature has been on the interactions of disordered proteins with other proteins, disorder is also frequently observed in nucleic acids (particularly RNA) and in the proteins that interact with t...

  2. The unfoldomics decade: an update on intrinsically disordered proteins

    OpenAIRE

    Vacic Vladimir; Chen Jessica; Yang Jack Y; Romero Pedro; Meng Jingwei; Oldfield Christopher J; Dunker A Keith; Obradovic Zoran; Uversky Vladimir N

    2008-01-01

    Abstract Background Our first predictor of protein disorder was published just over a decade ago in the Proceedings of the IEEE International Conference on Neural Networks (Romero P, Obradovic Z, Kissinger C, Villafranca JE, Dunker AK (1997) Identifying disordered regions in proteins from amino acid sequence. Proceedings of the IEEE International Conference on Neural Networks, 1: 90–95). By now more than twenty other laboratory groups have joined the efforts to improve the prediction of prote...

  3. DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder

    OpenAIRE

    Varadi, Mihaly; Guharoy, Mainak; Zsolyomi, Fruzsina; Tompa, Peter

    2015-01-01

    Background Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of th...

  4. Double Solution with Chaos Completion of de Broglie's Nonlinear Wave Mechanics and Its Intrinsic Unification with the Causally Extended Relativity

    CERN Document Server

    Kirilyuk, A P

    1999-01-01

    As was shown previously, a simple system of interacting electromagnetic and gravitational protofields with generic parameters shows intrinsic instability with respect to unceasing cycles of physically real auto-squeeze (reduction) to randomly chosen centres and the reverse extension which form the causally probabilistic process of quantum beat observed as an elementary particle (like electron). Here we show that the emerging wave-particle duality, space, and time lead to the well-known equations of special relativity and quantum mechanics thus providing their causal extension and intrinsic unification. The relativistic inertial mass (energy) is universally defined as the temporal rate (intensity) of the chaotic quantum beat process(es). The same complex-dynamical processes and the same mass-energy account for the universal gravitation, since any reduction event in the electromagnetic protofield is reproduced within the (directly unobservable) gravitational protofield leading to an increase of its tension whic...

  5. The importance of intrinsic disorder for protein phosphorylation

    OpenAIRE

    Lilia M Iakoucheva; Radivojac, Predrag; Celeste J Brown; O'Connor, Timothy R.; Sikes, Jason G.; Obradovic, Zoran; Dunker, A. Keith

    2004-01-01

    Reversible protein phosphorylation provides a major regulatory mechanism in eukaryotic cells. Due to the high variability of amino acid residues flanking a relatively limited number of experimentally identified phosphorylation sites, reliable prediction of such sites still remains an important issue. Here we report the development of a new web-based tool for the prediction of protein phosphorylation sites, DISPHOS (DISorder-enhanced PHOSphorylation predictor, http://www.ist.temple.edu/DISPHOS...

  6. Intrinsic structural disorder of mouse proNGF.

    Science.gov (United States)

    Paoletti, Francesca; Covaceuszach, Sonia; Konarev, Peter V; Gonfloni, Stefania; Malerba, Francesca; Schwarz, Elisabeth; Svergun, Dmitri I; Cattaneo, Antonino; Lamba, Doriano

    2009-06-01

    The unprocessed precursor of the Nerve Growth Factor (NGF), proNGF, has additional functions, besides its initially described role as a chaperone for NGF folding. The precursor protein endows apoptotic and/or neurotrophic properties, in contrast to the mature part. The structural and molecular basis for such distinct activities are presently unknown. Aiming to gain insights into the specific molecular interactions that govern rm-proNGF biological activities versus those of its mature counterpart, a structural study by synchrotron small angle X-ray scattering (SAXS) in solution was carried out. The different binding properties of the two proteins were investigated by surface plasmon resonance (SPR) using, as structural probes, a panel of anti-NGF antibodies and the soluble forms of TrkA and p75(NTR) receptors. SAXS measurements revealed the rm-proNGF to be dimeric and anisometric, with the propeptide domain being intrinsically unstructured. Ab initio reconstructions assuming twofold symmetry generated two types of structural models, a globular "crab-like" and an elongated shape that resulted in equally good fits of the scattering data. A novel method accounting for possible coexistence of different conformations contributing to the experimental scattering pattern, with no symmetry constraints, suggests the "crab-like" to be a more likely proNGF conformation. To exploit the potential of chemical stabilizers affecting the existing conformational protein populations, SAXS data were also collected in the presence of ammonium sulphate. An increase of the proNGF compactness was observed. SPR data pinpoints that the propeptide of proNGF may act as an intrinsically unstructured protein domain, characterized by a molecular promiscuity in the interaction/binding to multiple partners (TrkA and p75(NTR) receptors and a panel of neutralizing anti-NGF antibodies) depending on the physiological conditions of the cell. These data provide a first insight into the structural basis

  7. The intrinsic disorder related alloy scattering in ZrNiSn half-Heusler thermoelectric materials

    OpenAIRE

    Hanhui Xie; Heng Wang; Chenguang Fu; Yintu Liu; G. Jeffrey Snyder; Xinbing Zhao; Tiejun Zhu

    2014-01-01

    The intrinsic structural disorder dramatically affects the thermal and electronic transport in semiconductors. Although normally considered an ordered compound, the half-Heusler ZrNiSn displays many transport characteristics of a disordered alloy. Similar to the (Zr,Hf)NiSn based solid solutions, the unsubstituted ZrNiSn compound also exhibits charge transport dominated by alloy scattering, as demonstrated in this work. The unexpected charge transport, even in ZrNiSn which is normally conside...

  8. Abundance of intrinsic structural disorder in the histone H1 subtypes.

    Science.gov (United States)

    Kowalski, Andrzej

    2015-12-01

    The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes. PMID:26366527

  9. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

    OpenAIRE

    Davey, Norman E.; Cowan, Joanne L; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J; Edwards, Richard J

    2012-01-01

    Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use ...

  10. High dimensional and high resolution pulse sequences for backbone resonance assignment of intrinsically disordered proteins

    Czech Academy of Sciences Publication Activity Database

    Zawadzka-Kazimierczuk, A.; Kozminski, W.; Šanderová, Hana; Krásný, Libor

    2012-01-01

    Roč. 52, č. 4 (2012), s. 329-337. ISSN 0925-2738 R&D Projects: GA ČR GA204/09/0583 Institutional research plan: CEZ:AV0Z50200510 Keywords : Intrinsically disordered proteins * Non-uniform sampling * Backbone assignment Subject RIV: EE - Microbiology, Virology Impact factor: 2.845, year: 2012

  11. The roles of intrinsic disorder in orchestrating the Wnt-pathway.

    Science.gov (United States)

    Xue, Bin; Dunker, A Keith; Uversky, Vladimir N

    2012-01-01

    The canonical Wnt-pathway plays a number of crucial roles in the development of organism. Malfunctions of this pathway lead to various diseases including cancer. In the inactivated state, this pathway involves five proteins, Axin, CKI-α, GSK-3β, APC, and β-catenin. We analyzed these proteins by a number of computational tools, such as PONDR(r)VLXT, PONDR(r)VSL2, MoRF-II predictor and Hydrophobic Cluster Analysis (HCA) to show that each of the Wnt-pathway proteins contains several intrinsically disordered regions. Based on a comprehensive analysis of published data we conclude that these disordered regions facilitate protein-protein interactions, post-translational modifications, and signaling. The scaffold protein Axin and another large protein, APC, act as flexible concentrators in gathering together all other proteins involved in the Wnt-pathway, emphasizing the role of intrinsically disordered regions in orchestrating the complex protein-protein interactions. We further explore the intricate roles of highly disordered APC in regulation of β-catenin function. Intrinsically disordered APC helps the collection of β-catenin from cytoplasm, facilitates the b-catenin delivery to the binding sites on Axin, and controls the final detachment of β-catenin from Axin. PMID:22292947

  12. Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions.

    Science.gov (United States)

    Gruet, Antoine; Dosnon, Marion; Blocquel, David; Brunel, Joanna; Gerlier, Denis; Das, Rahul K; Bonetti, Daniela; Gianni, Stefano; Fuxreiter, Monika; Longhi, Sonia; Bignon, Christophe

    2016-02-01

    Despite the partial disorder-to-order transition that intrinsically disordered proteins often undergo upon binding to their partners, a considerable amount of residual disorder may be retained in the bound form, resulting in a fuzzy complex. Fuzzy regions flanking molecular recognition elements may enable partner fishing through non-specific, transient contacts, thereby facilitating binding, but may also disfavor binding through various mechanisms. So far, few computational or experimental studies have addressed the effect of fuzzy appendages on partner recognition by intrinsically disordered proteins. In order to shed light onto this issue, we used the interaction between the intrinsically disordered C-terminal domain of the measles virus (MeV) nucleoprotein (NTAIL ) and the X domain (XD) of the viral phosphoprotein as model system. After binding to XD, the N-terminal region of NTAIL remains conspicuously disordered, with α-helical folding taking place only within a short molecular recognition element. To study the effect of the N-terminal fuzzy region on NTAIL /XD binding, we generated N-terminal truncation variants of NTAIL , and assessed their binding abilities towards XD. The results revealed that binding increases with shortening of the N-terminal fuzzy region, with this also being observed with hsp70 (another MeV NTAIL binding partner), and for the homologous NTAIL /XD pairs from the Nipah and Hendra viruses. Finally, similar results were obtained when the MeV NTAIL fuzzy region was replaced with a highly dissimilar artificial disordered sequence, supporting a sequence-independent inhibitory effect of the fuzzy region. PMID:26684000

  13. Test and Evaluation of ff99IDPs Force Field for Intrinsically Disordered Proteins.

    Science.gov (United States)

    Ye, Wei; Ji, Dingjue; Wang, Wei; Luo, Ray; Chen, Hai-Feng

    2015-05-26

    Over 40% of eukaryotic proteomic sequences have been predicted to be intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) and confirmed to be associated with many diseases. However, widely used force fields cannot well reproduce the conformers of IDPs. Previously the ff99IDPs force field was released to simulate IDPs with CMAP energy corrections for the eight disorder-promoting residues. In order to further confirm the performance of ff99IDPs, three representative IDP systems (arginine-rich HIV-1 Rev, aspartic proteinase inhibitor IA3, and α-synuclein) were used to test and evaluate the simulation results. The results show that for free disordered proteins, the chemical shifts from the ff99IDPs simulations are in quantitative agreement with those from reported NMR measurements and better than those from ff99SBildn. Thus, ff99IDPs can sample more clusters of disordered conformers than ff99SBildn. For structural proteins, both ff99IDPs and ff99SBildn can well reproduce the conformations. In general, ff99IDPs can successfully be used to simulate the conformations of IDPs and IDRs in both bound and free states. However, relative errors could still be found at the boundaries of ordered residues scattered in long disorder-promoting sequences. Therefore, polarizable force fields might be one of the possible ways to further improve the performance on IDPs. PMID:25919886

  14. On the abundance of intrinsically disordered proteins in the human proteome and its relation to diseases: there is no enrichment

    OpenAIRE

    Deiana, Antonio; Giansanti, Andrea

    2014-01-01

    Intrinsically disordered proteins are fascinating the community of protein science since the last decade, at least. There is a well-established line of research that intends to reveal the crucial role played by intrinsically disordered proteins (IDPs) in the development of human diseases. The main argument is that IDPs are differentially more present in groups of disease-related proteins. In this note we compare the frequency of disorder in human proteins, both disease-related and not. The fr...

  15. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins

    Science.gov (United States)

    Schirò, Giorgio; Fichou, Yann; Gallat, Francois-Xavier; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin

    2015-03-01

    Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity.

  16. Dancing Protein Clouds: The Strange Biology and Chaotic Physics of Intrinsically Disordered Proteins.

    Science.gov (United States)

    Uversky, Vladimir N

    2016-03-25

    Biologically active but floppy proteins represent a new reality of modern protein science. These intrinsically disordered proteins (IDPs) and hybrid proteins containing ordered and intrinsically disordered protein regions (IDPRs) constitute a noticeable part of any given proteome. Functionally, they complement ordered proteins, and their conformational flexibility and structural plasticity allow them to perform impossible tricks and be engaged in biological activities that are inaccessible to well folded proteins with their unique structures. The major goals of this minireview are to show that, despite their simplified amino acid sequences, IDPs/IDPRs are complex entities often resembling chaotic systems, are structurally and functionally heterogeneous, and can be considered an important part of the structure-function continuum. Furthermore, IDPs/IDPRs are everywhere, and are ubiquitously engaged in various interactions characterized by a wide spectrum of binding scenarios and an even wider spectrum of structural and functional outputs. PMID:26851286

  17. Polymer scaling laws of unfolded and intrinsically disordered proteins quantified with single-molecule spectroscopy.

    OpenAIRE

    Hofmann H.; Soranno A; Borgia A; Gast K; Nettels D; Schuler B.

    2012-01-01

    The dimensions of unfolded and intrinsically disordered proteins are highly dependent on their amino acid composition and solution conditions, especially salt and denaturant concentration. However, the quantitative implications of this behavior have remained unclear, largely because the effective theta-state, the central reference point for the underlying polymer collapse transition, has eluded experimental determination. Here, we used single-molecule fluorescence spectroscopy and two-focus c...

  18. Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins.

    OpenAIRE

    Schirò, Giorgio; Fichou, Yann; Paciaroni, Alessandro; Wuttke, Joachim; Tobias, Douglas J.; Weik, Martin; Gallat, Francois-Xavier,; Wood, Kathleen; Gabel, Frank; Moulin, Martine; Härtlein, Michael; Heyden, Matthias; Colletier, Jacques-Philippe; Orecchini, Andrea

    2015-01-01

    Hydration ​water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between ​water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration ​water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human pr...

  19. NMR contributions to structural dynamics studies of intrinsically disordered proteins ☆

    OpenAIRE

    Konrat, Robert

    2014-01-01

    Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will...

  20. A decade and a half of protein intrinsic disorder: Biology still waits for physics

    OpenAIRE

    Vladimir N Uversky

    2013-01-01

    The abundant existence of proteins and regions that possess specific functions without being uniquely folded into unique 3D structures has become accepted by a significant number of protein scientists. Sequences of these intrinsically disordered proteins (IDPs) and IDP regions (IDPRs) are characterized by a number of specific features, such as low overall hydrophobicity and high net charge which makes these proteins predictable. IDPs/IDPRs possess large hydrodynamic volumes, low contents of o...

  1. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues

    OpenAIRE

    Das, Rahul K.; Pappu, Rohit V.

    2013-01-01

    The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequence–ensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyamphol...

  2. Hamiltonian Mapping Revisited: Calibrating Minimalist Models to Capture Molecular Recognition by Intrinsically Disordered Proteins

    OpenAIRE

    Law, Sean M.; Ahlstrom, Logan S.; Panahi, Afra; Brooks, Charles L.

    2014-01-01

    Molecular recognition by intrinsically disordered proteins (IDPs) plays a central role in many critical cellular processes. Toward achieving detailed mechanistic understanding of IDP–target interactions, here we employ the “Hamiltonian mapping” methodology, which is rooted in the weighted histogram analysis method (WHAM), for the fast and efficient calibration of structure-based models in studies of IDPs. By performing reference simulations on a given Hamiltonian, we illustrate for two model ...

  3. Exploring the psychosis functional connectome: aberrant intrinsic networks in schizophrenia and bipolar disorder

    Directory of Open Access Journals (Sweden)

    VinceDCalhoun

    2012-01-01

    Full Text Available Intrinsic functional brain networks (INs are regions showing temporal coherence with one another. These INs are present in the context of a task (as opposed to an undirected task such as rest, albeit modulated to a degree both spatially and temporally. Prominent networks include the default mode, attentional fronto-parietal, executive control, bilateral temporal lobe and motor networks. The characterization of INs has recently gained considerable momentum, however; most previous studies evaluate only a small subset of the intrinsic networks (e.g. default mode. In this paper we use independent component analysis to study INs decomposed from fMRI data collected in a large group of schizophrenia patients, healthy controls, and individuals with bipolar disorder, while performing an auditory oddball task. Schizophrenia and bipolar disorder share significant overlap in clinical symptoms, brain characteristics, and risk genes which motivates our goal of identifying whether functional imaging data can differentiate the two disorders. We tested for group differences in properties of all identified intrinsic networks including spatial maps, spectra, and functional network connectivity. A small set of default mode, temporal lobe, and frontal networks with default mode regions appearing to play a key role in all comparisons. Bipolar subjects showed more prominent changes in ventromedial and prefrontal default mode regions whereas schizophrenia patients showed changes in posterior default mode regions. Anti-correlations between left parietal areas and dorsolateral prefrontal cortical areas were different in bipolar and schizophrenia patients and amplitude was significantly different from healthy controls in both patient groups. Patients exhibited similar frequency behavior across multiple networks with decreased low frequency power. In summary, a comprehensive analysis of intrinsic networks reveals a key role for the default mode in both schizophrenia and

  4. Liquid demixing of intrinsically disordered proteins is seeded by poly(ADP-ribose)

    DEFF Research Database (Denmark)

    Altmeyer, Matthias; Neelsen, Kai J; Teloni, Federico;

    2015-01-01

    Intrinsically disordered proteins can phase separate from the soluble intracellular space, and tend to aggregate under pathological conditions. The physiological functions and molecular triggers of liquid demixing by phase separation are not well understood. Here we show in vitro and in vivo...... disordered proteins at DNA break sites. Demixing, which relies on electrostatic interactions between positively charged RGG repeats and negatively charged PAR, is amplified by aggregation-prone prion-like domains, and orchestrates the earliest cellular responses to DNA breakage. We propose that PAR......-seeded liquid demixing is a general mechanism to dynamically reorganize the soluble nuclear space with implications for pathological protein aggregation caused by derailed phase separation....

  5. The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

    Science.gov (United States)

    Shirai, Nobu C.; Kikuchi, Macoto

    2016-02-01

    α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy.

  6. Electrostatics and Intrinsic Disorder Drive Translocon Binding of the SRP Receptor FtsY.

    Science.gov (United States)

    Lakomek, Nils-Alexander; Draycheva, Albena; Bornemann, Thomas; Wintermeyer, Wolfgang

    2016-08-01

    Integral membrane proteins in bacteria are co-translationally targeted to the SecYEG translocon for membrane insertion via the signal recognition particle (SRP) pathway. The SRP receptor FtsY and its N-terminal A domain, which is lacking in any structural model of FtsY, were studied using NMR and fluorescence spectroscopy. The A domain is mainly disordered and highly flexible; it binds to lipids via its N terminus and the C-terminal membrane targeting sequence. The central A domain binds to the translocon non-specifically and maintains disorder. Translocon targeting and binding of the A domain is driven by electrostatic interactions. The intrinsically disordered A domain tethers FtsY to the translocon, and because of its flexibility, allows the FtsY NG domain to scan a large area for binding to the NG domain of ribosome-bound SRP, thereby promoting the formation of the quaternary transfer complex at the membrane. PMID:27346853

  7. SLiMPrints: conservation-based discovery of functional motif fingerprints in intrinsically disordered protein regions

    Science.gov (United States)

    Davey, Norman E.; Cowan, Joanne L.; Shields, Denis C.; Gibson, Toby J.; Coldwell, Mark J.; Edwards, Richard J.

    2012-01-01

    Large portions of higher eukaryotic proteomes are intrinsically disordered, and abundant evidence suggests that these unstructured regions of proteins are rich in regulatory interaction interfaces. A major class of disordered interaction interfaces are the compact and degenerate modules known as short linear motifs (SLiMs). As a result of the difficulties associated with the experimental identification and validation of SLiMs, our understanding of these modules is limited, advocating the use of computational methods to focus experimental discovery. This article evaluates the use of evolutionary conservation as a discriminatory technique for motif discovery. A statistical framework is introduced to assess the significance of relatively conserved residues, quantifying the likelihood a residue will have a particular level of conservation given the conservation of the surrounding residues. The framework is expanded to assess the significance of groupings of conserved residues, a metric that forms the basis of SLiMPrints (short linear motif fingerprints), a de novo motif discovery tool. SLiMPrints identifies relatively overconstrained proximal groupings of residues within intrinsically disordered regions, indicative of putatively functional motifs. Finally, the human proteome is analysed to create a set of highly conserved putative motif instances, including a novel site on translation initiation factor eIF2A that may regulate translation through binding of eIF4E. PMID:22977176

  8. Intrinsically disordered amphiphilic peptides as potential targets in drug delivery vehicles.

    Science.gov (United States)

    Vincenzi, Marian; Accardo, Antonella; Costantini, Susan; Scala, Stefania; Portella, Luigi; Trotta, Annamaria; Ronga, Luisa; Guillon, Jean; Leone, Marilisa; Colonna, Giovanni; Rossi, Filomena; Tesauro, Diego

    2015-11-01

    Intrinsically disordered proteins/peptides play a crucial role in many physiological and pathological events and may assume a precise conformation upon binding to a specific target. Recently, we have described the conformational and functional properties of two linear ester peptides provided with the following sequences: Y-G-E-C-P-C-K-OAllyl (PepK) and Y-G-E-C-P-C-E-OAllyl (PepE). Both peptides are characterized by the presence of the "CPC" motif together with a few amino acids able to promote disorder. The CPC sequence is a binding motif for the CXCR4 receptor that represents a well-known target for cancer therapies. In this paper, we report on synthetic amphiphilic peptides that consist of lipophilic derivatives of PepE and PepK bearing two stearic alkyl chains and/or an ethoxylic spacer. These peptide amphiphiles form stable supramolecular aggregates; they present conformational features that are typical of intrinsically disordered molecules as shown by CD spectroscopy. Solution fluorescence and DLS studies have been performed to evaluate Critical Micellar Concentrations and the dimension of supramolecular aggregates. Moreover, preliminary in vitro cell-based assays have been conducted to investigate the molecular recognition processes involving the CXCR4 receptor. In the end, the results obtained have been compared with the previous data generated by the corresponding non-amphiphilic peptides (PepE and PepK). PMID:26263446

  9. Deducing conformational variability of intrinsically disordered proteins from infrared spectroscopy with Bayesian statistics

    International Nuclear Information System (INIS)

    Highlights: • Deduce secondary structure content of intrinsically disordered proteins from IR spectra. • Bayesian analysis to infer conformations of disordered regions of proteins from IR. • Comparison of measured and calculated IR spectra to obtain thermodynamic weights. - Abstract: As it remains practically impossible to generate ergodic ensembles for large intrinsically disordered proteins (IDP) with molecular dynamics (MD) simulations, it becomes critical to compare spectroscopic characteristics of the theoretically generated ensembles to corresponding measurements. We develop a Bayesian framework to infer the ensemble properties of an IDP using a combination of conformations generated by MD simulations and its measured infrared spectrum. We performed 100 different MD simulations totaling more than 10 μs to characterize the conformational ensemble of α-synuclein, a prototypical IDP, in water. These conformations are clustered based on solvent accessibility and helical content. We compute the amide-I band for these clusters and predict the thermodynamic weights of each cluster given the measured amide-I band. Bayesian analysis produces a reproducible and non-redundant set of thermodynamic weights for each cluster, which can then be used to calculate the ensemble properties. In a rigorous validation, these weights reproduce measured chemical shifts

  10. Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an "Elephant and Blind Men" Situation.

    Science.gov (United States)

    Uversky, Vladimir N

    2015-01-01

    Intrinsically disordered proteins (IDPs) and hybrid proteins possessing ordered domains and intrinsically disordered protein regions (IDPRs) are highly abundant in various proteomes. They are different from ordered proteins at many levels, and an unambiguous representation of an IDP structure is a difficult task. In fact, IDPs show an extremely wide diversity in their structural properties, being able to attain extended conformations (random coil-like) or to remain globally collapsed (molten globule-like). Disorder can differently affect different parts of a protein, with some regions being more ordered than others. IDPs and IDPRs exist as dynamic ensembles, resembling "protein-clouds". IDP structures are best presented as conformational ensembles that contain highly dynamic structures interconverting on a number of timescales. The determination of a unique high-resolution structure is not possible for an isolated IDP, and a detailed structural and dynamic characterization of IDPs cannot typically be provided by a single tool. Therefore, accurate descriptions of IDPs/IDPRs rely on a multiparametric approach that includes a host of biophysical methods that can provide information on the overall compactness of IDPs and their conformational stability, shape, residual secondary structure, transient long-range contacts, regions of restricted or enhanced mobility, etc. The goal of this chapter is to provide a brief overview of some of the components of this multiparametric approach. PMID:26387104

  11. Structure of an Intrinsically Disordered Stress Protein Alone and Bound to a Membrane Surface.

    Science.gov (United States)

    Atkinson, John; Clarke, Matthew W; Warnica, Josephine M; Boddington, Kelly F; Graether, Steffen P

    2016-08-01

    Dehydrins are a group of intrinsically disordered proteins that protect plants from damage caused by drought, cold, and high salinity. Like other intrinsically disordered proteins, dehydrins can gain structure when bound to a ligand. Previous studies have shown that dehydrins are able to protect liposomes from cold damage, but the interactions that drive membrane binding and the detailed structure of the bound and unbound forms are not known. We use an ensemble-structure approach to generate models of a dehydrin known as K2 in the presence and absence of sodium dodecyl sulfate micelles, and we docked the bound structure to the micelle. The collection of residual dipolar coupling data, amide protection factors, and paramagnetic relaxation enhancement distances, in combination with chemical shifts and relaxation measurements, allows for determining plausible structures that are not otherwise visible in time-averaged structural data. The results show that in the bound structure, the conserved lysines are important for membrane binding, whereas the flanking hydrophobic residues play a lesser role. The unbound structure shows a high level of disorder and an extended structure. We propose that the structural differences between bound and unbound forms allow dehydrins to act as molecular shields in their unbound state and as membrane protectants in their bound state. Unlike α-synuclein, the significant gain of α-helicity in K2 at low concentrations of sodium dodecyl sulfate is not due to a decrease in the critical micelle concentration. The study provides structural insight into how a disordered protein can interact with a membrane surface. PMID:27508433

  12. Effect of O-Linked Glycosylation on the Equilibrium Structural Ensemble of Intrinsically Disordered Polypeptides.

    Science.gov (United States)

    Zerze, Gül H; Mittal, Jeetain

    2015-12-24

    Glycosylation is one of the most common post-translational modifications (PTMs), which provides a large proteome diversity. Previous work on glycosylation of globular proteins has revealed remarkable effects of glycosylation on protein function, altering the folding stability and structure and/or altering the protein surface which affects their binding characteristics. Intrinsically disordered proteins (IDPs) or intrinsically disordered regions (IDRs) of large proteins are also frequently glycosylated, yet how glycosylation affects their function remains to be elucidated. An important open question is, does glycosylation affect IDP structure or binding characteristics or both? In this work, we particularly address the structural effects of O-linked glycosylation by investigating glycosylated and unglycosylated forms of two different IDPs, tau174-183 and human islet amyloid polypeptide (hIAPP), by all-atom explicit solvent simulations. We simulate these IDPs in aqueous solution for O-linked glycosylated and unglycosylated forms by employing two modern all-atom force fields for which glycan parameters are also available. We find that O-linked glycosylation only has a modest effect on equilibrium structural ensembles of IDPs, for the cases studied here, which suggests that the functional role of glycosylation may be primarily exerted by modulation of the protein binding characteristics rather than structure. PMID:26618856

  13. Actin capping protein and its inhibitor CARMIL: how intrinsically disordered regions function

    International Nuclear Information System (INIS)

    The actin capping protein (CP) tightly binds to the barbed end of actin filaments to block further elongation. The β-tentacle in CP is an important region that ensures stable interaction with actin filaments. CARMIL inhibits the interaction of CP with actin filaments via the C-terminal portion containing the CP-binding motif, located in an intrinsically disordered region. We have proposed an allosteric inhibition model in which CARMIL suppresses CP by the population shift mechanism. Here, we solved a crystal structure of CP in complex with a CARMIL-derived peptide, CA32. The new structure clearly represents the α-helical form of the β-tentacle that was invisible in other CP/CARMIL peptide complex structures. In addition, we exhaustively performed a normal mode analysis with the elastic network model on all available crystal structures of the CP/CARMIL peptide complexes, including the new structure. We concluded that the CP-binding motif is necessary and sufficient for altering the fluctuation of CP, which is essential for attenuating the barbed-end-capping activity along the population shift mechanism. The roles and functions of the β-tentacle and the CP-binding motif are discussed in terms of their intrinsically disordered nature

  14. Reduced intrinsic connectivity of amygdala in adults with major depressive disorder

    Directory of Open Access Journals (Sweden)

    RajamannarRamasubbu

    2014-02-01

    Full Text Available Imaging studies of major depressive disorder (MDD have demonstrated enhanced resting-state activity of the amygdala as well as exaggerated reactivity to negative emotional stimuli relative to healthy controls. However, the abnormalities in the intrinsic connectivity of the amygdala in MDD still remain unclear. As the resting-state activity and functional connectivity (RSFC reflect fundamental brain processes, we compared the RSFC of the amygdala between unmedicated MDD patients and healthy controls. Seventy-four subjects, 55 adults meeting the DSM IV criteria for MDD and 19 healthy controls, underwent a resting state 3-T functional magnetic resonance imaging (fMRI scan. An amygdala seed-based low frequency RSFC map for the whole brain was generated for each group. Compared with healthy controls, MDD patients showed a wide-spread reduction in the intrinsic connectivity of the amygdala with a variety of brain regions involved in emotional processing and regulation, including the ventrolateral prefrontal cortex, insula, caudate, middle and superior temporal regions, occipital cortex, and cerebellum, as well as increased connectivity with the bilateral temporal poles (p< 0.05 corrected. The increase in the intrinsic connectivity of amygdala with the temporal poles was inversely correlated with symptom severity and anxiety scores. Although the directionality of connections between regions cannot be inferred from temporal correlations, the reduced intrinsic connectivity of the amygdala predominantly with regions involved in emotional processing may reflect impaired bottom-up signaling for top-down cortical modulation of limbic regions leading to abnormal affect regulation in MDD.

  15. Disordered nucleiome: Abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea.

    Science.gov (United States)

    Wang, Chen; Uversky, Vladimir N; Kurgan, Lukasz

    2016-05-01

    Intrinsically disordered proteins (IDPs) are abundant in various proteomes, where they play numerous important roles and complement biological activities of ordered proteins. Among functions assigned to IDPs are interactions with nucleic acids. However, often, such assignments are made based on the guilty-by-association principle. The validity of the extension of these correlations to all nucleic acid binding proteins has never been analyzed on a large scale across all domains of life. To fill this gap, we perform a comprehensive computational analysis of the abundance of intrinsic disorder and intrinsically disordered domains in nucleiomes (∼548 000 nucleic acid binding proteins) of 1121 species from Archaea, Bacteria and Eukaryota. Nucleiome is a whole complement of proteins involved in interactions with nucleic acids. We show that relative to other proteins in the corresponding proteomes, the DNA-binding proteins have significantly increased disorder content and are significantly enriched in disordered domains in Eukaryotes but not in Archaea and Bacteria. The RNA-binding proteins are significantly enriched in the disordered domains in Bacteria, Archaea and Eukaryota, while the overall abundance of disorder in these proteins is significantly increased in Bacteria, Archaea, animals and fungi. The high abundance of disorder in nucleiomes supports the notion that the nucleic acid binding proteins often require intrinsic disorder for their functions and regulation. PMID:27037624

  16. The intrinsic disorder related alloy scattering in ZrNiSn half-Heusler thermoelectric materials.

    Science.gov (United States)

    Xie, Hanhui; Wang, Heng; Fu, Chenguang; Liu, Yintu; Snyder, G Jeffrey; Zhao, Xinbing; Zhu, Tiejun

    2014-01-01

    The intrinsic structural disorder dramatically affects the thermal and electronic transport in semiconductors. Although normally considered an ordered compound, the half-Heusler ZrNiSn displays many transport characteristics of a disordered alloy. Similar to the (Zr,Hf)NiSn based solid solutions, the unsubstituted ZrNiSn compound also exhibits charge transport dominated by alloy scattering, as demonstrated in this work. The unexpected charge transport, even in ZrNiSn which is normally considered fully ordered, can be explained by the Ni partially filling interstitial sites in this half-Heusler system. The influence of the disordering and defects in crystal structure on the electron transport process has also been quantitatively analyzed in ZrNiSn1-xSbx with carrier concentration nH ranging from 5.0 × 10(19) to 2.3 × 10(21) cm(-3) by changing Sb dopant content. The optimized carrier concentration nH ≈ 3-4 × 10(20) cm(-2) results in ZT ≈ 0.8 at 875K. This work suggests that MNiSn (M = Hf, Zr, Ti) and perhaps most other half-Heusler thermoelectric materials should be considered highly disordered especially when trying to understand the electronic and phonon structure and transport features. PMID:25363573

  17. There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order".

    Science.gov (United States)

    Nielsen, Jakob T; Mulder, Frans A A

    2016-01-01

    The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence. PMID:26904549

  18. Mapping the potential energy landscape of intrinsically disordered proteins at amino acid resolution.

    Science.gov (United States)

    Ozenne, Valéry; Schneider, Robert; Yao, Mingxi; Huang, Jie-rong; Salmon, Loïc; Zweckstetter, Markus; Jensen, Malene Ringkjøbing; Blackledge, Martin

    2012-09-12

    Intrinsically disordered regions are predicted to exist in a significant fraction of proteins encoded in eukaryotic genomes. The high levels of conformational plasticity of this class of proteins endows them with unique capacities to act in functional modes not achievable by folded proteins, but also places their molecular characterization beyond the reach of classical structural biology. New techniques are therefore required to understand the relationship between primary sequence and biological function in this class of proteins. Although dependences of some NMR parameters such as chemical shifts (CSs) or residual dipolar couplings (RDCs) on structural propensity are known, so that sampling regimes are often inferred from experimental observation, there is currently no framework that allows for a statistical mapping of the available Ramachandran space of each amino acid in terms of conformational propensity. In this study we develop such an approach, combining highly efficient conformational sampling with ensemble selection to map the backbone conformational sampling of IDPs on a residue specific level. By systematically analyzing the ability of NMR data to map the conformational landscape of disordered proteins, we identify combinations of RDCs and CSs that can be used to raise conformational degeneracies inherent to different data types, and apply these approaches to characterize the conformational behavior of two intrinsically disordered proteins, the K18 domain from Tau protein and N(TAIL) from measles virus nucleoprotein. In both cases, we identify the enhanced populations of turn and helical regions in key regions of the proteins, as well as contiguous strands that show clear and enhanced polyproline II sampling. PMID:22901047

  19. Colored chaos

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, B.

    1997-09-22

    The report contains viewgraphs on the following: ergodicity and chaos; Hamiltonian dynamics; metric properties; Lyapunov exponents; KS entropy; dynamical realization; lattice formulation; and numerical results.

  20. Correlating Flavivirus virulence and levels of intrinsic disorder in shell proteins: protective roles vs. immune evasion.

    Science.gov (United States)

    Goh, Gerard Kian-Meng; Dunker, A Keith; Uversky, Vladimir N

    2016-05-24

    Computational analyses revealed correlations between the intrinsic disorder propensity of shell proteins and case fatality rates (CFRs) among Flaviviruses and within at least two Flavivirus species, such as tick-borne encephalitis virus (TBEV) and dengue virus (DENV). The shell proteins analyzed in this study are capsid (C) and membrane (PrM, Pr, and M) proteins. The highest correlations can be found when regression analyses were conducted using Pr (Flavivirus: r(2) = 0.78, p fever virus (YFV), which is the most virulent virus in the sample, has the highest PID levels, whereas the second most virulent TBEV FE subtype has the second highest PID score due to its C protein, and the least virulent West Nile virus (WNV) has the least disordered C protein. This knowledge can be used while working on the development and identification of attenuated strains for vaccine. Curiously, unlike Flaviviruses, a disordered outer shell was described for hepatitis C virus (HCV), human immunodeficiency virus (HIV), and human simplex virus 2 (HSV-2), which currently have no effective vaccine. PMID:27102744

  1. Patterns in chaos

    International Nuclear Information System (INIS)

    Classification of chaotic patterns in classical Hamiltonian systems is given as a series of levels with increasing disorder. Hamiltonian dynamics is presented, including the renormalization chaos, based upon the fairly simple resonant theory. First estimates for the critical structure and related statistical anomalies in arbitrary dimensions are discussed. 49 refs

  2. Shifted intrinsic connectivity of central executive and salience network in borderline personality disorder

    Directory of Open Access Journals (Sweden)

    Anselm eDoll

    2013-10-01

    Full Text Available Borderline personality disorder (BPD is characterized by stable instability of emotions and behavior and their regulation. This emotional and behavioral instability corresponds with a neurocognitive triple network model of psychopathology, which suggests that aberrant emotional saliency and cognitive control is associated with aberrant interaction across three intrinsic connectivity networks (ICN (i.e. the salience, default mode, and central executive network, SN, DMN, CEN. The objective of the current study was to investigate whether and how such triple network intrinsic functional connectivity (iFC is changed in patients with BPD. We acquired resting-state functional magnetic resonance imaging (rs-fMRI data from fourteen patients with BPD and sixteen healthy controls (HC. High-model order independent component analysis (ICA was used to extract spatiotemporal patterns of ongoing, coherent blood-oxygen-level-dependent (BOLD signal fluctuations from rs-fMRI data. Main outcome measures were iFC within networks (intra-iFC and between networks (i.e. network time course correlation inter-iFC.Aberrant intra-iFC was found in patients’ DMN, SN, and CEN, consistent with previous findings. While patients’ inter-iFC of the CEN was decreased, inter-iFC of the SN was increased. In particular, a balance index reflecting the relationship of CEN-and SN-inter-iFC across networks was strongly shifted from CEN to SN connectivity in patients. Results provide first preliminary evidence for aberrant triple network intrinsic functional connectivity in BPD. Our data suggest a shift of inter-network iFC from networks involved in cognitive control to those of emotion-related activity in BPD, potentially reflecting the persistent instability of emotion regulation in patients.

  3. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex.

    Science.gov (United States)

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick Yh; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. PMID:27198189

  4. Sequence heuristics to encode phase behaviour in intrinsically disordered protein polymers

    Science.gov (United States)

    Quiroz, Felipe García; Chilkoti, Ashutosh

    2015-11-01

    Proteins and synthetic polymers that undergo aqueous phase transitions mediate self-assembly in nature and in man-made material systems. Yet little is known about how the phase behaviour of a protein is encoded in its amino acid sequence. Here, by synthesizing intrinsically disordered, repeat proteins to test motifs that we hypothesized would encode phase behaviour, we show that the proteins can be designed to exhibit tunable lower or upper critical solution temperature (LCST and UCST, respectively) transitions in physiological solutions. We also show that mutation of key residues at the repeat level abolishes phase behaviour or encodes an orthogonal transition. Furthermore, we provide heuristics to identify, at the proteome level, proteins that might exhibit phase behaviour and to design novel protein polymers consisting of biologically active peptide repeats that exhibit LCST or UCST transitions. These findings set the foundation for the prediction and encoding of phase behaviour at the sequence level.

  5. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    Science.gov (United States)

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-06-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed `clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

  6. Improving the chemical shift dispersion of multidimensional NMR spectra of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Bermel, Wolfgang [Bruker BioSpin GmbH (Germany); Bruix, Marta [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain); Felli, Isabella C., E-mail: felli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Kumar, M.V. Vasantha [University of Florence, Magnetic Resonance Center (Italy); Pierattelli, Roberta, E-mail: pierattelli@cerm.unifi.it [University of Florence, Department of Chemistry ' Ugo Shiff' (Italy); Serrano, Soraya [Consejo Superior de Investigaciones Cientificas, Instituto de Quimica Fisica ' ' Rocasolano' ' (Spain)

    2013-03-15

    Intrinsically disordered proteins (IDPs) have recently attracted the attention of the scientific community challenging the well accepted structure-function paradigm. In the characterization of the dynamic features of proteins nuclear magnetic resonance spectroscopy (NMR) is a strategic tool of investigation. However the peculiar properties of IDPs, with the lack of a unique 3D structure and their high flexibility, have a strong impact on NMR observables (low chemical shift dispersion, efficient solvent exchange broadening) and thus on the quality of NMR spectra. Key aspects to be considered in the design of new NMR experiments optimized for the study of IDPs are discussed. A new experiment, based on direct detection of {sup 13}C{sup {alpha}}, is proposed.

  7. Exploring the psychosis functional connectome: aberrant intrinsic networks in schizophrenia and bipolar disorder.

    Science.gov (United States)

    Calhoun, Vince D; Sui, Jing; Kiehl, Kent; Turner, Jessica; Allen, Elena; Pearlson, Godfrey

    2011-01-01

    Intrinsic functional brain networks (INs) are regions showing temporal coherence with one another. These INs are present in the context of a task (as opposed to an undirected task such as rest), albeit modulated to a degree both spatially and temporally. Prominent networks include the default mode, attentional fronto-parietal, executive control, bilateral temporal lobe, and motor networks. The characterization of INs has recently gained considerable momentum, however; most previous studies evaluate only a small subset of the INs (e.g., default mode). In this paper we use independent component analysis to study INs decomposed from functional magnetic resonance imaging data collected in a large group of schizophrenia patients, healthy controls, and individuals with bipolar disorder, while performing an auditory oddball task. Schizophrenia and bipolar disorder share significant overlap in clinical symptoms, brain characteristics, and risk genes which motivates our goal of identifying whether functional imaging data can differentiate the two disorders. We tested for group differences in properties of all identified INs including spatial maps, spectra, and functional network connectivity. A small set of default mode, temporal lobe, and frontal networks with default mode regions appearing to play a key role in all comparisons. Bipolar subjects showed more prominent changes in ventromedial and prefrontal default mode regions whereas schizophrenia patients showed changes in posterior default mode regions. Anti-correlations between left parietal areas and dorsolateral prefrontal cortical areas were different in bipolar and schizophrenia patients and amplitude was significantly different from healthy controls in both patient groups. Patients exhibited similar frequency behavior across multiple networks with decreased low frequency power. In summary, a comprehensive analysis of INs reveals a key role for the default mode in both schizophrenia and bipolar disorder. PMID

  8. There is Diversity in Disorder-"In all Chaos there is a Cosmos, in all Disorder a Secret Order"

    DEFF Research Database (Denmark)

    Nielsen, Jakob T; Mulder, Frans A A

    2016-01-01

    The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part,...

  9. Identifying intrinsically disordered protein regions likely to undergo binding-induced helical transitions.

    Science.gov (United States)

    Glover, Karen; Mei, Yang; Sinha, Sangita C

    2016-10-01

    Many proteins contain intrinsically disordered regions (IDRs) lacking stable secondary and ordered tertiary structure. IDRs are often implicated in macromolecular interactions, and may undergo structural transitions upon binding to interaction partners. However, as binding partners of many protein IDRs are unknown, these structural transitions are difficult to verify and often are poorly understood. In this study we describe a method to identify IDRs that are likely to undergo helical transitions upon binding. This method combines bioinformatics analyses followed by circular dichroism spectroscopy to monitor 2,2,2-trifluoroethanol (TFE)-induced changes in secondary structure content of these IDRs. Our results demonstrate that there is no significant change in the helicity of IDRs that are not predicted to fold upon binding. IDRs that are predicted to fold fall into two groups: one group does not become helical in the presence of TFE and includes examples of IDRs that form β-strands upon binding, while the other group becomes more helical and includes examples that are known to fold into helices upon binding. Therefore, we propose that bioinformatics analyses combined with experimental evaluation using TFE may provide a general method to identify IDRs that undergo binding-induced disorder-to-helix transitions. PMID:27179590

  10. Effects of molecular crowding on the dynamics of intrinsically disordered proteins.

    Directory of Open Access Journals (Sweden)

    Elio A Cino

    Full Text Available Inside cells, the concentration of macromolecules can reach up to 400 g/L. In such crowded environments, proteins are expected to behave differently than in vitro. It has been shown that the stability and the folding rate of a globular protein can be altered by the excluded volume effect produced by a high density of macromolecules. However, macromolecular crowding effects on intrinsically disordered proteins (IDPs are less explored. These proteins can be extremely dynamic and potentially sample a wide ensemble of conformations under non-denaturing conditions. The dynamic properties of IDPs are intimately related to the timescale of conformational exchange within the ensemble, which govern target recognition and how these proteins function. In this work, we investigated the macromolecular crowding effects on the dynamics of several IDPs by measuring the NMR spin relaxation parameters of three disordered proteins (ProTα, TC1, and α-synuclein with different extents of residual structures. To aid the interpretation of experimental results, we also performed an MD simulation of ProTα. Based on the MD analysis, a simple model to correlate the observed changes in relaxation rates to the alteration in protein motions under crowding conditions was proposed. Our results show that 1 IDPs remain at least partially disordered despite the presence of high concentration of other macromolecules, 2 the crowded environment has differential effects on the conformational propensity of distinct regions of an IDP, which may lead to selective stabilization of certain target-binding motifs, and 3 the segmental motions of IDPs on the nanosecond timescale are retained under crowded conditions. These findings strongly suggest that IDPs function as dynamic structural ensembles in cellular environments.

  11. Native globular actin has a thermodynamically unstable quasi-stationary structure with elements of intrinsic disorder.

    Science.gov (United States)

    Kuznetsova, Irina M; Povarova, Olga I; Uversky, Vladimir N; Turoverov, Konstantin K

    2016-02-01

    The native form of globular actin, G-actin, is formed in vivo as a result of complex post-translational folding processes that require ATP energy expenditure and are assisted by the 70 kDa heat shock protein, prefoldin and chaperonin containing TCP-1. G-actin is stabilized by the binding of one ATP molecule and one Ca(2+) ion (or Mg(2+) in vivo). Chemical denaturants, heating or Ca(2+) removal transform native actin (N) into 'inactivated actin' (I), a compact oligomer comprising 14-16 subunits. Viscogenic and crowding agents slow this process but do not stop it. The lack of calcium in the solution accelerates the spontaneous N → I transition. Thus, native G-actin has a kinetically stable (as a result of the high free energy barrier between the N and I states) but thermodynamically unstable structure, which, in the absence of Ca(2+) or other bivalent metal ions, spontaneously converts to the thermodynamically stable I state. It was noted that native actin has much in common with intrinsically disordered proteins: it has functionally important disordered regions; it is constantly in complex with one of its numerous partners; and it plays key roles in many cellular processes, in a manner similar to disordered hub proteins. By analyzing actin folding in vivo and unfolding in vitro, we advanced the hypothesis that proteins in a native state may have a thermodynamically unstable quasi-stationary structure. The kinetically stable native state of these proteins appears forcibly under the influence of intracellular folding machinery. The denaturation of such proteins is always irreversible because the inactivated state, for which the structure is determined by the amino acid sequence of a protein, comprises the thermodynamically stable state under physiological conditions. PMID:26460158

  12. Microsecond molecular dynamics simulations of intrinsically disordered proteins involved in the oxidative stress response.

    Directory of Open Access Journals (Sweden)

    Elio A Cino

    Full Text Available Intrinsically disordered proteins (IDPs are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTα and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2, with a common binding partner, Kelch-like ECH-associated protein 1(Keap1, are essential for regulating cellular response to oxidative stress. Misregulation of this pathway can lead to neurodegenerative diseases, premature aging and cancer. In order to understand the mechanisms these two disordered proteins employ to bind to Keap1, we performed extensive 0.5-1.0 microsecond atomistic molecular dynamics (MD simulations and isothermal titration calorimetry experiments to investigate the structure/dynamics of free-state ProTα and Neh2 and their thermodynamics of bindings. The results show that in their free states, both ProTα and Neh2 have propensities to form bound-state-like β-turn structures but to different extents. We also found that, for both proteins, residues outside the Keap1-binding motifs may play important roles in stabilizing the bound-state-like structures. Based on our findings, we propose that the binding of disordered ProTα and Neh2 to Keap1 occurs synergistically via preformed structural elements (PSEs and coupled folding and binding, with a heavy bias towards PSEs, particularly for Neh2. Our results provide insights into the molecular mechanisms Neh2 and ProTα bind to Keap1, information that is useful for developing therapeutics to enhance the oxidative stress response.

  13. Maternal empathy, family chaos, and the etiology of borderline personality disorder.

    Science.gov (United States)

    Golomb, A; Ludolph, P; Westen, D; Block, M J; Maurer, P; Wiss, F C

    1994-01-01

    Psychoanalytic writers have traced the etiology of borderline personality disorder (BPD) to be a preoedipal disturbance in the mother-child relationship. Despite the prevalence of theories focusing on the role of mothering in the development of BPD, few empirical studies have tested the hypothesis that borderlines were the recipients of unempathic mothering. The current preliminary study compared 13 mothers of borderline adolescents with 13 mothers of normal adolescents. This study found that mothers of borderlines tended to conceive of their children egocentrically, as need-gratifying objects, rather than as individuals with distinct and evolving personalities. This study also found that the mothers of borderlines reported raising their daughters in extremely chaotic families struggling to cope with multiple hardships, including divorce and financial worries. The stressful environmental circumstances reported by the mothers likely affected the borderline daughters directly as well as the mothers' ability to parent effectively and empathically. The results of this study suggest that, as predicted by psychoanalytic theory, a problematic mother-child relationship may play a significant role in the genesis of borderline pathology; however, the life circumstances that contextualize the mother-child relationship also need to be considered when accounting for the etiology of BPD. PMID:8040554

  14. SASSIE: A program to study intrinsically disordered biological molecules and macromolecular ensembles using experimental scattering restraints

    Science.gov (United States)

    Curtis, Joseph E.; Raghunandan, Sindhu; Nanda, Hirsh; Krueger, Susan

    2012-02-01

    A program to construct ensembles of biomolecular structures that are consistent with experimental scattering data are described. Specifically, we generate an ensemble of biomolecular structures by varying sets of backbone dihedral angles that are then filtered using experimentally determined restraints to rapidly determine structures that have scattering profiles that are consistent with scattering data. We discuss an application of these tools to predict a set of structures for the HIV-1 Gag protein, an intrinsically disordered protein, that are consistent with small-angle neutron scattering experimental data. We have assembled these algorithms into a program called SASSIE for structure generation, visualization, and analysis of intrinsically disordered proteins and other macromolecular ensembles using neutron and X-ray scattering restraints. Program summaryProgram title: SASSIE Catalogue identifier: AEKL_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKL_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License v3 No. of lines in distributed program, including test data, etc.: 3 991 624 No. of bytes in distributed program, including test data, etc.: 826 Distribution format: tar.gz Programming language: Python, C/C++, Fortran Computer: PC/Mac Operating system: 32- and 64-bit Linux (Ubuntu 10.04, Centos 5.6) and Mac OS X (10.6.6) RAM: 1 GB Classification: 3 External routines: Python 2.6.5, numpy 1.4.0, swig 1.3.40, scipy 0.8.0, Gnuplot-py-1.8, Tcl 8.5, Tk 8.5, Mac installation requires aquaterm 1.0 (or X window system) and Xcode 3 development tools. Nature of problem: Open source software to generate structures of disordered biological molecules that subsequently allow for the comparison of computational and experimental results is limiting the use of scattering resources. Solution method: Starting with an all atom model of a protein, for example, users can input

  15. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR

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    Natsuko Goda

    2015-07-01

    Full Text Available Intrinsically disordered proteins (IDPs that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an “indirect/reflected” detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR. This approach employs a “chimeric membrane protein”-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding-fold domain (named NfeDC domain, connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.

  16. Structural and Functional Insights into the Cryoprotection of Membranes by the Intrinsically Disordered Dehydrins.

    Science.gov (United States)

    Clarke, Matthew W; Boddington, Kelly F; Warnica, Josephine M; Atkinson, John; McKenna, Sarah; Madge, Jeffrey; Barker, Christine H; Graether, Steffen P

    2015-11-01

    Dehydration can be due to desiccation caused by a lack of environmental water or to freezing caused by a lack of liquid water. Plants have evolved a large family of proteins called LEA (late embryogenesis abundant) proteins, which include the intrinsically disordered dehydrin (dehydration protein) family, to combat these abiotic stresses. Although transcription and translation studies have shown a correlation between dehydration stress and the presence of dehydrins, the biochemical mechanisms have remained somewhat elusive. We examine here the effect and structure of a small model dehydrin (Vitis riparia K2) on the protection of membranes from freeze-thaw stress. This protein is able to bind to liposomes containing phosphatidic acid and protect the liposomes from fusing after freeze-thaw treatment. The presence of K2 did not measurably affect liposome surface accessibility or lipid mobility but did lower its membrane transition temperature by 3 °C. Using sodium dodecyl sulfate as a membrane model, we examined the NMR structure of K2 in the presence and absence of the micelle. Biochemical and NMR experiments show that the conserved, lysine-rich segments are involved in the binding of the dehydrin to a membrane, whereas the poorly conserved φ segments play no role in binding or protection. PMID:26370084

  17. NS3 Protease from Hepatitis C Virus: Biophysical Studies on an Intrinsically Disordered Protein Domain

    Directory of Open Access Journals (Sweden)

    Adrian Velazquez-Campoy

    2013-06-01

    Full Text Available The nonstructural protein 3 (NS3 from the hepatitis C virus (HCV is responsible for processing the non-structural region of the viral precursor polyprotein in infected hepatic cells. NS3 protease activity, located at the N-terminal domain, is a zinc-dependent serine protease. A zinc ion, required for the hydrolytic activity, has been considered as a structural metal ion essential for the structural integrity of the protein. In addition, NS3 interacts with another cofactor, NS4A, an accessory viral protein that induces a conformational change enhancing the hydrolytic activity. Biophysical studies on the isolated protease domain, whose behavior is similar to that of the full-length protein (e.g., catalytic activity, allosteric mechanism and susceptibility to inhibitors, suggest that a considerable global conformational change in the protein is coupled to zinc binding. Zinc binding to NS3 protease can be considered as a folding event, an extreme case of induced-fit binding. Therefore, NS3 protease is an intrinsically (partially disordered protein with a complex conformational landscape due to its inherent plasticity and to the interaction with its different effectors. Here we summarize the results from a detailed biophysical characterization of this enzyme and present new experimental data.

  18. Looking at the carcinogenicity of human insulin analogues via the intrinsic disorder prism.

    Science.gov (United States)

    Redwan, Elrashdy M; Linjawi, Moustafa H; Uversky, Vladimir N

    2016-01-01

    Therapeutic insulin, in its native and biosynthetic forms as well as several currently available insulin analogues, continues to be the protein of most interest to researchers. From the time of its discovery to the development of modern insulin analogues, this important therapeutic protein has passed through several stages and product generations. Beside the well-known link between diabetes and cancer risk, the currently used therapeutic insulin analogues raised serious concerns due to their potential roles in cancer initiation and/or progression. It is possible that structural variations in some of the insulin analogues are responsible for the appearance of new oncogenic species with high binding affinity to the insulin-like growth factor 1 (IGF1) receptor. The question we are trying to answer in this work is: are there any specific features of the distribution of intrinsic disorder propensity within the amino acid sequences of insulin analogues that may provide an explanation for the carcinogenicity of the altered insulin protein? PMID:26983499

  19. Calcium ion binding properties and the effect of phosphorylation on the intrinsically disordered Starmaker protein.

    Science.gov (United States)

    Wojtas, Magdalena; Hołubowicz, Rafał; Poznar, Monika; Maciejewska, Marta; Ożyhar, Andrzej; Dobryszycki, Piotr

    2015-10-27

    Starmaker (Stm) is an intrinsically disordered protein (IDP) involved in otolith biomineralization in Danio rerio. Stm controls calcium carbonate crystal formation in vivo and in vitro. Phosphorylation of Stm affects its biomineralization properties. This study examined the effects of calcium ions and phosphorylation on the structure of Stm. We have shown that CK2 kinase phosphorylates 25 or 26 residues in Stm. Furthermore, we have demonstrated that Stm's affinity for calcium binding is dependent on its phosphorylation state. Phosphorylated Stm (StmP) has an estimated 30 ± 1 calcium binding sites per protein molecule with a dissociation constant (KD) of 61 ± 4 μM, while the unphosphorylated protein has 28 ± 3 sites and a KD of 210 ± 22 μM. Calcium ion binding induces a compaction of the Stm molecule, causing a significant decrease in its hydrodynamic radius and the formation of a secondary structure. The screening effect of Na(+) ions on calcium binding was also observed. Analysis of the hydrodynamic properties of Stm and StmP showed that Stm and StmP molecules adopt the structure of native coil-like proteins. PMID:26445027

  20. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

    Science.gov (United States)

    Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J; Zweckstetter, Markus; de Groot, Bert L; Grubmüller, Helmut

    2015-11-10

    Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles generated by eight all-atom empirical force fields against primary small-angle X-ray scattering (SAXS) and NMR data. Ensembles obtained with different force fields exhibit marked differences in chain dimensions, hydrogen bonding, and secondary structure content. These differences are unexpectedly large: changing the force field is found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performs best in this force field comparison: it has the lowest error in chemical shifts and J-couplings and agrees well with the SAXS data. A high population of left-handed α-helix is present in the CHARMM 36 ensemble, which is inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty is shown to be much smaller than the observed differences. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. PMID:26574339

  1. Hyperphosphorylation of intrinsically disordered tau protein induces an amyloidogenic shift in its conformational ensemble.

    Directory of Open Access Journals (Sweden)

    Shaolong Zhu

    Full Text Available Tau is an intrinsically disordered protein (IDP whose primary physiological role is to stabilize microtubules in neuronal axons at all stages of development. In Alzheimer's and other tauopathies, tau forms intracellular insoluble amyloid aggregates known as neurofibrillary tangles, a process that appears in many cases to be preceded by hyperphosphorylation of tau monomers. Understanding the shift in conformational bias induced by hyperphosphorylation is key to elucidating the structural factors that drive tau pathology, however, as an IDP, tau is not amenable to conventional structural characterization. In this work, we employ a straightforward technique based on Time-Resolved ElectroSpray Ionization Mass Spectrometry (TRESI-MS and Hydrogen/Deuterium Exchange (HDX to provide a detailed picture of residual structure in tau, and the shifts in conformational bias induced by hyperphosphorylation. By comparing the native and hyperphosphorylated ensembles, we are able to define specific conformational biases that can easily be rationalized as enhancing amyloidogenic propensity. Representative structures for the native and hyperphosphorylated tau ensembles were generated by refinement of a broad sample of conformations generated by low-computational complexity modeling, based on agreement with the TRESI-HDX profiles.

  2. Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder.

    Directory of Open Access Journals (Sweden)

    James J Valdés

    Full Text Available BACKGROUND: A salivary proteome-transcriptome project on the hard tick Ixodes scapularis revealed that Kunitz peptides are the most abundant salivary proteins. Ticks use Kunitz peptides (among other salivary proteins to combat host defense mechanisms and to obtain a blood meal. Most of these Kunitz peptides, however, remain functionally uncharacterized, thus limiting our knowledge about their biochemical interactions. RESULTS: We discovered an unusual cysteine motif in a Kunitz peptide. This peptide inhibits several serine proteases with high affinity and was named tryptogalinin due to its high affinity for β-tryptase. Compared with other functionally described peptides from the Acari subclass, we showed that tryptogalinin is phylogenetically related to a Kunitz peptide from Rhipicephalus appendiculatus, also reported to have a high affinity for β-tryptase. Using homology-based modeling (and other protein prediction programs we were able to model and explain the multifaceted function of tryptogalinin. The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases. CONCLUSIONS: By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.

  3. Prediction of Spontaneous Protein Deamidation from Sequence-Derived Secondary Structure and Intrinsic Disorder.

    Directory of Open Access Journals (Sweden)

    J Ramiro Lorenzo

    Full Text Available Asparagine residues in proteins undergo spontaneous deamidation, a post-translational modification that may act as a molecular clock for the regulation of protein function and turnover. Asparagine deamidation is modulated by protein local sequence, secondary structure and hydrogen bonding. We present NGOME, an algorithm able to predict non-enzymatic deamidation of internal asparagine residues in proteins in the absence of structural data, using sequence-based predictions of secondary structure and intrinsic disorder. Compared to previous algorithms, NGOME does not require three-dimensional structures yet yields better predictions than available sequence-only methods. Four case studies of specific proteins show how NGOME may help the user identify deamidation-prone asparagine residues, often related to protein gain of function, protein degradation or protein misfolding in pathological processes. A fifth case study applies NGOME at a proteomic scale and unveils a correlation between asparagine deamidation and protein degradation in yeast. NGOME is freely available as a webserver at the National EMBnet node Argentina, URL: http://www.embnet.qb.fcen.uba.ar/ in the subpage "Protein and nucleic acid structure and sequence analysis".

  4. Homodimerization propensity of the intrinsically disordered N-terminal domain of Ultraspiracle from Aedes aegypti.

    Science.gov (United States)

    Pieprzyk, Joanna; Zbela, Agnieszka; Jakób, Michał; Ożyhar, Andrzej; Orłowski, Marek

    2014-06-01

    The mosquito Aedes aegypti is the principal vector of dengue, one of the most devastating arthropod-borne viral infections in humans. The isoform specific A/B region, called the N-terminal domain (NTD), is hypervariable in sequence and length and is poorly conserved within the Ultraspiracle (Usp) family. The Usp protein together with ecdysteroid receptor (EcR) forms a heterodimeric complex. Up until now, there has been little data on the molecular properties of the isolated Usp-NTD. Here, we describe the biochemical and biophysical properties of the recombinant NTD of the Usp isoform B (aaUsp-NTD) from A. aegypti. These results, in combination with in silico bioinformatics approaches, indicate that aaUsp-NTD exhibits properties of an intrinsically disordered protein (IDP). We also present the first experimental evidence describing the dimerization propensity of the isolated NTD of Usp. These characteristics also appear for other members of the Usp family in different species, for example, in the Usp-NTD from Drosophila melanogaster and Bombyx mori. However, aaUsp-NTD exhibits the strongest homodimerization potential. We postulate that the unique dimerization of the NTD might be important for Usp function by providing an additional platform for interactions, in addition to the nuclear receptor superfamily dimerization via DNA binding domains and ligand binding domains that has already been extensively documented. Furthermore, the unique NTD-NTD interaction that was observed might contribute new insight into the dimerization propensities of nuclear receptors. PMID:24704038

  5. Age-related changes in intrinsic function of the superior temporal sulcus in autism spectrum disorders.

    Science.gov (United States)

    Alaerts, Kaat; Nayar, Kritika; Kelly, Clare; Raithel, Jessica; Milham, Michael P; Di Martino, Adriana

    2015-10-01

    Currently, the developmental trajectories of neural circuits implicated in autism spectrum disorders (ASD) are largely unknown. Here, we specifically focused on age-related changes in the functional circuitry of the posterior superior temporal sulcus (pSTS), a key hub underlying social-cognitive processes known to be impaired in ASD. Using a cross-sectional approach, we analysed resting-state functional magnetic resonance imaging (fMRI) data collected from children, adolescents and adults available through the autism brain imaging data exchange repository [n = 106 with ASD and n = 109 typical controls (TC), ages 7-30 years]. The observed age-related changes of pSTS intrinsic functional connectivity (iFC) suggest that no single developmental pattern characterizes ASD. Instead, pSTS circuitry displayed a complex developmental picture, with some functional circuits showing patterns consistent with atypical development in ASD relative to TC (pSTS-iFC with fusiform gyrus and angular gyrus) and others showing delayed maturation (pSTS-iFC with regions of the action perception network). Distinct developmental trajectories in different functional circuits in ASD likely reflect differential age-related changes in the socio-cognitive processes they underlie. Increasing insight on these mechanisms is a critical step in the development of age-specific interventions in ASD. PMID:25809403

  6. Proteins with Intrinsically Disordered Domains Are Preferentially Recruited to Polyglutamine Aggregates.

    Directory of Open Access Journals (Sweden)

    Maggie P Wear

    Full Text Available Intracellular protein aggregation is the hallmark of several neurodegenerative diseases. Aggregates formed by polyglutamine (polyQ-expanded proteins, such as Huntingtin, adopt amyloid-like structures that are resistant to denaturation. We used a novel purification strategy to isolate aggregates formed by human Huntingtin N-terminal fragments with expanded polyQ tracts from both yeast and mammalian (PC-12 cells. Using mass spectrometry we identified the protein species that are trapped within these polyQ aggregates. We found that proteins with very long intrinsically-disordered (ID domains (≥ 100 amino acids and RNA-binding proteins were disproportionately recruited into aggregates. The removal of the ID domains from selected proteins was sufficient to eliminate their recruitment into polyQ aggregates. We also observed that several neurodegenerative disease-linked proteins were reproducibly trapped within the polyQ aggregates purified from mammalian cells. Many of these proteins have large ID domains and are found in neuronal inclusions in their respective diseases. Our study indicates that neurodegenerative disease-associated proteins are particularly vulnerable to recruitment into polyQ aggregates via their ID domains. Also, the high frequency of ID domains in RNA-binding proteins may explain why RNA-binding proteins are frequently found in pathological inclusions in various neurodegenerative diseases.

  7. Simple biophysics underpins collective conformations of the intrinsically disordered proteins of the Nuclear Pore Complex

    Science.gov (United States)

    Vovk, Andrei; Gu, Chad; Opferman, Michael G; Kapinos, Larisa E; Lim, Roderick YH; Coalson, Rob D; Jasnow, David; Zilman, Anton

    2016-01-01

    Nuclear Pore Complexes (NPCs) are key cellular transporter that control nucleocytoplasmic transport in eukaryotic cells, but its transport mechanism is still not understood. The centerpiece of NPC transport is the assembly of intrinsically disordered polypeptides, known as FG nucleoporins, lining its passageway. Their conformations and collective dynamics during transport are difficult to assess in vivo. In vitro investigations provide partially conflicting results, lending support to different models of transport, which invoke various conformational transitions of the FG nucleoporins induced by the cargo-carrying transport proteins. We show that the spatial organization of FG nucleoporin assemblies with the transport proteins can be understood within a first principles biophysical model with a minimal number of key physical variables, such as the average protein interaction strengths and spatial densities. These results address some of the outstanding controversies and suggest how molecularly divergent NPCs in different species can perform essentially the same function. DOI: http://dx.doi.org/10.7554/eLife.10785.001 PMID:27198189

  8. BOOK REVIEW: Critical Phenomena in Natural Sciences: Chaos, Fractals, Selforganization and Disorder: Concepts and Tools

    Science.gov (United States)

    Franz, S.

    2004-10-01

    complicated concepts are always explained by means of simple examples, important results are often mentioned but not derived or discussed in depth. Most of the time this style of exposition manages to successfully convey the essential information, other times unfortunately, e.g. in the case of the chapter on disordered systems, the presentation appears rather superficial. This is the price we pay for a book covering an impressively vast subject area and the huge bibliography (more than 1000 references) furnishes a necessary guide for acquiring the working knowledge of the subject covered. I would recommend it to teachers planning introductory courses on the field of complex systems and to researchers wanting to learn about an area of great contemporary interest.

  9. Critical Phenomena in Natural Sciences: Chaos, Fractals, Selforganization and Disorder: Concepts and Tools

    International Nuclear Information System (INIS)

    complicated concepts are always explained by means of simple examples, important results are often mentioned but not derived or discussed in depth. Most of the time this style of exposition manages to successfully convey the essential information, other times unfortunately, e.g. in the case of the chapter on disordered systems, the presentation appears rather superficial. This is the price we pay for a book covering an impressively vast subject area and the huge bibliography (more than 1000 references) furnishes a necessary guide for acquiring the working knowledge of the subject covered. I would recommend it to teachers planning introductory courses on the field of complex systems and to researchers wanting to learn about an area of great contemporary interest. (book review)

  10. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues.

    Science.gov (United States)

    Das, Rahul K; Pappu, Rohit V

    2013-08-13

    The functions of intrinsically disordered proteins (IDPs) are governed by relationships between information encoded in their amino acid sequences and the ensembles of conformations that they sample as autonomous units. Most IDPs are polyampholytes, with sequences that include both positively and negatively charged residues. Accordingly, we focus here on the sequence-ensemble relationships of polyampholytic IDPs. The fraction of charged residues discriminates between weak and strong polyampholytes. Using atomistic simulations, we show that weak polyampholytes form globules, whereas the conformational preferences of strong polyampholytes are determined by a combination of fraction of charged residues values and the linear sequence distributions of oppositely charged residues. We quantify the latter using a patterning parameter κ that lies between zero and one. The value of κ is low for well-mixed sequences, and in these sequences, intrachain electrostatic repulsions and attractions are counterbalanced, leading to the unmasking of preferences for conformations that resemble either self-avoiding random walks or generic Flory random coils. Segregation of oppositely charged residues within linear sequences leads to high κ-values and preferences for hairpin-like conformations caused by long-range electrostatic attractions induced by conformational fluctuations. We propose a scaling theory to explain the sequence-encoded conformational properties of strong polyampholytes. We show that naturally occurring strong polyampholytes have low κ-values, and this feature implies a selection for random coil ensembles. The design of sequences with different κ-values demonstrably alters the conformational preferences of polyampholytic IDPs, and this ability could become a useful tool for enabling direct inquiries into connections between sequence-ensemble relationships and functions of IDPs. PMID:23901099

  11. Subregional differences in intrinsic amygdala hyperconnectivity and hypoconnectivity in autism spectrum disorder.

    Science.gov (United States)

    Kleinhans, Natalia M; Reiter, Maya A; Neuhaus, Emily; Pauley, Greg; Martin, Nathalie; Dager, Stephen; Estes, Annette

    2016-07-01

    The amygdala is a complex structure with distinct subregions and dissociable functional networks. The laterobasal subregion of the amygdala is hypothesized to mediate the presentation and severity of autism symptoms, although very little data are available regarding amygdala dysfunction at the subregional level. In this study, we investigated the relationship between abnormal amygdalar intrinsic connectivity, autism symptom severity, and anxiety and depressive symptoms. We collected resting state fMRI data on 31 high functioning adolescents and adults with autism spectrum disorder and 38 typically developing (TD) controls aged 14-45. Twenty-five participants with ASD and 28 TD participants were included in the final analyses. ASD participants were administered the Autism Diagnostic Interview-Revised and the Autism Diagnostic Observation Schedule. Adult participants were administered the Beck Depression Inventory II and the Beck Anxiety Inventory. Functional connectivity analyses were conducted from three amygdalar subregions: centromedial (CM), laterobasal (LB) and superficial (SF). In addition, correlations with the behavioral measures were tested in the adult participants. In general, the ASD group showed significantly decreased connectivity from the LB subregion and increased connectivity from the CM and SF subregions compared to the TD group. We found evidence that social symptoms are primarily associated with under-connectivity from the LB subregion whereas over-connectivity and under-connectivity from the CM, SF and LB subregions are related to co-morbid depression and anxiety in ASD, in brain regions that were distinct from those associated with social dysfunction, and in different patterns than were observed in mildly symptomatic TD participants. Our findings provide new evidence for functional subregional differences in amygdala pathophysiology in ASD. Autism Res 2016, 9: 760-772. © 2015 International Society for Autism Research, Wiley Periodicals, Inc

  12. On the importance of polar interactions for complexes containing intrinsically disordered proteins.

    Directory of Open Access Journals (Sweden)

    Eric T C Wong

    Full Text Available There is a growing recognition for the importance of proteins with large intrinsically disordered (ID segments in cell signaling and regulation. ID segments in these proteins often harbor regions that mediate molecular recognition. Coupled folding and binding of the recognition regions has been proposed to confer high specificity to interactions involving ID segments. However, researchers recently questioned the origin of the interaction specificity of ID proteins because of the overrepresentation of hydrophobic residues in their interaction interfaces. Here, we focused on the role of polar and charged residues in interactions mediated by ID segments. Making use of the extended nature of most ID segments when in complex with globular proteins, we first identified large numbers of complexes between globular proteins and ID segments by using radius-of-gyration-based selection criteria. Consistent with previous studies, we found the interfaces of these complexes to be enriched in hydrophobic residues, and that these residues contribute significantly to the stability of the interaction interface. However, our analyses also show that polar interactions play a larger role in these complexes than in structured protein complexes. Computational alanine scanning and salt-bridge analysis indicate that interfaces in ID complexes are highly complementary with respect to electrostatics, more so than interfaces of globular proteins. Follow-up calculations of the electrostatic contributions to the free energy of binding uncovered significantly stronger Coulombic interactions in complexes harbouring ID segments than in structured protein complexes. However, they are counter-balanced by even higher polar-desolvation penalties. We propose that polar interactions are a key contributing factor to the observed high specificity of ID segment-mediated interactions.

  13. Phosphorylation Regulates the Bound Structure of an Intrinsically Disordered Protein: The p53-TAZ2 Case.

    Directory of Open Access Journals (Sweden)

    Raúl Esteban Ithuralde

    Full Text Available Disordered regions and Intrinsically Disordered Proteins (IDPs are involved in critical cellular processes and may acquire a stable three-dimensional structure only upon binding to their partners. IDPs may follow a folding-after-binding process, known as induced folding, or a folding-before-binding process, known as conformational selection. The transcription factor p53 is involved in the regulation of cellular events that arise upon stress or DNA damage. The p53 domain structure is composed of an N-terminal transactivation domain (p53TAD, a DNA Binding Domain and a tetramerization domain. The activity of TAD is tightly regulated by interactions with cofactors, inhibitors and phosphorylation. To initiate transcription, p53TAD binds to the TAZ2 domain of CBP, a co-transcription factor, and undergoes a folding and binding process, as revealed by the recent NMR structure of the complex. The activity of p53 is regulated by phosphorylation at multiple sites on the TAD domain and recent studies have shown that modifications at three residues affect the binding towards TAZ2. However, we still do not know how these phosphorylations affect the structure of the bound state and, therefore, how they regulate the p53 function. In this work, we have used computational simulations to understand how phosphorylation affects the structure of the p53TAD:TAZ2 complex and regulates the recognition mechanism. Phosphorylation has been proposed to enhance binding by direct interaction with the folded protein or by changing the unbound conformation of IDPs, for example by pre-folding the protein favoring the recognition mechanism. Here, we show an interesting turn in the p53 case: phosphorylation mainly affects the bound structure of p53TAD, highlighting the complexity of IDP protein-protein interactions. Our results are in agreement with previous experimental studies, allowing a clear picture of how p53 is regulated by phosphorylation and giving new insights into how

  14. A comparative study of the relationship between protein structure and beta-aggregation in globular and intrinsically disordered proteins

    DEFF Research Database (Denmark)

    Linding, Rune; Schymkowitz, Joost; Rousseau, Frederic;

    2004-01-01

    solubility problems. Further, some IDPs such as the human prion protein, synuclein and Tau protein are related to major protein conformational diseases. However, this scenario contrasts with the large number of unstructured proteins identified, especially in higher eukaryotes, and the fact that the......A growing number of proteins are being identified that are biologically active though intrinsically disordered, in sharp contrast with the classic notion that proteins require a well-defined globular structure in order to be functional. At the same time recent work showed that aggregation and...... amyloidosis are initiated in amino acid sequences that have specific physico-chemical properties in terms of secondary structure propensities, hydrophobicity and charge. In intrinsically disordered proteins (IDPs) such sequences would be almost exclusively solvent-exposed and therefore cause serious...

  15. The Intracellular Distal Tail of the Na+/H+ Exchanger NHE1 Is Intrinsically Disordered

    DEFF Research Database (Denmark)

    Nørholm, Ann-Beth; Hendus-Altenburger, Ruth; Bjerre, Gabriel;

    2011-01-01

    dysfunction is implicated in several clinically important diseases. This study shows, for the first time for any carrier protein, that the distal part of the C-terminal intracellular tail (the cdt, residues V686-Q815) from human (h) NHE1 is intrinsically disordered. Further, we experimentally demonstrated the...... disrupted the putative binding feature. When this mutant NHE1 was expressed in full length NHE1 in AP1 cells, it exhibited impaired trafficking to the plasma membrane. This study demonstrated that the distal regulatory domain of NHE1 is intrinsically disordered yet contains conserved regions of transient...... structure. We suggest that normal NHE1 function depends on a protein recognition element within the ID region that may be linked to NHE1 trafficking via an acidic ER export motif....

  16. The structural basis for the intrinsic disorder of the actin filament: the "lateral slipping" model.

    Science.gov (United States)

    Bremer, A; Millonig, R C; Sütterlin, R; Engel, A; Pollard, T D; Aebi, U

    1991-11-01

    contributes to the outer part of the massive base. Quantitative evaluation of successive crossover spacings along individual F-actin filaments revealed the deviations from the mean repeat to be compensatory, i.e., short crossovers frequently followed long ones and vice versa. The variable crossover spacings and diameter of the F-actin filament together with the local unraveling of the two long-pitch helical strands are explained in terms of varying amounts of compensatory "lateral slipping" of the two strands past each other roughly perpendicular to the filament axis. This intrinsic disorder of the actin filament may enable the actin moiety to play a more active role in actin-myosin-based force generation than merely act as a rigid passive cable as has hitherto been assumed. PMID:1918159

  17. Biochemical and Molecular Characterization of a Novel Cu/Zn Superoxide Dismutase from Amaranthus hypochondriacus L.: an Intrinsically Disordered Protein.

    Science.gov (United States)

    Montero-Morán, Gabriela M; Sampedro, José G; Saab-Rincón, Gloria; Cervantes-González, Miguel A; Huerta-Ocampo, José Á; De León-Rodríguez, Antonio; Barba de la Rosa, Ana P

    2015-08-01

    A novel Cu/ZnSOD from Amaranthus hypochondriacus was cloned, expressed, and characterized. Nucleotide sequence analysis showed an open reading frame (ORF) of 456 bp, which was predicted to encode a 15.6-kDa molecular weight protein with a pI of 5.4. Structural analysis showed highly conserved amino acid residues involved in Cu/Zn binding. Recombinant amaranth superoxide dismutase (rAhSOD) displayed more than 50 % of catalytic activity after incubation at 100 °C for 30 min. In silico analysis of Amaranthus hypochondriacus SOD (AhSOD) amino acid sequence for globularity and disorder suggested that this protein is mainly disordered; this was confirmed by circular dichroism, which showed the lack of secondary structure. Intrinsic fluorescence studies showed that rAhSOD undergoes conformational changes in two steps by the presence of Cu/Zn, which indicates the presence of two binding sites displaying different affinities for metals ions. Our results show that AhSOD could be classified as an intrinsically disordered protein (IDP) that is folded when metals are bound and with high thermal stability. PMID:26129702

  18. Phosphoproteomic analysis reveals major default phosphorylation sites outside long intrinsically disordered regions of Arabidopsis plasma membrane proteins

    Directory of Open Access Journals (Sweden)

    Nespoulous Claude

    2012-10-01

    Full Text Available Abstract Background Genome-wide statistics established that long intrinsically disordered regions (over 30 residues are predicted in a large part of proteins in all eukaryotes, with a higher ratio in trans-membrane proteins. At functional level, such unstructured and flexible regions were suggested for years to favour phosphorylation events. In plants, despite increasing evidence of the regulation of transport and signalling processes by phosphorylation events, only few data are available without specific information regarding plasma membrane proteins, especially at proteome scale. Results Using a dedicated phosphoproteomic workflow, 75 novel and unambiguous phosphorylation sites were identified in Arabidopsis plasma membrane. Bioinformatics analysis showed that this new dataset concerned mostly integral proteins involved in key functions of the plasma membrane (such as transport and signal transduction, including protein phosphorylation. It thus expanded by 15% the directory of phosphosites previously characterized in signalling and transport proteins. Unexpectedly, 66% of phosphorylation sites were predicted to be located outside long intrinsically disordered regions. This result was further corroborated by analysis of publicly available data for the plasma membrane. Conclusions The new phosphoproteomics data presented here, with published datasets and functional annotation, suggest a previously unexpected topology of phosphorylation in the plant plasma membrane proteins. The significance of these new insights into the so far overlooked properties of the plant plasma membrane phosphoproteome and the long disordered regions is discussed.

  19. Dynamics of GCN4 facilitate DNA interaction: a model-free analysis of an intrinsically disordered region.

    Science.gov (United States)

    Gill, Michelle L; Byrd, R Andrew; Palmer Iii, Arthur G

    2016-02-17

    Intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered regions (IDRs) are known to play important roles in regulatory and signaling pathways. A critical aspect of these functions is the ability of IDP/IDRs to form highly specific complexes with target molecules. However, elucidation of the contributions of conformational dynamics to function has been limited by challenges associated with structural heterogeneity of IDP/IDRs. Using NMR spin relaxation parameters ((15)N R1, (15)N R2, and {(1)H}-(15)N heteronuclear NOE) collected at four static magnetic fields ranging from 14.1 to 21.1 T, we have analyzed the backbone dynamics of the basic leucine-zipper (bZip) domain of the Saccharomyces cerevisiae transcription factor GCN4, whose DNA binding domain is intrinsically disordered in the absence of DNA substrate. We demonstrate that the extended model-free analysis can be applied to proteins with IDRs such as apo GCN4 and that these results significantly extend previous NMR studies of GCN4 dynamics performed using a single static magnetic field of 11.74 T [Bracken, et al., J. Mol. Biol., 1999, 285, 2133-2146] and correlate well with molecular dynamics simulations [Robustelli, et al., J. Chem. Theory Comput., 2013, 9, 5190-5200]. In contrast to the earlier work, data at multiple static fields allows the time scales of internal dynamics of GCN4 to be reliably quantified. Large amplitude dynamic fluctuations in the DNA-binding region have correlation times (τs ≈ 1.4-2.5 ns) consistent with a two-step mechanism in which partially ordered bZip conformations of GCN4 form initial encounter complexes with DNA and then rapidly rearrange to the high affinity state with fully formed basic region recognition helices. PMID:26661739

  20. CHAOS IN ECONOMY (COMMODITIES

    Directory of Open Access Journals (Sweden)

    A. Bonatto

    2015-06-01

    Full Text Available Chaos is based on nonlinear phenomena occurring everywhere, but it brings stability and its own structure. Many are the linear realities, but there are phenomena to which mathematical systems do not describe acceptably. Charting these relationships is challenging to obtain a representative model of reality. In the chaos, a small disturbance will amplify, and initially close trajectories diverge. The instability leads to new aspects. This helps in the process of modeling for the study of simulations that are applied in the financial and economic fields, showing that the market continues to disorder in an organized manner. Research in the last 25 years focus on the risk and volatility of the behavior of commodity prices. The analysis and forecast of price behavior in commodity markets are relevant both for producers, cooperatives and industries and for global financial markets. These applications aim to enable projections of future commodity prices, improving decision-making in the future. In modeling commodity time series we must take into account several factors such as seasonality in prices due to fluctuations in supply and demand during periods of crop and season. The analysis of the behavior of prices of an asset is important for predicting future revenue, past behavior analysis of a series of prices and study of the historical price of a product. That's one reason the applicability of chaos theory: the ability to identify and explain fluctuations in the markets that appear to be random, but actually are not.

  1. Intrinsic Functional Connectivity of Amygdala-Based Networks in Adolescent Generalized Anxiety Disorder

    Science.gov (United States)

    Roy, Amy K.; Fudge, Julie L.; Kelly, Clare; Perry, Justin S. A.; Daniele, Teresa; Carlisi, Christina; Benson, Brenda; Castellanos, F. Xavier; Milham, Michael P.; Pine, Daniel S.; Ernst, Monique

    2013-01-01

    Objective: Generalized anxiety disorder (GAD) typically begins during adolescence and can persist into adulthood. The pathophysiological mechanisms underlying this disorder remain unclear. Recent evidence from resting state functional magnetic resonance imaging (R-fMRI) studies in adults suggests disruptions in amygdala-based circuitry; the…

  2. Exploring the Psychosis Functional Connectome: Aberrant Intrinsic Networks in Schizophrenia and Bipolar Disorder

    OpenAIRE

    Calhoun, Vince D.; Sui, Jing; Kiehl, Kent; Turner, Jessica; Allen, Elena; Pearlson, Godfrey

    2012-01-01

    Intrinsic functional brain networks (INs) are regions showing temporal coherence with one another. These INs are present in the context of a task (as opposed to an undirected task such as rest), albeit modulated to a degree both spatially and temporally. Prominent networks include the default mode, attentional fronto-parietal, executive control, bilateral temporal lobe, and motor networks. The characterization of INs has recently gained considerable momentum, however; most previous studies ev...

  3. Exploring the psychosis functional connectome: aberrant intrinsic networks in schizophrenia and bipolar disorder

    OpenAIRE

    VinceDCalhoun; GodfreyPearlson

    2012-01-01

    Intrinsic functional brain networks (INs) are regions showing temporal coherence with one another. These INs are present in the context of a task (as opposed to an undirected task such as rest), albeit modulated to a degree both spatially and temporally. Prominent networks include the default mode, attentional fronto-parietal, executive control, bilateral temporal lobe and motor networks. The characterization of INs has recently gained considerable momentum, however; most previous studies eva...

  4. Actinidia DRM1 - An Intrinsically Disordered Protein Whose mRNA Expression Is Inversely Correlated with Spring Budbreak in Kiwifruit

    Science.gov (United States)

    Wood, Marion; Rae, Georgina M.; Wu, Rong-Mei; Walton, Eric F.; Xue, Bin; Hellens, Roger P.; Uversky, Vladimir N.

    2013-01-01

    Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein levels. It is predicted to be an intrinsically disordered protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia. PMID:23516402

  5. Discriminating binding mechanisms of an intrinsically disordered protein via a multi-state coarse-grained model

    Energy Technology Data Exchange (ETDEWEB)

    Knott, Michael [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Best, Robert B., E-mail: robertbe@helix.nih.gov [Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW (United Kingdom); Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520 (United States)

    2014-05-07

    Many proteins undergo a conformational transition upon binding to their cognate binding partner, with intrinsically disordered proteins (IDPs) providing an extreme example in which a folding transition occurs. However, it is often not clear whether this occurs via an “induced fit” or “conformational selection” mechanism, or via some intermediate scenario. In the first case, transient encounters with the binding partner favour transitions to the bound structure before the two proteins dissociate, while in the second the bound structure must be selected from a subset of unbound structures which are in the correct state for binding, because transient encounters of the incorrect conformation with the binding partner are most likely to result in dissociation. A particularly interesting situation involves those intrinsically disordered proteins which can bind to different binding partners in different conformations. We have devised a multi-state coarse-grained simulation model which is able to capture the binding of IDPs in alternate conformations, and by applying it to the binding of nuclear coactivator binding domain (NCBD) to either ACTR or IRF-3 we are able to determine the binding mechanism. By all measures, the binding of NCBD to either binding partner appears to occur via an induced fit mechanism. Nonetheless, we also show how a scenario closer to conformational selection could arise by choosing an alternative non-binding structure for NCBD.

  6. There is Diversity in Disorder—“In all Chaos there is a Cosmos, in all Disorder a Secret Order”

    Science.gov (United States)

    Nielsen, Jakob T.; Mulder, Frans A. A.

    2016-01-01

    The protein universe consists of a continuum of structures ranging from full order to complete disorder. As the structured part of the proteome has been intensively studied, stably folded proteins are increasingly well documented and understood. However, proteins that are fully, or in large part, disordered are much less well characterized. Here we collected NMR chemical shifts in a small database for 117 protein sequences that are known to contain disorder. We demonstrate that NMR chemical shift data can be brought to bear as an exquisite judge of protein disorder at the residue level, and help in validation. With the help of secondary chemical shift analysis we demonstrate that the proteins in the database span the full spectrum of disorder, but still, largely segregate into two classes; disordered with small segments of order scattered along the sequence, and structured with small segments of disorder inserted between the different structured regions. A detailed analysis reveals that the distribution of order/disorder along the sequence shows a complex and asymmetric distribution, that is highly protein-dependent. Access to ratified training data further suggests an avenue to improving prediction of disorder from sequence. PMID:26904549

  7. Protein intrinsic disorder in Arabidopsis NAC transcription factors

    DEFF Research Database (Denmark)

    O'Shea, Charlotte; Jensen, Mikael Kryger; Stender, Emil G.P.;

    2015-01-01

    transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies...

  8. Aberrant Intrinsic Connectivity of Hippocampus and Amygdala Overlap in the Fronto-Insular and Dorsomedial-Prefrontal Cortex in Major Depressive Disorder

    OpenAIRE

    Tahmasian, Masoud; Knight, David C.; Manoliu, Andrei; Schwerthöffer, Dirk; Scherr, Martin; Meng, Chun; Shao, Junming; Peters, Henning; Doll, Anselm; Khazaie, Habibolah; Drzezga, Alexander; Bäuml, Josef; Zimmer, Claus; Förstl, Hans; Wohlschläger, Afra M.

    2013-01-01

    Neuroimaging studies of major depressive disorder (MDD) have consistently observed functional and structural changes of the hippocampus (HP) and amygdale (AY). Thus, these brain regions appear to be critical elements of the pathophysiology of MDD. The HP and AY directly interact and show broad and overlapping intrinsic functional connectivity (iFC) to other brain regions. Therefore, we hypothesized the HP and AY would show a corresponding pattern of aberrant intrinsic connectivity in MDD. Res...

  9. Solvent effects in the helix-coil transition model can explain the unusual biophysics of intrinsically disordered proteins

    Science.gov (United States)

    Badasyan, Artem; Mamasakhlisov, Yevgeni Sh.; Podgornik, Rudolf; Parsegian, V. Adrian

    2015-07-01

    We analyze a model statistical description of the polypeptide chain helix-coil transition, where we take into account the specificity of its primary sequence, as quantified by the phase space volume ratio of the number of all accessible states to the number corresponding to a helical conformation. The resulting transition phase diagram is then juxtaposed with the unusual behavior of the secondary structures in Intrinsically Disordered Proteins (IDPs) and a number of similarities are observed, even if the protein folding is a more complex transition than the helix-coil transition. In fact, the deficit in bulky and hydrophobic amino acids observed in IDPs, translated into larger values of phase space volume, allows us to locate the region in parameter space of the helix-coil transition that would correspond to the secondary structure transformations that are intrinsic to conformational transitions in IDPs and that is characterized by a modified phase diagram when compared to globular proteins. Here, we argue how the nature of this modified phase diagram, obtained from a model of the helix-coil transition in a solvent, would illuminate the turned-out response of IDPs to the changes in the environment conditions that follow straightforwardly from the re-entrant (cold denaturation) branch in their folding phase diagram.

  10. Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

    Directory of Open Access Journals (Sweden)

    Omar Awile

    Full Text Available The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.

  11. IDPT: Insights into potential intrinsically disordered proteins through transcriptomic analysis of genes for prostate carcinoma epigenetic data.

    Science.gov (United States)

    Mallik, Saurav; Sen, Sagnik; Maulik, Ujjwal

    2016-07-15

    Involvement of intrinsically disordered proteins (IDPs) with various dreadful diseases like cancer is an interesting research topic. In order to gain novel insights into the regulation of IDPs, in this article, we perform a transcriptomic analysis of mRNAs (genes) for transcripts encoding IDPs on a human multi-omics prostate carcinoma dataset having both gene expression and methylation data. In this regard, firstly the genes that consist of both the expression and methylation data, and that are corresponding to the cancer-related prostate-tissue-specific disordered proteins of MobiDb database, are selected. We apply standard t-test for determining differentially expressed genes as well as differentially methylated genes. A network having these genes and their targeter miRNAs from Diana Tarbase v7.0 database and corresponding Transcription Factors from TRANSFAC and ITFP databases, is then built. Thereafter, we perform literature search, and KEGG pathway and Gene Ontology analyses using DAVID database. Finally, we report several significant potential gene-markers (with the corresponding IDPs) that have inverse relationship between differential expression and methylation patterns, and that are hub genes of the TF-miRNA-gene network. PMID:27060408

  12. Membrane binding mode of intrinsically disordered cytoplasmic domains of T cell receptor signaling subunits depends on lipid composition

    International Nuclear Information System (INIS)

    Intrinsically disordered cytoplasmic domains of T cell receptor (TCR) signaling subunits including ζcyt and CD3εcyt all contain one or more copies of an immunoreceptor tyrosine-based activation motif (ITAM), tyrosine residues of which are phosphorylated upon receptor triggering. Membrane binding-induced helical folding of ζcyt and CD3εcyt ITAMs is thought to control TCR activation. However, the question whether or not lipid binding of ζcyt and CD3εcyt is necessarily accompanied by a folding transition of ITAMs remains open. In this study, we investigate whether the membrane binding mechanisms of ζcyt and CD3εcyt depend on the membrane model used. Circular dichroic and fluorescence data indicate that binding of ζcyt and CD3εcyt to detergent micelles and unstable vesicles is accompanied by a disorder-to-order transition, whereas upon binding to stable vesicles these proteins remain unfolded. Using electron microscopy and dynamic light scattering, we show that upon protein binding, unstable vesicles fuse and rupture. In contrast, stable vesicles remain intact under these conditions. This suggests different membrane binding modes for ζcyt and CD3εcyt depending on the bilayer stability: (1) coupled binding and folding, and (2) binding without folding. These findings explain the long-standing puzzle in the literature and highlight the importance of the choice of an appropriate membrane model for protein-lipid interactions studies.

  13. On the intrinsic disorder status of the major players in programmed cell death pathways [v1; ref status: indexed, http://f1000r.es/1me

    Directory of Open Access Journals (Sweden)

    Alexey V Uversky

    2013-09-01

    Full Text Available Earlier computational and bioinformatics analysis of several large protein datasets across 28 species showed that proteins involved in regulation and execution of programmed cell death (PCD possess substantial amounts of intrinsic disorder. Based on the comprehensive analysis of these datasets by a wide array of modern bioinformatics tools it was concluded that disordered regions of PCD-related proteins are involved in a multitude of biological functions and interactions with various partners, possess numerous posttranslational modification sites, and have specific evolutionary patterns (Peng et al. 2013. This study extends our previous work by providing information on the intrinsic disorder status of some of the major players of the three major PCD pathways: apoptosis, autophagy, and necroptosis. We also present a detailed description of the disorder status and interactomes of selected proteins that are involved in the p53-mediated apoptotic signaling pathways.

  14. Monitoring structural changes in intrinsically disordered proteins using QCM-D: application to the bacterial cell division protein ZipA.

    Science.gov (United States)

    Mateos-Gil, Pablo; Tsortos, Achilleas; Vélez, Marisela; Gizeli, Electra

    2016-05-01

    The sensitivity of QCM-D to molecular hydrodynamic properties is applied in this work to study conformational changes of the intrinsically disordered protein ZipA. Acoustic measurements can clearly follow ZipA's unstructured domain expansion and contraction with salt content and be correlated with changes in the hydrodynamic radius of 1.8 nm or less. PMID:27109863

  15. Embrace the Chaos

    Science.gov (United States)

    Huwe, Terence K.

    2009-01-01

    "Embracing the chaos" is an ongoing challenge for librarians. Embracing the chaos means librarians must have a plan for responding to the flood of new products, widgets, web tools, and gizmos that students use daily. In this article, the author argues that library instruction and access services have been grappling with that chaos with some degree…

  16. Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex.

    Science.gov (United States)

    Moussavi-Baygi, R; Mofrad, M R K

    2016-01-01

    Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores. PMID:27470900

  17. Reconfiguration dynamics in folded and intrinsically disordered protein with internal friction: Effect of solvent quality and denaturant

    Science.gov (United States)

    Samanta, Nairhita; Chakrabarti, Rajarshi

    2016-05-01

    We consider a flexible chain with internal friction in a harmonic confinement and extend it to include the effects of solvent quality at the mean field level by introducing a Flory type exponent ν. The strength of the harmonic confinement (kc) accounts for the denaturant concentration and connects to the internal friction of the chain (ξint) through an ansatz. Our calculated reconfiguration times falling in the range of 5-50 ns are found out to be within 10%-15% of the experimentally measured reconfiguration times of the folded cold shock protein and the intrinsically disordered protein prothymosin α. In addition, our calculations show that the reconfiguration time scales with the chain length N as ∼Nα, where α depends weakly on the internal friction but has rather stronger dependence on the solvent quality. In the absence of any internal friction, α = 2 ν + 1 and it goes down in the presence of internal friction, but chain reconfiguration slows down in general. On the contrary, in a poorer solvent chain reconfiguration and looping become faster even though the internal friction is higher in the collapsed state.

  18. Rapid Brownian Motion Primes Ultrafast Reconstruction of Intrinsically Disordered Phe-Gly Repeats Inside the Nuclear Pore Complex

    Science.gov (United States)

    Moussavi-Baygi, R.; Mofrad, M. R. K.

    2016-01-01

    Conformational behavior of intrinsically disordered proteins, such as Phe-Gly repeat domains, alters drastically when they are confined in, and tethered to, nan channels. This has challenged our understanding of how they serve to selectively facilitate translocation of nuclear transport receptor (NTR)-bearing macromolecules. Heterogeneous FG-repeats, tethered to the NPC interior, nonuniformly fill the channel in a diameter-dependent manner and adopt a rapid Brownian motion, thereby forming a porous and highly dynamic polymeric meshwork that percolates in radial and axial directions and features two distinguishable zones: a dense hydrophobic rod-like zone located in the center, and a peripheral low-density shell-like zone. The FG-meshwork is locally disrupted upon interacting with NTR-bearing macromolecules, but immediately reconstructs itself between 0.44 μs and 7.0 μs, depending on cargo size and shape. This confers a perpetually-sealed state to the NPC, and is solely due to rapid Brownian motion of FG-repeats, not FG-repeat hydrophobic bonds. Elongated-shaped macromolecules, both in the presence and absence of NTRs, penetrate more readily into the FG-meshwork compared to their globular counterparts of identical volume and surface chemistry, highlighting the importance of the shape effects in nucleocytoplasmic transport. These results can help our understanding of geometrical effects in, and the design of, intelligent and responsive biopolymer-based materials in nanofiltration and artificial nanopores. PMID:27470900

  19. Concentrated Solutions of Single-Chain Nanoparticles: A Simple Model for Intrinsically Disordered Proteins under Crowding Conditions.

    Science.gov (United States)

    Moreno, Angel J; Lo Verso, Federica; Arbe, Arantxa; Pomposo, José A; Colmenero, Juan

    2016-03-01

    By means of large-scale computer simulations and small-angle neutron scattering (SANS), we investigate solutions of single-chain nanoparticles (SCNPs), covering the whole concentration range from infinite dilution to melt density. The analysis of the conformational properties of the SCNPs reveals that these synthetic nano-objects share basic ingredients with intrinsically disordered proteins (IDPs), as topological polydispersity, generally sparse conformations, and locally compact domains. We investigate the role of the architecture of the SCNPs in their collapse behavior under macromolecular crowding. Unlike in the case of linear macromolecules, which experience the usual transition from self-avoiding to Gaussian random-walk conformations, crowding leads to collapsed conformations of SCNPs resembling those of crumpled globules. This behavior is already found at volume fractions (about 30%) that are characteristic of crowding in cellular environments. The simulation results are confirmed by the SANS experiments. Our results for SCNPs-a model system free of specific interactions-propose a general scenario for the effect of steric crowding on IDPs: collapse from sparse conformations at high dilution to crumpled globular conformations in cell environments. PMID:26894933

  20. Transcriptional repressor domain of MBD1 is intrinsically disordered and interacts with its binding partners in a selective manner.

    KAUST Repository

    Hameed, Umar Farook Shahul

    2014-05-09

    Methylation of DNA CpG sites is a major mechanism of epigenetic gene silencing and plays important roles in cell division, development and carcinogenesis. One of its regulators is the 64-residue C-terminal Transcriptional Repressor Domain (the TRD) of MBD1, which recruits several repressor proteins such as MCAF1, HDAC3 and MPG that are essential for the gene silencing. Using NMR spectroscopy, we have characterized the solution structure of the C-terminus of MBD1 (MBD1-c, residues D507 to Q605), which included the TRD (A529 to P592). Surprisingly, the MBD1-c is intrinsically disordered. Despite its lack of a tertiary folding, MBD1-c could still bind to different partner proteins in a selective manner. MPG and MCAF1Δ8 showed binding to both the N-terminal and C-terminal residues of MBD1-c but HDAC3 preferably bound to the C-terminal region. This study reveals how MBD1-c discriminates different binding partners, and thus, expands our understanding of the mechanisms of gene regulation by MBD1.

  1. Universal quantification for deterministic chaos in dynamical systems

    OpenAIRE

    Selvam, A. Mary

    2000-01-01

    A cell dynamical system model for deterministic chaos enables precise quantification of the round-off error growth,i.e., deterministic chaos in digital computer realizations of mathematical models of continuum dynamical systems. The model predicts the following: (a) The phase space trajectory (strange attractor) when resolved as a function of the computer accuracy has intrinsic logarithmic spiral curvature with the quasiperiodic Penrose tiling pattern for the internal structure. (b) The unive...

  2. Manifestation of resonance-related chaos in coupled Josephson junctions

    International Nuclear Information System (INIS)

    Manifestation of chaos in the temporal dependence of the electric charge is demonstrated through the calculation of the maximal Lyapunov exponent, phase–charge and charge–charge Lissajous diagrams and correlation functions. It is found that the number of junctions in the stack strongly influences the fine structure in the current–voltage characteristics and a strong proximity effect results from the nonperiodic boundary conditions. The observed resonance-related chaos exhibits intermittency. The criteria for a breakpoint region with no chaos are obtained. Such criteria could clarify recent experimental observations of variations in the power output from intrinsic Josephson junctions in high temperature superconductors.

  3. Altered temporal features of intrinsic connectivity networks in boys with combined type of attention deficit hyperactivity disorder

    International Nuclear Information System (INIS)

    Highlights: • Temporal patterns within ICNs provide new way to investigate ADHD brains. • ADHD exhibits enhanced temporal activities within and between ICNs. • Network-wise ALFF influences functional connectivity between ICNs. • Univariate patterns within ICNs are correlated to behavior scores. - Abstract: Purpose: Investigating the altered temporal features within and between intrinsic connectivity networks (ICNs) for boys with attention-deficit/hyperactivity disorder (ADHD); and analyzing the relationships between altered temporal features within ICNs and behavior scores. Materials and methods: A cohort of boys with combined type of ADHD and a cohort of age-matched healthy boys were recruited from ADHD-200 Consortium. All resting-state fMRI datasets were preprocessed and normalized into standard brain space. Using general linear regression, 20 ICNs were taken as spatial templates to analyze the time-courses of ICNs for each subject. Amplitude of low frequency fluctuations (ALFFs) were computed as univariate temporal features within ICNs. Pearson correlation coefficients and node strengths were computed as bivariate temporal features between ICNs. Additional correlation analysis was performed between temporal features of ICNs and behavior scores. Results: ADHD exhibited more activated network-wise ALFF than normal controls in attention and default mode-related network. Enhanced functional connectivities between ICNs were found in ADHD. The network-wise ALFF within ICNs might influence the functional connectivity between ICNs. The temporal pattern within posterior default mode network (pDMN) was positively correlated to inattentive scores. The subcortical network, fusiform-related DMN and attention-related networks were negatively correlated to Intelligence Quotient (IQ) scores. Conclusion: The temporal low frequency oscillations of ICNs in boys with ADHD were more activated than normal controls during resting state; the temporal features within ICNs could

  4. Altered temporal features of intrinsic connectivity networks in boys with combined type of attention deficit hyperactivity disorder

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xun-Heng, E-mail: xhwang@hdu.edu.cn [College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China); School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096 (China); Li, Lihua [College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou 310018 (China)

    2015-05-15

    Highlights: • Temporal patterns within ICNs provide new way to investigate ADHD brains. • ADHD exhibits enhanced temporal activities within and between ICNs. • Network-wise ALFF influences functional connectivity between ICNs. • Univariate patterns within ICNs are correlated to behavior scores. - Abstract: Purpose: Investigating the altered temporal features within and between intrinsic connectivity networks (ICNs) for boys with attention-deficit/hyperactivity disorder (ADHD); and analyzing the relationships between altered temporal features within ICNs and behavior scores. Materials and methods: A cohort of boys with combined type of ADHD and a cohort of age-matched healthy boys were recruited from ADHD-200 Consortium. All resting-state fMRI datasets were preprocessed and normalized into standard brain space. Using general linear regression, 20 ICNs were taken as spatial templates to analyze the time-courses of ICNs for each subject. Amplitude of low frequency fluctuations (ALFFs) were computed as univariate temporal features within ICNs. Pearson correlation coefficients and node strengths were computed as bivariate temporal features between ICNs. Additional correlation analysis was performed between temporal features of ICNs and behavior scores. Results: ADHD exhibited more activated network-wise ALFF than normal controls in attention and default mode-related network. Enhanced functional connectivities between ICNs were found in ADHD. The network-wise ALFF within ICNs might influence the functional connectivity between ICNs. The temporal pattern within posterior default mode network (pDMN) was positively correlated to inattentive scores. The subcortical network, fusiform-related DMN and attention-related networks were negatively correlated to Intelligence Quotient (IQ) scores. Conclusion: The temporal low frequency oscillations of ICNs in boys with ADHD were more activated than normal controls during resting state; the temporal features within ICNs could

  5. Chaos theory in politics

    CERN Document Server

    Erçetin, Şefika; Tekin, Ali

    2014-01-01

    The present work investigates global politics and political implications of social science and management with the aid of the latest complexity and chaos theories. Until now, deterministic chaos and nonlinear analysis have not been a focal point in this area of research. This book remedies this deficiency by utilizing these methods in the analysis of the subject matter. The authors provide the reader a detailed analysis on politics and its associated applications with the help of chaos theory, in a single edited volume.

  6. The human selenoprotein VCP-interacting membrane protein (VIMP) is non-globular and harbors a reductase function in an intrinsically disordered region

    DEFF Research Database (Denmark)

    Christensen, Lea Cecilie; Jensen, Njal Winther; Lages Lino Vala, Andrea;

    2012-01-01

    The human selenoprotein VIMP (VCP-interacting membrane protein)/SelS (selenoprotein S) localizes to the endoplasmic reticulum (ER) membrane and is involved in the process of ER-associated degradation (ERAD). To date, little is known about the presumed redox activity of VIMP, its structure and how...... reductase, and we speculate that the plasticity of the intrinsically disordered C-terminal region allows the protein to access many different and structurally diverse substrates....

  7. Aberrant intrinsic connectivity of hippocampus and amygdala overlap in the fronto-insular and dorsomedial-prefrontal cortex in major depressive disorder

    Directory of Open Access Journals (Sweden)

    Masoud Tahmasian

    2013-10-01

    Full Text Available Neuroimaging studies of major depressive disorder (MDD have consistently observed functional and structural changes of the hippocampus (HP and amygdale (AY. Thus, these brain regions appear to be critical elements of the pathophysiology of MDD. The HP and AY directly interact and show broad and overlapping intrinsic functional connectivity (iFC to other brain regions. Therefore, we hypothesized the HP and AY would show a corresponding pattern of aberrant intrinsic connectivity in MDD. Resting-state functional MRI was acquired from 21 patients with MDD and 20 healthy controls. ß-maps of region-of-interest-based FC for bilateral body of the HP and basolateral AY were used as surrogates for iFC of the HP and AY. ANOVA was used to compare ß-maps between MDD and healthy control groups, and included covariates for age and gender as well as grey matter volume of the HP and AY. The HP and AY of MDD patient’s showed an overlapping pattern of reduced FC to the dorsomedial prefrontal cortex and fronto-insular operculum. Both of these regions are known to regulate the interactions among intrinsic networks (i.e. default mode, central executive, and salience networks that are disrupted in MDD. These results provide the first evidence of overlapping aberrant HP and AY intrinsic connectivity in MDD. Our findings suggest that aberrant HP and AY connectivity may interact with dysfunctional intrinsic network activity in MDD.

  8. Quantum Chaos and Statistical Mechanics

    OpenAIRE

    Srednicki, Mark

    1994-01-01

    We briefly review the well known connection between classical chaos and classical statistical mechanics, and the recently discovered connection between quantum chaos and quantum statistical mechanics.

  9. Understanding Chaos via Nuclei

    OpenAIRE

    Cejnar, Pavel; Stránský, Pavel

    2014-01-01

    We use two models of nuclear collective dynamics - the geometric collective model and the interacting boson model - to illustrate principles of classical and quantum chaos. We propose these models as a suitable testing ground for further elaborations of the general theory of chaos in both classical and quantum domains.

  10. Coherence and chaos in extended dynamical systems

    International Nuclear Information System (INIS)

    Coherence, chaos, and pattern formation are characteristic elements of the nonequilibrium statistical mechanics controlling mesoscopic order and disorder in many-degree-of-freedom nonlinear dynamical systems. Competing length scales and/or time scales are the underlying microscopic driving forces for many of these aspects of ''complexity.'' We illustrate the basic concepts with some model examples of classical and quantum, ordered and disordered, nonlinear systems

  11. Clinical Practice Guideline for the Treatment of Intrinsic Circadian Rhythm Sleep-Wake Disorders: Advanced Sleep-Wake Phase Disorder (ASWPD), Delayed Sleep-Wake Phase Disorder (DSWPD), Non-24-Hour Sleep-Wake Rhythm Disorder (N24SWD), and Irregular Sleep-Wake Rhythm Disorder (ISWRD). An Update for 2015: An American Academy of Sleep Medicine Clinical Practice Guideline

    OpenAIRE

    Auger, R. Robert; Burgess, Helen J.; Emens, Jonathan S.; Deriy, Ludmila V.; Thomas, Sherene M.; Sharkey, Katherine M.

    2015-01-01

    A systematic literature review and meta-analyses (where appropriate) were performed and the GRADE approach was used to update the previous American Academy of Sleep Medicine Practice Parameters on the treatment of intrinsic circadian rhythm sleep-wake disorders. Available data allowed for positive endorsement (at a second-tier degree of confidence) of strategically timed melatonin (for the treatment of DSWPD, blind adults with N24SWD, and children/ adolescents with ISWRD and comorbid neurolog...

  12. Probing Structural Transitions in the Intrinsically Disordered C-Terminal Domain of the Measles Virus Nucleoprotein by Vibrational Spectroscopy of Cyanylated Cysteines

    Science.gov (United States)

    Bischak, Connor G.; Longhi, Sonia; Snead, David M.; Costanzo, Stéphanie; Terrer, Elodie; Londergan, Casey H.

    2010-01-01

    Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (NTAIL) were cyanylated at cysteine and their infrared spectra in the C≡N stretching region were recorded both in the absence and in the presence of one of the physiological partners of NTAIL, namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within NTAIL, the C≡N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level. PMID:20816082

  13. Science of Chaos or Chaos in Science?

    OpenAIRE

    Bricmont, Jean

    1996-01-01

    I try to clarify several confusions in the popular literature concerning chaos, determinism, the arrow of time, entropy and the role of probability in physics. Classical ideas going back to Laplace and Boltzmann are explained and defended while some recent views on irreversibility, due to Prigogine, are criticized.

  14. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

    We conjecture a sharp bound on the rate of growth of chaos in thermal quantum systems with a large number of degrees of freedom. Chaos can be diagnosed using an out-of-time-order correlation function closely related to the commutator of operators separated in time. We conjecture that the influence of chaos on this correlator can develop no faster than exponentially, with Lyapunov exponent $\\lambda_L \\le 2 \\pi k_B T/\\hbar$. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  15. Paths to chaos

    International Nuclear Information System (INIS)

    Rapid growth in the study of nonlinear dynamics and chaos in classical mechanics, has led physicists to reappraise their abandonment of this definition of atomic theory in favour of quantum mechanics adopted earlier this century. The concept of chaos in classical mechanics is examined in this paper and manifestations of chaos in quantum mechanics are explored. While quantum mechanics teaches that atomic particles must not be pictured as moving sharply in defined orbits, these precise orbits can be used to describe essential features of the measurable quantum mechanical spectra. (UK)

  16. Chaos applications in telecommunications

    CERN Document Server

    Stavroulakis, Peter

    2005-01-01

    IntroductionPeter StavroulakisChaotic Signal Generation and Transmission Antonio Cândido Faleiros,Waldecir João Perrella,TâniaNunes Rabello,Adalberto Sampaio Santos, andNeiYoshihiro SomaChaotic Transceiver Design Arthur Fleming-DahlChaos-Based Modulation and DemodulationTechniques Francis C.M. Lau and Chi K. TseA Chaos Approach to Asynchronous DS-CDMASystems S. Callegari, G. Mazzini, R. Rovatti, and G. SettiChannel Equalization in Chaotic CommunicationSystems Mahmut CiftciOptical Communications using ChaoticTechniques Gregory D. VanWiggerenAPPENDIX AFundamental Concepts of the Theory ofChaos a

  17. Combining a PagP fusion protein system with nickel ion-catalyzed cleavage to produce intrinsically disordered proteins in E. coli.

    Science.gov (United States)

    Zahran, Somaya; Pan, Jonathan S; Liu, Philip B; Hwang, Peter M

    2015-12-01

    Many proteins contain intrinsically disordered regions that are highly solvent-exposed and susceptible to post-translational modifications. Studying these protein segments is critical to understanding their physiologic regulation, but proteolytic degradation can make them difficult to express and purify. We have designed a new protein expression vector that fuses the target protein to the N-terminus of the integral membrane protein, PagP. The two proteins are connected by a short linker containing the sequence SRHW, previously shown to be optimal for nickel ion-catalyzed cleavage. The methodology is demonstrated for an intrinsically disordered segment of cardiac troponin I. cTnI[135-209]-SRHW-PagP-His6 fusion protein was overexpressed in Escherichia coli, accumulating in insoluble inclusion bodies. The protein was solubilized, purified using nickel affinity chromatography, and then cleaved with 0.5mM NiSO4 at pH 9.0 and 45 °C, all in 6M guanidine-HCl. Nickel ion-catalyzed peptide bond hydrolysis is an effective chemical cleavage technique under denaturing conditions that preclude the use of proteases. Moreover, nickel-catalyzed cleavage is more specific than the most commonly used agent, cyanogen bromide, which cleaves C-terminal to methionine residues. We were able to produce 15 mg of purified cTnI[135-209] from 1L of M9 minimal media using this protocol. The methodology is more generally applicable to the production of intrinsically disordered protein segments. PMID:26297994

  18. Chaos and Preheating

    CERN Document Server

    Jorás, S E; Jor\\'as, Sergio E.

    2003-01-01

    We show evidence for a relationship between chaos and parametric resonance both in a classical system and in the semiclassical process of particle creation. We apply our considerations in a toy model for preheating after inflation.

  19. Exploiting chaos for applications

    International Nuclear Information System (INIS)

    We discuss how understanding the nature of chaotic dynamics allows us to control these systems. A controlled chaotic system can then serve as a versatile pattern generator that can be used for a range of application. Specifically, we will discuss the application of controlled chaos to the design of novel computational paradigms. Thus, we present an illustrative research arc, starting with ideas of control, based on the general understanding of chaos, moving over to applications that influence the course of building better devices

  20. Chaos in quantum channels

    OpenAIRE

    Hosur, Pavan; Qi, Xiao-Liang; Roberts, Daniel; Yoshida, Beni(Institute for Quantum Information & Matter and Walter Burke Institute for Theoretical Physics, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA, 91125, U.S.A.)

    2016-01-01

    We study chaos and scrambling in unitary channels by considering their entanglement properties as states. Using out-of-time-order correlation functions to diagnose chaos, we characterize the ability of a channel to process quantum information. We show that the generic decay of such correlators implies that any input subsystem must have near vanishing mutual information with almost all partitions of the output. Additionally, we propose the negativity of the tripartite information of the channe...

  1. Exploiting chaos for applications

    Energy Technology Data Exchange (ETDEWEB)

    Ditto, William L., E-mail: wditto@hawaii.edu [Department of Physics and Astronomy, University of Hawaii at Mānoa, Honolulu, Hawaii 96822 (United States); Sinha, Sudeshna, E-mail: sudeshna@iisermohali.ac.in [Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector 81, SAS Nagar, PO Manauli 140306, Punjab (India)

    2015-09-15

    We discuss how understanding the nature of chaotic dynamics allows us to control these systems. A controlled chaotic system can then serve as a versatile pattern generator that can be used for a range of application. Specifically, we will discuss the application of controlled chaos to the design of novel computational paradigms. Thus, we present an illustrative research arc, starting with ideas of control, based on the general understanding of chaos, moving over to applications that influence the course of building better devices.

  2. Phosphorylation at intrinsically disordered regions of PAM2 motif-containing proteins modulates their interactions with PABPC1 and influences mRNA fate.

    Science.gov (United States)

    Huang, Kai-Lieh; Chadee, Amanda B; Chen, Chyi-Ying A; Zhang, Yueqiang; Shyu, Ann-Bin

    2013-03-01

    Cytoplasmic poly(A)-binding protein (PABP) C1 recruits different interacting partners to regulate mRNA fate. The majority of PABP-interacting proteins contain a PAM2 motif to mediate their interactions with PABPC1. However, little is known about the regulation of these interactions or the corresponding functional consequences. Through in silico analysis, we found that PAM2 motifs are generally embedded within an extended intrinsic disorder region (IDR) and are located next to cluster(s) of potential serine (Ser) or threonine (Thr) phosphorylation sites within the IDR. We hypothesized that phosphorylation at these Ser/Thr sites regulates the interactions between PAM2-containing proteins and PABPC1. In the present study, we have tested this hypothesis using complementary approaches to increase or decrease phosphorylation. The results indicate that changing the extent of phosphorylation of three PAM2-containing proteins (Tob2, Pan3, and Tnrc6c) alters their ability to interact with PABPC1. Results from experiments using phospho-blocking or phosphomimetic mutants in PAM2-containing proteins further support our hypothesis. Moreover, the phosphomimetic mutations appreciably affected the functions of these proteins in mRNA turnover and gene silencing. Taken together, these results provide a new framework for understanding the roles of intrinsically disordered proteins in the dynamic and signal-dependent control of cytoplasmic mRNA functions. PMID:23340509

  3. Frozen spatial chaos induced by boundaries

    CERN Document Server

    Eguiluz, V M; Piro, O; Balle, S; Eguiluz, Victor M.; Hernandez-Garcia, Emilio; Piro, Oreste; Balle, Salvador

    1999-01-01

    We show that rather simple but non-trivial boundary conditions could induce the appearance of spatial chaos (that is stationary, stable, but spatially disordered configurations) in extended dynamical systems with very simple dynamics. We exemplify the phenomenon with a nonlinear reaction-diffusion equation in a two-dimensional undulated domain. Concepts from the theory of dynamical systems, and a transverse-single-mode approximation are used to describe the spatially chaotic structures.

  4. The gene expression profiling of hepatocellular carcinoma by a network analysis approach shows a dominance of intrinsically disordered proteins (IDPs) between hub nodes.

    Science.gov (United States)

    Singh, Sakshi; Colonna, Giovanni; Di Bernardo, Giovanni; Bergantino, Francesca; Cammarota, Marcella; Castello, Giuseppe; Costantini, Susan

    2015-11-01

    We have analyzed the transcriptomic data from patients with hepatocellular carcinoma (HCC) after viral HCV infection at the various stages of the disease by means of a networking analysis using the publicly available E-MTAB-950 dataset. The data was compared with those obtained in our group from HepG2 cells, a cancer cell line that lacks the viral infection. By sequential pruning of data, and also taking into account the data from cells of healthy patients as blanks, we were able to obtain a distribution of hub genes for the various stages that characterize the disease and finally, we isolated a metabolic sub-net specific to HCC alone. The general picture is that the basic organization to energetically and metabolically sustain the cells in both the normal and diseased conditions is the same, but a complex cluster of sub-networks controlled by hub genes drives the HCC progression with high metabolic flexibility and plasticity. In particular, we have extracted a sub-net of genes strictly correlated to other hub genes of the network from HepG2 cells, but specific for the HCC and mainly devoted to: (i) control at chromatin levels of cell division; (ii) control of ergastoplasmatic stress through protein degradation and misfolding; (iii) control of the immune response also through an increase of mature T-cells in the thymus. This sub-net is characterized by 26 hub genes coding for intrinsically disordered proteins with a high ability to interact with numerous molecular partners. Moreover, we have also noted that periphery molecules, that is, with one or very few interactions (e.g., cytokines or post-translational enzymes), which do not have a central role in the clusters that make up the global metabolic network, essentially have roles as information transporters. The results evidence a strong presence of intrinsically disordered proteins with key roles as hubs in the sub-networks that characterize the various stages of the disease, conferring a structural plasticity to

  5. Biophysical characterization of the structural change of Nopp140, an intrinsically disordered protein, in the interaction with CK2α.

    Science.gov (United States)

    Na, Jung-Hyun; Lee, Won-Kyu; Kim, Yuyoung; Jeong, Cherlhyun; Song, Seung Soo; Cha, Sun-Shin; Han, Kyou-Hoon; Shin, Yeon-Kyun; Yu, Yeon Gyu

    2016-08-19

    Nucleolar phosphoprotein 140 (Nopp140) is a nucleolar protein, more than 80% of which is disordered. Previous studies have shown that the C-terminal region of Nopp140 (residues 568-596) interacts with protein kinase CK2α, and inhibits the catalytic activity of CK2. Although the region of Nopp140 responsible for the interaction with CK2α was identified, the structural features and the effect of this interaction on the structure of Nopp140 have not been defined due to the difficulty of structural characterization of disordered protein. In this study, the disordered feature of Nopp140 and the effect of CK2α on the structure of Nopp140 were examined using single-molecule fluorescence resonance energy transfer (smFRET) and electron paramagnetic resonance (EPR). The interaction with CK2α was increased conformational rigidity of the CK2α-interacting region of Nopp140 (Nopp140C), suggesting that the disordered and flexible conformation of Nopp140C became more rigid conformation as it binds to CK2α. In addition, site specific spin labeling and EPR analysis confirmed that the residues 574-589 of Nopp140 are critical for binding to CK2α. Similar technical approaches can be applied to analyze the conformational changes in other IDPs during their interactions with binding partners. PMID:27297113

  6. Deterministic chaos an introduction

    CERN Document Server

    Schuster, Heinz Georg

    2005-01-01

    A new edition of this well-established monograph, this volume provides a comprehensive overview over the still fascinating field of chaos research. The authors include recent developments such as systems with restricted degrees of freedom but put also a strong emphasis on the mathematical foundations. Partly illustrated in color, this fourth edition features new sections from applied nonlinear science, like control of chaos, synchronisation of nonlinear systems, and turbulence, as well as recent theoretical concepts like strange nonchaotic attractors, on-off intermittency and spatio-temporal chaotic motion

  7. Chaos in Magnetoplasmas

    Directory of Open Access Journals (Sweden)

    B. Buti

    1999-01-01

    Full Text Available A nonlinear wave, in general, is equivalent to a nonlinear dynamical system, which exhibits the phenomena of chaos. By means of techniques of nonlinear dynamical systems, we have investigated the conditions under which nonlinear Alfvén waves and lower-hybrid waves can become chaotic. The role of heavy ions, in controlling the chaos in magnetoplasmas, is examined. Chaotic routes to Alfvénic turbulence, with k-1 spectra, are observed in case of externally driven nonlinear Alfvén waves. Anomalous heating and particle acceleration resulting from chaotic fields, generated by lower-hybrid waves, are briefly outlined.

  8. Morphogenesis of Chaos

    OpenAIRE

    Akhmet, Marat; Fen, Mehmet Onur

    2012-01-01

    Morphogenesis, as it is understood in a wide sense by Ren\\'e Thom, is considered for various types of chaos. That is, those, obtained by period-doubling cascade, Devaney's and Li-Yorke chaos. Moreover, in discussion form we consider inheritance of intermittency, the double-scroll Chua's attractor and quasiperiodical motions as a possible skeleton of a chaotic attractor. To make our introduction of the paper more clear, we have to say that one may consider other various accompanying concepts o...

  9. Dissipative structures and chaos

    CERN Document Server

    Mori, Hazime

    1998-01-01

    This monograph consists of two parts and gives an approach to the physics of open nonequilibrium systems. Part I derives the phenomena of dissipative structures on the basis of reduced evolution equations and includes Bénard convection and Belousov-Zhabotinskii chemical reactions. Part II discusses the physics and structures of chaos. While presenting a construction of the statistical physics of chaos, the authors unify the geometrical and statistical descriptions of dynamical systems. The shape of chaotic attractors is characterized, as are the mixing and diffusion of chaotic orbits and the fluctuation of energy dissipation exhibited by chaotic systems.

  10. Automatic Bayesian classification of healthy controls, bipolar disorder and schizophrenia using intrinsic connectivity maps from fMRI data

    OpenAIRE

    Arribas, Juan I.; Calhoun, Vince D.; Adalı, Tülay

    2010-01-01

    We present a method for supervised, automatic and reliable classification of healthy controls, patients with bipolar disorder and patients with schizophrenia using brain imaging data. The method uses four supervised classification learning machines trained with a stochastic gradient learning rule based on the minimization of Kullback-Leibler divergence and an optimal model complexity search through posterior probability estimation. Prior to classification, given the high dimensionality of fun...

  11. Altered intrinsic functional connectivity of anterior and posterior insular regions in high-functioning participants with autism spectrum disorder

    OpenAIRE

    Ebisch, S.; Gallese, V.; Willems, R.; Mantini, D.; Groen, W; Romani, G; Buitelaar, J.; Bekkering, H

    2011-01-01

    Impaired understanding of others' sensations and emotions as well as abnormal experience of their own emotions and sensations is frequently reported in individuals with Autism Spectrum Disorder (ASD). It is hypothesized that these abnormalities are based on altered connectivity within “shared” neural networks involved in emotional awareness of self and others. The insula is considered a central brain region in a network underlying these functions, being located at the transition of informatio...

  12. Chaos in drive systems

    Directory of Open Access Journals (Sweden)

    Kratochvíl C.

    2007-10-01

    Full Text Available The purpose of this article is to provide an elementary introduction to the subject of chaos in the electromechanical drive systems. In this article, we explore chaotic solutions of maps and continuous time systems. These solutions are also bounded like equilibrium, periodic and quasiperiodic solutions.

  13. Neural chaos and schizophrenia

    Czech Academy of Sciences Publication Activity Database

    Bob, P.; Chládek, Jan; Šusta, M.; Glaslová, K.; Jagla, F.; Kukleta, M.

    2007-01-01

    Roč. 26, č. 4 (2007), s. 298-305. ISSN 0231-5882 Institutional research plan: CEZ:AV0Z20650511 Keywords : EDA * Lyapunov exponent * schizophrenia * chaos Subject RIV: FL - Psychiatry, Sexuology Impact factor: 1.286, year: 2007

  14. Chaos in GDP

    Directory of Open Access Journals (Sweden)

    R. Kříž

    2011-01-01

    Full Text Available This paper presents an analysis of GDP and finds chaos in GDP. I tried to find a nonlinear lower-dimensional discrete dynamic macroeconomic model that would characterize GDP. This model is represented by a set of differential equations. I have used the Mathematica and MS Excel programs for the analysis.

  15. Chaos in GDP

    OpenAIRE

    R. Kříž

    2011-01-01

    This paper presents an analysis of GDP and finds chaos in GDP. I tried to find a nonlinear lower-dimensional discrete dynamic macroeconomic model that would characterize GDP. This model is represented by a set of differential equations. I have used the Mathematica and MS Excel programs for the analysis.

  16. Tick receptor for outer surface protein A from Ixodes ricinus — the first intrinsically disordered protein involved in vector-microbe recognition

    Science.gov (United States)

    Urbanowicz, Anna; Lewandowski, Dominik; Szpotkowski, Kamil; Figlerowicz, Marek

    2016-04-01

    The tick receptor for outer surface protein A (TROSPA) is the only identified factor involved in tick gut colonization by various Borrelia species. TROSPA is localized in the gut epithelium and can recognize and bind the outer surface bacterial protein OspA via an unknown mechanism. Based on earlier reports and our latest observations, we considered that TROSPA would be the first identified intrinsically disordered protein (IDP) involved in the interaction between a vector and a pathogenic microbe. To verify this hypothesis, we performed structural studies of a TROSPA mutant from Ixodes ricinus using both computational and experimental approaches. Irrespective of the method used, we observed that the secondary structure content of the TROSPA polypeptide chain is low. In addition, the collected SAXS data indicated that this protein is highly extended and exists in solution as a set of numerous conformers. These features are all commonly considered hallmarks of IDPs. Taking advantage of our SAXS data, we created structural models of TROSPA and proposed a putative mechanism for the TROSPA-OspA interaction. The disordered nature of TROSPA may explain the ability of a wide spectrum of Borrelia species to colonize the tick gut.

  17. High-dimensional chaos from self-sustained collisions of solitons

    International Nuclear Information System (INIS)

    We experimentally demonstrate chaos generation based on collisions of electrical solitons on a nonlinear transmission line. The nonlinear line creates solitons, and an amplifier connected to it provides gain to these solitons for their self-excitation and self-sustenance. Critically, the amplifier also provides a mechanism to enable and intensify collisions among solitons. These collisional interactions are of intrinsically nonlinear nature, modulating the phase and amplitude of solitons, thus causing chaos. This chaos generated by the exploitation of the nonlinear wave phenomena is inherently high-dimensional, which we also demonstrate.

  18. The bacterial tubulin FtsZ requires its intrinsically disordered linker to direct robust cell wall construction.

    Science.gov (United States)

    Sundararajan, Kousik; Miguel, Amanda; Desmarais, Samantha M; Meier, Elizabeth L; Casey Huang, Kerwyn; Goley, Erin D

    2015-01-01

    The bacterial GTPase FtsZ forms a cytokinetic ring at midcell, recruits the division machinery and orchestrates membrane and peptidoglycan cell wall invagination. However, the mechanism for FtsZ regulation of peptidoglycan metabolism is unknown. The FtsZ GTPase domain is separated from its membrane-anchoring C-terminal conserved (CTC) peptide by a disordered C-terminal linker (CTL). Here we investigate CTL function in Caulobacter crescentus. Strikingly, production of FtsZ lacking the CTL (ΔCTL) is lethal: cells become filamentous, form envelope bulges and lyse, resembling treatment with β-lactam antibiotics. This phenotype is produced by FtsZ polymers bearing the CTC and a CTL shorter than 14 residues. Peptidoglycan synthesis still occurs downstream of ΔCTL; however, cells expressing ΔCTL exhibit reduced peptidoglycan crosslinking and longer glycan strands than wild type. Importantly, midcell proteins are still recruited to sites of ΔCTL assembly. We propose that FtsZ regulates peptidoglycan metabolism through a CTL-dependent mechanism that extends beyond simple protein recruitment. PMID:26099469

  19. Fuzzy controller based on chaos optimal design and its application

    Institute of Scientific and Technical Information of China (English)

    邹恩; 李祥飞; 张泰山

    2004-01-01

    In order to overcome difficulty of tuning parameters of fuzzy controller, a chaos optimal design method based on annealing strategy is proposed. First, apply the chaotic variables to search for parameters of fuzzy controller, and transform the optimal variables into chaotic variables by carrier-wave method. Making use of the intrinsic stochastic property and ergodicity of chaos movement to escape from the local minimum and direct optimization searching within global range, an approximate global optimal solution is obtained. Then, the chaos local searching and optimization based on annealing strategy are cited, the parameters are optimized again within the limits of the approximate global optimal solution, the optimization is realized by means of combination of global and partial chaos searching, which can converge quickly to global optimal value. Finally, the third order system and discrete nonlinear system are simulated and compared with traditional method of fuzzy control. The results show that the new chaos optimal design method is superior to fuzzy control method, and that the control results are of high precision, with no overshoot and fast response.

  20. A Structure behind Primitive Chaos

    Science.gov (United States)

    Ogasawara, Yoshihito

    2015-06-01

    Recently, a new concept, primitive chaos, has been proposed as a concept closely related to the fundamental problems of physics itself such as determinism, causality, free will, predictability, and irreversibility [J. Phys. Soc. Jpn. 79, 015002 (2010)]. This paper reveals a structure hidden behind the primitive chaos; under some conditions, a new primitive chaos is constructed from the original primitive chaos, this procedure can be repeated, and the hierarchical structure of the primitive chaos is obtained. This implies such a picture that new events and causality are constructed from the old ones, with the aid of the concept of a coarse graining. As an application of this structure, interesting facts are revealed for the essential condition of the primitive chaos and for chaotic behaviors.

  1. The joy of transient chaos

    Energy Technology Data Exchange (ETDEWEB)

    Tél, Tamás [Institute for Theoretical Physics, Eötvös University, and MTA-ELTE Theoretical Physics Research Group, Pázmány P. s. 1/A, Budapest H-1117 (Hungary)

    2015-09-15

    We intend to show that transient chaos is a very appealing, but still not widely appreciated, subfield of nonlinear dynamics. Besides flashing its basic properties and giving a brief overview of the many applications, a few recent transient-chaos-related subjects are introduced in some detail. These include the dynamics of decision making, dispersion, and sedimentation of volcanic ash, doubly transient chaos of undriven autonomous mechanical systems, and a dynamical systems approach to energy absorption or explosion.

  2. Chaos detection and predictability

    CERN Document Server

    Gottwald, Georg; Laskar, Jacques

    2016-01-01

    Distinguishing chaoticity from regularity in deterministic dynamical systems and specifying the subspace of the phase space in which instabilities are expected to occur is of utmost importance in as disparate areas as astronomy, particle physics and climate dynamics.   To address these issues there exists a plethora of methods for chaos detection and predictability. The most commonly employed technique for investigating chaotic dynamics, i.e. the computation of Lyapunov exponents, however, may suffer a number of problems and drawbacks, for example when applied to noisy experimental data.   In the last two decades, several novel methods have been developed for the fast and reliable determination of the regular or chaotic nature of orbits, aimed at overcoming the shortcomings of more traditional techniques. This set of lecture notes and tutorial reviews serves as an introduction to and overview of modern chaos detection and predictability techniques for graduate students and non-specialists.   The book cover...

  3. Chaos in quantum channels

    CERN Document Server

    Hosur, Pavan; Roberts, Daniel A; Yoshida, Beni

    2015-01-01

    We study chaos and scrambling in unitary channels by considering their entanglement properties as states. Using out-of-time-order correlation functions to diagnose chaos, we characterize the ability of a channel to process quantum information. We show that the generic decay of such correlators implies that any input subsystem must have near vanishing mutual information with almost all partitions of the output. Additionally, we propose the negativity of the tripartite information of the channel as a general diagnostic of scrambling. This measures the delocalization of information and is closely related to the decay of out-of-time-order correlators. We back up our results with numerics in two non-integrable models and analytic results in a perfect tensor network model of chaotic time evolution. These results show that the butterfly effect in quantum systems implies the information-theoretic definition of scrambling.

  4. Recent Progress in Controlling Chaos

    CERN Document Server

    Sanjuan, Miguel AF

    2010-01-01

    This book provides a collection of research papers on one of the topics where the applications of chaos have been more fruitful: controlling chaos. Here, new theoretical ideas, as experimental implementations of controlling chaos, are included, while the applications contained in this volume can be referred to turbulent magnetized plasmas, chaotic neural networks, modeling city traffic and models of interest in celestial mechanics. "Recent Progress in Controlling Chaos" will provide an overview of the recent progress in this field, which will be very useful for students and researche

  5. Robust chaos and its applications

    CERN Document Server

    Zeraoulia, Elhadj

    2011-01-01

    Robust chaos is defined by the absence of periodic windows and coexisting attractors in some neighborhoods in the parameter space of a dynamical system. This unique book explores the definition, sources, and roles of robust chaos. The book is written in a reasonably self-contained manner and aims to provide students and researchers with the necessary understanding of the subject. Most of the known results, experiments, and conjectures about chaos in general and about robust chaos in particular are collected here in a pedagogical form. Many examples of dynamical systems, ranging from purely mat

  6. Martingales, Nonlinearity, and Chaos

    OpenAIRE

    Barnett, William A.; Apostolos Serletis

    1998-01-01

    In this article we provide a review of the literature with respect to the efficient markets hypothesis and chaos. In doing so, we contrast the martingale behavior of asset prices to nonlinear chaotic dynamics, discuss some recent techniques used in distinguishing between probabilistic and deterministic behavior in asset prices, and report some evidence. Moreover, we look at the controversies that have arisen about the available tests and results, and raise the issue of whether dynamical syste...

  7. Chaos on hyperspace

    Czech Academy of Sciences Publication Activity Database

    Beran, Zdeněk; Čelikovský, Sergej

    2013-01-01

    Roč. 23, č. 5 (2013), 1350084-1-1350084-9. ISSN 0218-1274 R&D Projects: GA ČR GA13-20433S Institutional support: RVO:67985556 Keywords : Hyperspace * chaos * shadowing * Bernoulli shift Subject RIV: BC - Control Systems Theory Impact factor: 1.017, year: 2013 http://library.utia.cas.cz/separaty/2013/TR/beran-0392926.pdf

  8. Fractals and chaos

    CERN Document Server

    Earnshow, R; Jones, H

    1991-01-01

    This volume is based upon the presentations made at an international conference in London on the subject of 'Fractals and Chaos'. The objective of the conference was to bring together some of the leading practitioners and exponents in the overlapping fields of fractal geometry and chaos theory, with a view to exploring some of the relationships between the two domains. Based on this initial conference and subsequent exchanges between the editors and the authors, revised and updated papers were produced. These papers are contained in the present volume. We thank all those who contributed to this effort by way of planning and organisation, and also all those who helped in the production of this volume. In particular, we wish to express our appreciation to Gerhard Rossbach, Computer Science Editor, Craig Van Dyck, Production Director, and Nancy A. Rogers, who did the typesetting. A. J. Crilly R. A. Earnshaw H. Jones 1 March 1990 Introduction Fractals and Chaos The word 'fractal' was coined by Benoit Mandelbrot i...

  9. Chaos in hadrons

    International Nuclear Information System (INIS)

    In the last decade quantum chaos has become a well established discipline with outreach to different fields, from condensed-matter to nuclear physics. The most important signature of quantum chaos is the statistical analysis of the energy spectrum, which distinguishes between systems with integrable and chaotic classical analogues. In recent years, spectral statistical techniques inherited from quantum chaos have been applied successfully to the baryon spectrum revealing its likely chaotic behaviour even at the lowest energies. However, the theoretical spectra present a behaviour closer to the statistics of integrable systems which makes theory and experiment statistically incompatible. The usual statement of missing resonances in the experimental spectrum when compared to the theoretical ones cannot account for the discrepancies. In this communication we report an improved analysis of the baryon spectrum, taking into account the low statistics and the error bars associated with each resonance. Our findings give a major support to the previous conclusions. Besides, analogue analyses are performed in the experimental meson spectrum, with comparison to theoretical models.

  10. Novel circular single-stranded DNA viruses identified in marine invertebrates reveal high sequence diversity and consistent predicted intrinsic disorder patterns within putative structural proteins

    Directory of Open Access Journals (Sweden)

    Karyna eRosario

    2015-07-01

    Full Text Available Viral metagenomics has recently revealed the ubiquitous and diverse nature of single-stranded DNA (ssDNA viruses that encode a conserved replication initiator protein (Rep in the marine environment. Although eukaryotic circular Rep-encoding ssDNA (CRESS-DNA viruses were originally thought to only infect plants and vertebrates, recent studies have identified these viruses in a number of invertebrates. To further explore CRESS-DNA viruses in the marine environment, this study surveyed CRESS-DNA viruses in various marine invertebrate species. A total of 27 novel CRESS-DNA genomes, with Reps that share less than 60.1% identity with previously reported viruses, were recovered from 21 invertebrate species, mainly crustaceans. Phylogenetic analysis based on the Rep revealed a novel clade of CRESS-DNA viruses that included approximately one third of the marine invertebrate associated viruses identified here and whose members may represent a novel family. Investigation of putative capsid proteins (Cap encoded within the eukaryotic CRESS-DNA viral genomes from this study and those in GenBank demonstrated conserved patterns of predicted intrinsically disordered regions (IDRs, which can be used to complement similarity-based searches to identify divergent structural proteins within novel genomes. Overall, this study expands our knowledge of CRESS-DNA viruses associated with invertebrates and explores a new tool to evaluate divergent structural proteins encoded by these viruses.

  11. Continuous wave W- and D-Band EPR spectroscopy offer “sweet-spots” for characterizing conformational changes and dynamics in intrinsically disordered proteins

    International Nuclear Information System (INIS)

    Highlights: • W- and D-Band line shapes are sensitive to motions in the 0.1–2 ns time regime. • These frequencies effectively report on conformational dynamics of IDPs. • W-band spectra reflecting helical formation in IA3 is experimentally demonstrated. - Abstract: Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA3, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs

  12. Evidence for an Induced-Fit Process Underlying the Activation of Apoptotic BAX by an Intrinsically Disordered BimBH3 Peptide.

    Science.gov (United States)

    Jhong, Siao-Ru; Li, Ching-Yu; Sung, Tai-Ching; Lan, Yu-Jing; Chang, Kuo-Jung; Chiang, Yun-Wei

    2016-03-17

    Apoptotic BAX protein functions as a critical gateway to mitochondria-mediated apoptosis. A diversity of stimuli has been implicated in initiating BAX activation, but the triggering mechanism remains elusive. Here we study the interaction of BAX with an intrinsically disordered BH3 motif of Bim protein (BimBH3) using ESR techniques. Upon incubation with BAX, BimBH3 binds to BAX at helices 1/6 trigger site to initiate conformational changes of BAX, which in turn promotes the formation of BAX oligomers. The study strategy is twofold: while BAX oligomerization was monitored through spectral changes of spin-labeled BAX, the binding kinetics was studied by observing time-dependent changes of spin-labeled BimBH3. Meanwhile, conformational transition between the unstructured and structured BimBH3 was measured. We show that helical propensity of the BimBH3 is increased upon binding to BAX but is then reduced after being released from the activated BAX; the release is due to the BimBH3-induced conformational change of BAX that is a prerequisite for the oligomer assembling. Intermediate states are identified, offering a key snapshot of the coupled folding and binding process. Our results provide a quantitative mechanistic description of the BAX activation and reveal new insights into the mechanism underlying the interactions between BAX and BH3-mimetic peptide. PMID:26913490

  13. Intrinsically disordered region of influenza A NP regulates viral genome packaging via interactions with viral RNA and host PI(4,5)P2.

    Science.gov (United States)

    Kakisaka, Michinori; Yamada, Kazunori; Yamaji-Hasegawa, Akiko; Kobayashi, Toshihide; Aida, Yoko

    2016-09-01

    To be incorporated into progeny virions, the viral genome must be transported to the inner leaflet of the plasma membrane (PM) and accumulate there. Some viruses utilize lipid components to assemble at the PM. For example, simian virus 40 (SV40) targets the ganglioside GM1 and human immunodeficiency virus type 1 (HIV-1) utilizes phosphatidylinositol (4,5) bisphosphate [PI(4,5)P2]. Recent studies clearly indicate that Rab11-mediated recycling endosomes are required for influenza A virus (IAV) trafficking of vRNPs to the PM but it remains unclear how IAV vRNP localized or accumulate underneath the PM for viral genome incorporation into progeny virions. In this study, we found that the second intrinsically disordered region (IDR2) of NP regulates two binding steps involved in viral genome packaging. First, IDR2 facilitates NP oligomer binding to viral RNA to form vRNP. Secondly, vRNP assemble by interacting with PI(4,5)P2 at the PM via IDR2. These findings suggest that PI(4,5)P2 functions as the determinant of vRNP accumulation at the PM. PMID:27289560

  14. Prostate-associated gene 4 (PAGE4), an intrinsically disordered cancer/testis antigen, is a novel therapeutic target for prostate cancer

    Science.gov (United States)

    Kulkarni, Prakash; Dunker, A Keith; Weninger, Keith; Orban, John

    2016-01-01

    Prostate-associated gene 4 (PAGE4) is a remarkably prostate-specific Cancer/Testis Antigen that is highly upregulated in the human fetal prostate and its diseased states but not in the adult normal gland. PAGE4 is an intrinsically disordered protein (IDP) that functions as a stress-response protein to suppress reactive oxygen species as well as prevent DNA damage. In addition, PAGE4 is also a transcriptional regulator that potentiates transactivation by the oncogene c-Jun. c-Jun forms the AP-1 complex by heterodimerizing with members of the Fos family and plays an important role in the development and pathology of the prostate gland, underscoring the importance of the PAGE4/c-Jun interaction. HIPK1, also a component of the stress-response pathway, phosphorylates PAGE4 at T51 which is critical for its transcriptional activity. Phosphorylation induces conformational and dynamic switching in the PAGE4 ensemble leading to a new cellular function. Finally, bioinformatics evidence suggests that the PAGE4 mRNA could be alternatively spliced resulting in four potential isoforms of the polypeptide alluding to the possibility of a range of conformational ensembles with latent functions. Considered together, the data suggest that PAGE4 may represent the first molecular link between stress and prostate cancer (PCa). Thus, pharmacologically targeting PAGE4 may be a novel opportunity for treating and managing patients with PCa, especially patients with low-risk disease. PMID:27270343

  15. The TFE-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of Escherichia coli RNA polymerase.

    Science.gov (United States)

    Kaczka, Piotr; Winiewska, Maria; Zhukov, Igor; Rempoła, Bożenna; Bolewska, Krystyna; Łoziński, Tomasz; Ejchart, Andrzej; Poznańska, Anna; Wierzchowski, Kazimierz L; Poznański, Jarosław

    2014-12-01

    The transient folding of domain 4 of an E. coli RNA polymerase σ⁷⁰ subunit (rECσ₄⁷⁰) induced by an increasing concentration of 2,2,2-trifluoroethanol (TFE) in an aqueous solution was monitored by means of CD and heteronuclear NMR spectroscopy. NMR data, collected at a 30% TFE, allowed the estimation of the population of a locally folded rECσ₄⁷⁰ structure (CSI descriptors) and of local backbone dynamics ((15)N relaxation). The spontaneous organization of the helical regions of the initially unfolded protein into a TFE-induced 3D structure was revealed from structural constraints deduced from (15)N- to (13)C-edited NOESY spectra. In accordance with all the applied criteria, three highly populated α-helical regions, separated by much more flexible fragments, form a transient HLHTH motif resembling those found in PDB structures resolved for homologous proteins. All the data taken together demonstrate that TFE induces a transient native-like structure in the intrinsically disordered protein. PMID:25261014

  16. The edge of chaos: A nonlinear view of psychoanalytic technique.

    Science.gov (United States)

    Galatzer-Levy, Robert M

    2016-04-01

    The field of nonlinear dynamics (or chaos theory) provides ways to expand concepts of psychoanalytic process that have implications for the technique of psychoanalysis. This paper describes how concepts of "the edge of chaos," emergence, attractors, and coupled oscillators can help shape analytic technique resulting in an approach to doing analysis which is at the same time freer and more firmly based in an enlarged understanding of the ways in which psychoanalysis works than some current recommendation about technique. Illustrations from a lengthy analysis of an analysand with obsessive-compulsive disorder show this approach in action. PMID:27030426

  17. Chaos Theory and Post Modernism

    Science.gov (United States)

    Snell, Joel

    2009-01-01

    Chaos theory is often associated with post modernism. However, one may make the point that both terms are misunderstood. The point of this article is to define both terms and indicate their relationship. Description: Chaos theory is associated with a definition of a theory dealing with variables (butterflies) that are not directly related to a…

  18. Chaos Criminology: A critical analysis

    Science.gov (United States)

    McCarthy, Adrienne L.

    There has been a push since the early 1980's for a paradigm shift in criminology from a Newtonian-based ontology to one of quantum physics. Primarily this effort has taken the form of integrating Chaos Theory into Criminology into what this thesis calls 'Chaos Criminology'. However, with the melding of any two fields, terms and concepts need to be translated properly, which has yet to be done. In addition to proving a translation between fields, this thesis also uses a set of criteria to evaluate the effectiveness of the current use of Chaos Theory in Criminology. While the results of the theory evaluation reveal that the current Chaos Criminology work is severely lacking and in need of development, there is some promise in the development of Marx's dialectical materialism with Chaos Theory.

  19. Transition to Chaos in Random Neuronal Networks

    Science.gov (United States)

    Kadmon, Jonathan; Sompolinsky, Haim

    2015-10-01

    Firing patterns in the central nervous system often exhibit strong temporal irregularity and considerable heterogeneity in time-averaged response properties. Previous studies suggested that these properties are the outcome of the intrinsic chaotic dynamics of the neural circuits. Indeed, simplified rate-based neuronal networks with synaptic connections drawn from Gaussian distribution and sigmoidal nonlinearity are known to exhibit chaotic dynamics when the synaptic gain (i.e., connection variance) is sufficiently large. In the limit of an infinitely large network, there is a sharp transition from a fixed point to chaos, as the synaptic gain reaches a critical value. Near the onset, chaotic fluctuations are slow, analogous to the ubiquitous, slow irregular fluctuations observed in the firing rates of many cortical circuits. However, the existence of a transition from a fixed point to chaos in neuronal circuit models with more realistic architectures and firing dynamics has not been established. In this work, we investigate rate-based dynamics of neuronal circuits composed of several subpopulations with randomly diluted connections. Nonzero connections are either positive for excitatory neurons or negative for inhibitory ones, while single neuron output is strictly positive with output rates rising as a power law above threshold, in line with known constraints in many biological systems. Using dynamic mean field theory, we find the phase diagram depicting the regimes of stable fixed-point, unstable-dynamic, and chaotic-rate fluctuations. We focus on the latter and characterize the properties of systems near this transition. We show that dilute excitatory-inhibitory architectures exhibit the same onset to chaos as the single population with Gaussian connectivity. In these architectures, the large mean excitatory and inhibitory inputs dynamically balance each other, amplifying the effect of the residual fluctuations. Importantly, the existence of a transition to chaos

  20. The Retentivity of Chaos under Topological Conjugation

    OpenAIRE

    Tianxiu Lu; Peiyong Zhu; Xinxing Wu

    2013-01-01

    The definitions of Devaney chaos (DevC), exact Devaney chaos (EDevC), mixing Devaney chaos (MDevC), and weak mixing Devaney chaos (WMDevC) are extended to topological spaces. This paper proves that these chaotic properties are all preserved under topological conjugation. Besides, an example is given to show that the Li-Yorke chaos is not preserved under topological conjugation if the domain is extended to a general metric space.

  1. Chaos a very short introduction

    CERN Document Server

    Smith, Leonard

    2007-01-01

    Chaos: A Very Short Introduction shows that we all have an intuitive understanding of chaotic systems. It uses accessible maths and physics (replacing complex equations with simple examples like pendulums, railway lines, and tossing coins) to explain the theory, and points to numerous examples in philosophy and literature (Edgar Allen Poe, Chang-Tzu, and Arthur Conan Doyle) that illuminate the problems. The beauty of fractal patterns and their relation to chaos, as well as the history of chaos, and its uses in the real world and implications for the philosophy of science are all discussed in this Very Short Introduction.

  2. Containers of disorder: Generator of comfort place by the chaos of objects; El contenedor de desorden: Generador de espacios confortables mediante el caos objetual

    Energy Technology Data Exchange (ETDEWEB)

    D Lacoste P, Laura C; Machado P, Maria V. [Universidad del Zulia-LUZ, Maracaibo (Venezuela)

    2000-07-01

    In an urban context at side to any consideration of bioclimatic conditioning, the buildings are defined as repetitive and independent unites apparently homogeneous, characterized as isolated cellular elements, without responding to the climatic conditions of Maracaibo city; as high temperature values and relative humidity during all the year, north-northeast winds, low precipitation and the year average values of solar radiation. This is why it appears a sequence of buildings, that in first place, they are the reproduction of these cellular elements which in their evolution, suffer a series of changes, to acquire more sensibility with the context, generation the house as containers of disorder; being the container whom assume the responsibilities of ventilation, sunning, natural illumination, etc.; and the contained objects disposed in a random or an ordered way, since they have been freed of bioclimatic and contextual responsibilities. The container of disorder is a pure prismatic volume, that regards objects in different forms and functions, disposed in a hazard way in two strips: the mass strip where it is disposed the space separator objects, that is the equipment; and the light strip, where the objects are punctured by the structure of the container. Some of the bioclimatic principle used for the designing of this container were the minimization of heat gain by radiation and conduction; wind control; vegetation; selection of recyclable and recycled materials; the utilization of gray water and rain water. This proposal has been evaluated through the thermal simulation program CODYBA and a French model heliodom to determine the evolution of interior temperature, the values of comfort and the solar protection effectiveness. This permitted to know that the interior media temperature was 2 Celsius degrees less than the exterior media temperature, concluding that with the usage of a macro cover that assume bioclimatic responsibilities, it is possible to increase the

  3. really intrinsic

    Directory of Open Access Journals (Sweden)

    Goldsmith Brendan

    2015-10-01

    Full Text Available The intrinsic algebraic entropy ent(ɸ of an endomorphism ɸ of an Abelian group G can be computed using fully inert subgroups of ɸ-invariant sections of G, instead of the whole family of ɸ-inert subgroups. For a class of groups containing the groups of finite rank, aswell as those groupswhich are trajectories of finitely generated subgroups, it is proved that only fully inert subgroups of the group itself are needed to comput ent(ɸ. Examples show how the situation may be quite different outside of this class.

  4. Self-organization of chaos in mythology from a scientific point of view

    Science.gov (United States)

    Melker, Alexander I.

    2007-04-01

    In this contribution ancient Greek myths describing world's creation are analyzed as if they were a scientific paper. The 'paper' divided into the following parts: initial and boundary conditions, self-organization of chaos, world lines of self-organization, conclusion. It is shown that the self-organization of chaos consists of several stages during which two motive forces (attractive and repulsive) are generated, and totally disordered chaos transforms into partially ordered. It is found that there are five world lines of self-organization: water, light, cosmos-weather, water-fire, and State evolution.

  5. A Chaos Conveyor Belt

    Science.gov (United States)

    Schmidt, Britney E.

    2013-10-01

    A critical question for the habitability of Europa remains: how does the ice shell work? The detection of shallow subsurface lenses below Europa’s chaos implies that the ice shell is recycled rapidly and that Europa may be currently active. While this is not the first time liquid water has been implicated for Europa, the location of these features combined with new perspective on their dynamics frames the question in a new way. Melt lenses are intriguing potential habitats. Moreover, their formation requires the existence of impurities within the upper ice shell that may be sources of energy for microorganisms. Geomorphic evidence also exists for hydraulic redistribution of fluids both vertically and horizontally through pores and fractures. This process, observed in terrestrial ice shelves, may preserve liquid water within the ice matrix over many kilometers from the source. Horizontal transport of material may produce interconnectivity between distinct regions of Europa, thus preserving habitable conditions within the ice over a longer duration. At a surface age of 40-90 Myr, with 25-50% covered by chaos terrain, Europa's resurfacing rate is very high and water likely plays a significant role. Because of the vigor of overturn implied by this new work, it is likely that surface and subsurface materials are well-mixed within the largest and deepest lenses, providing a mechanism for bringing oxidants and other surface contaminants to the deeper ice shell where it can reach the ocean by convective or compositional effects. The timescales over which large lenses refreeze are large compared to the timescales for vertical transport, while the timescales for smaller lenses are comparable to or shorter than convective timescales. Moreover, marine ice accretion at the bottom of the ice shell may be contributing to a compositional buoyancy engine that would change the makeup of the ice shell. From this point of view, we evaluate the habitability of Europa’s ice and

  6. Ancient and Current Chaos Theories

    Directory of Open Access Journals (Sweden)

    Güngör Gündüz

    2006-07-01

    Full Text Available Chaos theories developed in the last three decades have made very important contributions to our understanding of dynamical systems and natural phenomena. The meaning of chaos in the current theories and in the past is somewhat different from each other. In this work, the properties of dynamical systems and the evolution of chaotic systems were discussed in terms of the views of ancient philosophers. The meaning of chaos in Anaximenes’ philosophy and its role in the Ancient natural philosophy has been discussed in relation to other natural philosophers such as of Anaximander, Parmenides, Heraclitus, Empedocles, Leucippus (i.e. atomists and Aristotle. In addition, the fundamental concepts of statistical mechanics and the current chaos theories were discussed in relation to the views in Ancient natural philosophy. The roots of the scientific concepts such as randomness, autocatalysis, nonlinear growth, information, pattern, etc. in the Ancient natural philosophy were investigated.

  7. Cryptography with chaos and shadowing

    Energy Technology Data Exchange (ETDEWEB)

    Smaoui, Nejib [Department of Mathematics and Computer Science, Kuwait University, P.O. Box 5969, Safat 13060 (Kuwait)], E-mail: nsmaoui64@yahoo.com; Kanso, Ali [Department of Mathematics and Computer Science, Kuwait University, P.O. Box 5969, Safat 13060 (Kuwait)], E-mail: akanso@hotmail.com

    2009-11-30

    In this paper, we present a novel approach to encrypt a message (a text composed by some alphabets) using chaos and shadowing. First, we generate a numerical chaotic orbit based on the logistic map, and use the shadowing algorithm of Smaoui and Kostelich [Smaoui N, Kostelich E. Using chaos to shadow the quadratic map for all time. Int J Comput Math 1998;70:117-29] to show that there exists a finite number of true orbits that shadow the numerical orbit. Then, the finite number of maps generated is used in Baptista's algorithm [Baptista MS. Cryptography with chaos. Phys Lett A 1998;240:50-4] to encrypt each character of the message. It is shown that the use of chaos and shadowing in the encryption process enhances the security level.

  8. Quantum Instantons and Quantum Chaos

    OpenAIRE

    Jirari, H.; Kröger, H.; Luo, X. Q.; Moriarty, K. J. M.; Rubin, S. G.

    1999-01-01

    Based on a closed form expression for the path integral of quantum transition amplitudes, we suggest rigorous definitions of both, quantum instantons and quantum chaos. As an example we compute the quantum instanton of the double well potential.

  9. Cryptography with chaos and shadowing

    International Nuclear Information System (INIS)

    In this paper, we present a novel approach to encrypt a message (a text composed by some alphabets) using chaos and shadowing. First, we generate a numerical chaotic orbit based on the logistic map, and use the shadowing algorithm of Smaoui and Kostelich [Smaoui N, Kostelich E. Using chaos to shadow the quadratic map for all time. Int J Comput Math 1998;70:117-29] to show that there exists a finite number of true orbits that shadow the numerical orbit. Then, the finite number of maps generated is used in Baptista's algorithm [Baptista MS. Cryptography with chaos. Phys Lett A 1998;240:50-4] to encrypt each character of the message. It is shown that the use of chaos and shadowing in the encryption process enhances the security level.

  10. Quantum Chaos and Quantum Computers

    CERN Document Server

    Shepelyansky, D L

    2001-01-01

    The standard generic quantum computer model is studied analytically and numerically and the border for emergence of quantum chaos, induced by imperfections and residual inter-qubit couplings, is determined. This phenomenon appears in an isolated quantum computer without any external decoherence. The onset of quantum chaos leads to quantum computer hardware melting, strong quantum entropy growth and destruction of computer operability. The time scales for development of quantum chaos and ergodicity are determined. In spite the fact that this phenomenon is rather dangerous for quantum computing it is shown that the quantum chaos border for inter-qubit coupling is exponentially larger than the energy level spacing between quantum computer eigenstates and drops only linearly with the number of qubits n. As a result the ideal multi-qubit structure of the computer remains rather robust against imperfections. This opens a broad parameter region for a possible realization of quantum computer. The obtained results are...

  11. Ergodic cobweb chaos

    Directory of Open Access Journals (Sweden)

    Akio Matsumoto

    1997-01-01

    Full Text Available This study augments the traditional linear cobweb model with lower and upper bounds for variations of output. Its purpose is to detect the relationship between the output constraints and the dynamics of the modified model. Due to the upper and lower bounds, a transitional function takes on a tilted z-profile having three piecewise segments with two turning points. It prevents the price (or quantity dynamics from explosive oscillations. This study demonstrates, by presenting numerical examples, that the modified cobweb model can generate various dynamics ranging from stable periodic cycles to ergodic chaos if a product of the marginal propensity to consume and the marginal product is greater than unity.

  12. Partially predictable chaos

    CERN Document Server

    Wernecke, Hendrik; Gros, Claudius

    2016-01-01

    For a chaotic system pairs of initially close-by trajectories become eventually fully uncorrelated on the attracting set. This process of decorrelation is split into an initial decrease characterized by the maximal Lyapunov exponent and a subsequent diffusive process on the chaotic attractor causing the final loss of predictability. The time scales of both processes can be either of the same or of very different orders of magnitude. In the latter case the two trajectories linger within a finite but small distance (with respect to the overall size of the attractor) for exceedingly long times and therefore remain partially predictable. We introduce a 0-1 indicator for chaos capable of describing this scenario, arguing, in addition, that the chaotic closed braids found close to a period-doubling transition are generically partially predictable.

  13. The Chaos Within Sudoku

    CERN Document Server

    Ercsey-Ravasz, Maria

    2012-01-01

    The mathematical structure of the widely popular Sudoku puzzles is akin to typical hard constraint satisfaction problems that lie at the heart of many applications, including protein folding and the general problem of finding the ground state of a glassy spin system. Via an exact mapping of Sudoku into a deterministic, continuous-time dynamical system, here we show that the difficulty of Sudoku translates into transient chaotic behavior exhibited by the dynamical system. In particular, we show that the escape rate $\\kappa$, an invariant characteristic of transient chaos, provides a single scalar measure of the puzzle's hardness, which correlates well with human difficulty level ratings. Accordingly, $\\eta = -\\log_{10}{\\kappa}$ can be used to define a "Richter"-type scale for puzzle hardness, with easy puzzles falling in the range $0 3$. To our best knowledge, there are no known puzzles with $\\eta > 4$.

  14. Chaos in Partial Differential Equations

    OpenAIRE

    Li, Y. Charles

    2009-01-01

    This is a survey on Chaos in Partial Differential Equations. First we classify soliton equations into three categories: 1. (1+1)-dimensional soliton equations, 2. soliton lattices, 3. (1+n)-dimensional soliton equations (n greater than 1). A systematic program has been established by the author and collaborators, for proving the existence of chaos in soliton equations under perturbations. For each category, we pick a representative to present the results. Then we review some initial results o...

  15. Chaos in circuits and systems

    CERN Document Server

    Chen, Guanrong

    2002-01-01

    In this volume, leading experts present current achievements in the forefront of research in the challenging field of chaos in circuits and systems, with emphasis on engineering perspectives, methodologies, circuitry design techniques, and potential applications of chaos and bifurcation. A combination of overview, tutorial and technical articles, the book describes state-of-the-art research on significant problems in this field. It is suitable for readers ranging from graduate students, university professors, laboratory researchers and industrial practitioners to applied mathematicians and phy

  16. ORDER IN THE CHAOS IN SPORTS ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Mehran Azarian

    2014-07-01

    Full Text Available Purpose: Nowadays, scientists consider the world as a combination of some systems that work in a self -organizing way and the result of such a way is unpredictable and accidential states. Compulsory Natural rules are affective in such circumstances. Also it is known that systems work in a circular form in which order ends in disorder and vice versa. The idea of world as something simple has already replaced by a complicated and contradictory world. The study aim is to survey chaordic organizations characters of sport organizations. Materials and methods : For this purpose we used a standard questionnaire with appropriate reliability and validity. The statistical population of the study are whole staff of sport and youth head-quarter of west Azarbaijan province that are 89 (sample number is equal to the population's. We used Kolmogrov- Smirnov test to study data normal distribution, and in respect of normal distribution of data to test hypothesis we used sample t test and also descriptive statistical methods like mean and standard deviation, through SPSS 18. Questionnaires were filled out by whole staff of sport and youth head-quarters of west Azarbaijan province. Results: Results of this study, which have got through a single-sample t-test, show that sport organizations have six characteristics of welcoming to innovation, coherence, uncertainty, non-linearity, unpredictability, and ugly structure. It’s just the grade of the characteristic of recruiting competent staffs that is low in sport organizations; in fact they don’t enjoy it. But, within assessing the main hypothesis of the research that was around the feature of chaos-order, it was resulted that sport organizations have characteristics of a chaos-order organization and they can be considered as a chaos-order organization. Conclusions: According to the results of this study and t-table we can deduce that sport organizations are chaordic organization.

  17. Stimulus-dependent suppression of chaos in recurrent neural networks

    International Nuclear Information System (INIS)

    Neuronal activity arises from an interaction between ongoing firing generated spontaneously by neural circuits and responses driven by external stimuli. Using mean-field analysis, we ask how a neural network that intrinsically generates chaotic patterns of activity can remain sensitive to extrinsic input. We find that inputs not only drive network responses, but they also actively suppress ongoing activity, ultimately leading to a phase transition in which chaos is completely eliminated. The critical input intensity at the phase transition is a nonmonotonic function of stimulus frequency, revealing a 'resonant' frequency at which the input is most effective at suppressing chaos even though the power spectrum of the spontaneous activity peaks at zero and falls exponentially. A prediction of our analysis is that the variance of neural responses should be most strongly suppressed at frequencies matching the range over which many sensory systems operate.

  18. 2012 Symposium on Chaos, Complexity and Leadership

    CERN Document Server

    Erçetin, Şefika

    2014-01-01

    These proceedings from the 2012 symposium on "Chaos, complexity and leadership"  reflect current research results from all branches of Chaos, Complex Systems and their applications in Management. Included are the diverse results in the fields of applied nonlinear methods, modeling of data and simulations, as well as theoretical achievements of Chaos and Complex Systems. Also highlighted are  Leadership and Management applications of Chaos and Complexity Theory.

  19. Decoherence, determinism and chaos

    International Nuclear Information System (INIS)

    The author claims by now to have made his case that modern work on fractals and chaos theory has already removed the presumption that classical physics is 'deterministic'. Further, he claims that in so far as classical relativistic field theory (i.e. electromagnetism and gravitation) are scale invariant, they are self-consistent only if the idea of 'test-particle' is introduced from outside the theory. Einstein spent the last years of his life trying to use singularities in the metric as 'particles' or to get them out of the non-linearities in a grand unified theory -- in vain. So classical physics in this sense cannot be the fundamental theory. However, the author claims to have shown that if he introduces a 'scale invariance bounded from below' by measurement accuracy, then Tanimura's generalization of the Feynman proof as reconstructed by Dyson allows him to make a consistent classical theory for decoherent sources sinks. Restoring coherence to classical physics via relativistic action-at-a distance is left as a task for the future. Relativistic quantum mechanics, properly reconstructed from a finite and discrete basis, emerges in much better shape. The concept of 'particles has to be replaced by NO-YES particulate events, and particle-antiparticle pair creation and annihilation properly formulated

  20. Chaos of chiral condensate

    CERN Document Server

    Hashimoto, Koji; Yoshida, Kentaroh

    2016-01-01

    Assigning a chaos index for vacua of generic quantum field theories is a challenging problem. We find chaotic behavior of chiral condensates of a quantum gauge theory at strong coupling limit, by using the AdS/CFT correspondence. We evaluate the time evolution of homogeneous quark condensates and in an N=2 supersymmetric QCD with the SU(N_c) gauge group at large N_c and at large 't Hooft coupling lambda. At an equivalent classical gravity picture, a Lyapunov exponent is readily defined. We show that the condensates exhibit chaotic behavior for energy density E > (6x10^2) (N_c/lambda^2) (m_q)^4 where m_q is the quark mass. The energy region of the chaotic vacua of the N=2 supersymmetric QCD increases for smaller N_c or larger lambda. The Lyapunov exponent is calculated as a function of the theory (N_c,lambda,E), showing that the N=2 supersymmetric QCD is more chaotic for smaller N_c.

  1. Decoherence, determinism and chaos

    Energy Technology Data Exchange (ETDEWEB)

    Noyes, H.P.

    1994-01-01

    The author claims by now to have made his case that modern work on fractals and chaos theory has already removed the presumption that classical physics is `deterministic`. Further, he claims that in so far as classical relativistic field theory (i.e. electromagnetism and gravitation) are scale invariant, they are self-consistent only if the idea of `test-particle` is introduced from outside the theory. Einstein spent the last years of his life trying to use singularities in the metric as `particles` or to get them out of the non-linearities in a grand unified theory -- in vain. So classical physics in this sense cannot be the fundamental theory. However, the author claims to have shown that if he introduces a `scale invariance bounded from below` by measurement accuracy, then Tanimura`s generalization of the Feynman proof as reconstructed by Dyson allows him to make a consistent classical theory for decoherent sources sinks. Restoring coherence to classical physics via relativistic action-at-a distance is left as a task for the future. Relativistic quantum mechanics, properly reconstructed from a finite and discrete basis, emerges in much better shape. The concept of `particles has to be replaced by NO-YES particulate events, and particle-antiparticle pair creation and annihilation properly formulated.

  2. Intrinsic n

    International Nuclear Information System (INIS)

    ZnO typifies a class of materials that can be doped via native defects in only one way: either n type or p type. We explain this asymmetry in ZnO via a study of its intrinsic defect physics, including ZnO, Zni, VO, Oi, and VZn and n-type impurity dopants, Al and F. We find that ZnO is n type at Zn-rich conditions. This is because (i) the Zn interstitial, Zni, is a shallow donor, supplying electrons; (ii) its formation enthalpy is low for both Zn-rich and O-rich conditions, so this defect is abundant; and (iii) the native defects that could compensate the n-type doping effect of Zni (interstitial O, Oi, and Zn vacancy, VZn), have high formation enthalpies for Zn-rich conditions, so these ''electron killers'' are not abundant. We find that ZnO cannot be doped p type via native defects (Oi,VZn) despite the fact that they are shallow (i.e., supplying holes at room temperature). This is because at both Zn-rich and O-rich conditions, the defects that could compensate p-type doping (VO,Zni,ZnO) have low formation enthalpies so these ''hole killers'' form readily. Furthermore, we identify electron-hole radiative recombination at the VO center as the source of the green luminescence. In contrast, a large structural relaxation of the same center upon double hole capture leads to slow electron-hole recombination (either radiative or nonradiative) responsible for the slow decay of photoconductivity

  3. On CFT and Quantum Chaos

    CERN Document Server

    Turiaci, Gustavo

    2016-01-01

    We make three observations that help clarify the relation between CFT and quantum chaos. We show that any 1+1-D system in which conformal symmetry is non-linearly realized exhibits two main characteristics of chaos: maximal Lyapunov behavior and a spectrum of Ruelle resonances. We use this insight to identify a lattice model for quantum chaos, built from parafermionic spin variables with an equation of motion given by a Y-system. Finally we point to a relation between the spectrum of Ruelle resonances of a CFT and the analytic properties of OPE coefficients between light and heavy operators. In our model, this spectrum agrees with the quasi-normal modes of the BTZ black hole.

  4. Chaos, decoherence and quantum cosmology

    International Nuclear Information System (INIS)

    In this topical review we discuss the connections between chaos, decoherence and quantum cosmology. We understand chaos as classical chaos in systems with a finite number of degrees of freedom, decoherence as environment induced decoherence and quantum cosmology as the theory of the Wheeler-DeWitt equation or else the consistent history formulation thereof, first in mini super spaces and later through its extension to midi super spaces. The overall conclusion is that consideration of decoherence is necessary (and probably sufficient) to sustain an interpretation of quantum cosmology based on the wavefunction of the Universe adopting a Wentzel-Kramers-Brillouin form for large Universes, but a definitive account of the semiclassical transition in classically chaotic cosmological models is not available in the literature yet. (topical review)

  5. Quantum chaos in multiwell potentials

    International Nuclear Information System (INIS)

    Till the present time signatures of quantum chaos were studied mostly for the billiard-type systems, for dumped one-dimensional systems or for two-dimensional systems with potential energy surface of simple geometry. Almost nothing is known about the quantum chaos for generic Hamiltonian systems, including multiwell potentials, though those are the models describing the dynamics of transition between different states, for example, nuclear isomeric transitions and decay of superdeformed states of nuclei. An important feature of classical dynamics in generic multiwell potentials is the so-called mixed state, namely: regular and chaotic regimes coexist at the same energy, being localized in different local minima of the potential. The aim of our work is to show that studies of quantum chaos in the mixed state are promising and in many cases optimal. (author)

  6. Deterministic polarization chaos from a laser diode

    CERN Document Server

    Virte, Martin; Thienpont, Hugo; Sciamanna, Marc

    2014-01-01

    Fifty years after the invention of the laser diode and fourty years after the report of the butterfly effect - i.e. the unpredictability of deterministic chaos, it is said that a laser diode behaves like a damped nonlinear oscillator. Hence no chaos can be generated unless with additional forcing or parameter modulation. Here we report the first counter-example of a free-running laser diode generating chaos. The underlying physics is a nonlinear coupling between two elliptically polarized modes in a vertical-cavity surface-emitting laser. We identify chaos in experimental time-series and show theoretically the bifurcations leading to single- and double-scroll attractors with characteristics similar to Lorenz chaos. The reported polarization chaos resembles at first sight a noise-driven mode hopping but shows opposite statistical properties. Our findings open up new research areas that combine the high speed performances of microcavity lasers with controllable and integrated sources of optical chaos.

  7. Solitons and chaos in plasma

    International Nuclear Information System (INIS)

    Plasma exhibits a full of variety of nonlinear phenomena. Active research in nonlinear plasma physics contributed to explore the concepts of soliton and chaos. Structure of soliton equations and dynamics of low dimensional Hamiltonian systems are discussed to emphasize the universality of these novel concepts in the wide branch of science and engineering. (author) 52 refs

  8. Distributed chaos in turbulent wakes

    CERN Document Server

    Bershadskii, A

    2016-01-01

    Soft and hard spontaneous breaking of space translational symmetry (homogeneity) have been studied in turbulent wakes by means of distributed chaos. In the case of the soft translational symmetry breaking the vorticity correlation integral $\\int_{V} \\langle {\\boldsymbol \\omega} ({\\bf x},t) \\cdot {\\boldsymbol \\omega} ({\\bf x} + {\\bf r},t) \\rangle_{V} d{\\bf r}$ dominates the distributed chaos and the chaotic spectra $\\exp-(k/k_{\\beta})^{\\beta }$ have $\\beta =1/2$. In the case of the hard translational symmetry breaking, control on the distributed chaos is switched from one type of fundamental symmetry to another (in this case to Lagrangian relabeling symmetry). Due to the Noether's theorem the relabeling symmetry results in the inviscid helicity conservation and helicity correlation integral $I=\\int \\langle h({\\bf x},t)~h({\\bf x}+{\\bf r}, t)\\rangle d{\\bf r}$ (Levich-Tsinober invariant) dominates the distributed chaos with $\\beta =1/3$. Good agreement with the experimatal data has been established for turbulent ...

  9. Chaos Behaviour of Molecular Orbit

    Institute of Scientific and Technical Information of China (English)

    LIU Shu-Tang; SUN Fu-Yan; SHEN Shu-Lan

    2007-01-01

    Based on H(u)ckel's molecular orbit theory,the chaos and;bifurcation behaviour of a molecular orbit modelled by a nonlinear dynamic system is studied.The relationship between molecular orbit and its energy level in the nonlinear dynamic system is obtained.

  10. MHD turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

    It is shown, using results of recent direct numerical simulations, that spectral properties of distributed chaos in MHD turbulence with zero mean magnetic field are similar to those of hydrodynamic turbulence. An exception is MHD spontaneous breaking of space translational symmetry, when the stretched exponential spectrum $\\exp(-k/k_{\\beta})^{\\beta}$ has $\\beta=4/7$.

  11. Chaos Synthesis by Evolutionary Algorithms

    Czech Academy of Sciences Publication Activity Database

    Zelinka, I.; Chen, G.; Čelikovský, Sergej

    Berlin : Springer-Verlag, 2010 - (Zelinka, I.; Čelikovský, S.; Richter, H.; Chen, G.), s. 345-382 ISBN 978-3-642-10706-1. - (Studies in Computational Intelligence. 267) Institutional research plan: CEZ:AV0Z10750506 Keywords : chaos synthesis * evolutionary algorithms * self organizingmigrating * evolutionary computing Subject RIV: BC - Control Systems Theory

  12. Chaos and remedial investigations

    International Nuclear Information System (INIS)

    Current research into the nature of chaos indicates that even for systems that are well known and easily modeled, slight changes in the scale used to measure the input have unpredictable results in the model output. The conduct of a remedial investigation (RI) is dictated by well-established rules of investigation and management, yet small changes in project orientation, regulatory environment, or site conditions have unpredictable consequences to the project. The consequences can lead to either brilliant success or utter failure. The chaotic effect of a change in scale is most often illustrated by an exercise in measuring the length of the coast of Great Britain. If a straight ruler 10-kilometers long is used, the sum of the 10-kilometer increments gives the length of the coast. If the ruler is changed to five kilometers long and the exercise is repeated, the sum of the five-kilometer increments will not be the same as the sum of the 10-kilometer increments. Nor is there a way to predict what the length of the coast will be using any other scale. Several examples from the Fernald Project RI are used to illustrate open-quotes changes in scaleclose quotes in both technical and management situations. Given that there is no way to predict the outcome of scale changes in a RI, technical and project management must be alert to the fact that a scale has changed and the investigation is no longer on the path it was thought to be on. The key to success, therefore, is to develop specific units of measure for a number of activities, in addition to cost and schedule, and track them regularly. An example for tracking a portion of the field investigation is presented. The determination of effective units of measure is perhaps the most difficult aspect of any project. Changes in scale sometimes go unnoticed until suddenly the budget is expended and only a portion of the work is completed. Remedial investigations on large facilities provide new and complex challenges

  13. Hamiltonian Chaos and Fractional Dynamics

    International Nuclear Information System (INIS)

    This book provides an introduction and discussion of the main issues in the current understanding of classical Hamiltonian chaos, and of its fractional space-time structure. It also develops the most complex and open problems in this context, and provides a set of possible applications of these notions to some fundamental questions of dynamics: complexity and entropy of systems, foundation of classical statistical physics on the basis of chaos theory, and so on. Starting with an introduction of the basic principles of the Hamiltonian theory of chaos, the book covers many topics that can be found elsewhere in the literature, but which are collected here for the readers' convenience. In the last three parts, the author develops topics which are not typically included in the standard textbooks; among them are: - the failure of the traditional description of chaotic dynamics in terms of diffusion equations; - he fractional kinematics, its foundation and renormalization group analysis; - 'pseudo-chaos', i.e. kinetics of systems with weak mixing and zero Lyapunov exponents; - directional complexity and entropy. The purpose of this book is to provide researchers and students in physics, mathematics and engineering with an overview of many aspects of chaos and fractality in Hamiltonian dynamical systems. In my opinion it achieves this aim, at least provided researchers and students (mainly those involved in mathematical physics) can complement this reading with comprehensive material from more specialized sources which are provided as references and 'further reading'. Each section contains introductory pedagogical material, often illustrated by figures coming from several numerical simulations which give the feeling of what's going on, and thus is very useful to the reader who is not very familiar with the topics presented. Some problems are included at the end of most sections to help the reader to go deeper into the subject. My one regret is that the book does not

  14. First-principles evaluation of intrinsic, side-jump, and skew-scattering parts of anomalous Hall conductivities in disordered alloys

    OpenAIRE

    Hyodo, K; Kota, Y; Sakuma, A.

    2016-01-01

    We develop a first-principles procedure for the individual evaluation of the intrinsic, side-jump, and skew-scattering contributions to the anomalous Hall conductivity ${\\sigma}_{xy}$. This method is based on the different microscopic conductive processes of each origin of ${\\sigma}_{xy}$ in the Kubo-Streda formula. We also present an approach for implementing this scheme in the tight-binding linear muffin-tin orbital (TB-LMTO) method with the coherent potential approximation (CPA). The valid...

  15. Advances in chaos theory and intelligent control

    CERN Document Server

    Vaidyanathan, Sundarapandian

    2016-01-01

    The book reports on the latest advances in and applications of chaos theory and intelligent control. Written by eminent scientists and active researchers and using a clear, matter-of-fact style, it covers advanced theories, methods, and applications in a variety of research areas, and explains key concepts in modeling, analysis, and control of chaotic and hyperchaotic systems. Topics include fractional chaotic systems, chaos control, chaos synchronization, memristors, jerk circuits, chaotic systems with hidden attractors, mechanical and biological chaos, and circuit realization of chaotic systems. The book further covers fuzzy logic controllers, evolutionary algorithms, swarm intelligence, and petri nets among other topics. Not only does it provide the readers with chaos fundamentals and intelligent control-based algorithms; it also discusses key applications of chaos as well as multidisciplinary solutions developed via intelligent control. The book is a timely and comprehensive reference guide for graduate s...

  16. Recent Developments on Chaos in Mechanical Systems

    OpenAIRE

    Mohammad Sajid

    2013-01-01

    Recent advancements in complexity of mechanical systems have led to the application of chaos theory. In this paper, some recent developments on chaos in mechanical systems are explored. The aim is to bring together researchers from various interests of mechanical systems, exposing them to chaos theory. This exposure gives researchers from the discipline of mechanical systems to find opportunity of cross disciplinary research, which may ultimately lead to novel solutions and understanding of m...

  17. A Quantum Correction To Chaos

    CERN Document Server

    Fitzpatrick, A Liam

    2016-01-01

    We use results on Virasoro conformal blocks to study chaotic dynamics in CFT$_2$ at large central charge c. The Lyapunov exponent $\\lambda_L$, which is a diagnostic for the early onset of chaos, receives $1/c$ corrections that may be interpreted as $\\lambda_L = \\frac{2 \\pi}{\\beta} \\left( 1 + \\frac{12}{c} \\right)$. However, out of time order correlators receive other equally important $1/c$ suppressed contributions that do not have such a simple interpretation. We revisit the proof of a bound on $\\lambda_L$ that emerges at large $c$, focusing on CFT$_2$ and explaining why our results do not conflict with the analysis leading to the bound. We also comment on relationships between chaos, scattering, causality, and bulk locality.

  18. Scrambling without chaos in RCFT

    CERN Document Server

    Caputa, Pawel; Veliz-Osorio, Alvaro

    2016-01-01

    In this letter we investigate measures of chaos and entanglement scrambling in rational conformal field theories in 1+1 dimensions. First, we derive a formula for the late time value of the out-of-time-order correlators for these class of theories. Our universal result can be expressed as a particular combination of the modular S-matrix elements known as anyon monodromy scalar. Next, in the explicit setup of a $SU(N)_k$ WZW model, we compare the late time behaviour of the out-of-time correlators and the purity. Interestingly, in the large-c limit, the purity grows logarithmically but the out-of-time-order correlators remain constant. Therefore, we find that some systems may display entanglement scrambling in the absence of chaos.

  19. Spatiotemporal chaos from bursting dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Berenstein, Igal; De Decker, Yannick [Nonlinear Physical Chemistry Unit and Interdisciplinary Center for Nonlinear Phenomena and Complex Systems (CENOLI), Faculté des Sciences, Université libre de Bruxelles (ULB), Campus Plaine, C.P. 231, B-1050 Brussels (Belgium)

    2015-08-14

    In this paper, we study the emergence of spatiotemporal chaos from mixed-mode oscillations, by using an extended Oregonator model. We show that bursting dynamics consisting of fast/slow mixed mode oscillations along a single attractor can lead to spatiotemporal chaotic dynamics, although the spatially homogeneous solution is itself non-chaotic. This behavior is observed far from the Hopf bifurcation and takes the form of a spatiotemporal intermittency where the system locally alternates between the fast and the slow phases of the mixed mode oscillations. We expect this form of spatiotemporal chaos to be generic for models in which one or several slow variables are coupled to activator-inhibitor type of oscillators.

  20. On the definition of 'chaos'

    International Nuclear Information System (INIS)

    A new definition of a chaotic invariant set is given for a continuous semiflow in a metric space. It generalizes the well-known definition due to Devaney and allows one to take into account a special feature occurring in the non-compact infinite-dimensional case: so-called turbulent chaos. The paper consists of two sections. The first contains several well-known facts from chaotic dynamics, together with new definitions and results. The second presents a concrete example demonstrating that our definition of chaos is meaningful. Namely, an infinite-dimensional system of ordinary differential equations is investigated having an attractor that is chaotic in the sense of the new definition but not in the sense of Devaney or Knudsen. Bibliography: 65 titles.

  1. Chaos, turbulence and strange attractors

    International Nuclear Information System (INIS)

    Using the turbulence example, the author recalls the two different conceptions of the nature of an erratic regime: the one in which a great number of elementary events are concerned (Landau) and the other one in which, on the contrary, a few number of elementary events are concerned (Ruelle and Takens). The last type of erratic comportment has a deterministic origin and is pointed by the adjective chaotic. Phase space for a dynamic system is presented and so the attractor nation. Chaos and notion of sensitiveness to initial conditions are defined. In scrutining the geometry of an attractor corresponding to a chaotic regime, the notion of strange attractor is shown. Some experiments results are given as illustration. Application field is recalled: for example, studies on hamiltonian chaos are made at DRFC (Department of research on controlled fusion at CEA) in relation with plasma instabilities

  2. Master stability analysis in transient spatiotemporal chaos.

    Science.gov (United States)

    Wackerbauer, Renate

    2007-11-01

    The asymptotic stability of spatiotemporal chaos is difficult to determine, since transient spatiotemporal chaos may be extremely long lived. A master stability analysis reveals that the asymptotic state of transient spatiotemporal chaos in the Gray-Scott system and in the Bär-Eiswirth system is characterized by negative transverse Lyapunov exponents on the attractor of the invariant synchronization manifold. The average lifetime of transient spatiotemporal chaos depends on the number of transverse directions that are unstable along a typical excitation cycle. PMID:18233739

  3. The chaos cookbook a practical programming guide

    CERN Document Server

    Pritchard, Joe

    2014-01-01

    The Chaos Cookbook: A Practical Programming Guide discusses the use of chaos in computer programming. The book is comprised of 11 chapters that tackle various topics relevant to chaos and programming. Chapter 1 reviews the concept of chaos, and Chapter 2 discusses the iterative functions. Chapters 3 and 4 cover differential and Lorenz equations. Chapter 5 talks about strange attractors, while Chapter 6 deals with the fractal link. The book also discusses the Mandelbrot set, and then covers the Julia sets. The other fractal systems and the cellular automata are also explained. The last chapter

  4. Chaos in the library environment

    OpenAIRE

    Κατσιρίκου, Ανθή

    2001-01-01

    Describes the impact of chaos theory in social systems and the phenomena that result from it, drawing attention to related phenomena in the state of the library today. Then considers the factors that lead library systems to exhibit chaotic behaviour. These factors are the plethora of technological tools and the variety of software and interfaces, the dependence of resource providers and the increasing supply and diversity of information resources. The changes dictated by these factors influen...

  5. Relative chaos in stellar systems

    International Nuclear Information System (INIS)

    Statistical properties of many-dimensional dynamical system -s tellar systems of different types, are investigated by means of estimation of Ricci curvature in the direction of the velocity of geodesics. Numerical experiment is performed to calculate the Ricci and scalar curvatures for systems with equal total energy. The results of calculations enable one to obtain schematic classification of stellar systems by increasing degree of chaos

  6. Analysis of FBC deterministic chaos

    Energy Technology Data Exchange (ETDEWEB)

    Daw, C.S.

    1996-06-01

    It has recently been discovered that the performance of a number of fossil energy conversion devices such as fluidized beds, pulsed combustors, steady combustors, and internal combustion engines are affected by deterministic chaos. It is now recognized that understanding and controlling the chaotic elements of these devices can lead to significantly improved energy efficiency and reduced emissions. Application of these techniques to key fossil energy processes are expected to provide important competitive advantages for U.S. industry.

  7. Chaos and multiple photon absorption

    International Nuclear Information System (INIS)

    An anharmonic vibrational mode of a molecule, driven by an intense infrared laser and coupled to a quasi-continuum of background modes, is found to undergo chaotic oscillations. This chaos leads to predominantly fluence-dependent rather than intensity-dependent multiple-photon absorption, as is found experimentally. The loss of coherence is associated with the decay of temporal correlation of background-mode oscillations

  8. Model for Shock Wave Chaos

    KAUST Repository

    Kasimov, Aslan R.

    2013-03-08

    We propose the following model equation, ut+1/2(u2−uus)x=f(x,us) that predicts chaotic shock waves, similar to those in detonations in chemically reacting mixtures. The equation is given on the half line, x<0, and the shock is located at x=0 for any t≥0. Here, us(t) is the shock state and the source term f is taken to mimic the chemical energy release in detonations. This equation retains the essential physics needed to reproduce many properties of detonations in gaseous reactive mixtures: steady traveling wave solutions, instability of such solutions, and the onset of chaos. Our model is the first (to our knowledge) to describe chaos in shock waves by a scalar first-order partial differential equation. The chaos arises in the equation thanks to an interplay between the nonlinearity of the inviscid Burgers equation and a novel forcing term that is nonlocal in nature and has deep physical roots in reactive Euler equations.

  9. Hamiltonian chaos and fractional dynamics

    CERN Document Server

    Zaslavsky, George M

    2008-01-01

    The dynamics of realistic Hamiltonian systems has unusual microscopic features that are direct consequences of its fractional space-time structure and its phase space topology. The book deals with the fractality of the chaotic dynamics and kinetics, and also includes material on non-ergodic and non-well-mixing Hamiltonian dynamics. The book does not follow the traditional scheme of most of today's literature on chaos. The intention of the author has been to put together some of the most complex and yet open problems on the general theory of chaotic systems. The importance of the discussed issues and an understanding of their origin should inspire students and researchers to touch upon some of the deepest aspects of nonlinear dynamics. The book considers the basic principles of the Hamiltonian theory of chaos and some applications including for example, the cooling of particles and signals, control and erasing of chaos, polynomial complexity, Maxwell's Demon, and others. It presents a new and realistic image ...

  10. Dynamical chaos and power spectra in toy models of heteropolymers and proteins

    OpenAIRE

    Li, Mai Suan; Cieplak, Marek; Sushko, Nazar

    2000-01-01

    The dynamical chaos in Lennard-Jones toy models of heteropolymers is studied by molecular dynamics simulations. It is shown that two nearby trajectories quickly diverge from each other if the heteropolymer corresponds to a random sequence. For good folders, on the other hand, two nearby trajectories may initially move apart but eventually they come together. Thus good folders are intrinsically non-chaotic. A choice of a distance of the initial conformation from the native state affects the wa...

  11. Selection for intrinsic endurance modifies endocrine stress responsiveness

    OpenAIRE

    Waters, R Parrish; Renner, Kenneth J.; Summers, Cliff H.; Watt, Michael L; Forster, Gina L.; Koch, Lauren G.; Britton, Steven L.; Swallow, John G.

    2010-01-01

    Physical exercise dampens an individual’s stress response and decreases symptoms of anxiety and depression disorders. While the extrinsic relationship of exercise and psychological state are established, their intrinsic relationship is unresolved. We investigated the potential intrinsic relationship of exercise with stress responsiveness using NIH rats bidirectionally selected for intrinsic endurance capacity. Selection resulted in two populations, one with high intrinsic endurance (high capa...

  12. Discretization chaos - Feedback control and transition to chaos

    Science.gov (United States)

    Grantham, Walter J.; Athalye, Amit M.

    1990-01-01

    Problems in the design of feedback controllers for chaotic dynamical systems are considered theoretically, focusing on two cases where chaos arises only when a nonchaotic continuous-time system is discretized into a simpler discrete-time systems (exponential discretization and pseudo-Euler integration applied to Lotka-Volterra competition and prey-predator systems). Numerical simulation results are presented in extensive graphs and discussed in detail. It is concluded that care must be taken in applying standard dynamical-systems methods to control systems that may be discontinuous or nondifferentiable.

  13. PHASE CHAOS IN THE DISCRETE KURAMOTO MODEL

    DEFF Research Database (Denmark)

    Maistrenko, V.; Vasylenko, A.; Maistrenko, Y.; Mosekilde, Erik

    2010-01-01

    The paper describes the appearance of a novel, high-dimensional chaotic regime, called phase chaos, in a time-discrete Kuramoto model of globally coupled phase oscillators. This type of chaos is observed at small and intermediate values of the coupling strength. It arises from the nonlinear inter...

  14. Chaos and fractals. Applications to nuclear engineering

    International Nuclear Information System (INIS)

    This work presents a description of the research lines carried out by the authors on chaos and fractal theories, oriented to the nuclear field. The possibilities that appear in the nuclear security branch where the information deriving from chaos and fractal techniques may help to the development of better criteria and more reliable designs, are of special importance. (Author)

  15. Chaos in nonlinear oscillations controlling and synchronization

    CERN Document Server

    Lakshamanan, M

    1996-01-01

    This book deals with the bifurcation and chaotic aspects of damped and driven nonlinear oscillators. The analytical and numerical aspects of the chaotic dynamics of these oscillators are covered, together with appropriate experimental studies using nonlinear electronic circuits. Recent exciting developments in chaos research are also discussed, such as the control and synchronization of chaos and possible technological applications.

  16. "Chaos" Theory: Implications for Educational Research.

    Science.gov (United States)

    Lindsay, Jean S.

    "Chaos" theory is a revolutionary new paradigm developed by scientists to study the behavior of natural systems. "Chaos" refers to the tendency of dynamic non-linear systems toward irregular, sometimes unpredictable, yet deterministic behavior. Major tenets of the theory are presented. The precedent for use of models developed in the natural…

  17. The CHAOS-4 geomagnetic field model

    DEFF Research Database (Denmark)

    Olsen, Nils; Lühr, H.; Finlay, Chris;

    2014-01-01

    We present CHAOS-4, a new version in the CHAOS model series, which aims to describe the Earth's magnetic field with high spatial and temporal resolution. Terms up to spherical degree of at least n = 85 for the lithospheric field, and up to n = 16 for the time-varying core field are robustly deter...

  18. The CHAOS-4 Geomagnetic Field Model

    DEFF Research Database (Denmark)

    Olsen, Nils; Finlay, Chris; Lühr, H.;

    We present CHAOS-4, a new version in the CHAOS model series, which aims at describing the Earth's magnetic field with high spatial resolution (terms up to spherical degree n=90 for the crustal field, and up to n=16 for the time-varying core field are robustly determined) and high temporal resolut...

  19. Easy and unambiguous sequential assignments of intrinsically disordered proteins by correlating the backbone {sup 15}N or {sup 13}C′ chemical shifts of multiple contiguous residues in highly resolved 3D spectra

    Energy Technology Data Exchange (ETDEWEB)

    Yoshimura, Yuichi; Kulminskaya, Natalia V.; Mulder, Frans A. A., E-mail: fmulder@chem.au.dk [Aarhus University, Department of Chemistry and Interdisciplinary Nanoscience Center (iNANO) (Denmark)

    2015-02-15

    Sequential resonance assignment strategies are typically based on matching one or two chemical shifts of adjacent residues. However, resonance overlap often leads to ambiguity in resonance assignments in particular for intrinsically disordered proteins. We investigated the potential of establishing connectivity through the three-bond couplings between sequentially adjoining backbone carbonyl carbon nuclei, combined with semi-constant time chemical shift evolution, for resonance assignments of small folded and larger unfolded proteins. Extended sequential connectivity strongly lifts chemical shift degeneracy of the backbone nuclei in disordered proteins. We show here that 3D (H)N(COCO)NH and (HN)CO(CO)NH experiments with relaxation-optimized multiple pulse mixing correlate up to seven adjacent backbone amide nitrogen or carbonyl carbon nuclei, respectively, and connections across proline residues are also obtained straightforwardly. Multiple, recurrent long-range correlations with ultra-high resolution allow backbone {sup 1}H{sup N}, {sup 15}N{sup H}, and {sup 13}C′ resonance assignments to be completed from a single pair of 3D experiments.

  20. 4th international interdisciplinary chaos symposium

    CERN Document Server

    Banerjee, Santo; Caglar, Suleyman; Ozer, Mehmet; Chaos and complex systems

    2013-01-01

    Complexity Science and Chaos Theory are fascinating areas of scientific research with wide-ranging applications.  The interdisciplinary nature and ubiquity of complexity and chaos are features that provides scientists with a motivation to pursue general theoretical tools and frameworks. Complex systems give rise to emergent behaviors, which in turn produce novel and interesting phenomena in science, engineering, as well as in the socio-economic sciences. The aim of all Symposia on Chaos and Complex Systems (CCS) is to bring together scientists, engineers, economists and social scientists, and to discuss the latest insights and results obtained in the area of corresponding nonlinear-system complex (chaotic) behavior. Especially for the “4th International Interdisciplinary Chaos Symposium on Chaos and Complex Systems,” which took place April 29th to May 2nd, 2012 in Antalya, Turkey, the scope of the symposium had been further enlarged so as to encompass the presentation of work from circuits to econophysic...

  1. Semiconductor Lasers Stability, Instability and Chaos

    CERN Document Server

    Ohtsubo, Junji

    2013-01-01

    This third edition of “Semiconductor Lasers, Stability, Instability and Chaos” was significantly extended.  In the previous edition, the dynamics and characteristics of chaos in semiconductor lasers after the introduction of the fundamental theory of laser chaos and chaotic dynamics induced by self-optical feedback and optical injection was discussed. Semiconductor lasers with new device structures, such as vertical-cavity surface-emitting lasers and broad-area semiconductor lasers, are interesting devices from the viewpoint of chaotic dynamics since they essentially involve chaotic dynamics even in their free-running oscillations. These topics are also treated with respect to the new developments in the current edition. Also the control of such instabilities and chaos control are critical issues for applications. Another interesting and important issue of semiconductor laser chaos in this third edition is chaos synchronization between two lasers and the application to optical secure communication. One o...

  2. Chaos the science of predictable random motion

    CERN Document Server

    Kautz, Richard

    2011-01-01

    Based on only elementary mathematics, this engaging account of chaos theory bridges the gap between introductions for the layman and college-level texts. It develops the science of dynamics in terms of small time steps, describes the phenomenon of chaos through simple examples, and concludes with a close look at a homoclinic tangle, the mathematical monster at the heart of chaos. The presentation is enhanced by many figures, animations of chaotic motion (available on a companion CD), and biographical sketches of the pioneers of dynamics and chaos theory. To ensure accessibility to motivated high school students, care has been taken to explain advanced mathematical concepts simply, including exponentials and logarithms, probability, correlation, frequency analysis, fractals, and transfinite numbers. These tools help to resolve the intriguing paradox of motion that is predictable and yet random, while the final chapter explores the various ways chaos theory has been put to practical use.

  3. Decoherence, determinism and chaos revisited

    Energy Technology Data Exchange (ETDEWEB)

    Noyes, H.P.

    1994-11-15

    We suggest that the derivation of the free space Maxwell Equations for classical electromagnetism, using a discrete ordered calculus developed by L.H. Kauffman and T. Etter, necessarily pushes the discussion of determinism in natural science down to the level of relativistic quantum mechanics and hence renders the mathematical phenomena studied in deterministic chaos research irrelevant to the question of whether the world investigated by physics is deterministic. We believe that this argument reinforces Suppes` contention that the issue of determinism versus indeterminism should be viewed as a Kantian antinomy incapable of investigation using currently available scientific tools.

  4. Quelques aspects de Chaos Quantique

    OpenAIRE

    Nonnenmacher, Stéphane

    2009-01-01

    Ce mémoire résume mes travaux dans 3 domaines reliés au "chaos quantique". J'y aborde tout d'abord les questions de répartition spatiale des fonctions propres de systèmes quantiques classiquement chaotiques. Dans une seconde partie, je résume mes travaux sur la distribution des résonances pour les systèmes de diffusion dont l'ensemble des trajectoires captées est fractal, et supporte une dynamique chaotique. Enfin, je mentionne des résultats obtenus sur les transformations chaotiques bruitées...

  5. Periodic orbits in arithmetical chaos

    International Nuclear Information System (INIS)

    Length spectra of periodic orbits are investigated for some chaotic dynamical systems whose quantum energy spectra show unexpected statistical properties and for which the notion of arithmetical chaos has been introduced recently. These systems are defined as the unconstrained motions of particles on two dimensional surfaces of constant negative curvature whose fundamental groups are given by number theoretical statements (arithmetic Fuchsian groups). It is shown that the mean multiplicity of lengths l of periodic orbits grows asymptotically like c x el/2/l, l → ∞. Moreover, the constant c (depending on the arithmetic group) is determined. (orig.)

  6. Decoherence, determinism and chaos revisited

    International Nuclear Information System (INIS)

    We suggest that the derivation of the free space Maxwell Equations for classical electromagnetism, using a discrete ordered calculus developed by L.H. Kauffman and T. Etter, necessarily pushes the discussion of determinism in natural science down to the level of relativistic quantum mechanics and hence renders the mathematical phenomena studied in deterministic chaos research irrelevant to the question of whether the world investigated by physics is deterministic. We believe that this argument reinforces Suppes' contention that the issue of determinism versus indeterminism should be viewed as a Kantian antinomy incapable of investigation using currently available scientific tools

  7. Chaos and gauge field theory

    CERN Document Server

    Biro, TS; Mueller, B

    1995-01-01

    This book introduces a rapidly growing new research area - the study of dynamical properties of elementary fields. The methods used in this field range from algebraic topology to parallel computer programming. The main aim of this research is to understand the behavior of elementary particles and fields under extreme circumstances, first of all at high temperature and energy density generated in the largest accelerators of the world and supposed to be present in the early evolution of our Universe shortly after the Big Bang.In particular, chaos is rediscovered in a new appearance in these stud

  8. Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation.

    Science.gov (United States)

    Balu, Rajkamal; Mata, Jitendra P; Knott, Robert; Elvin, Christopher M; Hill, Anita J; Choudhury, Namita R; Dutta, Naba K

    2016-07-14

    In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles. PMID:27281267

  9. Unstable periodic orbits and noise in chaos computing.

    Science.gov (United States)

    Kia, Behnam; Dari, Anna; Ditto, William L; Spano, Mark L

    2011-12-01

    Different methods to utilize the rich library of patterns and behaviors of a chaotic system have been proposed for doing computation or communication. Since a chaotic system is intrinsically unstable and its nearby orbits diverge exponentially from each other, special attention needs to be paid to the robustness against noise of chaos-based approaches to computation. In this paper unstable periodic orbits, which form the skeleton of any chaotic system, are employed to build a model for the chaotic system to measure the sensitivity of each orbit to noise, and to select the orbits whose symbolic representations are relatively robust against the existence of noise. Furthermore, since unstable periodic orbits are extractable from time series, periodic orbit-based models can be extracted from time series too. Chaos computing can be and has been implemented on different platforms, including biological systems. In biology noise is always present; as a result having a clear model for the effects of noise on any given biological implementation has profound importance. Also, since in biology it is hard to obtain exact dynamical equations of the system under study, the time series techniques we introduce here are of critical importance. PMID:22225394

  10. An Experimental Investigation of Secure Communication With Chaos Masking

    CERN Document Server

    Dhar, Sourav

    2007-01-01

    The most exciting recent development in nonlinear dynamics is realization that chaos can be useful. One application involves "Secure Communication". Two piecewise linear systems with switching nonlinearities have been taken as chaos generators. In the present work the phenomenon of secure communication with chaos masking has been investigated experimentally. In this investigation chaos which is generated from two chaos generators is masked with the massage signal to be transmitted, thus makes communication is more secure.

  11. Quantifying chaos for ecological stoichiometry

    Science.gov (United States)

    Duarte, Jorge; Januário, Cristina; Martins, Nuno; Sardanyés, Josep

    2010-09-01

    The theory of ecological stoichiometry considers ecological interactions among species with different chemical compositions. Both experimental and theoretical investigations have shown the importance of species composition in the outcome of the population dynamics. A recent study of a theoretical three-species food chain model considering stoichiometry [B. Deng and I. Loladze, Chaos 17, 033108 (2007)] shows that coexistence between two consumers predating on the same prey is possible via chaos. In this work we study the topological and dynamical measures of the chaotic attractors found in such a model under ecological relevant parameters. By using the theory of symbolic dynamics, we first compute the topological entropy associated with unimodal Poincaré return maps obtained by Deng and Loladze from a dimension reduction. With this measure we numerically prove chaotic competitive coexistence, which is characterized by positive topological entropy and positive Lyapunov exponents, achieved when the first predator reduces its maximum growth rate, as happens at increasing δ1. However, for higher values of δ1 the dynamics become again stable due to an asymmetric bubble-like bifurcation scenario. We also show that a decrease in the efficiency of the predator sensitive to prey's quality (increasing parameter ζ) stabilizes the dynamics. Finally, we estimate the fractal dimension of the chaotic attractors for the stoichiometric ecological model.

  12. Chaos suppression through asymmetric coupling

    Science.gov (United States)

    Bragard, J.; Vidal, G.; Mancini, H.; Mendoza, C.; Boccaletti, S.

    2007-12-01

    We study pairs of identical coupled chaotic oscillators. In particular, we have used Roessler (in the funnel and no funnel regimes), Lorenz, and four-dimensional chaotic Lotka-Volterra models. In all four of these cases, a pair of identical oscillators is asymmetrically coupled. The main result of the numerical simulations is that in all cases, specific values of coupling strength and asymmetry exist that render the two oscillators periodic and synchronized. The values of the coupling strength for which this phenomenon occurs is well below the previously known value for complete synchronization. We have found that this behavior exists for all the chaotic oscillators that we have used in the analysis. We postulate that this behavior is presumably generic to all chaotic oscillators. In order to complete the study, we have tested the robustness of this phenomenon of chaos suppression versus the addition of some Gaussian noise. We found that chaos suppression is robust for the addition of finite noise level. Finally, we propose some extension to this research.

  13. Competitive coexistence in stoichiometric chaos

    Science.gov (United States)

    Deng, Bo; Loladze, Irakli

    2007-09-01

    Classical predator-prey models, such as Lotka-Volterra, track the abundance of prey, but ignore its quality. Yet, in the past decade, some new and occasionally counterintuitive effects of prey quality on food web dynamics emerged from both experiments and mathematical modeling. The underpinning of this work is the theory of ecological stoichiometry that is centered on the fact that each organism is a mixture of multiple chemical elements such as carbon (C), nitrogen (N), and phosphorus (P). The ratios of these elements can vary within and among species, providing simple ways to represent prey quality as its C:N or C:P ratios. When these ratios modeled to vary, as they frequently do in nature, seemingly paradoxical results can arise such as the extinction of a predator that has an abundant and accessible prey. Here, for the first time, we show analytically that the reduction in prey quality can give rise to chaotic oscillations. In particular, when competing predators differ in their sensitivity to prey quality then all species can coexist via chaotic fluctuations. The chaos generating mechanism is based on the existence of a junction-fold point on the nullcline surfaces of the species. Conditions on parameters are found for such a point, and the singular perturbation method and the kneading sequence analysis are used to demonstrate the existence of a period-doubling cascade to chaos as a result of the point.

  14. Chua's circuit a paradigm for chaos

    CERN Document Server

    1993-01-01

    For uninitiated researchers, engineers, and scientists interested in a quick entry into the subject of chaos, this book offers a timely collection of 55 carefully selected papers covering almost every aspect of this subject. Because Chua's circuit is endowed with virtually every bifurcation phenomena reported in the extensive literature on chaos, and because it is the only chaotic system which can be easily built by a novice, simulated in a personal computer, and tractable mathematically, it has become a paradigm for chaos, and a vehicle for illustrating this ubiquitous phenomenon. Its supreme

  15. Edge of Chaos and Genesis of Turbulence

    CERN Document Server

    Chian, Abraham C -L; Rempel, Erico

    2013-01-01

    The edge of chaos is analyzed in a spatially extended system, modeled by the regularized long-wave equation, prior to the transition to permanent spatiotemporal chaos. In the presence of coexisting attractors, a chaotic saddle is born at the basin boundary due to a smooth-fractal metamorphosis. As a control parameter is varied, the chaotic transient evolves to well-developed transient turbulence via a cascade of fractal-fractal metamorphoses. The edge state responsible for the edge of chaos and the genesis of turbulence is an unstable travelling wave in the laboratory frame, corresponding to a saddle point lying at the basin boundary in the Fourier space.

  16. Physics and Applications of Laser Diode Chaos

    CERN Document Server

    Sciamanna, Marc

    2015-01-01

    An overview of chaos in laser diodes is provided which surveys experimental achievements in the area and explains the theory behind the phenomenon. The fundamental physics underpinning this behaviour and also the opportunities for harnessing laser diode chaos for potential applications are discussed. The availability and ease of operation of laser diodes, in a wide range of configurations, make them a convenient test-bed for exploring basic aspects of nonlinear and chaotic dynamics. It also makes them attractive for practical tasks, such as chaos-based secure communications and random number generation. Avenues for future research and development of chaotic laser diodes are also identified.

  17. Distributed chaos and helicity in turbulence

    CERN Document Server

    Bershadskii, A

    2016-01-01

    The distributed chaos driven by Levich-Tsinober (helicity) integral: $I=\\int \\langle h({\\bf x},t)~h({\\bf x}+{\\bf r}, t)\\rangle d{\\bf r}$ has been studied. It is shown that the helical distributed chaos can be considered as basis for complex turbulent flows with interplay between large-scale coherent structures and small-scale turbulence, such as Cuette-Taylor flow, wake behind cylinder and turbulent flow in the Large Plasma Device (LAPD) with inserted limiters. In the last case appearance of the helical distributed chaos, caused by the limiters, results in improvement of radial particle confinement.

  18. From Hamiltonian chaos to Maxwell's Demon

    International Nuclear Information System (INIS)

    The problem of the existence of Maxwell's Demon (MD) is formulated for systems with dynamical chaos. Property of stickiness of individual trajectories, anomalous distribution of the Poincare recurrence time, and anomalous (non-Gaussian) transport for a typical system with Hamiltonian chaos results in a possibility to design a situation equivalent to the MD operation. A numerical example demonstrates a possibility to set without expenditure of work a thermodynamically non-equilibrium state between two contacted domains of the phase space lasting for an arbitrarily long time. This result offers a new view of the Hamiltonian chaos and its role in the foundation of statistical mechanics. copyright 1995 American Institute of Physics

  19. Chaos dynamic characteristics during mine fires

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Mine fires break out and continue in confmed scopes, studying mine fire dynamics characteristics is very usefulto prevent and control fire. The judgement index of fire chaos characteristics was introduced, chaos analysis of mine Fireprocess was described, and the reconstruction of phase space was also presented. An example of mine fire was calculated.The computations show that it is feasible to analyze mine fire dynamic characteristics with chaos theory, and indicate thatfire preoeas is a catastrophe, that is to say, the fire system changes from one state to another during mine fire

  20. Chaos from simple models to complex systems

    CERN Document Server

    Cencini, Massimo; Vulpiani, Angelo

    2010-01-01

    Chaos: from simple models to complex systems aims to guide science and engineering students through chaos and nonlinear dynamics from classical examples to the most recent fields of research. The first part, intended for undergraduate and graduate students, is a gentle and self-contained introduction to the concepts and main tools for the characterization of deterministic chaotic systems, with emphasis to statistical approaches. The second part can be used as a reference by researchers as it focuses on more advanced topics including the characterization of chaos with tools of information theor

  1. Strong intrinsic motivation

    OpenAIRE

    Dessi, Roberta; Rustichini, Aldo

    2015-01-01

    A large literature in psychology, and more recently in economics, has argued that monetary rewards can reduce intrinsic motivation. We investigate whether the negative impact persists when intrinsic motivation is strong, and test this hypothesis experimentally focusing on the motivation to undertake interesting and challenging tasks, informative about individual ability. We find that this type of task can generate strong intrinsic motivation, that is impervious to the effect of monetary incen...

  2. Quantum Correlations, Chaos and Information

    Science.gov (United States)

    Madhok, Vaibhav

    Quantum chaos is the study of quantum systems whose classical description is chaotic. How does chaos manifest itself in the quantum world? In this spirit, we study the dynamical generation of entanglement as a signature of chaos in a system of periodically kicked coupled-tops, where chaos and entanglement arise from the same physical mechanism. The long-time entanglement as a function of the position of an initially localized wave packet very closely correlates with the classical phase space surface of section - it is nearly uniform in the chaotic sea, and reproduces the detailed structure of the regular islands. The uniform value in the chaotic sea is explained by the random state conjecture. As classically chaotic dynamics take localized distributions in phase space to random distributions, quantized versions take localized coherent states to pseudo-random states in Hilbert space. Such random states are highly entangled, with an average value near that of the maximally entangled state. For a map with global chaos, we derive that value based on new analytic results for the entropy of random states. For a mixed phase space, we use the Percival conjecture to identify a "chaotic subspace" of the Hilbert space. The typical entanglement, averaged over the unitarily invariant Haar measure in this subspace, agrees with the long-time averaged entanglement for initial states in the chaotic sea. In all cases the dynamically generated entanglement is that of a random complex vector, even though the system is time-reversal invariant, and the Floquet operator is a member of the circular orthogonal ensemble. Continuing on our journey to find the footprints of chaos in the quantum world, we explore quantum signatures of classical chaos by studying the rate of information gain in quantum tomography. The measurement record is obtained as a sequence of expectation values of a Hermitian operator evolving under repeated application of the Floquet operator of the quantum kicked top on

  3. NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics.

    Science.gov (United States)

    Gupta, Garvita; Lim, Liangzhong; Song, Jianxing

    2015-01-01

    Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its "complete insolubility", the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48-100) or the full-length NS2B (1-130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48-100;Δ77-84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection. PMID:26258523

  4. Altered intrinsic organisation of brain networks implicated in attentional processes in adult attention-deficit/hyperactivity disorder: a resting-state study of attention, default mode and salience network connectivity.

    Science.gov (United States)

    Sidlauskaite, Justina; Sonuga-Barke, Edmund; Roeyers, Herbert; Wiersema, Jan R

    2016-06-01

    Deficits in task-related attentional engagement in attention-deficit/hyperactivity disorder (ADHD) have been hypothesised to be due to altered interrelationships between attention, default mode and salience networks. We examined the intrinsic connectivity during rest within and between these networks. Six-minute resting-state scans were obtained. Using a network-based approach, connectivity within and between the dorsal and ventral attention, the default mode and the salience networks was compared between the ADHD and control group. The ADHD group displayed hyperconnectivity between the two attention networks and within the default mode and ventral attention network. The salience network was hypoconnected to the dorsal attention network. There were trends towards hyperconnectivity within the dorsal attention network and between the salience and ventral attention network in ADHD. Connectivity within and between other networks was unrelated to ADHD. Our findings highlight the altered connectivity within and between attention networks, and between them and the salience network in ADHD. One hypothesis to be tested in future studies is that individuals with ADHD are affected by an imbalance between ventral and dorsal attention systems with the former playing a dominant role during task engagement, making individuals with ADHD highly susceptible to distraction by salient task-irrelevant stimuli. PMID:26260900

  5. Superfluid (quantum) turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

    Properties of distributed chaos in superfluid (quantum) turbulence have been studied using the data of recent direct numerical simulations (HVBK two-fluid model for He II, and a moving grid in the frames of Gross-Pitaevskii model of the Bose-Einstein condensates at low temperatures). It is found that for the viscous (normal) component of the velocity field in He II the viscosity dominates the distributed chaos with the stretched exponential spectrum $\\exp(-k/k_{\\beta})^{\\beta}$ and $\\beta = 2/3$. For the superfluid component the distributed chaos is dominated by the vorticity correlation integral with $\\beta =1/2$ (the soft spontaneous breaking of the space translational symmetry - homogeneity). For very low temperature the distributed chaos is tuned to the large-scale coherent motions: the viscous (normal) component is tuned to the fundamental mode, whereas the superfluid component is subharmonically tuned. For the Gross-Pitaevskii superfluid turbulence incompressible part of the energy spectrum (containing ...

  6. Coherence and chaos in condensed matter

    International Nuclear Information System (INIS)

    This paper discusses the following topics: nonlinearity in condensed matter; coherence and chaos in spatially extended condensed matter systems; nonlinearity and magnetism; and solitons and conducting polymers. 52 refs., 7 figs

  7. Symmetry vs. Chaos in collective dynamics

    International Nuclear Information System (INIS)

    Models of nuclear collective dynamics are used to study the interplay of order (approximate dynamical symmetry) and chaos in general physical systems. We report on some recent results obtained within the interacting boson model and the geometric model. (author)

  8. Geodesics deviation equation approach to chaos

    OpenAIRE

    Dobrowolski, Tomasz; Szczesny, Jerzy

    1999-01-01

    Geodesics deviation equation (GDE) is itroduced. In "adiabatic" approximation exact solution of the GDE if found. Perturbation theory in general case is formulated. Geometrical criterion of local instability which may lead to chaos is formulated.

  9. Chaos on the conveyor belt

    CERN Document Server

    Sándor, Bulcsú; Tél, Tamás; Néda, Zoltán

    2013-01-01

    The dynamics of a spring-block train placed on a moving conveyor belt is investigated both by simple experiments and computer simulations. The first block is connected by spring to an external static point, and due to the dragging effect of the belt the blocks undergo complex stick-slip dynamics. A qualitative agreement with the experimental results can only be achieved by taking into account the spatial inhomogeneity of the friction force on the belt's surface, modeled as noise. As a function of the velocity of the conveyor belt and the noise strength, the system exhibits complex, self-organized critical, sometimes chaotic dynamics and phase transition-like behavior. Noise induced chaos and intermittency is also observed. Simulations suggest that the maximum complexity of the dynamical states is achieved for a relatively small number of blocks, around five.

  10. The Minerals of Aureum Chaos

    Science.gov (United States)

    2008-01-01

    [figure removed for brevity, see original site] Click on image for animation of 3-dimensional model with 5x vertical exaggeration This image of chaotic terrain in the Aureum Chaos region of Mars was taken by the Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) at 0858UTC (3:58 a.m. EST) on January 24, 2008, near 3.66 degrees south latitude, 26.5 degrees west longitude. The image was taken in 544 colors covering 0.36-3.92 micrometers, and shows features as small as 18 meters (60 feet) across. The image is about 10 kilometers (6.2 miles) wide at its narrowest point. Aureum Chaos is a 368 kilometer (229 mile) wide area of chaotic terrain in the eastern part of Valles Marineris. The chaotic terrain is thought to have formed by collapse of the surrounding Margaritifer Terra highland region. Aureum Chaos contains heavily eroded, randomly oriented mesas, plateaus, and knobs many revealing distinct layered deposits along their slopes. These deposits may be formed from remnants of the collapsed highlands, sand carried by Martian winds, dust or volcanic ash that settled out of the atmosphere, or sediments laid down on the floor of an ancient lake. The top panel in the montage above shows the location of the CRISM image on a mosaic taken by the Mars Odyssey spacecraft's Thermal Emission Imaging System (THEMIS). The CRISM data cover a narrow plateau near the edge of the chaotic terrain, that stretches across from the southwest to the northeast. The lower left image, an infrared false color image, reveals the plateau and several eroded knobs of varying sizes. The plateau's layer-cake structure is similar to that of other layered outcrops in Valles Marineris. The lower right image reveals the strengths of mineral spectral features overlain on a black-and-white version of the infrared image. Areas shaded in red hold more of the mineral pyroxene, a primary component of basaltic rocks that are prevalent in the highlands. Spots of green indicate monohydrated sulfate

  11. Chaos in junctions and devices

    International Nuclear Information System (INIS)

    The plan of the paper is as follows. Section 2 is an introduction into chaos in dissipative systems with an emphasis on period doubling and intermittency. The logistic map and the circle map are discussed and their significance as describing systems of continuous dynamics is emphasized. Section 3 is subdivided into two parts after the introduction of the RSJ equations. The first is on the ac driven Josephson junction without a dc bias and the second on the same with a dc current. Each of these subdivisions includes a discussion of experiments as well. There is also a section on investigations that do not fit into either of the above categories. Section 4 is devoted to the dc-SQUID, in the first part as a magnetic flux gauge and in the second as a four dimensional dynamical system, which can be simulated with great accuracy and compared with one dimensional models. (orig./BUD)

  12. Chaos

    OpenAIRE

    P. Tallapragada; Ross, Shane. D.; Schmale, D. G., III

    2011-01-01

    Many microorganisms are advected in the lower atmosphere from one habitat to another with scales of motion being hundreds to thousands of kilometers. The concentration of these microbes in the lower atmosphere at a single geographic location can show rapid temporal changes. We used autonomous unmanned aerial vehicles equipped with microbe-sampling devices to collect fungi in the genus Fusarium 100 m above ground level at a single sampling location in Blacksburg, Virginia, USA. Some Fusarium s...

  13. Detecting nonlinearity and chaos in epidemic data

    Energy Technology Data Exchange (ETDEWEB)

    Ellner, S.; Gallant, A.R. [North Carolina State Univ., Raleigh, NC (United States). Dept. of Statistics; Theiler, J. [Santa Fe Inst., NM (United States)]|[Los Alamos National Lab., NM (United States)

    1993-08-01

    Historical data on recurrent epidemics have been central to the debate about the prevalence of chaos in biological population dynamics. Schaffer and Kot who first recognized that the abundance and accuracy of disease incidence data opened the door to applying a range of methods for detecting chaos that had been devised in the early 1980`s. Using attractor reconstruction, estimates of dynamical invariants, and comparisons between data and simulation of SEIR models, the ``case for chaos in childhood epidemics`` was made through a series of influential papers beginning in the mid 1980`s. The proposition that the precise timing and magnitude of epidemic outbreaks are deterministic but chaotic is appealing, since it raises the hope of finding determinism and simplicity beneath the apparently stochastic and complicated surface of the data. The initial enthusiasm for methods of detecting chaos in data has been followed by critical re-evaluations of their limitations. Early hopes of a ``one size fits all`` algorithm to diagnose chaos vs. noise in any data set have given way to a recognition that a variety of methods must be used, and interpretation of results must take into account the limitations of each method and the imperfections of the data. Our goals here are to outline some newer methods for detecting nonlinearity and chaos that have a solid statistical basis and are suited to epidemic data, and to begin a re-evaluation of the claims for nonlinear dynamics and chaos in epidemics using these newer methods. We also identify features of epidemic data that create problems for the older, better known methods of detecting chaos. When we ask ``are epidemics nonlinear?``, we are not questioning the existence of global nonlinearities in epidemic dynamics, such as nonlinear transmission rates. Our question is whether the data`s deviations from an annual cyclic trend (which would reflect global nonlinearities) are described by a linear, noise-driven stochastic process.

  14. Polynomial chaos representation of a stochastic preconditioner

    OpenAIRE

    Desceliers, Christophe; Ghanem, R; Soize, Christian

    2005-01-01

    A method is developed in this paper to accelerate the convergence in computing the solution of stochastic algebraic systems of equations. The method is based on computing, via statistical sampling, a polynomial chaos decomposition of a stochastic preconditioner to the system of equations. This preconditioner can subsequently be used in conjunction with either chaos representations of the solution or with approaches based on Monte Carlo sampling. In addition to presenting the supporting theory...

  15. Microscopic theory of intrinsic shear and bulk viscosities

    International Nuclear Information System (INIS)

    A microscopic theory of intrinsic shear and bulk viscosities of solutions is given for a model of particles that interact with hard-sphere cores and weak long-range attraction. The approximation considered (the velocity chaos assumption of the Enskog theory) can be expected to yield quantitatively useful values for viscosities of the model solute-solvent system when the solute particles are not much larger than the solvent particles. Under solute-solvent mixing conditions of constant pressure and temperature, it is found that the intrinsic viscosities of a hard-sphere solute in a hard-sphere solvent can be positive or negative, depending upon size and mass ratios; for solute and solvent particles whose mass ratio equals their volume ratio, the intrinsic shear and bulk viscosities are always positive for solute particles larger than solvent particles: in the opposite case, the intrinsic shear viscosity is always negative while the intrinsic bulk viscosity is for the most part negative, becoming positive again when the solute particle is sufficiently small. For solute particles smaller than solvent particles, this result is sensitive to change in mass ratio. The addition of solvent-solvent attraction is found to lower the intrinsic viscosities substantially; the addition of solute-solvent attraction raises it. Detailed quantitative analysis of these effects is given

  16. On indeterminism, chaos, and small number particle systems in the brain.

    Science.gov (United States)

    Lewis, Edwin R; MacGregor, Ronald J

    2006-06-01

    This paper presents rational, theoretical, and empirical grounds for doubting the principle of determinism in nature and in the brain, and discusses implications of this for free will and the chaos model of the brain. Small number particle systems are practically indeterministic and may be intrinsically indeterministic. Determinism in nature has often been taken to preclude free will. Strict determinism is a concept frequently applied to systems theory, establishing, e.g., the uniqueness of state-space trajectories. In order to consider determinism as a law of nature, however, one must be able to subject it to empirical tests. Presently, one is not able to and whether this can be shown to enable free will or not is not clear. It does remove, at least for the present, determinism itself as a rationale for precluding free will. The work partially supports the chaos model, but weakens the computational computer metaphor of brain function. PMID:16783870

  17. Spatial interaction creates period-doubling bifurcation and chaos of urbanization

    International Nuclear Information System (INIS)

    This paper provides a new way of looking at complicated dynamics of simple mathematical models. The complicated behavior of simple equations is one of the headstreams of chaos theory. However, a recent study based on dynamical equations of urbanization shows that there are still some undiscovered secrets behind the simple mathematical models such as logistic equation. The rural-urban interaction model can also display varied kinds of complicated dynamics, including period-doubling bifurcation and chaos. The two-dimension map of urbanization presents the same dynamics as that from the one-dimension logistic map. In theory, the logistic equation can be derived from the two-population interaction model. This seems to suggest that the complicated behavior of simple models results from interaction rather than pure intrinsic randomicity. In light of this idea, the classical predator-prey interaction model can be revised to explain the complex dynamics of logistic equation in physical and social sciences.

  18. Accessing Creativity: Jungian Night Sea Journeys, Wandering Minds, and Chaos.

    Science.gov (United States)

    Rosen, Diane

    2016-01-01

    NDS theory has been meaningfully applied to the dynamics of creativity and psychology. These complex systems have much in common, including a broad definition of "product" as new order emerging from disorder, a new whole (etymologically, 'health') out of disintegration or destabilization. From a nonlinear dynamical systems perspective, this paper explores the far-from-equilibrium zone of creative incubation: first in the Jungian night sea journey, a primordial myth of psychological and creative transformation; then in the neuroscience of mind wandering, the well-spring of creative ideation within the larger neural matrix. Finally, chaos theory grounds the elusive subject of creativity, modeling chaotic generation of idea elements that tend toward strange attractors, combine unpredictably, and produce change by means of tension between opposites, particularly notes consciousness (light) and the poetic unconscious (darkness). Examples from my own artwork illustrate this dialectical process. Considered together, the unconscious mythic sea journey, the unknowing wandering mind, and the generative paradigm of deterministic chaos suggest conditions that facilitate creativity across disciplines, providing fresh indications that the darkness of the unknown or irrational is, paradoxically, the illuminative source and strength of creativity. PMID:26639923

  19. Input-dependent Suppression of Chaos in Recurrent Neural Networks

    Science.gov (United States)

    Rajan, K.; Abbott, L. F.; Sompolinsky, H.

    2010-03-01

    Neuronal responses arise from an interaction between spontaneous activity and responses driven by external inputs. Experiments studying cortical circuits reveal a striking similarity between the magnitude and complexity of intrinsic and input-generated activity. How does a network generating complex activity remain sensitive to external inputs? This seems unlikely for a network in which input-driven responses add linearly to ongoing activity generated by stochastic noise generators. We developed a mean-field theory and used recurrent network models to distinguish between this type of external noise and chaotic background generated by strong coupling within the circuit. As a result of a highly nonlinear relationship between input- and internally generated activity, we show that intrinsic noise is sensitive to the amplitude and the spatiotemporal structure of the input. We find that input not only drives responses, it also actively suppresses spontaneous activity, leading to a phase transition in which the chaotic background is absent. Although the power spectrum of the spontaneous activity falls exponentially from zero, the phase transition reveals a resonant frequency at which relatively a weak input suppresses chaos. As long as the input drives the system across the phase transition, a spontaneously active network can work with coupling strong enough to allow large signal amplification and selectivity without the complex background interfering with sensory processing.

  20. Chaos forgets and remembers: Measuring information creation, destruction, and storage

    Energy Technology Data Exchange (ETDEWEB)

    James, Ryan G., E-mail: rgjames@ucdavis.edu [Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States); Burke, Korana, E-mail: kburke@ucdavis.edu [Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States); Crutchfield, James P., E-mail: chaos@ucdavis.edu [Complexity Sciences Center and Physics Department, University of California at Davis, One Shields Avenue, Davis, CA 95616 (United States); Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501 (United States)

    2014-06-13

    Highlights: • Kolmogorov–Sinai entropy measures information creation in dynamical systems. • It decomposes into information remembered (bound) and that forgotten (ephemeral). • Thus chaotic dynamical systems compute: they actively store and destroy information. • This is easily estimated and, in many cases, analytically computed. • Decomposition illustrated for the Logistic, Tent, and Lozi discrete-time maps. - Abstract: The hallmark of deterministic chaos is that it creates information—the rate being given by the Kolmogorov–Sinai metric entropy. Since its introduction half a century ago, the metric entropy has been used as a unitary quantity to measure a system's intrinsic unpredictability. Here, we show that it naturally decomposes into two structurally meaningful components: A portion of the created information—the ephemeral information—is forgotten and a portion—the bound information—is remembered. The bound information is a new kind of intrinsic computation that differs fundamentally from information creation: it measures the rate of active information storage. We show that it can be directly and accurately calculated via symbolic dynamics, revealing a hitherto unknown richness in how dynamical systems compute.

  1. CHAOS III: Gas-Phase Abundances in NGC5457

    CERN Document Server

    Croxall, Kevin; Berg, Danielle A; Skillman, Evan D; Moustakas, John

    2016-01-01

    The CHemical Abundances of Spirals (CHAOS) project leverages the combined power of the Large Binocular Telescope with the broad spectral range and sensitivity of the Multi Object Double Spectrograph (MODS) to measure direct abundances in large samples of HII regions in spiral galaxies. We present LBT MODS observations of 109 Hii regions in NGC5457, of which 74 have robust measurements of key auroral lines, a factor of 3 larger than all previous published detections of auroral lines in the HII regions of NGC5457. Comparing the temperatures derived from the different ionic species we find: (1) strong correlations of T[NII] with T[SIII] and T[OIII], consistent with little or no intrinsic scatter; (2) a correlation of T[SIII] with T[OIII], but with significant intrinsic dispersion; (3) overall agreement between T[NII], T[SII], and T[OII], as expected, but with significant outliers; (4) the correlations of T[NII] with T[SIII] and T[OIII] match the predictions of photoionization modeling while the correlation of T[...

  2. HN-NCA heteronuclear TOCSY-NH experiment for {sup 1}H{sup N} and {sup 15}N sequential correlations in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Wiedemann, Christoph; Goradia, Nishit; Häfner, Sabine [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany); Herbst, Christian [Ubon Ratchathani University, Department of Physics, Faculty of Science (Thailand); Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai, E-mail: raman@fli-leibniz.de [Leibniz Institute for Age Research, Fritz Lipmann Institute, Research Group Biomolecular NMR Spectroscopy (Germany)

    2015-10-15

    A simple triple resonance NMR experiment that leads to the correlation of the backbone amide resonances of each amino acid residue ‘i’ with that of residues ‘i−1’ and ‘i+1’ in ({sup 13}C, {sup 15}N) labelled intrinsically disordered proteins (IDPs) is presented. The experimental scheme, {HN-NCA heteronuclear TOCSY-NH}, exploits the favourable relaxation properties of IDPs and the presence of {sup 1}J{sub CαN} and {sup 2}J{sub CαN} couplings to transfer the {sup 15}N{sub x} magnetisation from amino acid residue ‘i’ to adjacent residues via the application of a band-selective {sup 15}N–{sup 13}C{sup α} heteronuclear cross-polarisation sequence of ∼100 ms duration. Employing non-uniform sampling in the indirect dimensions, the efficacy of the approach has been demonstrated by the acquisition of 3D HNN chemical shift correlation spectra of α-synuclein. The experimental performance of the RF pulse sequence has been compared with that of the conventional INEPT-based HN(CA)NH pulse scheme. As the availability of data from both the HCCNH and HNN experiments will make it possible to use the information extracted from one experiment to simplify the analysis of the data of the other and lead to a robust approach for unambiguous backbone and side-chain resonance assignments, a time-saving strategy for the simultaneous collection of HCCNH and HNN data is also described.

  3. Intrinsic Spin Hall Effect

    OpenAIRE

    Murakami, Shuichi

    2005-01-01

    A brief review is given on the spin Hall effect, where an external electric field induces a transverse spin current. It has been recognized over 30 years that such effect occurs due to impurities in the presence of spin-orbit coupling. Meanwhile, it was proposed recently that there is also an intrinsic contribution for this effect. We explain the mechanism for this intrinsic spin Hall effect. We also discuss recent experimental observations of the spin Hall effect.

  4. Intrinsic Prices Of Risk

    OpenAIRE

    Truc Le

    2014-01-01

    We review the nature of some well-known phenomena such as volatility smiles, convexity adjustments and parallel derivative markets. We propose that the market is incomplete and postulate the existence of intrinsic risks in every contingent claim as a basis for understanding these phenomena. In a continuous time framework, we bring together the notion of intrinsic risk and the theory of change of measures to derive a probability measure, namely risk-subjective measure, for evaluating contingen...

  5. 2nd International Symposium on Chaos, Complexity and Leadership

    CERN Document Server

    Banerjee, Santo

    2015-01-01

    These proceedings from the 2013 symposium on "Chaos, complexity and leadership" reflect current research results from all branches of Chaos, Complex Systems and their applications in Management. Included are the diverse results in the fields of applied nonlinear methods, modeling of data and simulations, as well as theoretical achievements of Chaos and Complex Systems. Also highlighted are Leadership and Management applications of Chaos and Complexity Theory.

  6. Chaos Theory and Literature from an Existentialist Perspective

    OpenAIRE

    Khamees Ragab Aman, Yasser

    2007-01-01

    Yasser Khamees Ragab Aman proposes in his article "Chaos Theory and Literature from an Existentialist Perspective" that in literature the relation, principles, and processes of chaos and order can be analyzed from an existentialist perspective. Chaos lies at the heart of nothingness and order is the appearance of the achievement it tries to realize, temporary it may seem. Aman argues that with the application of chaos theory to works of literature may yield new insight and applies in his pape...

  7. Nuclear collective dynamics and chaos

    International Nuclear Information System (INIS)

    The present status and future problems in both the classical-level theory and full quantum theory of nuclear collective dynamics are discussed by putting special emphasis on their relation to the classical and quantum order-to-chaos transition dynamics, respectively. The nonlinear dynamics between the collective and single-particle excitation modes of motion specific for the finite, self-sustained and self-organizing system as the nucleus is discussed within the time-dependent Hartree-Fock (TDHF) theory, the basic equation of which is shown to be formally equivalent to the Hamilton's canonical equations of motion in the classical nonlinear dynamical system. An importance to relate the structure of the TDHF symplectic manifold with an inexhaustible rich structure of the classical phase space in the nonlinear system is stressed. A full quantum theory of nuclear collective dynamics is proposed under a dictation of what has been developed in the classical-level TDHF theory. It is shown that the proposed quantum theory enables us to explore exceeding complexity of the Hilbert space. It is discussed that a resonant denominator known as a source of the extraordinary rich structure of the phase space trajectories, also plays a decisive role in generating a rich structure of the quantum Hilbert space. (author) 87 refs

  8. Generic superweak chaos induced by Hall effect

    Science.gov (United States)

    Ben-Harush, Moti; Dana, Itzhack

    2016-05-01

    We introduce and study the "kicked Hall system" (KHS), i.e., charged particles periodically kicked in the presence of uniform magnetic (B ) and electric (E ) fields that are perpendicular to each other and to the kicking direction. We show that for resonant values of B and E and in the weak-chaos regime of sufficiently small nonintegrability parameter κ (the kicking strength), there exists a generic family of periodic kicking potentials for which the Hall effect from B and E significantly suppresses the weak chaos, replacing it by "superweak" chaos (SWC). This means that the system behaves as if the kicking strength were κ2 rather than κ . For E =0 , SWC is known to be a classical fingerprint of quantum antiresonance, but it occurs under much less generic conditions, in particular only for very special kicking potentials. Manifestations of SWC are a decrease in the instability of periodic orbits and a narrowing of the chaotic layers, relative to the ordinary weak-chaos case. Also, for global SWC, taking place on an infinite "stochastic web" in phase space, the chaotic diffusion on the web is much slower than the weak-chaos one. Thus, the Hall effect can be relatively stabilizing for small κ . In some special cases, the effect is shown to cause ballistic motion for almost all parameter values. The generic global SWC on stochastic webs in the KHS appears to be the two-dimensional closest analog to the Arnol'd web in higher dimensional systems.

  9. Household Chaos--Links with Parenting and Child Behaviour

    Science.gov (United States)

    Coldwell, Joanne; Pike, Alison; Dunn, Judy

    2006-01-01

    Background: The study aimed to confirm previous findings showing links between household chaos and parenting in addition to examining whether household chaos was predictive of children's behaviour over and above parenting. In addition, we investigated whether household chaos acts as a moderator between parenting and children's behaviour. Method:…

  10. God's Stuff: The Constructive Powers of Chaos for Teaching Religion

    Science.gov (United States)

    Willhauck, Susan

    2010-01-01

    Order and organization are valued in the classroom, and there is a prevailing understanding that chaos should be avoided. Yet chaos can also be potent space or a source from which new things spring forth. This article investigates biblical, scientific, and cultural understandings of chaos to discover how these contribute to a revelatory metaphor…

  11. Reliable Computational Predictions by Modeling Uncertainties Using Arbitrary Polynomial Chaos

    OpenAIRE

    Witteveen, J.A.S.; Bijl, H

    2006-01-01

    Inherent physical uncertainties can have a significant influence on computational predictions. It is therefore important to take physical uncertainties into account to obtain more reliable computational predictions. The Galerkin polynomial chaos method is a commonly applied uncertainty quantification method. However, the polynomial chaos expansion has some limitations. Firstly, the polynomial chaos expansion based on classical polynomials can achieve exponential convergence for a limited set ...

  12. Anti-control of chaos of single time scale brushless dc motors and chaos synchronization of different order systems

    International Nuclear Information System (INIS)

    Anti-control of chaos of single time scale brushless dc motors (BLDCM) and chaos synchronization of different order systems are studied in this paper. By addition of an external nonlinear term, we can obtain anti-control of chaos. Then, by addition of the coupling terms, by the use of Lyapunov stability theorem and by the linearization of the error dynamics, chaos synchronization between a third-order BLDCM and a second-order Duffing system are presented

  13. Chaos Concepts, Control and Constructive Use

    CERN Document Server

    Bolotin, Yurii; Yanovsky, Vladimir

    2009-01-01

    The study of chaotic behaviour in nonlinear, dynamical systems is now a well established research domain with ramifications into all fields of sciences, spanning a vast range of applications, from celestial mechanics, via climate change, to the functioning of brownian motors in cells. A more recent discovery is that chaos can be controlled and, under appropriate conditions, can actually be constructive in the sense of becoming a control parameter itself for the system under investigation, stochastic resonance being a prime example. The present work is putting emphasis on the latter aspects, and after recalling the paradigm changes introduced by the concept of chaos, leads the reader skillfully through the basics of chaos control by detailing relevant algorithms for both Hamiltonian and dissipative systems amongst others. The main part of the book is then devoted to the issue of synchronization in chaotic systems, an introduction to stochastic resonance and a survey of ratchet models. This short and concise pr...

  14. Associative memory with spatiotemporal chaos control

    Science.gov (United States)

    Kushibe, Masanori; Liu, Yun; Ohtsubo, Junji

    1996-05-01

    Control of spatiotemporal chaos in a neural network with discrete time and continuous state variables is investigated. The chaos control is performed with the knowledge of only a part of the target information in the memory patterns. The success rate for the pattern associations and the dependence of the search time on the sampling number in the proposed chaos neural network are studied. By the introduction of the reinforcement factor in the learning process, the recognition rate of the network can be much enhanced. Random and regular samplings of the pattern for the control are tested and the successful results of the associations are demonstrated. The chaotic behavior and recalling ability of the system are evaluated based on the analysis of the Lyapunov spectrum of the network.

  15. Improved particle swarm optimization combined with chaos

    International Nuclear Information System (INIS)

    As a novel optimization technique, chaos has gained much attention and some applications during the past decade. For a given energy or cost function, by following chaotic ergodic orbits, a chaotic dynamic system may eventually reach the global optimum or its good approximation with high probability. To enhance the performance of particle swarm optimization (PSO), which is an evolutionary computation technique through individual improvement plus population cooperation and competition, hybrid particle swarm optimization algorithm is proposed by incorporating chaos. Firstly, adaptive inertia weight factor (AIWF) is introduced in PSO to efficiently balance the exploration and exploitation abilities. Secondly, PSO with AIWF and chaos are hybridized to form a chaotic PSO (CPSO), which reasonably combines the population-based evolutionary searching ability of PSO and chaotic searching behavior. Simulation results and comparisons with the standard PSO and several meta-heuristics show that the CPSO can effectively enhance the searching efficiency and greatly improve the searching quality

  16. Nonlinear dynamics and quantum chaos an introduction

    CERN Document Server

    Wimberger, Sandro

    2014-01-01

    The field of nonlinear dynamics and chaos has grown very much over the last few decades and is becoming more and more relevant in different disciplines. This book presents a clear and concise introduction to the field of nonlinear dynamics and chaos, suitable for graduate students in mathematics, physics, chemistry, engineering, and in natural sciences in general. It provides a thorough and modern introduction to the concepts of Hamiltonian dynamical systems' theory combining in a comprehensive way classical and quantum mechanical description. It covers a wide range of topics usually not found in similar books. Motivations of the respective subjects and a clear presentation eases the understanding. The book is based on lectures on classical and quantum chaos held by the author at Heidelberg University. It contains exercises and worked examples, which makes it ideal for an introductory course for students as well as for researchers starting to work in the field.

  17. Experimental Evidence of Chaos from Memristors

    Science.gov (United States)

    Gambuzza, Lucia Valentina; Fortuna, Luigi; Frasca, Mattia; Gale, Ella

    Until now, most memristor-based chaotic circuits proposed in the literature are based on mathematical models which assume ideal characteristics such as piecewise-linear or cubic nonlinearities. The idea, illustrated here and originating from the experimental approach for device characterization, is to realize a chaotic system exploiting the nonlinearity of only one memristor with a very simple experimental set-up using feedback. In this way, a simple circuit is obtained and chaos is experimentally observed and is confirmed by the calculation of the largest Lyapunov exponent. Numerical results using the Strukov model support the existence of robust chaos in our circuit. To our knowledge, this is the first experimental demonstration of chaos in a real memristor circuit and suggests that memristors are well placed for hardware encryption.

  18. Towards CHAOS-5 - How can Swarm contribute?

    DEFF Research Database (Denmark)

    Finlay, Chris; Olsen, Nils; Tøffner-Clausen, Lars

    2014-01-01

    The launch of ESA's satellite trio Swarm in November 2013 opens an exciting new chapter in the observation and monitoring of Earth's magnetic field from space. We report preliminary results from an extension of the CHAOS series of geomagnetic field models to include both scalar and vector field...... observations from the three Swarm satellites, along with the most recent quasi-definitive ground observatory data. The fit of this new update CHAOS field model to the Swarm observations will be presented in detail providing useful insight the initial Swarm data. Enhancements of the CHAOS modelling scheme...... include a 1 minute time resolution for the RC index and anisotropic weighting of vector field data depending on quasi-dipole latitude. We shall also report on the perspective given by the initial Swarm data on rapid field changes currently taking place in the Atlantic sector....

  19. Nonlinear Physics Integrability, Chaos and Beyond

    CERN Document Server

    Lakshmanan, M

    1997-01-01

    Integrability and chaos are two of the main concepts associated with nonlinear physical systems which have revolutionized our understanding of them. Highly stable exponentially localized solitons are often associated with many of the important integrable nonlinear systems while motions which are sensitively dependent on initial conditions are associated with chaotic systems. Besides dramatically raising our perception of many natural phenomena, these concepts are opening up new vistas of applications and unfolding technologies: Optical soliton based information technology, magnetoelectronics, controlling and synchronization of chaos and secure communications, to name a few. These developments have raised further new interesting questions and potentialities. We present a particular view of some of the challenging problems and payoffs ahead in the next few decades by tracing the early historical events, summarizing the revolutionary era of 1950-70 when many important new ideas including solitons and chaos were ...

  20. Polynomial chaos functions and stochastic differential equations

    International Nuclear Information System (INIS)

    The Karhunen-Loeve procedure and the associated polynomial chaos expansion have been employed to solve a simple first order stochastic differential equation which is typical of transport problems. Because the equation has an analytical solution, it provides a useful test of the efficacy of polynomial chaos. We find that the convergence is very rapid in some cases but that the increased complexity associated with many random variables can lead to very long computational times. The work is illustrated by exact and approximate solutions for the mean, variance and the probability distribution itself. The usefulness of a white noise approximation is also assessed. Extensive numerical results are given which highlight the weaknesses and strengths of polynomial chaos. The general conclusion is that the method is promising but requires further detailed study by application to a practical problem in transport theory

  1. Etiology of dental erosion--intrinsic factors.

    Science.gov (United States)

    Scheutzel, P

    1996-04-01

    Dental erosion due to intrinsic factors is caused by gastric acid reaching the oral cavity and the teeth as a result of vomiting or gastroesophageal reflux. Since clinical manifestation of dental erosion does not occur until gastric acid has acted on the dental hard tissues regularly over a period of several years, dental erosion caused by intrinsic factors has been observed only in those diseases which are associated with chronic vomiting or persistent gastroesophageal reflux over a long period. Examples of such conditions include disorders of the upper alimentary tract, specific metabolic and endocrine disorders, cases of medication side-effects and drug abuse, and certain psychosomatic disorders, e.g. stress-induced psychosomatic vomiting, anorexia and bulimia nervosa or rumination. Based on a review of the medical and dental literature, the main symptoms of all disorders which must be taken into account as possible intrinsic etiological factors of dental erosion are thoroughly discussed with respect to the clinical picture, prevalence and risk of erosion. PMID:8804885

  2. Chaos in periodically forced Holling type IV predator-prey system with impulsive perturbations

    International Nuclear Information System (INIS)

    The effect of periodic forcing and impulsive perturbations on predator-prey model with Holling type IV functional response is investigated. The periodic forcing is affected by assuming a periodic variation in the intrinsic growth rate of the prey. The impulsive perturbations are affected by introducing periodic constant impulsive immigration of predator. The dynamical behavior of the system is simulated and bifurcation diagrams are obtained for different parameters. The results show that periodic forcing and impulsive perturbation can easily give rise to complex dynamics, including (1) quasi-periodic oscillating, (2) period doubling cascade, (3) chaos, (4) period halfing cascade

  3. Chaos in periodically forced Holling type II predator-prey system with impulsive perturbations

    International Nuclear Information System (INIS)

    The effect of periodic forcing and impulsive perturbations on predator-prey model with Holling type II functional response is investigated. The periodic forcing is affected by assuming a periodic variation in the intrinsic growth rate of prey. The impulsive perturbation is affected by introducing periodic constant impulsive immigration of predator. The dynamical behavior of the system is simulated and bifurcation diagrams are obtained for different parameters. The results show that periodic forcing and impulsive perturbation can very easily give rise to complex dynamics, including (1) quasi-periodic oscillating, (2) period doubling cascade, (3) chaos, (4) period halfing cascade, (5) non-unique dynamics

  4. Transition to chaos of thermocapillary convection

    Science.gov (United States)

    Li, Kai; Tang, Ze Mei; Aa, Yan; Hu, Wen-Rui

    Transition of fluid convection to chaos in dissipative dynamical systems is a subject of great interest for both its theoretical and practical aspects in the fluid mechanics. Extensive studies have shown that there are several routes of the buoyant natural convection to chaos depending on parameters of the dissipative dynamical systems such as the Rayleigh number, the Prandtl number and geometry aspect. Another important type of natural convection is thermocapillary convection driven by the surface-tension gradient prominent in fluid systems with interface in the microgravity condition or in small-scaled terrestrial configurations (The relative importance of the gravity effect to the capillary effect is scaled by the static Bond number, , and the dynamic Bond number, , the geometrical scale of the system in the terrestrial experiments, therefore, was significantly reduced to make the capillary effect dominant). The thermocapillary convection has become one of the fundamental subjects in the microgravity fluid physics and space fluid/heat management. However, most studies now available were focused on the onset of oscillatory thermocapillary convection, the initial regime of the route to chaos. A complete route to chaos in such a new sort of dissipative system is still an attractive open question, especially in the experimental study. In present study, the route to chaos of the thermocapillary convection has been investigated. Several routes to chaos, e.g. period oscillatory convection to quasi-period oscillatory convection with 2 to 3 major frequencies, a series of successive period doubling bifurcations and their combination, of the thermocapillary flow is reported through the temperature measurements and the corresponding real time analysis of frequency spectra accomplished by Fast-Fourier-Transformation (FFT) or numerically. The corresponding phase diagrams are also provided.

  5. Chaos, brain and divided consciousness.

    Science.gov (United States)

    Bob, Petr

    2007-01-01

    Modern trends in psychology and cognitive neuroscience suggest that applications of nonlinear dynamics, chaos and self-organization seem to be particularly important for research of some fundamental problems regarding mind-brain relationship. Relevant problems among others are formations of memories during alterations of mental states and nature of a barrier that divides mental states, and leads to the process called dissociation. This process is related to a formation of groups of neurons which often synchronize their firing patterns in a unique spatial maner. Central theme of this study is the relationship between level of moving and oscilating mental processes and their neurophysiological substrate. This opens a question about principles of organization of conscious experiences and how these experiences arise in the brain. Chaotic self-organization provides a unique theoretical and experimental tool for deeper understanding of dissociative phenomena and enables to study how dissociative phenomena can be linked to epileptiform discharges which are related to various forms of psychological and somatic manifestations. Organizing principles that constitute human consciousness and other mental phenomena from this point of view may be described by analysis and reconstruction of underlying dynamics of psychological or psychophysiological measures. These nonlinear methods in this study were used for analysis of characteristic changes in EEG and bilateral electrodermal activity (EDA) during reliving of dissociated traumatic and stressful memories and during psychopathological states. Analysis confirms a possible role of chaotic transitions in the processing of dissociated memory. Supportive finding for a possible chaotic process related to dissociation found in this study represent also significant relationship of dissociation, epileptiform discharges measured by typical psychopathological manifestations and characteristic laterality changes in bilateral EDA in patients

  6. Distributed chaos and inertial ranges in turbulence

    CERN Document Server

    Bershadskii, A

    2016-01-01

    It is shown that appearance of inertial range of scales, adjacent to distributed chaos range, results in adiabatic invariance of an energy correlation integral for isotropic homogeneous turbulence and for buoyancy driven turbulence (with stable or unstable stratification, including Rayleigh-Taylor mixing zone). Power spectrum of velocity field for distributed chaos dominated by this adiabatic invariant has a stretched exponential form $\\propto \\exp(-k/k_{\\beta})^{3/5}$. Results of recent direct numerical simulations have been used in order to support these conclusions.

  7. Controlling chaos in an economic model

    Science.gov (United States)

    Chen, Liang; Chen, Guanrong

    2007-01-01

    A Cournot duopoly, with a bounded inverse demand function and different constant marginal production costs, can be modeled as a discrete-time dynamical system, which exhibits complex bifurcating and chaotic behaviors. Based on some essential features of the model, we show how bifurcation and chaos can be controlled via the delayed feedback control method. We then propose and evaluate an adaptive parameter-tuning algorithm for control. In addition, we discuss possible economic implications of the chaos control strategies described in the paper.

  8. USING OPTIMAL FEEDBACK CONTROL FOR CHAOS TARGETING

    Institute of Scientific and Technical Information of China (English)

    PENG ZHAO-WANG; ZHONG TING-XIU

    2000-01-01

    Since the conventional open-loop optimal targeting of chaos is very sensitive to noise, a close-loop optimal targeting method is proposed to improve the targeting performance under noise. The present optimal targeting model takes into consideration both precision and speed of the targeting procedure. The parameters, rather than the output, of the targeting controller, are directly optimized to obtain optimal chaos targeting. Analysis regarding the mechanism is given from physics aspect and numerical experiment on the Hénon map is carried out to compare the targeting performance under noise between the close-loop and the open-loop methods.

  9. On chaos synchronization and secure communication.

    Science.gov (United States)

    Kinzel, W; Englert, A; Kanter, I

    2010-01-28

    Chaos synchronization, in particular isochronal synchronization of two chaotic trajectories to each other, may be used to build a means of secure communication over a public channel. In this paper, we give an overview of coupling schemes of Bernoulli units deduced from chaotic laser systems, different ways to transmit information by chaos synchronization and the advantage of bidirectional over unidirectional coupling with respect to secure communication. We present the protocol for using dynamical private commutative filters for tap-proof transmission of information that maps the task of a passive attacker to the class of non-deterministic polynomial time-complete problems. PMID:20008407

  10. Lorentz invariant intrinsic decoherence

    CERN Document Server

    Milburn, G J

    2003-01-01

    Quantum decoherence can arise due to classical fluctuations in the parameters which define the dynamics of the system. In this case decoherence, and complementary noise, is manifest when data from repeated measurement trials are combined. Recently a number of authors have suggested that fluctuations in the space-time metric arising from quantum gravity effects would correspond to a source of intrinsic noise, which would necessarily be accompanied by intrinsic decoherence. This work extends a previous heuristic modification of Schr\\"{o}dinger dynamics based on discrete time intervals with an intrinsic uncertainty. The extension uses unital semigroup representations of space and time translations rather than the more usual unitary representation, and does the least violence to physically important invariance principles. Physical consequences include a modification of the uncertainty principle and a modification of field dispersion relations, in a way consistent with other modifications suggested by quantum grav...

  11. Intrinsic time quantum geometrodynamics

    Science.gov (United States)

    Ita, Eyo Eyo; Soo, Chopin; Yu, Hoi-Lai

    2015-08-01

    Quantum geometrodynamics with intrinsic time development and momentric variables is presented. An underlying SU(3) group structure at each spatial point regulates the theory. The intrinsic time behavior of the theory is analyzed, together with its ground state and primordial quantum fluctuations. Cotton-York potential dominates at early times when the universe was small; the ground state naturally resolves Penrose's Weyl curvature hypothesis, and thermodynamic and gravitational "arrows of time" point in the same direction. Ricci scalar potential corresponding to Einstein's general relativity emerges as a zero-point energy contribution. A new set of fundamental commutation relations without Planck's constant emerges from the unification of gravitation and quantum mechanics.

  12. Intrinsic Time Quantum Geometrodynamics

    CERN Document Server

    Ita, Eyo Eyo; Yu, Hoi-Lai

    2015-01-01

    Quantum Geometrodynamics with intrinsic time development and momentric variables is presented. An underlying SU(3) group structure at each spatial point regulates the theory. The intrinsic time behavior of the theory is analyzed, together with its ground state and primordial quantum fluctuations. Cotton-York potential dominates at early times when the universe was small; the ground state naturally resolves Penrose's Weyl Curvature Hypothesis, and thermodynamic and gravitational `arrows of time' point in the same direction. Ricci scalar potential corresponding to Einstein's General Relativity emerges as a zero-point energy contribution. A new set of fundamental canonical commutation relations without Planck's constant emerges from the unification of Gravitation and Quantum Mechanics.

  13. Predicting Intrinsic Motivation

    Science.gov (United States)

    Martens, Rob; Kirschner, Paul A.

    2004-01-01

    Intrinsic motivation can be predicted from participants' perceptions of the social environment and the task environment (Ryan & Deci, 2000)in terms of control, relatedness and competence. To determine the degree of independence of these factors 251 students in higher vocational education (physiotherapy and hotel management) indicated the extent to…

  14. Chaos control applied to heart rhythm dynamics

    International Nuclear Information System (INIS)

    Highlights: → A natural cardiac pacemaker is modeled by a modified Van der Pol oscillator. → Responses related to normal and chaotic, pathological functioning of the heart are investigated. → Chaos control methods are applied to avoid pathological behaviors of heart dynamics. → Different approaches are treated: stabilization of unstable periodic orbits and chaos suppression. - Abstract: The dynamics of cardiovascular rhythms have been widely studied due to the key aspects of the heart in the physiology of living beings. Cardiac rhythms can be either periodic or chaotic, being respectively related to normal and pathological physiological functioning. In this regard, chaos control methods may be useful to promote the stabilization of unstable periodic orbits using small perturbations. In this article, the extended time-delayed feedback control method is applied to a natural cardiac pacemaker described by a mathematical model. The model consists of a modified Van der Pol equation that reproduces the behavior of this pacemaker. Results show the ability of the chaos control strategy to control the system response performing either the stabilization of unstable periodic orbits or the suppression of chaotic response, avoiding behaviors associated with critical cardiac pathologies.

  15. Chaos in schizophrenia associations, reality or metaphor?

    Czech Academy of Sciences Publication Activity Database

    Bob, P.; Šusta, M.; Chládek, Jan; Glaslová, K.; Paluš, Milan

    2009-01-01

    Roč. 73, č. 3 (2009), s. 179-185. ISSN 0167-8760 Institutional research plan: CEZ:AV0Z20650511; CEZ:AV0Z10300504 Keywords : Chaos * Schizophrenia * Associations * Electrodermal activity * Lyapunov exponent Subject RIV: FH - Neurology Impact factor: 3.045, year: 2009

  16. Order, chaos and nuclear dynamics: An introduction

    International Nuclear Information System (INIS)

    This is an introductory lecture illustrating by simple examples the anticipated effect on collective nuclear dynamics of a transition from order to chaos in the motions of nucleons inside an idealized nucleus. The destruction of order is paralleled by a transition from a rubber-like to a honey-like behaviour of the independent-particle nuclear model. 10 refs., 6 figs

  17. Chaos theory: A fascinating concept for oncologists

    International Nuclear Information System (INIS)

    The oncologist is confronted daily by questions related to the fact that any patient presents a specific evolution for his cancer: he is challenged by very different, unexpected and often unpredictable outcomes, in some of his patients. The mathematical approach used today to describe this evolution has recourse to statistics and probability laws: such an approach does not ultimately apply to one particular patient, but to a given more or less heterogeneous population. This approach therefore poorly characterizes the dynamics of this disease and does not allow to state whether a patient is cured, to predict if he will relapse and when this could occur, and in what form, nor to predict the response to treatment and, in particular, to radiation therapy. Chaos theory, not well known by oncologists, could allow a better understanding of these issues. Developed to investigate complex systems producing behaviours that cannot be predicted due to a great sensitivity to initial conditions, chaos theory is rich of suitable concepts for a new approach of cancer dynamics. This article is three-fold: to provide a brief introduction to chaos theory, to clarify the main connecting points between chaos and carcinogenesis and to point out few promising research perspectives, especially in radiotherapy. (authors)

  18. Chaos in a Bose—Einstein condensate

    International Nuclear Information System (INIS)

    It is demonstrated that Smale-horseshoe chaos exists in the time evolution of the one-dimensional Bose—Einstein condensate driven by time-periodic harmonic or inverted-harmonic potential. A formally exact solution of the time-dependent Gross—Pitaevskii equation is constructed, which describes the matter shock waves with chaotic or periodic amplitudes and phases

  19. The chaos machine: analogue computing rediscovered (1)

    OpenAIRE

    Ambaum, Maarten H. P.; Harrison, R. Giles

    2011-01-01

    Analogue computers provide actual rather than virtual representations of model systems. They are powerful and engaging computing machines that are cheap and simple to build. This two-part Retronics article helps you build (and understand!) your own analogue computer to simulate the Lorenz butterfly that's become iconic for Chaos theory.

  20. Chaos in a Bose-Einstein condensate

    Institute of Scientific and Technical Information of China (English)

    Wang Zhi-Xia; Ni Zheng-Guo; Cong Fu-Zhong; Liu Xue-Shen; Chen Lei

    2010-01-01

    It is demonstrated that Smale-horseshoe chaos exists in the time evolution of the one-dimensional Bose-Einstein condensate driven by time-periodic harmonic or inverted-harmonic potential.A formally exact solution of the timedependent Gross-Pitaevskii equation is constructed,which describes the matter shock waves with chaotic or periodic amplitudes and phases.

  1. Chaos and fractals an elementary introduction

    CERN Document Server

    Feldman, David P

    2012-01-01

    For students with a background in elementary algebra, this text provides a vivid introduction to the key phenomena and ideas of chaos and fractals, including the butterfly effect, strange attractors, fractal dimensions, Julia sets and the Mandelbrot set, power laws, and cellular automata.

  2. Chaos control applied to heart rhythm dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Borem Ferreira, Bianca, E-mail: biaborem@gmail.com [Universidade Federal do Rio de Janeiro, COPPE, Department of Mechanical Engineering, P.O. Box 68.503, 21.941.972 Rio de Janeiro, RJ (Brazil); Souza de Paula, Aline, E-mail: alinedepaula@unb.br [Universidade de Brasi' lia, Department of Mechanical Engineering, 70.910.900 Brasilia, DF (Brazil); Amorim Savi, Marcelo, E-mail: savi@mecanica.ufrj.br [Universidade Federal do Rio de Janeiro, COPPE, Department of Mechanical Engineering, P.O. Box 68.503, 21.941.972 Rio de Janeiro, RJ (Brazil)

    2011-08-15

    Highlights: > A natural cardiac pacemaker is modeled by a modified Van der Pol oscillator. > Responses related to normal and chaotic, pathological functioning of the heart are investigated. > Chaos control methods are applied to avoid pathological behaviors of heart dynamics. > Different approaches are treated: stabilization of unstable periodic orbits and chaos suppression. - Abstract: The dynamics of cardiovascular rhythms have been widely studied due to the key aspects of the heart in the physiology of living beings. Cardiac rhythms can be either periodic or chaotic, being respectively related to normal and pathological physiological functioning. In this regard, chaos control methods may be useful to promote the stabilization of unstable periodic orbits using small perturbations. In this article, the extended time-delayed feedback control method is applied to a natural cardiac pacemaker described by a mathematical model. The model consists of a modified Van der Pol equation that reproduces the behavior of this pacemaker. Results show the ability of the chaos control strategy to control the system response performing either the stabilization of unstable periodic orbits or the suppression of chaotic response, avoiding behaviors associated with critical cardiac pathologies.

  3. Chaos and Interactions in Quantum Dots

    OpenAIRE

    Alhassid, Y.

    2001-01-01

    Quantum dots are small conducting devices containing up to several thousand electrons. We focus here on closed dots whose single-electron dynamics are mostly chaotic. The mesoscopic fluctuations of the conduction properties of such dots reveal the effects of one-body chaos, quantum coherence and electron-electron interactions.

  4. Chaos synthesis by means of evolutionary algorithms

    Czech Academy of Sciences Publication Activity Database

    Zelinka, I.; Chen, G.; Čelikovský, Sergej

    2008-01-01

    Roč. 18, č. 4 (2008), s. 911-942. ISSN 0218-1274 R&D Projects: GA ČR(CZ) GA102/08/0186 Institutional research plan: CEZ:AV0Z10750506 Keywords : Chaos * evolution * synthesis Subject RIV: BC - Control Systems Theory Impact factor: 0.870, year: 2008

  5. Stabilizing the Richardson Algorithm by Controlling Chaos

    OpenAIRE

    He, Song

    1996-01-01

    By viewing the operations of the Richardson purification algorithm as a discrete time dynamical process, we propose a method to overcome the instability of the algorithm by controlling chaos. We present theoretical analysis and numerical results on the behavior and performance of the stabilized algorithm.

  6. Chaos: A Very Short Introduction

    International Nuclear Information System (INIS)

    This book is a new volume of a series designed to introduce the curious reader to anything from ancient Egypt and Indian philosophy to conceptual art and cosmology. Very handy in pocket size, Chaos promises an introduction to fundamental concepts of nonlinear science by using mathematics that is 'no more complicated than X=2. Anyone who ever tried to give a popular science account of research knows that this is a more challenging task than writing an ordinary research article. Lenny Smith brilliantly succeeds to explain in words, in pictures and by using intuitive models the essence of mathematical dynamical systems theory and time series analysis as it applies to the modern world. In a more technical part he introduces the basic terms of nonlinear theory by means of simple mappings. He masterly embeds this analysis into the social, historical and cultural context by using numerous examples, from poems and paintings over chess and rabbits to Olbers' paradox, card games and 'phynance'. Fundamental problems of the modelling of nonlinear systems like the weather, sun spots or golf balls falling through an array of nails are discussed from the point of view of mathematics, physics and statistics by touching upon philosophical issues. At variance with Laplace's demon, Smith's 21st century demon makes 'real world' observations only with limited precision. This poses a severe problem to predictions derived from complex chaotic models, where small variations of initial conditions typically yield totally different outcomes. As Smith argues, this difficulty has direct implications on decision-making in everyday modern life. However, it also asks for an inherently probabilistic theory, which somewhat reminds us of what we are used to in the microworld. There is little to criticise in this nice little book except that some figures are of poor quality thus not really reflecting the beauty of fractals and other wonderful objects in this field. I feel that occasionally the book

  7. Chaos: A Very Short Introduction

    Energy Technology Data Exchange (ETDEWEB)

    Klages, R [School of Mathematical Sciences, Mile End Road, London, E1 4NS (United Kingdom)

    2007-07-20

    This book is a new volume of a series designed to introduce the curious reader to anything from ancient Egypt and Indian philosophy to conceptual art and cosmology. Very handy in pocket size, Chaos promises an introduction to fundamental concepts of nonlinear science by using mathematics that is 'no more complicated than X=2. Anyone who ever tried to give a popular science account of research knows that this is a more challenging task than writing an ordinary research article. Lenny Smith brilliantly succeeds to explain in words, in pictures and by using intuitive models the essence of mathematical dynamical systems theory and time series analysis as it applies to the modern world. In a more technical part he introduces the basic terms of nonlinear theory by means of simple mappings. He masterly embeds this analysis into the social, historical and cultural context by using numerous examples, from poems and paintings over chess and rabbits to Olbers' paradox, card games and 'phynance'. Fundamental problems of the modelling of nonlinear systems like the weather, sun spots or golf balls falling through an array of nails are discussed from the point of view of mathematics, physics and statistics by touching upon philosophical issues. At variance with Laplace's demon, Smith's 21st century demon makes 'real world' observations only with limited precision. This poses a severe problem to predictions derived from complex chaotic models, where small variations of initial conditions typically yield totally different outcomes. As Smith argues, this difficulty has direct implications on decision-making in everyday modern life. However, it also asks for an inherently probabilistic theory, which somewhat reminds us of what we are used to in the microworld. There is little to criticise in this nice little book except that some figures are of poor quality thus not really reflecting the beauty of fractals and other wonderful objects in this

  8. CHAOS-BASED ADVANCED ENCRYPTION STANDARD

    KAUST Repository

    Abdulwahed, Naif B.

    2013-05-01

    This thesis introduces a new chaos-based Advanced Encryption Standard (AES). The AES is a well-known encryption algorithm that was standardized by U.S National Institute of Standard and Technology (NIST) in 2001. The thesis investigates and explores the behavior of the AES algorithm by replacing two of its original modules, namely the S-Box and the Key Schedule, with two other chaos- based modules. Three chaos systems are considered in designing the new modules which are Lorenz system with multiplication nonlinearity, Chen system with sign modules nonlinearity, and 1D multiscroll system with stair case nonlinearity. The three systems are evaluated on their sensitivity to initial conditions and as Pseudo Random Number Generators (PRNG) after applying a post-processing technique to their output then performing NIST SP. 800-22 statistical tests. The thesis presents a hardware implementation of dynamic S-Boxes for AES that are populated using the three chaos systems. Moreover, a full MATLAB package to analyze the chaos generated S-Boxes based on graphical analysis, Walsh-Hadamard spectrum analysis, and image encryption analysis is developed. Although these S-Boxes are dynamic, meaning they are regenerated whenever the encryption key is changed, the analysis results show that such S-Boxes exhibit good properties like the Strict Avalanche Criterion (SAC) and the nonlinearity and in the application of image encryption. Furthermore, the thesis presents a new Lorenz-chaos-based key expansion for the AES. Many researchers have pointed out that there are some defects in the original key expansion of AES and thus have motivated such chaos-based key expansion proposal. The new proposed key schedule is analyzed and assessed in terms of confusion and diffusion by performing the frequency and SAC test respectively. The obtained results show that the new proposed design is more secure than the original AES key schedule and other proposed designs in the literature. The proposed

  9. THEORY OF SECULAR CHAOS AND MERCURY'S ORBIT

    International Nuclear Information System (INIS)

    We study the chaotic orbital evolution of planetary systems, focusing on secular (i.e., orbit-averaged) interactions, which dominate on long timescales. We first focus on the evolution of a test particle that is forced by multiple planets. To linear order in eccentricity and inclination, its orbit precesses with constant frequencies. But nonlinearities modify the frequencies, and can shift them into and out of resonance with either the planets' eigenfrequencies (forming eccentricity or inclination secular resonances), or with linear combinations of those frequencies (forming mixed high-order secular resonances). The overlap of these nonlinear secular resonances drives secular chaos. We calculate the locations and widths of nonlinear secular resonances, display them together on a newly developed map (the 'map of the mean momenta'), and find good agreement between analytical and numerical results. This map also graphically demonstrates how chaos emerges from overlapping secular resonances. We then apply this newfound understanding to Mercury to elucidate the origin of its orbital chaos. We find that since Mercury's two free precession frequencies (in eccentricity and inclination) lie within ∼25% of two other eigenfrequencies in the solar system (those of the Jupiter-dominated eccentricity mode and the Venus-dominated inclination mode), secular resonances involving these four modes overlap and cause Mercury's chaos. We confirm this with N-body integrations by showing that a slew of these resonant angles alternately librate and circulate. Our new analytical understanding allows us to calculate the criterion for Mercury to become chaotic: Jupiter and Venus must have eccentricity and inclination of a few percent. The timescale for Mercury's chaotic diffusion depends sensitively on the forcing. As it is, Mercury appears to be perched on the threshold for chaos, with an instability timescale comparable to the lifetime of the solar system.

  10. Controlling halo-chaos via wavelet-based feedback

    Directory of Open Access Journals (Sweden)

    Geng Zhao

    2002-01-01

    Full Text Available Halo-chaos in high-current accelerator has become one of the key issues because it can cause excessive radioactivity from the accelerators and significantly limits the applications of the new accelerators in industrial and other fields. Some general engineering methods for chaos control have been developed, but they generally are unsuccessful for halo-chaos suppression due to many technical constraints. In this article, controllability condition for beam halo-chaos is analyzed qualitatively. Then Particles-in-Cell (PIC simulations explore the nature of beam halo-chaos formation. A nonlinear control method and wavelet function feedback controller are proposed for controlling beam halo-chaos. After control of beam halo-chaos for initial proton beam with water bag distributions, the beam halo strength factor H is reduced to zero, and other statistical physical quantities of beam halo-chaos are doubly reduced. The results show that the developed methods in this paper are very effective for proton beam halo-chaos suppression. Potential application of the halo-chaos control method is finally pointed out.

  11. Proceedings of the 2nd Experimental Chaos Conference

    Science.gov (United States)

    Ditto, William; Pecora, Lou; Shlesinger, Michael; Spano, Mark; Vohra, Sandeep

    1995-02-01

    The Table of Contents for the full book PDF is as follows: * Introduction * Spatiotemporal Phenomena * Experimental Studies of Chaotic Mixing * Using Random Maps in the Analysis of Experimental Fluid Flows * Transition to Spatiotemporal Chaos in a Reaction-Diffusion System * Ion-Dynamical Chaos in Plasmas * Optics * Chaos in a Synchronously Driven Optical Resonator * Chaos, Patterns and Defects in Stimulated Scattering Phenomena * Test of the Normal Form for a Subcritical Bifurcation * Observation of Bifurcations and Chaos in a Driven Fiber Optic Coil * Applications -- Communications * Robustness and Signal Recovery in a Synchronized Chaotic System * Synchronizing Nonautonomous Chaotic Circuits * Synchronization of Pulse-Coupled Chaotic Oscillators * Ocean Transmission Effects on Chaotic Signals * Controlling Symbolic Dynamics for Communication * Applications -- Control * Analysis of Nonlinear Actuators Using Chaotic Waveforms * Controlling Chaos in a Quasiperiodic Electronic System * Control of Chaos in a CO2 Laser * General Research * Video-Based Analysis of Bifurcation Phenomena in Radio-Frequency-Excited Inert Gas Plasmas * Transition from Soliton to Chaotic Motion During the Impact of a Nonlinear Structure * Sonoluminescence in a Single Bubble: Periodic, Quasiperiodic and Chaotic Light Source * Quantum Chaos Experiments Using Microwave Cavities * Experiments on Quantum Chaos With and Without Time Reversibility * When Small Noise Imposed on Deterministic Dynamics Becomes Important * Biology * Chaos Control for Cardiac Arrhythmias * Irregularities in Spike Trains of Cat Retinal Ganglion Cells * Broad-Band Synchronization in Monkey Neocortex * Applicability of Correlation Dimension Calculations to Blood Pressure Signal in Rats * Tests for Deterministic Chaos in Noisy Time Series * The Crayfish Mechanoreceptor Cell: A Biological Example of Stochastic Resonance * Chemistry * Chaos During Heterogeneous Chemical Reactions * Stabilizing and Tracking Unstable Periodic

  12. Intrinsic Time Quantum Gravity

    OpenAIRE

    Yu, Hoi Lai

    2016-01-01

    Correct identification of the true gauge symmetry of General Relativity being 3d spatial diffeomorphism invariant(3dDI) (not the conventional infinite tensor product group with principle fibre bundle structure), together with intrinsic time extracted from clean decomposition of the canonical structure yields a self-consistent theory of quantum gravity. A new set of fundamental commutation relations is also presented. The basic variables are the eight components of the unimodular part of the s...

  13. Chaos in electric drive systems analysis control and application

    CERN Document Server

    Chau, K T

    2011-01-01

    In Chaos in Electric Drive Systems: Analysis, Control and Application authors Chau and Wang systematically introduce an emerging technology of electrical engineering that bridges abstract chaos theory and practical electric drives. The authors consolidate all important information in this interdisciplinary technology, including the fundamental concepts, mathematical modeling, theoretical analysis, computer simulation, and hardware implementation. The book provides comprehensive coverage of chaos in electric drive systems with three main parts: analysis, control and application. Corresponding drive systems range from the simplest to the latest types: DC, induction, synchronous reluctance, switched reluctance, and permanent magnet brushless drives.The first book to comprehensively treat chaos in electric drive systemsReviews chaos in various electrical engineering technologies and drive systemsPresents innovative approaches to stabilize and stimulate chaos in typical drivesDiscusses practical application of cha...

  14. Optomechanically induced stochastic resonance and chaos transfer between optical fields

    Science.gov (United States)

    Monifi, Faraz; Zhang, Jing; Özdemir, Şahin Kaya; Peng, Bo; Liu, Yu-Xi; Bo, Fang; Nori, Franco; Yang, Lan

    2016-06-01

    Chaotic dynamics has been reported in many physical systems and has affected almost every field of science. Chaos involves hypersensitivity to the initial conditions of a system and introduces unpredictability into its output. Thus, it is often unwanted. Interestingly, the very same features make chaos a powerful tool to suppress decoherence, achieve secure communication and replace background noise in stochastic resonance—a counterintuitive concept that a system's ability to transfer information can be coherently amplified by adding noise. Here, we report the first demonstration of chaos-induced stochastic resonance in an optomechanical system, as well as the optomechanically mediated chaos transfer between two optical fields such that they follow the same route to chaos. These results will contribute to the understanding of nonlinear phenomena and chaos in optomechanical systems, and may find applications in the chaotic transfer of information and for improving the detection of otherwise undetectable signals in optomechanical systems.

  15. A novel 2D wavelength-time chaos code in optical CDMA system

    Science.gov (United States)

    Zhang, Qi; Xin, Xiangjun; Wang, Yongjun; Zhang, Lijia; Yu, Chongxiu; Meng, Nan; Wang, Houtian

    2012-11-01

    Two-dimensional wavelength-time chaos code is proposed and constructed for a synchronous optical code division multiple access system. The access performance is compared between one-dimensional chaos code, WDM/chaos code and the proposed code. Comparison shows that two-dimensional wavelength-time chaos code possesses larger capacity, better spectral efficiency and bit-error ratio than WDM/chaos combinations and one-dimensional chaos code.

  16. CONGENITAL HIGH AIRWAY OBSTRUCTION (CHAOS SYNDROME: A RARE CASE PRESENTATION

    Directory of Open Access Journals (Sweden)

    Dinakara

    2014-04-01

    Full Text Available Congenital high airway obstruction syndrome (CHAOS results in a predictable constellation of findings: large echogenic lungs flattened or inverted diaphragms, dilated airways distal to the obstruction, and fetal ascites and/or hydrops.1 The finding of CHAOS on prenatal ultrasound examination is diagnostic of complete or near-complete obstruction of the fetal upper airway, most likely caused by laryngeal atresia. A greater understanding of the natural history of CHAOS may permit improved prenatal and perinatal management

  17. Comments on microcausality, chaos, and gravitational observables

    Science.gov (United States)

    Marolf, Donald

    2015-12-01

    Observables in gravitational systems must be non-local so as to be invariant under diffeomorphism gauge transformations. But at the classical level some such observables can nevertheless satisfy an exact form of microcausality. This property is conjectured to remain true at all orders in the semiclassical expansion, though with limitations at finite ℏ or {{\\ell }}{Planck}. We also discuss related issues concerning observables in black hole spacetimes and comment on the senses in which they do and do not experience the form of chaos identified by Shenker and Stanford. In particular, in contrast to the situation in a reflecting cavity, this chaos does not afflict observables naturally associated with Hawking radiation for evaporating black holes.

  18. Comments on Microcausality, Chaos, and Gravitational Observables

    CERN Document Server

    Marolf, Donald

    2015-01-01

    Observables in gravitational systems must be non-local so as to be invariant under diffeomorphism gauge transformations. But at the classical level some such observables can nevertheless satisfy an exact form of microcausality. This property is conjectured to remain true at all orders in the semiclassical expansion, though with limitations at finite $\\hbar$ or $\\ell_{Planck}$. We also discuss related issues concerning observables in black hole spacetimes and comment on the senses in which they do and do not experience the form of chaos identified by Shenker and Stanford. In particular, in contrast to the situation in a reflecting cavity, this chaos does not afflict observables naturally associated with Hawking radiation for evaporating black holes.

  19. Chaos synchronization in networks of semiconductor superlattices

    Science.gov (United States)

    Li, Wen; Aviad, Yaara; Reidler, Igor; Song, Helun; Huang, Yuyang; Biermann, Klaus; Rosenbluh, Michael; Zhang, Yaohui; Grahn, Holger T.; Kanter, Ido

    2015-11-01

    Chaos synchronization has been demonstrated as a useful building block for various tasks in secure communications, including a source of all-electronic ultrafast physical random number generators based on room temperature spontaneous chaotic oscillations in a DC-biased weakly coupled GaAs/Al0.45Ga0.55As semiconductor superlattice (SSL). Here, we experimentally demonstrate the emergence of several types of chaos synchronization, e.g. leader-laggard, face-to-face and zero-lag synchronization in network motifs of coupled SSLs consisting of unidirectional and mutual coupling as well as self-feedback coupling. Each type of synchronization clearly reflects the symmetry of the topology of its network motif. The emergence of a chaotic SSL without external feedback and synchronization among different structured SSLs open up the possibility for advanced secure multi-user communication methods based on large networks of coupled SSLs.

  20. Chaos theory perspective for industry clusters development

    Science.gov (United States)

    Yu, Haiying; Jiang, Minghui; Li, Chengzhang

    2016-03-01

    Industry clusters have outperformed in economic development in most developing countries. The contributions of industrial clusters have been recognized as promotion of regional business and the alleviation of economic and social costs. It is no doubt globalization is rendering clusters in accelerating the competitiveness of economic activities. In accordance, many ideas and concepts involve in illustrating evolution tendency, stimulating the clusters development, meanwhile, avoiding industrial clusters recession. The term chaos theory is introduced to explain inherent relationship of features within industry clusters. A preferred life cycle approach is proposed for industrial cluster recessive theory analysis. Lyapunov exponents and Wolf model are presented for chaotic identification and examination. A case study of Tianjin, China has verified the model effectiveness. The investigations indicate that the approaches outperform in explaining chaos properties in industrial clusters, which demonstrates industrial clusters evolution, solves empirical issues and generates corresponding strategies.

  1. Experimental chaos detection in the Duffing oscillator

    Science.gov (United States)

    Eyebe Fouda, J. S. Armand; Bodo, Bertrand; Djeufa, Guy M. D.; Sabat, Samrat L.

    2016-04-01

    This paper presents a comparative study of four algorithms namely the maximal Lyapunov exponent (MLE), 0-1 test, conditional entropy of ordinal patterns (CPE) and recently developed permutation largest slope entropy (PLSE) algorithm for experimental chaos detection in the Duffing oscillator. We consider an electrical model of the Duffing oscillator and its equivalent electronic circuit for generating the data to validate the effectiveness of the algorithms. The performance of the PLSE is compared with the 0-1 test and the CPE algorithms on the data set obtained from the simulated circuit; and with the MLE for the data collected from the experimental circuit. The experimental data are acquired using a digital oscilloscope with 1 MHz sampling frequency. From the comparison of the experimental spectra of the four methods with the analog phase portraits of the real system, it appears that the PLSE is the more reliable algorithm for chaos detection from experimental data.

  2. Experimental Study of the Sampled Labyrinth Chaos

    Directory of Open Access Journals (Sweden)

    J. Petrzela

    2011-12-01

    Full Text Available In this paper, some new numerical as well as experimental results connected with the so-called labyrinth chaos are presented. This very unusual chaotic motion can be generated by mathematical model involving the scalar goniometrical functions which makes a three-dimensional autonomous dynamical system strongly nonlinear. Final circuitry implementation with analog core and digital parts can be used for modeling Brownian motion. From the viewpoint of generating chaotic motion by some electronic circuit, first step is to solve problems associated with the two-port nonlinear transfer functions synthesis. In the case of labyrinth chaos the finite dynamical range of the input variables introduced by the used active elements usually limits the performance greatly, similarly as it holds for the multi-grid spiral attractors. This paper shows an elegant way how to remove these obstacles by using uni-versal multiple-port with internal digital signal processing.

  3. Chaos in a Hydraulic Control Valve

    Science.gov (United States)

    Hayashi, S.; Hayase, T.; Kurahashi, T.

    1997-08-01

    In this paper we have studied the instability and chaos occurring in a pilot-type poppet valve circuit. The system consists of a poppet valve, an upstream plenum chamber, a supply pipeline and an orifice inserted between the pelnum and the pipeline. Although the poppet valve rests on the seat stably for a supply pressure lower than the cracking pressure, the circuit becomes unstable for an initial disturbance beyond a critical value and develops a self-excited vibration. In this unstable region, chaotic vibration appears at the period-doubling bifurcation. We have investigated the stability of the circuit and the chaotic phenomenon numerically, and elucidated it by power spectra, a bifurcation diagram and Lyapunov exponent calculations, showing that the phenomenon follows the Feigenbaum route to chaos.Copyright 1997 Academic Press Limited

  4. Buoyancy driven turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

    It is shown, using results of recent direct numerical simulations, laboratory experiments and atmospheric measurements, that buoyancy driven turbulence exhibits a broad diversity of the types of distributed chaos with its stretched exponential spectrum $\\exp(-k/k_{\\beta})^{\\beta}$. The distributed chaos with $\\beta = 1/3$ (determined by the helicity correlation integral) is the most common feature of the stably stratified turbulence (due to the strong helical waves presence). These waves mostly dominate spectral properties of the vertical component of velocity field, while the horizontal component is dominated by the diffusive processes both for the weak and strong stable stratification ($\\beta =2/3$). For the last case influence of the low boundary can overcome the wave effects and result in $\\beta =1/2$ for the vertical component of the velocity field (the spontaneous breaking of the space translational symmetry - homogeneity). For the unstably stratified turbulence in the Rayleigh-Taylor mixing zone the di...

  5. Chaos in hydrodynamic BL Herculis models

    CERN Document Server

    Smolec, R

    2014-01-01

    We present non-linear, convective, BL Her-type hydrodynamic models that show complex variability characteristic for deterministic chaos. The bifurcation diagram reveals a rich structure, with many phenomena detected for the first time in hydrodynamic models of pulsating stars. The phenomena include not only period doubling cascades en route to chaos (detected in earlier studies) but also periodic windows within chaotic band, type-I and type-III intermittent behaviour, interior crisis bifurcation and others. Such phenomena are known in many textbook chaotic systems, from the simplest discrete logistic map, to more complex systems like Lorenz equations. We discuss the physical relevance of our models. Although except of period doubling such phenomena were not detected in any BL Her star, chaotic variability was claimed in several higher luminosity siblings of BL Her stars - RV Tau variables, and also in longer-period, luminous irregular pulsators. Our models may help to understand these poorly studied stars. Pa...

  6. An exploration of dynamical systems and chaos

    CERN Document Server

    Argyris, John H; Haase, Maria; Friedrich, Rudolf

    2015-01-01

    This book is conceived as a comprehensive and detailed text-book on non-linear dynamical systems with particular emphasis on the exploration of chaotic phenomena. The self-contained introductory presentation is addressed both to those who wish to study the physics of chaotic systems and non-linear dynamics intensively as well as those who are curious to learn more about the fascinating world of chaotic phenomena. Basic concepts like Poincaré section, iterated mappings, Hamiltonian chaos and KAM theory, strange attractors, fractal dimensions, Lyapunov exponents, bifurcation theory, self-similarity and renormalisation and transitions to chaos are thoroughly explained. To facilitate comprehension, mathematical concepts and tools are introduced in short sub-sections. The text is supported by numerous computer experiments and a multitude of graphical illustrations and colour plates emphasising the geometrical and topological characteristics of the underlying dynamics. This volume is a completely revised and enlar...

  7. Chaos A Program Collection for the PC

    CERN Document Server

    Korsch, Hans Jürgen; Hartmann, Timo

    2008-01-01

    This new edition strives yet again to provide readers with a working knowledge of chaos theory and dynamical systems through parallel introductory explanations in the book and interaction with carefully-selected programs supplied on the accompanying diskette. The programs enable readers, especially advanced-undergraduate students in physics, engineering, and math, to tackle relevant physical systems quickly on their PCs, without distraction from algorithmic details. For the third edition of Chaos: A Program Collection for the PC, each of the previous twelve programs is polished and rewritten in C++ (both Windows and Linux versions are included). A new program treats kicked systems, an important class of two-dimensional problems, which is introduced in Chapter 13. Each chapter follows the structure: theoretical background; numerical techniques; interaction with the program; computer experiments; real experiments and empirical evidence; reference. Interacting with the many numerical experiments have proven to h...

  8. Nonlinear physics: Catastrophe, chaos and complexity

    International Nuclear Information System (INIS)

    Currently in the world of physics, there is open debate on the role of the three C's - catastrophe, chaos and complexity. Seen as new ideas or paradigms, incapable of being harmonized within the realm of traditional physics, these terms seem to be creating turmoil in the classical physics establishment whose foundations date back to the early seventeenth century. This paper first defines catastrophe, chaos and complexity and shows how these terms are all connected to nonlinear dynamics and how they have long since been present within scientific treatises. It also evidences the relationship of the three C's with the concept of organization, inappropriately called self-organization, and with recognition and decisional strategies of cognitive systems. Relevant to natural science, the development of these considerations is necessitating the re-examination of the role and capabilities of human knowledge and a return to inter-disciplinary scientific-philosophical debate

  9. Nonlinear Dynamics In Quantum Physics -- Quantum Chaos and Quantum Instantons

    OpenAIRE

    Kröger, H.

    2003-01-01

    We discuss the recently proposed quantum action - its interpretation, its motivation, its mathematical properties and its use in physics: quantum mechanical tunneling, quantum instantons and quantum chaos.

  10. Complex motions and chaos in nonlinear systems

    CERN Document Server

    Machado, José; Zhang, Jiazhong

    2016-01-01

    This book brings together 10 chapters on a new stream of research examining complex phenomena in nonlinear systems—including engineering, physics, and social science. Complex Motions and Chaos in Nonlinear Systems provides readers a particular vantage of the nature and nonlinear phenomena in nonlinear dynamics that can develop the corresponding mathematical theory and apply nonlinear design to practical engineering as well as the study of other complex phenomena including those investigated within social science.

  11. Topological Chaos in Spatially Periodic Mixers

    OpenAIRE

    Finn, Matthew D.; Thiffeault, Jean-Luc; Gouillart, Emmanuelle

    2005-01-01

    Topologically chaotic fluid advection is examined in two-dimensional flows with either or both directions spatially periodic. Topological chaos is created by driving flow with moving stirrers whose trajectories are chosen to form various braids. For spatially periodic flows, in addition to the usual stirrer-exchange braiding motions, there are additional topologically-nontrivial motions corresponding to stirrers traversing the periodic directions. This leads to a study of the braid group on t...

  12. Les ordinateurs quantiques affrontent le chaos

    OpenAIRE

    Georgeot, Bertrand; Shepelyansky, Dima L.

    2003-01-01

    Quantum computers facing chaos. Quantum parallelism allows to perform computation in a radically new manner. A quantum computer based on these new principles may resolve certain problems exponentially faster than a classical computer. We discuss how quantum computers can simulate complex dynamics, in particularly the dynamics of chaotic systems, where the errors of classical computation grow exponentially fast. ----- Le parallelisme autorise par la mecanique quantique permet d'effectuer des c...

  13. Delayed Self-Synchronization in Homoclinic Chaos

    OpenAIRE

    Arecchi, F. T.; Meucci, R.; E. Allaria; Di Garbo, A.; Tsimring, L. S.

    2001-01-01

    The chaotic spike train of a homoclinic dynamical system is self-synchronized by re-inserting a small fraction of the delayed output. Due to the sensitive nature of the homoclinic chaos to external perturbations, stabilization of very long periodic orbits is possible. On these orbits, the dynamics appears chaotic over a finite time, but then it repeats with a recurrence time that is slightly longer than the delay time. The effect, called delayed self-synchronization (DSS), displays analogies ...

  14. Gravity Waves, Chaos, and Spinning Compact Binaries

    OpenAIRE

    Levin, Janna

    1999-01-01

    Spinning compact binaries are shown to be chaotic in the Post-Newtonian expansion of the two body system. Chaos by definition is the extreme sensitivity to initial conditions and a consequent inability to predict the outcome of the evolution. As a result, the spinning pair will have unpredictable gravitational waveforms during coalescence. This poses a challenge to future gravity wave observatories which rely on a match between the data and a theoretical template.

  15. Chaos Theory for Evolutionary Algorithms Researchers

    Czech Academy of Sciences Publication Activity Database

    Čelikovský, Sergej; Zelinka, I.

    Berlin : Springer-Verlag, 2010 - (Zelinka, I.; Čelikovský, S.; Richter, H.; Chen, G.), s. 89-143 ISBN 978-3-642-10706-1. - (Studies in Computational Intelligence. 267) R&D Projects: GA ČR(CZ) GA102/08/0186 Institutional research plan: CEZ:AV0Z10750506 Keywords : Complex Systems * Computational Intelligence * Deterministic Chaos * Evolutionary Computation Subject RIV: BC - Control Systems Theory http://library.utia.cas.cz/separaty/2010/TR/celikovsky-0340153.pdf

  16. Signatures of homoclinic motion in quantum chaos

    OpenAIRE

    Wisniacki, D. A.; Vergini, E.; Benito, R. M.; Borondo, F.

    2004-01-01

    Homoclinic motion plays a key role in the organization of classical chaos in Hamiltonian systems. In this Letter, we show that it also imprints a clear signature in the corresponding quantum spectra. By numerically studying the fluctuations of the widths of wavefunctions localized along periodic orbits we reveal the existence of an oscillatory behavior, that is explained solely in terms of the primary homoclinic motion. Furthermore, our results indicate that it survives the semiclassical limit.

  17. Quantum chaos in small quantum networks

    CERN Document Server

    Kim, I; Kim, Ilki; Mahler, Guenter

    1999-01-01

    We study a 2-spin quantum Turing architecture, in which discrete local rotations \\alpha_m of the Turing head spin alternate with quantum controlled NOT-operations. We show that a single chaotic parameter input \\alpha_m leads to a chaotic dynamics in the entire Hilbert space. The instability of periodic orbits on the Turing head and `chaos swapping' onto the Turing tape are demonstrated explicitly as well as exponential parameter sensitivity of the Bures metric.

  18. Generic Superweak Chaos Induced by Hall Effect

    OpenAIRE

    Ben-Harush, Moti; Dana, Itzhack

    2016-01-01

    We introduce and study the "kicked Hall system" (KHS), i.e., charged particles periodically kicked in the presence of uniform magnetic ($\\mathbf{B}$) and electric ($\\mathbf{E}$) fields that are perpendicular to each other and to the kicking direction. We show that for resonant values of $B$ and $E$ and in the weak-chaos regime of sufficiently small nonintegrability parameter $\\kappa$ (the kicking strength), there exists a \\emph{generic} family of periodic kicking potentials for which the Hall...

  19. Classical and Quantum Chaos in Atom Optics

    OpenAIRE

    Saif, Farhan

    2006-01-01

    The interaction of an atom with an electromagnetic field is discussed in the presence of a time periodic external modulating force. It is explained that a control on atom by electromagnetic fields helps to design the quantum analog of classical optical systems. In these atom optical systems chaos may appear at the onset of external fields. The classical and quantum chaotic dynamics is discussed, in particular in an atom optics Fermi accelerator. It is found that the quantum dynamics exhibits ...

  20. Information-theoretic characterization of quantum chaos

    CERN Document Server

    Schack, R

    1995-01-01

    Hypersensitivity to perturbation is a criterion for chaos based on the question of how much information about a perturbing environment is needed to keep the entropy of a Hamiltonian system from increasing. We demonstrate numerically that hypersensitivity to perturbation is present in the following quantum maps: the quantum kicked top, the quantum baker's map, the quantum lazy baker's map, and the quantum sawtooth and cat maps.

  1. Modulational instability and spatiotemporal transition to chaos

    International Nuclear Information System (INIS)

    The one-dimensional generalized modified complex Ginzburg-Landau equation [Malomed BA, Stenflo L. J Phys A: Math Gen 1991;24:L1149] is considered. The linear stability analysis is used in order to derive the conditions for modulational instability. We obtained the generalized Lange and Newell's criterion for modulational instability. Numerical simulation shows the validity of the analytical approach. The model presents a rich variety of patterns propagating in the system and a spatiotemporal transition to chaos

  2. Li-Yorke chaos in linear dynamics

    Czech Academy of Sciences Publication Activity Database

    Bernardes Jr., N.C.; Bonilla, A.; Müller, Vladimír; Peris, A.

    2015-01-01

    Roč. 35, č. 6 (2015), s. 1723-1745. ISSN 0143-3857 R&D Projects: GA ČR GA201/09/0473; GA AV ČR IAA100190903 Institutional support: RVO:67985840 Keywords : Li-York chaos * Banach space * Fréchet space Subject RIV: BA - General Mathematics Impact factor: 0.778, year: 2014 http://journals.cambridge.org/action/displayAbstract?fromPage=online&aid=9884748&fileId=S0143385714000200

  3. Dynamics and chaos control of gyrostat satellite

    International Nuclear Information System (INIS)

    Highlights: ► Free dual-spin gyrostat with a small rotor asymmetry is considered. ► Equations in Andoyer-Deprit canonical dimensionless variables are obtained. ► Phase space heteroclinic and homoclinic trajectories are written in closed form. ► Modified Melnikov function is used to construct the control that eliminates chaos. - Abstract: We consider the chaotic motion of the free gyrostat consisting of a platform with a triaxial inertia ellipsoid and a rotor with a small asymmetry with respect to the axis of rotation. Dimensionless equations of motion of the system with perturbations caused by small asymmetries of the rotor are written in Andoyer-Deprit variables. These perturbations lead to separatrix chaos. For gyrostats with different ratios of moments of inertia heteroclinic and homoclinic trajectories are written in closed-form. These trajectories are used for constructing modified Melnikov function, which is used for determine the control that eliminates separatrix chaos. Melnikov function and phase space trajectory are built to show the effectiveness of the control.

  4. Quantum chaos in open quantum dot arrays

    International Nuclear Information System (INIS)

    Full text: The discovery of chaos in macro-scale physical systems led to the emergence of a new understanding of laws in nature. Chaos should not exist at all in quantum systems - as laws of quantum mechanics actually forbid it. We will show in this work the footprints of quantum chaos in the dynamics of electron transport by studying ballistic open quantum dot arrays. We will apply quantum mechanical calculations and classical calculations in order to explain the low field magneto-transport through open quantum dots. To characterize the quantum/classical correspondence in this system and to understand the transport, it is necessary to invoke dynamical tunneling, a quantum-mechanical mechanism which allows tunneling of electrons between chaotic and regular regions in the phase space, a process which is classically forbidden. The relevant conclusions regarding dynamical tunneling are drawn by using Husimi representations. By comparing the classical trajectories with the electron probability density high accordance is achieved. The Husimi plots are used to visualize the wave function distribution in the vx-x-plane of the Poincare section. We show in the Husimi plots that the wave function has weight on the regular and chaotic regions alike. This represents a distribution in the phase space that cannot be generated by classical dynamics and supports the interpretation including dynamical tunneling. (author)

  5. Stable chaos in fluctuation driven neural circuits

    International Nuclear Information System (INIS)

    Highlights: • Nonlinear instabilities in fluctuation driven (balanced) neural circuits are studied. • Balanced networks display chaos and stable phases at different post-synaptic widths. • Linear instabilities coexists with nonlinear ones in the chaotic regime. • Erratic motion appears also in linearly stable phase due to stable chaos. - Abstract: We study the dynamical stability of pulse coupled networks of leaky integrate-and-fire neurons against infinitesimal and finite perturbations. In particular, we compare mean versus fluctuations driven networks, the former (latter) is realized by considering purely excitatory (inhibitory) sparse neural circuits. In the excitatory case the instabilities of the system can be completely captured by an usual linear stability (Lyapunov) analysis, whereas the inhibitory networks can display the coexistence of linear and nonlinear instabilities. The nonlinear effects are associated to finite amplitude instabilities, which have been characterized in terms of suitable indicators. For inhibitory coupling one observes a transition from chaotic to non chaotic dynamics by decreasing the pulse-width. For sufficiently fast synapses the system, despite showing an erratic evolution, is linearly stable, thus representing a prototypical example of stable chaos

  6. Energy Factor Modelling and Model Reference Adaptive Control of Chaos in Boost Converter

    Directory of Open Access Journals (Sweden)

    R Mani Kumar

    2012-05-01

    Full Text Available Chaos is an apparently disordered deterministic behavior, which is universally occurring in many systems in all areas of science. In this paper, chaos in boost converter has been analyzed by taking the load and supply voltage as a bifurcation parameter under open loop condition. The mathematical model of the boost converter is obtained using Energy Factor modeling approach. A Lyapunov’s stability based Model Reference Adaptive controller (MRAC is designed for the boost converter and is implemented to control chaos by keeping the system stable from chaotic stage. The proposed adaptive controller, in the on line mode has the ability to track a specific high-frequency reference voltage and also to adapt for the variations in the load and high-frequency pulsed supply voltage. The simulation results show that the proposed method updates the adjustable parameter values to guarantee stable operation from chaotic stage and also to provide good dynamical responses than the conventional Proportional Integral Derivative (PID controller.

  7. The chaos and order in nuclear molecular dynamics; Chaos i porzadek w jadrowej dynamice molekularnej

    Energy Technology Data Exchange (ETDEWEB)

    Srokowski, T. [Institute of Nuclear Physics, Cracow (Poland)

    1995-12-31

    The subject of the presented report is role of chaos in scattering processes in the frame of molecular dynamics. In this model, it is assumed that scattering particles (nuclei) consist of not-interacted components as alpha particles or {sup 12}C, {sup 16}O and {sup 20}Ne clusters. The results show such effects as dynamical in stabilities and fractal structure as well as compound nuclei decay and heavy-ion fusion. The goal of the report is to make the reader more familiar with the chaos model and its application to nuclear phenomena. 157 refs, 40 figs.

  8. Application of Chaos Theory to Psychological Models

    Science.gov (United States)

    Blackerby, Rae Fortunato

    This dissertation shows that an alternative theoretical approach from physics--chaos theory--offers a viable basis for improved understanding of human beings and their behavior. Chaos theory provides achievable frameworks for potential identification, assessment, and adjustment of human behavior patterns. Most current psychological models fail to address the metaphysical conditions inherent in the human system, thus bringing deep errors to psychological practice and empirical research. Freudian, Jungian and behavioristic perspectives are inadequate psychological models because they assume, either implicitly or explicitly, that the human psychological system is a closed, linear system. On the other hand, Adlerian models that require open systems are likely to be empirically tenable. Logically, models will hold only if the model's assumptions hold. The innovative application of chaotic dynamics to psychological behavior is a promising theoretical development because the application asserts that human systems are open, nonlinear and self-organizing. Chaotic dynamics use nonlinear mathematical relationships among factors that influence human systems. This dissertation explores these mathematical relationships in the context of a sample model of moral behavior using simulated data. Mathematical equations with nonlinear feedback loops describe chaotic systems. Feedback loops govern the equations' value in subsequent calculation iterations. For example, changes in moral behavior are affected by an individual's own self-centeredness, family and community influences, and previous moral behavior choices that feed back to influence future choices. When applying these factors to the chaos equations, the model behaves like other chaotic systems. For example, changes in moral behavior fluctuate in regular patterns, as determined by the values of the individual, family and community factors. In some cases, these fluctuations converge to one value; in other cases, they diverge in

  9. Intrinsic Time Quantum Gravity

    CERN Document Server

    Yu, Hoi Lai

    2016-01-01

    Correct identification of the true gauge symmetry of General Relativity being 3d spatial diffeomorphism invariant(3dDI) (not the conventional infinite tensor product group with principle fibre bundle structure), together with intrinsic time extracted from clean decomposition of the canonical structure yields a self-consistent theory of quantum gravity. A new set of fundamental commutation relations is also presented. The basic variables are the eight components of the unimodular part of the spatial dreibein and eight SU(3) generators which correspond to Klauder's momentric variables that characterize a free theory of quantum gravity. The commutation relations are not canonical, but have well defined group theoretical meanings. All fundamental entities are dimensionless; and the quantum wave functionals are preferentially in the dreibein representation. The successful quantum theory of gravity involves only broad spectrum of knowledge and deep insights but no exotic idea.

  10. Intrinsic anion oxidation potentials.

    Science.gov (United States)

    Johansson, Patrik

    2006-11-01

    Anions of lithium battery salts have been investigated by electronic structure calculations with the objective to find a computational measure to correlate with the observed (in)stability of nonaqueous lithium battery electrolytes vs oxidation often encountered in practice. Accurate prediction of intrinsic anion oxidation potentials is here made possible by computing the vertical free energy difference between anion and neutral radical (Delta Gv) and further strengthened by an empirical correction using only the anion volume as a parameter. The 6-311+G(2df,p) basis set, the VSXC functional, and the C-PCM SCRF algorithm were used. The Delta Gv calculations can be performed using any standard computational chemistry software. PMID:17078600

  11. Controlling Beam Halo-Chaos via Time-Delayed Feedback

    Institute of Scientific and Technical Information of China (English)

    FANG Jin-Qing; WENG Jia-Qiang; ZHU Lun-Wu; LUO Xiao-Shu

    2004-01-01

    The study of controlling high-current proton beam halo-chaos has become a key concerned issue for many important applications. In this paper, time-delayed feedback control method is proposed for beam halo-chaos. Particle in cell simulation results show that the method is very effective and has some advantages for high-current beam experiments and engineering.

  12. Toward a definition of chaos for general relativity

    OpenAIRE

    Witt, Donald; Schleich, Kristin

    1996-01-01

    General relativity exhibits a unique feature not represented in standard examples of chaotic systems; it is a spacetime diffeomorphism invariant theory. Thus many characterizations of chaos do not work. It is therefore necessary to develop a definition of chaos suitable for application to general relativity. This presentation will present results towards this goal.

  13. Using a quantum computer to investigate quantum chaos

    OpenAIRE

    Schack, Ruediger

    1997-01-01

    We show that the quantum baker's map, a prototypical map invented for theoretical studies of quantum chaos, has a very simple realization in terms of quantum gates. Chaos in the quantum baker's map could be investigated experimentally on a quantum computer based on only 3 qubits.

  14. Research on a family of n-scroll chaos generators

    International Nuclear Information System (INIS)

    This paper studies a family of n-scroll chaos generators using a modified Chua's circuit. A mathematic model of the generators is established, the relationship between equilibrium points and scrolls is also analyzed, and a general theorem for generation of n-scroll chaos attractors is given. Numerical simulation is illustrated, showing excellent agreement with our theoretical predictions

  15. Master Teachers: Making a Difference on the Edge of Chaos

    Science.gov (United States)

    Chapin, Dexter

    2008-01-01

    The No Child Left Behind legislation, by legitimizing a stark, one-size-fits-all, industrial model of education, has denied the inherent complexity and richness of what teachers do. Discussing teaching in terms of Chaos Theory, Chapin explains that while excellent teaching may occur at the edge of chaos, it is not chaotic. There are patterns…

  16. Chaos: A Topic for Interdisciplinary Education in Physics

    Science.gov (United States)

    Bae, Saebyok

    2009-01-01

    Since society and science need interdisciplinary works, the interesting topic of chaos is chosen for interdisciplinary education in physics. The educational programme contains various university-level activities such as computer simulations, chaos experiment and team projects besides ordinary teaching. According to the participants, the programme…

  17. The "Chaos" Pattern in Piaget's Theory of Cognitive Development.

    Science.gov (United States)

    Lindsay, Jean S.

    Piaget's theory of the cognitive development of the child is related to the recently developed non-linear "chaos" model. The term "chaos" refers to the tendency of dynamical, non-linear systems toward irregular, sometimes unpredictable, deterministic behavior. Piaget identified this same pattern in his model of cognitive development in children.…

  18. Major open problems in chaos theory and nonlinear dynamics

    CERN Document Server

    Li, Y Charles

    2013-01-01

    Nowadays, chaos theory and nonlinear dynamics lack research focuses. Here we mention a few major open problems: 1. an effective description of chaos and turbulence, 2. rough dependence on initial data, 3. arrow of time, 4. the paradox of enrichment, 5. the paradox of pesticides, 6. the paradox of plankton.

  19. Nonlinear Resonance Leading to Beam Halo-chaos-complexity

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In this paper,nonlinear resonances of the particle-core taken placed in a space-charge dominatedbeam are suited. Overlapping resonance leads to chaos and halo formation. That is one of most importantphysical mechanisms. Duo to beam halo-chaos is essentially a spatiotemporal chaotic motion, Such beam

  20. Torus Destruction and Chaos-Chaos Intermittency in a Commodity Distribution Chain

    DEFF Research Database (Denmark)

    Sosnovtseva, O.; Mosekilde, Erik

    1997-01-01

    The destruction of two-dimensional tori T2 and the transitions to chaos are studied in a high-dimensional model describing the decision-making behavior of human subjects in a simulated managerial environment (the beer production-distribution model). Two different routes from quasiperiodicity to c...

  1. Quantitative and qualitative Kac's chaos on the Boltzmann's sphere

    CERN Document Server

    Carrapatoso, Kleber

    2012-01-01

    We investigate the construction of chaotic probability measures on the Boltzmann's sphere, which is the state space of the stochastic process of a many-particle system undergoing a dynamics preserving energy and momentum. Firstly, based on a version of the local Central Limit Theorem (or Berry-Essenn theorem), we construct a sequence of probabilities that is Kac chaotic and we prove a quantitative rate of convergence. Then, we investigate a stronger notion of chaos, namely entropic chaos introduced in \\cite{CCLLV}, and we prove, with quantitative rate, that this same sequence is also entropically chaotic. Furthermore, we investigate more general class of probability measures on the Boltzmann's sphere. Using the HWI inequality we prove that a Kac chaotic probability with bounded Fisher's information is entropically chaotic and we give a quantitative rate. We also link different notions of chaos, proving that Fisher's information chaos, introduced in \\cite{HaurayMischler}, is stronger than entropic chaos, which...

  2. A new approach for realizing electronic chaos generators

    International Nuclear Information System (INIS)

    A dictionary definition of chaos is a 'formless primordial matter, utter confusion' [1]. The study of chaos is part of a larger program of study of so-called strongly nonlinear systems. No strict definition of chaos yet exists, however, nonrandom complicated motions that exhibit a very rapid growth of errors and that, despite perfect determinism, inhibit any ability to render accurate long-term prediction are usually termed chaotic. In other words, chaos may be referred to as deterministic randomness since it is the phenomenon where deterministic laws, are sometimes extremely simple, show random (or random-like) behaviours while random (or random-like) motions happen to follow strict deterministic laws. The sense of order in chaos can be usually observed in the space of dimensions where time is not a dimension, while the sense of randomness is usually evident when time is incorporated. 10 refs., 29 figs

  3. Dynamical chaos in chip-scale optomechanical oscillators

    CERN Document Server

    Wu, Jiagui; Huang, Yongjun; Zhou, Hao; Yang, Jinghui; Liu, Jia-Ming; Yu, Mingbin; Lo, Guoqiang; Kwong, Dim-Lee; Xia, Guangqiong; Wong, Chee Wei

    2016-01-01

    Chaos has revolutionized the field of nonlinear science and stimulated foundational studies from neural networks, extreme event statistics, to physics of electron transport. Recent studies in cavity optomechanics provide a new platform to uncover quintessential architectures of chaos generation and the underlying physics. Here we report the first generation of dynamical chaos in silicon optomechanical oscillators, enabled by the strong and coupled nonlinearities of Drude electron-hole plasma. Deterministic chaotic oscillation is achieved, and statistical and entropic characterization quantifies the complexity of chaos. The correlation dimension D2 is determined at ~ 1.67 for the chaotic attractor, along with a maximal Lyapunov exponent rate about 2.94*the fundamental optomechanical oscillation. The corresponding nonlinear dynamical maps demonstrate the plethora of subharmonics, bifurcations, and stable regimes, along with distinct transitional routes into chaotic states. The chaos generation in our mesoscopic...

  4. Replication of chaos in neural networks, economics and physics

    CERN Document Server

    Akhmet, Marat

    2016-01-01

    This book presents detailed descriptions of chaos for continuous-time systems. It is the first-ever book to consider chaos as an input for differential and hybrid equations. Chaotic sets and chaotic functions are used as inputs for systems with attractors: equilibrium points, cycles and tori. The findings strongly suggest that chaos theory can proceed from the theory of differential equations to a higher level than previously thought. The approach selected is conducive to the in-depth analysis of different types of chaos. The appearance of deterministic chaos in neural networks, economics and mechanical systems is discussed theoretically and supported by simulations. As such, the book offers a valuable resource for mathematicians, physicists, engineers and economists studying nonlinear chaotic dynamics.

  5. Chaos in closed FRW: an imaginary approach

    CERN Document Server

    Jorás, S E

    2003-01-01

    In this work we study the existence of mechanisms of transition to global chaos in a closed Friedmann-Robertson-Walker universe with a massive conformally coupled scalar field. We propose a complexification of the radius of the universe so that the global dynamics can be understood. We show numerically the existence of heteroclinic connections of the unstable and stable manifolds to periodic orbits associated to the saddle-center equilibrium points. We find two bifurcations which are crucial in creating non-collapsing universes both in the real and imaginary version of the models. The techniques presented here can be employed in any cosmological model.

  6. Feigenbaum graphs at the onset of chaos

    International Nuclear Information System (INIS)

    We analyze the properties of networks obtained from the trajectories of unimodal maps at the transition to chaos via the horizontal visibility (HV) algorithm. We find that the network degrees fluctuate at all scales with amplitude that increases as the size of the network grows, and can be described by a spectrum of graph-theoretical generalized Lyapunov exponents. We further define an entropy growth rate that describes the amount of information created along paths in network space, and find that such entropy growth rate coincides with the spectrum of generalized graph-theoretical exponents, constituting a set of Pesin-like identities for the network.

  7. Integrability and chaos: the classical uncertainty

    International Nuclear Information System (INIS)

    In recent years there has been a considerable increase in the publishing of textbooks and monographs covering what was formerly known as random or irregular deterministic motion, now referred to as deterministic chaos. There is still substantial interest in a matter that is included in many graduate and even undergraduate courses on classical mechanics. Based on the Hamiltonian formalism, the main objective of this paper is to provide, from the physicist's point of view, an overall and intuitive review of this broad subject (with some emphasis on the Kolmogorov-Arnold-Moser theorem and the stability of planetary motions) which may be useful to both students and instructors.

  8. Delayed self-synchronization in homoclinic chaos

    Science.gov (United States)

    Arecchi, F. T.; Meucci, R.; Allaria, E.; di Garbo, A.; Tsimring, L. S.

    2002-04-01

    The chaotic spike train of a homoclinic dynamical system is self-synchronized by applying a time-delayed correction proportional to the laser output intensity. Due to the sensitive nature of the homoclinic chaos to external perturbations, stabilization of very long-periodic orbits is possible. On these orbits, the dynamics appears chaotic over a finite time, but then it repeats with a recurrence time that is slightly longer than the delay time. The effect, called delayed self-synchronization, displays analogies with neurodynamic events that occur in the buildup of long-term memories.

  9. Quantum chaos and nuclear mass systematics

    International Nuclear Information System (INIS)

    The presence of quantum chaos in nuclear mass systematics is analyzed by considering the differences between measured and calculated nuclear masses as a time series described by the power law 1fα. While for the liquid droplet model plus shell corrections a quantum chaotic behavior α∼1 is found, errors in the microscopic mass formula have α∼0.5, closer to white noise. The chaotic behavior seems to arise from many body effects not included in the mass formula

  10. Cryptography with chaos at the physical level

    International Nuclear Information System (INIS)

    In this work, we devise a chaos-based secret key cryptography scheme for digital communication where the encryption is realized at the physical level, that is, the encrypting transformations are applied to the wave signal instead to the symbolic sequence. The encryption process consists of transformations applied to a two-dimensional signal composed of the message carrying signal and an encrypting signal that has to be a chaotic one. The secret key, in this case, is related to the number of times the transformations are applied. Furthermore, we show that due to its chaotic nature, the encrypting signal is able to hide the statistics of the original signal

  11. Chaos in the BMN matrix model

    Science.gov (United States)

    Asano, Yuhma; Kawai, Daisuke; Yoshida, Kentaroh

    2015-06-01

    We study classical chaotic motions in the Berenstein-Maldacena-Nastase (BMN) matrix model. For this purpose, it is convenient to focus upon a reduced system composed of two-coupled anharmonic oscillators by supposing an ansatz. We examine three ansätze: 1) two pulsating fuzzy spheres, 2) a single Coulomb-type potential, and 3) integrable fuzzy spheres. For the first two cases, we show the existence of chaos by computing Poincaré sections and a Lyapunov spectrum. The third case leads to an integrable system. As a result, the BMN matrix model is not integrable in the sense of Liouville, though there may be some integrable subsectors.

  12. Chaos in the BMN matrix model

    CERN Document Server

    Asano, Yuhma; Yoshida, Kentaroh

    2015-01-01

    We study classical chaotic motions in the Berenstein-Maldacena-Nastase (BMN) matrix model. For this purpose, it is convenient to focus upon a reduced system composed of two-coupled anharmonic oscillators by supposing an ansatz. We examine three ans\\"atze: 1) two pulsating fuzzy spheres, 2) a single Coulomb-type potential, and 3) integrable fuzzy spheres. For the first two cases, we show the existence of chaos by computing Poincar\\'e sections and a Lyapunov spectrum. The third case leads to an integrable system. As a result, the BMN matrix model is not integrable in the sense of Liouville, though there may be some integrable subsectors.

  13. Importance of packing in spiral defect chaos

    Indian Academy of Sciences (India)

    Kapilanjan Krishna

    2008-04-01

    We develop two measures to characterize the geometry of patterns exhibited by the state of spiral defect chaos, a weakly turbulent regime of Rayleigh-Bénard convection. These describe the packing of contiguous stripes within the pattern by quantifying their length and nearest-neighbor distributions. The distributions evolve towards unique distribution with increasing Rayleigh number that suggests power-law scaling for the dynamics in the limit of infinite system size. The techniques are generally applicable to patterns that are reducible to a binary representation.

  14. Topological organization of (low-dimensional) chaos

    International Nuclear Information System (INIS)

    Recent progress toward classifying low-dimensional chaos measured from time series data is described. This classification theory assigns a template to the time series once the time series is embedded in three dimensions. The template describes the primary folding and stretching mechanisms of phase space responsible for the chaotic motion. Topological invariants of the unstable periodic orbits in the closure of the strange set are calculated from the (reconstructed) template. These topological invariants must be consistent with ampersand ny model put forth to describe the time series data, and are useful in invalidating (or gaining confidence in) any model intended to describe the dynamical system generating the time series

  15. Regularity and chaos in nuclear structure

    International Nuclear Information System (INIS)

    The BSC pairing gap, obtained from nuclear masses, shows large structural effects. A periodic orbit theory for the pairing gap has been developed, and generic expressions for the pairing gap fluctuations are derived, stressing the role of regularity/chaos. Results from the theory are compared to pairing gaps obtained from nuclear masses, calculated as well as measured. The comparison provides another quality control of nuclear mass formula, and gives additional insight in the nuclear pairing phenomenon. The theory can be applied to pairing fluctuations in other finite-size Fermi systems, as ultracold atomic gases or small metallic grains

  16. A pseudo-matched filter for chaos

    OpenAIRE

    Cohen, Seth D.; Gauthier, Daniel J

    2012-01-01

    A matched filter maximizes the signal-to-noise ratio of a signal. In the recent work of Corron et al. [Chaos 20, 023123 (2010)], a matched filter is derived for the chaotic waveforms produced by a piecewise-linear system. Motivated by these results, we describe a pseudo-matched filter, which removes noise from the same chaotic signal. It consists of a notch filter followed by a first-order, low-pass filter. We compare quantitatively the matched filter's performance to that of our pseudo-match...

  17. Chaos in Multi-Valued Dynamical Systems

    Czech Academy of Sciences Publication Activity Database

    Beran, Zdeněk; Čelikovský, S.

    Vegazana Campus of the University of León: Universidad de León, 2011, s. 1-5. [Physcon 2011 - 5th International Scientific Conference on Physics and Control. León (ES), 05.09.2011-08.09.2011] R&D Projects: GA ČR(CZ) GAP103/10/0628 Institutional research plan: CEZ:AV0Z10750506 Keywords : Multi-valued dynamical systems * chaos * differential inclusions Subject RIV: BC - Control Systems Theory http://physcon.unileon.es/wp-content/uploads/Finalprogram.pdf

  18. Chaos caused by fatigue crack growth

    International Nuclear Information System (INIS)

    The nonlinear dynamic responses including chaotic oscillations caused by a fatigue crack growth are presented. Fatigue tests have been conducted on a novel fatigue-testing rig, where the loading is generated from inertial forces. The nonlinearity is in the form of discontinuous stiffness caused by the opening and closing of a growing crack. Nonlinear dynamic tools such as Poincare maps and bifurcation diagrams are used to unveil the global dynamics of the system. The results obtained indicate that fatigue crack growth strongly influences the dynamic response of the system leading to chaos

  19. Chaos caused by fatigue crack growth

    Energy Technology Data Exchange (ETDEWEB)

    Foong, C.-H.; Pavlovskaia, Ekaterina; Wiercigroch, Marian; Deans, William

    2003-06-01

    The nonlinear dynamic responses including chaotic oscillations caused by a fatigue crack growth are presented. Fatigue tests have been conducted on a novel fatigue-testing rig, where the loading is generated from inertial forces. The nonlinearity is in the form of discontinuous stiffness caused by the opening and closing of a growing crack. Nonlinear dynamic tools such as Poincare maps and bifurcation diagrams are used to unveil the global dynamics of the system. The results obtained indicate that fatigue crack growth strongly influences the dynamic response of the system leading to chaos.

  20. Enlightening complexity: making energy with chaos

    CERN Document Server

    Molinari, D

    2011-01-01

    We study the energy harvesting of photons undergoing chaotic dynamics with different complexity degrees. Our theory employs a multiscale analysis, which combines Hamiltonian billiards, time-dependent coupled mode theory and ab-initio simulations. In analogy to classical thermodynamics, where the presence of microscopic chaos leads to a single direction for time and entropy, an increased complexity in the motion of photons yields to a monotonic accumulation of energy, which dramatically grows thanks to a constructive mechanism of energy buildup. This result could lead to the realization of novel complexity-driven, energy harvesting architectures.

  1. Toward analytical chaos in nonlinear systems

    CERN Document Server

    Luo, Albert C J

    2014-01-01

    Exact analytical solutions to periodic motions in nonlinear dynamical systems are almost not possible. Since the 18th century, one has extensively used techniques such as perturbation methods to obtain approximate analytical solutions of periodic motions in nonlinear systems. However, the perturbation methods cannot provide the enough accuracy of analytical solutions of periodic motions in nonlinear dynamical systems. So the bifurcation trees of periodic motions to chaos cannot be achieved analytically.  The author has developed an analytical technique that is more effective to achieve period

  2. Congenital laryngomucocoele: a rare cause for CHAOS

    OpenAIRE

    M. Cunha; Janeiro, P; Fernandes, R.; Carreiro, H; Laurini, R

    2009-01-01

    Congenital high airway obstruction syndrome (CHAOS) is a rare but life-threatening condition that results from the obstruction of the upper airways. We describe a female newborn, from a Grávida II, Para 0, 36-year-old woman, with a routine ultrasound at 30 weeks’ gestation that showed polyhydramnios. She delivered a live-born female baby at 36 weeks without any dismorphic features but with respiratory distress. Attempts at endotracheal intubation were unsuccessful due to the presence of a ...

  3. Chaos and complexity in nonlinear electronic circuits

    CERN Document Server

    Ogorzalek, MJ

    1997-01-01

    The basic procedures for designing and analysing electronic systems are based largely on the assumptions of linear behavior of the system. Nonlinearities inherent in all real applications very often cause unexpected and even strange behavior. This book presents an electronic engineer's perspective on chaos and complex behavior. It starts from basic mathematical notions which enable understanding of the observed phenomena, and guides the reader through the methodology and tools used in the laboratory and numerical experiments to interpretation and explanation of basic mechanisms. On typical cir

  4. Controlling chaos in Internet congestion control model

    International Nuclear Information System (INIS)

    The TCP end-to-end congestion control plus RED router queue management can be modeled as a discrete-time dynamical system, which may create complex bifurcating and chaotic behavior. Based on the basic features of the TCP-RED model, we propose a time-dependent delayed feedback control algorithm to control chaos in the system by perturbing the accessible RED parameter pmax. This method is able to stabilized a router queue occupancy at a level without knowing the exact knowledge of the network. Further, we study the situation of the presence of the UDP traffic

  5. Quantum chaos and the black hole horizon

    CERN Document Server

    CERN. Geneva

    2016-01-01

    Thanks to AdS/CFT, the analogy between black holes and thermal systems has become a practical tool, shedding light on thermalization, transport, and entanglement dynamics. Continuing in this vein, recent work has shown how chaos in the boundary CFT can be analyzed in terms of high energy scattering right on the horizon of the dual black hole. The analysis revolves around certain out-of-time-order correlation functions, which are simple diagnostics of the butterfly effect. We will review this work, along with a general bound on these functions that implies black holes are the most chaotic systems in quantum mechanics. (NB Room Change to Main Auditorium)

  6. Staircase functions, spectral regidity and a rule for quantizing chaos

    International Nuclear Information System (INIS)

    Considering the Selberg trace formula as an exact version of Gutzwiller's semiclassical periodic-orbit theory in the case of the free motion on compact Riemann surfaces with constant negative curvature (Hadamard-Gutzwiller model), we study two complementary basic problems in quantum chaology: the computation of the calssical staircase N(l), the number of periodic orbits with length shorter than l, in terms of the quantal energy spectrum {En}, the computation of the spectral staircase N (E), the number of quantal energies below the energy E, in terms of the length spectrum {ln} of the classical periodic orbits. A formulation of the periodic-orbit theory is presented which is intrinsically unsmoothed, but for which an effective smoothing arises from the limited 'input data', i.e. from the limited knowledge of the periodic orbits in the case of N(E) and the limited knowledge of quantal energies in the case of N(l). Based on the periodic-orbit formula for N(E), we propose a new rule for quantizing chaos, which simply states that the quantal energies are determined by the zeros of the function ξ1(E) = cos (πN(E)). The formulas for N(l) and N(E) as well as the new quantization condition are tested numerically. Furthermore, it is shown that the staircase N(E) computed from the length spectrum yields (up to a constant) a good description of the spectral rigidity Δ3(L), being the first numerical attempt to compute a statistical property of the quantal energy spectrum of a chaotic system from classical periodic orbits. (orig.)

  7. Experimental Chaos - Proceedings of the 3rd Conference

    Science.gov (United States)

    Harrison, Robert G.; Lu, Weiping; Ditto, William; Pecora, Lou; Spano, Mark; Vohra, Sandeep

    1996-10-01

    The Table of Contents for the full book PDF is as follows: * Preface * Spatiotemporal Chaos and Patterns * Scale Segregation via Formation of Domains in a Nonlinear Optical System * Laser Dynamics as Hydrodynamics * Spatiotemporal Dynamics of Human Epileptic Seizures * Experimental Transition to Chaos in a Quasi 1D Chain of Oscillators * Measuring Coupling in Spatiotemporal Dynamical Systems * Chaos in Vortex Breakdown * Dynamical Analysis * Radial Basis Function Modelling and Prediction of Time Series * Nonlinear Phenomena in Polyrhythmic Hand Movements * Using Models to Diagnose, Test and Control Chaotic Systems * New Real-Time Analysis of Time Series Data with Physical Wavelets * Control and Synchronization * Measuring and Controlling Chaotic Dynamics in a Slugging Fluidized Bed * Control of Chaos in a Laser with Feedback * Synchronization and Chaotic Diode Resonators * Control of Chaos by Continuous-time Feedback with Delay * A Framework for Communication using Chaos Sychronization * Control of Chaos in Switching Circuits * Astrophysics, Meteorology and Oceanography * Solar-Wind-Magnetospheric Dynamics via Satellite Data * Nonlinear Dynamics of the Solar Atmosphere * Fractal Dimension of Scalar and Vector Variables from Turbulence Measurements in the Atmospheric Surface Layer * Mechanics * Escape and Overturning: Subtle Transient Behavior in Nonlinear Mechanical Models * Organising Centres in the Dynamics of Parametrically Excited Double Pendulums * Intermittent Behaviour in a Heating System Driven by Phase Transitions * Hydrodynamics * Size Segregation in Couette Flow of Granular Material * Routes to Chaos in Rotational Taylor-Couette Flow * Experimental Study of the Laminar-Turbulent Transition in an Open Flow System * Chemistry * Order and Chaos in Excitable Media under External Forcing * A Chemical Wave Propagation with Accelerating Speed Accompanied by Hydrodynamic Flow * Optics * Instabilities in Semiconductor Lasers with Optical Injection * Spatio

  8. The dream's navel between chaos and thought.

    Science.gov (United States)

    Scalzone, F; Zontini, G

    2001-04-01

    The authors begin by drawing attention to the problem of the transition from the biological to the psychic, noting that Freud himself, with his background in the neurosciences, grappled with it throughout his career. Certain recent paradigms more commonly applied to the natural sciences, such as in particular chaos and complexity theory, can in their view prove fruitful in psychoanalysis too, and it is shown how these notions are inherent in some of Freud's conceptions. The unconscious is stated to operate like a neural network, performing the kind of parallel processing used in the computing of highly complex situations, whereas the conscious mind is sequential. Dreams, in the authors' opinion, are organisers of the mind, imparting order to the turbulence of the underlying wishes and unconscious fantasies and structuring them through the dream work. Through dreams, the structured linearity of conscious thought can emerge out of the non-linear chaos of the drives. The dream's navel can be seen as the chaotic link, or interface, between the unconscious wish, which constitutes an attractor, and the conscious thought. The attractor may be visualised as having an hourglass or clepsydra shape, the narrow section being the dream's navel, and, being the same at any scale of observation, has the property of fractality. PMID:11341062

  9. Order and chaos in soft condensed matter

    Indian Academy of Sciences (India)

    A K Sood; Rajesh Ganapathy

    2006-07-01

    Soft matter, like colloidal suspensions and surfactant gels, exhibit strong response to modest external perturbations. This paper reviews our recent experiments on the nonlinear flow behaviour of surfactant worm-like micellar gels. A rich dynamic behaviour exhibiting regular, quasi-periodic, intermittency and chaos is observed. In particular, we have shown experimentally that the route to chaos is via Type-II intermittency in shear thinning worm-like micellar solution of cetyltrimethylammonium tosylate where the strength of flow-concentration coupling is tuned by the addition of sodium chloride. A Poincaré first return map of the time series and the probability distribution of laminar length between burst events show that our data are consistent with Type-II intermittency. The existence of a `Butterfly' intensity pattern in small angle light scattering (SALS) measurements performed simultaneously with the rheological measurements confirms the coupling of flow to concentration fluctuations in the system under study. The scattered depolarised intensity in SALS, sensitive to orientational order fluctuations, shows the same time-dependence (like intermittency) as that of shear stress.

  10. The intrinsic vasculature of the cat facial nerve.

    Science.gov (United States)

    Balkany, T

    1986-01-01

    Treatment of facial nerve disorders is based in part on assumptions regarding the intrinsic blood supply of the nerve. This study was designed to comprehensively delineate the intrinsic facial nerve microcirculation and its relation to the extrinsic circulation in an animal model. Twenty-eight cat facial nerves were removed intact from brain stem to stylomastoid foramen following intravital fixation. Specimens were studied by gross dissection, silicone injection and tissue clearing, complete vessel counts on serial cross sections of individual nerves, and scanning electron microscopy or transmission electron microscopy. The labyrinthine segment of the cat facial nerve contains strikingly fewer intrinsic blood vessels than the mastoid and tympanic segments. The geniculate ganglion, however, has a distinct, rich vascular plexus. The ultrastructure of the intrinsic facial nerve vessels is similar to other small vessels of the body with tight junctions of the endothelium and overlapping spiral smooth muscle fibers of arterioles, as well as surrounding pericytes. PMID:3510355

  11. Associations of personality with intrinsic motivation in schizophrenia.

    Science.gov (United States)

    Vohs, Jenifer L; Lysaker, Paul H; Nabors, Lori

    2013-06-30

    Motivation is often disturbed in patients with schizophrenia, but little is known about how it relates to personality. We examined intrinsic motivation (IM), two personality domains from the NEO Five-Factor Inventory, and symptoms in 58 male patients with schizophrenia spectrum disorders. Analyses revealed IM may be linked to Extraversion, Neuroticism, and negative symptoms. PMID:23566367

  12. Time generated by intrinsic observers

    CERN Document Server

    Svozil, Karl

    2009-01-01

    We shortly review the construction of knowledge by intrinsic observers. Intrinsic observers are embedded in a system and are inseparable parts thereof. The intrinsic viewpoint has to be contrasted with an extrinsic, "God's eye" viewpoint, from which the system can be observed externally without in any way changing it. This epistemological distinction has concrete, formalizable consequences. One consequence is the emergence of "complementarity" for intrinsic observers, even if the underlying system is totally deterministic (computable). Another consequence is the appearence of time and inertial frames for intrinsic observers. The necessary operational techniques are developed in the context of Cellular Automata. We finish with a somewhat speculative question. Given space-time frames generated by clocks which use sound waves for synchronization; why could supersonic travel not cause time paradoxes?

  13. Topological chaos of the spatial prisoner׳s dilemma game on regular networks.

    Science.gov (United States)

    Jin, Weifeng; Chen, Fangyue

    2016-02-21

    The spatial version of evolutionary prisoner׳s dilemma on infinitely large regular lattice with purely deterministic strategies and no memories among players is investigated in this paper. Based on the statistical inferences, it is pertinent to confirm that the frequency of cooperation for characterizing its macroscopic behaviors is very sensitive to the initial conditions, which is the most practically significant property of chaos. Its intrinsic complexity is then justified on firm ground from the theory of symbolic dynamics; that is, this game is topologically mixing and possesses positive topological entropy on its subsystems. It is demonstrated therefore that its frequency of cooperation could not be adopted by simply averaging over several steps after the game reaches the equilibrium state. Furthermore, the chaotically changing spatial patterns via empirical observations can be defined and justified in view of symbolic dynamics. It is worth mentioning that the procedure proposed in this work is also applicable to other deterministic spatial evolutionary games therein. PMID:26646768

  14. Chaos in temporarily destabilized regular systems with the slow passage effect

    International Nuclear Information System (INIS)

    We provide evidences for chaotic behaviour in temporarily destabilized regular systems. In particular, we focus on time-continuous systems with the slow passage effect. The extreme sensitivity of the slow passage phase enables the existence of long chaotic transients induced by random pulsatile perturbations, thereby evoking chaotic behaviour in an initially regular system. We confirm the chaotic behaviour of the temporarily destabilized system by calculating the largest Lyapunov exponent. Moreover, we show that the newly obtained unstable periodic orbits can be easily controlled with conventional chaos control techniques, thereby guaranteeing a rich diversity of accessible dynamical states that is usually expected only in intrinsically chaotic systems. Additionally, we discuss the biological importance of presented results

  15. Evolution to the Edge of Chaos in Imitation Game

    CERN Document Server

    Kaneko, K; Kaneko, Kunihiko; Suzuki, Junji

    1993-01-01

    Motivated by the evolution of complex bird songs, an abstract imitation game is proposed to study the increase of dynamical complexity: Artificial "birds" display a "song" time series to each other, and those that imitate the other's song better win the game. With the introduction of population dynamics according to the score of the game and the mutation of parameters for the song dynamics, the dynamics is found to evolve towards the borderline between chaos and a periodic window, after punctuated equilibria. The importance of edge of chaos with topological chaos for complexity is stressed.

  16. Theory of the nucleus as applied to quantum chaos

    Energy Technology Data Exchange (ETDEWEB)

    Bunakov, V. E., E-mail: bunakov@VB13190.spb.edu [St. Petersburg State University, Petersburg Nuclear Physics Institute, National Research Center Kurchatov Institute (Russian Federation)

    2014-12-15

    A critical analysis of the present-day concept of chaos in quantum systems as nothing but a quantum signature of chaos in classical mechanics is given. It is proposed to specify a regular versus a chaotic behavior on the basis of symmetries of the system being considered and global integrals of motion that are associated with these symmetries in accordance with the Liouville-Arnold theorem rather than on the basis of the concept of Lyapunov’s instability of trajectories. Numerical criteria of quantum chaos that follow from the proposed concept are analyzed.

  17. Contributions of plasma physics to chaos and nonlinear dynamics

    CERN Document Server

    Escande, Dominique

    2016-01-01

    This topical review focusses on the contributions of plasma physics to chaos and nonlinear dynamics bringing new methods which are or can be used in other scientific domains. It starts with the development of the theory of Hamiltonian chaos, and then deals with order or quasi order, for instance adiabatic and soliton theories. It ends with a shorter account of dissipative and high dimensional Hamiltonian dynamics, and of quantum chaos. Most of these contributions are a spin-off of the research on thermonuclear fusion by magnetic confinement, which started in the fifties. Their presentation is both exhaustive and compact. [15 April 2016

  18. From chaos to order methodologies, perspectives and applications

    CERN Document Server

    Chen Guan Rong

    1998-01-01

    Chaos control has become a fast-developing interdisciplinary research field in recent years. This book is for engineers and applied scientists who want to have a broad understanding of the emerging field of chaos control. It describes fundamental concepts, outlines representative techniques, provides case studies, and highlights recent developments, putting the reader at the forefront of current research.Important topics presented in the book include: Fundamentals of nonlinear dynamical systems, essential for understanding and developing chaos control methods.; Parametric variation and paramet

  19. Controlling beam halo-chaos via backstepping design

    Institute of Scientific and Technical Information of China (English)

    Gao Yuan; Kong Feng

    2008-01-01

    A backstepping control method is proposed for controlling beam halo-chaos in the periodic focusing channels PFCs) of high-current ion accelerator. The analysis and numerical results show that the method, via adjusting an exterior magnetic field, is effective to control beam halo chaos with five types of initial distribution ion beams, all statistical quantities of the beam halo-chaos are largely reduced, and the uniformity of ion beam is improved. This control method has an important value of application, for the exterior magnetic field can be easily adjusted in the periodical magnetic focusing channels in experiment.

  20. Chaos behavior in the discrete Fitzhugh nerve system

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The discrete Fitzhugh nerve systems obtained by the Euler method is investigated and it is proved that there exist chaotic phenomena in the sense of Marotto's definition of chaos. And numerical simulations not only show the consistence with the theoretical analysis but also exhibit the complex dynamical behaviors, including the ten-periodic orbit, a cascade of period-doubling bifurcation, quasiperiodic orbits and the chaotic orbits and intermittent chaos. The computations of Lyapunov exponents confirm the chaos behaviors. Moreover we also find a strange attractor having the self-similar orbit structure as that of Henon attractor.

  1. Chaos-based hash function (CBHF) for cryptographic applications

    International Nuclear Information System (INIS)

    As the core of cryptography, hash is the basic technique for information security. Many of the hash functions generate the message digest through a randomizing process of the original message. Subsequently, a chaos system also generates a random behavior, but at the same time a chaos system is completely deterministic. In this paper, an algorithm for one-way hash function construction based on chaos theory is introduced. Theoretical analysis and computer simulation indicate that the algorithm can satisfy all performance requirements of hash function in an efficient and flexible manner and secure against birthday attacks or meet-in-the-middle attacks, which is good choice for data integrity or authentication.

  2. Intrinsic time geometrodynamics: explicit examples

    CERN Document Server

    Lin, Huei-Chen

    2016-01-01

    Intrinsic time quantum geometrodynamics resolved `the problem of time' and bridged the deep divide between quantum mechanics and canonical quantum gravity with a Schrodinger equation which describes evolution in intrinsic time variable. In this formalism, Einstein's general relativity is a particular realization of a wider class of theories. Explicit classical black hole and cosmological solutions and the motion of test particles are derived and analyzed in this work in the context of constant three-curvature solutions in intrinsic time geometrodynamics; and we exemplify how this formalism yields results which agree with the predictions of Einstein's theory.

  3. Intrinsic Negative Mass from Nonlinearity

    Science.gov (United States)

    Di Mei, F.; Caramazza, P.; Pierangeli, D.; Di Domenico, G.; Ilan, H.; Agranat, A. J.; Di Porto, P.; DelRe, E.

    2016-04-01

    We propose and provide experimental evidence of a mechanism able to support negative intrinsic effective mass. The idea is to use a shape-sensitive nonlinearity to change the sign of the mass in the leading linear propagation equation. Intrinsic negative-mass dynamics is reported for light beams in a ferroelectric crystal substrate, where the diffusive photorefractive nonlinearity leads to a negative-mass Schrödinger equation. The signature of inverted dynamics is the observation of beams repelled from strongly guiding integrated waveguides irrespective of wavelength and intensity and suggests shape-sensitive nonlinearity as a basic mechanism leading to intrinsic negative mass.

  4. A Non-symmetric Digital Image Secure Communication Scheme Based on Generalized Chaos Synchronization System

    International Nuclear Information System (INIS)

    Based on a generalized chaos synchronization system and a discrete Sinai map, a non-symmetric true color (RGB) digital image secure communication scheme is proposed. The scheme first changes an ordinary RGB digital image with 8 bits into unrecognizable disorder codes and then transforms the disorder codes into an RGB digital image with 16 bits for transmitting. A receiver uses a non-symmetric key to verify the authentication of the received data origin, and decrypts the ciphertext. The scheme can encrypt and decrypt most formatted digital RGB images recognized by computers, and recover the plaintext almost without any errors. The scheme is suitable to be applied in network image communications. The analysis of the key space, sensitivity of key parameters, and correlation of encrypted images imply that this scheme has sound security.

  5. A Non-symmetric Digital Image Secure Communication Scheme Based on Generalized Chaos Synchronization System

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiao-Hong; MIN Le-Quan

    2005-01-01

    Based on a generalized chaos synchronization system and a discrete Sinai map, a non-symmetric true color(RGB) digital image secur e communication scheme is proposed. The scheme first changes an ordinary RGB digital image with 8 bits into unrecognizable disorder codes and then transforms the disorder codes into an RGB digital image with 16 bits for transmitting. A receiver uses a non-symmetric key to verify the authentication of the received data origin,and decrypts the ciphertext. The scheme can encrypt and decrypt most formatted digital RGB images recognized by computers, and recover the plaintext almost without any errors. The scheme is suitable to be applied in network image communications. The analysis of the key space, sensitivity of key parameters, and correlation of encrypted images imply that this scheme has sound security.

  6. WHAT DOES CHAOS HAVE TO DO WITH SYSTEMS AND CONTROL ENGINEERING?

    Institute of Scientific and Technical Information of China (English)

    CHEN Guanrong

    2001-01-01

    Chaos as a very special type of complex dynamical behaviors hasbeen studied for about four decades. Yet the traditional trend of analyzing and understanding chaos has evolved to controlling and utilizing chaos today. Research in the field of chaos modeling,control, and synchronization includes not only ordering chaos, which means to weaken or completely suppress chaos when it is harmful, but also chaotification, which refers to enhancing existing chaos or creating chaos purposely when it is useful, by any means of control technology. This article offers a brief overview about the potential impact of controlled chaos on beneficial applications in science and engineering, and introduces some recent progress in chaotification via feedback control methods.

  7. Introduction aux méthodes semiclassiques en chaos quantique

    OpenAIRE

    Mouchet, Amaury

    1996-01-01

    On replace les méthodes semiclassiques en chaos quantique dans une perspective historique, peu technique, étayée par une bibliographie abondante mais non exhaustive allant jusqu'au milieu des années 90.

  8. Strategic leadership: a view from quantum and chaos theories.

    Science.gov (United States)

    McDaniel, R R

    1997-01-01

    Viewing health care from the perspective of chaos and quantum theories offers new insights into management techniques for effective and efficient delivery of health care services. This article introduces these concepts and gives specific prescriptions for managerial action. PMID:9058085

  9. Complex Nonlinearity Chaos, Phase Transitions, Topology Change and Path Integrals

    CERN Document Server

    Ivancevic, Vladimir G

    2008-01-01

    Complex Nonlinearity: Chaos, Phase Transitions, Topology Change and Path Integrals is a book about prediction & control of general nonlinear and chaotic dynamics of high-dimensional complex systems of various physical and non-physical nature and their underpinning geometro-topological change. The book starts with a textbook-like expose on nonlinear dynamics, attractors and chaos, both temporal and spatio-temporal, including modern techniques of chaos–control. Chapter 2 turns to the edge of chaos, in the form of phase transitions (equilibrium and non-equilibrium, oscillatory, fractal and noise-induced), as well as the related field of synergetics. While the natural stage for linear dynamics comprises of flat, Euclidean geometry (with the corresponding calculation tools from linear algebra and analysis), the natural stage for nonlinear dynamics is curved, Riemannian geometry (with the corresponding tools from nonlinear, tensor algebra and analysis). The extreme nonlinearity – chaos – corresponds to th...

  10. CHAOS-BASED FEEDFORWARD OUTPUT FUNCTIONS FOR COMBINING KEYSTREAM GENERATORS

    Institute of Scientific and Technical Information of China (English)

    Sang Tao; Wang Ruli; Yan Yixun

    2001-01-01

    The chaos-based feedforward output functions for combining keystream generators are proposed according to chaotic dynamic theory. The generated binary signals are independently and identically distributed, and have predictable periods. All experiments correspond to the theoretical prediction very well.

  11. The transition to chaos conservative classical systems and quantum manifestations

    CERN Document Server

    Reichl, Linda E

    2004-01-01

    This book provides a thorough and comprehensive discussion of classical and quantum chaos theory for bounded systems and for scattering processes Specific discussions include • Noether’s theorem, integrability, KAM theory, and a definition of chaotic behavior • Area-preserving maps, quantum billiards, semiclassical quantization, chaotic scattering, scaling in classical and quantum dynamics, dynamic localization, dynamic tunneling, effects of chaos in periodically driven systems and stochastic systems • Random matrix theory and supersymmetry The book is divided into several parts Chapters 2 through 4 deal with the dynamics of nonlinear conservative classical systems Chapter 5 and several appendices give a thorough grounding in random matrix theory and supersymmetry techniques Chapters 6 and 7 discuss the manifestations of chaos in bounded quantum systems and open quantum systems respectively Chapter 8 focuses on the semiclassical description of quantum systems with underlying classical chaos, and Chapt...

  12. Chaos in monopole sector of the Georgi-Glashow model

    OpenAIRE

    Dobrowolski, Tomasz; Szczesny, Jerzy

    1999-01-01

    A spherically symmetric excitations of the Polyakov - t' Hooft monopole are considered. In the framework of the geodesics deviation equation it is found that in the large mass Higgs sector a signature of chaos occurs.

  13. Chaos-assisted, broadband trapping of light in optical resonators

    CERN Document Server

    Liu, C; Molinari, D; Khan, Y; Ooi, B S; Krauss, T F; Fratalocchi, A

    2012-01-01

    Chaos is a phenomenon that occurs in many aspects of contemporary science. In classical dynamics, chaos is defined as a hypersensitivity to initial conditions. The presence of chaos is often unwanted, as it introduces unpredictability, which makes it difficult to predict or explain experimental results. Conversely, we demonstrate here how chaos can be used to enhance the ability of an optical resonator to store energy. We combine analytic theory with ab-initio simulations and experiments in photonic crystal resonators to show that a chaotic resonator can store six times more energy than its classical counterpart of the same volume. We explain the observed increase with the equipartition of energy among all degrees of freedom of the chaotic resonator, i.e. the cavity modes, which is evident from the convergence of their lifetime towards a single value. A compelling illustration of the theory is provided by demonstrating enhanced absorption in deformed polystyrene microspheres.

  14. Discrete chaos in fractional sine and standard maps

    Energy Technology Data Exchange (ETDEWEB)

    Wu, Guo-Cheng, E-mail: wuguocheng@gmail.com [Key Laboratory of Numerical Simulation of Sichuan Province, College of Mathematics and Information Science, Neijiang Normal University, Neijiang 641112 (China); College of Water Resource and Hydropower, Sichuan University, Chengdu 610065 (China); Baleanu, Dumitru, E-mail: dumitru@cankaya.edu.tr [Department of Chemical and Materials Engineering, Faculty of Engineering, King Abdulaziz University, PO Box 80204, Jeddah 21589 (Saudi Arabia); Department of Mathematics and Computer Sciences, Faculty of Arts and Sciences, Cankaya University, 06530 Balgat, Ankara (Turkey); Institute of Space Sciences, Magurele-Bucharest (Romania); Zeng, Sheng-Da [School of Science, Guangxi University for Nationalities, Nanning 530006 (China)

    2014-01-24

    Fractional standard and sine maps are proposed by using the discrete fractional calculus. The chaos behaviors are then numerically discussed when the difference order is a fractional one. The bifurcation diagrams and the phase portraits are presented, respectively.

  15. Fractional Chaos Based Communication Systems-An Introduction

    Institute of Scientific and Technical Information of China (English)

    Juebang Yu

    2008-01-01

    As one of secure communication means, chaotic communication systems has been well-developed during the past three decades. Technical papers, both for theoretical and practical investigations, have reached a huge amount in number. On the other hand, fractional chaos, as a parallel ongoing research topic, also attracts many researchers to investigate. As far as the IT field is concerned, the research on control systems by using fractional chaos known as FOC (fractional order control) has been a hot issue for quite a long time. As a comparison, interesting enough, up to now we have not found any research result related to Fractional Chaos Communi cation (FCC) system, Le., a system based on fractional chaos. The motivation of the present article is to reveal the feasibility of realizing communication systems based upon FCC and their superiority over the conventional integer chaotic communication systems. Principles of FCC and its advantages over integer chaotic communication systems are also discussed.

  16. Filtering with Marked Point Process Observations via Poisson Chaos Expansion

    International Nuclear Information System (INIS)

    We study a general filtering problem with marked point process observations. The motivation comes from modeling financial ultra-high frequency data. First, we rigorously derive the unnormalized filtering equation with marked point process observations under mild assumptions, especially relaxing the bounded condition of stochastic intensity. Then, we derive the Poisson chaos expansion for the unnormalized filter. Based on the chaos expansion, we establish the uniqueness of solutions of the unnormalized filtering equation. Moreover, we derive the Poisson chaos expansion for the unnormalized filter density under additional conditions. To explore the computational advantage, we further construct a new consistent recursive numerical scheme based on the truncation of the chaos density expansion for a simple case. The new algorithm divides the computations into those containing solely system coefficients and those including the observations, and assign the former off-line.

  17. Chaos as a Source of Complexity and Diversity in Evolution

    CERN Document Server

    Kaneko, K

    1993-01-01

    The relevance of chaos to evolution is discussed in the context of the origin and maintenance of diversity and complexity. Evolution to the edge of chaos is demonstrated in an imitation game. As an origin of diversity, dynamic clustering of identical chaotic elements, globally coupled each to other, is briefly reviewed. The clustering is extended to nonlinear dynamics on hypercubic lattices, which enables us to construct a self-organizing genetic algorithm. A mechanism of maintenance of diversity, ``homeochaos", is given in an ecological system with interaction among many species. Homeochaos provides a dynamic stability sustained by high-dimensional weak chaos. A novel mechanism of cell differentiation is presented, based on dynamic clustering. Here, a new concept -- ``open chaos" -- is proposed for the instability in a dynamical system with growing degrees of freedom. It is suggested that studies based on interacting chaotic elements can replace both top-down and bottom-up approaches.

  18. Biological conditions for oscillations and chaos generated by multispecies competition

    NARCIS (Netherlands)

    Huisman, J; Weissing, FJ

    2001-01-01

    We investigate biological mechanisms that generate oscillations and chaos in multispecies competition models. For this purpose, we use a competition model concerned with competition for abiotic essential resources. Because phytoplankton and plants consume quite a number of abiotic essential resource

  19. Spatial chaos-based image encryption design

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In recent years, the chaos based cryptographic algorithms have suggested some new and efficient ways to develop secure image encryption techniques, but the drawbacks of small key space and weak security in one-dimensional chaotic cryptosystems are obvious. In this paper, permutation and sub- stitution methods are incorporated to present a stronger image encryption algorithm. Spatial chaotic maps are used to realize the position permutation, and to confuse the relationship between the ci- pher-image and the plain-image. The experimental results demonstrate that the suggested encryption scheme of image has the advantages of large key space and high security; moreover, the distribution of grey values of the encrypted image has a random-like behavior.

  20. Spatial chaos-based image encryption design

    Institute of Scientific and Technical Information of China (English)

    LIU ShuTang; SUN FuYan

    2009-01-01

    In recent years, the chaos based cryptographic algorithms have suggested some new and efficient ways to develop secure image encryption techniques, but the drawbacks of small key space and weak security in one-dimensional chaotic cryptosystems are obvious. In this paper, permutation and sub-stitution methods are incorporated to present a stronger image encryption algorithm. Spatial chaotic maps are used to realize the position permutation, and to confuse the relationship between the ci-pher-image and the plain-image. The experimental results demonstrate that the suggested encryption scheme of image has the advantages of large key space and high security; moreover, the distribution of grey values of the encrypted image has a random-like behavior.

  1. Food chain chaos due to transcritical point

    Science.gov (United States)

    Deng, Bo; Hines, Gwendolen

    2003-06-01

    Chaotic dynamics of a classical prey-predator-superpredator ecological model are considered. Although much is known about the behavior of the model numerically, very few results have been proven analytically. A new analytical result is obtained. It is demonstrated that there exists a subset on which a singular Poincaré map generated by the model is conjugate to the shift map on two symbols. The existence of such a Poincaré map is due to two conditions: the assumption that each species has its own time scale ranging from fast for the prey to slow for the superpredator, and the existence of transcritical points, leading to the classical mathematical phenomenon of Pontryagin's delay of loss of stability. This chaos generating mechanism is new, neither suspected in abstract form nor recognized in numerical experiments in the literature.

  2. Quantifying chaos: A tale of two maps

    International Nuclear Information System (INIS)

    In many applications, there is a desire to determine if the dynamics of interest are chaotic or not. Since positive Lyapunov exponents are a signature for chaos, they are often used to determine this. Reliable estimates of Lyapunov exponents should demonstrate evidence of convergence; but literature abounds in which this evidence lacks. This Letter presents two maps through which it highlights the importance of providing evidence of convergence of Lyapunov exponent estimates. The results suggest cautious conclusions when confronted with real data. Moreover, the maps are interesting in their own right. -- Highlights: → We highlight the importance of verifying convergence of Lyapunov exponent estimates. → We emphasise a distributional approach to verifying convergence. → We illustrate with two novel nonlinear maps. → We suggest a way to deal with finite real data.

  3. Secure communication based on spatiotemporal chaos

    Science.gov (United States)

    Ren, Hai-Peng; Bai, Chao

    2015-08-01

    In this paper, we propose a novel approach to secure communication based on spatiotemporal chaos. At the transmitter end, the state variables of the coupled map lattice system are divided into two groups: one is used as the key to encrypt the plaintext in the N-shift encryption function, and the other is used to mix with the output of the N-shift function to further confuse the information to transmit. At the receiver end, the receiver lattices are driven by the received signal to synchronize with the transmitter lattices and an inverse procedure of the encoding is conducted to decode the information. Numerical simulation and experiment based on the TI TMS320C6713 Digital Signal Processor (DSP) show the feasibility and the validity of the proposed scheme. Project supported by the National Natural Science Foundation of China (Grant No. 61172070) and the Funds from the Science and Technology Innovation Team of Shaanxi Province, China (Grant No. 2013CKT-04).

  4. An introduction to chaos and randomness

    International Nuclear Information System (INIS)

    Chaos provides a link between determinism and randomness. It demonstrates that even very simple systems are capable of random behavior, and that randomness does not necessarily depend on the complexity of initial data. Instead, nonlinear geometrical relationships in the laws of motion cause mixing of nearby initial conditions, so that the states of the system are shuffled, much like a deck of cards. Even though the geometric relationships dictated by the laws of motion may be quite simple, the resulting trajectories can be highly complex. Small changes in initial conditions are amplified into very large changes in long-term behavior, making the relationship between cause and effect so complicated as to be effectively random. This complexity is generated internally, rather than externally. From any practical point of view the result is random. 150 refs., 43 figs

  5. Digital Communications Using Chaos and Nonlinear Dynamics

    CERN Document Server

    Larson, Lawrence E; Liu, Jia-Ming

    2006-01-01

    This book introduces readers to a new and exciting cross-disciplinary field of digital communications with chaos. This field was born around 15 years ago, when it was first demonstrated that nonlinear systems which produce complex non-periodic noise-like chaotic signals, can be synchronized and modulated to carry useful information. Thus, chaotic signals can be used instead of pseudo-random digital sequences for spread-spectrum and private communication applications. This deceptively simple idea spun hundreds of research papers, and many novel communication schemes based on chaotic signals have been proposed. However, only very recently researchers have begun to make a transition from academic studies toward practical implementation issues, and many "promising" schemes had to be discarded or re-formulated. This book describes the state of the art (both theoretical and experimental) of this novel field. The book is written by leading experts in the fields of Nonlinear Dynamics and Electrical Engineering who pa...

  6. Chaos embedded particle swarm optimization algorithms

    International Nuclear Information System (INIS)

    This paper proposes new particle swarm optimization (PSO) methods that use chaotic maps for parameter adaptation. This has been done by using of chaotic number generators each time a random number is needed by the classical PSO algorithm. Twelve chaos-embedded PSO methods have been proposed and eight chaotic maps have been analyzed in the benchmark functions. It has been detected that coupling emergent results in different areas, like those of PSO and complex dynamics, can improve the quality of results in some optimization problems. It has been also shown that, some of the proposed methods have somewhat increased the solution quality, that is in some cases they improved the global searching capability by escaping the local solutions.

  7. Stratified chaos in a sand pile formation

    CERN Document Server

    Poortinga, Ate; Ritsema, Coen J

    2014-01-01

    Sand pile formation is often used to describe stratified chaos in dynamic systems due to self-emergent and scale invariant behaviour. Cellular automata (Bak-Tang-Wiesenfeld model) are often used to describe chaotic behaviour, as simulating physical interactions between individual particles is computationally demanding. In this study, we use a state-of-the-art parallel implementation of the discrete element method on the graphical processing unit to simulate sand pile formation. Interactions between individual grains were simulated using a contact model in an Euler integration scheme. Results show non-linear self-emergent behaviour which is in good agreement with experimental results, theoretical work and self organized criticality (SOC) approaches. Moreover, it was found that the fully deterministic model, where the position and forces on every individual particle can be determined every iteration has a brown noise signal in the x and y direction, where the signal is the z direction is closer to a white noise...

  8. Theory of Secular Chaos and Mercury's Orbit

    CERN Document Server

    Lithwick, Yoram

    2010-01-01

    We study the chaotic orbital evolution of planetary systems, focusing on secular (i.e., orbit-averaged) interactions, because these often dominate on long timescales. We first focus on the evolution of a test particle that is forced by multiple massive planets. To linear order in eccentricity and inclination, its orbit precesses with constant frequencies. But nonlinearities can shift the frequencies into and out of secular resonance with the planets' eigenfrequencies, or with linear combinations of those frequencies. The overlap of these nonlinear secular resonances drive secular chaos in planetary systems. We quantify the resulting dynamics for the first time by calculating the locations and widths of nonlinear secular resonances. When results from both analytical calculations and numerical integrations are displayed together in a newly developed "map of the mean momenta" (MMM), the agreement is excellent. This map is particularly revealing for non-coplanar planetary systems and demonstrates graphically that...

  9. Chaos, Dirac observables and constraint quantization

    CERN Document Server

    Dittrich, Bianca; Koslowski, Tim A; Nelson, Mike I

    2015-01-01

    There is good evidence that full general relativity is non-integrable or even chaotic. We point out the severe repercussions: differentiable Dirac observables and a reduced phase space do not exist in non-integrable constrained systems and are thus unlikely to occur in a generic general relativistic context. Instead, gauge invariant quantities generally become discontinuous, thus not admitting Poisson-algebraic structures and posing serious challenges to a quantization. Non-integrability also renders the paradigm of relational dynamics cumbersome, thereby straining common interpretations of the dynamics. We illustrate these conceptual and technical challenges with simple toy models. In particular, we exhibit reparametrization invariant models which fail to be integrable and, as a consequence, can either not be quantized with standard methods or lead to sick quantum theories without a semiclassical limit. These troubles are qualitatively distinct from semiclassical subtleties in unconstrained quantum chaos and...

  10. From Cool Cash to Coded Chaos

    DEFF Research Database (Denmark)

    Rennison, Betina Wolfgang

    Communication makes a difference. The manner in which we communicate creates the phenomena we communicate about. It can seem obvious, but we are nevertheless seldom aware of the complexity this constructivist assumption implies. Through an analysis of a new salary system in the public sector of...... Denmark (called New Wage), this paper theorizes this complexity in terms of Niklas Luhmann's systems theory. It identifies four wholly different `codes' of communication: legal, economic, pedagogical and intimate. Each of them shapes the phenomena of `pay', the construal of the employee and the form of...... management differently. In this chaos of codes the managerial challenge is to take a second order position in order to strategically manage the communication that manages management itself. Key words: Management; personnel management; human-relations; pay-system; communication; system-theory; discursive...

  11. Stochastic chaos in a turbulent swirling flow

    CERN Document Server

    Faranda, Davide; Saint-Michel, Brice; Wiertel, Cecile; Padilla, Vincent; Dubrulle, Berengere; Daviaud, Francois

    2016-01-01

    We report the experimental evidence of the existence of a random attractor in a fully developed turbulent swirling flow. By defining a global observable which tracks the asymmetry in the flux of angular momentum imparted to the flow, we can first reconstruct the associated turbulent attractor and then follow its route towards chaos. We further show that the experimental attractor can be modeled by stochastic Duffing equations, that match the quantitative properties of the experimental flow, namely the number of quasi-stationary states and transition rates among them, the effective dimensions, and the continuity of the first Lyapunov exponents. Such properties can neither be recovered using deterministic models nor using stochastic differential equations based on effective potentials obtained by inverting the probability distributions of the experimental global observables. Our findings open the way to low dimensional modeling of systems featuring a large number of degrees of freedom and multiple quasi-station...

  12. Controlling chaos using an exponential control

    CERN Document Server

    Gadre, S D; Gadre, Sangeeta D; Varma, V S

    1995-01-01

    We demonstrate that chaos can be controlled using a multiplicative exponential feedback control. All three types of unstable orbits - unstable fixed points, limit cycles and chaotic trajectories can be stabilized using this control. The control is effective both for maps and flows. The control is significant, particularly for systems with several degrees of freedom, as knowledge of only one variable on the desired unstable orbit is sufficient to settle the system on to that orbit. We find, that in all the cases studied, the transient time is a decreasing function of the stiffness of control. But increasing the stiffness beyond an optimum value can increase the transient time. The control can also be used to create suitable new stable attractors in a map, which did not exist in the original system.

  13. Chaos in attitude dynamics of spacecraft

    CERN Document Server

    Liu, Yanzhu

    2013-01-01

    Attitude dynamics is the theoretical basis of attitude control of spacecrafts in aerospace engineering. With the development of nonlinear dynamics, chaos in spacecraft attitude dynamics has drawn great attention since the 1990's. The problem of the predictability and controllability of the chaotic attitude motion of a spacecraft has a practical significance in astronautic science. This book aims to summarize basic concepts, main approaches, and recent progress in this area. It focuses on the research work of the author and other Chinese scientists in this field, providing new methods and viewpoints in the investigation of spacecraft attitude motion, as well as new mathematical models, with definite engineering backgrounds, for further analysis. Professor Yanzhu Liu was the Director of the Institute of Engineering Mechanics, Shanghai Jiao Tong University, China. Dr. Liqun Chen is a Professor at the Department of Mechanics, Shanghai University, China.

  14. Mechanics From Newton's Laws to Deterministic Chaos

    CERN Document Server

    Scheck, Florian

    2010-01-01

    This book covers all topics in mechanics from elementary Newtonian mechanics, the principles of canonical mechanics and rigid body mechanics to relativistic mechanics and nonlinear dynamics. It was among the first textbooks to include dynamical systems and deterministic chaos in due detail. As compared to the previous editions the present fifth edition is updated and revised with more explanations, additional examples and sections on Noether's theorem. Symmetries and invariance principles, the basic geometric aspects of mechanics as well as elements of continuum mechanics also play an important role. The book will enable the reader to develop general principles from which equations of motion follow, to understand the importance of canonical mechanics and of symmetries as a basis for quantum mechanics, and to get practice in using general theoretical concepts and tools that are essential for all branches of physics. The book contains more than 120 problems with complete solutions, as well as some practical exa...

  15. Time reversibility, computer simulation, algorithms, chaos

    CERN Document Server

    Hoover, William Graham

    2012-01-01

    A small army of physicists, chemists, mathematicians, and engineers has joined forces to attack a classic problem, the "reversibility paradox", with modern tools. This book describes their work from the perspective of computer simulation, emphasizing the author's approach to the problem of understanding the compatibility, and even inevitability, of the irreversible second law of thermodynamics with an underlying time-reversible mechanics. Computer simulation has made it possible to probe reversibility from a variety of directions and "chaos theory" or "nonlinear dynamics" has supplied a useful vocabulary and a set of concepts, which allow a fuller explanation of irreversibility than that available to Boltzmann or to Green, Kubo and Onsager. Clear illustration of concepts is emphasized throughout, and reinforced with a glossary of technical terms from the specialized fields which have been combined here to focus on a common theme. The book begins with a discussion, contrasting the idealized reversibility of ba...

  16. Intrinsic motivation and learning dynamics

    CERN Document Server

    Zgonnikov, Arkady

    2013-01-01

    We investigate the effects of intrinsic motivation on the dynamics of learning processes. We construct a simple model of a single agent adapting to unknown environment. Performing a repeated choice between a number of initially unexplored alternatives, the agent gains rewards for each selected alternative and in doing so gradually comprehends the environment. In our model the agent choice is governed by two stimuli. The traditional extrinsic motive inclines the agent to maximize the cumulative payoff throughout the process, while the second, intrinsic one, biases the agent towards the novel options that she inherently likes. We show that the intrinsic motivation can induce an instability and periodic dynamics of the learning process which is always stationary in the case of selfish, rational agent. Interestingly, the opposite effect can arise as well: when the impact of intrinsic motivation on the agent choice is strong, the equiprobable choice equilibrium strategy becomes stable. Based on the presented resul...

  17. Thermal conductivity of nonlinear waves in disordered chains

    Indian Academy of Sciences (India)

    Sergej Flach; Mikhail Ivanchenko; Nianbei Li

    2011-11-01

    We present computational data on the thermal conductivity of nonlinear waves in disordered chains. Disorder induces Anderson localization for linear waves and results in a vanishing conductivity. Cubic nonlinearity restores normal conductivity, but with a strongly temperature-dependent conductivity (). We find indications for an asymptotic low-temperature ∼ 4 and intermediate temperature ∼ 2 laws. These findings are in accord with theoretical studies of wave packet spreading, where a regime of strong chaos is found to be intermediate, followed by an asymptotic regime of weak chaos (Laptyeva et al, Europhys. Lett. 91, 30001 (2010)).

  18. Secure Communication System Based on Chaos in Optical Fibre

    Institute of Scientific and Technical Information of China (English)

    Pak; L; Chu; Fan; Zhang; William; Mak; Robust; Lai

    2003-01-01

    1 IntroductionRecently, there have been intense research activities on the study of synchronized chaos generated by fibre lasers and its application to secure communication systems. So far, all studies concentrate on two aspects: (1) the effect of the transmission channel between the transmitter and the receiver has been neglected, and (2) the chaos and the signal are carried by one wavelength. Both theoretical and experimental investigations make

  19. Fluctuations of Spatial Patterns as a Measure of Classical Chaos

    CERN Document Server

    Cao, Z J; Cao, Zhen; Hwa, Rudolph C.

    1997-01-01

    In problems where the temporal evolution of a nonlinear system cannot be followed, a method for studying the fluctuations of spatial patterns has been developed. That method is applied to well-known problems in deterministic chaos (the logistic map and the Lorenz model) to check its effectiveness in characterizing the dynamical behaviors. It is found that the indices $\\mu _q$ are as useful as the Lyapunov exponents in providing a quantitative measure of chaos.

  20. High precision framework for chaos many-body engine

    Science.gov (United States)

    Grossu, I. V.; Besliu, C.; Felea, D.; Jipa, Al.

    2014-04-01

    In this paper we present a C# 4.0 high precision framework for simulation of relativistic many-body systems. In order to benefit from the, previously developed, chaos analysis instruments, all new modules were integrated with Chaos Many-Body Engine (Grossu et al. 2010, 2013). As a direct application, we used 46 digits precision for analyzing the "Butterfly Effect" of the gravitational force in a specific relativistic nuclear collision toy-model.

  1. Relations between distributional, Li-Yorke and {omega} chaos

    Energy Technology Data Exchange (ETDEWEB)

    Guirao, Juan Luis Garcia [Departamento de Matematica Aplicada y Estadistica, Universidad Politecnica de Cartagena, C/Paseo Alfonso XIII, 30203-Cartagena (Region de Murcia) (Spain)]. E-mail: juan.garcia@upct.es; Lampart, Marek [Mathematical Institute at Opava, Silesian University at Opava, Na Rybnicku 1, 746 01 Opava (Czech Republic)]. E-mail: marek.lampart@math.slu.cz

    2006-05-15

    The forcing relations between notions of distributional, Li-Yorke and {omega} chaos were studied by many authors. In this paper we summarize all known connections between these three different types of chaos and fulfill the results for general compact metric spaces by the construction of a selfmap on a compact perfect set which is {omega} chaotic, not distributionally chaotic and has zero topological entropy.

  2. Chaos and Nonlinear Dynamics in a Quantum Artificial Economy

    CERN Document Server

    Gonçalves, Carlos Pedro

    2012-01-01

    Chaos and nonlinear economic dynamics are addressed for a quantum coupled map lattice model of an artificial economy, with quantized supply and demand equilibrium conditions. The measure theoretic properties and the patterns that emerge in both the economic business volume dynamics' diagrams as well as in the quantum mean field averages are addressed and conclusions are drawn in regards to the application of quantum chaos theory to address signatures of chaotic dynamics in relevant discrete economic state variables.

  3. Tropic of Chaos: An Evening with Christian Parenti

    OpenAIRE

    Parenti, Christian

    2011-01-01

    Christian Parenti talks about his latest book, 'Tropic of Chaos: Climate Change and the New Geography of Violence', a "brilliant weather report from the near future of world politics" (Mike Davis). The era of climate war is upon us. Extreme weather brought on by global warming is unleashing cascades of unrest and violence across the globe, from Africa to Asia to the Americas. In Tropic of Chaos, award-winning journalist and sociologists Christian Parenti reports from the front lines of this ...

  4. Quantum Graphs: Applications to Quantum Chaos and Universal Spectral Statistics

    OpenAIRE

    Gnutzmann, Sven; Smilansky, Uzy

    2006-01-01

    During the last years quantum graphs have become a paradigm of quantum chaos with applications from spectral statistics to chaotic scattering and wave function statistics. In the first part of this review we give a detailed introduction to the spectral theory of quantum graphs and discuss exact trace formulae for the spectrum and the quantum-to-classical correspondence. The second part of this review is devoted to the spectral statistics of quantum graphs as an application to quantum chaos. E...

  5. Fibonacci order in the period-doubling cascade to chaos

    International Nuclear Information System (INIS)

    In this contribution, we describe how the Fibonacci sequence appears within the Feigenbaum scaling of the period-doubling cascade to chaos. An important consequence of this discovery is that the ratio of successive Fibonacci numbers converges to the golden mean in every period-doubling sequence and therefore the convergence to φ, the most irrational number, occurs in concert with the onset of deterministic chaos

  6. Adaptive SAGA Based on Mutative Scale Chaos Optimization Strategy

    OpenAIRE

    Haichang Gao; Boqin Feng; Yun Hou; Bin Guo; Li Zhu

    2006-01-01

    A hybrid adaptive SAGA based on mutative scale chaos optimization strategy (CASAGA) is proposed to solve the slow convergence, incident getting into local optimum characteristics of the Standard Genetic Algorithm (SGA). The algorithm combined the parallel searching structure of Genetic Algorithm (GA) with the probabilistic jumping property of Simulated Annealing (SA), also used adaptive crossover and mutation operators. The mutative scale Chaos optimization strategy was used to accelerate the...

  7. Quantum manifestations of chaos in elastic atom-surface scattering

    OpenAIRE

    Guantes, R.; Miret-Artés, Salvador; Borondo, Florentino

    2001-01-01

    Quantum manifestations of chaos in the diffraction of atoms from corrugated surfaces, for a range of initial conditions easily attainable in scattering experiments, are presented and discussed. The appearance of strong oscillations in diffraction patterns is shown to be directly related to the presence of classical chaos and threshold effects. We also show that the autocorrelation function for some of the collision S-matrix elements over incident angles is sensitive to the character, hyperbol...

  8. Chaos, CNN, memristors and beyond a festschrift for Leon Chua

    CERN Document Server

    Adamatzky, Andrew

    2013-01-01

    This invaluable book is a unique collection of tributes to outstanding discoveries pioneered by Leon Chua in nonlinear circuits, cellular neural networks, and chaos. It is comprised of three parts. The first - cellular nonlinear networks, nonlinear circuits and cellular automata - deals with Chua's Lagrangian circuits, cellular wave computers, bio-inspired robotics and neuro-morphic architectures, toroidal chaos, synaptic cellular automata, history of Chua's circuits, cardiac arrhythmias, local activity principle, symmetry breaking and complexity, bifurcation trees, and Chua's views on nonline

  9. A Note on Intrinsic Correlation

    OpenAIRE

    Du, Songzi

    2008-01-01

    In this note we characterize the strategic implication of intrinsic correlation, introduced by Brandenburger and Friedenberg (2008), in the subjective correlated equilibrium setting of a complete information game. Intrinsic correlation restricts correlation devices to variables within the game, i.e. players's beliefs (and higher order beliefs) about each other's strategies, in contrast to signals or sunspots from the "outside." The characterization is a strengthening of best-response set wi...

  10. OnN Kac's Chaos and Related Problems

    CERN Document Server

    Hauray, Maxime

    2012-01-01

    This paper is devoted to establish quantitative and qualitative estimates related to the notion of chaos as firstly formulated by M. Kac [37] in his study of mean-field limit for systems of N undistinguishable particles as N \\rightarrow \\infty. First, we quantitatively liken three usual measures of Kac's chaos, some involving the all N variables, other involving a finite fixed number of variables. The cornerstone of the proof is a new representation of the Monge-Kantorovich-Wasserstein (MKW) distance for symmetric N-particle probabilities in terms of the distance between the law of the associated empirical measures on the one hand, and a new estimate on some MKW distance on probability spaces endowed with a suitable Hilbert norm taking advantage of the associated good algebraic structure. Next, we define the notion of entropy chaos and Fisher information chaos in a similar way as defined by Carlen et al [17]. We show that Fisher information chaos is stronger than entropy chaos, which in turn is stronger than ...

  11. The chaos avant-garde memories of the early days of chaos theory

    CERN Document Server

    Abraham, Ralph H

    2001-01-01

    This book is an authoritative and unique reference for the history of chaos theory, told by the pioneers themselves. It also provides an excellent historical introduction to the concepts. There are eleven contributions, and six of them are published here for the first time - two by Steve Smale, three by Yoshisuke Ueda, and one each by Ralph Abraham, Edward Lorenz, Christian Mira, Floris Takens, T Y Li and James A Yorke, and Otto E Rossler. Contents: On How I Got Started in Dynamical Systems 1959-1962 (S Smale); Finding a Horseshoe on the Beaches of Rio (S Smale); Strange Attractors and the Ori

  12. Dictature et chaos dans le roman du dictateur hispano-américain

    Directory of Open Access Journals (Sweden)

    Cécile Brochard

    2008-07-01

    Full Text Available Le chaos est l’adversaire de la dictature : celle-ci recherche l’ordre et l’unité, incarnés par le dictateur. Pourtant, loin de reproduire l’idéologie autoritaire, le roman du dictateur hispano-américain choisit le désordre et inscrit la confusion au cœur de la dictature : l’identité du chef, soumise à la duplicité, se fractionne et la parole unique est concurrencée par la polyphonie. Ainsi le roman du dictateur se développe-t-il en contrepoint de la dictature.Chaos is the enemy of dictatorship, which searches for order and unity, materialized by the dictator. Nevertheless, far from reproducing this authoritative ideology, the Hispano-American dictator novel chooses disorder and inserts confusion at the heart of dictatorship : the leader’s identity, subject to duplicity, splits and his speech competes with polyphony. Thus, the dictator novel is written and built as a counterpoint to dictatorship itself.

  13. Sleep Quality Estimation based on Chaos Analysis for Heart Rate Variability

    Science.gov (United States)

    Fukuda, Toshio; Wakuda, Yuki; Hasegawa, Yasuhisa; Arai, Fumihito; Kawaguchi, Mitsuo; Noda, Akiko

    In this paper, we propose an algorithm to estimate sleep quality based on a heart rate variability using chaos analysis. Polysomnography(PSG) is a conventional and reliable system to diagnose sleep disorder and to evaluate its severity and therapeatic effect, by estimating sleep quality based on multiple channels. However, a recording process requires a lot of time and a controlled environment for measurement and then an analyzing process of PSG data is hard work because the huge sensed data should be manually evaluated. On the other hand, it is focused that some people make a mistake or cause an accident due to lost of regular sleep and of homeostasis these days. Therefore a simple home system for checking own sleep is required and then the estimation algorithm for the system should be developed. Therefore we propose an algorithm to estimate sleep quality based only on a heart rate variability which can be measured by a simple sensor such as a pressure sensor and an infrared sensor in an uncontrolled environment, by experimentally finding the relationship between chaos indices and sleep quality. The system including the estimation algorithm can inform patterns and quality of own daily sleep to a user, and then the user can previously arranges his life schedule, pays more attention based on sleep results and consult with a doctor.

  14. Element-specific structure of materials with intrinsic disorder by high-energy resonant x-ray diffraction and differential atomic pair-distribution functions: A study of PtPd nanosized catalysts

    Science.gov (United States)

    Petkov, V.; Shastri, S. D.

    2010-04-01

    We demonstrate how high-energy resonant x-ray diffraction (XRD) and differential atomic-pair-distribution function (PDF) analysis can be used to characterize the atomic ordering in materials of limited structural coherence with both excellent spatial resolution and element specificity. First we prove that this experimental approach is feasible by probing the K -absorption edge of Au(˜81keV) atoms in chemically ordered and disordered bulk Cu3Au alloys. The resulting Au-differential PDFs show very clearly the different ways Au atoms are known to occupy the sites of otherwise identical cubic lattices of those materials. Next we apply it to a more complex material: PtPd alloy and core-shell nanosized (˜2-4nm) particles by probing the K -absorption edge of Pt(˜78keV) . The resulting Pt-differential atomic PDFs reveal how exactly the atomic ordering of catalytically active Pt atoms is affected by the nanoparticles’ design, thus providing a firm structural basis for understanding their properties. The work is a step forward in expanding the limits of applicability of nontraditional XRD to the rapidly growing field of materials of unusual structural complexity.

  15. Intrinsically Unstructured Proteins: Potential Targets for Drug Discovery

    Directory of Open Access Journals (Sweden)

    Pathan Salma

    2009-01-01

    Full Text Available Problem statement: The function of a protein is dependent on its three-dimensional structure. However, numerous proteins lacking intrinsic globular 3D structure under physiological conditions had been recognized. These proteins are frequently involved in some of the most critical cellular control mechanisms and it appears that their rapid turnover, aided by their unstructured nature in the unbound state, provides a level of control that allows rapid and accurate responses of the cell to changing environmental conditions. Approach: A significant number of proteins known to be involved in protein deposition disorders were now considered to Be Intrinsically Unstructured Proteins (IUPs. For example, Aß peptide and tau protein in Alzheimer’s disease, PrP in Prion’s disease and a-Synuclein in Parkinson’s disease. The disorder of intrinsically unstructured proteins (IUP's was crucial to their functions. They may adopt defined but extended structures when bound to cognate ligands. Their amino acid compositions were less hydrophobic than those of soluble proteins. They lack hydrophobic cores and hence did not become insoluble when heated. About 40% of eukaryotic proteins had at least one long (>50 residues disordered region. Roughly 10% of proteins in various genomes had been predicted to be fully disordered. Presently over 100 IUP's had been identified; none are enzymes. Obviously, IUP's were greatly underrepresented in the Protein Data Bank, although there were few cases of an IUP bound to a folded (intrinsically structured protein. Results: The five functional categories for intrinsically unstructured proteins and domains were entropic chains (bristles to ensure spacing, springs, flexible spacers/linkers, effectors (inhibitors and disassemblers, scavengers, assemblers and display sites. These IUPs could serve as potential targets for Structure Based Drug Design (SBDD which stress on the transition

  16. Stability Analysis of Nonlinear Feedback Control Methods for Beam Halo-chaos

    Institute of Scientific and Technical Information of China (English)

    WANGZhong-sheng; FANGJin-qing; CHENGuan-rong

    2003-01-01

    Control of beam halo-chaos has been a more challenge subject in recent years, in which nonlinear feedback method for beam halo-chaos has been developed for control of beam halo-chaos in high-current proton linear accelerators. However, stability analysis of nonlinear feedback control methods for beam halo-chaos has still been an open and important topic in this field. In this letter.

  17. Experimental study of chaos synchronization in the Belousov-Zhabotinsky chemical system

    International Nuclear Information System (INIS)

    Employing self-adaptive parameter regulation scheme, chaos synchronization in the Belousov-Zhabotinsky-CSTR chemical system has been studied experimentally. By optimizing the combination of regulation parameters, the trend of chaos synchronization is observed and the prediction of chaos synchronization from numerical simulation is thus verified by the experiment. In addition, the difference of sensitivity to noise with the mass coupling scheme and the self-adaptive parameter regulation scheme in chaos synchronization has also been discussed

  18. Time-dependent generalized polynomial chaos

    International Nuclear Information System (INIS)

    Generalized polynomial chaos (gPC) has non-uniform convergence and tends to break down for long-time integration. The reason is that the probability density distribution (PDF) of the solution evolves as a function of time. The set of orthogonal polynomials associated with the initial distribution will therefore not be optimal at later times, thus causing the reduced efficiency of the method for long-time integration. Adaptation of the set of orthogonal polynomials with respect to the changing PDF removes the error with respect to long-time integration. In this method new stochastic variables and orthogonal polynomials are constructed as time progresses. In the new stochastic variable the solution can be represented exactly by linear functions. This allows the method to use only low order polynomial approximations with high accuracy. The method is illustrated with a simple decay model for which an analytic solution is available and subsequently applied to the three mode Kraichnan-Orszag problem with favorable results.

  19. Nonlinear Dynamics: Integrability, Chaos and Patterns

    International Nuclear Information System (INIS)

    When the editorial office of Journal of Physics A: Mathematical and General of the Institute of Physics Publishing asked me to review a book on nonlinear dynamics I experienced an undeniable apprehension. Indeed, the domain is a rapidly expanding one and writing a book aiming at a certain degree of completeness looks like an almost impossible task. My uneasiness abated somewhat when I saw the names of the authors, two well-known specialists of the nonlinear domain, but it was only when I held the book in my hands that I felt really reassured. The book is not just a review of the recent (and less so) findings on nonlinear systems. It is also a textbook. The authors set out to provide a detailed, step by step, introduction to the domain of nonlinearity and its various subdomains: chaos, integrability and pattern formation (although this last topic is treated with far less detail than the other two). The public they have in mind is obviously that of university students, graduate or undergraduate, who are interested in nonlinear phenomena. I suspect that a non-negligible portion of readers will be people who have to teach topics which figure among those included in the book: they will find this monograph an excellent companion to their course. The book is written in a pedagogical way, with a profusion of examples, detailed explanations and clear diagrams. The point of view is that of a physicist, which to my eyes is a major advantage. The mathematical formulation remains simple and perfectly intelligible. Thus the reader is not bogged down by fancy mathematical formalism, which would have discouraged the less experienced ones. A host of exercises accompanies every chapter. This will give the novice the occasion to develop his/her problem-solving skills and acquire competence in the use of nonlinear techniques. Some exercises are quite straightforward, like 'verify the relation 14.81'. Others are less so, such as 'prepare a write-up on a) frequency-locking and b) devil

  20. Implementation of LT codes based on chaos

    Institute of Scientific and Technical Information of China (English)

    Zhou Qian; Li Liang; Chen Zeng-Qiang; Zhao Jia-Xiang

    2008-01-01

    Fountain codes provide an efficient way to transfer information over erasure channels like the Internet.LT codes are the first codes fully realizing the digital fountain concept.They are asymptotically optimal rateless erasure codes with highly efficient encoding and decoding algorithms.In theory,for each encoding symbol of LT codes,its degree is randomly chosen according to a predetermined degree distribution,and its neighbours used to generate that encoding symbol are chosen uniformly at random.Practical implementation of LT codes usually realizes the randomness through pseudo-randomness number generator like linear congruential method.This paper applies the pseudo-randomness of chaotic sequence in the implementation of LT codes.Two Kent chaotic maps are used to determine the degree and neighbour(s)of each encoding symbol.It is shown that the implemented LT codes based on chaos perform better than the LT codes implemented by the traditional pseudo-randomness number generator.