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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. Unusual biophysics of intrinsically disordered proteins.

    Science.gov (United States)

    Uversky, Vladimir N

    2013-05-01

    Research of a past decade and a half leaves no doubt that complete understanding of protein functionality requires close consideration of the fact that many functional proteins do not have well-folded structures. These intrinsically disordered proteins (IDPs) and proteins with intrinsically disordered protein regions (IDPRs) are highly abundant in nature and play a number of crucial roles in a living cell. Their functions, which are typically associated with a wide range of intermolecular interactions where IDPs possess remarkable binding promiscuity, complement functional repertoire of ordered proteins. All this requires a close attention to the peculiarities of biophysics of these proteins. In this review, some key biophysical features of IDPs are covered. In addition to the peculiar sequence characteristics of IDPs these biophysical features include sequential, structural, and spatiotemporal heterogeneity of IDPs; their rough and relatively flat energy landscapes; their ability to undergo both induced folding and induced unfolding; the ability to interact specifically with structurally unrelated partners; the ability to gain different structures at binding to different partners; and the ability to keep essential amount of disorder even in the bound form. IDPs are also characterized by the "turned-out" response to the changes in their environment, where they gain some structure under conditions resulting in denaturation or even unfolding of ordered proteins. It is proposed that the heterogeneous spatiotemporal structure of IDPs/IDPRs can be described as a set of foldons, inducible foldons, semi-foldons, non-foldons, and unfoldons. They may lose their function when folded, and activation of some IDPs is associated with the awaking of the dormant disorder. It is possible that IDPs represent the "edge of chaos" systems which operate in a region between order and complete randomness or chaos, where the complexity is maximal. This article is part of a Special Issue

  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. 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.

  8. 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.

  9. 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...

  10. 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....

  11. 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.

  12. Helical propensity in an intrinsically disordered protein accelerates ligand binding

    DEFF Research Database (Denmark)

    Iesmantavicius, Vytautas; Dogan, Jakob; Jemth, Per;

    2014-01-01

    Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activation...... domain of the activator for thyroid hormone and retinoid receptors (ACTR) is intrinsically disordered and folds upon binding to the nuclear coactivator binding domain (NCBD) of the CREB binding protein. A number of mutants was designed that selectively perturbs the amount of secondary structure...... in unbound ACTR without interfering with the intermolecular interactions between ACTR and NCBD. Using NMR spectroscopy and fluorescence-monitored stopped-flow kinetic measurements we show that the secondary structure content in helix 1 of ACTR indeed influences the binding kinetics. The results thus support...

  13. 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.

  14. Experiments on intrinsic and thermally induced chaos in an rf-driven Josephson junction

    DEFF Research Database (Denmark)

    Davidson, A.; Dueholm, B.; Beasley, M. R.

    1986-01-01

    We report detailed measurements of low-frequency noise due to microwaves applied to a real Josephson tunnel junction. An intrinsically chaotic region is apparently identified, but the effects of thermal noise are shown to be significant. In particular we show experimental data that we interpret a...

  15. 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...

  16. Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment

    Science.gov (United States)

    Mollica, Luca; Bessa, Luiza M.; Hanoulle, Xavier; Jensen, Malene Ringkjøbing; Blackledge, Martin; Schneider, Robert

    2016-01-01

    In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context.

  17. Binding Mechanisms of Intrinsically Disordered Proteins: Theory, Simulation, and Experiment

    Science.gov (United States)

    Mollica, Luca; Bessa, Luiza M.; Hanoulle, Xavier; Jensen, Malene Ringkjøbing; Blackledge, Martin; Schneider, Robert

    2016-01-01

    In recent years, protein science has been revolutionized by the discovery of intrinsically disordered proteins (IDPs). In contrast to the classical paradigm that a given protein sequence corresponds to a defined structure and an associated function, we now know that proteins can be functional in the absence of a stable three-dimensional structure. In many cases, disordered proteins or protein regions become structured, at least locally, upon interacting with their physiological partners. Many, sometimes conflicting, hypotheses have been put forward regarding the interaction mechanisms of IDPs and the potential advantages of disorder for protein-protein interactions. Whether disorder may increase, as proposed, e.g., in the “fly-casting” hypothesis, or decrease binding rates, increase or decrease binding specificity, or what role pre-formed structure might play in interactions involving IDPs (conformational selection vs. induced fit), are subjects of intense debate. Experimentally, these questions remain difficult to address. Here, we review experimental studies of binding mechanisms of IDPs using NMR spectroscopy and transient kinetic techniques, as well as the underlying theoretical concepts and numerical methods that can be applied to describe these interactions at the atomic level. The available literature suggests that the kinetic and thermodynamic parameters characterizing interactions involving IDPs can vary widely and that there may be no single common mechanism that can explain the different binding modes observed experimentally. Rather, disordered proteins appear to make combined use of features such as pre-formed structure and flexibility, depending on the individual system and the functional context. PMID:27668217

  18. DSS1/Sem1, a multifunctional and intrinsically disordered protein

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Schenstrøm, Signe Marie; 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 transcription; and the TREX-2 complex, involved in nuclear export of mRNA and transcription elongation. As a subunit of the proteasome, DSS1 functions both in complex assembly and possibly as a ubiquitin receptor. Here, we summarise structural and functional aspects of DSS1/Sem1 with particular emphasis on its...... multifunctional and disordered properties. We suggest that DSS1/Sem1 can act as a polyanionic adhesive to prevent nonproductive interactions during construction of protein assemblies, uniquely employing different structures when associating with the diverse multisubunit complexes....

  19. 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.

  20. 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.

  1. 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......, which allows the accurate random coil chemical shifts to be obtained at any pH. By correcting the random coil chemical shifts for the effects of temperature and pH, systematic biases of the secondary chemical shifts are minimized, which will improve the reliability of detection of transient secondary...

  2. 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

  3. 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

  4. 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)

  5. 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.

  6. 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

  7. 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

    2016-01-18

    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.

  8. 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…

  9. Intrinsic disorder in graphene on transition metal dichalcogenide heterostructures

    Science.gov (United States)

    Yankowitz, Matthew; Larentis, Stefano; Kim, Kyounghwam; Xue, Jiamin; McKenzie, Devin; Huang, Shengqiang; Paggen, Marina; Ali, Mazhar; Cava, Robert; Tutuc, Emanuel; Leroy, Brian J.

    2015-03-01

    Recently, semiconducting materials in the transition metal dichalcogenide (TMD) family have gained great popularity for use in novel graphene-based heterostructure devices such as tunneling transistors, highly efficient flexible photovoltaic devices, and nonvolatile memory cells. TMDs have also been explored as alternatives to hexagonal boron nitride (hBN) as substrates for pristine graphene devices. However, their quality has thus far been significantly worse than comparable hBN devices. We examine graphene on numerous TMD substrates (MoS2, WS2, WSe2, MoTe2) with scanning tunneling microscopy and spectroscopy and find that point and line defects intrinsic to all TMD crystals (both of natural and synthetic origin) result in scattering of electrons in graphene. Our findings suggest that the quality of graphene on TMD heterostructures is limited by the intrinsic crystalline quality of the TMDs.

  10. 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...

  11. 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...

  12. 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

  13. Quantum Chaos

    Science.gov (United States)

    Casati, Giulio; Chirikov, Boris

    2006-11-01

    Preface; Acknowledgments; Introduction: 1. The legacy of chaos in quantum mechanics G. Casati and B. V. Chirikov; Part I. Classical Chaos and Quantum Localization: 2. Stochastic behaviour of a quantum pendulum under a periodic perturbation G. Casati, B. V. Chirikov, F. M. Izrailev and J. Ford; 3. Quantum dynamics of a nonintegrable system D. R. Grempel, R. E. Prange and S. E. Fishman; 4. Excitation of molecular rotation by periodic microwave pulses. A testing ground for Anderson localization R. Blümel, S. Fishman and U. Smilansky; 5. Localization of diffusive excitation in multi-level systems D. K. Shepelyansky; 6. Classical and quantum chaos for a kicked top F. Haake, M. Kus and R. Scharf; 7. Self-similarity in quantum dynamics L. E. Reichl and L. Haoming; 8. Time irreversibility of classically chaotic quantum dynamics K. Ikeda; 9. Effect of noise on time-dependent quantum chaos E. Ott, T. M. Antonsen Jr and J. D. Hanson; 10. Dynamical localization, dissipation and noise R. F. Graham; 11. Maximum entropy models and quantum transmission in disordered systems J.-L. Pichard and M. Sanquer; 12. Solid state 'atoms' in intense oscillating fields M. S. Sherwin; Part II. Atoms in Strong Fields: 13. Localization of classically chaotic diffusion for hydrogen atoms in microwave fields J. E. Bayfield, G. Casati, I. Guarneri and D. W. Sokol; 14. Inhibition of quantum transport due to 'scars' of unstable periodic orbits R. V. Jensen, M. M. Sanders, M. Saraceno and B. Sundaram; 15. Rubidium Rydberg atoms in strong fields G. Benson, G. Raithel and H. Walther; 16. Diamagnetic Rydberg atom: confrontation of calculated and observed spectra C.-H. Iu, G. R. Welch, M. M. Kash, D. Kleppner, D. Delande and J. C. Gay; 17. Semiclassical approximation for the quantum states of a hydrogen atom in a magnetic field near the ionization limit M. Y. Kuchiev and O. P. Sushkov; 18. The semiclassical helium atom D. Wintgen, K. Richter and G. Tanner; 19. Stretched helium: a model for quantum chaos

  14. 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

  15. 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

  16. 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...

  17. 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

    2015-01-01

    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 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.

  18. 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.

  19. 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

  20. Subgroup-specific intrinsic disorder profiles of arabidopsis NAC transcription factors

    DEFF Research Database (Denmark)

    Stender, Emil G.; O'Shea, Charlotte; Skriver, Karen

    2015-01-01

    Protein intrinsic disorder (ID), referring to the lack of a fixed tertiary structure, is significant in signaling and transcription. We recently characterized ID in 6 phylogenetically representative Arabidopsis thaliana NAC transcription factors. Their transcription regulatory domains are mostly.......g. transcriptional activation and interactions. Based on our analysis, we suggest that ID profiling of regulatory proteins in general can be used to guide identification of interaction partners of network proteins....

  1. 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...

  2. 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...

  3. 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...

  4. 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...

  5. 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 ...

  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. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer

    Science.gov (United States)

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease. PMID:27453073

  8. Unfoldomics of prostate cancer: on the abundance and roles of intrinsically disordered proteins in prostate cancer.

    Science.gov (United States)

    Landau, Kevin S; Na, Insung; Schenck, Ryan O; Uversky, Vladimir N

    2016-01-01

    Prostatic diseases such as prostate cancer and benign prostatic hyperplasia are highly prevalent among men. The number of studies focused on the abundance and roles of intrinsically disordered proteins in prostate cancer is rather limited. The goal of this study is to analyze the prevalence and degree of disorder in proteins that were previously associated with the prostate cancer pathogenesis and to compare these proteins to the entire human proteome. The analysis of these datasets provides means for drawing conclusions on the roles of disordered proteins in this common male disease. We also hope that the results of our analysis can potentially lead to future experimental studies of these proteins to find novel pathways associated with this disease.

  9. Quantifying the intrinsic amount of fabrication disorder in photonic-crystal waveguides from optical far-field intensity measurements

    DEFF Research Database (Denmark)

    Garcia-Fernandez, Pedro David; Javadi, Alisa; Nielsen, Henri Thyrrestrup;

    2013-01-01

    Residual disorder due to fabrication imperfections has important impact in nanophotonics where it may degrade device performance by increasing radiation loss or spontaneously trap light by Anderson localization. We propose and demonstrate experimentally a method of quantifying the intrinsic amount...

  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. 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

  12. 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).

  13. Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation.

    Science.gov (United States)

    Noval, María G; Gallo, Mariana; Perrone, Sebastián; Salvay, Andres G; Chemes, Lucía B; de Prat-Gay, Gonzalo

    2013-01-01

    Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N). Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29), while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII) structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus. PMID:24086265

  14. Primary structure and solution conditions determine conformational ensemble properties of intrinsically disordered proteins

    Science.gov (United States)

    Mao, Hsuan-Han Alberto

    Intrinsically disordered proteins (IDPs) are a class of proteins that do not exhibit well-defined three-dimensional structures. The absence of structure is intrinsic to their amino acid sequences, which are characterized by low hydrophobicity and high net charge per residue compared to folded proteins. Contradicting the classic structure-function paradigm, IDPs are capable of interacting with high specificity and affinity, often acquiring order in complex with protein and nucleic acid binding partners. This phenomenon is evident during cellular activities involving IDPs, which include transcriptional and translational regulation, cell cycle control, signal transduction, molecular assembly, and molecular recognition. Although approximately 30% of eukaryotic proteomes are intrinsically disordered, the nature of IDP conformational ensembles remains unclear. In this dissertation, we describe relationships connecting characteristics of IDP conformational ensembles to their primary structures and solution conditions. Using molecular simulations and fluorescence experiments on a set of base-rich IDPs, we find that net charge per residue segregates conformational ensembles along a globule-to-coil transition. Speculatively generalizing this result, we propose a phase diagram that predicts an IDP's average size and shape based on sequence composition and use it to generate hypotheses for a broad set of intrinsically disordered regions (IDRs). Simulations reveal that acid-rich IDRs, unlike their oppositely charged base-rich counterparts, exhibit disordered globular ensembles despite intra-chain repulsive electrostatic interactions. This apparent asymmetry is sensitive to simulation parameters for representing alkali and halide salt ions, suggesting that solution conditions modulate IDP conformational ensembles. We refine the ion parameters using a calibration procedure that relies exclusively on crystal lattice properties. Simulations with these parameters recover swollen

  15. 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

  16. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins

    Science.gov (United States)

    Sormanni, Pietro; Aprile, Francesco A.; Vendruscolo, Michele

    2015-01-01

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions. PMID:26216991

  17. Rational design of antibodies targeting specific epitopes within intrinsically disordered proteins.

    Science.gov (United States)

    Sormanni, Pietro; Aprile, Francesco A; Vendruscolo, Michele

    2015-08-11

    Antibodies are powerful tools in life sciences research, as well as in diagnostic and therapeutic applications, because of their ability to bind given molecules with high affinity and specificity. Using current methods, however, it is laborious and sometimes difficult to generate antibodies to target specific epitopes within a protein, in particular if these epitopes are not effective antigens. Here we present a method to rationally design antibodies to enable them to bind virtually any chosen disordered epitope in a protein. The procedure consists in the sequence-based design of one or more complementary peptides targeting a selected disordered epitope and the subsequent grafting of such peptides on an antibody scaffold. We illustrate the method by designing six single-domain antibodies to bind different epitopes within three disease-related intrinsically disordered proteins and peptides (α-synuclein, Aβ42, and IAPP). Our results show that all these designed antibodies bind their targets with good affinity and specificity. As an example of an application, we show that one of these antibodies inhibits the aggregation of α-synuclein at substoichiometric concentrations and that binding occurs at the selected epitope. Taken together, these results indicate that the design strategy that we propose makes it possible to obtain antibodies targeting given epitopes in disordered proteins or protein regions.

  18. 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

  19. 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.

  20. 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

  1. Genome-scale prediction of proteins with long intrinsically disordered regions.

    Science.gov (United States)

    Peng, Zhenling; Mizianty, Marcin J; Kurgan, Lukasz

    2014-01-01

    Proteins with long disordered regions (LDRs), defined as having 30 or more consecutive disordered residues, are abundant in eukaryotes, and these regions are recognized as a distinct class of biologically functional domains. LDRs facilitate various cellular functions and are important for target selection in structural genomics. Motivated by the lack of methods that directly predict proteins with LDRs, we designed Super-fast predictor of proteins with Long Intrinsically DisordERed regions (SLIDER). SLIDER utilizes logistic regression that takes an empirically chosen set of numerical features, which consider selected physicochemical properties of amino acids, sequence complexity, and amino acid composition, as its inputs. Empirical tests show that SLIDER offers competitive predictive performance combined with low computational cost. It outperforms, by at least a modest margin, a comprehensive set of modern disorder predictors (that can indirectly predict LDRs) and is 16 times faster compared to the best currently available disorder predictor. Utilizing our time-efficient predictor, we characterized abundance and functional roles of proteins with LDRs over 110 eukaryotic proteomes. Similar to related studies, we found that eukaryotes have many (on average 30.3%) proteins with LDRs with majority of proteomes having between 25 and 40%, where higher abundance is characteristic to proteomes that have larger proteins. Our first-of-its-kind large-scale functional analysis shows that these proteins are enriched in a number of cellular functions and processes including certain binding events, regulation of catalytic activities, cellular component organization, biogenesis, biological regulation, and some metabolic and developmental processes. A webserver that implements SLIDER is available at http://biomine.ece.ualberta.ca/SLIDER/.

  2. Insights into the Immunological Properties of Intrinsically Disordered Malaria Proteins Using Proteome Scale Predictions.

    Directory of Open Access Journals (Sweden)

    Andrew J Guy

    Full Text Available Malaria remains a significant global health burden. The development of an effective malaria vaccine remains as a major challenge with the potential to significantly reduce morbidity and mortality. While Plasmodium spp. have been shown to contain a large number of intrinsically disordered proteins (IDPs or disordered protein regions, the relationship of protein structure to subcellular localisation and adaptive immune responses remains unclear. In this study, we employed several computational prediction algorithms to identify IDPs at the proteome level of six Plasmodium spp. and to investigate the potential impact of protein disorder on adaptive immunity against P. falciparum parasites. IDPs were shown to be particularly enriched within nuclear proteins, apical proteins, exported proteins and proteins localised to the parasitophorous vacuole. Furthermore, several leading vaccine candidates, and proteins with known roles in host-cell invasion, have extensive regions of disorder. Presentation of peptides by MHC molecules plays an important role in adaptive immune responses, and we show that IDP regions are predicted to contain relatively few MHC class I and II binding peptides owing to inherent differences in amino acid composition compared to structured domains. In contrast, linear B-cell epitopes were predicted to be enriched in IDPs. Tandem repeat regions and non-synonymous single nucleotide polymorphisms were found to be strongly associated with regions of disorder. In summary, immune responses against IDPs appear to have characteristics distinct from those against structured protein domains, with increased antibody recognition of linear epitopes but some constraints for MHC presentation and issues of polymorphisms. These findings have major implications for vaccine design, and understanding immunity to malaria.

  3. Origins of Myc proteins--using intrinsic protein disorder to trace distant relatives.

    Directory of Open Access Journals (Sweden)

    Amir Mahani

    , that have high levels of intrinsic disorder.

  4. Conformational dissection of a viral intrinsically disordered domain involved in cellular transformation.

    Directory of Open Access Journals (Sweden)

    María G Noval

    Full Text Available Intrinsic disorder is abundant in viral genomes and provides conformational plasticity to its protein products. In order to gain insight into its structure-function relationships, we carried out a comprehensive analysis of structural propensities within the intrinsically disordered N-terminal domain from the human papillomavirus type-16 E7 oncoprotein (E7N. Two E7N segments located within the conserved CR1 and CR2 regions present transient α-helix structure. The helix in the CR1 region spans residues L8 to L13 and overlaps with the E2F mimic linear motif. The second helix, located within the highly acidic CR2 region, presents a pH-dependent structural transition. At neutral pH the helix spans residues P17 to N29, which include the retinoblastoma tumor suppressor LxCxE binding motif (residues 21-29, while the acidic CKII-PEST region spanning residues E33 to I38 populates polyproline type II (PII structure. At pH 5.0, the CR2 helix propagates up to residue I38 at the expense of loss of PII due to charge neutralization of acidic residues. Using truncated forms of HPV-16 E7, we confirmed that pH-induced changes in α-helix content are governed by the intrinsically disordered E7N domain. Interestingly, while at both pH the region encompassing the LxCxE motif adopts α-helical structure, the isolated 21-29 fragment including this stretch is unable to populate an α-helix even at high TFE concentrations. Thus, the E7N domain can populate dynamic but discrete structural ensembles by sampling α-helix-coil-PII-ß-sheet structures. This high plasticity may modulate the exposure of linear binding motifs responsible for its multi-target binding properties, leading to interference with key cell signaling pathways and eventually to cellular transformation by the virus.

  5. High-throughput prediction of RNA, DNA and protein binding regions mediated by intrinsic disorder.

    Science.gov (United States)

    Peng, Zhenling; Kurgan, Lukasz

    2015-10-15

    Intrinsically disordered proteins and regions (IDPs and IDRs) lack stable 3D structure under physiological conditions in-vitro, are common in eukaryotes, and facilitate interactions with RNA, DNA and proteins. Current methods for prediction of IDPs and IDRs do not provide insights into their functions, except for a handful of methods that address predictions of protein-binding regions. We report first-of-its-kind computational method DisoRDPbind for high-throughput prediction of RNA, DNA and protein binding residues located in IDRs from protein sequences. DisoRDPbind is implemented using a runtime-efficient multi-layered design that utilizes information extracted from physiochemical properties of amino acids, sequence complexity, putative secondary structure and disorder and sequence alignment. Empirical tests demonstrate that it provides accurate predictions that are competitive with other predictors of disorder-mediated protein binding regions and complementary to the methods that predict RNA- and DNA-binding residues annotated based on crystal structures. Application in Homo sapiens, Mus musculus, Caenorhabditis elegans and Drosophila melanogaster proteomes reveals that RNA- and DNA-binding proteins predicted by DisoRDPbind complement and overlap with the corresponding known binding proteins collected from several sources. Also, the number of the putative protein-binding regions predicted with DisoRDPbind correlates with the promiscuity of proteins in the corresponding protein-protein interaction networks. Webserver: http://biomine.ece.ualberta.ca/DisoRDPbind/.

  6. 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

  7. 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.

  8. Intrinsic Affective Network Is Impaired in Children with Attention-Deficit/Hyperactivity Disorder.

    Science.gov (United States)

    Ho, New-Fei; Chong, Joanna S X; Koh, Hui Li; Koukouna, Eleni; Lee, Tih-Shih; Fung, Daniel; Lim, Choon Guan; Zhou, Juan

    2015-01-01

    Deficits in impulsivity and affect dysregulation are key features of attention-deficit/hyperactivity disorder (ADHD) besides impairing levels of hyperactivity and/or inattention. However, the neural substrates underlying these traits are relatively under-investigated. In this study, we use resting-state functional magnetic resonance imaging to test the hypothesis of diminished functional integration within the affective/limbic network (which includes the amygdala, hippocampus, subgenual cingulate cortex, orbitofrontal cortex and nucleus accumbens) of children with ADHD, which is associated with their behavioral measures of emotional control deficits. Resting state-fMRI data were obtained from 12 healthy control subjects and 15 children with ADHD, all who had a minimum one-month washout period for medications and supplements. Children with ADHD demonstrated less integrated affective network, evidenced by increased bilateral amygdalar and decreased left orbitofrontal connectivity within the affective network compared to healthy controls. The hyper-connectivity at the left amygdalar within the affective network was associated with increased aggressiveness and conduct problems, as well as decline in functioning in children with ADHD. Similar findings in affective network dysconnectivity were replicated in a subset of children with ADHD three months later. Our findings of divergent changes in amygdala and orbitofrontal intrinsic connectivity support the hypothesis of an impaired functional integration within the affective network in childhood ADHD. Larger prospective studies of the intrinsic affective network in ADHD are required, which may provide further insight on the biological mechanisms of emotional control deficits observed in ADHD. PMID:26406311

  9. Intrinsic Affective Network Is Impaired in Children with Attention-Deficit/Hyperactivity Disorder.

    Directory of Open Access Journals (Sweden)

    New-Fei Ho

    Full Text Available Deficits in impulsivity and affect dysregulation are key features of attention-deficit/hyperactivity disorder (ADHD besides impairing levels of hyperactivity and/or inattention. However, the neural substrates underlying these traits are relatively under-investigated. In this study, we use resting-state functional magnetic resonance imaging to test the hypothesis of diminished functional integration within the affective/limbic network (which includes the amygdala, hippocampus, subgenual cingulate cortex, orbitofrontal cortex and nucleus accumbens of children with ADHD, which is associated with their behavioral measures of emotional control deficits. Resting state-fMRI data were obtained from 12 healthy control subjects and 15 children with ADHD, all who had a minimum one-month washout period for medications and supplements. Children with ADHD demonstrated less integrated affective network, evidenced by increased bilateral amygdalar and decreased left orbitofrontal connectivity within the affective network compared to healthy controls. The hyper-connectivity at the left amygdalar within the affective network was associated with increased aggressiveness and conduct problems, as well as decline in functioning in children with ADHD. Similar findings in affective network dysconnectivity were replicated in a subset of children with ADHD three months later. Our findings of divergent changes in amygdala and orbitofrontal intrinsic connectivity support the hypothesis of an impaired functional integration within the affective network in childhood ADHD. Larger prospective studies of the intrinsic affective network in ADHD are required, which may provide further insight on the biological mechanisms of emotional control deficits observed in ADHD.

  10. 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.

  11. Study conformational dynamics of intrinsically disordered protein by PET-FCS (Conference Presentation)

    Science.gov (United States)

    Enderlein, Joerg; Zhou, Man; Van, Qui; Gregor, Ingo

    2016-02-01

    Intrinsically disordered proteins (IDP) form a large and functionally important class of proteins that lack an ordered three-dimensional structure. IDPs play an important role in cell signaling, transcription, or chromatin remodeling. The discovery of IDPs has challenged the traditional paradigm of protein structure which states that protein function depends on a well-defined three-dimensional structure. Due to their high conformational flexibility and the lack of ordered secondary structure, it is challenging to study the flexible structure, dynamics and energetics of these proteins with conventional methods. In our work, we employ photoinduced electron transfer (PET) combined with fluorescence correlation spectroscopy (FCS) for studying the conformational dynamics of one specific class of IDPs: phenylalanine-glycine rich protein domains (FG repeats) which are dominant building blocks within the pore of nuclear pore complexes. Nuclear pore complexes are large protein assemblies that cross the nuclear envelope and form selective barrier, which regulate bidirectional exchange between nucleus and cytoplasm.

  12. The intrinsically disordered RNR inhibitor Sml1 is a dynamic dimer

    DEFF Research Database (Denmark)

    Danielsson, Jens; Liljedahl, Leena; Ba´ra´ny-Wallje, Elsa;

    2008-01-01

    . Sml1 belongs to the class of intrinsically disordered proteins with a high degree of dynamics and very little stable structure. Earlier suggestions for a dimeric structure of Sml1 were confirmed, and from translation diffusion NMR measurements, a dimerization dissociation constant of 0.1 mM at 4...... degrees C could be determined. The hydrodynamic radius for the monomeric form of Sml1 was determined to be 23.4 A, corresponding to a protein size between those of a globular protein and a coil. Formation of a dimer results in a hydrodynamic radius of 34.4 A. The observed chemical shifts showed...... folds onto the C-terminal domain. Importantly, protease degradation studies combined with mass spectrometry indicated that the N-terminal domain is degraded before the C-terminal region and thus may serve as a protection against proteolysis of the functionally important C-terminal region. Dimer...

  13. 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

  14. In-cell NMR of intrinsically disordered proteins in prokaryotic cells.

    Science.gov (United States)

    Ito, Yutaka; Mikawa, Tsutomu; Smith, Brian O

    2012-01-01

    In-cell NMR, i.e., the acquisition of heteronuclear multidimensional NMR of biomacromolecules inside living cells, is, to our knowledge, the only method for investigating the three-dimensional structure and dynamics of proteins at atomic detail in the intracellular environment. Since the inception of the method, intrinsically disordered proteins have been regarded as particular targets for in-cell NMR, due to their expected sensitivity to the molecular crowding in the intracellular environment. While both prokaryotic and eukaryotic cells can be used as host cells for in-cell NMR, prokaryotic in-cell NMR, particularly employing commonly used protein overexpression systems in Escherichia coli cells, is the most accessible approach. In this chapter we describe general procedures for obtaining in-cell NMR spectra in E. coli cells.

  15. 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.

  16. 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.

  17. 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,...

  18. pE-DB: a database of structural ensembles of intrinsically disordered and of unfolded proteins

    Science.gov (United States)

    Varadi, Mihaly; Kosol, Simone; Lebrun, Pierre; Valentini, Erica; Blackledge, Martin; Dunker, A. Keith; Felli, Isabella C.; Forman-Kay, Julie D.; Kriwacki, Richard W.; Pierattelli, Roberta; Sussman, Joel; Svergun, Dmitri I.; Uversky, Vladimir N.; Vendruscolo, Michele; Wishart, David; Wright, Peter E.; Tompa, Peter

    2014-01-01

    The goal of pE-DB (http://pedb.vib.be) is to serve as an openly accessible database for the deposition of structural ensembles of intrinsically disordered proteins (IDPs) and of denatured proteins based on nuclear magnetic resonance spectroscopy, small-angle X-ray scattering and other data measured in solution. Owing to the inherent flexibility of IDPs, solution techniques are particularly appropriate for characterizing their biophysical properties, and structural ensembles in agreement with these data provide a convenient tool for describing the underlying conformational sampling. Database entries consist of (i) primary experimental data with descriptions of the acquisition methods and algorithms used for the ensemble calculations, and (ii) the structural ensembles consistent with these data, provided as a set of models in a Protein Data Bank format. PE-DB is open for submissions from the community, and is intended as a forum for disseminating the structural ensembles and the methodologies used to generate them. While the need to represent the IDP structures is clear, methods for determining and evaluating the structural ensembles are still evolving. The availability of the pE-DB database is expected to promote the development of new modeling methods and leads to a better understanding of how function arises from disordered states. PMID:24174539

  19. 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

  20. 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.

  1. 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

    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 amy...

  2. 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

  3. 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

  4. 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.

  5. 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

  6. 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

  7. 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.

  8. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  10. "CON-CON" assignment strategy for highly flexible intrinsically disordered proteins.

    Science.gov (United States)

    Piai, Alessandro; Hošek, Tomáš; Gonnelli, Leonardo; Zawadzka-Kazimierczuk, Anna; Koźmiński, Wiktor; Brutscher, Bernhard; Bermel, Wolfgang; Pierattelli, Roberta; Felli, Isabella C

    2014-12-01

    Intrinsically disordered proteins (IDPs) are a class of highly flexible proteins whose characterization by NMR spectroscopy is complicated by severe spectral overlaps. The development of experiments designed to facilitate the sequence-specific assignment procedure is thus very important to improve the tools for the characterization of IDPs and thus to be able to focus on IDPs of increasing size and complexity. Here, we present and describe the implementation of a set of novel ¹H-detected 5D experiments, (HACA)CON(CACO)NCO(CA)HA, BT-(H)NCO(CAN)CONNH and BT-HN(COCAN)CONNH, optimized for the study of highly flexible IDPs that exploit the best resolved correlations, those involving the carbonyl and nitrogen nuclei of neighboring amino acids, to achieve sequence-specific resonance assignment. Together with the analogous recently proposed pulse schemes based on ¹³C detection, they form a complete set of experiments for sequence-specific assignment of highly flexible IDPs. Depending on the particular sample conditions (concentration, lifetime, pH, temperature, etc.), these experiments present certain advantages and disadvantages that will be discussed. Needless to say, that the availability of a variety of complementary experiments will be important for accurate determination of resonance frequencies in complex IDPs.

  11. 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

  12. 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

  13. An Intrinsically Disordered Motif Mediates Diverse Actions of Monomeric C-reactive Protein.

    Science.gov (United States)

    Li, Hai-Yun; Wang, Jing; Meng, Fan; Jia, Zhe-Kun; Su, Yang; Bai, Qi-Feng; Lv, Ling-Ling; Ma, Fu-Rong; Potempa, Lawrence A; Yan, Yong-Bin; Ji, Shang-Rong; Wu, Yi

    2016-04-15

    Most proinflammatory actions of C-reactive protein (CRP) are only expressed following dissociation of its native pentameric assembly into monomeric form (mCRP). However, little is known about what underlies the greatly enhanced activities of mCRP. Here we show that a single sequence motif, i.e. cholesterol binding sequence (CBS; a.a. 35-47), is responsible for mediating the interactions of mCRP with diverse ligands. The binding of mCRP to lipoprotein component ApoB, to complement component C1q, to extracellular matrix components fibronectin and collagen, to blood coagulation component fibrinogen, and to membrane lipid component cholesterol, are all found to be markedly inhibited by the synthetic CBS peptide but not by other CRP sequences tested. Likewise, mutating CBS in mCRP also greatly impairs these interactions. Functional experiments further reveal that CBS peptide significantly reduces the effects of mCRP on activation of endothelial cells in vitro and on acute induction of IL-6 in mice. The potency and specificity of CBS are critically determined by the N-terminal residues Cys-36, Leu-37, and His-38; while the versatility of CBS appears to originate from its intrinsically disordered conformation polymorphism. Together, these data unexpectedly identify CBS as the major recognition site of mCRP and suggest that this motif may be exploited to tune the proinflammatory actions of mCRP.

  14. 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.

  15. 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".

  16. 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.

  17. 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)

  18. 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.

  19. 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

  20. The large intracellular loop of hZIP4 is an intrinsically disordered zinc binding domain†

    Science.gov (United States)

    Bafaro, Elizabeth M.; Antala, Sagar; Nguyen, Tuong-Vi; Dzul, Stephen P.; Doyon, Brian; Stemmler, Timothy L.; Dempski, Robert E.

    2015-01-01

    The human (h) ZIP4 transporter is a plasma membrane protein which functions to increase the cytosolic concentration of zinc. hZIP4 transports zinc into intestinal cells and therefore has a central role in the absorption of dietary zinc. hZIP4 has eight transmembrane domains and encodes a large intracellular loop between transmembrane domains III and IV, M3M4. Previously, it has been postulated that this domain regulates hZIP4 levels in the plasma membrane in a zinc-dependent manner. The objective of this research was to examine the zinc binding properties of the large intracellular loop of hZIP4. Therefore, we have recombineantly expressed and purified M3M4 and showed that this domain binds two zinc ions. Using a combination of site-directed mutagenesis, metal binding affinity assays, and X-ray absorption spectroscopy, we demonstrated that the two Zn2+ ions bind sequentially, with the first Zn2+ binding to a CysHis3 site with a nanomolar binding affinity, and the second Zn2+ binding to a His4 site with a weaker affinity. Circular dichroism spectroscopy revealed that the M3M4 domain is intrinsically disordered, with only a small structural change induced upon Zn2+ coordination. Our data supports a model in which the intracellular M3M4 domain senses high cytosolic Zn2+ concentrations and regulates the plasma membrane levels of the hZIP4 transporter in response to Zn2+ binding. PMID:25882556

  1. 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

  2. Robust Chaos

    CERN Document Server

    Banerjee, S; Grebogi, C; Banerjee, Soumitro; Yorke, James A.; Grebogi, Celso

    1998-01-01

    It has been proposed to make practical use of chaos in communication, in enhancing mixing in chemical processes and in spreading the spectrum of switch-mode power suppies to avoid electromagnetic interference. It is however known that for most smooth chaotic systems, there is a dense set of periodic windows for any range of parameter values. Therefore in practical systems working in chaotic mode, slight inadvertent fluctuation of a parameter may take the system out of chaos. We say a chaotic attractor is robust if, for its parameter values there exists a neighborhood in the parameter space with no periodic attractor and the chaotic attractor is unique in that neighborhood. In this paper we show that robust chaos can occur in piecewise smooth systems and obtain the conditions of its occurrence. We illustrate this phenomenon with a practical example from electrical engineering.

  3. 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

  4. 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...... 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....

  5. Discrete Chaos

    CERN Document Server

    Waelbroeck, H

    1999-01-01

    We propose a theory of deterministic chaos for discrete systems, based on their representations in symbolic history spaces Ømega. These are spaces of semi-infinite sequences, as the one-sided shift spaces, but endowed with a more general topology which we call a semicausal topology. We show that define metrical properties, including the correlation dimension of the attractor. Examples are considered: Asymmetric neural networks and random cellular automata are not chaotic. A neural network model with memory, on the other hand, does appear to be an example of discrete chaos.

  6. gH625 is a viral derived peptide for effective delivery of intrinsically disordered proteins

    Directory of Open Access Journals (Sweden)

    Smaldone G

    2013-07-01

    Full Text Available Giovanni Smaldone,1,2 Annarita Falanga,3 Domenica Capasso,4 Daniela Guarnieri,5,6 Stefania Correale,1,7 Massimiliano Galdiero,8 Paolo A Netti,4 Massimo Zollo,9 Stefania Galdiero,1,2 Sonia Di Gaetano,1 Emilia Pedone1 1Institute of Biostructures and Bioimaging, National Research Council, Naples, Italy; 2Department of Pharmacy and Interuniversity Research Center on Bioactive Peptides, Federico II University of Naples, Naples, Italy; 3Molecular Diagnostics and Pharmaceuticals Scarl, Naples, Italy; 4Special Center for Biotechnology, Federico II University of Naples, Naples, Italy; 5Center for Advanced Biomaterials for Health Care, Interdisciplinary Research Centre on Biomaterials, Italian Institute of Technology, Naples, Italy; 6Interdisciplinary Research Centre on Biomaterials, Federico II University of Naples, Naples, Italy; 7Kedrion S.p.A, Sant'antimo, Naples, Italy; 8Department of Experimental Medicine, Federico II University of Naples, Naples, Italy; 9CEINGE – Advanced Biotechnology Scarl, Naples, Italy Abstract: A genetically modified recombinant gH625-c-prune was prepared through conjugation of c-prune with gH625, a peptide encompassing 625–644 residues of the glycoprotein H of herpes simplex virus 1, which has been proved to possess the ability to carry cargo molecules across cell membranes. C-prune is the C-terminal domain of h-prune, overexpressed in breast, colorectal, and gastric cancers, interacting with multiple partners, and representing an ideal target for inhibition of cancer development. Its C-terminal domain results in an intrinsically disordered domain (IDD, and the peculiar properties of gH625 render it an optimal candidate to act as a carrier for this net negatively charged molecule by comparison with the positively charged TAT. A characterization of the recombinant gH625-c-prune fusion protein was conducted by biochemical, cellular biology and confocal microscopy means in comparison with TAT-c-prune. The results showed that

  7. 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

  8. Wiener Chaos

    CERN Document Server

    Peccati, Giovanni

    2011-01-01

    The concept of Wiener chaos generalizes to an infinite-dimensional setting the properties of orthogonal polynomials associated with probability distributions on the real line. It plays a crucial role in modern probability theory, with applications ranging from Malliavin calculus to stochastic differential equations and from probabilistic approximations to mathematical finance. This book is concerned with combinatorial structures arising from the study of chaotic random variables related to infinitely divisible random measures. The combinatorial structures involved are those of partitions of fi

  9. 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

  10. 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.

  11. 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

  12. 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…

  13. Evolutionarily conserved and conformationally constrained short peptides might serve as DNA recognition elements in intrinsically disordered regions.

    Science.gov (United States)

    Tayal, Nitish; Choudhary, Preeti; Pandit, Shashi B; Sandhu, Kuljeet Singh

    2014-06-01

    Despite recent advances, it is yet not clear how intrinsically disordered regions in proteins recognize their targets without any defined structures. Short linear motifs had been proposed to mediate molecular recognition by disordered regions; however, the underlying structural prerequisite remains elusive. Moreover, the role of short linear motifs in DNA recognition has not been studied. We report a repertoire of short evolutionarily Conserved Recognition Elements (CoREs) in long intrinsically disordered regions, which have very distinct amino-acid propensities from those of known motifs, and exhibit a strong tendency to retain their three-dimensional conformations compared to adjacent regions. The majority of CoREs directly interact with the DNA in the available 3D structures, which is further supported by literature evidence, analyses of ΔΔG values of DNA-binding energies and threading-based prediction of DNA binding potential. CoREs were enriched in cancer-associated missense mutations, further strengthening their functional nature. Significant enrichment of glycines in CoREs and the preference of glycyl ϕ-Ψ values within the left-handed bridge range in the l-disallowed region of the Ramachandran plot suggest that Gly-to-nonGly mutations within CoREs might alter the backbone conformation and consequently the function, a hypothesis that we reconciled using available mutation data. We conclude that CoREs might serve as bait for DNA recognition by long disordered regions and that certain mutations in these peptides can disrupt their DNA binding potential and consequently the protein function. We further hypothesize that the preferred conformations of CoREs and of glycyl residues therein might play an important role in DNA binding. The highly ordered nature of CoREs hints at a therapeutic strategy to inhibit malicious molecular interactions using small molecules mimicking CoRE conformations.

  14. Computational Prediction of O-linked Glycosylation Sites that Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins

    Directory of Open Access Journals (Sweden)

    Satoshi Fukuchi

    2010-12-01

    Full Text Available O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability.

  15. The Relationships Among MicroRNA Regulation, Intrinsically Disordered Regions, and Other Indicators of Protein Evolutionary Rate

    Science.gov (United States)

    Chen, Sean Chun-Chang; Chuang, Trees-Juen; Li, Wen-Hsiung

    2011-01-01

    Many indicators of protein evolutionary rate have been proposed, but some of them are interrelated. The purpose of this study is to disentangle their correlations. We assess the strength of each indicator by controlling for the other indicators under study. We find that the number of microRNA (miRNA) types that regulate a gene is the strongest rate indicator (a negative correlation), followed by disorder content (the percentage of disordered regions in a protein, a positive correlation); the strength of disorder content as a rate indicator is substantially increased after controlling for the number of miRNA types. By dividing proteins into lowly and highly intrinsically disordered proteins (L-IDPs and H-IDPs), we find that proteins interacting with more H-IDPs tend to evolve more slowly, which largely explains the previous observation of a negative correlation between the number of protein–protein interactions and evolutionary rate. Moreover, all of the indicators examined here, except for the number of miRNA types, have different strengths in L-IDPs and in H-IDPs. Finally, the number of phosphorylation sites is weakly correlated with the number of miRNA types, and its strength as a rate indicator is substantially reduced when other indicators are considered. Our study reveals the relative strength of each rate indicator and increases our understanding of protein evolution. PMID:21398349

  16. 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

    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...

  17. Intrinsic Affective Network Is Impaired in Children with Attention-Deficit/Hyperactivity Disorder

    OpenAIRE

    New-Fei Ho; Joanna S X Chong; Hui Li Koh; Eleni Koukouna; Tih-Shih Lee; Daniel Fung; Choon Guan Lim; Juan Zhou

    2015-01-01

    Deficits in impulsivity and affect dysregulation are key features of attention-deficit/hyperactivity disorder (ADHD) besides impairing levels of hyperactivity and/or inattention. However, the neural substrates underlying these traits are relatively under-investigated. In this study, we use resting-state functional magnetic resonance imaging to test the hypothesis of diminished functional integration within the affective/limbic network (which includes the amygdala, hippocampus, subgenual cingu...

  18. 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...... because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large...

  19. 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.

  20. Intrinsic disorder as a generalizable strategy for the rational design of highly responsive, allosterically cooperative receptors

    Science.gov (United States)

    Simon, Anna J.; Vallée-Bélisle, Alexis; Ricci, Francesco; Plaxco, Kevin W.

    2014-01-01

    Control over the sensitivity with which biomolecular receptors respond to small changes in the concentration of their target ligand is critical for the proper function of many cellular processes. Such control could likewise be of utility in artificial biotechnologies, such as biosensors, genetic logic gates, and “smart” materials, in which highly responsive behavior is of value. In nature, the control of molecular responsiveness is often achieved using “Hill-type” cooperativity, a mechanism in which sequential binding events on a multivalent receptor are coupled such that the first enhances the affinity of the next, producing a steep, higher-order dependence on target concentration. Here, we use an intrinsic-disorder–based mechanism that can be implemented without requiring detailed structural knowledge to rationally introduce this potentially useful property into several normally noncooperative biomolecules. To do so, we fabricate a tandem repeat of the receptor that is destabilized (unfolded) via the introduction of a long, unstructured loop. The first binding event requires the energetically unfavorable closing of this loop, reducing its affinity relative to that of the second binding event, which, in contrast occurs at a preformed site. Using this approach, we have rationally introduced cooperativity into three unrelated DNA aptamers, achieving in the best of these a Hill coefficient experimentally indistinguishable from the theoretically expected maximum. The extent of cooperativity and thus the steepness of the binding transition are, moreover, well modeled as simple functions of the energetic cost of binding-induced folding, speaking to the quantitative nature of this design strategy. PMID:25288724

  1. Intrinsic order and disorder in the bcl-2 member harakiri: insights into its proapoptotic activity.

    Directory of Open Access Journals (Sweden)

    Susana Barrera-Vilarmau

    Full Text Available Harakiri is a BH3-only member of the Bcl-2 family that localizes in membranes and induces cell death by binding to prosurvival Bcl-x(L and Bcl-2. The cytosolic domain of Harakiri is largely disorder with residual α-helical conformation according to previous structural studies. As these helical structures could play an important role in Harakiri's function, we have used NMR and circular dichroism to fully characterize them at the residue-atomic level. In addition, we report structural studies on a peptide fragment spanning Harakiri's C-terminal hydrophobic sequence, which potentially operates as a transmembrane domain. We initially checked by enzyme immunoassays and NMR that peptides encompassing different lengths of the cytosolic domain are functional as they bind Bcl-x(L and Bcl-2. The structural data in water indicate that the α-helical conformation is restricted to a 25-residue segment comprising the BH3 domain. However, structure calculation was precluded because of insufficient NMR restraints. To bypass this problem we used alcohol-water mixture to increase structure population and confirmed by NMR that the conformation in both milieus is equivalent. The resulting three-dimensional structure closely resembles that of peptides encompassing the BH3 domain of BH3-only members in complex with their prosurvival partners, suggesting that preformed structural elements in the disordered protein are central to binding. In contrast, the transmembrane domain forms in micelles a monomeric α-helix with a population close to 100%. Its three-dimensional structure here reported reveals features that explain its function as membrane anchor. Altogether these results are used to propose a tentative structural model of how Harakiri works.

  2. 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…

  3. Some chaotic features of intrinsically coupled Josephson junctions

    Energy Technology Data Exchange (ETDEWEB)

    Kolahchi, M.R., E-mail: kolahchi@iasbs.ac.ir [Institute for Advanced Studies in Basic Sciences, Zanjan 45195-1159 (Iran, Islamic Republic of); Shukrinov, Yu.M. [BLTP, JINR, Dubna, Moscow Region 141980 (Russian Federation); Max-Planck-Institute for the Physics of Complex Systems, 01187 Dresden (Germany); Hamdipour, M. [Institute for Advanced Studies in Basic Sciences, Zanjan 45195-1159 (Iran, Islamic Republic of); BLTP, JINR, Dubna, Moscow Region 141980 (Russian Federation); Botha, A.E. [Department of Physics, University of South Africa, P.O. Box 392, Pretoria 0003 (South Africa); Suzuki, M. [Photonics and Electronics Science and Engineering Center and Department of Electronic Science and Engineering, Kyoto University, Kyoto 615-8510 (Japan)

    2013-08-15

    Highlights: ► Intrinsically coupled Josephson junctions model a high-T{sub c} superconductor. ► Intrinsically coupled Josephson junctions can act as a chaotic nonlinear system. ► Chaos could be due to resonance overlap. ► Avoiding parameters that lead to chaos is important for the design of resonators. -- Abstract: We look for chaos in an intrinsically coupled system of Josephson junctions. This study has direct applications for the high-T{sub c} resonators which require coherence amongst the junctions.

  4. Effects of Linker Length and Transient Secondary Structure Elements in the Intrinsically Disordered Notch RAM Region on Notch Signaling.

    Science.gov (United States)

    Sherry, Kathryn P; Johnson, Scott E; Hatem, Christine L; Majumdar, Ananya; Barrick, Doug

    2015-11-01

    Formation of the bivalent interaction between the Notch intracellular domain (NICD) and the transcription factor CBF-1/RBP-j, Su(H), Lag-1 (CSL) is a key event in Notch signaling because it switches Notch-responsive genes from a repressed state to an activated state. Interaction of the intrinsically disordered RBP-j-associated molecule (RAM) region of NICD with CSL is thought to both disrupt binding of corepressor proteins to CSL and anchor NICD to CSL, promoting interaction of the ankyrin domain of NICD with CSL through an effective concentration mechanism. To quantify the role of disorder in the RAM linker region on the effective concentration enhancement of Notch transcriptional activation, we measured the effects of linker length variation on activation. The resulting activation profile has general features of a worm-like chain model for effective concentration. However, deviations from the model for short sequence deletions suggest that RAM contains sequence-specific structural elements that may be important for activation. Structural characterization of the RAM linker with sedimentation velocity analytical ultracentrifugation and NMR spectroscopy reveals that the linker is compact and contains three transient helices and two extended and dynamic regions. To test if these secondary structure elements are important for activation, we made sequence substitutions to change the secondary structure propensities of these elements and measured transcriptional activation of the resulting variants. Substitutions to two of these nonrandom elements (helix 2, extended region 1) have effects on activation, but these effects do not depend on the nature of the substituting residues. Thus, the primary sequences of these elements, but not their secondary structures, are influencing signaling.

  5. The effects of cognitive-behavioral therapy on intrinsic functional brain networks in adults with attention-deficit/hyperactivity disorder.

    Science.gov (United States)

    Wang, Xiaoli; Cao, Qingjiu; Wang, Jinhui; Wu, Zhaomin; Wang, Peng; Sun, Li; Cai, Taisheng; Wang, Yufeng

    2016-01-01

    Cognitive-behavioral therapy (CBT) is an efficacious psychological treatment for adults with attention-deficit/hyperactivity disorder (ADHD), but the neural processes underlying the benefits of CBT are not well understood. This study aims to unravel psychosocial mechanisms for treatment ADHD by exploring the effects of CBT on functional brain networks. Ten adults with ADHD were enrolled and resting-state functional magnetic resonance imaging scans were acquired before and after a 12-session CBT. Twelve age- and gender-matched healthy controls were also scanned. We constructed whole-brain functional connectivity networks using graph-theory approaches and further computed the changes of regional functional connectivity strength (rFCS) between pre- and post-CBT in ADHD for measuring the effects of CBT. The results showed that rFCS was increased in the fronto-parietal network and cerebellum, the brain regions that were most often affected by medication, in adults with ADHD following CBT. Furthermore, the enhanced functional coupling between bilateral superior parietal gyrus was positively correlated with the improvement of ADHD symptoms following CBT. Together, these findings provide evidence that CBT can selectively modulate the intrinsic network connectivity in the fronto-parietal network and cerebellum and suggest that the CBT may share common brain mechanism with the pharmacology in adults with ADHD.

  6. 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.

  7. 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

  8. 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

  9. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

    Shukrinov, Yu.M. [BLTP, JINR, Dubna, Moscow Region, 141980 (Russian Federation); Hamdipour, M. [BLTP, JINR, Dubna, Moscow Region, 141980 (Russian Federation); Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan (Iran, Islamic Republic of); Kolahchi, M.R. [Institute for Advanced Studies in Basic Sciences, P.O. Box 45195-1159, Zanjan (Iran, Islamic Republic of); Botha, A.E., E-mail: bothaae@unisa.ac.za [Department of Physics, University of South Africa, P.O. Box 392, Pretoria 0003 (South Africa); Suzuki, M. [Photonics and Electronics Science and Engineering Center and Department of Electronic Science and Engineering, Kyoto University, Kyoto 615-8510 (Japan)

    2012-11-01

    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.

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

    Science.gov (United States)

    Shukrinov, Yu. M.; Hamdipour, M.; Kolahchi, M. R.; Botha, A. E.; Suzuki, M.

    2012-11-01

    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.

  12. Dynamical Coupling of Intrinsically Disordered Proteins and Their Hydration Water: Comparison with Folded Soluble and Membrane Proteins

    Science.gov (United States)

    Gallat, F.-X.; Laganowsky, A.; Wood, K.; Gabel, F.; van Eijck, L.; Wuttke, J.; Moulin, M.; Härtlein, M.; Eisenberg, D.; Colletier, J.-P.; Zaccai, G.; Weik, M.

    2012-01-01

    Hydration water is vital for various macromolecular biological activities, such as specific ligand recognition, enzyme activity, response to receptor binding, and energy transduction. Without hydration water, proteins would not fold correctly and would lack the conformational flexibility that animates their three-dimensional structures. Motions in globular, soluble proteins are thought to be governed to a certain extent by hydration-water dynamics, yet it is not known whether this relationship holds true for other protein classes in general and whether, in turn, the structural nature of a protein also influences water motions. Here, we provide insight into the coupling between hydration-water dynamics and atomic motions in intrinsically disordered proteins (IDP), a largely unexplored class of proteins that, in contrast to folded proteins, lack a well-defined three-dimensional structure. We investigated the human IDP tau, which is involved in the pathogenic processes accompanying Alzheimer disease. Combining neutron scattering and protein perdeuteration, we found similar atomic mean-square displacements over a large temperature range for the tau protein and its hydration water, indicating intimate coupling between them. This is in contrast to the behavior of folded proteins of similar molecular weight, such as the globular, soluble maltose-binding protein and the membrane protein bacteriorhodopsin, which display moderate to weak coupling, respectively. The extracted mean square displacements also reveal a greater motional flexibility of IDP compared with globular, folded proteins and more restricted water motions on the IDP surface. The results provide evidence that protein and hydration-water motions mutually affect and shape each other, and that there is a gradient of coupling across different protein classes that may play a functional role in macromolecular activity in a cellular context. PMID:22828339

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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....

  18. Role of Intrinsic Protein Disorder in the Function and Interactions of the Transcriptional Coactivators CREB-binding Protein (CBP) and p300.

    Science.gov (United States)

    Dyson, H Jane; Wright, Peter E

    2016-03-25

    The transcriptional coactivators CREB-binding protein (CBP) and p300 undergo a particularly rich set of interactions with disordered and partly ordered partners, as a part of their ubiquitous role in facilitating transcription of genes. CBP and p300 contain a number of small structured domains that provide scaffolds for the interaction of disordered transactivation domains from a wide variety of partners, including p53, hypoxia-inducible factor 1α (HIF-1α), NF-κB, and STAT proteins, and are the targets for the interactions of disordered viral proteins that compete with cellular factors to disrupt signaling and subvert the cell cycle. The functional diversity of the CBP/p300 interactome provides an excellent example of the power of intrinsic disorder to facilitate the complexity of living systems.

  19. 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.

  20. Harnessing quantum transport by transient chaos.

    Science.gov (United States)

    Yang, Rui; Huang, Liang; Lai, Ying-Cheng; Grebogi, Celso; Pecora, Louis M

    2013-03-01

    Chaos has long been recognized to be generally advantageous from the perspective of control. In particular, the infinite number of unstable periodic orbits embedded in a chaotic set and the intrinsically sensitive dependence on initial conditions imply that a chaotic system can be controlled to a desirable state by using small perturbations. Investigation of chaos control, however, was largely limited to nonlinear dynamical systems in the classical realm. In this paper, we show that chaos may be used to modulate or harness quantum mechanical systems. To be concrete, we focus on quantum transport through nanostructures, a problem of considerable interest in nanoscience, where a key feature is conductance fluctuations. We articulate and demonstrate that chaos, more specifically transient chaos, can be effective in modulating the conductance-fluctuation patterns. Experimentally, this can be achieved by applying an external gate voltage in a device of suitable geometry to generate classically inaccessible potential barriers. Adjusting the gate voltage allows the characteristics of the dynamical invariant set responsible for transient chaos to be varied in a desirable manner which, in turn, can induce continuous changes in the statistical characteristics of the quantum conductance-fluctuation pattern. To understand the physical mechanism of our scheme, we develop a theory based on analyzing the spectrum of the generalized non-Hermitian Hamiltonian that includes the effect of leads, or electronic waveguides, as self-energy terms. As the escape rate of the underlying non-attracting chaotic set is increased, the imaginary part of the complex eigenenergy becomes increasingly large so that pointer states are more difficult to form, making smoother the conductance-fluctuation pattern.

  1. 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

  2. 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.

  3. 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

  4. 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...

  5. 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

  6. Six- and seven-dimensional experiments by combination of sparse random sampling and projection spectroscopy dedicated for backbone resonance assignment of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Żerko, Szymon; Koźmiński, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry, Biological and Chemical Research Centre (Poland)

    2015-11-15

    Two novel six- and seven-dimensional NMR experiments are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in four indirectly detected dimensions and synchronous sampling in the additional dimensions using projection spectroscopy principle. The resulted data sets could be processed as five-dimensional data using existing software. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel experiments were successfully tested using 1 mM sample of α-synuclein on 600 and 800 MHz NMR spectrometers equipped with standard room temperature probes. The experiments allowed backbone assignment from a 1-day acquisition.

  7. 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.

  8. 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

  9. 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...

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

    Science.gov (United States)

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

    2016-09-01

    We develop a first-principles procedure for the individual evaluation of the intrinsic, side-jump, and skew-scattering contributions to the anomalous Hall conductivity σx y. This method is based on the different microscopic conductive processes of each origin of σx y in the Kubo-Bastin 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 validity of this calculation method is demonstrated for disordered FePt and FePd alloys. We find that the estimated value of each origin of σx y exhibits reasonable dependencies on the electron scattering in these disordered alloys.

  11. Fractal Patterns and Chaos Games

    Science.gov (United States)

    Devaney, Robert L.

    2004-01-01

    Teachers incorporate the chaos game and the concept of a fractal into various areas of the algebra and geometry curriculum. The chaos game approach to fractals provides teachers with an opportunity to help students comprehend the geometry of affine transformations.

  12. 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.

  13. 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

  14. 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

  15. 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.

  16. 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

  17. 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.

  18. 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...

  19. 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...

  20. 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.

  1. 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.

  2. Inverse anticipating chaos synchronization.

    Science.gov (United States)

    Shahverdiev, E M; Sivaprakasam, S; Shore, K A

    2002-07-01

    We derive conditions for achieving inverse anticipating synchronization where a driven time-delay chaotic system synchronizes to the inverse future state of the driver. The significance of inverse anticipating chaos in delineating synchronization regimes in time-delay systems is elucidated. The concept is extended to cascaded time-delay systems.

  3. User-Driven CHAOS

    DEFF Research Database (Denmark)

    Lykke, Marianne; Lund, Haakon; Skov, Mette

    2016-01-01

    CHAOS (Cultural Heritage Archive Open System) provides streaming access to more than 500.000 broad-casts by the Danish Broadcast Corporation from 1931 and onwards. The archive is part of the LARM project with the purpose of enabling researchers to search, annotate, and interact with recordings. T...

  4. Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of the Ets-1 transcription factor.

    Science.gov (United States)

    Desjardins, Geneviève; Meeker, Charles A; Bhachech, Niraja; Currie, Simon L; Okon, Mark; Graves, Barbara J; McIntosh, Lawrence P

    2014-07-29

    The E26 transformation-specific (Ets-1) transcription factor is autoinhibited by a conformationally disordered serine-rich region (SRR) that transiently interacts with its DNA-binding ETS domain. In response to calcium signaling, autoinhibition is reinforced by calmodulin-dependent kinase II phosphorylation of serines within the SRR. Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine or tyrosine (ϕ) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-ϕ-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively charged DNA-recognition interface and an adjacent region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression.

  5. Chaos induced by coupling between Josephson junctions

    Science.gov (United States)

    Shukrinov, Yu. M.; Azemtsa-Donfack, H.; Botha, A. E.

    2015-02-01

    It is found that, in a stack of intrinsic Josephson junctions in layered high temperature superconductors under external electromagnetic radiation, the chaotic features are triggered by interjunction coupling, i.e., the coupling between different junctions in the stack. While the radiation is well known to produce chaotic effects in the single junction, the effect of interjunction coupling is fundamentally different and it can lead to the onset of chaos via a different route to that of the single junction. A precise numerical study of the phase dynamics of intrinsic Josephson junctions, as described by the CCJJ+DC model, is performed. We demonstrate the charging of superconducting layers, in a bias current interval corresponding to a Shapiro step subharmonic, due to the creation of a longitudinal plasma wave along the stack of junctions. With increase in radiation amplitude chaotic behavior sets in. The chaotic features of the coupled Josephson junctions are analyzed by calculations of the Lyapunov exponents. We compare results for a stack of junctions to the case of a single junction and prove that the observed chaos is induced by the coupling between the junctions. The use of Shapiro step subharmonics may allow longitudinal plasma waves to be excited at low radiation power.

  6. 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.

  7. Phase Desynchronization as a Mechanism for Transitions to High-Dimensional Chaos

    Institute of Scientific and Technical Information of China (English)

    ZHENG ZhiGang; HU Gang

    2001-01-01

    Phase is an important degree of freedom in studies of chaotic oscillations. Phase coherence and localization in coupled chaotic elements are studied. It is shown that phase desynchronization is a key mechanism responsible for the transitions from low- to high-dimensional chaos. The route from low-dimensional chaos to high-dimensional toroidal chaos is accompanied by a cascade of phase desynchronizations. Phase synchronization tree is adopted to exhibit the entrainment process. This bifurcation tree implies an intrinsic cascade of order embedded in irregular motions.``

  8. 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.

  9. 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

  10. 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.

  11. The joy of transient chaos

    Science.gov (United States)

    Tél, Tamás

    2015-09-01

    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.

  12. The Chinese chaos game

    Science.gov (United States)

    Matsushita, Raul; Gleria, Iram; Figueiredo, Annibal; Da Silva, Sergio

    2007-05-01

    The yuan-dollar returns prior to the 2005 revaluation show a Sierpinski triangle in an iterated function system clumpiness test. Yet the fractal vanishes after the revaluation. The Sierpinski commonly emerges in the chaos game, where randomness coexists with deterministic rules (M.F. Barnsley, Fractals Everywhere, Academic Press, San Diego, 1988; H.O. Peitgen, H. Jurgens, D. Saupe, Chaos and Fractals: New Frontiers of Science, Springer, New York, 1992). Here, it is explained by the yuan's pegs to the US dollar, which made more than half of the data points close to zero. Extra data from the Brazilian and Argentine experiences do confirm that the fractal emerges whenever exchange rate pegs are kept for too long.

  13. 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...

  14. Arithmetic quantum chaos

    CERN Document Server

    Marklof, J

    2005-01-01

    The central objective in the study of quantum chaos is to characterize universal properties of quantum systems that reflect the regular or chaotic features of the underlying classical dynamics. Most developments of the past 25 years have been influenced by the pioneering models on statistical properties of eigenstates (Berry 1977) and energy levels (Berry and Tabor 1977; Bohigas, Giannoni and Schmit 1984). Arithmetic quantum chaos (AQC) refers to the investigation of quantum system with additional arithmetic structures that allow a significantly more extensive analysis than is generally possible. On the other hand, the special number-theoretic features also render these systems non-generic, and thus some of the expected universal phenomena fail to emerge. Important examples of such systems include the modular surface and linear automorphisms of tori (`cat maps') which will be described below.

  15. 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.

  16. 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...

  17. The N-terminal cytoplasmic region of NCBE displays features of an intrinsic disordered structure and represents a novel target for specific drug screening

    Directory of Open Access Journals (Sweden)

    Kaare eBjerregaard-Andersen

    2013-11-01

    Full Text Available The sodium dependent bicarbonate transporter NCBE/NBCn2 is predominantly expressed in the central nervous system (CNS. The highest protein abundance is found in the choroid plexus. The primary function of this integral plasma membrane transport protein is to regulate intracellular neuronal pH and probably to maintain the pH homeostasis across the blood-cerebrospinal fluid barrier (CSFB. NCBE has a transmembrane region consisting of 10 predicted α-helices. The N- and C- termini are both cytoplasmic, with a large N-terminal domain (Nt-NCBE and a relatively small C-terminal domain (Ct-NCBE. The cytoplasmic N-terminal domain is likely involved in bicarbonate recognition and transport and contains key areas of regulation through pH sensing and protein - protein interactions (PPIs. Intrinsic disordered proteins (IDPs and regions (IDPRs are defined as not having any rigid three-dimensional structure under physiological conditions and are believed to be involved in signaling networks in which specific, though with low affinity, PPIs play an important role in the signaling event. We show that NCBE and other SLC4 family members have a high level of predicted intrinsic disorder prevalent in the cytoplasmic regions. To provide biophysical evidence for the IDPR predicted in Nt-NCBE, we isolated recombinant NCBE from E. coli and purified it to >99 % purity and used it to perform differential scanning fluorescence spectroscopy (DSF, in the search for small molecules that induce secondary or tertiary structure. This will promote the current need to develop selective drugs for individual SLC4 family members. We have also determined a low resolution X-ray crystal structure of the N-terminal core domain at 4.0 Å resolution. The N-terminal cytoplasmic domain of AE1 (cdb3 shares a similar fold with the N-terminal core domain of NCBE. The crystal conditions for the full-length N-terminal domain have been explored, however, only the core domain forms diffracting

  18. 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...

  19. Protein intrinsic disorder in Arabidopsis NAC transcription factors: transcriptional activation by ANAC013 and ANAC046 and their interactions with RCD1.

    Science.gov (United States)

    O'Shea, Charlotte; Kryger, Mikael; Stender, Emil G P; Kragelund, Birthe B; Willemoës, Martin; Skriver, Karen

    2015-01-15

    Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of the transcription regulatory domains (TRDs) of six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis 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 because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large regulatory domain is unlikely to contribute to the interaction, since the domain and truncations thereof have similar affinities for RCD1, which are also similar for ANAC013-RCD1 interactions. However, different enthalpic and entropic contributions to binding were revealed for ANAC046 and ANAC013, suggestive of differences in binding mechanisms. Although substitution of both hydrophobic and acidic residues of the ANAC046 MoRF region abolished binding, substitution of other residues, even with α-helix-breaking proline, was less disruptive. Together, the biophysical analyses suggest that RCD1-ANAC046 complex formation does not involve folding-upon-binding, but rather fuzziness or an unknown structure in ANAC046. We suggest that the ANAC046 regulatory domain functions as an entropic chain with a terminal hot spot interacting with RCD1. RCD1, a cellular hub, may be able to interact with many different TFs by exploiting their ID-based flexibility, as demonstrated for its interactions with ANAC046 and ANAC013.

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

    Energy Technology Data Exchange (ETDEWEB)

    Casey, Thomas M.; Liu, Zhanglong; Esquiaqui, Jackie M.; Pirman, Natasha L.; Milshteyn, Eugene; Fanucci, Gail E., E-mail: fanucci@chem.ufl.edu

    2014-07-18

    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 IA{sub 3} 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 IA{sub 3}, 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.

  1. 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.

  2. 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

  3. Spiritual well-being, intrinsic religiosity, and suicidal behavior in predominantly Catholic Croatian war veterans with chronic posttraumatic stress disorder: a case control study.

    Science.gov (United States)

    Nad, Sanea; Marcinko, Darko; Vuksan-Aeusa, Bjanka; Jakovljević, Miro; Jakovljevic, Gordana

    2008-01-01

    We investigated relationships between spiritual well-being (SWB), intrinsic religiosity (IR), and suicidal behavior in 45 Croatian war veterans with chronic posttraumatic stress disorder and 32 healthy volunteers. Compared with the volunteers, the veterans had significantly lower SWB scores (p = 0.000) and existential well-being (EWB) scores (p = 0.000). Scores on the religious well-being (RWB) subscale (p = 0.108) and the IR scale did not differ significantly between the groups (p = 0.803). Veterans' suicidality inversely correlated with SWB (p = 0.000), EWB (p = 0.000), RWB (p = 0.026), and IR (p = 0.041), with the association being stronger for the EWB subscale than for the RWB subscale. Veterans who had attempted suicide at least once in their lifetime had significantly higher Suicidal Assessment Scale scores and lower EWB scores than veterans who never attempted suicide. Low EWB scores may imply an increased risk of suicidality. Some religious activities were more frequent among the veterans than among the healthy volunteers, possibly reflecting the veterans' increased help-seeking behavior due to poor EWB.

  4. 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

  5. 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

  6. 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.

  7. Controlling Beam Halo-Chaos

    Institute of Scientific and Technical Information of China (English)

    方锦清; 罗晓曙; 陈关荣; 翁甲强

    2001-01-01

    Beam halo-chaos is essentially a complex spatiotemporal chaotic motion in a periodic-focusing channel of a highpower linear proton accelerator. The controllability condition for beam halo-chaos is analysed qualitatively. A special nonlinear control method, i.e. the wavelet-based function feedback, is proposed for controlling beam halochaos. Particle-in-cell simulations are used to explore the nature of halo-chaos formation, which has shown that the beam hMo-chaos is suppressed effectively after using nonlinear control for the proton beam with an initial full Gaussian distribution. The halo intensity factor Hav is reduced from 14%o to zero, and the other statistical physical quantities of beam halo-chaos are more than doubly reduced. The potential applications of such nonlinear control in experiments are briefly pointed out.

  8. 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

  9. Quantum bouncer with chaos

    Science.gov (United States)

    Dembiński, S. T.; Makowski, A. J.; Pepłowski, P.

    1993-02-01

    We report for the first time quantum calculations for the so-called bouncer model, the classical analog of which is well known to manifest a chaotic behavior. Three versions of our model are fully tractable quantum mechanically and are potentially a rich source of data for establishing properties of a quantum system of which the classical mechanics can be chaotic. Among the results presented here, consequences of the varying bandwidth of infinite-dimensional transition matrices on the use of the correspondence between classical chaos and non-Poissonian quasienergy statistics are discussed.

  10. Dynamical topology and statistical properties of spatiotemporal chaos.

    Science.gov (United States)

    Zhuang, Quntao; Gao, Xun; Ouyang, Qi; Wang, Hongli

    2012-12-01

    For spatiotemporal chaos described by partial differential equations, there are generally locations where the dynamical variable achieves its local extremum or where the time partial derivative of the variable vanishes instantaneously. To a large extent, the location and movement of these topologically special points determine the qualitative structure of the disordered states. We analyze numerically statistical properties of the topologically special points in one-dimensional spatiotemporal chaos. The probability distribution functions for the number of point, the lifespan, and the distance covered during their lifetime are obtained from numerical simulations. Mathematically, we establish a probabilistic model to describe the dynamics of these topologically special points. In spite of the different definitions in different spatiotemporal chaos, the dynamics of these special points can be described in a uniform approach.

  11. 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.

  12. 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

  13. 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

  14. 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.

  15. 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.

  16. Chaos and language.

    Science.gov (United States)

    Mitchener, W Garrett; Nowak, Martin A

    2004-04-01

    Human language is a complex communication system with unlimited expressibility. Children spontaneously develop a native language by exposure to linguistic data from their speech community. Over historical time, languages change dramatically and unpredictably by accumulation of small changes and by interaction with other languages. We have previously developed a mathematical model for the acquisition and evolution of language in heterogeneous populations of speakers. This model is based on game dynamical equations with learning. Here, we show that simple examples of such equations can display complex limit cycles and chaos. Hence, language dynamical equations mimic complicated and unpredictable changes of languages over time. In terms of evolutionary game theory, we note that imperfect learning can induce chaotic switching among strict Nash equilibria.

  17. 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 $\\eta > 4$.

  18. SPICE and Chaos

    DEFF Research Database (Denmark)

    Lindberg, Erik

    1996-01-01

    Can we believe in the results of our circuit simulators ? Is it possible to distinguish between results due to numerical chaos and resultsdue to the eventual chaotic nature of our modelsof physical systems ?. Three experiments with SPICE are presented: (1) A "stable" active RCcircuit with poles...... in the right half plane. (2) "Chaotic" steady state behaviour of a non-chaotic dc power supply. (3) Analysis of a Colpitts oscillator with chaotic behaviour. In order to obtain reliable results from the SPICE simulators the users of these programs need insight not only in the use of the programs but also...... in the models of the circuits to be analyzed. If trimmed properly SPICE normally gives the correct result....

  19. 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.

  20. 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.

  1. Chaos and complexity by design

    CERN Document Server

    Roberts, Daniel A

    2016-01-01

    We study the relationship between quantum chaos and pseudorandomness by developing probes of unitary design. A natural probe of randomness is the "frame potential," which is minimized by unitary $k$-designs and measures the $2$-norm distance between the Haar random unitary ensemble and another ensemble. A natural probe of quantum chaos is out-of-time-order (OTO) four-point correlation functions. We show that the norm squared of a generalization of out-of-time-order $2k$-point correlators is proportional to the $k$th frame potential, providing a quantitative connection between chaos and pseudorandomness. Additionally, we prove that these $2k$-point correlators for Pauli operators completely determine the $k$-fold channel of an ensemble of unitary operators. Finally, we use a counting argument to obtain a lower bound on the quantum circuit complexity in terms of the frame potential. This provides a direct link between chaos, complexity, and randomness.

  2. 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...

  3. Yersinia pestis Caf1 Protein: Effect of Sequence Polymorphism on Intrinsic Disorder Propensity, Serological Cross-Reactivity and Cross-Protectivity of Isoforms.

    Science.gov (United States)

    Kopylov, Pavel Kh; Platonov, Mikhail E; Ablamunits, Vitaly G; Kombarova, Tat'yana I; Ivanov, Sergey A; Kadnikova, Lidiya A; Somov, Aleksey N; Dentovskaya, Svetlana V; Uversky, Vladimir N; Anisimov, Andrey P

    2016-01-01

    Yersinia pestis Caf1 is a multifunctional protein responsible for antiphagocytic activity and is a key protective antigen. It is generally conserved between globally distributed Y. pestis strains, but Y. pestis subsp. microtus biovar caucasica strains circulating within populations of common voles in Georgia and Armenia were reported to carry a single substitution of alanine to serine. We investigated polymorphism of the Caf1 sequences among other Y. pestis subsp. microtus strains, which have a limited virulence in guinea pigs and in humans. Sequencing of caf1 genes from 119 Y. pestis strains belonging to different biovars within subsp. microtus showed that the Caf1 proteins exist in three isoforms, the global type Caf1NT1 (Ala48 Phe117), type Caf1NT2 (Ser48 Phe117) found in Transcaucasian-highland and Pre-Araks natural plague foci #4-7, and a novel Caf1NT3 type (Ala48 Val117) endemic in Dagestan-highland natural plague focus #39. Both minor types are the progenies of the global isoform. In this report, Caf1 polymorphism was analyzed by comparing predicted intrinsic disorder propensities and potential protein-protein interactivities of the three Caf1 isoforms. The analysis revealed that these properties of Caf1 protein are minimally affected by its polymorphism. All protein isoforms could be equally detected by an immunochromatography test for plague at the lowest protein concentration tested (1.0 ng/mL), which is the detection limit. When compared to the classic Caf1NT1 isoform, the endemic Caf1NT2 or Caf1NT3 had lower immunoreactivity in ELISA and lower indices of self- and cross-protection. Despite a visible reduction in cross-protection between all Caf1 isoforms, our data suggest that polymorphism in the caf1 gene may not allow the carriers of Caf1NT2 or Caf1NT3 variants escaping from the Caf1NT1-mediated immunity to plague in the case of a low-dose flea-borne infection. PMID:27606595

  4. Granular chaos and mixing: Whirled in a grain of sand

    Energy Technology Data Exchange (ETDEWEB)

    Shinbrot, Troy, E-mail: shinbrot@rutgers.edu [Department of Biomedical Engineering, Rutgers University, Piscataway, New Jersey 08854 (United States)

    2015-09-15

    In this paper, we overview examples of chaos in granular flows. We begin by reviewing several remarkable behaviors that have intrigued researchers over the past few decades, and we then focus on three areas in which chaos plays an intrinsic role in granular behavior. First, we discuss pattern formation in vibrated beds, which we show is a direct result of chaotic scattering combined with dynamical dissipation. Next, we consider stick-slip motion, which involves chaotic scattering on the micro-scale, and which results in complex and as yet unexplained peculiarities on the macro-scale. Finally, we examine granular mixing, which we show combines micro-scale chaotic scattering and macro-scale stick-slip motion into behaviors that are well described by dynamical systems tools, such as iterative mappings.

  5. 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.

  6. 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

  7. 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

  8. 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.

  9. 4D Non-uniformly sampled HCBCACON and {sup 1}J(NC{sup {alpha}})-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic); Haba, Noam Y.; Chill, Jordan H. [Bar Ilan University, Department of Chemistry (Israel); Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2012-06-15

    A pair of 4D NMR experiments for the backbone assignment of disordered proteins is presented. The experiments exploit {sup 13}C direct detection and non-uniform sampling of the indirectly detected dimensions, and provide correlations of the aliphatic proton (H{sup {alpha}}, and H{sup {beta}}) and carbon (C{sup {alpha}}, C{sup {beta}}) resonance frequencies to the protein backbone. Thus, all the chemical shifts regularly used to map the transient secondary structure motifs in the intrinsically disordered proteins (H{sup {alpha}}, C{sup {alpha}}, C{sup {beta}}, C Prime , and N) can be extracted from each spectrum. Compared to the commonly used assignment strategy based on matching the C{sup {alpha}} and C{sup {beta}} chemical shifts, inclusion of the H{sup {alpha}} and H{sup {beta}} provides up to three extra resonance frequencies that decrease the chance of ambiguous assignment. The experiments were successfully applied to the original assignment of a 12.8 kDa intrinsically disordered protein having a high content of proline residues (26 %) in the sequence.

  10. Chaos theory for the biomedical engineer.

    Science.gov (United States)

    Eberhart, R C

    1989-01-01

    A brief introduction to chaos theory is provided. Definitions of chaos and attributes of chaos and fractals are discussed. Several general examples are examined, and fractals are introduced with a brief look at the Mandelbrot and Julia sets. Biomedical examples of chaotic behaviour and fractals are presented.

  11. 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.

  12. 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)

  13. Chaos: A historical perspective

    Science.gov (United States)

    Lighthill, James

    In this introductory lecture I'd like to offer a broad historical perspective regarding the relatively recent general recognition: (a) that mechanical systems satisfying Newton's laws may be subject to the essentially unpredictable type of behavior which the word CHAOS describes—in other words, the recognition (b) that quantum effects are not required; (c) so that, notwithstanding Heisenberg, uncertainty is there on the basis of the good old classical mechanics based on Newton's Laws. But first of all I'll remind you that there are two kinds of laws in science, which we may exemplify by Kepler's Laws and Newton's Laws. Kepler in 1609 completed some very detailed observations of the motions of Mars; together with a full geometrical description of them, in the Copernican sun-centered flame of reference, as motions in a constant orbit in the shape of an ellipse with the Sun as focus. A decade later Kepler had published the Epitome Astronomiae Copernicanae (a rather more substantial work than the Dialogo which later got Galileo into some difficulties), and had there described in detail his most famous discovery: Kepler's three empirical laws concerning planetary orbits. These laws, of the elliptical shapes of orbits, of the radius covering equal areas in equal times, and of the proportionality of the square of the orbital period to the cube of the major axis, were shown from the observations to be closely satisfied by the Earth and by the five then known planets; and furthermore, by the four satellites of Jupiter which Galileo had recently discovered.

  14. 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.

  15. 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 ...

  16. Pioneer Women in Chaos Theory

    CERN Document Server

    Wang, Frank Y

    2009-01-01

    The general public has been made aware of the research field of "chaos" by the book of that title by James Gleick. This paper will focus on the achievements of Sonya Kovalevskaya, Mary Cartwright, and Mary Tsingou, whose pioneer works were not mentioned in Gleick's book.

  17. 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 $\\beta=4/7$.

  18. 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.

  19. Chaos, creativity, and substance abuse: the nonlinear dynamics of choice.

    Science.gov (United States)

    Zausner, Tobi

    2011-04-01

    Artists create their work in conditions of disequilibrium, states of creative chaos that may appear turbulent but are capable of bringing forth new order. By absorbing information from the environment and discharging it negentropically as new work, artists can be modeled as dissipative systems. A characteristic of chaotic systems is a heightened sensitivity to stimuli, which can generate either positive experiences or negative ones that can lead some artists to substance abuse and misguided searches for a creative chaos. Alcohol and drug use along with inadequately addressed co-occurring emotional disorders interfere with artists' quest for the nonlinearity of creativity. Instead, metaphorically modeled by a limit cycle of addiction and then a spiral to disorder, the joys of a creative chaos become an elusive chimera for them rather than a fulfilling experience. Untreated mental illness and addiction to substances have shortened the lives of artists such as Vincent Van Gogh, Frida Kahlo, Henri de Toulouse-Lautrec, and Jackson Pollock, all of whom committed suicide. In contrast Edvard Munch and John Callahan, who chose to address their emotional problems and substance abuse, continued to live and remain creative. Choosing to access previously avoided moments of pain can activate the nonlinear power of self-transformation.

  20. Random organization. Ordered chaos

    NARCIS (Netherlands)

    Frenkel, D.

    2008-01-01

    When we speak about self-organizing systems, we intuitively think of situations where an initially disordered state spontaneously evolves into an ordered one. On page 420 of this issue, Corté and co-workers present a combined numerical and experimental study1 of a driven system of spherical particle

  1. 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...

  2. 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...

  3. Controlling neuronal noise using chaos control

    CERN Document Server

    Christini, D J; Christini, David J; Collins, James J

    1995-01-01

    Chaos control techniques have been applied to a wide variety of experimental systems, including magneto-elastic ribbons, lasers, chemical reactions, arrhythmic cardiac tissue, and spontaneously bursting neuronal networks. An underlying assumption in all of these studies is that the system being controlled is chaotic. However, the identification of chaos in experimental systems, particularly physiological systems, is a difficult and often misleading task. Here we demonstrate that the chaos criteria used in a recent study can falsely classify a noise-driven, non-chaotic neuronal model as being chaotic. We apply chaos control, periodic pacing, and anticontrol to the non-chaotic model and obtain results which are similar to those reported for apparently chaotic, {\\em in vitro} neuronal networks. We also obtain similar results when we apply chaos control to a simple stochastic system. These novel findings challenge the claim that the aforementioned neuronal networks were chaotic and suggest that chaos control tech...

  4. 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...

  5. 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.

  6. 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.

  7. 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...

  8. 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

  9. Random Behaviour in Quantum Chaos

    CERN Document Server

    Garbaczewski, P

    2001-01-01

    We demonstrate that a family of radial Ornstein-Uhlenbeck stochastic processes displays an ergodic behaviour appropriate for known quantum chaos universality classes of nearest neighbour spacing distributions. A common feature of those parametric processes is an asymptotic balance between the radial (Bessel-type) repulsion and the harmonic attraction, as manifested in the general form of forward drifts $b(x) = {{N-1}\\over {2x}} - x$, ($N = 2,3,5$ correspond respectively to the familiar GOE, GUE and GSE cases).

  10. 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.

  11. 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

  12. 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

  13. 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 ...

  14. 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.

  15. Weak chaos in the asymmetric heavy top

    CERN Document Server

    Barrientos, M; Ranada, A F

    1995-01-01

    We consider the dynamics of the slightly asymmetric heavy top, a non-integrable system obtained from the Lagrange top by breaking the symmetry of its inertia tensor. It shows signs of weak chaos, which we study numerically. We argue that it is a good example for introducing students to non-integrability and chaos. (author)

  16. 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)

  17. Chaos desynchronization in strongly coupled systems

    Energy Technology Data Exchange (ETDEWEB)

    Wu Ye [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); School of Science, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Liu Weiqing [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100049 (China); School of Science, Beijing University of Posts and Telecommunications, Beijing 100876 (China); School of Science, Jiangxi University of Science and Technology, Ganzhou 341000 (China); Xiao, Jinghua [School of Science, Beijing University of Posts and Telecommunications, Beijing 100876 (China); Zhan Meng [Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071 (China)], E-mail: zhanmeng@wipm.ac.cn

    2007-10-01

    The dynamics of chaos desynchronization in strongly coupled oscillator systems is studied. We find a new bifurcation from synchronous chaotic state, chaotic short wave bifurcation, i.e. a chaotic desynchronization attractor is new born in the systems due to chaos desynchronization. In comparison with the usual periodic short wave bifurcation, very rich but distinct phenomena are observed.

  18. Radio lighting based on dynamic chaos generators

    CERN Document Server

    Dmitriev, Alexander; Gerasimov, Mark; Itskov, Vadim

    2016-01-01

    A problem of lighting objects and surfaces with artificial sources of noncoherent microwave radiation with the aim to observe them using radiometric equipment is considered. Transmitters based on dynamic chaos generators are used as sources of noncoherent wideband microwave radiation. An experimental sample of such a device, i.e., a radio lighting lamp based on a chaos microgenerator and its performance are presented.

  19. "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…

  20. 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...

  1. Path and semimartingale properties of chaos processes

    DEFF Research Database (Denmark)

    Basse-O'Connor, Andreas; Graversen, Svend-Erik

    2010-01-01

    The present paper characterizes various properties of chaos processes which in particular include processes where all time variables admit a Wiener chaos expansion of a fixed finite order. The main focus is on the semimartingale property, p-variation and continuity. The general results obtained a...

  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. 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...

  4. PHASE CHAOS IN THE DISCRETE KURAMOTO MODEL

    DEFF Research Database (Denmark)

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

    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...... interaction among the oscillators, while the individual oscillators behave periodically when left uncoupled. For the four-dimensional time-discrete Kuramoto model, we outline the region of phase chaos in the parameter plane and determine the regions where phase chaos coexists with different periodic...... attractors. We also study the subcritical frequency-splitting bifurcation at the onset of desynchronization and demonstrate that the transition to phase chaos takes place via a torus destruction process....

  5. 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...

  6. 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.

  7. Dazzled by unity? Order and chaos in public discourse on illicit drug use.

    Science.gov (United States)

    Fraser, Suzanne; Moore, David

    2008-02-01

    One of the ways in which researchers, policy makers and practitioners routinely characterise illicit drug use is through a taxonomy of two paired conditions, the negative state of 'chaos' and the positive state of 'order' in the form of 'stability.' In this article, we explore some of the ways in which this taxonomy operates in public discourse on illicit drug use. Google searches were conducted in order to gather a corpus of Australian, United Kingdom and United States materials making use of notions of chaos and stability in discussing illicit drug use. The chaos/stability pairing was identified in a large number of materials, including government policy documents, internet web sites for drug related services, newspaper articles and research papers. Drawing on the work of Michel Foucault and Michel Serres, we argue that references to chaos and stability within public discourse produce at least three different ontological registers in which drug users are positioned: (1) the drug user as chaotic, (2) the drug using way of life as chaotic and (3) drug use activities as chaotic. These registers produce different semantic effects in that each locates the 'problem' of chaos differently and invokes it for different political and regulatory ends. Further, we argue that the taxonomy serves mainly to affirm the illegitimacy of injecting drug use by establishing and policing boundaries between the ostensibly unproductive, disorderly lives of drug users and the 'normal,' orderly and productive lives of non-injecting drug users. In concluding, we question the adequacy of chaos, as conventionally defined, in accounting for the circumstances and actions of drug users, and canvass alternative ways of viewing chaos that might offer useful critical tools for drugs research, policy and practice.

  8. Some new surprises in chaos

    Energy Technology Data Exchange (ETDEWEB)

    Bunimovich, Leonid A., E-mail: bunimovh@math.gatech.edu [ABC Program, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States); Vela-Arevalo, Luz V., E-mail: luzvela@math.gatech.edu [School of Mathematics, Georgia Institute of Technology, Atlanta, Georgia 30332 (United States)

    2015-09-15

    A brief review is presented of some recent findings in the theory of chaotic dynamics. We also prove a statement that could be naturally considered as a dual one to the Poincaré theorem on recurrences. Numerical results demonstrate that some parts of the phase space of chaotic systems are more likely to be visited earlier than other parts. A new class of chaotic focusing billiards is discussed that clearly violates the main condition considered to be necessary for chaos in focusing billiards.

  9. On the Mechanisms Behind Chaos

    DEFF Research Database (Denmark)

    Lindberg, Erik

    2006-01-01

    Chaotic systems are observed everywhere. Electronic circuit analogues based on the differential equations of the models for the chaotic systems are often used to study the nature of chaotic systems. This tutorial is an attempt to classify electronic chaotic oscillators according to the mechanism...... behind the chaotic behavior, e.g. one group is based on the sudden interrupt of inductive currents, another group is based on the sudden parallel coupling of capacitors with different voltages, and a third group may be based on multiplication of signals. An example of chaos based on disturbance...

  10. 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.

  11. The IntFOLD server: an integrated web resource for protein fold recognition, 3D model quality assessment, intrinsic disorder prediction, domain prediction and ligand binding site prediction.

    Science.gov (United States)

    Roche, Daniel B; Buenavista, Maria T; Tetchner, Stuart J; McGuffin, Liam J

    2011-07-01

    The IntFOLD server is a novel independent server that integrates several cutting edge methods for the prediction of structure and function from sequence. Our guiding principles behind the server development were as follows: (i) to provide a simple unified resource that makes our prediction software accessible to all and (ii) to produce integrated output for predictions that can be easily interpreted. The output for predictions is presented as a simple table that summarizes all results graphically via plots and annotated 3D models. The raw machine readable data files for each set of predictions are also provided for developers, which comply with the Critical Assessment of Methods for Protein Structure Prediction (CASP) data standards. The server comprises an integrated suite of five novel methods: nFOLD4, for tertiary structure prediction; ModFOLD 3.0, for model quality assessment; DISOclust 2.0, for disorder prediction; DomFOLD 2.0 for domain prediction; and FunFOLD 1.0, for ligand binding site prediction. Predictions from the IntFOLD server were found to be competitive in several categories in the recent CASP9 experiment. The IntFOLD server is available at the following web site: http://www.reading.ac.uk/bioinf/IntFOLD/.

  12. 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.

  13. 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.

  14. 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.

  15. 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

  16. Nonlinear Dynamics and Chaos: Applications in Atmospheric Sciences

    CERN Document Server

    Selvam, A M

    2010-01-01

    Atmospheric flows, an example of turbulent fluid flows, exhibit fractal fluctuations of all space-time scales ranging from turbulence scale of mm - sec to climate scales of thousands of kilometers - years and may be visualized as a nested continuum of weather cycles or periodicities, the smaller cycles existing as intrinsic fine structure of the larger cycles. The power spectra of fractal fluctuations exhibit inverse power law form signifying long - range correlations identified as self - organized criticality and are ubiquitous to dynamical systems in nature and is manifested as sensitive dependence on initial condition or 'deterministic chaos' in finite precision computer realizations of nonlinear mathematical models of real world dynamical systems such as atmospheric flows. Though the self-similar nature of atmospheric flows have been widely documented and discussed during the last three to four decades, the exact physical mechanism is not yet identified. There now exists an urgent need to develop and inco...

  17. Physics and applications of laser diode chaos

    Science.gov (United States)

    Sciamanna, M.; Shore, K. A.

    2015-03-01

    This Review Article provides an overview of chaos in laser diodes by surveying experimental achievements in the area and explaining the theory behind the phenomenon. The fundamental physics underpinning laser diode chaos and also the opportunities for harnessing it for potential applications are discussed. The availability and ease of operation of laser diodes, in a wide range of configurations, make them a convenient testbed 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.

  18. 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

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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...

  4. Delay-range-dependent chaos synchronization approach under varying time-lags and delayed nonlinear coupling.

    Science.gov (United States)

    Zaheer, Muhammad Hamad; Rehan, Muhammad; Mustafa, Ghulam; Ashraf, Muhammad

    2014-11-01

    This paper proposes a novel state feedback delay-range-dependent control approach for chaos synchronization in coupled nonlinear time-delay systems. The coupling between two systems is esteemed to be nonlinear subject to time-lags. Time-varying nature of both the intrinsic and the coupling delays is incorporated to broad scope of the present study for a better-quality synchronization controller synthesis. Lyapunov-Krasovskii (LK) functional is employed to derive delay-range-dependent conditions that can be solved by means of the conventional linear matrix inequality (LMI)-tools. The resultant control approach for chaos synchronization of the master-slave time-delay systems considers non-zero lower bound of the intrinsic as well as the coupling time-delays. Further, the delay-dependent synchronization condition has been established as a special case of the proposed LK functional treatment. Furthermore, a delay-range-dependent condition, independent of the delay-rate, has been provided to address the situation when upper bound of the delay-derivative is unknown. A robust state feedback control methodology is formulated for synchronization of the time-delay chaotic networks against the L2 norm bounded perturbations by minimizing the L2 gain from the disturbance to the synchronization error. Numerical simulation results are provided for the time-delay chaotic networks to show effectiveness of the proposed delay-range-dependent chaos synchronization methodologies.

  5. 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...

  6. 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.

  7. Ergodic theory, randomness, and "chaos".

    Science.gov (United States)

    Ornstein, D S

    1989-01-13

    Ergodic theory is the theory of the long-term statistical behavior of dynamical systems. The baker's transformation is an object of ergodic theory that provides a paradigm for the possibility of deterministic chaos. It can now be shown that this connection is more than an analogy and that at some level of abstraction a large number of systems governed by Newton's laws are the same as the baker's transformation. Going to this level of abstraction helps to organize the possible kinds of random behavior. The theory also gives new concrete results. For example, one can show that the same process could be produced by a mechanism governed by Newton's laws or by a mechanism governed by coin tossing. It also gives a statistical analog of structural stability.

  8. 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 ...

  9. 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)

  10. 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.

  11. Intrinsic personality traits in patients with generalized anxiety disorder%广泛性焦虑症患者的自身内在人格特质

    Institute of Scientific and Technical Information of China (English)

    瞿玮; 覃园园

    2005-01-01

    强性、兴奋性与Zung焦虑自评量表评分呈显著负相关(r=-0.273,P<0.01;r=-0.217,P<0.05;r=-0.217,P<0.05),紧张性与Zung焦虑自评量表评分呈显著正相关(r--0.248,P<0.05).结论:焦虑症的发生与其自身人格特质有关,有稳定性、持强性、兴奋性低分和紧张性高分特征.这4种人格特质,可能是罹患焦虑症的易感人格特征,同时还影响着焦虑症的严重程度.%BACKGROUND: According to Eysenck's theory of personality, trait level belongs tolow-grade personality, which can better reflect characteristics of individual habitual behavior reaction.OBJECTIVE: To explore the correspondent relationship between generalized anxiety patient and internal personality trait through adopting Cattell's 16 Personality Factor Questionnaire (16PFQ) and Zung's Self-rating Anxiety Scale (SAS) to test generalized anxiety patients.DESIGN: A transectional sampling survey and data was compared with that of health adult norms.SETTING: Counseling clinic of out-patient in the Southwest Hospital of the Third Military Medical University of Chinese PLA.PARTICIPANTS: Totally 100 patients with generalized anxiety disorders who visited the clinical counseling clinic of out-patient in the Southwest Hospital, Third Military Medical University of Chinese PLA for the first time from August 2003 to March 2004 were included, including 40 men and 60 women.METHODS: Catell's 16PFQ was tested with Psychometric Toolbox Standard Edition V2.3 developed by the Insight Group of Peking University.The patients filled out the forms independently after the method being explained clearly by professional staff members. These 16 personality factors included warmth (reserved vs. warm; Factor A), reasoning (concrete vs.abstract; Factor B), emotional stability (reactive vs. emotionally stable;Factor C), dominance (deferential vs. dominant; Factor E), liveliness (serious vs. lively; Factor F), rule-consciousness (expedient vs. rule-conscious;Factor G

  12. Legal System and Legal Chaos Theory

    Directory of Open Access Journals (Sweden)

    Amir Syarifudin

    2015-08-01

    Full Text Available Order of the universe and other objects can be described either by cosmology and physics. But from of the regularity of the object there in terms or aspect of irregularity or fractal (broken that difficult to describe by Auklides and Calculus mathematical models. Benoit Medelbrot tried to explain the chaotic objects with fractal theory which basically a branch of mathematics. The fractal theory affect the view of the law that inspired Charles Sampford which then sparked a legal chaos theory. The core of legal chaos theory is (1 social relationships , including the relationship established based on the relationship of forces (power relation, (2 the parties who make that relationship does not have the same strength or balance, and (3 at the time of execution of the respective relations based on their subjective opinions. Those three thing that is causing chaos. But the atmosphere of chaos that would eventually return to the regularity, because of the strength towing (strange attractor that in the area of law is the law and the power of the state. Chaos basically contained in the freedom -based relationship beyond the confines of order. When the towing force managed to recover the chaos so as to create harmony between order and freedom, the peace that one of the legal goal is achieved.

  13. Chaos and Cosmos on The Streets of Gostivar

    Directory of Open Access Journals (Sweden)

    Barbara Turk Niskač

    2009-12-01

    Full Text Available This paper focuses on the streets in Gostivar, Macedonia, and how its young Albanian and Macedonian inhabitants perceive them. I am interested in how the ethnic division in the town influences perceptions and behavior. Macedonian girls are exposed to verbal sexual advances and harassment by Albanians, whereas boys are exposed to occasional fights. On the other hand, among Albanian youth the fear of the Other is not as present as among the Macedonians. In seeking the reasons for this situation, I deal with the concepts of chaos and cosmos, social control, gossip, cultural differences, kinship, and patriarchy. The streets are one of the spaces where identification takes place, and gender and ethnic identities are related to interactions in the streets. By defining boundaries in space, people create and maintain the boundaries between “us” and “them.” Identities are built in the process of interaction with others. The process of identification is connected to defining the similarities and differences in relation to “us.” People place themselves in the center, in the sphere of the cosmos, which they relate to home, the known, order, safety, and cleanliness. They place the Other in the sphere of chaos because the Other represents the distant, the foreign, the unknown, disorder, danger, and uncleanness. Public opinion is important in maintaining identities and boundaries. Girls in particular must safeguard their honor, which is constantly under surveillance. Identification is maintained by avoiding the space of the Other. Individuals avoid it in order to maintain their good name in the eyes of their group. Through the constant maintenance of the identities and boundaries between “us” and “them,” or between cosmos and chaos, one can trace the fear of losing one’s own identity. Each side is afraid that they might become like “them.”

  14. Genome chaos: survival strategy during crisis.

    Science.gov (United States)

    Liu, Guo; Stevens, Joshua B; Horne, Steven D; Abdallah, Batoul Y; Ye, Karen J; Bremer, Steven W; Ye, Christine J; Chen, David J; Heng, Henry H

    2014-01-01

    Genome chaos, a process of complex, rapid genome re-organization, results in the formation of chaotic genomes, which is followed by the potential to establish stable genomes. It was initially detected through cytogenetic analyses, and recently confirmed by whole-genome sequencing efforts which identified multiple subtypes including "chromothripsis", "chromoplexy", "chromoanasynthesis", and "chromoanagenesis". Although genome chaos occurs commonly in tumors, both the mechanism and detailed aspects of the process are unknown due to the inability of observing its evolution over time in clinical samples. Here, an experimental system to monitor the evolutionary process of genome chaos was developed to elucidate its mechanisms. Genome chaos occurs following exposure to chemotherapeutics with different mechanisms, which act collectively as stressors. Characterization of the karyotype and its dynamic changes prior to, during, and after induction of genome chaos demonstrates that chromosome fragmentation (C-Frag) occurs just prior to chaotic genome formation. Chaotic genomes seem to form by random rejoining of chromosomal fragments, in part through non-homologous end joining (NHEJ). Stress induced genome chaos results in increased karyotypic heterogeneity. Such increased evolutionary potential is demonstrated by the identification of increased transcriptome dynamics associated with high levels of karyotypic variance. In contrast to impacting on a limited number of cancer genes, re-organized genomes lead to new system dynamics essential for cancer evolution. Genome chaos acts as a mechanism of rapid, adaptive, genome-based evolution that plays an essential role in promoting rapid macroevolution of new genome-defined systems during crisis, which may explain some unwanted consequences of cancer treatment.

  15. 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[...

  16. 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

  17. 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.

  18. 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.

  19. 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...

  20. 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.

  1. Quantum chaos in nanoelectromechanical systems

    Science.gov (United States)

    Gusso, André; da Luz, M. G. E.; Rego, Luis G. C.

    2006-01-01

    We present a theoretical study of the electron-phonon coupling in suspended nanoelectromechanical systems and investigate the resulting quantum chaotic behavior. The phonons are associated with the vibrational modes of a suspended rectangular dielectric plate, with free or clamped boundary conditions, whereas the electrons are confined to a large quantum dot (QD) on the plate’s surface. The deformation potential and piezoelectric interactions are considered. By performing standard energy-level statistics we demonstrate that the spectral fluctuations exhibit the same distributions as those of the Gaussian orthogonal ensemble or the Gaussian unitary ensemble (GUE), therefore evidencing the emergence of quantum chaos. That is verified for a large range of material and geometry parameters. In particular, the GUE statistics occurs only in the case of a circular QD. It represents an anomalous phenomenon, previously reported for just a small number of systems, since the problem is time-reversal invariant. The obtained results are explained through a detailed analysis of the Hamiltonian matrix structure.

  2. Regularly timed events amid chaos

    Science.gov (United States)

    Blakely, Jonathan N.; Cooper, Roy M.; Corron, Ned J.

    2015-11-01

    We show rigorously that the solutions of a class of chaotic oscillators are characterized by regularly timed events in which the derivative of the solution is instantaneously zero. The perfect regularity of these events is in stark contrast with the well-known unpredictability of chaos. We explore some consequences of these regularly timed events through experiments using chaotic electronic circuits. First, we show that a feedback loop can be implemented to phase lock the regularly timed events to a periodic external signal. In this arrangement the external signal regulates the timing of the chaotic signal but does not strictly lock its phase. That is, phase slips of the chaotic oscillation persist without disturbing timing of the regular events. Second, we couple the regularly timed events of one chaotic oscillator to those of another. A state of synchronization is observed where the oscillators exhibit synchronized regular events while their chaotic amplitudes and phases evolve independently. Finally, we add additional coupling to synchronize the amplitudes, as well, however in the opposite direction illustrating the independence of the amplitudes from the regularly timed events.

  3. 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.

  4. Importance and challenges of measuring intrinsic foot muscle strength

    Directory of Open Access Journals (Sweden)

    Soysa Achini

    2012-11-01

    Full Text Available Abstract Background Intrinsic foot muscle weakness has been implicated in a range of foot deformities and disorders. However, to establish a relationship between intrinsic muscle weakness and foot pathology, an objective measure of intrinsic muscle strength is needed. The aim of this review was to provide an overview of the anatomy and role of intrinsic foot muscles, implications of intrinsic weakness and evaluate the different methods used to measure intrinsic foot muscle strength. Method Literature was sourced from database searches of MEDLINE, PubMed, SCOPUS, Cochrane Library, PEDro and CINAHL up to June 2012. Results There is no widely accepted method of measuring intrinsic foot muscle strength. Methods to estimate toe flexor muscle strength include the paper grip test, plantar pressure, toe dynamometry, and the intrinsic positive test. Hand-held dynamometry has excellent interrater and intrarater reliability and limits toe curling, which is an action hypothesised to activate extrinsic toe flexor muscles. However, it is unclear whether any method can actually isolate intrinsic muscle strength. Also most methods measure only toe flexor strength and other actions such as toe extension and abduction have not been adequately assessed. Indirect methods to investigate intrinsic muscle structure and performance include CT, ultrasonography, MRI, EMG, and muscle biopsy. Indirect methods often discriminate between intrinsic and extrinsic muscles, but lack the ability to measure muscle force. Conclusions There are many challenges to accurately measure intrinsic muscle strength in isolation. Most studies have measured toe flexor strength as a surrogate measure of intrinsic muscle strength. Hand-held dynamometry appears to be a promising method of estimating intrinsic muscle strength. However, the contribution of extrinsic muscles cannot be excluded from toe flexor strength measurement. Future research should clarify the relative contribution of

  5. The Capabilities of Chaos and Complexity

    Directory of Open Access Journals (Sweden)

    David L. Abel

    2009-01-01

    Full Text Available To what degree could chaos and complexity have organized a Peptide or RNA World of crude yet necessarily integrated protometabolism? How far could such protolife evolve in the absence of a heritable linear digital symbol system that could mutate, instruct, regulate, optimize and maintain metabolic homeostasis? To address these questions, chaos, complexity, self-ordered states, and organization must all be carefully defined and distinguished. In addition their cause-and-effect relationships and mechanisms of action must be delineated. Are there any formal (non physical, abstract, conceptual, algorithmic components to chaos, complexity, self-ordering and organization, or are they entirely physicodynamic (physical, mass/energy interaction alone? Chaos and complexity can produce some fascinating self-ordered phenomena. But can spontaneous chaos and complexity steer events and processes toward pragmatic benefit, select function over non function, optimize algorithms, integrate circuits, produce computational halting, organize processes into formal systems, control and regulate existing systems toward greater efficiency? The question is pursued of whether there might be some yet-to-be discovered new law of biology that will elucidate the derivation of prescriptive information and control. “System” will be rigorously defined. Can a low-informational rapid succession of Prigogine’s dissipative structures self-order into bona fide organization?

  6. 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 ...

  7. 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…

  8. FRUSTRATION EFFECT ON SYNCHRONIZATION AND CHAOS IN COUPLED OSCILLATORS

    Institute of Scientific and Technical Information of China (English)

    ZHENG ZHI-GANG

    2001-01-01

    Synchronization dynamics in an array of coupled periodic oscillators with quenched natural frequencies are discussed in the presence of homogeneous phase shifts (frustrations). Frustration-induced desynchronization and chaos are found. The torus-doubling route to chaos, toroidal chaos and torus crisis are investigated.

  9. Emergence of integer quantum Hall effect from chaos

    Science.gov (United States)

    Tian, Chushun; Chen, Yu; Wang, Jiao

    2016-02-01

    We present an analytic microscopic theory showing that in a large class of spin-1/2 quasiperiodic quantum kicked rotors, a dynamical analog of the integer quantum Hall effect (IQHE) emerges from an intrinsic chaotic structure. Specifically, the inverse of the Planck's quantum (he) and the rotor's energy growth rate mimic the "filling fraction" and the "longitudinal conductivity" in conventional IQHE, respectively, and a hidden quantum number is found to mimic the "quantized Hall conductivity." We show that for an infinite discrete set of critical values of he, the long-time energy growth rate is universal and of order of unity ("metallic" phase), but otherwise vanishes ("insulating" phase). Moreover, the rotor insulating phases are topological, each of which is characterized by a hidden quantum number. This number exhibits universal behavior for small he, i.e., it jumps by unity whenever he decreases, passing through each critical value. This intriguing phenomenon is not triggered by the likes of Landau band filling, well known to be the mechanism for conventional IQHE, and far beyond the canonical Thouless-Kohmoto-Nightingale-Nijs paradigm for quantum Hall transitions. Instead, this dynamical phenomenon is of strong chaos origin; it does not occur when the dynamics is (partially) regular. More precisely, we find that a topological object, similar to the topological theta angle in quantum chromodynamics, emerges from strongly chaotic motion at microscopic scales, and its renormalization gives the hidden quantum number. Our analytic results are confirmed by numerical simulations. Our findings indicate that rich topological quantum phenomena can emerge from chaos and might point to a new direction of study in the interdisciplinary area straddling chaotic dynamics and condensed matter physics. This work is a substantial extension of a short paper published earlier by two of us [Y. Chen and C. Tian, Phys. Rev. Lett. 113, 216802 (2014), 10.1103/PhysRevLett.113.216802].

  10. 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...

  11. Avoiding Quantum Chaos in Quantum Computation

    CERN Document Server

    Berman, G P; Izrailev, F M; Tsifrinovich, V I

    2001-01-01

    We study a one-dimensional chain of nuclear $1/2-$spins in an external time-dependent magnetic field. This model is considered as a possible candidate for experimental realization of quantum computation. According to the general theory of interacting particles, one of the most dangerous effects is quantum chaos which can destroy the stability of quantum operations. According to the standard viewpoint, the threshold for the onset of quantum chaos due to an interaction between spins (qubits) strongly decreases with an increase of the number of qubits. Contrary to this opinion, we show that the presence of a magnetic field gradient helps to avoid quantum chaos which turns out to disappear with an increase of the number of qubits. We give analytical estimates which explain this effect, together with numerical data supporting

  12. 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.

  13. 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....

  14. 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.

  15. 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

  16. 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

  17. 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

  18. Ventilatory chaos is impaired in carotid atherosclerosis.

    Directory of Open Access Journals (Sweden)

    Laurence Mangin

    Full Text Available Ventilatory chaos is strongly linked to the activity of central pattern generators, alone or influenced by respiratory or cardiovascular afferents. We hypothesized that carotid atherosclerosis should alter ventilatory chaos through baroreflex and autonomic nervous system dysfunctions. Chaotic dynamics of inspiratory flow was prospectively evaluated in 75 subjects undergoing carotid ultrasonography: 27 with severe carotid stenosis (>70%, 23 with moderate stenosis (<70%, and 25 controls. Chaos was characterized by the noise titration method, the correlation dimension and the largest Lyapunov exponent. Baroreflex sensitivity was estimated in the frequency domain. In the control group, 92% of the time series exhibit nonlinear deterministic chaos with positive noise limit, whereas only 68% had a positive noise limit value in the stenoses groups. Ventilatory chaos was impaired in the groups with carotid stenoses, with significant parallel decrease in the noise limit value, correlation dimension and largest Lyapunov exponent, as compared to controls. In multiple regression models, the percentage of carotid stenosis was the best in predicting the correlation dimension (p<0.001, adjusted R(2: 0.35 and largest Lyapunov exponent (p<0.001, adjusted R(2: 0.6. Baroreflex sensitivity also predicted the correlation dimension values (p = 0.05, and the LLE (p = 0.08. Plaque removal after carotid surgery reversed the loss of ventilatory complexity. To conclude, ventilatory chaos is impaired in carotid atherosclerosis. These findings depend on the severity of the stenosis, its localization, plaque surface and morphology features, and is independently associated with baroreflex sensitivity reduction. These findings should help to understand the determinants of ventilatory complexity and breathing control in pathological conditions.

  19. 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

  20. Chaos in an imperfectly premixed model combustor

    Energy Technology Data Exchange (ETDEWEB)

    Kabiraj, Lipika, E-mail: lipika.kabiraj@tu-berlin.de; Saurabh, Aditya; Paschereit, Christian O. [Hermann Föttinger Institut, Technische Universität Berlin (Germany); Karimi, Nader [School of Engineering, University of Glasgow (United Kingdom); Sailor, Anna [University of Wisconsin-Madison, Madison 53706 (United States); Mastorakos, Epaminondas; Dowling, Ann P. [Department of Engineering, University of Cambridge (United Kingdom)

    2015-02-15

    This article reports nonlinear bifurcations observed in a laboratory scale, turbulent combustor operating under imperfectly premixed mode with global equivalence ratio as the control parameter. The results indicate that the dynamics of thermoacoustic instability correspond to quasi-periodic bifurcation to low-dimensional, deterministic chaos, a route that is common to a variety of dissipative nonlinear systems. The results support the recent identification of bifurcation scenarios in a laminar premixed flame combustor (Kabiraj et al., Chaos: Interdiscip. J. Nonlinear Sci. 22, 023129 (2012)) and extend the observation to a practically relevant combustor configuration.

  1. Atoms in static fields Chaos or Diffraction?

    CERN Document Server

    Dando, P A

    1998-01-01

    A brief review of the manifestations of classical chaos observed in atomic systems is presented. Particular attention is paid to the analysis of atomic spectra by periodic orbit-type theories. For diamagnetic non-hydrogenic Rydberg atoms, the dynamical explanation for observed spectral features has been disputed. By building on our previous work on the photoabsorption spectrum, we show how, by the addition of diffractive terms, the spectral fluctuations in the energy level spectrum of general Rydberg atoms can be obtained with remarkable precision from the Gutzwiller trace formula. This provides further evidence that non-hydrogenic systems are most naturally described in terms of diffraction rather than classical chaos.

  2. 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.

  3. Quantum chaos on a critical Fermi surface

    CERN Document Server

    Patel, Aavishkar A

    2016-01-01

    We compute parameters characterizing many-body quantum chaos for a critical Fermi surface without quasiparticle excitations. We examine a theory of $N$ species of fermions at non-zero density coupled to a $U(1)$ gauge field in two spatial dimensions, and determine the Lyapunov rate and the butterfly velocity in an extended RPA approximation. The thermal diffusivity is found to be universally related to these chaos parameters, i.e. the relationship is independent of $N$, the gauge coupling constant, the Fermi velocity, the Fermi surface curvature, and high energy details.

  4. 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.

  5. 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.

  6. 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...

  7. Phase Chaos and Multistability in the Discrete Kuramoto Model

    DEFF Research Database (Denmark)

    Maistrenko, V. L.; Vasylenko, A. A.; Maistrenko, Y. L.;

    2008-01-01

    The paper describes the appearance of a novel high-dimensional chaotic regime, called phase chaos, in the discrete Kuramoto model of globally coupled phase oscillators. This type of chaos is observed at small and intermediate values of the coupling strength. It is caused by the nonlinear...... interaction of the oscillators, while the individual oscillators behave periodically when left uncoupled. For the four-dimensional discrete Kuramoto model, we outline the region of phase chaos in the parameter plane, distinguish the region where the phase chaos coexists with other periodic attractors......, and demonstrate, in addition, that the transition to the phase chaos takes place through the torus destruction scenario....

  8. 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.

  9. 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…

  10. 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

  11. 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

  12. Quantum dynamical entropies in discrete classical chaos

    Energy Technology Data Exchange (ETDEWEB)

    Benatti, Fabio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Cappellini, Valerio [Dipartimento di Fisica Teorica, Universita di Trieste, Strada Costiera 11, 34014 Trieste (Italy); Zertuche, Federico [Instituto de Matematicas, UNAM, Unidad Cuernavaca, AP 273-3, Admon. 3, 62251 Cuernavaca, Morelos (Mexico)

    2004-01-09

    We discuss certain analogies between quantization and discretization of classical systems on manifolds. In particular, we will apply the quantum dynamical entropy of Alicki and Fannes to numerically study the footprints of chaos in discretized versions of hyperbolic maps on the torus.

  13. Chaos in the Belousov-Zhabotinsky reaction

    Science.gov (United States)

    Field, Richard J.

    The dynamics of reacting chemical systems is governed by typically polynomial differential equations that may contain nonlinear terms and/or embedded feedback loops. Thus the dynamics of such systems may exhibit features associated with nonlinear dynamical systems, including (among others): temporal oscillations, excitability, multistability, reaction-diffusion-driven formation of spatial patterns, and deterministic chaos. These behaviors are exhibited in the concentrations of intermediate chemical species. Bifurcations occur between particular dynamic behaviors as system parameters are varied. The governing differential equations of reacting chemical systems have as variables the concentrations of all chemical species involved, as well as controllable parameters, including temperature, the initial concentrations of all chemical species, and fixed reaction-rate constants. A discussion is presented of the kinetics of chemical reactions as well as some thermodynamic considerations important to the appearance of temporal oscillations and other nonlinear dynamic behaviors, e.g., deterministic chaos. The behavior, chemical details, and mechanism of the oscillatory Belousov-Zhabotinsky Reaction (BZR) are described. Furthermore, experimental and mathematical evidence is presented that the BZR does indeed exhibit deterministic chaos when run in a flow reactor. The origin of this chaos seems to be in toroidal dynamics in which flow-driven oscillations in the control species bromomalonic acid couple with the BZR limit cycle...

  14. 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.

  15. 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.

  16. 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

  17. A Framework for Chaos Theory Career Counselling

    Science.gov (United States)

    Pryor, Robert G. L.

    2010-01-01

    Theory in career development counselling provides a map that counsellors can use to understand and structure the career counselling process. It also provides a means to communicate this understanding and structuring to their clients as part of the counselling intervention. The chaos theory of careers draws attention to the complexity,…

  18. 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.

  19. Spatio-temporal chaos : A solvable model

    NARCIS (Netherlands)

    Diks, C; Takens, F; DeGoede, J

    1997-01-01

    A solvable coupled map lattice model exhibiting spatio-temporal chaos is studied. Exact expressions are obtained for the spectra of Lyapunov exponents as a function of the model parameters. Although the model has spatio-temporal structure, the time series measured at a single lattice site are shown

  20. Many-body chaos at weak coupling

    Science.gov (United States)

    Stanford, Douglas

    2016-10-01

    The strength of chaos in large N quantum systems can be quantified using λ L , the rate of growth of certain out-of-time-order four point functions. We calculate λ L to leading order in a weakly coupled matrix Φ4 theory by numerically diagonalizing a ladder kernel. The computation reduces to an essentially classical problem.

  1. Dynamic system uncertainty propagation using polynomial chaos

    Institute of Scientific and Technical Information of China (English)

    Xiong Fenfen; Chen Shishi; Xiong Ying

    2014-01-01

    The classic polynomial chaos method (PCM), characterized as an intrusive methodology, has been applied to uncertainty propagation (UP) in many dynamic systems. However, the intrusive polynomial chaos method (IPCM) requires tedious modification of the governing equations, which might introduce errors and can be impractical. Alternative to IPCM, the non-intrusive polynomial chaos method (NIPCM) that avoids such modifications has been developed. In spite of the frequent application to dynamic problems, almost all the existing works about NIPCM for dynamic UP fail to elaborate the implementation process in a straightforward way, which is important to readers who are unfamiliar with the mathematics of the polynomial chaos theory. Meanwhile, very few works have compared NIPCM to IPCM in terms of their merits and applicability. Therefore, the mathematic procedure of dynamic UP via both methods considering parametric and initial condition uncertainties are comparatively discussed and studied in the present paper. Comparison of accuracy and efficiency in statistic moment estimation is made by applying the two methods to several dynamic UP problems. The relative merits of both approaches are discussed and summarized. The detailed description and insights gained with the two methods through this work are expected to be helpful to engineering designers in solving dynamic UP problems.

  2. 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

  3. 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.

  4. Controlling halo-chaos via wavelet-based feedback

    Directory of Open Access Journals (Sweden)

    Jin-Qing Fang

    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.

  5. 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

  6. 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...

  7. 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.

  8. 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...

  9. 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

  10. 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.

  11. 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.

  12. 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...

  13. 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...... resolution (allowing for investigations of sub-annual core field changes). More than 14 years of data from the satellites Ørsted (March 1999 to June 2013), CHAMP (July 2000 to September 2010) and SAC-C (2000 to 2004), augmented with ground observatory revised monthly mean values (1997 to 2013) have been used...... for this model. Maximum spherical harmonic degree of the static (crustal) field is n=100. The core field time changes are expressed by spherical harmonic expansion coefficients up to n=20, described by order 6 splines (with 6-month knot spacing) spanning the time interval 1997.0 to 2013.5. The third time...

  14. 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...

  15. 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.

  16. 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

  17. Quantum chaos in QCD and hadrons

    CERN Document Server

    Markum, H; Pullirsch, R; Sengl, B; Wagenbrunn, R F; Markum, Harald; Plessas, Willibald; Pullirsch, Rainer; Sengl, Bianka; Wagenbrunn, Robert F.

    2005-01-01

    This article is the written version of a talk delivered at the Workshop on Nonlinear Dynamics and Fundamental Interactions in Tashkent and starts with an introduction into quantum chaos and its relationship to classical chaos. The Bohigas-Giannoni-Schmit conjecture is formulated and evaluated within random-matrix theory. In accordance to the title, the presentation is twofold and begins with research results on quantum chromodynamics and the quark-gluon plasma. We conclude with recent research work on the spectroscopy of baryons. Within the framework of a relativistic constituent quark model we investigate the excitation spectra of the nucleon and the delta with regard to a possible chaotic behavior for the cases when a hyperfine interaction of either Goldstone-boson-exchange or one-gluon-exchange type is added to the confinement interaction. Agreement with predictions from the experimental hadron spectrum is established.

  18. 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.

  19. 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.

  20. Intrinsic Depletion or Not

    DEFF Research Database (Denmark)

    Klösgen, Beate; Bruun, Sara; Hansen, Søren;

    with an AFM (2).    The intuitive explanation for the depletion based on "hydrophobic mismatch" between the obviously hydrophilic bulk phase of water next to the hydrophobic polymer. It would thus be an intrinsic property of all interfaces between non-matching materials. The detailed physical interaction path......  The presence of a depletion layer of water along extended hydrophobic interfaces, and a possibly related formation of nanobubbles, is an ongoing discussion. The phenomenon was initially reported when we, years ago, chose thick films (~300-400Å) of polystyrene as cushions between a crystalline...

  1. Intrinsic Depletion or Not

    DEFF Research Database (Denmark)

    Klösgen, Beate; Bruun, Sara; Hansen, Søren;

    with an AFM (2). The intuitive explanation for the depletion based on "hydrophobic mismatch" between the obviously hydrophilic bulk phase of water next to the hydrophobic polymer. It would thus be an intrinsic property of all interfaces between non-matching materials. The detailed physical interaction path......  The presence of a depletion layer of water along extended hydrophobic interfaces, and a possibly related formation of nanobubbles, is an ongoing discussion. The phenomenon was initially reported when we, years ago, chose thick films (~300-400Å) of polystyrene as cushions between a crystalline...

  2. 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 ...

  3. 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.

  4. Legal System and Legal Chaos Theory

    OpenAIRE

    Amir Syarifudin; Indah Febriani

    2015-01-01

    Order of the universe and other objects can be described either by cosmology and physics. But from of the regularity of the object there in terms or aspect of irregularity or fractal (broken) that difficult to describe by Auklides and Calculus mathematical models. Benoit Medelbrot tried to explain the chaotic objects with fractal theory which basically a branch of mathematics. The fractal theory affect the view of the law that inspired Charles Sampford which then sparked a legal chaos theory....

  5. 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 ...

  6. 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.

  7. 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.

  8. Chaos in a topologically transitive system

    Institute of Scientific and Technical Information of China (English)

    XIONG; Jincheng

    2005-01-01

    The chaotic phenomena have been studied in a topologically transitive system and it has been shown that the erratic time dependence of orbits in such a topologically transitive system is more complicated than what described by the well-known technology "Li-Yorke chaos". The concept "sensitive dependency on initial conditions" has been generalized, and the chaotic phenomena has been discussed for transitive systems with the generalized sensitive dependency property.

  9. Reducing or enhancing chaos using periodic orbits.

    Science.gov (United States)

    Bachelard, R; Chandre, C; Leoncini, X

    2006-06-01

    A method to reduce or enhance chaos in Hamiltonian flows with two degrees of freedom is discussed. This method is based on finding a suitable perturbation of the system such that the stability of a set of periodic orbits changes (local bifurcations). Depending on the values of the residues, reflecting their linear stability properties, a set of invariant tori is destroyed or created in the neighborhood of the chosen periodic orbits. An application on a paradigmatic system, a forced pendulum, illustrates the method.

  10. Chaos in free electron laser oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Bruni, C. [Univ Paris 11, LAL, UMR 8607, F-91898 Orsay, (France); Bachelard, R.; Couprie, M.E. [Synchrotron SOLEIL, F-91192 Gif Sur Yvette, (France); Garzella, D. [CEA DSM DRECAM SPAM, F-91191 Gif Sur Yvette, (France); Orlandi, G.L. [CR Frascati FIM FISACC, ENEA, I-00044 Frascati, (Italy)

    2009-07-01

    The chaotic nature of a storage-ring free electron laser (FEL) is investigated. The derivation of a low embedding dimension for the dynamics allows the low-dimensionality of this complex system to be observed, whereas its unpredictability is demonstrated, in some ranges of parameters, by a positive Lyapounov exponent. The route to chaos is then explored by tuning a single control parameter, and a period-doubling cascade is evidenced, as well as intermittence. (authors)

  11. 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.

  12. Bifurcations and Chaos in Duffing Equation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    The Duffing equation with even-odd asymmetrical nonlinear-restoring force and one external forcing is investigated. The conditions of existence of primary resonance, second-order, third-order subharmonics, m-order subharmonics and chaos are given by using the second-averaging method, the Melnikov method and bifurcation theory. Numerical simulations including bifurcation diagram, bifurcation surfaces and phase portraits show the consistence with the theoretical analysis. The numerical results also exhibit new dynamical behaviors including onset of chaos, chaos suddenly disappearing to periodic orbit, cascades of inverse period-doubling bifurcations, period-doubling bifurcation, symmetry period-doubling bifurcations of period-3 orbit, symmetry-breaking of periodic orbits, interleaving occurrence of chaotic behaviors and period-one orbit, a great abundance of periodic windows in transient chaotic regions with interior crises and boundary crisis and varied chaotic attractors. Our results show that many dynamical behaviors are strictly departure from the behaviors of the Duffing equation with odd-nonlinear restoring force.

  13. 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.

  14. Chaos driven by interfering memory

    CERN Document Server

    Perrard, Stéphane; Fort, Emmanuel; Couder, Yves

    2016-01-01

    The transmission of information can couple two entities of very different nature, one of them serving as a memory for the other. Here we study the situation in which information is stored in a wave field and serves as a memory that pilots the dynamics of a particle. Such a system can be implemented by a bouncing drop generating surface waves sustained by a parametric forcing. The motion of the resulting "walker" when confined in a harmonic potential well is generally disordered. Here we show that these trajectories correspond to chaotic regimes characterized by intermittent transitions between a discrete set of states. At any given time, the system is in one of these states characterized by a double quantization of size and angular momentum. A low dimensional intermittency determines their respective probabilities. They thus form an eigenstate basis of decomposition for what would be observed as a superposition of states if all measurements were intrusive.

  15. 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.

  16. 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

  17. Using largest Lyapunov exponent to confirm the intrinsic stability of boiling water reactors

    Energy Technology Data Exchange (ETDEWEB)

    Gavilian-Moreno, Carlos [Iberdrola Generacion, S.A., Cofrentes Nuclear Power Plant, Project Engineering Department, Paraje le Plano S/N, Valencia (Spain); Espinosa-Paredes, Gilberto [Area de ingeniera en Recursos Energeticos, Universidad Autonoma Metropolitana-Iztapalapa, Mexico city (Mexico)

    2016-04-15

    The aim of this paper is the study of instability state of boiling water reactors with a method based in largest Lyapunov exponents (LLEs). Detecting the presence of chaos in a dynamical system is an important problem that is solved by measuring the LLE. Lyapunov exponents quantify the exponential divergence of initially close state-space trajectories and estimate the amount of chaos in a system. This method was applied to a set of signals from several nuclear power plant (NPP) reactors under commercial operating conditions that experienced instabilities events, apparently each of a different nature. Laguna Verde and Forsmark NPPs with in-phase instabilities, and Cofrentes NPP with out-of-phases instability. This study presents the results of intrinsic instability in the boiling water reactors of three NPPs. In the analyzed cases the limit cycle was not reached, which implies that the point of equilibrium exerts influence and attraction on system evolution.

  18. 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

  19. 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.

  20. 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.

  1. Stratified Spatiotemporal Chaos in Anisotropic Reaction-Diffusion Systems

    Energy Technology Data Exchange (ETDEWEB)

    Baer, M.; Thiele, U. [Max-Planck-Institut fuer Physik Komplexer Systeme, Noethnitzer Strasse 38, 01187 Dresden (Germany); Hagberg, A. [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545 (United States); Baer, M.; Meron, E. [The Jacob Blaustein Institute for Desert Research and the Physics Department, Ben-Gurion University, Sede Boker Campus 84990 (Israel); Thiele, U. [Instituto Pluridisciplinar, Universidad Complutense Madrid, Paseo Juan XXIII 1, E-28040 Madrid (Spain)

    1999-09-01

    Numerical simulations of two-dimensional pattern formation in an anisotropic bistable reaction-diffusion medium reveal a new dynamical state, stratified spatiotemporal chaos, characterized by strong correlations along one of the principal axes. Equations that describe the dependence of front motion on the angle illustrate the mechanism leading to stratified chaos. {copyright} {ital 1999} {ital The American Physical Society}

  2. 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.

  3. 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.

  4. 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.

  5. The Chaos Game on a General Iterated Function System

    CERN Document Server

    Barnsley, Michael

    2010-01-01

    The main theorem of this paper establishes conditions under which the "chaos game" algorithm almost surely yields the attractor of an iterated function system. The theorem holds in a very general setting, even for non contractive iterated function systems, and under weaker conditions on the random orbit of the chaos game than obtained previously.

  6. 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

  7. 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.…

  8. 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

  9. 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…

  10. 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...

  11. 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...

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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

  17. Time reversibility, computer simulation, and chaos

    CERN Document Server

    Hoover, William Graham

    1999-01-01

    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

  18. 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.

  19. A new optimization algorithm based on chaos

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    In this article, some methods are proposed for enhancing the converging velocity of the COA (chaos optimization algorithm) based on using carrier wave two times, which can greatly increase the speed and efficiency of the first carrier wave's search for the optimal point in implementing the sophisticated searching during the second carrier wave is faster and more accurate.In addition, the concept of using the carrier wave three times is proposed and put into practice to tackle the multi-variables optimization problems, where the searching for the optimal point of the last several variables is frequently worse than the first several ones.

  20. Bose-Hubbard Hamiltonian: Quantum chaos approach

    Science.gov (United States)

    Kolovsky, Andrey R.

    2016-03-01

    We discuss applications of the theory of quantum chaos to one of the paradigm models of many-body quantum physics — the Bose-Hubbard (BH) model, which describes, in particular, interacting ultracold Bose atoms in an optical lattice. After preliminary, pure quantum analysis of the system we introduce the classical counterpart of the BH model and the governing semiclassical equations of motion. We analyze these equations for the problem of Bloch oscillations (BOs) of cold atoms where a number of experimental results are available. The paper is written for nonexperts and can be viewed as an introduction to the field.

  1. The CHAOS-4 Geomagnetic Field Model

    Science.gov (United States)

    Olsen, N.; Finlay, C. C.; Luhr, H.; Sabaka, T. J.; Michaelis, I.; Rauberg, J.; Tøffner-clausen, L.

    2013-12-01

    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 resolution (allowing for investigations of sub-annual core field changes). More than 14 years of data from the satellites Ørsted (March 1999 to June 2013), CHAMP (July 2000 to September 2010) and SAC-C (2000 to 2004), augmented with ground observatory revised monthly mean values (1997 to 2013) have been used for this model. Maximum spherical harmonic degree of the static (crustal) field is n=100. The core field time changes are expressed by spherical harmonic expansion coefficients up to n=20, described by order 6 splines (with 6-month knot spacing) spanning the time interval 1997.0 to 2013.5. The third time derivative of the squared magnetic field intensity is regularized at the core-mantle boundary. No spatial regularization is applied for the core field, but the high-degree crustal field is regularized for n>85. As part of the modeling effort we co-estimate a model of the large-scale magnetospheric field (with expansions in the GSM and SM coordinate system up to degree n = 2 and parameterization of the time dependence using the decomposition of Dst into external (Est) and induced (Ist) parts) and perform an in-flight alignment of the vector data (co-estimation of the Euler describing the rotation between the coordinate systems of the vector magnetometer and of the star sensor providing attitude information). The final CHAOS-4 model is derived by merging two sub-models: its low-degree part has been obtained using similar model parameterization and data sets as used for previous CHAOS models (but of course including newer satellite observations), while its high-degree crustal field part is solely determined from low-altitude CHAMP satellite observations between January 2009 and

  2. 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

  3. 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.

  4. Chaos Synchronization in Two Coupled Duffing Oscillators

    Institute of Scientific and Technical Information of China (English)

    方见树; 荣曼生; 方焯; 刘小娟

    2001-01-01

    We have obtained two general unstable periodic solutions near the homoclinic orbits of two coupled Duffing oscillators with weak periodic perturbations by using the direct perturbation technique. Theoretical analysis reveals that the stable periodic orbits are embedded in the Melnikov chaotic attractors. The corresponding numerical results show that the phase portraits in the (x, u) and (y, v) planes are identical and are synchronized when the parameters of the two coupled oscillators are identical, but they are different and asynchronized when there is any difference between these parameters. It has been shown that the system parameters play a very important role in chaos control and synchronization.

  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. 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

  7. 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.

  8. 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.

  9. 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 ...

  10. 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.)

  11. 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

  12. Intrinsic Angular Momentum of Light.

    Science.gov (United States)

    Santarelli, Vincent

    1979-01-01

    Derives a familiar torque-angular momentum theorem for the electromagnetic field, and includes the intrinsic torques exerted by the fields on the polarized medium. This inclusion leads to the expressions for the intrinsic angular momentum carried by the radiation traveling through a charge-free medium. (Author/MA)

  13. 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

  14. 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.

  15. Chaos and structure of level densities

    Energy Technology Data Exchange (ETDEWEB)

    Moller, Peter [Los Alamos National Laboratory; Aberg, Sven [LUND SWEDEN; Uhrenholt, Henrik [LUND SWEDEN; Ickhikawa, Takatoshi [RIKEN

    2008-01-01

    The energy region of the first few MeV above the ground state shows interesting features of the nucleus. Beyond an ordered energy region just above the ground-state the dynamics changes, and chaotic features are observed in the neutron resonance region. The statistical properties of energies and wave-functions are common to all chaotic nuclei. However, if instead a global property, like the local level-density function is studied, strong structure effects emerge. In this contribution we discuss these two different facets of warm nuclei. In section 2 the onset of chaos with increasing excitation energy is discussed, with both experimental observations and proposed theoretical mechanisms as starting points. The structure of level densities in the same excitation energy region based on the two different starting points, is treated in section 3, where we give a short presentation of a newly developed combinatorial level-density modell. Some results from the model are presented and discussed. Two coexisting facets of warm nuclei, quantum chaos and structure of the level density, are considered. A newly developed combinatorial level-density model is presented, and the role of collective enhancements discussed. An example of extreme parity enhancement is shown.

  16. Equilibrium behavior of coarse-grained chaos

    Science.gov (United States)

    Egolf, David A.; Ballard, Christopher C.; Esty, C. Clark

    2015-03-01

    A wide variety of systems exhibiting spatiotemporal chaos have been shown to be extensive, in that their fractal dimensions grow linearly with volume. Ruelle argued that this extensivity is evidence that these systems can be viewed as a gas of weakly-interacting regions. We have tested this idea by performing large-scale computational studies of spatiotemporal chaos in the 1D complex Ginzburg-Landau equation, and we have found that aspects of the coarse-grained system are well-described not only as a gas, but as an equilibrium gas -- in particular, a Tonks gas (and variants) in the grand canonical ensemble. Furthermore, for small system sizes, the average number of particles in the corresponding Tonks gas exhibits oscillatory, decaying deviations from extensivity in agreement with deviations in the fractal dimension found by Fishman and Egolf. This result not only supports Ruelle's picture but also suggests that the coarse-grained behavior of this far-from-equilibrium system might be understood using equilibrium statistical mechanics.

  17. 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

  18. Decrease of cardiac chaos in congestive heart failure

    Science.gov (United States)

    Poon, Chi-Sang; Merrill, Christopher K.

    1997-10-01

    The electrical properties of the mammalian heart undergo many complex transitions in normal and diseased states. It has been proposed that the normal heartbeat may display complex nonlinear dynamics, including deterministic chaos,, and that such cardiac chaos may be a useful physiological marker for the diagnosis and management, of certain heart trouble. However, it is not clear whether the heartbeat series of healthy and diseased hearts are chaotic or stochastic, or whether cardiac chaos represents normal or abnormal behaviour. Here we have used a highly sensitive technique, which is robust to random noise, to detect chaos. We analysed the electrocardiograms from a group of healthy subjects and those with severe congestive heart failure (CHF), a clinical condition associated with a high risk of sudden death. The short-term variations of beat-to-beat interval exhibited strongly and consistently chaotic behaviour in all healthy subjects, but were frequently interrupted by periods of seemingly non-chaotic fluctuations in patients with CHF. Chaotic dynamics in the CHF data, even when discernible, exhibited a high degree of random variability over time, suggesting a weaker form of chaos. These findings suggest that cardiac chaos is prevalent in healthy heart, and a decrease in such chaos may be indicative of CHF.

  19. HOPF BIFURCATION AND CHAOS OF FINANCIAL SYSTEM ON CONDITION OF SPECIFIC COMBINATION OF PARAMETERS

    Institute of Scientific and Technical Information of China (English)

    Junhai MA; Yaqiang CUI; Lixia LIU

    2008-01-01

    This paper studies the global bifurcation and Hopf bifurcation of one kind of complicated financial system with different parameter combinations. Conditions on which bifurcation happens, and the critical system structure when the system transforms from one kind of topological structure to another are studied as well. The criterion for identifying Hopf bifurcation under different parameter combinations is also given. The chaotic character of this system under quasi-periodic force is finally studied. The bifurcation structure graphs are given when two parameters of the combination are fixed while the other parameter varies. The presence and stability of 2 and 3 dimensional torus bifurcation are studied. All of the Lyapunov exponents of the system with different bifurcation parameters and routes leading the system to chaos with different parameter combinations are studied. It is of important theoretical and practical meaning to probe the intrinsic mechanism of such continuous complicated financial system and to find the macro control policies for such kind of system.

  20. Study on Chaos Created by Hopf Bifurcation of One Kind of Financial System and Its Application

    Institute of Scientific and Technical Information of China (English)

    JunhaiMa; BiaoRen; YanGao

    2004-01-01

    From a mathematical model of one kind complicated financial system, corresponding local topological structures of such kind system on condition of certain parametercombination, unstable equilibrium point of the system, conditions on which Hopf bifurcation is created and stability of the limit circle corresponding to the Hopf bifurcation as well as condition on which the limit circle is stable have been studied. From relationship between each parameter and the Hopf bifurcation all the way to route which leads to chaos etc have been studied. Following the above, conditions on which complicated behaviors created locally in such kind system has been analyzed. By applying fractal dimension, Lyapunov index, the intrinsic complexity of the system on such condition has been studied, and result of the numerical simulation proves the theory of this paper correct.

  1. 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

  2. CHAOS THEORY: A CONTRIBUTION TO THE FORMATION OF STRATEGIES

    Directory of Open Access Journals (Sweden)

    Marcio Luiz Marietto

    2011-12-01

    Full Text Available It is our intention, through this work, to contribute to the understanding of the influence of chaos theory on the formation of organizational strategies in the dynamic and complex environment in which organizations are embedded. In this sense, we present a theoretical review, leveraged by a dialectical epistemology, in which we propose to show some attributes of chaos theory and theoretical assumptions to be considered in the context of different areas of organizational strategy, with the goal of trying to elucidate and approximate the analytical characteristics of both theories and make evident how chaos theory can contribute to and/or influence the formation of business strategies.

  3. Diffusive Lorenz dynamics: Coherent structures and spatiotemporal chaos

    Institute of Scientific and Technical Information of China (English)

    YuehongQIAN; HudongCHEN; Da-HsuanFENG

    2000-01-01

    In this paper, we are interested in collective behaviors of many interacting Lorenz strange attractors. With an intermediate diffusion coupling between the attractors,a new remarkable synchronization of well organized structures merges as a result of two competing mechanisms: temporal chaos and spatial diffusive stabilization. A window of the coupling parameter for coherent structures is found numerically. Different from all existing scenarios of routes to chaos (period doubling, intermittency and strange attractors), an algorithmetic increase of wavenumbers before an abrupt change to chaos (compared to the periodic doubling geometrical) is unexpectedly discovered. Meta-stable states are also observed in simulations.

  4. 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.

  5. 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

  6. New chaos-based encryption scheme for digital sequence

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhengwei; Fan Yangyu; Zeng Li

    2007-01-01

    To enhance the anti-breaking performance of privacy information, this article proposes a new encryption method utilizing the leaping peculiarity of the periodic orbits of chaos systems. This method maps the secret sequence to several chaos periodic orbits, and a short sequence obtained by evolving the system parameters of the periodic orbits in another nonlinear system will be the key to reconstruct these periodic orbits. In the decryption end, the shadowing method of chaos trajectory based on the modified Newton-Raphson algorithm is adopted to restore these system parameters. Through deciding which orbit each pair coordinate falls on, the original digital sequence can be decrypted.

  7. 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.

  8. Contributions of plasma physics to chaos and nonlinear dynamics

    Science.gov (United States)

    Escande, D. F.

    2016-11-01

    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

  9. 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

  10. 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.

  11. Quantum Chaos in Physical Systems from Super Conductors to Quarks

    CERN Document Server

    Bittner, E; Pullirsch, R; Bittner, Elmar; Markum, Harald; Pullirsch, Rainer

    2001-01-01

    This article is the written version of a talk delivered at the Bexbach Colloquium of Science 2000 and starts with an introduction into quantum chaos and its relationship to classical chaos. The Bohigas-Giannoni-Schmit conjecture is formulated and evaluated within random-matrix theory. Several examples of physical systems exhibiting quantum chaos ranging from nuclear to solid state physics are presented. The presentation concludes with recent research work on quantum chromodynamics and the quark-gluon plasma. In the case of a chemical potential the eigenvalue spectrum becomes complex and one has to deal with non-Hermitian random-matrix theory.

  12. Chaos and order in stateless societies: Intercommunity exchange as a factor impacting the population dynamical patterns

    Energy Technology Data Exchange (ETDEWEB)

    Medvinsky, Alexander B., E-mail: medvinsky@iteb.ru [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation); Rusakov, Alexey V. [Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino 142290, Moscow Region (Russian Federation)

    2011-06-15

    Highlights: > We model community dynamics in stateless societies. > Intercommunity barter is shown to be a factor impacting the societies dynamics. > Increase in the human population growth rate can lead to appearance of chaos. > Secular and millennial cycles are found to arise as a result of the barter. - Abstract: The once abstract notions of dynamical chaos now appear naturally in various systems [Kaplan D, Glass L. Understanding nonlinear dynamics. New York: Springer; 1995]. As a result, future trajectories of the systems may be difficult to predict. In this paper, we demonstrate the appearance of chaotic dynamics in model human communities, which consist of producers of agricultural product and producers of agricultural equipment. In the case of a solitary community, the horizon of predictability of the human population dynamics is shown to be dependent on both intrinsic instability of the dynamics and the chaotic attractor sizes. Since a separate community is usually a part of a larger commonality, we study the dynamics of social systems consisting of two interacting communities. We show that intercommunity barter can lead to stabilization of the dynamics in one of the communities, which implies persistence of stable equilibrium under changes of the maximum value of the human population growth rate. However, in the neighboring community, the equilibrium turns into a stable limit cycle as the maximum value of the human population growth rate increases. Following an increase in the maximum value of the human population growth rate leads to period-doubling bifurcations resulting in chaotic dynamics. The horizon of predictability of the chaotic oscillations is found to be limited by 5 years. We demonstrate that the intercommunity interaction can lead to the appearance of long-period harmonics in the chaotic time series. The period of the harmonics is of order 100 and 1000 years. Hence the long-period changes in the population size may be considered as an

  13. 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.

  14. 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.

  15. The International Classification of Headache Disorders

    DEFF Research Database (Denmark)

    Olesen, J.

    2008-01-01

    A set of related medical disorders that lack a proper classification system and diagnostic criteria is like a society without laws. The result is incoherence at best, chaos at worst. For this reason, the International Classification of Headache Disorders (ICHD) is arguably the single most important....... In summary, the ICHD has attained widespread acceptance at the international level and has substantially facilitated both clinical research and clinical care in the field of headache medicine Udgivelsesdato: 2008/5...

  16. 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...

  17. 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.

  18. Chaos synchronization based on intermittent state observer

    Institute of Scientific and Technical Information of China (English)

    Li Guo-Hui; Zhou Shi-Ping; Xu De-Ming

    2004-01-01

    This paper describes the method of synchronizing slave to the master trajectory using an intermittent state observer by constructing a synchronizer which drives the response system globally tracing the driving system asymptotically. It has been shown from the theory of synchronization error-analysis that a satisfactory result of chaos synchronization is expected under an appropriate intermittent period and state observer. Compared with continuous control method,the proposed intermittent method can target the desired orbit more efficiently. The application of the method is demonstrated on the hyperchaotic Rossler systems. Numerical simulations show that the length of the synchronization interval rs is of crucial importance for our scheme, and the method is robust with respect to parameter mismatch.

  19. 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.

  20. 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...

  1. 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.

  2. Chaos in body-vortex interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby; Aref, Hassan

    2010-01-01

    The model of body–vortex interactions, where the fluid flow is planar, ideal and unbounded, and the vortex is a point vortex, is studied. The body may have a constant circulation around it. The governing equations for the general case of a freely moving body of arbitrary shape and mass density...... of a circle is integrable. As the body is made slightly elliptic, a chaotic region grows from an unstable relative equilibrium of the circle-vortex case. The case of a cylindrical body of any shape moving in fluid otherwise at rest is also integrable. A second transition to chaos arises from the limit between...... and an arbitrary number of point vortices are presented. The case of a body and a single vortex is then investigated numerically in detail. In this paper, the body is a homogeneous, elliptical cylinder. For large body–vortex separations, the system behaves much like a vortex pair regardless of body shape. The case...

  3. 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...

  4. 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...

  5. 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...

  6. 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.

  7. 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

  8. Extension of spatiotemporal chaos in glow discharge-semiconductor systems

    Energy Technology Data Exchange (ETDEWEB)

    Akhmet, Marat, E-mail: marat@metu.edu.tr; Fen, Mehmet Onur [Department of Mathematics, Middle East Technical University, 06800 Ankara (Turkey); Rafatov, Ismail [Department of Physics, Middle East Technical University, 06800 Ankara (Turkey)

    2014-12-15

    Generation of chaos in response systems is discovered numerically through specially designed unidirectional coupling of two glow discharge-semiconductor systems. By utilizing the auxiliary system approach, [H. D. I. Abarbanel, N. F. Rulkov, and M. M. Sushchik, Phys. Rev. E 53, 4528–4535 (1996)] it is verified that the phenomenon is not a chaos synchronization. Simulations demonstrate various aspects of the chaos appearance in both drive and response systems. Chaotic control is through the external circuit equation and governs the electrical potential on the boundary. The expandability of the theory to collectives of glow discharge systems is discussed, and this increases the potential of applications of the results. Moreover, the research completes the previous discussion of the chaos appearance in a glow discharge-semiconductor system [D. D. Šijačić U. Ebert, and I. Rafatov, Phys. Rev. E 70, 056220 (2004).].

  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. 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.

  11. 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.

  12. 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...

  13. 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.

  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. 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.

  16. 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

  17. 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.

  18. 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...

  19. 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...

  20. Harmonic structures and intrinsic torsion

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

    2015-01-01

    We discuss the construction of Sp(2)Sp(1)-structures whose fundamental form is closed. In particular, we find 10 new examples of 8-dimensional nilmanifolds that admit an invariant closed 4-form with stabiliser Sp(2) Sp(1). Our constructions entail the notion of SO(4)-structures on 7-manifolds. We...... present a thorough investigation of the intrinsic torsion of such structures, leading to the construction of explicit Lie group examples with invariant intrinsic torsion....

  1. Harmonic structures and intrinsic torsion

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

    We discuss the construction of 8-manifolds with harmonic Sp(2)Sp(1)-structures. In particular, we find 10 new examples of nilmanifolds that admit a closed 4-form Omega whose stabiliser is Sp(2)Sp(1). Our constructions entail the notion of SO(4)-structures on 7-manifolds. We present a thorough inv...... investigation of the intrinsic torsion of such structures; in addition to the construction of harmonic structures, this analysis leads to explicit Lie group examples with invariant intrinsic torsion....

  2. Bifurcations and chaos control in discrete small-world networks

    Institute of Scientific and Technical Information of China (English)

    Li Ning; Sun Hai-Yi; Zhang Qing-Ling

    2012-01-01

    An impulsive delayed feedback control strategy to control period-doubling bifurcations and chaos is proposed.The control method is then applied to a discrete small-world network model.Qualitative analyses and simulations show that under a generic condition,the bifurcations and the chaos can be delayed or eliminated completely.In addition,the periodic orbits embedded in the chaotic attractor can be stabilized.

  3. 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...

  4. 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

  5. Chaos suppression in a spin-torque nano-oscillator

    Science.gov (United States)

    Xu, H. Z.; Chen, X.; Liu, J.-M.

    2008-11-01

    We propose a novel practicable self-control scheme to suppress chaos in a spin-torque nano-oscillator in the presence of spin-polarized dc and ac. The magnetization dynamics is investigated by performing micromagnetic simulation. A complete chaos control diagram is obtained, indicating that employment of this proper self-control scheme over a broad frequency range of the ac can greatly reduce the degree of chaoticity in the oscillator.

  6. 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.

  7. 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.

  8. 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.

  9. Coping with disorder

    DEFF Research Database (Denmark)

    Mosebo, Marianne Bach

    2008-01-01

    The traditionally pastoral people of Karamoja live in an environment fraught with violence, poverty and disorder. However, they also just live life. In this article, I speak out against an imbalance, which I claim exists in the literature on Karamoja; namely that it focuses primarily on the negat......The traditionally pastoral people of Karamoja live in an environment fraught with violence, poverty and disorder. However, they also just live life. In this article, I speak out against an imbalance, which I claim exists in the literature on Karamoja; namely that it focuses primarily...... in a drinking group can become a space of freedom, unity and order in lives lived in an area of chaos and disorder, how negative drinking behaviour is scorned and sanctioned in order to keep the negative sides to drinking under control, and how being a member of a drinking group can be a means to move forward...

  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. Chaos Suppression in a Sine Square Map through Nonlinear Coupling

    Institute of Scientific and Technical Information of China (English)

    Eduardo L. Brugnago; Paulo C. Rech

    2011-01-01

    We study a pair of nonlinearly coupled identical chaotic sine square maps.More specifically,we investigate the chaos suppression associated with the variation of two parameters.Two-dimensional parameter-space regions where the chaotic dynamics of the individual chaotic sine square map is driven towards regular dynamics are delimited.Additionally,the dynamics of the coupled system is numerically characterized as the parameters are changed.In recent years,many efforts have been devoted to chaos suppression in a nonlinear dynamics field.Iglesias et al.[1] reported a chaos suppression method through numerical truncation and rounding errors,with applications in discrete-time systems.Hénon map[2] and the Burgers map[3] were used to illustrate the method.A method of feedback impulsive chaos suppression was introduced by Osipov et al.[4]It is an algorithm of suppressing chaos in continuoustime dissipative systems with an external impulsive force,whose necessary condition is a reduction of the continuous flow to a discrete-time one-dimensional map.%We study a pair of nonlinearly coupled identical chaotic sine square maps. More specifically, we investigate the chaos suppression associated with the variation of two parameters. Two-dimensional parameter-space regions where the chaotic dynamics of the individual chaotic sine square map is driven towards regular dynamics are delimited. Additionally, the dynamics of the coupled system is numerically characterized as the parameters are changed.

  12. The bifurcation threshold value of the chaos detection system for a weak signal

    Institute of Scientific and Technical Information of China (English)

    李月; 杨宝俊; 杜立志; 袁野

    2003-01-01

    Recently, it has become an important problem to confirm the bifurcation threshold value of a chaos detectionsystem for a weak signal in the fields of chaos detection. It is directly related to whether the results of chaos detectionare correct or not. In this paper, the discrimination system for the dynamic behaviour of a chaos detection system fora weak signal is established by using the theory of linear differential equation with periodic coefficients and computingthe Lyapunov exponents of the chaos detection system; and then, the movement state of the chaos detection system isdefined. The simulation experiments show that this method can exactly confirm the bifurcation threshold value of thechaos detection system.

  13. 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)).

  14. 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

  15. Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos.

    Science.gov (United States)

    Yuwen, Tairan; Xue, Yi; Skrynnikov, Nikolai R

    2016-03-29

    to its (loose) association with the protein. Note that spin relaxation data are indispensable in determining the dynamic status of the peptide. Such data can be properly modeled only on a basis of bona fide MD simulations, as shown in our study. We anticipate that in future the field will move away from the ensemble view of protein disorder and toward more sophisticated MD models. This will require further optimization of force fields, aimed specifically at disordered systems. Efforts in this direction have been recently initiated by several research groups; the empirical salt-bridge correction proposed in our work falls in the same category. MD models obtained with the help of suitably refined force fields and guided by experimental NMR data will provide a powerful insight into an intricate world of disordered biomolecules.

  16. 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.

  17. 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.

  18. Chaos in the Showalter-Noyes-Bar-Eli model of the Belousov-Zhabotinskii reaction

    Science.gov (United States)

    Lindberg, David; Turner, Jack S.; Barkley, Dwight

    1990-03-01

    The observation of robust, large-scale chaos in the Showalter-Noyes-Bar-Eli model of the Belousov-Zhabotinskii reaction is reported. The chaos observed is comparable to that found in CSTR experiments at low flow rates.

  19. 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

  20. Asynchronous Rate Chaos in Spiking Neuronal Circuits

    Science.gov (United States)

    Harish, Omri; Hansel, David

    2015-01-01

    The brain exhibits temporally complex patterns of activity with features similar to those of chaotic systems. Theoretical studies over the last twenty years have described various computational advantages for such regimes in neuronal systems. Nevertheless, it still remains unclear whether chaos requires specific cellular properties or network architectures, or whether it is a generic property of neuronal circuits. We investigate the dynamics of networks of excitatory-inhibitory (EI) spiking neurons with random sparse connectivity operating in the regime of balance of excitation and inhibition. Combining Dynamical Mean-Field Theory with numerical simulations, we show that chaotic, asynchronous firing rate fluctuations emerge generically for sufficiently strong synapses. Two different mechanisms can lead to these chaotic fluctuations. One mechanism relies on slow I-I inhibition which gives rise to slow subthreshold voltage and rate fluctuations. The decorrelation time of these fluctuations is proportional to the time constant of the inhibition. The second mechanism relies on the recurrent E-I-E feedback loop. It requires slow excitation but the inhibition can be fast. In the corresponding dynamical regime all neurons exhibit rate fluctuations on the time scale of the excitation. Another feature of this regime is that the population-averaged firing rate is substantially smaller in the excitatory population than in the inhibitory population. This is not necessarily the case in the I-I mechanism. Finally, we discuss the neurophysiological and computational significance of our results. PMID:26230679

  1. Attractors, bifurcations, & chaos nonlinear phenomena in economics

    CERN Document Server

    Puu, Tönu

    2003-01-01

    The present book relies on various editions of my earlier book "Nonlinear Economic Dynamics", first published in 1989 in the Springer series "Lecture Notes in Economics and Mathematical Systems", and republished in three more, successively revised and expanded editions, as a Springer monograph, in 1991, 1993, and 1997, and in a Russian translation as "Nelineynaia Economicheskaia Dinamica". The first three editions were focused on applications. The last was differ­ ent, as it also included some chapters with mathematical background mate­ rial -ordinary differential equations and iterated maps -so as to make the book self-contained and suitable as a textbook for economics students of dynamical systems. To the same pedagogical purpose, the number of illus­ trations were expanded. The book published in 2000, with the title "A ttractors, Bifurcations, and Chaos -Nonlinear Phenomena in Economics", was so much changed, that the author felt it reasonable to give it a new title. There were two new math­ ematics ch...

  2. Chaos Synchronization in Navier-Stokes Turbulence

    Science.gov (United States)

    Lalescu, Cristian; Meneveau, Charles; Eyink, Gregory

    2013-03-01

    Chaos synchronization (CS) has been studied for some time now (Pecora & Carroll 1990), for systems with only a few degrees of freedom as well as for systems described by partial differential equations (Boccaletti et al 2002). CS in general is said to be present in coupled dynamical systems when a specific property of each system has the same time evolution for all, even though the evolution itself is chaotic. The Navier-Stokes (NS) equations describe the velocity for a wide range of fluids, and their solutions are usually called turbulent if fluctuation amplitudes decrease as a power of their wavenumber. There have been some studies of CS for continuous systems (Kocarev et al 1997), but CS for NS turbulence seems not to have been investigated so far. We focus on the synchronization of the small scales of a turbulent flow for which the time history of large scales is prescribed. Our DNS results show that high-wavenumbers in turbulence are fully slaved to modes with wavenumbers up to a critical fraction of the Kolmogorov dissipation wavenumber. The motivation for our work is to study deeply sub-Kolmogorov scales in fully developed turbulence (Schumacher 2007), which we found to be recoverable even at very high Reynolds number from simulations with moderate resolutions. This work is supported by the National Science Foundation's CDI-II program, project CMMI-0941530

  3. A route to chaos using FPGAs

    CERN Document Server

    Muthuswamy, Bharathwaj

    2015-01-01

    The purpose of this introductory book is to couple the teaching of chaotic circuit and systems theory with the use of field programmable gate arrays (FPGAs).     As such, it differs from other texts on chaos: first, it puts emphasis on combining theoretical methods, simulation tools and physical realization to help the reader gain an intuitive understanding of the properties of chaotic systems.  Second, the "medium" used for physical realization is the FPGA.  These devices are massively parallel architectures that can be configured to realize a variety of logic functions.  Hence, FPGAs can be configured to emulate systems of differential equations.  Nevertheless maximizing the capabilities of an FPGA requires the user to understand the underlying hardware and also FPGA design software.  This is achieved by the third distinctive feature of this book: a lab component in each chapter.  Here, readers are asked to experiment with computer simulations and FPGA designs, to further their understanding of con...

  4. Disentangling Complexity from Randomness and Chaos

    Directory of Open Access Journals (Sweden)

    Lena C. Zuchowski

    2012-02-01

    Full Text Available This study aims to disentangle complexity from randomness and chaos, and to present a definition of complexity that emphasizes its epistemically distinct qualities. I will review existing attempts at defining complexity and argue that these suffer from two major faults: a tendency to neglect the underlying dynamics and to focus exclusively on the phenomenology of complex systems; and linguistic imprecisions in describing these phenomenologies. I will argue that the tendency to discuss phenomenology removed from the underlying dynamics is the main root of the difficulties in distinguishing complex from chaotic or random systems. In my own definition, I will explicitly try to avoid these pitfalls. The theoretical contemplations in this paper will be tested on a sample of five models: the random Kac ring, the chaotic CA30, the regular CA90, the complex CA110 and the complex Bak-Sneppen model. Although these modelling studies are restricted in scope and can only be seen as preliminary, they still constitute on of the first attempts to investigate complex systems comparatively.

  5. Genotoxicity of drinking water from Chao Lake

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Q.; Jiao, Q.C. [Nanjing Univ. (China). Dept. of Biological Science and Technology; Huang, X.M.; Jiang, J.P.; Cui, S.Q.; Yao, G.H.; Jiang, Z.R.; Zhao, H.K.; Wang, N.Y. [Anhui Antiepidemic Station, Hefei (China)

    1999-02-01

    Genotoxic activity appears to originate primarily from reactions of chlorine with humic substances in the source waters. Comparisons of extracts of settled versus chlorinated water have confirmed that chlorinating during water treatment produces mutagenic activity in the mutagenicity tests. Present work on XAD-2 extracts of raw, chlorinated (treated), and settled water from the Chao Lake region of China has involved a battery of mutagenicity assays for various genetic endpoints: the Salmonella test, the sister-chromatid exchange (SCE) induction in Chinese hamster lung (CHL) cells, and the micronucleus (MN) induction in the peripheral blood erythrocytes of silver carp. Extracts of raw and treated water but not the settled water are mutagenic in the Salmonella assay. On the other hand, extracts of three water samples show activity in the SCE and MN assays, especially the raw and treated water. These data show that contamination and chlorinating contribute mutagens to drinking water and suggest that the mammalian assays may be more sensitive for detecting mutagenicity in aquatic environment than the Salmonella test.

  6. Nonadiabatic quantum chaos in atom optics

    CERN Document Server

    Prants, S V

    2012-01-01

    Coherent dynamics of atomic matter waves in a standing-wave laser field is studied. In the dressed-state picture, wave packets of ballistic two-level atoms propagate simultaneously in two optical potentials. The probability to make a transition from one potential to another one is maximal when centroids of wave packets cross the field nodes and is given by a simple formula with the single exponent, the Landau--Zener parameter $\\kappa$. If $\\kappa \\gg 1$, the motion is essentially adiabatic. If $\\kappa \\ll 1$, it is (almost) resonant and periodic. If $\\kappa \\simeq 1$, atom makes nonadiabatic transitions with a splitting of its wave packet at each node and strong complexification of the wave function as compared to the two other cases. This effect is referred as nonadiabatic quantum chaos. Proliferation of wave packets at $\\kappa \\simeq 1$ is shown to be connected closely with chaotic center-of-mass motion in the semiclassical theory of point-like atoms with positive values of the maximal Lyapunov exponent. Th...

  7. ICT Capstone projects: The edge of chaos

    Directory of Open Access Journals (Sweden)

    Sue Chard

    Full Text Available Capstone project processes and assessment methodologies continue to be problematic. Experience has led us to review our assessment rubrics and methods with every iteration in an attempt to refine and improve the practice and outcomes. This review has surveyed a broad range of capstone projects describing approaches to practice, assessment and sizing. In their widest sense capstone projects are described as being ambiguous and complex, tantamount, as the title of this paper implies, to artfully practising as if one is \\'on the edge of chaos.\\' There have been promising taxonomies mooted or developed to give insight into evidence of the skills, practice, knowledge and understanding associated with capstone projects. There appears to be, however, a dilemma in terms of creating a succinct vision that might inform the sizing and assessment of projects and enable us to capture its ephemeral nature. Complexity theory appears to go some way towards unpacking relevant factors which could inform the development of tools for assessment and sizing of projects. There are professional heuristics employed in the sizing of projects and standards for the assessment of capstone projects. From this review it can be seen that a fluid but accurate methodology should be developed which addresses the dilemma in such a way as to provide robust conceptual, pedagogical and sociological sizing and assessment practices.

  8. Kinematic dynamo, supersymmetry breaking, and chaos

    Science.gov (United States)

    Ovchinnikov, Igor V.; Enßlin, Torsten A.

    2016-04-01

    The kinematic dynamo (KD) describes the growth of magnetic fields generated by the flow of a conducting medium in the limit of vanishing backaction of the fields onto the flow. The KD is therefore an important model system for understanding astrophysical magnetism. Here, the mathematical correspondence between the KD and a specific stochastic differential equation (SDE) viewed from the perspective of the supersymmetric theory of stochastics (STS) is discussed. The STS is a novel, approximation-free framework to investigate SDEs. The correspondence reported here permits insights from the STS to be applied to the theory of KD and vice versa. It was previously known that the fast KD in the idealistic limit of no magnetic diffusion requires chaotic flows. The KD-STS correspondence shows that this is also true for the diffusive KD. From the STS perspective, the KD possesses a topological supersymmetry, and the dynamo effect can be viewed as its spontaneous breakdown. This supersymmetry breaking can be regarded as the stochastic generalization of the concept of dynamical chaos. As this supersymmetry breaking happens in both the diffusive and the nondiffusive cases, the necessity of the underlying SDE being chaotic is given in either case. The observed exponentially growing and oscillating KD modes prove physically that dynamical spectra of the STS evolution operator that break the topological supersymmetry exist with both real and complex ground state eigenvalues. Finally, we comment on the nonexistence of dynamos for scalar quantities.

  9. 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.

  10. 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.

  11. Controlling Chaos Probability of a Bose-Einstein Condensate in a Weak Optical Superlattice

    Institute of Scientific and Technical Information of China (English)

    XU Jun; LUO Xiao-Bing

    2009-01-01

    @@ The spatial chaos probability of a Bose-Einstein condensate perturbed by a weak optical superlattice is studied. It is demonstrated that the spatial chaotic solution appears with a certain probability in a given parameter region under a random boundary condition. The effects of the lattice depths and wave vectors on the chaos probability are illustrated, and different regions associated with different chaos probabilities are found. This suggests a feasible scheme for suppressing and strengthening chaos by adjusting the optical superlattice experimentally.

  12. 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

  13. Quantum signatures of chaos in a kicked top.

    Science.gov (United States)

    Chaudhury, S; Smith, A; Anderson, B E; Ghose, S; Jessen, P S

    2009-10-01

    Chaotic behaviour is ubiquitous and plays an important part in most fields of science. In classical physics, chaos is characterized by hypersensitivity of the time evolution of a system to initial conditions. Quantum mechanics does not permit a similar definition owing in part to the uncertainty principle, and in part to the Schrödinger equation, which preserves the overlap between quantum states. This fundamental disconnect poses a challenge to quantum-classical correspondence, and has motivated a long-standing search for quantum signatures of classical chaos. Here we present the experimental realization of a common paradigm for quantum chaos-the quantum kicked top- and the observation directly in quantum phase space of dynamics that have a chaotic classical counterpart. Our system is based on the combined electronic and nuclear spin of a single atom and is therefore deep in the quantum regime; nevertheless, we find good correspondence between the quantum dynamics and classical phase space structures. Because chaos is inherently a dynamical phenomenon, special significance attaches to dynamical signatures such as sensitivity to perturbation or the generation of entropy and entanglement, for which only indirect evidence has been available. We observe clear differences in the sensitivity to perturbation in chaotic versus regular, non-chaotic regimes, and present experimental evidence for dynamical entanglement as a signature of chaos. PMID:19812668

  14. Intrinsic Motivation in Physical Education

    Science.gov (United States)

    Davies, Benjamin; Nambiar, Nathan; Hemphill, Caroline; Devietti, Elizabeth; Massengale, Alexandra; McCredie, Patrick

    2015-01-01

    This article describes ways in which educators can use Harter's perceived competence motivation theory, the achievement goal theory, and self-determination theory to develop students' intrinsic motivation to maintain physical fitness, as demonstrated by the Sound Body Sound Mind curriculum and proven effective by the 2013 University of…

  15. When chaos meets hyperchaos: 4D Rössler model

    Energy Technology Data Exchange (ETDEWEB)

    Barrio, Roberto, E-mail: rbarrio@unizar.es [Departamento de Matemática Aplicada and IUMA, University of Zaragoza, E-50009 Zaragoza (Spain); Computational Dynamics group, University of Zaragoza, E-50009 Zaragoza (Spain); Angeles Martínez, M., E-mail: gelimc@unizar.es [Computational Dynamics group, University of Zaragoza, E-50009 Zaragoza (Spain); Serrano, Sergio, E-mail: sserrano@unizar.es [Departamento de Matemática Aplicada and IUMA, University of Zaragoza, E-50009 Zaragoza (Spain); Computational Dynamics group, University of Zaragoza, E-50009 Zaragoza (Spain); Wilczak, Daniel, E-mail: wilczak@ii.uj.edu.pl [Faculty of Mathematics and Computer Science, Jagiellonian University, Łojasiewicza 6, 30-348 Kraków (Poland)

    2015-10-09

    Chaotic behavior is a common feature of nonlinear dynamics, as well as hyperchaos in high-dimensional systems. In numerical simulations of these systems it is quite difficult to distinguish one from another behavior in some situations, as the results are frequently quite “noisy”. We show that in such systems a global hyperchaotic invariant set is present giving rise to long hyperchaotic transient behaviors. This fact provides a mechanism for these noisy results. The coexistence of chaos and hyperchaos is proved via Computer-Assisted Proofs techniques. - Highlights: • The coexistence of chaos and hyperchaos in the 4D Rössler system is proved via Computer-Assisted Proofs techniques. • A global hyperchaotic invariant set is present giving rise to long hyperchaotic transient behaviors. • The long transient behaviors make difficult in numerical simulations to distinguish chaos from hyperchaos in some situations.

  16. A novel image encryption scheme based on spatial chaos map

    Energy Technology Data Exchange (ETDEWEB)

    Sun Fuyan [College of Control Science and Engineering, Shandong University, Jinan 250061 (China)], E-mail: fuyan.sun@gmail.com; Liu Shutang [College of Control Science and Engineering, Shandong University, Jinan 250061 (China); Li Zhongqin [HeiLongJiang Institute of Science and Technology, Harbin 150027 (China); Lue Zongwang [Information and Communication College, Guilin University of Electronic and Technology, Guilin 541004 (China); Corporate Engineering Department, Johnson Electric Co. Ltd., Shenzhen 518125 (China)

    2008-11-15

    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, spatial chaos system are used for high degree security image encryption while its speed is acceptable. The proposed algorithm is described in detail. The basic idea is to encrypt the image in space with spatial chaos map pixel by pixel, and then the pixels are confused in multiple directions of space. Using this method one cycle, the image becomes indistinguishable in space due to inherent properties of spatial chaotic systems. Several experimental results, key sensitivity tests, key space analysis, and statistical analysis show that the approach for image cryptosystems provides an efficient and secure way for real time image encryption and transmission from the cryptographic viewpoint.

  17. Polymer additives in fluid turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

    The fluids and polymers have different fundamental symmetries. Namely, the Lagrangian relabeling symmetry of fluids is absent for polymers (while the translational and rotational symmetries are still present). This fact results in spontaneous breaking of the relabeling symmetry in fluid turbulence even at a tiny polymer addition. Since helicity conservation in inviscid fluid motions is a consequence of the relabeling symmetry (due to the Noether's theorem) violation of this conservation by the polymer additives results in the strong effects in the distributed chaos. The distributed chaos in turbulence with the spontaneously broken relabeling symmetry is characterized by stretched exponential spectra $\\propto \\exp(-k/k_{\\beta})^{\\beta}$ with $\\beta =2/5$. The spectral range of this distributed chaos is extended in direction of the small wavenumbers and $k_{\\beta}$ becomes much larger in comparison with the pure fluid (Newtonian) case. This results in substantial suppression of small-scale turbulence and large-...

  18. When chaos meets hyperchaos: 4D Rössler model

    International Nuclear Information System (INIS)

    Chaotic behavior is a common feature of nonlinear dynamics, as well as hyperchaos in high-dimensional systems. In numerical simulations of these systems it is quite difficult to distinguish one from another behavior in some situations, as the results are frequently quite “noisy”. We show that in such systems a global hyperchaotic invariant set is present giving rise to long hyperchaotic transient behaviors. This fact provides a mechanism for these noisy results. The coexistence of chaos and hyperchaos is proved via Computer-Assisted Proofs techniques. - Highlights: • The coexistence of chaos and hyperchaos in the 4D Rössler system is proved via Computer-Assisted Proofs techniques. • A global hyperchaotic invariant set is present giving rise to long hyperchaotic transient behaviors. • The long transient behaviors make difficult in numerical simulations to distinguish chaos from hyperchaos in some situations

  19. Applications of chaos and nonlinear dynamics in science and engineering

    CERN Document Server

    Rondoni, Lamberto; Mitra, Mala

    Chaos and nonlinear dynamics initially developed as a new emergent field with its foundation in physics and applied mathematics. The highly generic, interdisciplinary quality of the insights gained in the last few decades has spawned myriad applications in almost all branches of science and technology—and even well beyond. Wherever the quantitative modeling and analysis of complex, nonlinear phenomena are required, chaos theory and its methods can play a key role.    This second volume concentrates on reviewing further relevant, contemporary applications of chaotic nonlinear systems as they apply to the various cutting-edge branches of engineering. This encompasses, but is not limited to, topics such as the spread of epidemics; electronic circuits; chaos control in mechanical devices; secure communication; and digital watermarking. Featuring contributions from active and leading research groups, this collection is ideal both as a reference work and as a ‘recipe book’ full of tried and tested, successf...

  20. Color image authentication based on spatiotemporal chaos and SVD

    Energy Technology Data Exchange (ETDEWEB)

    Peng Zhenni [College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China)], E-mail: jennyp8201@yahoo.com.cn; Liu Wenbo [College of Automation Engineering, Nanjing University of Aeronautics and Astronautics, Nanjing 210016 (China)], E-mail: wenboliu@nuaa.edu.cn

    2008-05-15

    In this paper, a new semi-fragile watermarking scheme for color image authentication is proposed based on spatiotemporal chaos and SVD (singular value decomposition). Wavelet transform is applied to watermarking. In contrast to conventional approaches where the watermark is embedded directly on the wavelet coefficients, we embed the watermark onto the SVs (singular values) of the blocks within wavelet subband. In order to enhance the security, spatiotemporal chaos is employed to select the embedding positions for each watermark bit as well as for watermark encryption. The experiment results show that the proposed scheme is able to identify malicious attacks to the image, while is robust to JPEG compression. And due to the sensitivity to the initial conditions of the spatiotemporal chaos, the security of the scheme is greatly improved.

  1. A novel image encryption scheme based on spatial chaos map

    International Nuclear Information System (INIS)

    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, spatial chaos system are used for high degree security image encryption while its speed is acceptable. The proposed algorithm is described in detail. The basic idea is to encrypt the image in space with spatial chaos map pixel by pixel, and then the pixels are confused in multiple directions of space. Using this method one cycle, the image becomes indistinguishable in space due to inherent properties of spatial chaotic systems. Several experimental results, key sensitivity tests, key space analysis, and statistical analysis show that the approach for image cryptosystems provides an efficient and secure way for real time image encryption and transmission from the cryptographic viewpoint

  2. Color image authentication based on spatiotemporal chaos and SVD

    International Nuclear Information System (INIS)

    In this paper, a new semi-fragile watermarking scheme for color image authentication is proposed based on spatiotemporal chaos and SVD (singular value decomposition). Wavelet transform is applied to watermarking. In contrast to conventional approaches where the watermark is embedded directly on the wavelet coefficients, we embed the watermark onto the SVs (singular values) of the blocks within wavelet subband. In order to enhance the security, spatiotemporal chaos is employed to select the embedding positions for each watermark bit as well as for watermark encryption. The experiment results show that the proposed scheme is able to identify malicious attacks to the image, while is robust to JPEG compression. And due to the sensitivity to the initial conditions of the spatiotemporal chaos, the security of the scheme is greatly improved

  3. A NOVEL APPROACH TO GENERATE FRACTAL IMAGES USING CHAOS THEORY

    Directory of Open Access Journals (Sweden)

    K. Thamizhchelvy

    2014-08-01

    Full Text Available We propose the fractal generation method to generate the different types of fractals using chaos theory. The fractals are generated by Iterated Function System (IFS technique. The chaos theory is an unpredictable behavior arises in the dynamical system. Chaos in turns explains the nonlinearity and randomness. Chaotic behavior depends upon the initial condition called as “seed” or “key”. Pseudo Random Number Generator (PRNG fixes the initial condition from the difference equations. The system uses the PRNG value and it generates the fractals, also it is hard to break. We apply the rules to generate the fractals. The different types of fractals are generated for the same data, because of the great sensitivity to the initial condition. It can be used as a digital signature in online applications such as e-Banking and online shopping.

  4. Multistability, chaos, and random signal generation in semiconductor superlattices

    Science.gov (United States)

    Ying, Lei; Huang, Danhong; Lai, Ying-Cheng

    2016-06-01

    Historically, semiconductor superlattices, artificial periodic structures of different semiconductor materials, were invented with the purpose of engineering or manipulating the electronic properties of semiconductor devices. A key application lies in generating radiation sources, amplifiers, and detectors in the "unusual" spectral range of subterahertz and terahertz (0.1-10 THz), which cannot be readily realized using conventional radiation sources, the so-called THz gap. Efforts in the past three decades have demonstrated various nonlinear dynamical behaviors including chaos, suggesting the potential to exploit chaos in semiconductor superlattices as random signal sources (e.g., random number generators) in the THz frequency range. We consider a realistic model of hot electrons in semiconductor superlattice, taking into account the induced space charge field. Through a systematic exploration of the phase space we find that, when the system is subject to an external electrical driving of a single frequency, chaos is typically associated with the occurrence of multistability. That is, for a given parameter setting, while there are initial conditions that lead to chaotic trajectories, simultaneously there are other initial conditions that lead to regular motions. Transition to multistability, i.e., the emergence of multistability with chaos as a system parameter passes through a critical point, is found and argued to be abrupt. Multistability thus presents an obstacle to utilizing the superlattice system as a reliable and robust random signal source. However, we demonstrate that, when an additional driving field of incommensurate frequency is applied, multistability can be eliminated, with chaos representing the only possible asymptotic behavior of the system. In such a case, a random initial condition will lead to a trajectory landing in a chaotic attractor with probability 1, making quasiperiodically driven semiconductor superlattices potentially as a reliable

  5. Multistability, chaos, and random signal generation in semiconductor superlattices.

    Science.gov (United States)

    Ying, Lei; Huang, Danhong; Lai, Ying-Cheng

    2016-06-01

    Historically, semiconductor superlattices, artificial periodic structures of different semiconductor materials, were invented with the purpose of engineering or manipulating the electronic properties of semiconductor devices. A key application lies in generating radiation sources, amplifiers, and detectors in the "unusual" spectral range of subterahertz and terahertz (0.1-10 THz), which cannot be readily realized using conventional radiation sources, the so-called THz gap. Efforts in the past three decades have demonstrated various nonlinear dynamical behaviors including chaos, suggesting the potential to exploit chaos in semiconductor superlattices as random signal sources (e.g., random number generators) in the THz frequency range. We consider a realistic model of hot electrons in semiconductor superlattice, taking into account the induced space charge field. Through a systematic exploration of the phase space we find that, when the system is subject to an external electrical driving of a single frequency, chaos is typically associated with the occurrence of multistability. That is, for a given parameter setting, while there are initial conditions that lead to chaotic trajectories, simultaneously there are other initial conditions that lead to regular motions. Transition to multistability, i.e., the emergence of multistability with chaos as a system parameter passes through a critical point, is found and argued to be abrupt. Multistability thus presents an obstacle to utilizing the superlattice system as a reliable and robust random signal source. However, we demonstrate that, when an additional driving field of incommensurate frequency is applied, multistability can be eliminated, with chaos representing the only possible asymptotic behavior of the system. In such a case, a random initial condition will lead to a trajectory landing in a chaotic attractor with probability 1, making quasiperiodically driven semiconductor superlattices potentially as a reliable

  6. Predicting vibration signals of automobile engine using chaos theory

    Institute of Scientific and Technical Information of China (English)

    LIU Chun; ZHANG Laibin; WANG Zhaohui

    2004-01-01

    Condition monitoring and life prediction of the vehicle engine is an important and urgent problem during the vehicle development process. The vibration signals that are closely associated with the engine running condition and its development trend are complex and nonlinear. The chaos theory is used to treat the nonlinear dynamical system recently. A novel chaos method in conjunction with SVD (singular value decomposition)denoising skill are used to predict the vibration time series. Two types of time series and their prediction errors are provided to illustrate the practical utility of the method.

  7. Application of chaos and fractals to computer vision

    CERN Document Server

    Farmer, Michael E

    2014-01-01

    This book provides a thorough investigation of the application of chaos theory and fractal analysis to computer vision. The field of chaos theory has been studied in dynamical physical systems, and has been very successful in providing computational models for very complex problems ranging from weather systems to neural pathway signal propagation. Computer vision researchers have derived motivation for their algorithms from biology and physics for many years as witnessed by the optical flow algorithm, the oscillator model underlying graphical cuts and of course neural networks. These algorithm

  8. In the Wake of Chaos Unpredictable Order in Dynamical Systems

    CERN Document Server

    Kellert, Stephen H

    1993-01-01

    Chaos theory has captured scientific and popular attention. What began as the discovery of randomness in simple physical systems has become a widespread fascination with "chaotic" models of everything from business cycles to brainwaves to heart attacks. But what exactly does this explosion of new research into chaotic phenomena mean for our understanding of the world? In this timely book, Stephen Kellert takes the first sustained look at the broad intellectual and philosophical questions raised by recent advances in chaos theory—its implications for science as a source of knowledge a

  9. Quantum dissipative chaos in the statistics of excitation numbers

    CERN Document Server

    Kryuchkyan, G Y; Kryuchkyan, Gagik Yu.; Manvelyan, Suren B.

    2002-01-01

    A quantum manifestation of chaotic classical dynamics is found in the framework of oscillatory numbers statistics for the model of nonlinear dissipative oscillator. It is shown by numerical simulation of an ensemble of quantum trajectories that the probability distributions and variances of oscillatory number states are strongly transformed in the order-to-chaos transition. The nonclassical, sub-Poissonian statistics of oscillatory excitation numbers is established for chaotic dissipative dynamics in the framework of Fano factor and Wigner functions. These results are proposed for testing and experimental studing of quantum dissipative chaos.

  10. Dynamic Ice-Water Interactions Form Europa's Chaos Terrains

    Science.gov (United States)

    Blankenship, D. D.; Schmidt, B. E.; Patterson, G. W.; Schenk, P.

    2011-12-01

    Unique to the surface of Europa, chaos terrain is diagnostic of the properties and dynamics of its icy shell. We present a new model that suggests large melt lenses form within the shell and that water-ice interactions above and within these lenses drive the production of chaos. This model is consistent with key observations of chaos, predicts observables for future missions, and indicates that the surface is likely still active today[1]. We apply lessons from ice-water interaction in the terrestrial cryosphere to hypothesize a dynamic lense-collapse model to for Europa's chaos terrain. Chaos terrain morphology, like that of Conamara chaos and Thera Macula, suggests a four-phase formation [1]: 1) Surface deflection occurs as ice melts over ascending thermal plumes, as regularly occurs on Earth as subglacial volcanoes activate. The same process can occur at Europa if thermal plumes cause pressure melt as they cross ice-impurity eutectics. 2) Resulting hydraulic gradients and driving forces produce a sealed, pressurized melt lense, akin to the hydraulic sealing of subglacial caldera lakes. On Europa, the water cannot escape the lense due to the horizontally continuous ice shell. 3) Extension of the brittle ice lid above the lense opens cracks, allowing for the ice to be hydrofractured by pressurized water. Fracture, brine injection and percolation within the ice and possible iceberg toppling produces ice-melange-like granular matrix material. 4) Refreezing of the melt lense and brine-filled pores and cracks within the matrix results in raised chaos. Brine soaking and injection concentrates the ice in brines and adds water volume to the shell. As this englacial water freezes, the now water-filled ice will expand, not unlike the process of forming pingos and other "expansion ice" phenomena on Earth. The refreezing can raise the surface and create the oft-observed matrix "domes" In this presentation, we describe how catastrophic ice-water interactions on Earth have

  11. MPPT of PV array using stepped-up chaos optimization algorithm

    OpenAIRE

    Wang, Lihua; WEI, XUEYE; SHAO, YUQIN; ZHU, TIANLONG; ZHANG, JUNHONG

    2015-01-01

    In order to achieve maximum efficiency, a maximum power point tracking (MPPT) scheme should be applied in photovoltaic systems. Among all the MPPT schemes, the chaos optimization scheme is one of the hot topics in recent years. In this study, a novel stepped-up chaos optimization algorithm is presented. A chaos mapping $x_{n+1} =\\mu \\sin (\\pi x_{n} )$ is used as a chaos generator to produce a chaos variable. In the process of MPPT, a coarse search is done to find the current optimal solution ...

  12. Quasar redshifts: the intrinsic component

    Science.gov (United States)

    Hansen, Peter M.

    2016-09-01

    The large observed redshift of quasars has suggested large cosmological distances and a corresponding enormous energy output to explain the brightness or luminosity as seen at earth. Alternative or complementary sources of redshift have not been identified by the astronomical community. This study examines one possible source of additional redshift: an intrinsic component based on the plasma characteristics of high temperature and high electron density which are believed to be present.

  13. Decoherence: Intrinsic, Extrinsic, and Environmental

    Science.gov (United States)

    Stamp, Philip

    2012-02-01

    Environmental decoherence times have been difficult to predict in solid-state systems. In spin systems, environmental decoherence is predicted to arise from nuclear spins, spin-phonon interactions, and long-range dipolar interactions [1]. Recent experiments have confirmed these predictions quantitatively in crystals of Fe8 molecules [2]. Coherent spin dynamics was observed over macroscopic volumes, with a decoherence Q-factor Qφ= 1.5 x10^6 (the upper predicted limit in this system being Qφ= 6 x10^7). Decoherence from dipolar interactions is particularly complex, and depends on the shape and the quantum state of the system. No extrinsic ``noise'' decoherence was observed. The generalization to quantum dot and superconducting qubit systems is also discussed. We then discuss searches for ``intrinsic'' decoherence [3,4], coming from non-linear corrections to quantum mechanics. Particular attention is paid to condensed matter tests of such intrinsic decoherence, in hybrid spin/optomechanical systems, and to ways of distinguishing intrinsic decoherence from environmental and extrinsic decoherence sources. [4pt] [1] Morello, A. Stamp, P. C. E. & Tupitsyn, Phys. Rev. Lett. 97, 207206 (2006).[0pt] [2] S. Takahashi et al., Nature 476, 76 (2011).[0pt] [3] Stamp, P. C. E., Stud. Hist. Phil. Mod. Phys. 37, 467 (2006). [0pt] [4] Stamp, P.C.E., Phil. Trans. Roy. Soc. A (to be published)

  14. Experimental observation of a chaos-to-chaos transition in laser droplet generation

    CERN Document Server

    Krese, Blaz; Govekar, Edvard

    2010-01-01

    We examine the dynamics of laser droplet generation in dependence on the detachment pulse power. In the absence of the detachment pulse, undulating pendant droplets are formed at the end of a properly fed metal wire due to the impact of the primary laser pulse that induces melting. Eventually, these droplets detach, i.e. overcome the surface tension, because of their increasing mass. We show that this spontaneous dripping is deterministically chaotic by means of a positive largest Lyapunov exponent and a negative divergence. In the presence of the detachment pulse, however, the generation of droplets is fastened depending on the pulse power. At high powers, the spontaneity of dripping is completely overshadowed by the impact of the detachment pulse. Still, amplitude chaos can be detected, which similarly as the spontaneous dripping, is characterized by a positive largest Lyapunov exponent and a negative divergence, thus indicating that the observed dynamics is deterministically chaotic with an attractor as so...

  15. A New Type of Cascading Synchronization for Halo-Chaos and Its Potential for Communication Applications

    Institute of Scientific and Technical Information of China (English)

    FANG Jin-Qing; YU Xing-Huo

    2004-01-01

    @@ Study of beam halo-chaos has become a key issue of concern for many future important applications. Control of halo-chaos has been researched intensively. This is the first time that the synchronization of beam halo-chaos has been realized in this field so far. Two nonlinear feedback control methods are proposed for the cascading synchronizing halo-chaos in coupled lattices of a periodic focusing channel. The simulation results show that the methods are effective. The realization of the synchronization of beam halo-chaos is significant not only for halo-chaos control itself but also for halo-chaos-based secure communication which may become an innovative technique.

  16. The bifurcation threshold value of the chaos detection system for a weak signal

    Institute of Scientific and Technical Information of China (English)

    李月; 杨宝俊; 杜立志; 袁野

    2003-01-01

    Recently, it has become an important problem to confirm the bifurcation threshold value of a chaos detection system for a weak signal in the fields of chaos detection. It is directly related to whether the results of chaos detection are correct or not. In this paper, the discrimination system for the dynamic behaviour of a chaos detection system for a weak signal is established by using the theory of linear differential equation with periodic coefficients and computing the Lyapunov exponents of the chaos detection system; and then, the movement state of the chaos detection system is defined. The simulation experiments show that this method can exactly confirm the bifurcation threshold value of the chaos detection system.

  17. Intrinsic Patterns of Human Activity

    Science.gov (United States)

    Hu, Kun; Ivanov, Plamen Ch.; Chen, Zhi; Hilton, Michael; Stanley, H. Eugene; Shea, Steven

    2003-03-01

    Activity is one of the defining features of life. Control of human activity is complex, being influenced by many factors both extrinsic and intrinsic to the body. The most obvious extrinsic factors that affect activity are the daily schedule of planned events, such as work and recreation, as well as reactions to unforeseen or random events. These extrinsic factors may account for the apparently random fluctuations in human motion observed over short time scales. The most obvious intrinsic factors are the body clocks including the circadian pacemaker that influences our sleep/wake cycle and ultradian oscillators with shorter time scales [2, 3]. These intrinsic rhythms may account for the underlying regularity in average activity level over longer periods of up to 24 h. Here we ask if the known extrinsic and intrinsic factors fully account for all complex features observed in recordings of human activity. To this end, we measure activity over two weeks from forearm motion in subjects undergoing their regular daily routine. Utilizing concepts from statistical physics, we demonstrate that during wakefulness human activity possesses previously unrecognized complex dynamic patterns. These patterns of activity are characterized by robust fractal and nonlinear dynamics including a universal probability distribution and long-range power-law correlations that are stable over a wide range of time scales (from minutes to hours). Surprisingly, we find that these dynamic patterns are unaffected by changes in the average activity level that occur within individual subjects throughout the day and on different days of the week, and between subjects. Moreover, we find that these patterns persist when the same subjects undergo time-isolation laboratory experiments designed to account for the phase of the circadian pacemaker, and control the known extrinsic factors by restricting behaviors and manipulating scheduled events including the sleep/wake cycle. We attribute these newly

  18. vs. a polynomial chaos-based MCMC

    KAUST Repository

    Siripatana, Adil

    2014-08-01

    Bayesian Inference of Manning\\'s n coefficient in a Storm Surge Model Framework: comparison between Kalman lter and polynomial based method Adil Siripatana Conventional coastal ocean models solve the shallow water equations, which describe the conservation of mass and momentum when the horizontal length scale is much greater than the vertical length scale. In this case vertical pressure gradients in the momentum equations are nearly hydrostatic. The outputs of coastal ocean models are thus sensitive to the bottom stress terms de ned through the formulation of Manning\\'s n coefficients. This thesis considers the Bayesian inference problem of the Manning\\'s n coefficient in the context of storm surge based on the coastal ocean ADCIRC model. In the first part of the thesis, we apply an ensemble-based Kalman filter, the singular evolutive interpolated Kalman (SEIK) filter to estimate both a constant Manning\\'s n coefficient and a 2-D parameterized Manning\\'s coefficient on one ideal and one of more realistic domain using observation system simulation experiments (OSSEs). We study the sensitivity of the system to the ensemble size. we also access the benefits from using an in ation factor on the filter performance. To study the limitation of the Guassian restricted assumption on the SEIK lter, 5 we also implemented in the second part of this thesis a Markov Chain Monte Carlo (MCMC) method based on a Generalized Polynomial chaos (gPc) approach for the estimation of the 1-D and 2-D Mannning\\'s n coe cient. The gPc is used to build a surrogate model that imitate the ADCIRC model in order to make the computational cost of implementing the MCMC with the ADCIRC model reasonable. We evaluate the performance of the MCMC-gPc approach and study its robustness to di erent OSSEs scenario. we also compare its estimates with those resulting from SEIK in term of parameter estimates and full distributions. we present a full analysis of the solution of these two methods, of the

  19. BOOK REVIEW: Chaos: A Very Short Introduction

    Science.gov (United States)

    Klages, R.

    2007-07-01

    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

  20. Chaos at the Heart of Orion

    Science.gov (United States)

    2006-01-01

    NASA's Spitzer and Hubble Space Telescopes have teamed up to expose the chaos that baby stars are creating 1,500 light-years away in a cosmic cloud called the Orion nebula. This striking infrared and visible-light composite indicates that four monstrously massive stars at the center of the cloud may be the main culprits in the familiar Orion constellation. The stars are collectively called the 'Trapezium.' Their community can be identified as the yellow smudge near the center of the image. Swirls of green in Hubble's ultraviolet and visible-light view reveal hydrogen and sulfur gas that have been heated and ionized by intense ultraviolet radiation from the Trapezium's stars. Meanwhile, Spitzer's infrared view exposes carbon-rich molecules called polycyclic aromatic hydrocarbons in the cloud. These organic molecules have been illuminated by the Trapezium's stars, and are shown in the composite as wisps of red and orange. On Earth, polycyclic aromatic hydrocarbons are found on burnt toast and in automobile exhaust. Together, the telescopes expose the stars in Orion as a rainbow of dots sprinkled throughout the image. Orange-yellow dots revealed by Spitzer are actually infant stars deeply embedded in a cocoon of dust and gas. Hubble showed less embedded stars as specks of green, and foreground stars as blue spots. Stellar winds from clusters of newborn stars scattered throughout the cloud etched all of the well-defined ridges and cavities in Orion. The large cavity near the right of the image was most likely carved by winds from the Trapezium's stars. Located 1,500 light-years away from Earth, the Orion nebula is the brightest spot in the sword of the Orion, or the 'Hunter' constellation. The cosmic cloud is also our closest massive star-formation factory, and astronomers believe it contains more than 1,000 young stars. The Orion constellation is a familiar sight in the fall and winter night sky in the northern hemisphere. The nebula is invisible to the unaided eye