WorldWideScience

Sample records for chaos intrinsically disordered

  1. 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...... as evidence for thermally activated hopping and thermally affected chaos. The data are only in qualitative accord with recent ideas regarding the effect of thermal noise on intermittent chaos....

  2. [Shedding light on chaos theory].

    Science.gov (United States)

    Chou, Shieu-Ming

    2004-06-01

    Gleick (1987) said that only three twentieth century scientific theories would be important enough to continue be of use in the twenty-first century: The Theory of Relativity, Quantum Theory, and Chaos Theory. Chaos Theory has become a craze which is being used to forge a new scientific system. It has also been extensively applied in a variety of professions. The purpose of this article is to introduce chaos theory and its nursing applications. Chaos is a sign of regular order. This is to say that chaos theory emphasizes the intrinsic potential for regular order within disordered phenomena. It is to be hoped that this article will inspire more nursing scientists to apply this concept to clinical, research, or administrative fields in our profession.

  3. 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…

  4. Functional Anthology of Intrinsic Disorder. III. Ligands, Postranslational Modifications and Diseases Associated with Intrinsically Disordered Proteins

    Science.gov (United States)

    Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

    2008-01-01

    Currently, the understanding of the relationships between function, amino acid sequence and protein structure continues to represent one of the major challenges of the modern protein science. As much as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bioinformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200,000 proteins from Swiss-Prot database, each annotated with at least one of the 875 functional keywords was described in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Using this tool, we have found that out of the 711 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic

  5. Intrinsically Disordered Side of the Zika Virus Proteome

    Directory of Open Access Journals (Sweden)

    Rajanish Giri

    2016-11-01

    Full Text Available Over the last few decades, concepts of protein intrinsic disorder have been implicated in different biological processes. Recent studies have suggested that intrinsically disordered proteins (IDPs provide structural plasticity and functional diversity to viral proteins that are involved in rapid replication and immune evasion in host cells. In case of Zika virus, the roles of protein intrinsic disorder in mechanisms of pathogenesis are not completely understood. In this study, we have analyzed the prevalence of intrinsic disorder in Zika virus proteome (strain MR 766. Our analyses revealed that Zika virus polyprotein is enriched with intrinsically disordered protein regions (IDPRs and this finding is consistent with previous reports on the involvement of IDPs in shell formation and virulence of the Flaviviridae family. We found abundant IDPRs in Capsid, NS2B, NS3, NS4A, and NS5 proteins that are involved in mature particle formation and replication. In our view, the intrinsic disorder-focused analysis of ZIKV proteins could be important for the development of new disorder-based drugs.

  6. Digested disorder: Quarterly intrinsic disorder digest (January/February/March, 2013).

    Science.gov (United States)

    Uversky, Vladimir N

    2013-01-01

    The current literature on intrinsically disordered proteins is blooming. A simple PubMed search for "intrinsically disordered protein OR natively unfolded protein" returns about 1,800 hits (as of June 17, 2013), with many papers published quite recently. To keep interested readers up to speed with this literature, we are starting a "Digested Disorder" project, which will encompass a series of reader's digest type of publications aiming at the objective representation of the research papers and reviews on intrinsically disordered proteins. The only two criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest covers papers published during the period of January, February and March of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

  7. Some chaotic features of intrinsically coupled Josephson junctions

    International Nuclear Information System (INIS)

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

    2013-01-01

    Highlights: ► Intrinsically coupled Josephson junctions model a high-T 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 c resonators which require coherence amongst the junctions

  8. Digested disorder: Quarterly intrinsic disorder digest (April-May-June, 2013).

    Science.gov (United States)

    DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

    2013-01-01

    The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a series of reader's digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

  9. Functional anthology of intrinsic disorder. 3. Ligands, post-translational modifications, and diseases associated with intrinsically disordered proteins.

    Science.gov (United States)

    Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

    2007-05-01

    Currently, the understanding of the relationships between function, amino acid sequence, and protein structure continues to represent one of the major challenges of the modern protein science. As many as 50% of eukaryotic proteins are likely to contain functionally important long disordered regions. Many proteins are wholly disordered but still possess numerous biologically important functions. However, the number of experimentally confirmed disordered proteins with known biological functions is substantially smaller than their actual number in nature. Therefore, there is a crucial need for novel bionformatics approaches that allow projection of the current knowledge from a few experimentally verified examples to much larger groups of known and potential proteins. The elaboration of a bioinformatics tool for the analysis of functional diversity of intrinsically disordered proteins and application of this data mining tool to >200 000 proteins from the Swiss-Prot database, each annotated with at least one of the 875 functional keywords, was described in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V.N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Using this tool, we have found that out of the 710 Swiss-Prot functional keywords associated with at least 20 proteins, 262 were strongly positively correlated with long intrinsically disordered regions, and 302 were strongly negatively correlated. Illustrative examples of functional disorder or order were found for the vast majority of keywords showing strongest positive or negative correlation with intrinsic disorder, respectively. Some 80 Swiss-Prot keywords associated with disorder- and order-driven biological processes and protein functions were described in the first paper (see above). The second paper of the series was

  10. Digested disorder: Quarterly intrinsic disorder digest (July-August-September, 2013).

    Science.gov (United States)

    Reddy, Krishna D; DeForte, Shelly; Uversky, Vladimir N

    2014-01-01

    The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a "Digested Disorder" project and represent a new issue of reader's digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

  11. Hidden Structural Codes in Protein Intrinsic Disorder.

    Science.gov (United States)

    Borkosky, Silvia S; Camporeale, Gabriela; Chemes, Lucía B; Risso, Marikena; Noval, María Gabriela; Sánchez, Ignacio E; Alonso, Leonardo G; de Prat Gay, Gonzalo

    2017-10-17

    Intrinsic disorder is a major structural category in biology, accounting for more than 30% of coding regions across the domains of life, yet consists of conformational ensembles in equilibrium, a major challenge in protein chemistry. Anciently evolved papillomavirus genomes constitute an unparalleled case for sequence to structure-function correlation in cases in which there are no folded structures. E7, the major transforming oncoprotein of human papillomaviruses, is a paradigmatic example among the intrinsically disordered proteins. Analysis of a large number of sequences of the same viral protein allowed for the identification of a handful of residues with absolute conservation, scattered along the sequence of its N-terminal intrinsically disordered domain, which intriguingly are mostly leucine residues. Mutation of these led to a pronounced increase in both α-helix and β-sheet structural content, reflected by drastic effects on equilibrium propensities and oligomerization kinetics, and uncovers the existence of local structural elements that oppose canonical folding. These folding relays suggest the existence of yet undefined hidden structural codes behind intrinsic disorder in this model protein. Thus, evolution pinpoints conformational hot spots that could have not been identified by direct experimental methods for analyzing or perturbing the equilibrium of an intrinsically disordered protein ensemble.

  12. Differential scanning microcalorimetry of intrinsically disordered proteins.

    Science.gov (United States)

    Permyakov, Sergei E

    2012-01-01

    Ultrasensitive differential scanning calorimetry (DSC) is an indispensable thermophysical technique enabling to get direct information on enthalpies accompanying heating/cooling of dilute biopolymer solutions. The thermal dependence of protein heat capacity extracted from DSC data is a valuable source of information on intrinsic disorder level of a protein. Application details and limitations of DSC technique in exploration of protein intrinsic disorder are described.

  13. Functions of intrinsic disorder in transmembrane proteins

    DEFF Research Database (Denmark)

    Kjaergaard, Magnus; Kragelund, Birthe B.

    2017-01-01

    Intrinsic disorder is common in integral membrane proteins, particularly in the intracellular domains. Despite this observation, these domains are not always recognized as being disordered. In this review, we will discuss the biological functions of intrinsically disordered regions of membrane...... receptors. The functions of the disordered regions are many and varied. We will discuss selected examples including: (1) Organization of receptors, kinases, phosphatases and second messenger sources into signaling complexes. (2) Modulation of the membrane-embedded domain function by ball-and-chain like...... mechanisms. (3) Trafficking of membrane proteins. (4) Transient membrane associations. (5) Post-translational modifications most notably phosphorylation and (6) disorder-linked isoform dependent function. We finish the review by discussing the future challenges facing the membrane protein community regarding...

  14. Lost in the chaos: Flawed literature should not generate new disorders

    OpenAIRE

    Van Rooij, Antonius J.; Kardefelt-Winther, Daniel

    2017-01-01

    The paper by Kuss, Griffiths, and Pontes (2016) titled ?Chaos and confusion in DSM-5 diagnosis of Internet Gaming Disorder: Issues, concerns, and recommendations for clarity in the field? examines issues relating to the concept of Internet Gaming Disorder. We agree that there are serious issues and extend their arguments by suggesting that the field lacks basic theory, definitions, patient research, and properly validated and standardized assessment tools. As most studies derive data from sur...

  15. Digested disorder, Quarterly intrinsic disorder digest (October-November-December, 2013).

    Science.gov (United States)

    DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

    2015-01-01

    This is the 4th issue of the Digested Disorder series that represents reader's digest of the scientific literature on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the fourth quarter of 2013; i.e. during the period of October, November, and December of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings.

  16. Quarterly intrinsic disorder digest (January-February-March, 2014)

    OpenAIRE

    DeForte, Shelly; Reddy, Krishna D.; Uversky, Vladimir N.

    2016-01-01

    This is the 5th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during ...

  17. Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

    Science.gov (United States)

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

    2015-01-01

    Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.

  18. Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins.

    Directory of Open Access Journals (Sweden)

    Mihaly Varadi

    Full Text Available Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their functionality through a quantitative description of the evolutionary conservation of disordered segments involved in binding, and investigated the structural implications of flexibility in terms of conformational stability and interface formation. We conclude that the functional role of intrinsically disordered protein segments in RNA-binding is two-fold: first, these regions establish extended, conserved electrostatic interfaces with RNAs via induced fit. Second, conformational flexibility enables them to target different RNA partners, providing multi-functionality, while also ensuring specificity. These findings emphasize the functional importance of intrinsically disordered regions in RNA-binding proteins.

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

    Science.gov (United States)

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

    2015-09-11

    Cell-free protein synthesis is used to produce proteins with various structural traits. Recent bioinformatics analyses indicate that more than half of eukaryotic proteins possess long intrinsically disordered regions. However, no systematic study concerning the connection between intrinsic disorder and expression success of cell-free protein synthesis has been presented until now. To address this issue, we examined correlations of the experimentally observed cell-free protein expression yields with the contents of intrinsic disorder bioinformatically predicted in the expressed sequences. This analysis revealed strong relationships between intrinsic disorder and protein amenability to heterologous cell-free expression. On the one hand, elevated disorder content was associated with the increased ratio of soluble expression. On the other hand, overall propensity for detectable protein expression decreased with disorder content. We further demonstrated that these tendencies are rooted in some distinct features of intrinsically disordered regions, such as low hydrophobicity, elevated surface accessibility and high abundance of sequence motifs for proteolytic degradation, including sites of ubiquitination and PEST sequences. Our findings suggest that identification of intrinsically disordered regions in the expressed amino acid sequences can be of practical use for predicting expression success and optimizing cell-free protein synthesis.

  20. Intrinsic disorder here, there, and everywhere, and nowhere to escape from it.

    Science.gov (United States)

    Uversky, Vladimir N

    2017-09-01

    The concept of protein intrinsic disorder persistently penetrates into all areas of modern protein science. It cannot be ignored anymore, and cannot be shrugged off, as it represents a vital feature (or, more correctly, a broad spectrum of important features), which, when added to and mixed with features arising from the well established protein structure-function paradigm, complete the picture of a functioning protein. The field of protein intrinsic disorder is very dynamic and fast developing. This Multi-Author Review represents a snapshot of this field by introducing some recent advances. Articles assembled in this Multi-Author Review introduce some of the new aspects of intrinsic disorder, outline some fascinating ideas related to the intrinsically disordered proteins, their structure, and functionality, and show challenges related to the analysis of proteins carrying intrinsic disorder.

  1. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions.

    Science.gov (United States)

    Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Uversky, Vladimir N; Obradovic, Zoran

    2007-05-01

    Identifying relationships between function, amino acid sequence, and protein structure represents a major challenge. In this study, we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from the Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins, and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our

  2. Weak chaos in the disordered nonlinear Schroedinger chain: Destruction of Anderson localization by Arnold diffusion

    International Nuclear Information System (INIS)

    Basko, D.M.

    2011-01-01

    Research highlights: → In a one-dimensional disordered chain of oscillators all normal modes are localized. → Nonlinearity leads to chaotic dynamics. → Chaos is concentrated on rare chaotic spots. → Chaotic spots drive energy exchange between oscillators. → Macroscopic transport coefficients are obtained. - Abstract: The subject of this study is the long-time equilibration dynamics of a strongly disordered one-dimensional chain of coupled weakly anharmonic classical oscillators. It is shown that chaos in this system has a very particular spatial structure: it can be viewed as a dilute gas of chaotic spots. Each chaotic spot corresponds to a stochastic pump which drives the Arnold diffusion of the oscillators surrounding it, thus leading to their relaxation and thermalization. The most important mechanism of equilibration at long distances is provided by random migration of the chaotic spots along the chain, which bears analogy with variable-range hopping of electrons in strongly disordered solids. The corresponding macroscopic transport equations are obtained.

  3. Quarterly intrinsic disorder digest (January-February-March, 2014).

    Science.gov (United States)

    DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

    2016-01-01

    This is the 5 th issue of the Digested Disorder series that represents a reader's digest of the scientific literature on intrinsically disordered proteins. We continue to use only 2 criteria for inclusion of a paper to this digest: The publication date (a paper should be published within the covered time frame) and the topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the first quarter of 2014; i.e., during the period of January, February, and March of 2014. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included papers a short description is given on its major findings.

  4. Functional Anthology of Intrinsic Disorder. I. Biological Processes and Functions of Proteins with Long Disordered Regions

    Science.gov (United States)

    Xie, Hongbo; Vucetic, Slobodan; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Uversky, Vladimir N.; Obradovic, Zoran

    2008-01-01

    Identifying relationships between function, amino acid sequence and protein structure represents a major challenge. In this study we propose a bioinformatics approach that identifies functional keywords in the Swiss-Prot database that correlate with intrinsic disorder. A statistical evaluation is employed to rank the significance of these correlations. Protein sequence data redundancy and the relationship between protein length and protein structure were taken into consideration to ensure the quality of the statistical inferences. Over 200,000 proteins from Swiss-Prot database were analyzed using this approach. The predictions of intrinsic disorder were carried out using PONDR VL3E predictor of long disordered regions that achieves an accuracy of above 86%. Overall, out of the 710 Swiss-Prot functional keywords that were each associated with at least 20 proteins, 238 were found to be strongly positively correlated with predicted long intrinsically disordered regions, whereas 302 were strongly negatively correlated with such regions. The remaining 170 keywords were ambiguous without strong positive or negative correlation with the disorder predictions. These functions cover a large variety of biological activities and imply that disordered regions are characterized by a wide functional repertoire. Our results agree well with literature findings, as we were able to find at least one illustrative example of functional disorder or order shown experimentally for the vast majority of keywords showing the strongest positive or negative correlation with intrinsic disorder. This work opens a series of three papers, which enriches the current view of protein structure-function relationships, especially with regards to functionalities of intrinsically disordered proteins and provides researchers with a novel tool that could be used to improve the understanding of the relationships between protein structure and function. The first paper of the series describes our statistical

  5. What's in a name? : Why these proteins are intrinsically disordered: Why these proteins are intrinsically disordered

    NARCIS (Netherlands)

    Dunker, A Keith; Babu, M Madan; Barbar, Elisar; Blackledge, Martin; Bondos, Sarah E; Dosztányi, Zsuzsanna; Dyson, H Jane; Forman-Kay, Julie; Fuxreiter, Monika; Gsponer, Jörg; Han, Kyou-Hoon; Jones, David T; Longhi, Sonia; Metallo, Steven J; Nishikawa, Ken; Nussinov, Ruth; Obradovic, Zoran; Pappu, Rohit V; Rost, Burkhard; Selenko, Philipp; Subramaniam, Vinod; Sussman, Joel L; Tompa, Peter; Uversky, Vladimir N

    2013-01-01

    "What's in a name? That which we call a rose By any other name would smell as sweet." From "Romeo and Juliet", William Shakespeare (1594) This article opens a series of publications on disambiguation of the basic terms used in the field of intrinsically disordered proteins. We start from the

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

    Energy Technology Data Exchange (ETDEWEB)

    Yildirim, O. Ozgur, E-mail: donhee@seas.harvard.edu, E-mail: oozgury@gmail.com [Cavium, Inc., 600 Nickerson Rd., Marlborough, Massachusetts 01752 (United States); Ham, Donhee, E-mail: donhee@seas.harvard.edu, E-mail: oozgury@gmail.com [Harvard University, 33 Oxford St., Cambridge, Massachusetts 02138 (United States)

    2014-06-16

    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. Functional Advantages of Conserved Intrinsic Disorder in RNA-Binding Proteins

    OpenAIRE

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

    2015-01-01

    Proteins form large macromolecular assemblies with RNA that govern essential molecular processes. RNA-binding proteins have often been associated with conformational flexibility, yet the extent and functional implications of their intrinsic disorder have never been fully assessed. Here, through large-scale analysis of comprehensive protein sequence and structure datasets we demonstrate the prevalence of intrinsic structural disorder in RNA-binding proteins and domains. We addressed their func...

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

    International Nuclear Information System (INIS)

    Pham, Tuan D.; Thang, Truong Cong; Oyama-Higa, Mayumi; Sugiyama, Masahide

    2013-01-01

    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

  9. Resolving the ambiguity: Making sense of intrinsic disorder when PDB structures disagree.

    Science.gov (United States)

    DeForte, Shelly; Uversky, Vladimir N

    2016-03-01

    Missing regions in X-ray crystal structures in the Protein Data Bank (PDB) have played a foundational role in the study of intrinsically disordered protein regions (IDPRs), especially in the development of in silico predictors of intrinsic disorder. However, a missing region is only a weak indication of intrinsic disorder, and this uncertainty is compounded by the presence of ambiguous regions, where more than one structure of the same protein sequence "disagrees" in terms of the presence or absence of missing residues. The question is this: are these ambiguous regions intrinsically disordered, or are they the result of static disorder that arises from experimental conditions, ensembles of structures, or domain wobbling? A novel way of looking at ambiguous regions in terms of the pattern between multiple PDB structures has been demonstrated. It was found that the propensity for intrinsic disorder increases as the level of ambiguity decreases. However, it is also shown that ambiguity is more likely to occur as the protein region is placed within different environmental conditions, and even the most ambiguous regions as a set display compositional bias that suggests flexibility. The results suggested that ambiguity is a natural result for many IDPRs crystallized under different conditions and that static disorder and wobbling domains are relatively rare. Instead, it is more likely that ambiguity arises because many of these regions were conditionally or partially disordered. © 2016 The Protein Society.

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

    Science.gov (United States)

    Kowalski, Andrzej

    2015-12-01

    The intrinsically disordered proteins consist of partially structured regions linked to the unstructured stretches, which consequently form the transient and dynamic conformational ensembles. They undergo disorder to order transition upon binding their partners. Intrinsic disorder is attributed to histones H1, perceived as assemblers of chromatin structure and the regulators of DNA and proteins activity. In this work, the comparison of intrinsic disorder abundance in the histone H1 subtypes was performed both by the analysis of their amino acid composition and by the prediction of disordered stretches, as well as by identifying molecular recognition features (MoRFs) and ANCHOR protein binding regions (APBR) that are responsible for recognition and binding. Both human and model organisms-animals, plants, fungi and protists-have H1 histone subtypes with the properties typical of disordered state. They possess a significantly higher content of hydrophilic and charged amino acid residues, arranged in the long regions, covering over half of the whole amino acid residues in chain. Almost complete disorder corresponds to histone H1 terminal domains, including MoRFs and ANCHOR. Those motifs were also identified in a more ordered histone H1 globular domain. Compared to the control (globular and fibrous) proteins, H1 histones demonstrate the increased folding rate and a higher proportion of low-complexity segments. The results of this work indicate that intrinsic disorder is an inherent structural property of histone H1 subtypes and it is essential for establishing a protein conformation which defines functional outcomes affecting on DNA- and/or partner protein-dependent cell processes. Copyright © 2015 Elsevier Ltd. All rights reserved.

  11. Discursive Maps at the Edge of Chaos

    Science.gov (United States)

    2017-05-25

    Discursive Maps at the Edge of Chaos A Monograph by Major Mathieu Primeau Canadian Army, Royal Canadian Engineer School of Advanced Military...Master’s Thesis 3. DATES COVERED (From - To) JUN 2016 – MAY 2017 4. TITLE AND SUBTITLE Discursive Maps at the Edge of Chaos 5a. CONTRACT NUMBER 5b...meaning of boundaries and polarize conflict towards violence. The edge of chaos is the fine line between disorder and coherence. Discursive maps

  12. Genetic recombination is associated with intrinsic disorder in plant proteomes.

    Science.gov (United States)

    Yruela, Inmaculada; Contreras-Moreira, Bruno

    2013-11-09

    Intrinsically disordered proteins, found in all living organisms, are essential for basic cellular functions and complement the function of ordered proteins. It has been shown that protein disorder is linked to the G + C content of the genome. Furthermore, recent investigations have suggested that the evolutionary dynamics of the plant nucleus adds disordered segments to open reading frames alike, and these segments are not necessarily conserved among orthologous genes. In the present work the distribution of intrinsically disordered proteins along the chromosomes of several representative plants was analyzed. The reported results support a non-random distribution of disordered proteins along the chromosomes of Arabidopsis thaliana and Oryza sativa, two model eudicot and monocot plant species, respectively. In fact, for most chromosomes positive correlations between the frequency of disordered segments of 30+ amino acids and both recombination rates and G + C content were observed. These analyses demonstrate that the presence of disordered segments among plant proteins is associated with the rates of genetic recombination of their encoding genes. Altogether, these findings suggest that high recombination rates, as well as chromosomal rearrangements, could induce disordered segments in proteins during evolution.

  13. A Chaos Theory Perspective on International Migration

    Directory of Open Access Journals (Sweden)

    Anca Tănasie

    2017-12-01

    Full Text Available This paper aims at providing a different approach to international migration analysis, beyond classical models previously proposed by specialized literature. Chaos theory is getting more and more applied into macroeconomics once traditional linear models or even previous dynamic analysis become less suitable. Modern science sees chaos as unpredictable evolution, maybe even disorder. Still, chaos has got its own rules and can describe many dynamic phenomena within our world. Thus, we test whether international migration data falls under the rules of chaos and whether recent developments within the “European migration crisis” (the total daily migration inflows towards the coasts of Italy, by sea, from January 2014 to April 2017 could be described as chaotic.

  14. Convergence of Artificial Protein Polymers and Intrinsically Disordered Proteins.

    Science.gov (United States)

    Dzuricky, Michael; Roberts, Stefan; Chilkoti, Ashutosh

    2018-05-01

    A flurry of research in recent years has revealed the molecular origins of many membraneless organelles to be the liquid phase separation of intrinsically disordered proteins (IDPs). Consequently, protein disorder has emerged as an important driver of intracellular compartmentalization by providing specialized microenvironments chemically distinct from the surrounding medium. Though the importance of protein disorder and its relationship to intracellular phase behavior are clear, a detailed understanding of how such phase behavior can be predicted and controlled remains elusive. While research in IDPs has largely focused on the implications of structural disorder on cellular function and disease, another field, that of artificial protein polymers, has focused on the de novo design of protein polymers with controllable material properties. A subset of these polymers, specifically those derived from structural proteins such as elastin and resilin, are also disordered sequences that undergo liquid-liquid phase separation. This phase separation has been used in a variety of biomedical applications, and researchers studying these polymers have developed methods to precisely characterize and tune their phase behavior. Despite their disparate origins, both fields are complementary as they study the phase behavior of intrinsically disordered polypeptides. This Perspective hopes to stimulate collaborative efforts by highlighting the similarities between these two fields and by providing examples of how such collaboration could be mutually beneficial.

  15. Intrinsically disordered proteins as molecular shields†

    Science.gov (United States)

    Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Kaminski Schierle, Gabriele S.; Kurniawan, Davy P.; Kaminski, Clemens F.; Wise, Michael J.; Tunnacliffe, Alan

    2017-01-01

    The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 – while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins – HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability

  16. Intrinsically disordered proteins as molecular shields.

    Science.gov (United States)

    Chakrabortee, Sohini; Tripathi, Rashmi; Watson, Matthew; Schierle, Gabriele S Kaminski; Kurniawan, Davy P; Kaminski, Clemens F; Wise, Michael J; Tunnacliffe, Alan

    2012-01-01

    The broad family of LEA proteins are intrinsically disordered proteins (IDPs) with several potential roles in desiccation tolerance, or anhydrobiosis, one of which is to limit desiccation-induced aggregation of cellular proteins. We show here that this activity, termed molecular shield function, is distinct from that of a classical molecular chaperone, such as HSP70 - while HSP70 reduces aggregation of citrate synthase (CS) on heating, two LEA proteins, a nematode group 3 protein, AavLEA1, and a plant group 1 protein, Em, do not; conversely, the LEA proteins reduce CS aggregation on desiccation, while HSP70 lacks this ability. There are also differences in interaction with client proteins - HSP70 can be co-immunoprecipitated with a polyglutamine-containing client, consistent with tight complex formation, whereas the LEA proteins can not, although a loose interaction is observed by Förster resonance energy transfer. In a further exploration of molecular shield function, we demonstrate that synthetic polysaccharides, like LEA proteins, are able to reduce desiccation-induced aggregation of a water-soluble proteome, consistent with a steric interference model of anti-aggregation activity. If molecular shields operate by reducing intermolecular cohesion rates, they should not protect against intramolecular protein damage. This was tested using the monomeric red fluorescent protein, mCherry, which does not undergo aggregation on drying, but the absorbance and emission spectra of its intrinsic fluorophore are dramatically reduced, indicative of intramolecular conformational changes. As expected, these changes are not prevented by AavLEA1, except for a slight protection at high molar ratios, and an AavLEA1-mCherry fusion protein is damaged to the same extent as mCherry alone. A recent hypothesis proposed that proteomes from desiccation-tolerant species contain a higher degree of disorder than intolerant examples, and that this might provide greater intrinsic stability

  17. Chaos and non-linear phenomena in renal vascular control

    DEFF Research Database (Denmark)

    Yip, K P; Holstein-Rathlou, N H

    1996-01-01

    are an example of deterministic chaos. Experimental studies show that the development of hypertension is associated with an increase in strength of the interaction between nephrons. Mathematical models suggest that an increased nephron-nephron interaction could cause a bifurcation in the dynamics of TGF from...... periodic oscillations to deterministic chaos. In addition to the TGF mediated oscillation, experimental studies have also demonstrated the presence of a faster oscillation, this having a frequency of 120-160 mHz. This is caused by a mechanism intrinsic to the vascular wall, and presumably represents...

  18. Lost in the chaos: Flawed literature should not generate new disorders

    Science.gov (United States)

    Van Rooij, Antonius J.; Kardefelt-Winther, Daniel

    2017-01-01

    The paper by Kuss, Griffiths, and Pontes (2016) titled “Chaos and confusion in DSM-5 diagnosis of Internet Gaming Disorder: Issues, concerns, and recommendations for clarity in the field” examines issues relating to the concept of Internet Gaming Disorder. We agree that there are serious issues and extend their arguments by suggesting that the field lacks basic theory, definitions, patient research, and properly validated and standardized assessment tools. As most studies derive data from survey research in functional populations, they exclude people with severe functional impairment and provide only limited information on the hypothesized disorder. Yet findings from such studies are widely used and often exaggerated, leading many to believe that we know more about the problem behavior than we do. We further argue that video game play is associated with several benefits and that formalizing this popular hobby as a psychiatric disorder is not without risks. It might undermine children’s right to play or encourage repressive treatment programs, which ultimately threaten children’s right to protection against violence. While Kuss et al. (2016) express support for the formal implementation of a disorder, we argue that before we have a proper evidence base, a sound theory, and validated assessment tools, it is irresponsible to support a formal category of disorder and doing so would solidify a confirmatory approach to research in this area. PMID:28301968

  19. The dynamic multisite interactions between two intrinsically disordered proteins

    KAUST Repository

    Wu, Shaowen; Wang, Dongdong; Liu, Jin; Feng, Yitao; Weng, Jingwei; Li, Yu; Gao, Xin; Liu, Jianwei; Wang, Wenning

    2017-01-01

    Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a

  20. Patterns in chaos

    International Nuclear Information System (INIS)

    Chirikov, B.V.

    1990-01-01

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

  1. Early Exposure to Environmental Chaos and Children's Physical and Mental Health.

    Science.gov (United States)

    Coley, Rebekah Levine; Lynch, Alicia Doyle; Kull, Melissa

    Environmental chaos has been proposed as a central influence impeding children's health and development, with the potential for particularly pernicious effects during the earliest years when children are most susceptible to environmental insults. This study evaluated a high-risk sample, following 495 low-income children living in poor urban neighborhoods from infancy to age 6. Longitudinal multilevel models tested the main tenets of the ecobiodevelopmental theory, finding that: (1) numerous distinct domains of environmental chaos were associated with children's physical and mental health outcomes, including housing disorder, neighborhood disorder, and relationship instability, with no significant results for residential instability; (2) different patterns emerged in relation to the timing of exposure to chaos, with more proximal exposure most strongly associated with children's functioning; and (3) the intensity of chaos also was a robust predictor of child functioning. Contrary to expectations, neither biological vulnerability (proxied through low birth weight status), maternal sensitivity, nor maternal distress moderated the role of chaos. Rather, maternal psychological distress functioned as a pathway through which environmental chaos was associated with children's functioning.

  2. Intrinsic connectivity networks within cerebellum and beyond in eating disorders.

    Science.gov (United States)

    Amianto, F; D'Agata, F; Lavagnino, L; Caroppo, P; Abbate-Daga, G; Righi, D; Scarone, S; Bergui, M; Mortara, P; Fassino, S

    2013-10-01

    Cerebellum seems to have a role both in feeding behavior and emotion regulation; therefore, it is a region that warrants further neuroimaging studies in eating disorders, severe conditions that determine a significant impairment in the physical and psychological domain. The aim of this study was to examine the cerebellum intrinsic connectivity during functional magnetic resonance imaging resting state in anorexia nervosa (AN), bulimia nervosa (BN), and healthy controls (CN). Resting state brain activity was decomposed into intrinsic connectivity networks (ICNs) using group spatial independent component analysis on the resting blood oxygenation level dependent time courses of 12 AN, 12 BN, and 10 CN. We extracted the cerebellar ICN and compared it between groups. Intrinsic connectivity within the cerebellar network showed some common alterations in eating disordered compared to healthy subjects (e.g., a greater connectivity with insulae, vermis, and paravermis and a lesser connectivity with parietal lobe); AN and BN patients were characterized by some peculiar alterations in connectivity patterns (e.g., greater connectivity with the insulae in AN compared to BN, greater connectivity with anterior cingulate cortex in BN compared to AN). Our data are consistent with the presence of different alterations in the cerebellar network in AN and BN patients that could be related to psychopathologic dimensions of eating disorders.

  3. 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.

  4. Functional anthology of intrinsic disorder. 2. Cellular components, domains, technical terms, developmental processes, and coding sequence diversities correlated with long disordered regions.

    Science.gov (United States)

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M; Oldfield, Christopher J; Dunker, A Keith; Obradovic, Zoran; Uversky, Vladimir N

    2007-05-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie, H.; Vucetic, S.; Iakoucheva, L. M.; Oldfield, C. J.; Dunker, A. K.; Obradovic, Z.; Uversky, V. N. Functional anthology of intrinsic disorder. 1. Biological processes and functions of proteins with long disordered regions. J. Proteome Res. 2007, 5, 1882-1898). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes approximately 90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes, and coding sequence diversities possessing strong positive and negative correlation with long disordered regions.

  5. Functional Anthology of Intrinsic Disorder. II. Cellular Components, Domains, Technical Terms, Developmental Processes and Coding Sequence Diversities Correlated with Long Disordered Regions

    Science.gov (United States)

    Vucetic, Slobodan; Xie, Hongbo; Iakoucheva, Lilia M.; Oldfield, Christopher J.; Dunker, A. Keith; Obradovic, Zoran; Uversky, Vladimir N.

    2008-01-01

    Biologically active proteins without stable ordered structure (i.e., intrinsically disordered proteins) are attracting increased attention. Functional repertoires of ordered and disordered proteins are very different, and the ability to differentiate whether a given function is associated with intrinsic disorder or with a well-folded protein is crucial for modern protein science. However, there is a large gap between the number of proteins experimentally confirmed to be disordered and their actual number in nature. As a result, studies of functional properties of confirmed disordered proteins, while helpful in revealing the functional diversity of protein disorder, provide only a limited view. To overcome this problem, a bioinformatics approach for comprehensive study of functional roles of protein disorder was proposed in the first paper of this series (Xie H., Vucetic S., Iakoucheva L.M., Oldfield C.J., Dunker A.K., Obradovic Z., Uversky V.N. (2006) Functional anthology of intrinsic disorder. I. Biological processes and functions of proteins with long disordered regions. J. Proteome Res.). Applying this novel approach to Swiss-Prot sequences and functional keywords, we found over 238 and 302 keywords to be strongly positively or negatively correlated, respectively, with long intrinsically disordered regions. This paper describes ~90 Swiss-Prot keywords attributed to the cellular components, domains, technical terms, developmental processes and coding sequence diversities possessing strong positive and negative correlation with long disordered regions. PMID:17391015

  6. Chaos, complexity, and random matrices

    Science.gov (United States)

    Cotler, Jordan; Hunter-Jones, Nicholas; Liu, Junyu; Yoshida, Beni

    2017-11-01

    Chaos and complexity entail an entropic and computational obstruction to describing a system, and thus are intrinsically difficult to characterize. In this paper, we consider time evolution by Gaussian Unitary Ensemble (GUE) Hamiltonians and analytically compute out-of-time-ordered correlation functions (OTOCs) and frame potentials to quantify scrambling, Haar-randomness, and circuit complexity. While our random matrix analysis gives a qualitatively correct prediction of the late-time behavior of chaotic systems, we find unphysical behavior at early times including an O(1) scrambling time and the apparent breakdown of spatial and temporal locality. The salient feature of GUE Hamiltonians which gives us computational traction is the Haar-invariance of the ensemble, meaning that the ensemble-averaged dynamics look the same in any basis. Motivated by this property of the GUE, we introduce k-invariance as a precise definition of what it means for the dynamics of a quantum system to be described by random matrix theory. We envision that the dynamical onset of approximate k-invariance will be a useful tool for capturing the transition from early-time chaos, as seen by OTOCs, to late-time chaos, as seen by random matrix theory.

  7. Survival and weak chaos.

    Science.gov (United States)

    Nee, Sean

    2018-05-01

    Survival analysis in biology and reliability theory in engineering concern the dynamical functioning of bio/electro/mechanical units. Here we incorporate effects of chaotic dynamics into the classical theory. Dynamical systems theory now distinguishes strong and weak chaos. Strong chaos generates Type II survivorship curves entirely as a result of the internal operation of the system, without any age-independent, external, random forces of mortality. Weak chaos exhibits (a) intermittency and (b) Type III survivorship, defined as a decreasing per capita mortality rate: engineering explicitly defines this pattern of decreasing hazard as 'infant mortality'. Weak chaos generates two phenomena from the normal functioning of the same system. First, infant mortality- sensu engineering-without any external explanatory factors, such as manufacturing defects, which is followed by increased average longevity of survivors. Second, sudden failure of units during their normal period of operation, before the onset of age-dependent mortality arising from senescence. The relevance of these phenomena encompasses, for example: no-fault-found failure of electronic devices; high rates of human early spontaneous miscarriage/abortion; runaway pacemakers; sudden cardiac death in young adults; bipolar disorder; and epilepsy.

  8. Protein intrinsic disorder in plants.

    Science.gov (United States)

    Pazos, Florencio; Pietrosemoli, Natalia; García-Martín, Juan A; Solano, Roberto

    2013-09-12

    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 signaling 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 cannot 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.

  9. Describing intrinsically disordered proteins at atomic resolution by NMR

    International Nuclear Information System (INIS)

    Ringkjobing Jensen, Malene; Blackledge, Martin; Ruigrok, Rob WH

    2013-01-01

    There is growing interest in the development of physical methods to study the conformational behaviour and biological activity of intrinsically disordered proteins (IDPs). In this review recent advances in the elucidation of quantitative descriptions of disordered proteins from nuclear magnetic resonance spectroscopy are presented. Ensemble approaches are particularly well adapted to map the conformational energy landscape sampled by the protein at atomic resolution. Significant advances in development of calibrated approaches to the statistical representation of the conformational behaviour of IDPs are presented, as well as applications to some biologically important systems where disorder plays a crucial role. (authors)

  10. Early Exposure to Environmental Chaos and Children’s Physical and Mental Health

    Science.gov (United States)

    Coley, Rebekah Levine; Lynch, Alicia Doyle; Kull, Melissa

    2015-01-01

    Environmental chaos has been proposed as a central influence impeding children’s health and development, with the potential for particularly pernicious effects during the earliest years when children are most susceptible to environmental insults. This study evaluated a high-risk sample, following 495 low-income children living in poor urban neighborhoods from infancy to age 6. Longitudinal multilevel models tested the main tenets of the ecobiodevelopmental theory, finding that: (1) numerous distinct domains of environmental chaos were associated with children’s physical and mental health outcomes, including housing disorder, neighborhood disorder, and relationship instability, with no significant results for residential instability; (2) different patterns emerged in relation to the timing of exposure to chaos, with more proximal exposure most strongly associated with children’s functioning; and (3) the intensity of chaos also was a robust predictor of child functioning. Contrary to expectations, neither biological vulnerability (proxied through low birth weight status), maternal sensitivity, nor maternal distress moderated the role of chaos. Rather, maternal psychological distress functioned as a pathway through which environmental chaos was associated with children’s functioning. PMID:25844016

  11. The fragmented self: imbalance between intrinsic and extrinsic self-networks in psychotic disorders.

    Science.gov (United States)

    Ebisch, Sjoerd J H; Aleman, André

    2016-08-01

    Self-disturbances are among the core features of schizophrenia and related psychotic disorders. The basic structure of the self could depend on the balance between intrinsic and extrinsic self-processing. We discuss studies on self-related processing in psychotic disorders that provide converging evidence for disrupted communication between neural networks subserving the so-called intrinsic self and extrinsic self. This disruption might be mainly caused by impaired integrity of key brain hubs. The intrinsic self has been associated with cortical midline structures involved in self-referential processing, autobiographical memory, and emotional evaluation. Additionally, we highlight central aspects of the extrinsic self in its interaction with the environment using sensorimotor networks, including self-experience in sensation and actions. A deficient relationship between these self-aspects because of disrupted between-network interactions offers a framework to explain core clinical features of psychotic disorders. In particular, we show how relative isolation and reduced modularity of networks subserving intrinsic and extrinsic self-processing might trigger the emergence of hallucinations and delusions, and why patients with psychosis typically have difficulties with self-other relationships and do not recognise mental problems. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Folding propensity of intrinsically disordered proteins by osmotic stress

    International Nuclear Information System (INIS)

    Mansouri, Amanda L.; Grese, Laura N.; Rowe, Erica L.

    2016-01-01

    Proteins imparted with intrinsic disorder conduct a range of essential cellular functions. To better understand the folding and hydration properties of intrinsically disordered proteins (IDPs), we used osmotic stress to induce conformational changes in nuclear co-activator binding domain (NCBD) and activator for thyroid hormone and retinoid receptor (ACTR). Osmotic stress was applied by the addition of small and polymeric osmolytes, where we discovered that water contributions to NCBD folding always exceeded those for ACTR. Both NCBD and ACTR were found to gain a-helical structure with increasing osmotic stress, consistent with their folding upon NCBD/ACTR complex formation. Using small-angle neutron scattering (SANS), we further characterized NCBD structural changes with the osmolyte ethylene glycol. Here a large reduction in overall size initially occurred before substantial secondary structural change. In conclusion, by focusing on folding propensity, and linked hydration changes, we uncover new insights that may be important for how IDP folding contributes to binding.

  13. 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...... natively disordered proteins....

  14. Structural vs. intrinsic carriers: contrasting effects of cation chemistry and disorder on ionic conductivity in pyrochlores

    International Nuclear Information System (INIS)

    Perriot, Romain; Uberuaga, Blas P.

    2015-01-01

    We use molecular dynamics simulations to investigate the role of cation disorder on oxygen diffusion in Gd 2 Zr 2 O 7 (GZO) and Gd 2 Ti 2 O 7 (GTO) pyrochlores, a class of complex oxides which contain a structural vacancy relative to the basic fluorite structure. The introduction of disorder has distinct effects depending on the chemistry of the material, increasing the mobility of structural carriers by up to four orders of magnitude in GZO. In contrast, in GTO, there is no mobility at zero or low disorder on the ns timescale, but higher disorder liberates the otherwise immobile carriers, allowing diffusion with rates comparable to GZO for the fully disordered material. Here, we show that the cation disorder enhances the diffusivity by both increasing the concentration of mobile structural carriers and their individual mobility. The disorder also influences the diffusion in materials containing intrinsic carriers, such as additional vacancies VO or oxygen interstitials OI. And while in ordered GZO and GTO the contribution of the intrinsic carriers dominates the overall diffusion of oxygen, OI in GZO contributes along with structural carriers, and the total diffusion rate can be calculated by assuming simple additive contributions from the two sources. Although the disorder in the materials with intrinsic defects usually enhances the diffusivity as in the defect-free case, in low concentrations, cation antisites AB or BA, where A = Gd and B = Zr or Ti, can act as traps for fast intrinsic defects. The trapping results in a lowering of the diffusivity, and causes a non-monotonic behavior of the diffusivity with disorder. Conversely, in the case of slow intrinsic defects, the main effect of the disorder is to liberate the structural carriers, resulting in an increase of the diffusivity regardless of the defect trapping.

  15. 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.

  16. Chaos in World Politics: A Reflection

    Science.gov (United States)

    Ferreira, Manuel Alberto Martins; Filipe, José António Candeias Bonito; Coelho, Manuel F. P.; Pedro, Isabel C.

    Chaos theory results from natural scientists' findings in the area of non-linear dynamics. The importance of related models has increased in the last decades, by studying the temporal evolution of non-linear systems. In consequence, chaos is one of the concepts that most rapidly have been expanded in what research topics respects. Considering that relationships in non-linear systems are unstable, chaos theory aims to understand and to explain this kind of unpredictable aspects of nature, social life, the uncertainties, the nonlinearities, the disorders and confusion, scientifically it represents a disarray connection, but basically it involves much more than that. The existing close relationship between change and time seems essential to understand what happens in the basics of chaos theory. In fact, this theory got a crucial role in the explanation of many phenomena. The relevance of this kind of theories has been well recognized to explain social phenomena and has permitted new advances in the study of social systems. Chaos theory has also been applied, particularly in the context of politics, in this area. The goal of this chapter is to make a reflection on chaos theory - and dynamical systems such as the theories of complexity - in terms of the interpretation of political issues, considering some kind of events in the political context and also considering the macro-strategic ideas of states positioning in the international stage.

  17. Quantum signatures of chaos or quantum chaos?

    International Nuclear Information System (INIS)

    Bunakov, V. E.

    2016-01-01

    A critical analysis of the present-day concept of chaos in quantum systems as nothing but a “quantum signature” of chaos in classical mechanics is given. In contrast to the existing semi-intuitive guesses, a definition of classical and quantum chaos is proposed on the basis of the Liouville–Arnold theorem: a quantum chaotic system featuring N degrees of freedom should have M < N independent first integrals of motion (good quantum numbers) specified by the symmetry of the Hamiltonian of the system. Quantitative measures of quantum chaos that, in the classical limit, go over to the Lyapunov exponent and the classical stability parameter are proposed. The proposed criteria of quantum chaos are applied to solving standard problems of modern dynamical chaos theory.

  18. Quantum signatures of chaos or quantum chaos?

    Energy Technology Data Exchange (ETDEWEB)

    Bunakov, V. E., E-mail: bunakov@VB13190.spb.edu [St. Petersburg State University (Russian Federation)

    2016-11-15

    A critical analysis of the present-day concept of chaos in quantum systems as nothing but a “quantum signature” of chaos in classical mechanics is given. In contrast to the existing semi-intuitive guesses, a definition of classical and quantum chaos is proposed on the basis of the Liouville–Arnold theorem: a quantum chaotic system featuring N degrees of freedom should have M < N independent first integrals of motion (good quantum numbers) specified by the symmetry of the Hamiltonian of the system. Quantitative measures of quantum chaos that, in the classical limit, go over to the Lyapunov exponent and the classical stability parameter are proposed. The proposed criteria of quantum chaos are applied to solving standard problems of modern dynamical chaos theory.

  19. The intrinsic stochasticity of near-integrable Hamiltonian systems

    Energy Technology Data Exchange (ETDEWEB)

    Krlin, L [Ceskoslovenska Akademie Ved, Prague (Czechoslovakia). Ustav Fyziky Plazmatu

    1989-09-01

    Under certain conditions, the dynamics of near-integrable Hamiltonian systems appears to be stochastic. This stochasticity (intrinsic stochasticity, or deterministic chaos) is closely related to the Kolmogorov-Arnold-Moser (KAM) theorem of the stability of near-integrable multiperiodic Hamiltonian systems. The effect of the intrinsic stochasticity attracts still growing attention both in theory and in various applications in contemporary physics. The paper discusses the relation of the intrinsic stochasticity to the modern ergodic theory and to the KAM theorem, and describes some numerical experiments on related astrophysical and high-temperature plasma problems. Some open questions are mentioned in conclusion. (author).

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

    International Nuclear Information System (INIS)

    Salmon, Loic

    2010-01-01

    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)

  1. Intrinsic disorder in Viral Proteins Genome-Linked: experimental and predictive analyses

    Directory of Open Access Journals (Sweden)

    Van Dorsselaer Alain

    2009-02-01

    Full Text Available Abstract Background VPgs are viral proteins linked to the 5' end of some viral genomes. Interactions between several VPgs and eukaryotic translation initiation factors eIF4Es are critical for plant infection. However, VPgs are not restricted to phytoviruses, being also involved in genome replication and protein translation of several animal viruses. To date, structural data are still limited to small picornaviral VPgs. Recently three phytoviral VPgs were shown to be natively unfolded proteins. Results In this paper, we report the bacterial expression, purification and biochemical characterization of two phytoviral VPgs, namely the VPgs of Rice yellow mottle virus (RYMV, genus Sobemovirus and Lettuce mosaic virus (LMV, genus Potyvirus. Using far-UV circular dichroism and size exclusion chromatography, we show that RYMV and LMV VPgs are predominantly or partly unstructured in solution, respectively. Using several disorder predictors, we show that both proteins are predicted to possess disordered regions. We next extend theses results to 14 VPgs representative of the viral diversity. Disordered regions were predicted in all VPg sequences whatever the genus and the family. Conclusion Based on these results, we propose that intrinsic disorder is a common feature of VPgs. The functional role of intrinsic disorder is discussed in light of the biological roles of VPgs.

  2. The fragmented self : imbalance between intrinsic and extrinsic self-networks in psychotic disorders

    NARCIS (Netherlands)

    Ebisch, Sjoerd J. H.; Aleman, Andre

    Self-disturbances are among the core features of schizophrenia and related psychotic disorders. The basic structure of the self could depend on the balance between intrinsic and extrinsic self-processing. We discuss studies on self-related processing in psychotic disorders that provide converging

  3. Small-angle scattering studies of intrinsically disordered proteins and their complexes

    DEFF Research Database (Denmark)

    Cordeiro, Tiago N.; Herranz-Trillo, Fátima; Urbanek, Annika

    2017-01-01

    Intrinsically Disordered Proteins (IDPs) perform a broad range of biological functions. Their relevance has motivated intense research activity seeking to characterize their sequence/structure/function relationships. However, the conformational plasticity of these molecules hampers the applicatio...

  4. Comprehensive large-scale assessment of intrinsic protein disorder.

    Science.gov (United States)

    Walsh, Ian; Giollo, Manuel; Di Domenico, Tomás; Ferrari, Carlo; Zimmermann, Olav; Tosatto, Silvio C E

    2015-01-15

    Intrinsically disordered regions are key for the function of numerous proteins. Due to the difficulties in experimental disorder characterization, many computational predictors have been developed with various disorder flavors. Their performance is generally measured on small sets mainly from experimentally solved structures, e.g. Protein Data Bank (PDB) chains. MobiDB has only recently started to collect disorder annotations from multiple experimental structures. MobiDB annotates disorder for UniProt sequences, allowing us to conduct the first large-scale assessment of fast disorder predictors on 25 833 different sequences with X-ray crystallographic structures. In addition to a comprehensive ranking of predictors, this analysis produced the following interesting observations. (i) The predictors cluster according to their disorder definition, with a consensus giving more confidence. (ii) Previous assessments appear over-reliant on data annotated at the PDB chain level and performance is lower on entire UniProt sequences. (iii) Long disordered regions are harder to predict. (iv) Depending on the structural and functional types of the proteins, differences in prediction performance of up to 10% are observed. The datasets are available from Web site at URL: http://mobidb.bio.unipd.it/lsd. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  5. 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...

  6. Restless 'rest': intrinsic sensory hyperactivity and disinhibition in post-traumatic stress disorder.

    Science.gov (United States)

    Clancy, Kevin; Ding, Mingzhou; Bernat, Edward; Schmidt, Norman B; Li, Wen

    2017-07-01

    Post-traumatic stress disorder is characterized by exaggerated threat response, and theoretical accounts to date have focused on impaired threat processing and dysregulated prefrontal-cortex-amygdala circuitry. Nevertheless, evidence is accruing for broad, threat-neutral sensory hyperactivity in post-traumatic stress disorder. As low-level, sensory processing impacts higher-order operations, such sensory anomalies can contribute to widespread dysfunctions, presenting an additional aetiological mechanism for post-traumatic stress disorder. To elucidate a sensory pathology of post-traumatic stress disorder, we examined intrinsic visual cortical activity (based on posterior alpha oscillations) and bottom-up sensory-driven causal connectivity (Granger causality in the alpha band) during a resting state (eyes open) and a passive, serial picture viewing state. Compared to patients with generalized anxiety disorder (n = 24) and healthy control subjects (n = 20), patients with post-traumatic stress disorder (n = 25) demonstrated intrinsic sensory hyperactivity (suppressed posterior alpha power, source-localized to the visual cortex-cuneus and precuneus) and bottom-up inhibition deficits (reduced posterior→frontal Granger causality). As sensory input increased from resting to passive picture viewing, patients with post-traumatic stress disorder failed to demonstrate alpha adaptation, highlighting a rigid, set mode of sensory hyperactivity. Interestingly, patients with post-traumatic stress disorder also showed heightened frontal processing (augmented frontal gamma power, source-localized to the superior frontal gyrus and dorsal cingulate cortex), accompanied by attenuated top-down inhibition (reduced frontal→posterior causality). Importantly, not only did suppressed alpha power and bottom-up causality correlate with heightened frontal gamma power, they also correlated with increased severity of sensory and executive dysfunctions (i.e. hypervigilance and impulse control

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

    Directory of Open Access Journals (Sweden)

    Vince D Calhoun

    2012-01-01

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

  8. Coherence and chaos in extended dynamical systems

    International Nuclear Information System (INIS)

    Bishop, A.R.

    1994-01-01

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

  9. 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.

  10. 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.

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

    Science.gov (United States)

    Shinbrot, Troy

    2015-09-01

    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.

  12. Understanding the Role of Intrinsic Disorder of Viral Proteins in the Oncogenicity of Different Types of HPV.

    Science.gov (United States)

    Tamarozzi, Elvira Regina; Giuliatti, Silvana

    2018-01-09

    Intrinsic disorder is very important in the biological function of several proteins, and is directly linked to their foldability during interaction with their targets. There is a close relationship between the intrinsically disordered proteins and the process of carcinogenesis involving viral pathogens. Among these pathogens, we have highlighted the human papillomavirus (HPV) in this study. HPV is currently among the most common sexually transmitted infections, besides being the cause of several types of cancer. HPVs are divided into two groups, called high- and low-risk, based on their oncogenic potential. The high-risk HPV E6 protein has been the target of much research, in seeking treatments against HPV, due to its direct involvement in the process of cell cycle control. To understand the role of intrinsic disorder of the viral proteins in the oncogenic potential of different HPV types, the structural characteristics of intrinsically disordered regions of high and low-risk HPV E6 proteins were analyzed. In silico analyses of primary sequences, prediction of tertiary structures, and analyses of molecular dynamics allowed the observation of the behavior of such disordered regions in these proteins, thereby proving a direct relationship of structural variation with the degree of oncogenicity of HPVs. The results obtained may contribute to the development of new therapies, targeting the E6 oncoprotein, for the treatment of HPV-associated diseases.

  13. RNA chaperoning and intrinsic disorder in the core proteins of Flaviviridae.

    Science.gov (United States)

    Ivanyi-Nagy, Roland; Lavergne, Jean-Pierre; Gabus, Caroline; Ficheux, Damien; Darlix, Jean-Luc

    2008-02-01

    RNA chaperone proteins are essential partners of RNA in living organisms and viruses. They are thought to assist in the correct folding and structural rearrangements of RNA molecules by resolving misfolded RNA species in an ATP-independent manner. RNA chaperoning is probably an entropy-driven process, mediated by the coupled binding and folding of intrinsically disordered protein regions and the kinetically trapped RNA. Previously, we have shown that the core protein of hepatitis C virus (HCV) is a potent RNA chaperone that can drive profound structural modifications of HCV RNA in vitro. We now examined the RNA chaperone activity and the disordered nature of core proteins from different Flaviviridae genera, namely that of HCV, GBV-B (GB virus B), WNV (West Nile virus) and BVDV (bovine viral diarrhoea virus). Despite low-sequence similarities, all four proteins demonstrated general nucleic acid annealing and RNA chaperone activities. Furthermore, heat resistance of core proteins, as well as far-UV circular dichroism spectroscopy suggested that a well-defined 3D protein structure is not necessary for core-induced RNA structural rearrangements. These data provide evidence that RNA chaperoning-possibly mediated by intrinsically disordered protein segments-is conserved in Flaviviridae core proteins. Thus, besides nucleocapsid formation, core proteins may function in RNA structural rearrangements taking place during virus replication.

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

    International Nuclear Information System (INIS)

    Rajan, Kanaka; Abbott, L. F.; Sompolinsky, Haim

    2010-01-01

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

  15. Disease-associated mutations disrupt functionally important regions of intrinsic protein disorder.

    Directory of Open Access Journals (Sweden)

    Vladimir Vacic

    Full Text Available The effects of disease mutations on protein structure and function have been extensively investigated, and many predictors of the functional impact of single amino acid substitutions are publicly available. The majority of these predictors are based on protein structure and evolutionary conservation, following the assumption that disease mutations predominantly affect folded and conserved protein regions. However, the prevalence of the intrinsically disordered proteins (IDPs and regions (IDRs in the human proteome together with their lack of fixed structure and low sequence conservation raise a question about the impact of disease mutations in IDRs. Here, we investigate annotated missense disease mutations and show that 21.7% of them are located within such intrinsically disordered regions. We further demonstrate that 20% of disease mutations in IDRs cause local disorder-to-order transitions, which represents a 1.7-2.7 fold increase compared to annotated polymorphisms and neutral evolutionary substitutions, respectively. Secondary structure predictions show elevated rates of transition from helices and strands into loops and vice versa in the disease mutations dataset. Disease disorder-to-order mutations also influence predicted molecular recognition features (MoRFs more often than the control mutations. The repertoire of disorder-to-order transition mutations is limited, with five most frequent mutations (R→W, R→C, E→K, R→H, R→Q collectively accounting for 44% of all deleterious disorder-to-order transitions. As a proof of concept, we performed accelerated molecular dynamics simulations on a deleterious disorder-to-order transition mutation of tumor protein p63 and, in agreement with our predictions, observed an increased α-helical propensity of the region harboring the mutation. Our findings highlight the importance of mutations in IDRs and refine the traditional structure-centric view of disease mutations. The results of this study

  16. Quantum chaos

    International Nuclear Information System (INIS)

    Steiner, F.

    1994-01-01

    A short historical overview is given on the development of our knowledge of complex dynamical systems with special emphasis on ergodicity and chaos, and on the semiclassical quantization of integrable and chaotic systems. The general trace formular is discussed as a sound mathematical basis for the semiclassical quantization of chaos. Two conjectures are presented on the basis of which it is argued that there are unique fluctuation properties in quantum mechanics which are universal and, in a well defined sense, maximally random if the corresponding classical system is strongly chaotic. These properties constitute the quantum mechanical analogue of the phenomenon of chaos in classical mechanics. Thus quantum chaos has been found. (orig.)

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

    DEFF Research Database (Denmark)

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

    2015-01-01

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

  18. Exploring chaos a guide to the new science of disorder

    CERN Document Server

    1994-01-01

    Chaos Theory is giving scientists fresh insights into all sorts of unruly phenomena--from dripping faucets to swinging pendulums, from the vagaries of the weather to the movements of the planets, from heart rhythms to gold futures.

  19. Multiple structure-intrinsic disorder interactions regulate and coordinate Hox protein function

    Science.gov (United States)

    Bondos, Sarah

    During animal development, Hox transcription factors determine fate of developing tissues to generate diverse organs and appendages. Hox proteins are famous for their bizarre mutant phenotypes, such as replacing antennae with legs. Clearly, the functions of individual Hox proteins must be distinct and reliable in vivo, or the organism risks malformation or death. However, within the Hox protein family, the DNA-binding homeodomains are highly conserved and the amino acids that contact DNA are nearly invariant. These observations raise the question: How do different Hox proteins correctly identify their distinct target genes using a common DNA binding domain? One possible means to modulate DNA binding is through the influence of the non-homeodomain protein regions, which differ significantly among Hox proteins. However genetic approaches never detected intra-protein interactions, and early biochemical attempts were hindered because the special features of ``intrinsically disordered'' sequences were not appreciated. We propose the first-ever structural model of a Hox protein to explain how specific contacts between distant, intrinsically disordered regions of the protein and the homeodomain regulate DNA binding and coordinate this activity with other Hox molecular functions.

  20. Hyper-chaos encryption using convolutional masking and model free unmasking

    International Nuclear Information System (INIS)

    Qi Guo-Yuan; Matondo Sandra Bazebo

    2014-01-01

    In this paper, during the masking process the encrypted message is convolved and embedded into a Qi hyper-chaotic system characterizing a high disorder degree. The masking scheme was tested using both Qi hyper-chaos and Lorenz chaos and indicated that Qi hyper-chaos based masking can resist attacks of the filtering and power spectrum analysis, while the Lorenz based scheme fails for high amplitude data. To unmask the message at the receiving end, two methods are proposed. In the first method, a model-free synchronizer, i.e. a multivariable higher-order differential feedback controller between the transmitter and receiver is employed to de-convolve the message embedded in the receiving signal. In the second method, no synchronization is required since the message is de-convolved using the information of the estimated derivative. (general)

  1. DisoMCS: Accurately Predicting Protein Intrinsically Disordered Regions Using a Multi-Class Conservative Score Approach.

    Directory of Open Access Journals (Sweden)

    Zhiheng Wang

    Full Text Available The precise prediction of protein intrinsically disordered regions, which play a crucial role in biological procedures, is a necessary prerequisite to further the understanding of the principles and mechanisms of protein function. Here, we propose a novel predictor, DisoMCS, which is a more accurate predictor of protein intrinsically disordered regions. The DisoMCS bases on an original multi-class conservative score (MCS obtained by sequence-order/disorder alignment. Initially, near-disorder regions are defined on fragments located at both the terminus of an ordered region connecting a disordered region. Then the multi-class conservative score is generated by sequence alignment against a known structure database and represented as order, near-disorder and disorder conservative scores. The MCS of each amino acid has three elements: order, near-disorder and disorder profiles. Finally, the MCS is exploited as features to identify disordered regions in sequences. DisoMCS utilizes a non-redundant data set as the training set, MCS and predicted secondary structure as features, and a conditional random field as the classification algorithm. In predicted near-disorder regions a residue is determined as an order or a disorder according to the optimized decision threshold. DisoMCS was evaluated by cross-validation, large-scale prediction, independent tests and CASP (Critical Assessment of Techniques for Protein Structure Prediction tests. All results confirmed that DisoMCS was very competitive in terms of accuracy of prediction when compared with well-established publicly available disordered region predictors. It also indicated our approach was more accurate when a query has higher homologous with the knowledge database.The DisoMCS is available at http://cal.tongji.edu.cn/disorder/.

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

    Directory of Open Access Journals (Sweden)

    Daniela Marasco

    2015-04-01

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

  3. Partner-Mediated Polymorphism of an Intrinsically Disordered Protein.

    Science.gov (United States)

    Bignon, Christophe; Troilo, Francesca; Gianni, Stefano; Longhi, Sonia

    2017-11-29

    Intrinsically disordered proteins (IDPs) recognize their partners through molecular recognition elements (MoREs). The MoRE of the C-terminal intrinsically disordered domain of the measles virus nucleoprotein (N TAIL ) is partly pre-configured as an α-helix in the free form and undergoes α-helical folding upon binding to the X domain (XD) of the viral phosphoprotein. Beyond XD, N TAIL also binds the major inducible heat shock protein 70 (hsp70). So far, no structural information is available for the N TAIL /hsp70 complex. Using mutational studies combined with a protein complementation assay based on green fluorescent protein reconstitution, we have investigated both N TAIL /XD and N TAIL /hsp70 interactions. Although the same N TAIL region binds the two partners, the binding mechanisms are different. Hsp70 binding is much more tolerant of MoRE substitutions than XD, and the majority of substitutions lead to an increased N TAIL /hsp70 interaction strength. Furthermore, while an increased and a decreased α-helicity of the MoRE lead to enhanced and reduced interaction strength with XD, respectively, the impact on hsp70 binding is negligible, suggesting that the MoRE does not adopt an α-helical conformation once bound to hsp70. Here, by showing that the α-helical conformation sampled by the free form of the MoRE does not systematically commit it to adopt an α-helical conformation in the bound form, we provide an example of partner-mediated polymorphism of an IDP and of the relative insensitiveness of the bound structure to the pre-recognition state. The present results therefore contribute to shed light on the molecular mechanisms by which IDPs recognize different partners. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. 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…

  5. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

    NARCIS (Netherlands)

    Ketterer, Philip; Ananth, Adithya N; Laman Trip, Diederik S; Mishra, Ankur; Bertosin, Eva; Ganji, Mahipal; van der Torre, Jaco; Onck, Patrick; Dietz, Hendrik; Dekker, Cees

    2018-01-01

    The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize

  6. The dynamic multisite interactions between two intrinsically disordered proteins

    KAUST Repository

    Wu, Shaowen

    2017-05-11

    Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well characterized folding upon binding to dynamic fuzzy complex. To date, most studies concern the binding of an IDP to a structured protein, while the Interaction between two IDPs is poorly understood. In this study, we combined NMR, smFRET, and molecular dynamics (MD) simulation to characterize the interaction between two IDPs, the C-terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by MD and mutagenesis studies. Our study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.

  7. 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. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Chaos in neurons and its application: perspective of chaos engineering.

    Science.gov (United States)

    Hirata, Yoshito; Oku, Makito; Aihara, Kazuyuki

    2012-12-01

    We review our recent work on chaos in neurons and its application to neural networks from perspective of chaos engineering. Especially, we analyze a dataset of a squid giant axon by newly combining our previous work of identifying Devaney's chaos with surrogate data analysis, and show that an axon can behave chaotically. Based on this knowledge, we use a chaotic neuron model to investigate possible information processing in the brain.

  9. A multi-state coarse grained modeling approach for an intrinsically disordered peptide

    Science.gov (United States)

    Ramezanghorbani, Farhad; Dalgicdir, Cahit; Sayar, Mehmet

    2017-09-01

    Many proteins display a marginally stable tertiary structure, which can be altered via external stimuli. Since a majority of coarse grained (CG) models are aimed at structure prediction, their success for an intrinsically disordered peptide's conformational space with marginal stability and sensitivity to external stimuli cannot be taken for granted. In this study, by using the LKα 14 peptide as a test system, we demonstrate a bottom-up approach for constructing a multi-state CG model, which can capture the conformational behavior of this peptide in three distinct environments with a unique set of interaction parameters. LKα 14 is disordered in dilute solutions; however, it strictly adopts the α -helix conformation upon aggregation or when in contact with a hydrophobic/hydrophilic interface. Our bottom-up approach combines a generic base model, that is unbiased for any particular secondary structure, with nonbonded interactions which represent hydrogen bonds, electrostatics, and hydrophobic forces. We demonstrate that by using carefully designed all atom potential of mean force calculations from all three states of interest, one can get a balanced representation of the nonbonded interactions. Our CG model behaves intrinsically disordered in bulk water, folds into an α -helix in the presence of an interface or a neighboring peptide, and is stable as a tetrameric unit, successfully reproducing the all atom molecular dynamics simulations and experimental results.

  10. DNA origami scaffold for studying intrinsically disordered proteins of the nuclear pore complex

    NARCIS (Netherlands)

    Ketterer, Philip; Ananth, A.N.; Laman Trip, J.D.S.; Mishra, Ankur; Bertosin, Eva; Ganji, M.; van der Torre, J.; Onck, Patrick; Dietz, Hendrik; Dekker, C.

    2018-01-01

    The nuclear pore complex (NPC) is the gatekeeper for nuclear transport in eukaryotic cells. A key component of the NPC is the central shaft lined with intrinsically disordered proteins (IDPs) known as FG-Nups, which control the selective molecular traffic. Here, we present an approach to realize

  11. 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. Copyright © 2016 Institute of Psychoanalysis.

  12. 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.

  13. 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

    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......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...

  14. Order, disorder and chaos in crystal lattice

    International Nuclear Information System (INIS)

    Oliveira, M.J. de; Salinas, S.R.A.

    1985-01-01

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

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

    International Nuclear Information System (INIS)

    Takeda, Shuichi; Maéda, Yuichiro; Koike, Ryotaro; Ota, Motonori; Nitanai, Yasushi; Minakata, Shiho

    2011-01-01

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

  16. Cosmos To Chaos: A Way of Thinking Legal Teaching Warat’s Contribuitions

    Directory of Open Access Journals (Sweden)

    Ana Flávia Costa Eccard

    2016-06-01

    find the disorder (chaos and the teacher has a fundamental role in this transformation, because him seduces and frees. This liberating teaching is conducted by a different conception of rationality and emotion.

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

    International Nuclear Information System (INIS)

    Chen Yanguang

    2009-01-01

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

  18. Defining chaos.

    Science.gov (United States)

    Hunt, Brian R; Ott, Edward

    2015-09-01

    In this paper, we propose, discuss, and illustrate a computationally feasible definition of chaos which can be applied very generally to situations that are commonly encountered, including attractors, repellers, and non-periodically forced systems. This definition is based on an entropy-like quantity, which we call "expansion entropy," and we define chaos as occurring when this quantity is positive. We relate and compare expansion entropy to the well-known concept of topological entropy to which it is equivalent under appropriate conditions. We also present example illustrations, discuss computational implementations, and point out issues arising from attempts at giving definitions of chaos that are not entropy-based.

  19. Regularity and chaos in Vlasov evolution of nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Jacquot, B.; Guarnera, A.; Chomaz, Ph.; Colonna, M.

    1995-12-31

    A careful analysis of the mean-field dynamics inside the spinodal instability region is performed. It is shown that, conversely to some recently published results the mean-field evolution appears mostly regular over a long time scale, while some disorder is observed only very late, when fragments are already formed This onset of chaos can be related to the fragment interaction which induces some coalescence effects. Moreover it is shown that the time scale over which the chaos start to develop are very sensitive to the range of the considered force. All the presented results support the various analyses of spinodal instabilities obtained using stochastic mean field approaches. (author). 16 refs. Submitted to Physical Review, C (US).

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

    NARCIS (Netherlands)

    Cino, E.A.; Wong-ekkabut, J.; Karttunen, M.E.J.; Choy, W.-Y.

    2011-01-01

    Intrinsically disordered proteins (IDPs) are abundant in cells and have central roles in protein-protein interaction networks. Interactions between the IDP Prothymosin alpha (ProTa) and the Neh2 domain of Nuclear factor erythroid 2-related factor 2 (Nrf2), with a common binding partner, Kelch-like

  1. Intramolecular three-colour single pair FRET of intrinsically disordered proteins with increased dynamic range.

    Science.gov (United States)

    Milles, Sigrid; Koehler, Christine; Gambin, Yann; Deniz, Ashok A; Lemke, Edward A

    2012-10-01

    Single molecule observation of fluorescence resonance energy transfer can be used to provide insight into the structure and dynamics of proteins. Using a straightforward triple-colour labelling strategy, we present a measurement and analysis scheme that can simultaneously study multiple regions within single intrinsically disordered proteins.

  2. Li-Yorke chaos and synchronous chaos in a globally nonlocal coupled map lattice

    International Nuclear Information System (INIS)

    Khellat, Farhad; Ghaderi, Akashe; Vasegh, Nastaran

    2011-01-01

    Highlights: → A globally nonlocal coupled map lattice is introduced. → A sufficient condition for the existence of Li-Yorke chaos is determined. → A sufficient condition for synchronous behaviors is obtained. - Abstract: This paper investigates a globally nonlocal coupled map lattice. A rigorous proof to the existence of chaos in the scene of Li-Yorke in that system is presented in terms of the Marotto theorem. Analytical sufficient conditions under which the system is chaotic, and has synchronous behaviors are determined, respectively. The wider regions associated with chaos and synchronous behaviors are shown by simulations. Spatiotemporal chaos, synchronous chaos and some other synchronous behaviors such as fixed points, 2-cycles and 2 2 -cycles are also shown by simulations for some values of the parameters.

  3. Biographical and intrinsic disorder in some ionic crystals according to EPR data

    International Nuclear Information System (INIS)

    Angelov, S.

    1989-01-01

    CO 0 2 -radicals stabilised in SrCO 3 are examined as an example of disorder in diamagnetic matrices containing isolated paramagnetic centers. The genesis, stabilisation and further recombination of CO - 2 is connected with a specific biographical disorder in SrCO 3 , depending on the rate of decomposition of the initial SrC 2 O 4 .H 2 O. Depending on the electronic configuration of the EPR-active ion and the structure of the matrix (interionic distances and angles between them), the biographical and intrinsic disorder may influence different parameters of the exchange-narrowed EPR singlet line. For example, Co 3 O 4 has a rigid structure, varying slightly with the preparation temperature. The disorder affects only the local zero-field splittings of the 4 A 2 state of the Co 2+ -ions, the exchange field being insensitive to it. In the more flexible structure of Fe 2 (MoO 4 ) 3 , the disorder due to small deviations from stoichiometry changes the exchange field between Fe(III) ions, while the second moment of the EPR line remains constant. (author)

  4. Intrinsically Disordered Proteins in a Physics-Based World

    Directory of Open Access Journals (Sweden)

    Jianhan Chen

    2010-12-01

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

  5. Quantum chaos

    International Nuclear Information System (INIS)

    Cejnar, P.

    2007-01-01

    Chaos is a name given in physics to a branch which, within classical mechanics, studies the consequences of sensitive dependences of the behavior of physical systems on the starting conditions, i.e., the 'butterfly wing effect'. However, how to describe chaotic behavior in the world of quantum particles? It appears that quantum mechanics does not admit the sensitive dependence on the starting conditions, and moreover, predicts a substantial suppression of chaos also at the macroscopic level. Still, the quantum properties of systems that are chaotic in terms of classical mechanics differ basically from the properties of classically arranged systems. This topic is studied by a field of physics referred to as quantum chaos. (author)

  6. On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats

    Science.gov (United States)

    Yacoub, Haitham A.; Sadek, Mahmoud A.; Uversky, Vladimir N.

    2017-01-01

    ABSTRACT This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way. In fact, positions and intensities of disorder/flexibility “signals” in the corresponding disorder profiles are relatively unique for avian and animal species. Therefore, it is possible to devise a set of simple rules based on the peculiarities of disorder profiles of their mtCyt-b proteins to discriminate among species. This intrinsic disorder-based analysis represents a new technique that could be used to provide a promising solution for identification of the source of meats. PMID:28331777

  7. N-terminal segments modulate the α-helical propensities of the intrinsically disordered basic regions of bZIP proteins.

    Science.gov (United States)

    Das, Rahul K; Crick, Scott L; Pappu, Rohit V

    2012-02-17

    Basic region leucine zippers (bZIPs) are modular transcription factors that play key roles in eukaryotic gene regulation. The basic regions of bZIPs (bZIP-bRs) are necessary and sufficient for DNA binding and specificity. Bioinformatic predictions and spectroscopic studies suggest that unbound monomeric bZIP-bRs are uniformly disordered as isolated domains. Here, we test this assumption through a comparative characterization of conformational ensembles for 15 different bZIP-bRs using a combination of atomistic simulations and circular dichroism measurements. We find that bZIP-bRs have quantifiable preferences for α-helical conformations in their unbound monomeric forms. This helicity varies from one bZIP-bR to another despite a significant sequence similarity of the DNA binding motifs (DBMs). Our analysis reveals that intramolecular interactions between DBMs and eight-residue segments directly N-terminal to DBMs are the primary modulators of bZIP-bR helicities. We test the accuracy of this inference by designing chimeras of bZIP-bRs to have either increased or decreased overall helicities. Our results yield quantitative insights regarding the relationship between sequence and the degree of intrinsic disorder within bZIP-bRs, and might have general implications for other intrinsically disordered proteins. Understanding how natural sequence variations lead to modulation of disorder is likely to be important for understanding the evolution of specificity in molecular recognition through intrinsically disordered regions (IDRs). Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Molecular signaling involving intrinsically disordered proteins in prostate cancer

    Directory of Open Access Journals (Sweden)

    Anna Russo

    2016-01-01

    Full Text Available Investigations on cellular protein interaction networks (PINs reveal that proteins that constitute hubs in a PIN are notably enriched in Intrinsically Disordered Proteins (IDPs compared to proteins that constitute edges, highlighting the role of IDPs in signaling pathways. Most IDPs rapidly undergo disorder-to-order transitions upon binding to their biological targets to perform their function. Conformational dynamics enables IDPs to be versatile and to interact with a broad range of interactors under normal physiological conditions where their expression is tightly modulated. IDPs are involved in many cellular processes such as cellular signaling, transcriptional regulation, and splicing; thus, their high-specificity/low-affinity interactions play crucial roles in many human diseases including cancer. Prostate cancer (PCa is one of the leading causes of cancer-related mortality in men worldwide. Therefore, identifying molecular mechanisms of the oncogenic signaling pathways that are involved in prostate carcinogenesis is crucial. In this review, we focus on the aspects of cellular pathways leading to PCa in which IDPs exert a primary role.

  9. Chaos as a psychological construct: historical roots, principal findings, and current growth directions.

    Science.gov (United States)

    Guastello, Stephen J

    2009-07-01

    The landmarks in the use of chaos and related constructs in psychology were entwined with the growing use of other nonlinear dynamical constructs, especially catastrophes and self-organization. The growth in substantive applications of chaos in psychology is partially related to the development of methodologies that work within the constraints of psychological data. The psychological literature includes rigorous theory with testable propositions, lighter-weight metaphorical uses of the construct, and colloquial uses of "chaos" with no particular theoretical intent. The current state of the chaos construct and supporting empirical research in psychological theory is summarized in neuroscience, psychophysics, psychomotor skill and other learning phenomena, clinical and abnormal psychology, and group dynamics and organizational behavior. Trends indicate that human systems do not remain chaotic indefinitely; they eventually self-organize, and the concept of the complex adaptive system has become prominent. Chaotic turbulence is generally higher in healthy systems compared to unhealthy systems, although opposite appears true in mood disorders. Group dynamics research shows trends consistent with the complex adaptive system, whereas organizational behavior lags behind in empirical studies relative to the quantity of its theory. Future directions for research involving the chaos construct and other nonlinear dynamics are outlined.

  10. Intrinsic brain connectivity predicts impulse control disorders in patients with Parkinson's disease.

    Science.gov (United States)

    Tessitore, Alessandro; De Micco, Rosa; Giordano, Alfonso; di Nardo, Federica; Caiazzo, Giuseppina; Siciliano, Mattia; De Stefano, Manuela; Russo, Antonio; Esposito, Fabrizio; Tedeschi, Gioacchino

    2017-12-01

    Impulse control disorders can be triggered by dopamine replacement therapies in patients with PD. Using resting-state functional MRI, we investigated the intrinsic brain network connectivity at baseline in a cohort of drug-naive PD patients who successively developed impulse control disorders over a 36-month follow-up period compared with patients who did not. Baseline 3-Tesla MRI images of 30 drug-naive PD patients and 20 matched healthy controls were analyzed. The impulse control disorders' presence and severity at follow-up were assessed by the Questionnaire for Impulsive-Compulsive Disorders in Parkinson's Disease Rating Scale. Single-subject and group-level independent component analysis was used to investigate functional connectivity differences within the major resting-state networks. We also compared internetwork connectivity between patients. Finally, a multivariate Cox regression model was used to investigate baseline predictors of impulse control disorder development. At baseline, decreased connectivity in the default-mode and right central executive networks and increased connectivity in the salience network were detected in PD patients with impulse control disorders at follow-up compared with those without. Increased default-mode/central executive internetwork connectivity was significantly associated with impulse control disorders development (P impulse control disorders while on dopaminergic treatment. We hypothesize that these divergent cognitive and limbic network connectivity changes could represent a potential biomarker and an additional risk factor for the emergence of impulse control disorders. © 2017 International Parkinson and Movement Disorder Society. © 2017 International Parkinson and Movement Disorder Society.

  11. Paths to chaos

    International Nuclear Information System (INIS)

    Friedrich, H.

    1992-01-01

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

  12. Chaos-assisted tunneling in the presence of Anderson localization.

    Science.gov (United States)

    Doggen, Elmer V H; Georgeot, Bertrand; Lemarié, Gabriel

    2017-10-01

    Tunneling between two classically disconnected regular regions can be strongly affected by the presence of a chaotic sea in between. This phenomenon, known as chaos-assisted tunneling, gives rise to large fluctuations of the tunneling rate. Here we study chaos-assisted tunneling in the presence of Anderson localization effects in the chaotic sea. Our results show that the standard tunneling rate distribution is strongly modified by localization, going from the Cauchy distribution in the ergodic regime to a log-normal distribution in the strongly localized case, for both a deterministic and a disordered model. We develop a single-parameter scaling description which accurately describes the numerical data. Several possible experimental implementations using cold atoms, photonic lattices, or microwave billiards are discussed.

  13. CHAOS THEORY OF LAW: PENJELASAN ATAS KETERATURAN DAN KETIDAKTERATURAN DALAM HUKUM

    Directory of Open Access Journals (Sweden)

    . Sudjito

    2015-02-01

    Full Text Available It is of no posibilitiy to understand the complex reality of law by means of linear-mechanistic approach used to be ulitilized in rechtsdogmatiek or legal-positivism which is still dominant in the teaching of law. It needs our readiness to see the world of law not as in order but in chaos; and this is the basic reason to present the Chaos theory of law. It is hoped that this theory will enable us to explore and explain the law throroughly. Thus the law science will be the total science which does not limit itself to the positive law, the state law or the lawyer’s law. Furthermore this chaos theory is expected to give better description and comprehension of law. Order and disorder are not opposant, or white-black dichotomy, but they are interrelated, interwoven and having mutual fulfilment in a sustainably and continually change process. The Chaos theory of law, thus, constitutes a theory which is qualified to give good explanation of the complex reality of law and provide the best solution to the critical condition of law in our country.

  14. Deciphering RNA-Recognition Patterns of Intrinsically Disordered Proteins

    Directory of Open Access Journals (Sweden)

    Ambuj Srivastava

    2018-05-01

    Full Text Available Intrinsically disordered regions (IDRs and protein (IDPs are highly flexible owing to their lack of well-defined structures. A subset of such proteins interacts with various substrates; including RNA; frequently adopting regular structures in the final complex. In this work; we have analysed a dataset of protein–RNA complexes undergoing disorder-to-order transition (DOT upon binding. We found that DOT regions are generally small in size (less than 3 residues for RNA binding proteins. Like structured proteins; positively charged residues are found to interact with RNA molecules; indicating the dominance of electrostatic and cation-π interactions. However, a comparison of binding frequency shows that interface hydrophobic and aromatic residues have more interactions in only DOT regions than in a protein. Further; DOT regions have significantly higher exposure to water than their structured counterparts. Interactions of DOT regions with RNA increase the sheet formation with minor changes in helix forming residues. We have computed the interaction energy for amino acids–nucleotide pairs; which showed the preference of His–G; Asn–U and Ser–U at for the interface of DOT regions. This study provides insights to understand protein–RNA interactions and the results could also be used for developing a tool for identifying DOT regions in RNA binding proteins.

  15. Model for Shock Wave Chaos

    KAUST Repository

    Kasimov, Aslan R.; Faria, Luiz; Rosales, Rodolfo R.

    2013-01-01

    : 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

  16. Does chaos assist localization or delocalization?

    Science.gov (United States)

    Tan, Jintao; Lu, Gengbiao; Luo, Yunrong; Hai, Wenhua

    2014-12-01

    We aim at a long-standing contradiction between chaos-assisted tunneling and chaos-related localization study quantum transport of a single particle held in an amplitude-modulated and tilted optical lattice. We find some near-resonant regions crossing chaotic and regular regions in the parameter space, and demonstrate that chaos can heighten velocity of delocalization in the chaos-resonance overlapping regions, while chaos may aid localization in the other chaotic regions. The degree of localization enhances with increasing the distance between parameter points and near-resonant regions. The results could be useful for experimentally manipulating chaos-assisted transport of single particles in optical or solid-state lattices.

  17. 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/. Copyright © 2013 Wiley Periodicals, Inc.

  18. The role of intrinsic disorder and dynamics in the assembly and function of the type II secretion system.

    Science.gov (United States)

    Gu, Shuang; Shevchik, Vladimir E; Shaw, Rosie; Pickersgill, Richard W; Garnett, James A

    2017-10-01

    Many Gram-negative commensal and pathogenic bacteria use a type II secretion system (T2SS) to transport proteins out of the cell. These exported proteins or substrates play a major role in toxin delivery, maintaining biofilms, replication in the host and subversion of host immune responses to infection. We review the current structural and functional work on this system and argue that intrinsically disordered regions and protein dynamics are central for assembly, exo-protein recognition, and secretion competence of the T2SS. The central role of intrinsic disorder-order transitions in these processes may be a particular feature of type II secretion. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. Intrinsically Disordered Segments Affect Protein Half-Life in the Cell and during Evolution

    Directory of Open Access Journals (Sweden)

    Robin van der Lee

    2014-09-01

    Full Text Available Precise control of protein turnover is essential for cellular homeostasis. The ubiquitin-proteasome system is well established as a major regulator of protein degradation, but an understanding of how inherent structural features influence the lifetimes of proteins is lacking. We report that yeast, mouse, and human proteins with terminal or internal intrinsically disordered segments have significantly shorter half-lives than proteins without these features. The lengths of the disordered segments that affect protein half-life are compatible with the structure of the proteasome. Divergence in terminal and internal disordered segments in yeast proteins originating from gene duplication leads to significantly altered half-life. Many paralogs that are affected by such changes participate in signaling, where altered protein half-life will directly impact cellular processes and function. Thus, natural variation in the length and position of disordered segments may affect protein half-life and could serve as an underappreciated source of genetic variation with important phenotypic consequences.

  20. Invoking the muse: Dada's chaos.

    Science.gov (United States)

    Rosen, Diane

    2014-07-01

    Dada, a self-proclaimed (anti)art (non)movement, took shape in 1916 among a group of writers and artists who rejected the traditions of a stagnating bourgeoisie. Instead, they adopted means of creative expression that embraced chaos, stoked instability and undermined logic, an outburst that overturned centuries of classical and Romantic aesthetics. Paradoxically, this insistence on disorder foreshadowed a new order in understanding creativity. Nearly one hundred years later, Nonlinear Dynamical Systems theory (NDS) gives renewed currency to Dada's visionary perspective on chance, chaos and creative cognition. This paper explores commonalities between NDS-theory and this early precursor of the nonlinear paradigm, suggesting that their conceptual synergy illuminates what it means to 'be creative' beyond the disciplinary boundaries of either. Key features are discussed within a 5P model of creativity based on Rhodes' 4P framework (Person, Process, Press, Product), to which I add Participant-Viewer for the interactivity of observer-observed. Grounded in my own art practice, several techniques are then put forward as non-methodical methods that invoke creative border zones, those regions where Dada's chance and design are wedded in a dialectical tension of opposites.

  1. Death and revival of chaos.

    Science.gov (United States)

    Kaszás, Bálint; Feudel, Ulrike; Tél, Tamás

    2016-12-01

    We investigate the death and revival of chaos under the impact of a monotonous time-dependent forcing that changes its strength with a non-negligible rate. Starting on a chaotic attractor it is found that the complexity of the dynamics remains very pronounced even when the driving amplitude has decayed to rather small values. When after the death of chaos the strength of the forcing is increased again with the same rate of change, chaos is found to revive but with a different history. This leads to the appearance of a hysteresis in the complexity of the dynamics. To characterize these dynamics, the concept of snapshot attractors is used, and the corresponding ensemble approach proves to be superior to a single trajectory description, that turns out to be nonrepresentative. The death (revival) of chaos is manifested in a drop (jump) of the standard deviation of one of the phase-space coordinates of the ensemble; the details of this chaos-nonchaos transition depend on the ratio of the characteristic times of the amplitude change and of the internal dynamics. It is demonstrated that chaos cannot die out as long as underlying transient chaos is present in the parameter space. As a condition for a "quasistatically slow" switch-off, we derive an inequality which cannot be fulfilled in practice over extended parameter ranges where transient chaos is present. These observations need to be taken into account when discussing the implications of "climate change scenarios" in any nonlinear dynamical system.

  2. 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.

  3. Colpitts and Chaos

    DEFF Research Database (Denmark)

    Lindberg, Erik

    1996-01-01

    The chaotic behaviour of the Colpitts oscillator reported by M.P. Kennedy is further investigated by means of PSpice simulations. Chaos is also observed with the default Ebers-Moll BJT transistor model with no memory. When the model is extended with memory and losses chaos do not occur and a 3'rd...... order limit cycle is found. If the the forward Early voltage parameter is added chaos is observed again. An examination of the eigenvalues of the oscillator with the simple memoryless Ebers-Moll BJT injection model is presented. By adding bulk resistors to the model stable limit cycles of orders 1, 2, 3...

  4. Noise tolerant spatiotemporal chaos computing.

    Science.gov (United States)

    Kia, Behnam; Kia, Sarvenaz; Lindner, John F; Sinha, Sudeshna; Ditto, William L

    2014-12-01

    We introduce and design a noise tolerant chaos computing system based on a coupled map lattice (CML) and the noise reduction capabilities inherent in coupled dynamical systems. The resulting spatiotemporal chaos computing system is more robust to noise than a single map chaos computing system. In this CML based approach to computing, under the coupled dynamics, the local noise from different nodes of the lattice diffuses across the lattice, and it attenuates each other's effects, resulting in a system with less noise content and a more robust chaos computing architecture.

  5. Intrinsic gray-matter connectivity of the brain in adults with autism spectrum disorder.

    Science.gov (United States)

    Ecker, Christine; Ronan, Lisa; Feng, Yue; Daly, Eileen; Murphy, Clodagh; Ginestet, Cedric E; Brammer, Michael; Fletcher, Paul C; Bullmore, Edward T; Suckling, John; Baron-Cohen, Simon; Williams, Steve; Loth, Eva; Murphy, Declan G M

    2013-08-06

    Autism spectrum disorders (ASD) are a group of neurodevelopmental conditions that are accompanied by atypical brain connectivity. So far, in vivo evidence for atypical structural brain connectivity in ASD has mainly been based on neuroimaging studies of cortical white matter. However, genetic studies suggest that abnormal connectivity in ASD may also affect neural connections within the cortical gray matter. Such intrinsic gray-matter connections are inherently more difficult to describe in vivo but may be inferred from a variety of surface-based geometric features that can be measured using magnetic resonance imaging. Here, we present a neuroimaging study that examines the intrinsic cortico-cortical connectivity of the brain in ASD using measures of "cortical separation distances" to assess the global and local intrinsic "wiring costs" of the cortex (i.e., estimated length of horizontal connections required to wire the cortex within the cortical sheet). In a sample of 68 adults with ASD and matched controls, we observed significantly reduced intrinsic wiring costs of cortex in ASD, both globally and locally. Differences in global and local wiring cost were predominantly observed in fronto-temporal regions and also significantly predicted the severity of social and repetitive symptoms (respectively). Our study confirms that atypical cortico-cortical "connectivity" in ASD is not restricted to the development of white-matter connections but may also affect the intrinsic gray-matter architecture (and connectivity) within the cortical sheet. Thus, the atypical connectivity of the brain in ASD is complex, affecting both gray and white matter, and forms part of the core neural substrates underlying autistic symptoms.

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

    Energy Technology Data Exchange (ETDEWEB)

    Zawadzka-Kazimierczuk, Anna; Kozminski, Wiktor, E-mail: kozmin@chem.uw.edu.pl [University of Warsaw, Faculty of Chemistry (Poland); Sanderova, Hana; Krasny, Libor [Institute of Microbiology, Academy of Sciences of the Czech Republic, Laboratory of Molecular Genetics of Bacteria, Department of Bacteriology (Czech Republic)

    2012-04-15

    Four novel 5D (HACA(N)CONH, HNCOCACB, (HACA)CON(CA)CONH, (H)NCO(NCA)CONH), and one 6D ((H)NCO(N)CACONH) NMR pulse sequences are proposed. The new experiments employ non-uniform sampling that enables achieving high resolution in indirectly detected dimensions. The experiments facilitate resonance assignment of intrinsically disordered proteins. The novel pulse sequences were successfully tested using {delta} subunit (20 kDa) of Bacillus subtilis RNA polymerase that has an 81-amino acid disordered part containing various repetitive sequences.

  7. Enlightenment philosophers’ ideas about chaos

    Directory of Open Access Journals (Sweden)

    A. V. Kulik

    2014-07-01

     It is grounded that the philosopher and enlightener Johann Gottfried von Herder advanced an idea of objectivity of process of transformation chaos into order. It is shown that idea of «The law of nature» existing as for ordering chaos opened far­reaching prospects for researches of interaction with chaos.

  8. 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.

  9. Chaos excited chaos synchronizations of integral and fractional order generalized van der Pol systems

    International Nuclear Information System (INIS)

    Ge Zhengming; Hsu Maoyuan

    2008-01-01

    In this paper, chaos excited chaos synchronizations of generalized van der Pol systems with integral and fractional order are studied. Synchronizations of two identified autonomous generalized van der Pol chaotic systems are obtained by replacing their corresponding exciting terms by the same function of chaotic states of a third nonautonomous or autonomous generalized van der Pol system. Numerical simulations, such as phase portraits, Poincare maps and state error plots are given. It is found that chaos excited chaos synchronizations exist for the fractional order systems with the total fractional order both less than and more than the number of the states of the integer order generalized van der Pol system

  10. 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.

  11. Stochastic Estimation via Polynomial Chaos

    Science.gov (United States)

    2015-10-01

    AFRL-RW-EG-TR-2015-108 Stochastic Estimation via Polynomial Chaos Douglas V. Nance Air Force Research...COVERED (From - To) 20-04-2015 – 07-08-2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Stochastic Estimation via Polynomial Chaos ...This expository report discusses fundamental aspects of the polynomial chaos method for representing the properties of second order stochastic

  12. Chaos and noise.

    Science.gov (United States)

    He, Temple; Habib, Salman

    2013-09-01

    Simple dynamical systems--with a small number of degrees of freedom--can behave in a complex manner due to the presence of chaos. Such systems are most often (idealized) limiting cases of more realistic situations. Isolating a small number of dynamical degrees of freedom in a realistically coupled system generically yields reduced equations with terms that can have a stochastic interpretation. In situations where both noise and chaos can potentially exist, it is not immediately obvious how Lyapunov exponents, key to characterizing chaos, should be properly defined. In this paper, we show how to do this in a class of well-defined noise-driven dynamical systems, derived from an underlying Hamiltonian model.

  13. OPAL: prediction of MoRF regions in intrinsically disordered protein sequences.

    Science.gov (United States)

    Sharma, Ronesh; Raicar, Gaurav; Tsunoda, Tatsuhiko; Patil, Ashwini; Sharma, Alok

    2018-06-01

    Intrinsically disordered proteins lack stable 3-dimensional structure and play a crucial role in performing various biological functions. Key to their biological function are the molecular recognition features (MoRFs) located within long disordered regions. Computationally identifying these MoRFs from disordered protein sequences is a challenging task. In this study, we present a new MoRF predictor, OPAL, to identify MoRFs in disordered protein sequences. OPAL utilizes two independent sources of information computed using different component predictors. The scores are processed and combined using common averaging method. The first score is computed using a component MoRF predictor which utilizes composition and sequence similarity of MoRF and non-MoRF regions to detect MoRFs. The second score is calculated using half-sphere exposure (HSE), solvent accessible surface area (ASA) and backbone angle information of the disordered protein sequence, using information from the amino acid properties of flanks surrounding the MoRFs to distinguish MoRF and non-MoRF residues. OPAL is evaluated using test sets that were previously used to evaluate MoRF predictors, MoRFpred, MoRFchibi and MoRFchibi-web. The results demonstrate that OPAL outperforms all the available MoRF predictors and is the most accurate predictor available for MoRF prediction. It is available at http://www.alok-ai-lab.com/tools/opal/. ashwini@hgc.jp or alok.sharma@griffith.edu.au. Supplementary data are available at Bioinformatics online.

  14. "Chaos Rules" Revisited

    Science.gov (United States)

    Murphy, David

    2011-01-01

    About 20 years ago, while lost in the midst of his PhD research, the author mused over proposed titles for his thesis. He was pretty pleased with himself when he came up with "Chaos Rules" (the implied double meaning was deliberate), or more completely, "Chaos Rules: An Exploration of the Work of Instructional Designers in Distance Education." He…

  15. From Sequence and Forces to Structure, Function and Evolution of Intrinsically Disordered Proteins

    Science.gov (United States)

    Forman-Kay, Julie D.; Mittag, Tanja

    2015-01-01

    Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to structural biology due to the inapplicability of standard methods for characterization of folded proteins as well as their deviation from the dominant structure/function paradigm. Their widespread presence and involvement in biological function, however, has spurred the growing acceptance of the importance of IDPs and the development of new tools for studying their structure, dynamics and function. The interplay of folded and disordered domains or regions for function and the existence of a continuum of protein states with respect to conformational energetics, motional timescales and compactness is shaping a unified understanding of structure-dynamics-disorder/function relationships. On the 20th anniversary of this journal, Structure, we provide a historical perspective on the investigation of IDPs and summarize the sequence features and physical forces that underlie their unique structural, functional and evolutionary properties. PMID:24010708

  16. Chaos applications in telecommunications

    CERN Document Server

    Stavroulakis, Peter

    2005-01-01

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

  17. A bound on chaos

    Energy Technology Data Exchange (ETDEWEB)

    Maldacena, Juan [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States); Shenker, Stephen H. [Stanford Institute for Theoretical Physics and Department of Physics, Stanford University,382 Via Pueblo Mall, Stanford, CA (United States); Stanford, Douglas [School of Natural Sciences, Institute for Advanced Study,1 Einstein Drive, Princeton, NJ (United States)

    2016-08-17

    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 λ{sub L}≤2πk{sub B}T/ℏ. We give a precise mathematical argument, based on plausible physical assumptions, establishing this conjecture.

  18. Application of Chaos Theory to Engine Systems

    OpenAIRE

    Matsumoto, Kazuhiro; Diebner, Hans H.; Tsuda, Ichiro; Hosoi, Yukiharu

    2008-01-01

    We focus on the control issue for engine systems from the perspective of chaos theory, which is based on the fact that engine systems have a low-dimensional chaotic dynamics. Two approaches are discussed: controlling chaos and harnessing chaos, respectively. We apply Pyragas' chaos control method to an actual engine system. The experimental results show that the chaotic motion of an engine system may be stabilized to a periodic motion. Alternatively, harnessing chaos for engine systems is add...

  19. Hastily Formed Networks-Chaos to Recovery

    Science.gov (United States)

    2015-09-01

    NETWORKS— CHAOS TO RECOVERY by Mark Arezzi September 2015 Thesis Co-Advisors: Douglas J. MacKinnon Brian Steckler THIS PAGE......systems to self-organize, adapt, and exert control over the chaos . Defining the role of communications requires an understanding of complexity, chaos

  20. High GC content causes orphan proteins to be intrinsically disordered.

    Directory of Open Access Journals (Sweden)

    Walter Basile

    2017-03-01

    Full Text Available De novo creation of protein coding genes involves the formation of short ORFs from noncoding regions; some of these ORFs might then become fixed in the population. These orphan proteins need to, at the bare minimum, not cause serious harm to the organism, meaning that they should for instance not aggregate. Therefore, although the creation of short ORFs could be truly random, the fixation should be subjected to some selective pressure. The selective forces acting on orphan proteins have been elusive, and contradictory results have been reported. In Drosophila young proteins are more disordered than ancient ones, while the opposite trend is present in yeast. To the best of our knowledge no valid explanation for this difference has been proposed. To solve this riddle we studied structural properties and age of proteins in 187 eukaryotic organisms. We find that, with the exception of length, there are only small differences in the properties between proteins of different ages. However, when we take the GC content into account we noted that it could explain the opposite trends observed for orphans in yeast (low GC and Drosophila (high GC. GC content is correlated with codons coding for disorder promoting amino acids. This leads us to propose that intrinsic disorder is not a strong determining factor for fixation of orphan proteins. Instead these proteins largely resemble random proteins given a particular GC level. During evolution the properties of a protein change faster than the GC level causing the relationship between disorder and GC to gradually weaken.

  1. Puzzles in studies of quantum chaos

    International Nuclear Information System (INIS)

    Xu Gongou

    1994-01-01

    Puzzles in studies of quantum chaos are discussed. From the view of global properties of quantum states, it is clarified that quantum chaos originates from the break-down of invariant properties of quantum canonical transformations. There exist precise correspondences between quantum and classical chaos

  2. 3D pulsed chaos lidar system.

    Science.gov (United States)

    Cheng, Chih-Hao; Chen, Chih-Ying; Chen, Jun-Da; Pan, Da-Kung; Ting, Kai-Ting; Lin, Fan-Yi

    2018-04-30

    We develop an unprecedented 3D pulsed chaos lidar system for potential intelligent machinery applications. Benefited from the random nature of the chaos, conventional CW chaos lidars already possess excellent anti-jamming and anti-interference capabilities and have no range ambiguity. In our system, we further employ self-homodyning and time gating to generate a pulsed homodyned chaos to boost the energy-utilization efficiency. Compared to the original chaos, we show that the pulsed homodyned chaos improves the detection SNR by more than 20 dB. With a sampling rate of just 1.25 GS/s that has a native sampling spacing of 12 cm, we successfully achieve millimeter-level accuracy and precision in ranging. Compared with two commercial lidars tested side-by-side, namely the pulsed Spectroscan and the random-modulation continuous-wave Lidar-lite, the pulsed chaos lidar that is in compliance with the class-1 eye-safe regulation shows significantly better precision and a much longer detection range up to 100 m. Moreover, by employing a 2-axis MEMS mirror for active laser scanning, we also demonstrate real-time 3D imaging with errors of less than 4 mm in depth.

  3. Understanding diffusion of intrinsically disordered proteins in polymer solutions: A disorder plus collapse model

    Directory of Open Access Journals (Sweden)

    Juan Wang

    2017-11-01

    Full Text Available Understanding diffusion of intrinsically disordered proteins (IDPs under crowded environments is of ubiquitous importance to modelling related dynamics in biological systems. In the present work, we proposed a theoretical framework to study the diffusion behavior of IDPs in polymer solutions. IDP is modeled as an ensemble of particles with a wide range of gyration radius subject to Flory-Fisk distribution, where the collapse effect which leads to the shrink of IDP due to polymer crowding is included. The diffusion coefficient of IDP is calculated as the average, denoted by 〈D〉, over the values of the particle samples. By properly incorporating the scaling relations for diffusion coefficient of nanoparticle (NP in polymer solutions, we are able to evaluate 〈D〉 straightforwardly and reveal the disorder and collapse effects on IDP’s diffusion in an explicit manner. Particular attentions are paid on comparison between the diffusion coefficient of an IDP and that of a NP. Results demonstrate that both disorder and collapse can enhance IDP diffusion rate. Our analysis shows that the crossover behavior reported by experiments can be actually a general phenomenon, namely, while a NP with smaller size than that of an IDP diffuses faster in simple solutions, the IDP may become the faster one under crowded conditions. We apply our theory to analyze the diffusion of several types of IDP in a few different polymer solutions. Good agreements between the theoretical results and the experimental data are obtained.

  4. Recent development of chaos theory in topological dynamics

    OpenAIRE

    Li, Jian; Ye, Xiangdong

    2015-01-01

    We give a summary on the recent development of chaos theory in topological dynamics, focusing on Li-Yorke chaos, Devaney chaos, distributional chaos, positive topological entropy, weakly mixing sets and so on, and their relationships.

  5. Chaos at High School

    Directory of Open Access Journals (Sweden)

    Tamás Meszéna

    2017-04-01

    Full Text Available We are faced with chaotic processes in many segments of our life: meteorology, environmental pollution, financial and economic processes, sociology, mechanics, electronics, biology, chemistry. The spreading of high-performance computers and the development of simulation methods made the examination of these processes easily available. Regular, periodic motions (pendulum, harmonic oscillatory motion, bouncing ball, as taught at secondary level, become chaotic even due minor changes. If it is true that the most considerable achievements of twentieth century physics were the theory of relativity, quantum mechanics and chaos theory, then it is presumably time to think about, examine and test how and to what extent chaos can be presented to the students. Here I would like to introduce a 12 lesson long facultative curriculum framework on chaos designed for students aged seventeen. The investigation of chaos phenomenon in this work is based on a freeware, “Dynamics Solver”. This software, with some assistance from the teacher, is suitable for classroom use at secondary level.

  6. Triple resonance 15N NMR relaxation experiments for studies of intrinsically disordered proteins

    Czech Academy of Sciences Publication Activity Database

    Srb, Pavel; Nováček, J.; Kadeřávek, P.; Rabatinová, Alžběta; Krásný, Libor; Žídková, Jitka; Bobálová, Janette; Sklenář, V.; Žídek, L.

    2017-01-01

    Roč. 69, č. 3 (2017), s. 133-146 ISSN 0925-2738 R&D Projects: GA ČR GA13-16842S; GA MŠk(CZ) LO1304 Institutional support: RVO:61388963 ; RVO:61388971 ; RVO:68081715 Keywords : nuclear magnetic resonance * relaxation * non-uniform sampling * intrinsically disordered proteins Subject RIV: CB - Analytical Chemistry, Separation; EE - Microbiology, Virology (MBU-M); CB - Analytical Chemistry, Separation (UIACH-O) OBOR OECD: Analytical chemistry; Microbiology (MBU-M); Analytical chemistry (UIACH-O) Impact factor: 2.410, year: 2016

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

    International Nuclear Information System (INIS)

    Ge Zhengming; Chang Chingming; Chen Yensheng

    2006-01-01

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

  8. Bioinformatics analysis identifies several intrinsically disordered human E3 ubiquitin-protein ligases

    Directory of Open Access Journals (Sweden)

    Wouter Boomsma

    2016-02-01

    Full Text Available The ubiquitin-proteasome system targets misfolded proteins for degradation. Since the accumulation of such proteins is potentially harmful for the cell, their prompt removal is important. E3 ubiquitin-protein ligases mediate substrate ubiquitination by bringing together the substrate with an E2 ubiquitin-conjugating enzyme, which transfers ubiquitin to the substrate. For misfolded proteins, substrate recognition is generally delegated to molecular chaperones that subsequently interact with specific E3 ligases. An important exception is San1, a yeast E3 ligase. San1 harbors extensive regions of intrinsic disorder, which provide both conformational flexibility and sites for direct recognition of misfolded targets of vastly different conformations. So far, no mammalian ortholog of San1 is known, nor is it clear whether other E3 ligases utilize disordered regions for substrate recognition. Here, we conduct a bioinformatics analysis to examine >600 human and S. cerevisiae E3 ligases to identify enzymes that are similar to San1 in terms of function and/or mechanism of substrate recognition. An initial sequence-based database search was found to detect candidates primarily based on the homology of their ordered regions, and did not capture the unique disorder patterns that encode the functional mechanism of San1. However, by searching specifically for key features of the San1 sequence, such as long regions of intrinsic disorder embedded with short stretches predicted to be suitable for substrate interaction, we identified several E3 ligases with these characteristics. Our initial analysis revealed that another remarkable trait of San1 is shared with several candidate E3 ligases: long stretches of complete lysine suppression, which in San1 limits auto-ubiquitination. We encode these characteristic features into a San1 similarity-score, and present a set of proteins that are plausible candidates as San1 counterparts in humans. In conclusion, our work

  9. Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy.

    Science.gov (United States)

    Delaforge, Elise; Kragelj, Jaka; Tengo, Laura; Palencia, Andrés; Milles, Sigrid; Bouvignies, Guillaume; Salvi, Nicola; Blackledge, Martin; Jensen, Malene Ringkjøbing

    2018-01-24

    Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R 1ρ , Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions.

  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. Further discussion on chaos in duopoly games

    International Nuclear Information System (INIS)

    Lu, Tianxiu; Zhu, Peiyong

    2013-01-01

    In this paper, we study Li–Yorke chaos, distributional chaos in a sequence, Li–Yorke sensitivity, sensitivity and distributional chaos of two-dimensional dynamical system of the form Φ(x, y) = (f(y), g(x))

  13. 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.

  14. 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...... 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...

  15. Nonlinear chaos control and synchronization

    NARCIS (Netherlands)

    Huijberts, H.J.C.; Nijmeijer, H.; Schöll, E.; Schuster, H.G.

    2007-01-01

    This chapter contains sections titled: Introduction Nonlinear Geometric Control Some Differential Geometric Concepts Nonlinear Controllability Chaos Control Through Feedback Linearization Chaos Control Through Input-Output Linearization Lyapunov Design Lyapunov Stability and Lyapunov's First Method

  16. Cryptography with chaos and shadowing

    International Nuclear Information System (INIS)

    Smaoui, Nejib; Kanso, Ali

    2009-01-01

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

  17. Experimental Induction of Genome Chaos.

    Science.gov (United States)

    Ye, Christine J; Liu, Guo; Heng, Henry H

    2018-01-01

    Genome chaos, or karyotype chaos, represents a powerful survival strategy for somatic cells under high levels of stress/selection. Since the genome context, not the gene content, encodes the genomic blueprint of the cell, stress-induced rapid and massive reorganization of genome topology functions as a very important mechanism for genome (karyotype) evolution. In recent years, the phenomenon of genome chaos has been confirmed by various sequencing efforts, and many different terms have been coined to describe different subtypes of the chaotic genome including "chromothripsis," "chromoplexy," and "structural mutations." To advance this exciting field, we need an effective experimental system to induce and characterize the karyotype reorganization process. In this chapter, an experimental protocol to induce chaotic genomes is described, following a brief discussion of the mechanism and implication of genome chaos in cancer evolution.

  18. Cryptography with chaos and shadowing

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-11-30

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

  19. Using chaos theory: the implications for nursing.

    Science.gov (United States)

    Haigh, Carol

    2002-03-01

    The purpose of this paper is to review chaos theory and to examine the role that it may have in the discipline of nursing. In this paper, the fundamental ingredients of chaotic thinking are outlined. The earlier days of chaos thinking were characterized by an almost exclusively physiological focus. By the 21st century, nurse theorists were applying its principles to the organization and evaluation of care delivery with varying levels of success. Whilst the biological use of chaos has focused on pragmatic approaches to knowledge enhancement, nursing has often focused on the mystical aspects of chaos as a concept. The contention that chaos theory has yet to find a niche within nursing theory and practice is examined. The application of chaotic thinking across nursing practice, nursing research and statistical modelling is reviewed. The use of chaos theory as a way of identifying the attractor state of specific systems is considered and the suggestion is made that it is within statistical modelling of services that chaos theory is most effective.

  20. An Extended Guinier Analysis for Intrinsically Disordered Proteins.

    Science.gov (United States)

    Zheng, Wenwei; Best, Robert B

    2018-03-21

    Guinier analysis allows model-free determination of the radius of gyration (R g ) of a biomolecule from X-ray or neutron scattering data, in the limit of very small scattering angles. Its range of validity is well understood for globular proteins, but is known to be more restricted for unfolded or intrinsically disordered proteins (IDPs). We have used ensembles of disordered structures from molecular dynamics simulations to investigate which structural properties cause deviations from the Guinier approximation at small scattering angles. We find that the deviation from the Guinier approximation is correlated with the polymer scaling exponent ν describing the unfolded ensemble. We therefore introduce an empirical, ν-dependent, higher-order correction term, to augment the standard Guinier analysis. We test the new fitting scheme using all-atom simulation data for several IDPs and experimental data for both an IDP and a destabilized mutant of a folded protein. In all cases tested, we achieve an accuracy of the inferred R g within ∼3% of the true R g . The method is straightforward to implement and extends the range of validity to a maximum qR g of ∼2 versus ∼1.1 for Guinier analysis. Compared with the Guinier or Debye approaches, our method allows data from wider angles with lower noise to be used to analyze scattering data accurately. In addition to R g , our fitting scheme also yields estimates of the scaling exponent ν in excellent agreement with the reference ν determined from the underlying molecular ensemble. Published by Elsevier Ltd.

  1. Quantum chaos: Statistical relaxation in discrete spectrum

    International Nuclear Information System (INIS)

    Chirikov, B.V.

    1991-01-01

    The controversial phenomenon of quantum chaos is discussed using the quantized standard map, or the kicked rotator, as a simple model. The relation to the classical dynamical chaos is tracked down on the basis of the correspondence principle. Various mechanisms of the quantum suppression of classical chaos are considered with an application to the excitation and ionization of Rydberg atoms in a microwave field. Several definitions of the quantum chaos are discussed. (author). 27 refs

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

    DEFF Research Database (Denmark)

    Sosnovtseva, O.; Mosekilde, Erik

    1997-01-01

    The destruction of two-dimensional tori T2 and the transitions to chaos are studied in a high-dimensional model describing the decision-making behavior of human subjects in a simulated managerial environment (the beer production-distribution model). Two different routes from quasiperiodicity...... to chaos can be distinguished. Intermittency transitions between chaotic and hyperchaotic attractors are characterized, and transients in which the system "pursues the ghost" of a vanished hyperchaotic attractor are studied....

  3. Chaos Modelling with Computers

    Indian Academy of Sciences (India)

    Chaos is one of the major scientific discoveries of our times. In fact many scientists ... But there are other natural phenomena that are not predictable though ... characteristics of chaos. ... The position and velocity are all that are needed to determine the motion of a .... a system of equations that modelled the earth's weather ...

  4. Biophysical properties of intrinsically disordered p130Cas substrate domain--implication in mechanosensing.

    Directory of Open Access Journals (Sweden)

    Kinya Hotta

    2014-04-01

    Full Text Available Mechanical stretch-induced tyrosine phosphorylation in the proline-rich 306-residue substrate domain (CasSD of p130Cas (or BCAR1 has eluded an experimentally validated structural understanding. Cellular p130Cas tyrosine phosphorylation is shown to function in areas without internal actomyosin contractility, sensing force at the leading edge of cell migration. Circular dichroism shows CasSD is intrinsically disordered with dominant polyproline type II conformations. Strongly conserved in placental mammals, the proline-rich sequence exhibits a pseudo-repeat unit with variation hotspots 2-9 residues before substrate tyrosine residues. Atomic-force microscopy pulling experiments show CasSD requires minimal extension force and exhibits infrequent, random regions of weak stability. Proteolysis, light scattering and ultracentrifugation results show that a monomeric intrinsically disordered form persists for CasSD in solution with an expanded hydrodynamic radius. All-atom 3D conformer sampling with the TraDES package yields ensembles in agreement with experiment when coil-biased sampling is used, matching the experimental radius of gyration. Increasing β-sampling propensities increases the number of prolate conformers. Combining the results, we conclude that CasSD has no stable compact structure and is unlikely to efficiently autoinhibit phosphorylation. Taking into consideration the structural propensity of CasSD and the fact that it is known to bind to LIM domains, we propose a model of how CasSD and LIM domain family of transcription factor proteins may function together to regulate phosphorylation of CasSD and effect machanosensing.

  5. Quasiperiodic transition to chaos in a plasma

    International Nuclear Information System (INIS)

    Weixing, D.; Huang Wei; Wang Xiaodong; Yu, C.X.

    1993-01-01

    The quasiperiodic transition to chaos in an undriven discharge plasma has been investigated. Results from the power spectrum and Lyapunov exponents quantitatively confirm the transition to chaos through quasiperiodicity. A low-dimension strange attractor has been found for this kind of plasma chaos

  6. Towards chaos criterion in quantum field theory

    OpenAIRE

    Kuvshinov, V. I.; Kuzmin, A. V.

    2002-01-01

    Chaos criterion for quantum field theory is proposed. Its correspondence with classical chaos criterion in semi-classical regime is shown. It is demonstrated for real scalar field that proposed chaos criterion can be used to investigate stability of classical solutions of field equations.

  7. 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...

  8. 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...

  9. 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...... to the core field, but the high-degree lithospheric field is regularized for n > 85. CHAOS-4 model is derived by merging two submodels: its low-degree part has been derived using similar model parametrization and data sets as used for previous CHAOS models (but of course including more recent data), while its...

  10. Encounters with chaos and fractals

    CERN Document Server

    Gulick, Denny

    2012-01-01

    Periodic Points Iterates of Functions Fixed Points Periodic Points Families of Functions The Quadratic Family Bifurcations Period-3 Points The Schwarzian Derivative One-Dimensional Chaos Chaos Transitivity and Strong Chaos Conjugacy Cantor Sets Two-Dimensional Chaos Review of Matrices Dynamics of Linear FunctionsNonlinear Maps The Hénon Map The Horseshoe Map Systems of Differential Equations Review of Systems of Differential Equations Almost Linearity The Pendulum The Lorenz System Introduction to Fractals Self-Similarity The Sierpiński Gasket and Other "Monsters"Space-Filling Curves Similarity and Capacity DimensionsLyapunov Dimension Calculating Fractal Dimensions of Objects Creating Fractals Sets Metric Spaces The Hausdorff Metric Contractions and Affine Functions Iterated Function SystemsAlgorithms for Drawing Fractals Complex Fractals: Julia Sets and the Mandelbrot Set Complex Numbers and Functions Julia Sets The Mandelbrot Set Computer Programs Answers to Selected Exercises References Index.

  11. A phosphorylation-motif for tuneable helix stabilisation in intrinsically disordered proteins - Lessons from the sodium proton exchanger 1 (NHE1)

    DEFF Research Database (Denmark)

    Hendus-Altenburger, Ruth; Lambrughi, Matteo; Terkelsen, Thilde Bagger

    2017-01-01

    ). Using NMR spectroscopy, we found that two out of those six phosphorylation sites had a stabilizing effect on transient helices. One of these was further investigated by circular dichroism and NMR spectroscopy as well as by molecular dynamic simulations, which confirmed the stabilizing effect......-spread role in phosphorylation-mediated regulation of intrinsically disordered proteins. The identification of such motifs is important for understanding the molecular mechanism of cellular signalling, and is crucial for the development of predictors for the structural effect of phosphorylation; a tool......Intrinsically disordered proteins (IDPs) are involved in many pivotal cellular processes including phosphorylation and signalling. The structural and functional effects of phosphorylation of IDPs remain poorly understood and difficult to predict. Thus, a need exists to identify motifs that confer...

  12. 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...... of disorder in state-of-the-art photonic-crystal waveguides from far-field measurements of the Anderson-localized modes. This is achieved by comparing the spectral range where Anderson localization is observed to numerical simulations, and the method offers sensitivity down to 1nm....

  13. 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

  14. Chaos and routes to chaos in coupled Duffing oscillators with multiple degrees of freedom

    International Nuclear Information System (INIS)

    Musielak, D.E.; Musielak, Z.E.; Benner, J.W.

    2005-01-01

    New results are reported on the routes to chaos in increasingly complex Duffing oscillator systems, which are formed by coupling several oscillators, thereby increasing the number of degrees of freedom. Other forms of increasing system complexity through distributed excitation, different forcing function phasing, different excitation frequency ratios, and higher order coupling are also studied. Changes in the quantitative aspects of the chaotic regions and in the routes to chaos of complex Duffing systems are investigated by performing numerical simulations. It is shown that the number of chaotic regions in these systems is significantly reduced when compared to the original Duffing system, and that crisis replaces period doubling as the dominant route to chaos when the number of degrees of freedom is increased. A new discovered phenomenon is that chaos emerges in the symmetrically and asymmetrically coupled Duffing oscillators only after the quasi-periodic torus breaks down through a 3-periodic and 2-periodic window, respectively

  15. 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

    Science.gov (United States)

    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 neurological disorders), and light therapy with or without accompanying behavioral interventions (adults with ASWPD, children/adolescents with DSWPD, and elderly with dementia). Recommendations against the use of melatonin and discrete sleep-promoting medications are provided for demented elderly patients, at a second- and first-tier degree of confidence, respectively. No recommendations were provided for remaining treatments/ populations, due to either insufficient or absent data. Areas where further research is needed are discussed. Citation: Auger RR, Burgess HJ, Emens JS, Deriy LV, Thomas SM, Sharkey KM. 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. J Clin Sleep Med 2015;11(10):1199–1236. PMID:26414986

  16. 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...

  17. Chaos to periodicity and periodicity to chaos by periodic perturbations in the Belousov-Zhabotinsky reaction

    International Nuclear Information System (INIS)

    Li Qianshu; Zhu Rui

    2004-01-01

    A three-variable model of the Belousov-Zhabotinsky reaction system subject to external sinusoidal perturbations is investigated by means of frequency spectrum analysis. In the period-1 window of the model, the transitions from periodicity to chaos are observed; in the chaotic window, the transitions from chaos to periodicity are found. The former might be understood by the circle map of two coupled oscillators, and the latter is partly explained by the resonance between the main frequency of the chaos and the frequency of the external periodic perturbations

  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. Quantum chaos: statistical relaxation in discrete spectrum

    International Nuclear Information System (INIS)

    Chirikov, B.V.

    1990-01-01

    The controversial phenomenon of quantum chaos is discussed using the quantized standard map, or the kicked rotator, as a simple model. The relation to the classical dynamical chaos is tracked down on the basis of the correspondence principle. Several definitions of the quantum chaos are discussed. 27 refs

  20. Scaling of chaos in strongly nonlinear lattices.

    Science.gov (United States)

    Mulansky, Mario

    2014-06-01

    Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic observations still remain mostly in the dark. In this work, we numerically analyze the probability of chaos in strongly nonlinear Hamiltonian systems and find different scaling properties depending on the nonlinear structure of the model. We argue that these different scaling laws of chaos have definite consequences for the macroscopic diffusive behavior, as chaos is the microscopic mechanism of diffusion. This is compared with previous results on chaotic diffusion [M. Mulansky and A. Pikovsky, New J. Phys. 15, 053015 (2013)], and a relation between microscopic chaos and macroscopic diffusion is established.

  1. Chaos as an intermittently forced linear system.

    Science.gov (United States)

    Brunton, Steven L; Brunton, Bingni W; Proctor, Joshua L; Kaiser, Eurika; Kutz, J Nathan

    2017-05-30

    Understanding the interplay of order and disorder in chaos is a central challenge in modern quantitative science. Approximate linear representations of nonlinear dynamics have long been sought, driving considerable interest in Koopman theory. We present a universal, data-driven decomposition of chaos as an intermittently forced linear system. This work combines delay embedding and Koopman theory to decompose chaotic dynamics into a linear model in the leading delay coordinates with forcing by low-energy delay coordinates; this is called the Hankel alternative view of Koopman (HAVOK) analysis. This analysis is applied to the Lorenz system and real-world examples including Earth's magnetic field reversal and measles outbreaks. In each case, forcing statistics are non-Gaussian, with long tails corresponding to rare intermittent forcing that precedes switching and bursting phenomena. The forcing activity demarcates coherent phase space regions where the dynamics are approximately linear from those that are strongly nonlinear.The huge amount of data generated in fields like neuroscience or finance calls for effective strategies that mine data to reveal underlying dynamics. Here Brunton et al.develop a data-driven technique to analyze chaotic systems and predict their dynamics in terms of a forced linear model.

  2. Ancient and Current Chaos Theories

    Directory of Open Access Journals (Sweden)

    Güngör Gündüz

    2006-07-01

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

  3. Colored chaos

    International Nuclear Information System (INIS)

    Mueller, B.

    1997-01-01

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

  4. Colored chaos

    Energy Technology Data Exchange (ETDEWEB)

    Mueller, B.

    1997-09-22

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

  5. Chaos in body-vortex interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby; Aref, Hassan

    2010-01-01

    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...... rocking and tumbling motion of the body known in this case. In both instances, the chaos may be detected both in the body motion and in the vortex motion. The effect of increasing body mass at a fixed body shape is to damp the chaos....

  6. 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...

  7. Robinson's chaos in set-valued discrete systems

    International Nuclear Information System (INIS)

    Roman-Flores, Heriberto; Chalco-Cano, Y.

    2005-01-01

    Let (X,d) be a compact metric space and f:X->X a continuous function. If we consider the space (K(X),H) of all non-empty compact subsets of X endowed with the Hausdorff metric induced by d and f-bar :K(X)->K(X), f-bar (A)={f(a)/a-bar A}, then the aim of this work is to show that Robinson's chaos in f-bar implies Robinson's chaos in f. Also, we give an example showing that R-chaos in f does not implies R-chaos in f-bar

  8. A quantum harmonic oscillator and strong chaos

    International Nuclear Information System (INIS)

    Oprocha, Piotr

    2006-01-01

    It is known that many physical systems which do not exhibit deterministic chaos when treated classically may exhibit such behaviour if treated from the quantum mechanics point of view. In this paper, we will show that an annihilation operator of the unforced quantum harmonic oscillator exhibits distributional chaos as introduced in B Schweizer and J SmItal (1994 Trans. Am. Math. Soc. 344 737-54). Our approach strengthens previous results on chaos in this model and provides a very powerful tool to measure chaos in other (quantum or classical) models

  9. 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

  10. 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.

  11. Markov transitions and the propagation of chaos

    International Nuclear Information System (INIS)

    Gottlieb, A.

    1998-01-01

    The propagation of chaos is a central concept of kinetic theory that serves to relate the equations of Boltzmann and Vlasov to the dynamics of many-particle systems. Propagation of chaos means that molecular chaos, i.e., the stochastic independence of two random particles in a many-particle system, persists in time, as the number of particles tends to infinity. We establish a necessary and sufficient condition for a family of general n-particle Markov processes to propagate chaos. This condition is expressed in terms of the Markov transition functions associated to the n-particle processes, and it amounts to saying that chaos of random initial states propagates if it propagates for pure initial states. Our proof of this result relies on the weak convergence approach to the study of chaos due to Sztitman and Tanaka. We assume that the space in which the particles live is homomorphic to a complete and separable metric space so that we may invoke Prohorov's theorem in our proof. We also show that, if the particles can be in only finitely many states, then molecular chaos implies that the specific entropies in the n-particle distributions converge to the entropy of the limiting single-particle distribution

  12. How to test for partially predictable chaos.

    Science.gov (United States)

    Wernecke, Hendrik; Sándor, Bulcsú; Gros, Claudius

    2017-04-24

    For a chaotic system pairs of initially close-by trajectories become eventually fully uncorrelated on the attracting set. This process of decorrelation can split into an initial exponential decrease and a subsequent diffusive process on the chaotic attractor causing the final loss of predictability. Both processes can be either of the same or of very different time scales. In the latter case the two trajectories linger within a finite but small distance (with respect to the overall extent of the attractor) for exceedingly long times and remain partially predictable. Standard tests for chaos widely use inter-orbital correlations as an indicator. However, testing partially predictable chaos yields mostly ambiguous results, as this type of chaos is characterized by attractors of fractally broadened braids. For a resolution we introduce a novel 0-1 indicator for chaos based on the cross-distance scaling of pairs of initially close trajectories. This test robustly discriminates chaos, including partially predictable chaos, from laminar flow. Additionally using the finite time cross-correlation of pairs of initially close trajectories, we are able to identify laminar flow as well as strong and partially predictable chaos in a 0-1 manner solely from the properties of pairs of trajectories.

  13. Channeling and dynamic chaos

    Energy Technology Data Exchange (ETDEWEB)

    Bolotin, IU L; Gonchar, V IU; Truten, V I; Shulga, N F

    1986-01-01

    It is shown that axial channeling of relativistic electrons can give rise to the effect of dynamic chaos which involves essentially chaotic motion of a particle in the channel. The conditions leading to the effect of dynamic chaos and the manifestations of this effect in physical processes associated with the passage of particles through a crystal are examined using a silicon crystal as an example. 7 references.

  14. Homoclinic tubes and chaos in perturbed sine-Gordon equation

    International Nuclear Information System (INIS)

    Li, Y. Charles

    2004-01-01

    Sine-Gordon equation under a quasi-periodic perturbation or a chaotic perturbation is studied. Existence of a homoclinic tube is proved. Established are chaos associated with the homoclinic tube, and 'chaos cascade' referring to the embeddings of smaller scale chaos in larger scale chaos

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

    International Nuclear Information System (INIS)

    Zhang Shuwen; Tan Dejun; Chen Lansun

    2006-01-01

    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

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

    International Nuclear Information System (INIS)

    Zhang Shuwen; Tan Dejun; Chen Lansun

    2006-01-01

    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

  17. Chaos and complexity by design

    Energy Technology Data Exchange (ETDEWEB)

    Roberts, Daniel A. [Center for Theoretical Physics and Department of Physics,Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); School of Natural Sciences, Institute for Advanced Study,Princeton, NJ 08540 (United States); Yoshida, Beni [Perimeter Institute for Theoretical Physics,Waterloo, Ontario N2L 2Y5 (Canada)

    2017-04-20

    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 kth 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.

  18. Chaos and complexity by design

    International Nuclear Information System (INIS)

    Roberts, Daniel A.; Yoshida, Beni

    2017-01-01

    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 kth 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.

  19. Chaos in the atomic and subatomic world

    International Nuclear Information System (INIS)

    Nussenzveig, H.M.

    1992-01-01

    This work discusses the possibility of the existence of chaos in the quantum level. In the macroscopic scale, chaos can be explained by the use of classical mechanics. The problem is to know whether there is any manifestation of chaos in the evolution of a system following the quantum mechanical laws. (A.C.A.S.)

  20. Chaos Theory as a Model for Life Transitions Counseling: Nonlinear Dynamics and Life's Changes

    Science.gov (United States)

    Bussolari, Cori J.; Goodell, Judith A.

    2009-01-01

    Chaos theory is presented for counselors working with clients experiencing life transitions. It is proposed as a model that considers disorder, unpredictability, and lack of control as normal parts of transition processes. Nonlinear constructs from physics are adapted for use in counseling. The model provides a method clients can use to…

  1. Chaos in collective nuclei

    International Nuclear Information System (INIS)

    Whelan, N.D.

    1993-01-01

    Random Matrix Theory successfully describes the statistics of the low-lying spectra of some nuclei but not of others. It is currently believed that this theory applies to systems in which the corresponding classical motion is chaotic. This conjecture is tested for collective nuclei by studying the Interacting Boson Model. Quantum and classical measures of chaos are proposed and found to be in agreement throughout the parameter space of the model. For some parameter values the measures indicate the presence of a previously unknown approximate symmetry. A phenomenon called partial dynamical symmetry is explored and shown to lead to a suppression of chaos. A time dependent function calculated from the quantum spectrum is discussed. This function is sensitive to the extent of chaos and provides a robust method of analyzing experimental spectra

  2. Intrinsically disordered caldesmon binds calmodulin via the “buttons on a string” mechanism

    Directory of Open Access Journals (Sweden)

    Sergei E. Permyakov

    2015-09-01

    Full Text Available We show here that chicken gizzard caldesmon (CaD and its C-terminal domain (residues 636–771, CaD136 are intrinsically disordered proteins. The computational and experimental analyses of the wild type CaD136 and series of its single tryptophan mutants (W674A, W707A, and W737A and a double tryptophan mutant (W674A/W707A suggested that although the interaction of CaD136 with calmodulin (CaM can be driven by the non-specific electrostatic attraction between these oppositely charged molecules, the specificity of CaD136-CaM binding is likely to be determined by the specific packing of important CaD136 tryptophan residues at the CaD136-CaM interface. It is suggested that this interaction can be described as the “buttons on a charged string” model, where the electrostatic attraction between the intrinsically disordered CaD136 and the CaM is solidified in a “snapping buttons” manner by specific packing of the CaD136 “pliable buttons” (which are the short segments of fluctuating local structure condensed around the tryptophan residues at the CaD136-CaM interface. Our data also show that all three “buttons” are important for binding, since mutation of any of the tryptophans affects CaD136-CaM binding and since CaD136 remains CaM-buttoned even when two of the three tryptophans are mutated to alanines.

  3. Quantum chaos: diffusion photoeffect in hydrogen

    Energy Technology Data Exchange (ETDEWEB)

    Shepelyanskij, D L

    1987-05-01

    Ionization process in highly excited hydrogen atom in electromagnetic field is presented in the form of an extraordinary photoeffect, in which ionization at the frequency, being much lower than ionization energy, occurs much quicker than single-photon one. Such a quick ionization is explained by dynamic chaos occurence. Question, related to quantum effect influence on chaotic movement of the electron (quantum chaos) is considered. Electron excitation in the chaos area is described by a diffusional equation.

  4. Meaning Finds a Way: Chaos (Theory) and Composition

    Science.gov (United States)

    Kyburz, Bonnie Lenore

    2004-01-01

    The explanatory power provided by the chaos theory is explored. A dynamic and reciprocal relationship between culture and chaos theory indicates that the progressive cultural work may be formed by the cross-disciplinary resonance of chaos theory.

  5. Chaos theory in geophysics: past, present and future

    International Nuclear Information System (INIS)

    Sivakumar, B.

    2004-01-01

    The past two decades of research on chaos theory in geophysics has brought about a significant shift in the way we view geophysical phenomena. Research on chaos theory in geophysics continues to grow at a much faster pace, with applications to a wide variety of geophysical phenomena and geophysical problems. In spite of our success in understanding geophysical phenomena also from a different (i.e. chaotic) perspective, there still seems to be lingering suspicions on the scope of chaos theory in geophysics. The goal of this paper is to present a comprehensive account of the achievements and status of chaos theory in geophysics, and to disseminate the hope and scope for the future. A systematic review of chaos theory in geophysics, covering a wide spectrum of geophysical phenomena studied (e.g. rainfall, river flow, sediment transport, temperature, pressure, tree ring series, etc.), is presented to narrate our past achievements not only in understanding and predicting geophysical phenomena but also in improving the chaos identification and prediction techniques. The present state of chaos research in geophysics (in terms of geophysical phenomena, problems, and chaos methods) and potential for future improvements (in terms of where, why and possibly how) are also highlighted. Our popular views of nature (i.e. stochastic and deterministic), and of geophysical phenomena in particular, are discussed, and the usefulness of chaos theory as a bridge between such views is also put forth

  6. Interplay of Determinism and Randomness: From Irreversibility to Chaos, Fractals, and Stochasticity

    Science.gov (United States)

    Tsonis, A.

    2017-12-01

    We will start our discussion into randomness by looking exclusively at our formal mathematical system to show that even in this pure and strictly logical system one cannot do away with randomness. By employing simple mathematical models, we will identify the three possible sources of randomness: randomness due to inability to find the rules (irreversibility), randomness due to inability to have infinite power (chaos), and randomness due to stochastic processes. Subsequently we will move from the mathematical system to our physical world to show that randomness, through the quantum mechanical character of small scales, through chaos, and because of the second law of thermodynamics, is an intrinsic property of nature as well. We will subsequently argue that the randomness in the physical world is consistent with the three sources of randomness suggested from the study of simple mathematical systems. Many examples ranging from purely mathematical to natural processes will be presented, which clearly demonstrate how the combination of rules and randomness produces the world we live in. Finally, the principle of least effort or the principle of minimum energy consumption will be suggested as the underlying principle behind this symbiosis between determinism and randomness.

  7. Controllable chaos in hybrid electro-optomechanical systems

    Science.gov (United States)

    Wang, Mei; Lü, Xin-You; Ma, Jin-Yong; Xiong, Hao; Si, Liu-Gang; Wu, Ying

    2016-01-01

    We investigate the nonlinear dynamics of a hybrid electro-optomechanical system (EOMS) that allows us to realize the controllable opto-mechanical nonlinearity by driving the microwave LC resonator with a tunable electric field. A controllable optical chaos is realized even without changing the optical pumping. The threshold and lifetime of the chaos could be optimized by adjusting the strength, frequency, or phase of the electric field. This study provides a method of manipulating optical chaos with an electric field. It may offer the prospect of exploring the controllable chaos in on-chip optoelectronic devices and its applications in secret communication. PMID:26948505

  8. Controllable chaos in hybrid electro-optomechanical systems.

    Science.gov (United States)

    Wang, Mei; Lü, Xin-You; Ma, Jin-Yong; Xiong, Hao; Si, Liu-Gang; Wu, Ying

    2016-03-07

    We investigate the nonlinear dynamics of a hybrid electro-optomechanical system (EOMS) that allows us to realize the controllable opto-mechanical nonlinearity by driving the microwave LC resonator with a tunable electric field. A controllable optical chaos is realized even without changing the optical pumping. The threshold and lifetime of the chaos could be optimized by adjusting the strength, frequency, or phase of the electric field. This study provides a method of manipulating optical chaos with an electric field. It may offer the prospect of exploring the controllable chaos in on-chip optoelectronic devices and its applications in secret communication.

  9. Strong chaos in one-dimensional quantum system

    International Nuclear Information System (INIS)

    Yang, C.-D.; Wei, C.-H.

    2008-01-01

    According to the Poincare-Bendixson theorem, a minimum of three autonomous equations is required to exhibit deterministic chaos. Because a one-dimensional quantum system is described by only two autonomous equations using de Broglie-Bohm's trajectory interpretation, chaos in one-dimensional quantum systems has long been considered impossible. We will prove in this paper that chaos phenomenon does exist in one-dimensional quantum systems, if the domain of quantum motions is extended to complex space by noting that the quantum world is actually characterized by a four-dimensional complex spacetime according to the E (∞) theory. Furthermore, we point out that the interaction between the real and imaginary parts of complex trajectories produces a new chaos phenomenon unique to quantum systems, called strong chaos, which describes the situation that quantum trajectories may emerge and diverge spontaneously without any perturbation in the initial position

  10. Relativistic quantum chaos-An emergent interdisciplinary field.

    Science.gov (United States)

    Lai, Ying-Cheng; Xu, Hong-Ya; Huang, Liang; Grebogi, Celso

    2018-05-01

    Quantum chaos is referred to as the study of quantum manifestations or fingerprints of classical chaos. A vast majority of the studies were for nonrelativistic quantum systems described by the Schrödinger equation. Recent years have witnessed a rapid development of Dirac materials such as graphene and topological insulators, which are described by the Dirac equation in relativistic quantum mechanics. A new field has thus emerged: relativistic quantum chaos. This Tutorial aims to introduce this field to the scientific community. Topics covered include scarring, chaotic scattering and transport, chaos regularized resonant tunneling, superpersistent currents, and energy level statistics-all in the relativistic quantum regime. As Dirac materials have the potential to revolutionize solid-state electronic and spintronic devices, a good understanding of the interplay between chaos and relativistic quantum mechanics may lead to novel design principles and methodologies to enhance device performance.

  11. Chaos and bifurcations in periodic windows observed in plasmas

    International Nuclear Information System (INIS)

    Qin, J.; Wang, L.; Yuan, D.P.; Gao, P.; Zhang, B.Z.

    1989-01-01

    We report the experimental observations of deterministic chaos in a steady-state plasma which is not driven by any extra periodic forces. Two routes to chaos have been found, period-doubling and intermittent chaos. The fine structures in chaos such as periodic windows and bifurcations in windows have also been observed

  12. Order against chaos in nuclei

    International Nuclear Information System (INIS)

    Soloviev, V.G.

    1995-01-01

    Order and chaos and order-to-chaos transition are treated in terms of nuclear wave functions. A quasiparticle-phonon interaction is responsible for the fragmentation of one- and many-quasiparticle and phonon states and for the mixing of closely spaced states. Complete damping of one-quasiparticle states cannot be considered as a transition to chaos due to large many-quasiparticle or quasiparticle-phonon terms in their wave functions. An experimental investigation of the strength distribution of many-quasiparticle and quasiparticle-phonon states should uncover a new region of a regularity in nuclei at intermediate excitation energy. A chaotic behaviour of nuclear states can be shifted to higher excitation energies. ((orig.))

  13. Effects of maturation and acidosis on the chaos-like complexity of the neural respiratory output in the isolated brainstem of the tadpole, Rana esculenta

    Science.gov (United States)

    Samara, Ziyad; Fiamma, Marie-Noëlle; Bautin, Nathalie; Ranohavimparany, Anja; Le Coz, Patrick; Golmard, Jean-Louis; Darré, Pierre; Zelter, Marc; Poon, Chi-Sang; Similowski, Thomas

    2011-01-01

    Human ventilation at rest exhibits mathematical chaos-like complexity that can be described as long-term unpredictability mediated (in whole or in part) by some low-dimensional nonlinear deterministic process. Although various physiological and pathological situations can affect respiratory complexity, the underlying mechanisms remain incompletely elucidated. If such chaos-like complexity is an intrinsic property of central respiratory generators, it should appear or increase when these structures mature or are stimulated. To test this hypothesis, we employed the isolated tadpole brainstem model [Rana (Pelophylax) esculenta] and recorded the neural respiratory output (buccal and lung rhythms) of pre- (n = 8) and postmetamorphic tadpoles (n = 8), at physiologic (7.8) and acidic pH (7.4). We analyzed the root mean square of the cranial nerve V or VII neurograms. Development and acidosis had no effect on buccal period. Lung frequency increased with development (P Chaos-like complexity, assessed through the noise limit, increased from pH 7.8 to pH 7.4 (P chaos-like complexity, especially in the postmetamorphic stage and at low pH. According to the ventilatory generators homology theory, this may also be the case in mammals. PMID:21325645

  14. Universal signatures of quantum chaos

    International Nuclear Information System (INIS)

    Aurich, R.; Bolte, J.; Steiner, F.

    1994-02-01

    We discuss fingerprints of classical chaos in spectra of the corresponding bound quantum systems. A novel quantity to measure quantum chaos in spectra is proposed and a conjecture about its universal statistical behaviour is put forward. Numerical as well as theoretical evidence is provided in favour of the conjecture. (orig.)

  15. Combining short- and long-range fluorescence reporters with simulations to explore the intramolecular dynamics of an intrinsically disordered protein

    Science.gov (United States)

    Zosel, Franziska; Haenni, Dominik; Soranno, Andrea; Nettels, Daniel; Schuler, Benjamin

    2017-10-01

    Intrinsically disordered proteins (IDPs) are increasingly recognized as a class of molecules that can exert essential biological functions even in the absence of a well-defined three-dimensional structure. Understanding the conformational distributions and dynamics of these highly flexible proteins is thus essential for explaining the molecular mechanisms underlying their function. Single-molecule fluorescence spectroscopy in combination with Förster resonance energy transfer (FRET) is a powerful tool for probing intramolecular distances and the rapid long-range distance dynamics in IDPs. To complement the information from FRET, we combine it with photoinduced electron transfer (PET) quenching to monitor local loop-closure kinetics at the same time and in the same molecule. Here we employed this combination to investigate the intrinsically disordered N-terminal domain of HIV-1 integrase. The results show that both long-range dynamics and loop closure kinetics on the sub-microsecond time scale can be obtained reliably from a single set of measurements by the analysis with a comprehensive model of the underlying photon statistics including both FRET and PET. A more detailed molecular interpretation of the results is enabled by direct comparison with a recent extensive atomistic molecular dynamics simulation of integrase. The simulations are in good agreement with experiment and can explain the deviation from simple models of chain dynamics by the formation of persistent local secondary structure. The results illustrate the power of a close combination of single-molecule spectroscopy and simulations for advancing our understanding of the dynamics and detailed mechanisms in unfolded and intrinsically disordered proteins.

  16. Chaos in hadrons

    International Nuclear Information System (INIS)

    Muñoz, L; Fernández-Ramírez, C; Relaño, A; Retamosa, J

    2012-01-01

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

  17. Household chaos and family sleep during infants' first year.

    Science.gov (United States)

    Whitesell, Corey J; Crosby, Brian; Anders, Thomas F; Teti, Douglas M

    2018-05-21

    Household chaos has been linked with dysregulated family and individual processes. The present study investigated linkages between household chaos and infant and parent sleep, a self-regulated process impacted by individual, social, and environmental factors. Studies of relations between household chaos and child sleep have focused on older children and teenagers, with little attention given to infants or parent sleep. This study examines these relationships using objective measures of household chaos and sleep while controlling for, respectively, maternal emotional availability at bedtime and martial adjustment, in infant and parent sleep. Multilevel modeling examined mean and variability of sleep duration and fragmentation for infants, mothers, and fathers when infants were 1, 3, 6, 9, and 12 months (N = 167). Results indicated infants in higher chaos homes experienced delays in sleep consolidation patterns, with longer and more variable sleep duration, and greater fragmentation. Parent sleep was also associated with household chaos such that in higher chaos homes, mothers and fathers experienced greater variability in sleep duration, which paralleled infant findings. In lower chaos homes, parents' sleep fragmentation mirrored infants' decreasingly fragmented sleep across the first year and remained lower at all timepoints compared to parents and infants in high chaos homes. Collectively, these findings indicate that after controlling for maternal emotional availability and marital adjustment (respectively) household chaos has a dysregulatory impact on infant and parent sleep. Results are discussed in terms of the potential for chaos-induced poor sleep to dysregulate daytime functioning and, in turn, place parent-infant relationships at risk. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

  18. Wrecked regulation of intrinsically disordered proteins in diseases: Pathogenicity of deregulated regulators

    Directory of Open Access Journals (Sweden)

    Vladimir N. Uversky

    2014-07-01

    Full Text Available Biologically active proteins without stable tertiary structure are common in all known proteomes. Functions of these intrinsically disordered proteins (IDPs are typically related to regulation, signaling and control. Cellular levels of these important regulators are tightly regulated by a variety mechanisms ranging from firmly controlled expression to precisely targeted degradation. Functions of IDPs are controlled by binding to specific partners, alternative splicing, and posttranslational modifications among other means. In the norm, right amounts of precisely activated IDPs have to be present in right time at right places. Wrecked regulation brings havoc to the ordered world of disordered proteins, leading to protein misfolding, misidentification, and missignaling that give rise to numerous human diseases, such as cancer, cardiovascular disease, neurodegenerative diseases, and diabetes. Among factors inducing pathogenic transformations of IDPs are various cellular mechanisms, such as chromosomal translocations, damaged splicing, altered expression, frustrated posttranslational modifications, aberrant proteolytic degradation, and defective trafficking. This review presents some of the aspects of deregulated regulation of IDPs leading to human diseases.

  19. Quantum chaos in the Heisenberg picture

    International Nuclear Information System (INIS)

    McKellar, B.H.J.; Lancaster, M.; McCaw, J.

    2000-01-01

    Full text: We explore the possibility of defining quantum chaos in the algebra of quantum mechanical operators. The simple definition of the Lyapunov exponent in terms of a metric on that algebra has the expected properties for the quantum logistic map, as we confirm for the simple spin 1 system. We then show numerically and analytically that the Hamiltonian evolution of finite spin systems does not lead to chaos in this definition, and investigate alternative definitions of quantum chaos in the algebra of operators

  20. 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.

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

    International Nuclear Information System (INIS)

    Gavilian-Moreno, Carlos; Espinosa-Paredes, Gilberto

    2016-01-01

    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

  2. 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.

  3. Using Largest Lyapunov Exponent to Confirm the Intrinsic Stability of Boiling Water Reactors

    Directory of Open Access Journals (Sweden)

    Carlos J. Gavilán-Moreno

    2016-04-01

    Full Text Available 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.

  4. Resurvey of order and chaos in spinning compact binaries

    International Nuclear Information System (INIS)

    Wu Xin; Xie Yi

    2008-01-01

    This paper is mainly devoted to applying the invariant, fast, Lyapunov indicator to clarify some doubt regarding the apparently conflicting results of chaos in spinning compact binaries at the second-order post-Newtonian approximation of general relativity from previous literatures. It is shown with a number of examples that no single physical parameter or initial condition can be described as responsible for causing chaos, but a complicated combination of all parameters and initial conditions is responsible. In other words, a universal rule for the dependence of chaos on each parameter or initial condition cannot be found in general. Chaos does not depend only on the mass ratio, and the maximal spins do not necessarily bring the strongest effect of chaos. Additionally, chaos does not always become drastic when the initial spin vectors are nearly perpendicular to the orbital plane, and the alignment of spins cannot trigger chaos by itself

  5. Chaos Theory and Post Modernism

    Science.gov (United States)

    Snell, Joel

    2009-01-01

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

  6. The three versions of distributional chaos

    International Nuclear Information System (INIS)

    Balibrea, F.; Smital, J.; Stefankova, M.

    2005-01-01

    The notion of distributional chaos was introduced by Schweizer and Smital [Trans. Amer. Math. Soc. 344 (1994) 737] for continuous maps of the interval. However, it turns out that, for continuous maps of a compact metric space three mutually nonequivalent versions of distributional chaos, DC1-DC3, can be considered. In this paper we consider the weakest one, DC3. We show that DC3 does not imply chaos in the sense of Li and Yorke. We also show that DC3 is not invariant with respect to topological conjugacy. In other words, there are lower and upper distribution functions Φ xy and Φxy* generated by a continuous map f of a compact metric space (M, ρ) such that Φxy*(t)>Φxy(t) for all t in an interval. However, f on the same space M, but with a metric ρ' generating the same topology as ρ is no more DC3.Recall that, contrary to this, either DC1 or DC2 is topological conjugacy invariant and implies Li and Yorke chaos (cf. [Chaos, Solitons and Fractals 21 (2004) 1125])

  7. Chaotic dynamics and chaos control in nonlinear laser systems

    International Nuclear Information System (INIS)

    Fang Jinqing; Yao Weiguang

    2001-01-01

    Chaotic dynamics and chaos control have become a great challenge in nonlinear laser systems and its advances are reviewed mainly based on the ring cavity laser systems. The principle and stability conditions for time-delay feedback control are analyzed and applied to chaos control in the laser systems. Other advanced methods of chaos control, such as weak spatial perturbation and occasional proportional feedback technique, are discussed. Prospects of chaos control for application (such as improvement of laser power and performance, synchronized chaos secure communication and information processing) are pointed out finally

  8. !CHAOS: A cloud of controls

    Science.gov (United States)

    Angius, S.; Bisegni, C.; Ciuffetti, P.; Di Pirro, G.; Foggetta, L. G.; Galletti, F.; Gargana, R.; Gioscio, E.; Maselli, D.; Mazzitelli, G.; Michelotti, A.; Orrù, R.; Pistoni, M.; Spagnoli, F.; Spigone, D.; Stecchi, A.; Tonto, T.; Tota, M. A.; Catani, L.; Di Giulio, C.; Salina, G.; Buzzi, P.; Checcucci, B.; Lubrano, P.; Piccini, M.; Fattibene, E.; Michelotto, M.; Cavallaro, S. R.; Diana, B. F.; Enrico, F.; Pulvirenti, S.

    2016-01-01

    The paper is aimed to present the !CHAOS open source project aimed to develop a prototype of a national private Cloud Computing infrastructure, devoted to accelerator control systems and large experiments of High Energy Physics (HEP). The !CHAOS project has been financed by MIUR (Italian Ministry of Research and Education) and aims to develop a new concept of control system and data acquisition framework by providing, with a high level of aaabstraction, all the services needed for controlling and managing a large scientific, or non-scientific, infrastructure. A beta version of the !CHAOS infrastructure will be released at the end of December 2015 and will run on private Cloud infrastructures based on OpenStack.

  9. !CHAOS: A cloud of controls

    International Nuclear Information System (INIS)

    Angius, S.; Bisegni, C.; Ciuffetti, P.

    2016-01-01

    The paper is aimed to present the !CHAOS open source project aimed to develop a prototype of a national private Cloud Computing infrastructure, devoted to accelerator control systems and large experiments of High Energy Physics (HEP). The !CHAOS project has been financed by MIUR (Italian Ministry of Research and Education) and aims to develop a new concept of control system and data acquisition framework by providing, with a high level of abstraction, all the services needed for controlling and managing a large scientific, or non-scientific, infrastructure. A beta version of the !CHAOS infrastructure will be released at the end of December 2015 and will run on private Cloud infrastructures based on OpenStack.

  10. On CFT and quantum chaos

    International Nuclear Information System (INIS)

    Turiaci, Gustavo J.; Verlinde, Herman

    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.

  11. Nuclear spectroscopy and quantum chaos

    International Nuclear Information System (INIS)

    Sakata, Fumihiko; Marumori, Toshio; Hashimoto, Yukio; Yamamoto, Yoshifumi; Tsukuma, Hidehiko; Iwasawa, Kazuo.

    1990-05-01

    In this paper, a recent development of INS-TSUKUBA joint research project on large-amplitude collective motion is summerized. The classical theory of nuclear collective dynamics formulated within the time-dependent Hartree-Fock theory is recapitulated and decisive role of the level crossing in the single-particle dynamics on the order-to-chaos transition of collective motion is discussed in detail. Extending the basic idea of the classical theory, we discuss a quantum theory of nuclear collective dynamics which allows us to properly define a concept of quantum chaos for each eigenfunction. By using numerical calculation, we illustrate what the quantum chaos for each eigenfunction means and its relation to usual definition based on the random matrix theory. (author)

  12. Quantum mechanical suppression of chaos

    International Nuclear Information System (INIS)

    Bluemel, R.; Smilansky, U.

    1990-01-01

    The relation between determinism and predictability is the central issue in the study of 'deterministic chaos'. Much knowledge has been accumulated in the past 10 years about the chaotic dynamics of macroscopic (classical) systems. The implications of chaos in the microscopic quantum world is examined, in other words, how to reconcile the correspondence principle with the inherent uncertainties which reflect the wave nature of quantum dynamics. Recent atomic physics experiments demonstrate clearly that chaos is relevant to the microscopic world. In particular, such experiments emphasise the urgent need to clarify the genuine quantum mechanism which imposes severe limitations on quantum dynamics, and renders it so very different from its classical counterpart. (author)

  13. On CFT and quantum chaos

    Energy Technology Data Exchange (ETDEWEB)

    Turiaci, Gustavo J. [Physics Department, Princeton University,Princeton NJ 08544 (United States); Verlinde, Herman [Physics Department, Princeton University,Princeton NJ 08544 (United States); Princeton Center for Theoretical Science, Princeton University,Princeton NJ 08544 (United States)

    2016-12-21

    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.

  14. Semiconductor lasers stability, instability and chaos

    CERN Document Server

    Ohtsubo, Junji

    2017-01-01

    This book describes the fascinating recent advances made concerning the chaos, stability and instability of semiconductor lasers, and discusses their applications and future prospects in detail. It emphasizes the dynamics in semiconductor lasers by optical and electronic feedback, optical injection, and injection current modulation. Applications of semiconductor laser chaos, control and noise, and semiconductor lasers are also demonstrated. Semiconductor lasers with new structures, such as vertical-cavity surface-emitting lasers and broad-area semiconductor lasers, are intriguing and promising devices. Current topics include fast physical number generation using chaotic semiconductor lasers for secure communication, development of chaos, quantum-dot semiconductor lasers and quantum-cascade semiconductor lasers, and vertical-cavity surface-emitting lasers. This fourth edition has been significantly expanded to reflect the latest developments. The fundamental theory of laser chaos and the chaotic dynamics in se...

  15. Homoclinic chaos and energy condition violation

    International Nuclear Information System (INIS)

    Heinzle, J. Mark; Roehr, Niklas; Uggla, Claes

    2006-01-01

    In this letter we discuss the connection between so-called homoclinic chaos and the violation of energy conditions in locally rotationally symmetric Bianchi type IX models, where the matter is assumed to be nontilted dust and a positive cosmological constant. We show that homoclinic chaos in these models is an artifact of unphysical assumptions: it requires that there exist solutions with positive matter energy density ρ>0 that evolve through the singularity and beyond as solutions with negative matter energy density ρ<0. Homoclinic chaos is absent when it is assumed that the dust particles always retain their positive mass. In addition, we discuss more general models: for solutions that are not locally rotationally symmetric we demonstrate that the construction of extensions through the singularity, which is required for homoclinic chaos, is not possible in general

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-05-07

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

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

    International Nuclear Information System (INIS)

    Knott, Michael; Best, Robert B.

    2014-01-01

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

  18. Iani Chaos

    Science.gov (United States)

    2005-01-01

    [figure removed for brevity, see original site] Context image for PIA03200 Iani Chaos This VIS image of Iani Chaos shows the layered deposit that occurs on the floor. It appears that the layers were deposited after the chaos was formed. Image information: VIS instrument. Latitude 2.3S, Longitude 342.3E. 17 meter/pixel resolution. Note: this THEMIS visual image has not been radiometrically nor geometrically calibrated for this preliminary release. An empirical correction has been performed to remove instrumental effects. A linear shift has been applied in the cross-track and down-track direction to approximate spacecraft and planetary motion. Fully calibrated and geometrically projected images will be released through the Planetary Data System in accordance with Project policies at a later time. NASA's Jet Propulsion Laboratory manages the 2001 Mars Odyssey mission for NASA's Office of Space Science, Washington, D.C. The Thermal Emission Imaging System (THEMIS) was developed by Arizona State University, Tempe, in collaboration with Raytheon Santa Barbara Remote Sensing. The THEMIS investigation is led by Dr. Philip Christensen at Arizona State University. Lockheed Martin Astronautics, Denver, is the prime contractor for the Odyssey project, and developed and built the orbiter. Mission operations are conducted jointly from Lockheed Martin and from JPL, a division of the California Institute of Technology in Pasadena.

  19. Semiconductor Lasers Stability, Instability and Chaos

    CERN Document Server

    Ohtsubo, Junji

    2008-01-01

    This monograph describes fascinating recent progress in the field of chaos, stability and instability of semiconductor lasers. Applications and future prospects are discussed in detail. The book emphasizes the various dynamics induced in semiconductor lasers by optical and electronic feedback, optical injection, and injection current modulation. Recent results of both theoretical and experimental investigations are presented. Demonstrating applications of semiconductor laser chaos, control and noise, Semiconductor Lasers describes suppression and chaotic secure communications. For those who are interested in optics but not familiar with nonlinear systems, a brief introduction to chaos analysis is presented.

  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. The Strength of Chaos: Accurate Simulation of Resonant Electron Scattering by Many-Electron Ions and Atoms in the Presence of Quantum Chaos

    Science.gov (United States)

    2017-01-20

    AFRL-AFOSR-JP-TR-2017-0012 The Strength of Chaos : accurate simulation of resonant electron scattering by many-electron ions and atoms in the presence...of quantum chaos Igor Bray CURTIN UNIVERSITY OF TECHNOLOGY Final Report 01/20/2017 DISTRIBUTION A: Distribution approved for public release. AF...SUBTITLE The Strength of Chaos : accurate simulation of resonant electron scattering by many- electron ions and atoms in the presence of quantum chaos

  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. The Impact of O-Glycan Chemistry on the Stability of Intrinsically Disordered Proteins

    Energy Technology Data Exchange (ETDEWEB)

    Beckham, Gregg T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Prates, Erica T [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Crowley, Michael F [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Guan, Xiaoyang [University of Colorado; Li, Yaohao [University of Colorado; Wang, Xinfeng [University of Colorado; Chaffey, Patrick K. [University of Colorado; Skaf, Munir S. [University of Campinas; Tan, Zhongping [University of Colorado

    2018-03-02

    Protein glycosylation is a diverse post-translational modification that serves myriad biological functions. O-linked glycans in particular vary widely in extent and chemistry in eukaryotes, with secreted proteins from fungi and yeast commonly exhibiting O-mannosylation in intrinsically disordered regions of proteins, likely for proteolysis protection, among other functions. However, it is not well understood why mannose is often the preferred glycan, and more generally, if the neighboring protein sequence and glycan have coevolved to protect against proteolysis in glycosylated intrinsically disordered proteins (IDPs). Here, we synthesized variants of a model IDP, specifically a natively O-mannosylated linker from a fungal enzyme, with a-O-linked mannose, glucose, and galactose moieties, along with a non-glycosylated linker. Upon exposure to thermolysin, O-mannosylation, by far, provides the highest extent of proteolysis protection. To explain this observation, extensive molecular dynamics simulations were conducted, revealing that the axial configuration of the C2-hydroxyl group (2-OH) of a-mannose adjacent to the glycan-peptide bond strongly influences the conformational features of the linker. Specifically, a-mannose restricts the torsions of the IDP main chain more than other glycans whose equatorial 2-OH groups exhibit interactions that favor perpendicular glycan-protein backbone orientation. We suggest that IDP stiffening due to O-mannosylation impairs protease action, with contributions from protein-glycan interactions, protein flexibility, and protein stability. Our results further imply that resistance to proteolysis is an important driving force for evolutionary selection of a-mannose in eukaryotic IDPs, and more broadly, that glycan motifs for proteolysis protection likely coevolve with the protein sequence to which they attach.

  4. Intrinsically Disordered Proteins and the Origins of Multicellular Organisms

    Science.gov (United States)

    Dunker, A. Keith

    In simple multicellular organisms all of the cells are in direct contact with the surrounding milieu, whereas in complex multicellular organisms some cells are completely surrounded by other cells. Current phylogenetic trees indicate that complex multicellular organisms evolved independently from unicellular ancestors about 10 times, and only among the eukaryotes, including once for animals, twice each for green, red, and brown algae, and thrice for fungi. Given these multiple independent evolutionary lineages, we asked two questions: 1. Which molecular functions underpinned the evolution of multicellular organisms?; and, 2. Which of these molecular functions depend on intrinsically disordered proteins (IDPs)? Compared to unicellularity, multicellularity requires the advent of molecules for cellular adhesion, for cell-cell communication and for developmental programs. In addition, the developmental programs need to be regulated over space and time. Finally, each multicellular organism has cell-specific biochemistry and physiology. Thus, the evolution of complex multicellular organisms from unicellular ancestors required five new classes of functions. To answer the second question we used Key-words in Swiss Protein ranked for associations with predictions of protein structure or disorder. With a Z-score of 18.8 compared to random-function proteins, à differentiation was the biological process most strongly associated with IDPs. As expected from this result, large numbers of individual proteins associated with differentiation exhibit substantial regions of predicted disorder. For the animals for which there is the most readily available data all five of the underpinning molecular functions for multicellularity were found to depend critically on IDP-based mechanisms and other evidence supports these ideas. While the data are more sparse, IDPs seem to similarly underlie the five new classes of functions for plants and fungi as well, suggesting that IDPs were indeed

  5. The α-Helical Structure of Prodomains Promotes Translocation of Intrinsically Disordered Neuropeptide Hormones into the Endoplasmic Reticulum*

    Science.gov (United States)

    Dirndorfer, Daniela; Seidel, Ralf P.; Nimrod, Guy; Miesbauer, Margit; Ben-Tal, Nir; Engelhard, Martin; Zimmermann, Richard; Winklhofer, Konstanze F.; Tatzelt, Jörg

    2013-01-01

    Different neuropeptide hormones, which are either too small to adopt a stable conformation or are predicted to be intrinsically disordered, are synthesized as larger precursors containing a prodomain in addition to an N-terminal signal peptide. We analyzed the biogenesis of three unstructured neuropeptide hormones and observed that translocation of these precursors into the lumen of the endoplasmic reticulum (ER) is critically dependent on the presence of the prodomain. The hormone domains could be deleted from the precursors without interfering with ER import and secretion, whereas constructs lacking the prodomain remained in the cytosol. Domain-swapping experiments revealed that the activity of the prodomains to promote productive ER import resides in their ability to adopt an α-helical structure. Removal of the prodomain from the precursor did not interfere with co-translational targeting of the nascent chain to the Sec61 translocon but with its subsequent productive translocation into the ER lumen. Our study reveals a novel function of prodomains to enable import of small or intrinsically disordered secretory proteins into the ER based on their ability to adopt an α-helical conformation. PMID:23532840

  6. 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.

  7. Prediction based chaos control via a new neural network

    International Nuclear Information System (INIS)

    Shen Liqun; Wang Mao; Liu Wanyu; Sun Guanghui

    2008-01-01

    In this Letter, a new chaos control scheme based on chaos prediction is proposed. To perform chaos prediction, a new neural network architecture for complex nonlinear approximation is proposed. And the difficulty in building and training the neural network is also reduced. Simulation results of Logistic map and Lorenz system show the effectiveness of the proposed chaos control scheme and the proposed neural network

  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. Exploiting chaos for applications.

    Science.gov (United States)

    Ditto, William L; Sinha, Sudeshna

    2015-09-01

    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.

  10. 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.

  11. Chaos, decoherence and quantum cosmology

    International Nuclear Information System (INIS)

    Calzetta, Esteban

    2012-01-01

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

  12. Intrinsically disordered proteins--relation to general model expressing the active role of the water environment.

    Science.gov (United States)

    Kalinowska, Barbara; Banach, Mateusz; Konieczny, Leszek; Marchewka, Damian; Roterman, Irena

    2014-01-01

    This work discusses the role of unstructured polypeptide chain fragments in shaping the protein's hydrophobic core. Based on the "fuzzy oil drop" model, which assumes an idealized distribution of hydrophobicity density described by the 3D Gaussian, we can determine which fragments make up the core and pinpoint residues whose location conflicts with theoretical predictions. We show that the structural influence of the water environment determines the positions of disordered fragments, leading to the formation of a hydrophobic core overlaid by a hydrophilic mantle. This phenomenon is further described by studying selected proteins which are known to be unstable and contain intrinsically disordered fragments. Their properties are established quantitatively, explaining the causative relation between the protein's structure and function and facilitating further comparative analyses of various structural models. © 2014 Elsevier Inc. All rights reserved.

  13. Linear Matrix Inequality Based Fuzzy Synchronization for Fractional Order Chaos

    Directory of Open Access Journals (Sweden)

    Bin Wang

    2015-01-01

    Full Text Available This paper investigates fuzzy synchronization for fractional order chaos via linear matrix inequality. Based on generalized Takagi-Sugeno fuzzy model, one efficient stability condition for fractional order chaos synchronization or antisynchronization is given. The fractional order stability condition is transformed into a set of linear matrix inequalities and the rigorous proof details are presented. Furthermore, through fractional order linear time-invariant (LTI interval theory, the approach is developed for fractional order chaos synchronization regardless of the system with uncertain parameters. Three typical examples, including synchronization between an integer order three-dimensional (3D chaos and a fractional order 3D chaos, anti-synchronization of two fractional order hyperchaos, and the synchronization between an integer order 3D chaos and a fractional order 4D chaos, are employed to verify the theoretical results.

  14. Chaos, Chaos Control and Synchronization of a Gyrostat System

    Science.gov (United States)

    GE, Z.-M.; LIN, T.-N.

    2002-03-01

    The dynamic behavior of a gyrostat system subjected to external disturbance is studied in this paper. By applying numerical results, phase diagrams, power spectrum, period-T maps, and Lyapunov exponents are presented to observe periodic and choatic motions. The effect of the parameters changed in the system can be found in the bifurcation and parametric diagrams. For global analysis, the basins of attraction of each attractor of the system are located by employing the modified interpolated cell mapping (MICM) method. Several methods, the delayed feedback control, the addition of constant torque, the addition of periodic force, the addition of periodic impulse torque, injection of dither signal control, adaptive control algorithm (ACA) control and bang-bang control are used to control chaos effectively. Finally, synchronization of chaos in the gyrostat system is studied.

  15. Chaos and its Role in Design and Simulation of Railway Vehicles

    DEFF Research Database (Denmark)

    True, Hans

    1996-01-01

    First certain important properties of nonlinear problems are discussed. Thenthe concept of chaos is described. It can only appear in nonlinear systemsand it is very common in the real world. Certain characteristic features ofdeterministic chaos and in relation hereto tests for the existence...... of chaos indynamical systems are presented.\\ Next the relevance of chaos for railwaydynamics is discussed and examples of chaotic oscillations in railwaydynamical model are shown, whereby the distinction between a chaoticattractor and transient chaos is introduces. Some causes of chaos in railwaytechnology...... are discussed. Finally the effects of chaos on field tests andnumerical simulations are discussed....

  16. A-coupled-expanding and distributional chaos

    International Nuclear Information System (INIS)

    Kim, Cholsan; Ju, Hyonhui; Chen, Minghao; Raith, Peter

    2015-01-01

    The concept of A-coupled-expanding maps is one of the more natural and useful ideas generalized from the horseshoe map which is commonly known as a criterion of chaos. It is well known that distributional chaos is one of the concepts which reflect strong chaotic behavior. In this paper, we focus on the relationship between A-coupled-expanding and distributional chaos. We prove two theorems which give sufficient conditions for a strictly A-coupled-expanding map to be distributionally chaotic in the senses of two kinds, where A is an m × m irreducible transition matrix

  17. Chaos on the interval

    CERN Document Server

    Ruette, Sylvie

    2017-01-01

    The aim of this book is to survey the relations between the various kinds of chaos and related notions for continuous interval maps from a topological point of view. The papers on this topic are numerous and widely scattered in the literature; some of them are little known, difficult to find, or originally published in Russian, Ukrainian, or Chinese. Dynamical systems given by the iteration of a continuous map on an interval have been broadly studied because they are simple but nevertheless exhibit complex behaviors. They also allow numerical simulations, which enabled the discovery of some chaotic phenomena. Moreover, the "most interesting" part of some higher-dimensional systems can be of lower dimension, which allows, in some cases, boiling it down to systems in dimension one. Some of the more recent developments such as distributional chaos, the relation between entropy and Li-Yorke chaos, sequence entropy, and maps with infinitely many branches are presented in book form for the first time. The author gi...

  18. 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 interact......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...

  19. Deterministic Chaos - Complex Chance out of Simple Necessity ...

    Indian Academy of Sciences (India)

    This is a very lucid and lively book on deterministic chaos. Chaos is very common in nature. However, the understanding and realisation of its potential applications is very recent. Thus this book is a timely addition to the subject. There are several books on chaos and several more are being added every day. In spite of this ...

  20. Chaos of discrete dynamical systems in complete metric spaces

    International Nuclear Information System (INIS)

    Shi Yuming; Chen Guanrong

    2004-01-01

    This paper is concerned with chaos of discrete dynamical systems in complete metric spaces. Discrete dynamical systems governed by continuous maps in general complete metric spaces are first discussed, and two criteria of chaos are then established. As a special case, two corresponding criteria of chaos for discrete dynamical systems in compact subsets of metric spaces are obtained. These results have extended and improved the existing relevant results of chaos in finite-dimensional Euclidean spaces

  1. Confirmatory Factor Analysis of the Malay Version of the Confusion, Hubbub and Order Scale (CHAOS-6) among Myocardial Infarction Survivors in a Malaysian Cardiac Healthcare Facility.

    Science.gov (United States)

    Ganasegeran, Kurubaran; Selvaraj, Kamaraj; Rashid, Abdul

    2017-08-01

    The six item Confusion, Hubbub and Order Scale (CHAOS-6) has been validated as a reliable tool to measure levels of household disorder. We aimed to investigate the goodness of fit and reliability of a new Malay version of the CHAOS-6. The original English version of the CHAOS-6 underwent forward-backward translation into the Malay language. The finalised Malay version was administered to 105 myocardial infarction survivors in a Malaysian cardiac health facility. We performed confirmatory factor analyses (CFAs) using structural equation modelling. A path diagram and fit statistics were yielded to determine the Malay version's validity. Composite reliability was tested to determine the scale's reliability. All 105 myocardial infarction survivors participated in the study. The CFA yielded a six-item, one-factor model with excellent fit statistics. Composite reliability for the single factor CHAOS-6 was 0.65, confirming that the scale is reliable for Malay speakers. The Malay version of the CHAOS-6 was reliable and showed the best fit statistics for our study sample. We thus offer a simple, brief, validated, reliable and novel instrument to measure chaos, the Skala Kecelaruan, Keriuhan & Tertib Terubahsuai (CHAOS-6) , for the Malaysian population.

  2. Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

    Energy Technology Data Exchange (ETDEWEB)

    Launay, Hélène; Barré, Patrick [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Puppo, Carine [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Manneville, Stéphanie [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France); Gontero, Brigitte [Aix-Marseille Université, Centre National de la Recherche Scientifique, UMR 7281, Laboratoire de Bioénergétique et Ingénierie des Protéines, 31 Chemin Joseph Aiguier, 13402, Marseille Cedex 20 (France); Receveur-Bréchot, Véronique, E-mail: veronique.brechot@inserm.fr [Laboratory of integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Aix-Marseille Universités, Marseille 13009 (France)

    2016-08-12

    The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

  3. Absence of residual structure in the intrinsically disordered regulatory protein CP12 in its reduced state

    International Nuclear Information System (INIS)

    Launay, Hélène; Barré, Patrick; Puppo, Carine; Manneville, Stéphanie; Gontero, Brigitte; Receveur-Bréchot, Véronique

    2016-01-01

    The redox switch protein CP12 is a key player of the regulation of the Benson–Calvin cycle. Its oxidation state is controlled by the formation/dissociation of two intramolecular disulphide bridges during the day/night cycle. CP12 was known to be globally intrinsically disordered on a large scale in its reduced state, while being partly ordered in the oxidised state. By combining Nuclear Magnetic Resonance and Small Angle X-ray Scattering experiments, we showed that, contrary to secondary structure or disorder predictions, reduced CP12 is fully disordered, with no transient or local residual structure likely to be precursor of the structures identified in the oxidised active state and/or in the bound state with GAPDH or PRK. These results highlight the diversity of the mechanisms of regulation of conditionally disordered redox switches, and question the stability of oxidised CP12 scaffold. - Highlights: • CP12 is predicted to form two helices in its N-terminal sequence. • Reduced CP12 is disordered as a random coil according to SAXS. • Limited or no transient structures are observed in reduced CP12 by NMR.

  4. Chaos concepts, control and constructive use

    CERN Document Server

    Bolotin, Yurii; Yanovsky, Vladimir

    2017-01-01

    This book offers a short and concise introduction to the many facets of chaos theory. While the study of chaotic behavior in nonlinear, dynamical systems is a well-established research field with ramifications in all areas of science, there is a lot to be learnt about how chaos can be controlled and, under appropriate conditions, can actually be constructive in the sense of becoming a control parameter for the system under investigation, stochastic resonance being a prime example. The present work stresses 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 the relevant algorithms for both Hamiltonian and dissipative systems, among 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. In this second, revised and enlarged edition, two more chapters explore the many interf...

  5. Evolutionary conservation of the polyproline II conformation surrounding intrinsically disordered phosphorylation sites.

    Science.gov (United States)

    Elam, W Austin; Schrank, Travis P; Campagnolo, Andrew J; Hilser, Vincent J

    2013-04-01

    Intrinsically disordered (ID) proteins function in the absence of a unique stable structure and appear to challenge the classic structure-function paradigm. The extent to which ID proteins take advantage of subtle conformational biases to perform functions, and whether signals for such mechanism can be identified in proteome-wide studies is not well understood. Of particular interest is the polyproline II (PII) conformation, suggested to be highly populated in unfolded proteins. We experimentally determine a complete calorimetric propensity scale for the PII conformation. Projection of the scale into representative eukaryotic proteomes reveals significant PII bias in regions coding for ID proteins. Importantly, enrichment of PII in ID proteins, or protein segments, is also captured by other PII scales, indicating that this enrichment is robustly encoded and universally detectable regardless of the method of PII propensity determination. Gene ontology (GO) terms obtained using our PII scale and other scales demonstrate a consensus for molecular functions performed by high PII proteins across the proteome. Perhaps the most striking result of the GO analysis is conserved enrichment (P ontology reveals an enrichment of PII bias near disordered phosphorylation sites that is conserved throughout eukaryotes. Copyright © 2013 The Protein Society.

  6. Global chaos synchronization with channel time-delay

    International Nuclear Information System (INIS)

    Jiang Guoping; Zheng Weixing; Chen Guanrong

    2004-01-01

    This paper addresses a practical issue in chaos synchronization where there is a time-delay in the receiver as compared with the transmitter. A new synchronization scheme and a general criterion for global chaos synchronization are proposed and developed from the approach of unidirectional linear error feedback coupling with time-delay. The chaotic Chua's circuit is used for illustration, where the coupling parameters are determined according to the criterion under which the global chaos synchronization of the time-delay coupled systems is achieved

  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

    2016-01-01

    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.

  8. Some open questions in 'wave chaos'

    International Nuclear Information System (INIS)

    Nonnenmacher, Stéphane

    2008-01-01

    The subject area referred to as 'wave chaos', 'quantum chaos' or 'quantum chaology' has been investigated mostly by the theoretical physics community in the last 30 years. The questions it raises have more recently also attracted the attention of mathematicians and mathematical physicists, due to connections with number theory, graph theory, Riemannian, hyperbolic or complex geometry, classical dynamical systems, probability, etc. After giving a rough account on 'what is quantum chaos?', I intend to list some pending questions, some of them having been raised a long time ago, some others more recent. The choice of problems (and of references) is of course partial and personal. (open problem)

  9. Nuclear physics, symmetries, and quantum chaos

    International Nuclear Information System (INIS)

    Bunakov, V.E.

    1999-01-01

    The reasons why the problem of chaos is of great topical interest in modern physics are briefly summarized, and it is indicated that ambiguities in the concept of quantum chaos present the greatest difficulties in these realms. The theory of random matrices and strength functions are generalized to demonstrate that chaotization of a system is associated with the violation of its symmetries. A criterion of quantum chaoticity is formulated in terms of the spreading width Γ spr . In the classical limit, this criterion reduces to Lyapunov's stability criteria. It is shown that the proposed criterion is applicable to standard problems of the modern theory of dynamical chaos

  10. L'ordre du chaos

    CERN Document Server

    1989-01-01

    Le mouvement brownien ; la mémoire des atomes ; le chaos ; déterminisme et prédictabilité ; déterminisme et chaos ; les phénomènes de physique et les échelles de longueur ; un ordre caché dans la matière désordonnée ; les verres de spin et l'étude des milieux désordonnés ; la convection ; la croissance fractale ; la physique de la matière hétérogène ; la matière ultradivisée.

  11. Defining intrinsic vs. extrinsic atopic dermatitis.

    Science.gov (United States)

    Karimkhani, Chante; Silverberg, Jonathan I; Dellavalle, Robert P

    2015-06-16

    Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin condition characterized by eczematous lesions, i.e. ill-demarcated erythematous patches and plaques. AD is commonly associated with elevated immunoglobulin E (IgE) and atopic disorders, such as asthma, hay fever, and food allergies. Rackemann and Mallory were some of the first to distinguish between asthma based on the presence ("extrinsic") or absence ("intrinsic") of allergy. This distinction has subsequently been applied to AD based on the presence ("extrinsic") or absence ("intrinsic") of increased IgE and atopic disease. Although the distinction between intrinsic and extrinsic AD is widely used, it remains controversial.

  12. A new approach for realizing electronic chaos generators

    International Nuclear Information System (INIS)

    Elwakeel, A.E.

    1997-01-01

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

  13. 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?

  14. The Six Fundamental Characteristics of Chaos and Their Clinical Relevance to Psychiatry: a New Hypothesis for the Origin of Psychosis

    Science.gov (United States)

    Schmid, Gary Bruno

    Underlying idea: A new hypothesis about how the mental state of psychosis may arise in the brain as a "linear" information processing pathology is briefly introduced. This hypothesis is proposed in the context of a complementary approach to psychiatry founded in the logical paradigm of chaos theory. To best understand the relation between chaos theory and psychiatry, the semantic structure of chaos theory is analyzed with the help of six general, and six specific, fundamental characteristics which can be directly inferred from empirical observations on chaotic systems. This enables a mathematically and physically stringent perspective on psychological phenomena which until now could only be grasped intuitively: Chaotic systems are in a general sense dynamic, intrinsically coherent, deterministic, recursive, reactive and structured: in a specific sense, self-organizing, unpredictable, nonreproducible, triadic, unstable and self-similar. To a great extent, certain concepts of chaos theory can be associated with corresponding concepts in psychiatry, psychology and psychotherapy, thus enabling an understanding of the human psyche in general as a (fractal) chaotic system and an explanation of certain mental developments, such as the course of schizophrenia, the course of psychosis and psychotherapy as chaotic processes. General overview: A short comparison and contrast of classical and chaotic physical theory leads to four postulates and one hypothesis motivating a new, dynamic, nonlinear approach to classical, causal psychiatry: Process-Oriented PSYchiatry or "POPSY", for short. Four aspects of the relationship between chaos theory and POPSY are discussed: (1) The first of these, namely, Identification of Chaos / Picture of Illness involves a definition of Chaos / Psychosis and a discussion of the 6 logical characteristics of each. This leads to the concept of dynamical disease (definition, characteristics and examples) and to the idea of "psychological disturbance as

  15. Particle ratios, quarks, and Chao-Yang statistics

    Energy Technology Data Exchange (ETDEWEB)

    Chew, C K; Low, G B; Lo, S Y [Nanyang Univ. (Singapore). Dept. of Physics; Phua, K K [Argonne National Lab., IL (USA)

    1980-01-01

    By introducing quarks into Chao-Yang statistics for 'violent' collisions, particle ratios are obtained which are consistent with the Chao-Yang results. The present method can also be extended to baryon-meson and baryon-antibaryon ratios.

  16. 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.

  17. Approximate motion integrals and the quantum chaos problem

    International Nuclear Information System (INIS)

    Bunakov, V.E.; Ivanov, I.B.

    2001-01-01

    One discusses the problem of occurrence and seek for the motion integrals in the stationary quantum mechanics and its relation to the quantum chaos. One studies decomposition of quantum numbers and derives the criterion of chaos. To seek the motion integrals one applies the convergence method. One derived the approximate integrals in the Hennone-Hales problem. One discusses the problem of compatibility of chaos and integrability [ru

  18. Quantum chaos and holographic tensor models

    Energy Technology Data Exchange (ETDEWEB)

    Krishnan, Chethan [Center for High Energy Physics, Indian Institute of Science,Bangalore 560012 (India); Sanyal, Sambuddha [International Center for Theoretical Sciences, Tata Institute of Fundamental Research,Bangalore 560089 (India); Subramanian, P.N. Bala [Center for High Energy Physics, Indian Institute of Science,Bangalore 560012 (India)

    2017-03-10

    A class of tensor models were recently outlined as potentially calculable examples of holography: their perturbative large-N behavior is similar to the Sachdev-Ye-Kitaev (SYK) model, but they are fully quantum mechanical (in the sense that there is no quenched disorder averaging). These facts make them intriguing tentative models for quantum black holes. In this note, we explicitly diagonalize the simplest non-trivial Gurau-Witten tensor model and study its spectral and late-time properties. We find parallels to (a single sample of) SYK where some of these features were recently attributed to random matrix behavior and quantum chaos. In particular, the spectral form factor exhibits a dip-ramp-plateau structure after a running time average, in qualitative agreement with SYK. But we also observe that even though the spectrum has a unique ground state, it has a huge (quasi-?)degeneracy of intermediate energy states, not seen in SYK. If one ignores the delta function due to the degeneracies however, there is level repulsion in the unfolded spacing distribution hinting chaos. Furthermore, there are gaps in the spectrum. The system also has a spectral mirror symmetry which we trace back to the presence of a unitary operator with which the Hamiltonian anticommutes. We use it to argue that to the extent that the model exhibits random matrix behavior, it is controlled not by the Dyson ensembles, but by the BDI (chiral orthogonal) class in the Altland-Zirnbauer classification.

  19. Quantum chaos and holographic tensor models

    International Nuclear Information System (INIS)

    Krishnan, Chethan; Sanyal, Sambuddha; Subramanian, P.N. Bala

    2017-01-01

    A class of tensor models were recently outlined as potentially calculable examples of holography: their perturbative large-N behavior is similar to the Sachdev-Ye-Kitaev (SYK) model, but they are fully quantum mechanical (in the sense that there is no quenched disorder averaging). These facts make them intriguing tentative models for quantum black holes. In this note, we explicitly diagonalize the simplest non-trivial Gurau-Witten tensor model and study its spectral and late-time properties. We find parallels to (a single sample of) SYK where some of these features were recently attributed to random matrix behavior and quantum chaos. In particular, the spectral form factor exhibits a dip-ramp-plateau structure after a running time average, in qualitative agreement with SYK. But we also observe that even though the spectrum has a unique ground state, it has a huge (quasi-?)degeneracy of intermediate energy states, not seen in SYK. If one ignores the delta function due to the degeneracies however, there is level repulsion in the unfolded spacing distribution hinting chaos. Furthermore, there are gaps in the spectrum. The system also has a spectral mirror symmetry which we trace back to the presence of a unitary operator with which the Hamiltonian anticommutes. We use it to argue that to the extent that the model exhibits random matrix behavior, it is controlled not by the Dyson ensembles, but by the BDI (chiral orthogonal) class in the Altland-Zirnbauer classification.

  20. Quantum chaos and conductivity in disordered systems

    International Nuclear Information System (INIS)

    Suzuki, A.; Matsutani, S.

    2001-01-01

    The hopping conductivity in a disordered system which is composed of small (semi-) metallic granules is presented. Due to the irregular shape of each granule, the level statistics of a free electron in granule is expressed by a random matrix, and a formula for the temperature-dependent conductivity (TDC) is obtained for such a disordered system. This TDC shows an apparent metal-insulator transition and is in good agreement with experimental results for disordered carbons

  1. Intrinsically disordered proteins aggregate at fungal cell-to-cell channels and regulate intercellular connectivity.

    Science.gov (United States)

    Lai, Julian; Koh, Chuan Hock; Tjota, Monika; Pieuchot, Laurent; Raman, Vignesh; Chandrababu, Karthik Balakrishna; Yang, Daiwen; Wong, Limsoon; Jedd, Gregory

    2012-09-25

    Like animals and plants, multicellular fungi possess cell-to-cell channels (septal pores) that allow intercellular communication and transport. Here, using a combination of MS of Woronin body-associated proteins and a bioinformatics approach that identifies related proteins based on composition and character, we identify 17 septal pore-associated (SPA) proteins that localize to the septal pore in rings and pore-centered foci. SPA proteins are not homologous at the primary sequence level but share overall physical properties with intrinsically disordered proteins. Some SPA proteins form aggregates at the septal pore, and in vitro assembly assays suggest aggregation through a nonamyloidal mechanism involving mainly α-helical and disordered structures. SPA loss-of-function phenotypes include excessive septation, septal pore degeneration, and uncontrolled Woronin body activation. Together, our data identify the septal pore as a complex subcellular compartment and focal point for the assembly of unstructured proteins controlling diverse aspects of intercellular connectivity.

  2. 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.

  3. Observation of Hamiltonian chaos and its control in wave-particle interaction

    International Nuclear Information System (INIS)

    Doveil, F; Macor, A; Aissi, A

    2007-01-01

    Wave-particle interactions are central in plasma physics. They can be studied in a traveling wave tube (TWT) to avoid intrinsic plasma noise. This led to detailed experimental analysis of the self-consistent interaction between unstable waves and an either cold or warm beam. More recently a test cold electron beam has been used to observe its non-self-consistent interaction with externally excited wave(s). The velocity distribution function of the electron beam is recorded with a trochoidal energy analyzer at the output of the TWT. An arbitrary waveform generator is used to launch a prescribed spectrum of waves along the slow wave structure (a 4 m long helix) of the TWT. The nonlinear synchronization of particles by a single wave responsible for Landau damping is observed. The resonant velocity domain associated with a single wave is also observed, as well as the transition to large scale chaos when the resonant domains of two waves and their secondary resonances overlap. This transition exhibits a 'devil's staircase' behavior when increasing the excitation amplitude in agreement with numerical simulation. A new strategy for control of chaos by building barriers of transport which prevent electrons from escaping from a given velocity region as well as its robustness are successfully tested. The underlying concepts extend far beyond the field of electron devices and plasma physics

  4. Nuclear physics and ideas of quantum chaos

    International Nuclear Information System (INIS)

    Zelevinsky, V.G.

    2002-01-01

    The field nowadays called 'many-body quantum chaos' was started in 1939 with the article by I.I. Gurevich studying the regularities of nuclear spectra. The field has been extensively developed recently, both mathematically and in application to mesoscopic systems and quantum fields. We argue that nuclear physics and the theory of quantum chaos are mutually beneficial. Many ideas of quantum chaos grew up from the factual material of nuclear physics; this enrichment still continues to take place. On the other hand, many phenomena in nuclear structure and reactions, as well as the general problem of statistical physics of finite strongly interacting systems, can be understood much deeper with the help of ideas and methods borrowed from the field of quantum chaos. A brief review of the selected topics related to the recent development is presented

  5. Chaos based encryption system for encrypting electroencephalogram signals.

    Science.gov (United States)

    Lin, Chin-Feng; Shih, Shun-Han; Zhu, Jin-De

    2014-05-01

    In the paper, we use the Microsoft Visual Studio Development Kit and C# programming language to implement a chaos-based electroencephalogram (EEG) encryption system involving three encryption levels. A chaos logic map, initial value, and bifurcation parameter for the map were used to generate Level I chaos-based EEG encryption bit streams. Two encryption-level parameters were added to these elements to generate Level II chaos-based EEG encryption bit streams. An additional chaotic map and chaotic address index assignment process was used to implement the Level III chaos-based EEG encryption system. Eight 16-channel EEG Vue signals were tested using the encryption system. The encryption was the most rapid and robust in the Level III system. The test yielded superior encryption results, and when the correct deciphering parameter was applied, the EEG signals were completely recovered. However, an input parameter error (e.g., a 0.00001 % initial point error) causes chaotic encryption bit streams, preventing the recovery of 16-channel EEG Vue signals.

  6. 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

  7. 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...

  8. Controlling chaos in a pendulum equation with ultra-subharmonic resonances

    International Nuclear Information System (INIS)

    Yang Jianping; Jing Zhujun

    2009-01-01

    Analytical and numerical results concerning control of chaos in a pendulum equation with parametric and external excitations are given by using Melnikov methods. We give the necessary conditions of chaos control with ultra-subharmonic resonances (i.e. Ω/ω=p/q,q>1,p,q are prime), where homoclinic chaos or heteroclinic chaos can be inhibited. Numerical simulations show that chaotic behavior can be converted to period-nq (n element of Z + ) orbits by adjusting amplitude and phase-difference of parametric excitation, and the distribution of maximum Lyapunov exponents in parameter-plane (Ψ,β) gives the regions in which chaos can be controlled.

  9. Noise induced chaos in optically driven colloidal rings.

    Science.gov (United States)

    Roichman, Yael; Zaslavsky, George; Grier, David G.

    2007-03-01

    Given a constant flux of energy, many driven dissipative systems rapidly organize themselves into configurations that support steady state motion. Examples include swarming of bacterial colonies, convection in shaken sandpiles, and synchronization in flowing traffic. How simple objects interacting in simple ways self-organize generally is not understood, mainly because so few of the available experimental systems afford the necessary access to their microscopic degrees of freedom. This talk introduces a new class of model driven dissipative systems typified by three colloidal spheres circulating around a ring-like optical trap known as an optical vortex. By controlling the interplay between hydrodynamic interactions and fixed disorder we are able to drive a transition from a previously predicted periodic steady state to fully developed chaos. In addition, by tracking both microscopic trajectories and macroscopic collective fluctuations the relation between the onset of microscopic weak chaos and the evolution of space-time self-similarity in macroscopic transport properties is revealed. In a broader scope, several optical vortices can be coupled to create a large dissipative system where each building block has internal degrees of freedom. In such systems the little understood dynamics of processes like frustration and jamming, fluctuation-dissipation relations and the propagation of collective motion can be tracked microscopically.

  10. Ray and wave chaos in underwater acoustic waveguides

    International Nuclear Information System (INIS)

    Virovlyansky, Anatolii L; Makarov, Denis V; Prants, Sergei V

    2012-01-01

    In the 1990s, the study of the chaotic behavior of ray trajectories in inhomogeneous waveguides emerged as a new field in ocean acoustics. It turned out that at ranges on the order of or larger than 1000 km ray chaos is well developed and should be taken into account when describing long-range sound propagation in the ocean. The theoretical analysis of ray chaos and of its finite-wavelength manifestation, wave chaos, is to a large extent based on well-known methods and ideas from the theory of dynamical and quantum chaos. Concrete examples are used to review the results obtained in this field over the last two decades. (reviews of topical problems)

  11. Chaos desynchronization in strongly coupled systems

    International Nuclear Information System (INIS)

    Wu Ye; Liu Weiqing; Xiao, Jinghua; Zhan Meng

    2007-01-01

    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

  12. Galloping instability to chaos of cables

    CERN Document Server

    Luo, Albert C J

    2017-01-01

    This book provides students and researchers with a systematic solution for fluid-induced structural vibrations, galloping instability and the chaos of cables. They will also gain a better understanding of stable and unstable periodic motions and chaos in fluid-induced structural vibrations. Further, the results presented here will help engineers effectively design and analyze fluid-induced vibrations.

  13. Control of chaos in a three-well duffing system

    International Nuclear Information System (INIS)

    Yang Jianping; Jing Zhujun

    2009-01-01

    Analytical and numerical results concerning control of chaos in a three-well duffing system with two external excitations are given by using the Melnikov methods proposed by Chacon et al. [Chacon R. General results on chaos suppression for biharmonically driven dissipative systems. Phys Lett A 1999;257:293-300, Chacon R, Palmero F, Balibrea F. Taming chaos in a driven Josephson Junction. Int J Bifurc Chaos 2001;11(7):1897-909, Chacon R. Role of ultrasubharmonic resonances in taming chaos by weak harmonic perturbations. Europhys Lett 2001;54(2):148C153]. We theoretically give the parameter-space region and intervals of initial phase difference for primary and subharmonic resonance and the necessary condition for the superharmonic and supersubharmonic resonance, where homoclinic chaos or heteroclinic chaos can be suppressed. Numerical simulations show the consistency and difference with theoretical analysis and the chaotic behavior can be converted to periodic orbits by adjusting amplitude and phase-difference of inhibiting excitation. Moreover, we consider the influence of parametric frequency on maximum Lyapunov exponent (LE) for different phase-differences, and give the distribution of maximum Lyapunov exponents in parameter-plane, which indicates the regions of non-chaotic states (non-positive LE) and chaotic states (positive LE).

  14. CHAOS: An SDN-Based Moving Target Defense System

    Directory of Open Access Journals (Sweden)

    Yuan Shi

    2017-01-01

    Full Text Available Moving target defense (MTD has provided a dynamic and proactive network defense to reduce or move the attack surface that is available for exploitation. However, traditional network is difficult to realize dynamic and active security defense effectively and comprehensively. Software-defined networking (SDN points out a brand-new path for building dynamic and proactive defense system. In this paper, we propose CHAOS, an SDN-based MTD system. Utilizing the programmability and flexibility of SDN, CHAOS obfuscates the attack surface including host mutation obfuscation, ports obfuscation, and obfuscation based on decoy servers, thereby enhancing the unpredictability of the networking environment. We propose the Chaos Tower Obfuscation (CTO method, which uses the Chaos Tower Structure (CTS to depict the hierarchy of all the hosts in an intranet and define expected connection and unexpected connection. Moreover, we develop fast CTO algorithms to achieve a different degree of obfuscation for the hosts in each layer. We design and implement CHAOS as an application of SDN controller. Our approach makes it very easy to realize moving target defense in networks. Our experimental results show that a network protected by CHAOS is capable of decreasing the percentage of information disclosure effectively to guarantee the normal flow of traffic.

  15. Spin squeezing as an indicator of quantum chaos in the Dicke model.

    Science.gov (United States)

    Song, Lijun; Yan, Dong; Ma, Jian; Wang, Xiaoguang

    2009-04-01

    We study spin squeezing, an intrinsic quantum property, in the Dicke model without the rotating-wave approximation. We show that the spin squeezing can reveal the underlying chaotic and regular structures in phase space given by a Poincaré section, namely, it acts as an indicator of quantum chaos. Spin squeezing vanishes after a very short time for an initial coherent state centered in a chaotic region, whereas it persists over a longer time for the coherent state centered in a regular region of the phase space. We also study the distribution of the mean spin directions when quantum dynamics takes place. Finally, we discuss relations among spin squeezing, bosonic quadrature squeezing, and two-qubit entanglement in the dynamical processes.

  16. 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...

  17. Controlling beam halo-chaos via backstepping design

    International Nuclear Information System (INIS)

    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

  18. Fast hydrogen exchange affects 15N relaxation measurements in intrinsically disordered proteins

    International Nuclear Information System (INIS)

    Kim, Seho; Wu, Kuen-Phon; Baum, Jean

    2013-01-01

    Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, 1 H– 15 N HSQC, is used to measure the 15 N transverse relaxation rate (R 2 ), the measured R 2 rate is convoluted with the HX rate (k HX ) and has higher apparent R 2 values. Since the 15 N R 2 measurement is important for analyzing protein backbone dynamics, the HX effect on the R 2 measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing 15 N R 2 CPMG experiments on α-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R 2 CPMG can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D 2 O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R 2 CPMG values be obtained by methods described herein.

  19. Chaos in the Solar System

    Science.gov (United States)

    Lecar, Myron; Franklin, Fred A.; Holman, Matthew J.; Murray, Norman J.

    2001-01-01

    The physical basis of chaos in the solar system is now better understood: In all cases investigated so far, chaotic orbits result from overlapping resonances. Perhaps the clearest examples are found in the asteroid belt. Overlapping resonances account for its kirkwood gaps and were used to predict and find evidence for very narrow gaps in the outer belt. Further afield, about one new "short-peroid" comet is discovered each year. They are believed to come from the "Kuiper Belt" (at 40 AU or more) via chaotic orbits produced by mean-motion and secular resonances with Neptune. Finally, the planetary system itself is not immune from chaos. In the inner solar system, overlapping secular resonances have been identified as the possible source of chaos. For example, Mercury in 1012 years, may suffer a close encounter with Venus or plunge into the Sun. In the outer solar system, three-body resonances have been identified as a source of chaos, but on an even longer time scale of 109 times the age of the solar system. On the human time scale, the planets do follow their orbits in a stately procession, and we can predict their trajectories for hundreds of thousands of years. That is because the mavericks, with shorter instability times, have long since been ejected. The solar system is not stable; it is just old!

  20. Hyperbolic Chaos A Physicist’s View

    CERN Document Server

    Kuznetsov, Sergey P

    2012-01-01

    "Hyperbolic Chaos: A Physicist’s View” presents recent progress on uniformly hyperbolic attractors in dynamical systems from a physical rather than mathematical perspective (e.g. the Plykin attractor, the Smale – Williams solenoid). The structurally stable attractors manifest strong stochastic properties, but are insensitive to variation of functions and parameters in the dynamical systems. Based on these characteristics of hyperbolic chaos, this monograph shows how to find hyperbolic chaotic attractors in physical systems and how to design a physical systems that possess hyperbolic chaos.   This book is designed as a reference work for university professors and researchers in the fields of physics, mechanics, and engineering.   Dr. Sergey P. Kuznetsov is a professor at the Department of Nonlinear Processes, Saratov State University, Russia.  

  1. The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

    Science.gov (United States)

    Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

    2015-10-26

    The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

  2. Effortful control and school adjustment: The moderating role of classroom chaos.

    Science.gov (United States)

    Berger, Rebecca H; Valiente, Carlos; Eisenberg, Nancy; Hernandez, Maciel M; Thompson, Marilyn; Spinrad, Tracy; VanSchyndel, Sarah; Silva, Kassondra; Southworth, Jody

    2017-11-01

    Guided by the person by environment framework, the primary goal of this study was to determine whether classroom chaos moderated the relation between effortful control and kindergarteners' school adjustment. Classroom observers reported on children's ( N = 301) effortful control in the fall. In the spring, teachers reported on classroom chaos and school adjustment outcomes (teacher-student relationship closeness and conflict, and school liking and avoidance). Cross-level interactions between effortful control and classroom chaos predicting school adjustment outcomes were assessed. A consistent pattern of interactions between effortful control and classroom chaos indicated that the relations between effortful control and the school adjustment outcomes were strongest in high chaos classrooms. Post-hoc analyses indicated that classroom chaos was associated with poor school adjustment when effortful control was low, suggesting that the combination of high chaos and low effortful control was associated with the poorest school outcomes.

  3. Chaos as a Social Determinant of Child Health: Reciprocal Associations?

    Science.gov (United States)

    Schmeer, Kammi K.; Taylor, Miles

    2013-01-01

    This study informs the social determinants of child health by exploring an understudied aspect of children’s social contexts: chaos. Chaos has been conceptualized as crowded, noisy, disorganized, unpredictable settings for child development (Evans et al., 2010). We measure chaos at two levels of children’s ecological environment - the microsystem (household) and the mesosystem (work-family-child care nexus) – and at two points in early childhood (ages 3 and 5). Using data from the Fragile Families and Child Wellbeing Study (N=3288), a study of predominantly low-income women and their partners in large US cities, we develop structural equation models that assess how maternal-rated child health (also assessed at ages 3 and 5) is associated with latent constructs of chaos, and whether there are important reciprocal effects. Autoregressive crosslagged path analysis suggest that increasing chaos (at both the household and maternal work levels) is associated with worse child health, controlling for key confounders like household economic status, family structure, and maternal health status. Child health has little effect on chaos, providing further support for the hypothesis that chaos is an important social determinant of child health in this sample of relatively disadvantaged children. This suggests child health may be improved by supporting families in ways that reduce chaos in their home and work/family environments, and that as researchers move beyond SES, race, and family structure to explore other sources of health inequalities, chaos and its proximate determinants may be a promising avenue for future research. PMID:23541250

  4. Chaos: Choto delat?

    Science.gov (United States)

    Campbell, David

    1987-11-01

    I provide a brief overview of the current status of the field of deterministic "chaos" stressing its interrelations and applications to other fields and suggesting a number of important open problems for future study.

  5. Chaos in plasma simulation and experiment

    International Nuclear Information System (INIS)

    Watts, C.; Sprott, J.C.

    1993-09-01

    We investigate the possibility that chaos and simple determinism are governing the dynamics of reversed field pinch (RFP) plasmas using data from both numerical simulations and experiment. A large repertoire of nonlinear analysis techniques is used to identify low dimensional chaos. These tools include phase portraits and Poincard sections, correlation dimension, the spectrum of Lyapunov exponents and short term predictability. In addition, nonlinear noise reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulate the plasma dynamics. These are -the DEBS code, which models global RFP dynamics, and the dissipative trapped electron mode (DTEM) model, which models drift wave turbulence. Data from both simulations show strong indications of low,dimensional chaos and simple determinism. Experimental data were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low dimensional chaos or other simple determinism. Moreover, most of the analysis tools indicate the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system

  6. Chaos in plasma simulation and experiment

    Energy Technology Data Exchange (ETDEWEB)

    Watts, C. [Texas Univ., Austin, TX (United States). Fusion Research Center; Newman, D.E. [Oak Ridge National Lab., TN (United States); Sprott, J.C. [Wisconsin Univ., Madison, WI (United States). Plasma Physics Research

    1993-09-01

    We investigate the possibility that chaos and simple determinism are governing the dynamics of reversed field pinch (RFP) plasmas using data from both numerical simulations and experiment. A large repertoire of nonlinear analysis techniques is used to identify low dimensional chaos. These tools include phase portraits and Poincard sections, correlation dimension, the spectrum of Lyapunov exponents and short term predictability. In addition, nonlinear noise reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulate the plasma dynamics. These are -the DEBS code, which models global RFP dynamics, and the dissipative trapped electron mode (DTEM) model, which models drift wave turbulence. Data from both simulations show strong indications of low,dimensional chaos and simple determinism. Experimental data were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low dimensional chaos or other simple determinism. Moreover, most of the analysis tools indicate the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system.

  7. How Robust Is the Mechanism of Folding-Upon-Binding for an Intrinsically Disordered Protein?

    Science.gov (United States)

    Bonetti, Daniela; Troilo, Francesca; Brunori, Maurizio; Longhi, Sonia; Gianni, Stefano

    2018-04-24

    The mechanism of interaction of an intrinsically disordered protein (IDP) with its physiological partner is characterized by a disorder-to-order transition in which a recognition and a binding step take place. Even if the mechanism is quite complex, IDPs tend to bind their partner in a cooperative manner such that it is generally possible to detect experimentally only the disordered unbound state and the structured complex. The interaction between the disordered C-terminal domain of the measles virus nucleoprotein (N TAIL ) and the X domain (XD) of the viral phosphoprotein allows us to detect and quantify the two distinct steps of the overall reaction. Here, we analyze the robustness of the folding of N TAIL upon binding to XD by measuring the effect on both the folding and binding steps of N TAIL when the structure of XD is modified. Because it has been shown that wild-type XD is structurally heterogeneous, populating an on-pathway intermediate under native conditions, we investigated the binding to 11 different site-directed variants of N TAIL of one particular variant of XD (I504A XD) that populates only the native state. Data reveal that the recognition and the folding steps are both affected by the structure of XD, indicating a highly malleable pathway. The experimental results are briefly discussed in the light of previous experiments on other IDPs. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  8. On the efficiency of chaos optimization algorithms for global optimization

    International Nuclear Information System (INIS)

    Yang Dixiong; Li Gang; Cheng Gengdong

    2007-01-01

    Chaos optimization algorithms as a novel method of global optimization have attracted much attention, which were all based on Logistic map. However, we have noticed that the probability density function of the chaotic sequences derived from Logistic map is a Chebyshev-type one, which may affect the global searching capacity and computational efficiency of chaos optimization algorithms considerably. Considering the statistical property of the chaotic sequences of Logistic map and Kent map, the improved hybrid chaos-BFGS optimization algorithm and the Kent map based hybrid chaos-BFGS algorithm are proposed. Five typical nonlinear functions with multimodal characteristic are tested to compare the performance of five hybrid optimization algorithms, which are the conventional Logistic map based chaos-BFGS algorithm, improved Logistic map based chaos-BFGS algorithm, Kent map based chaos-BFGS algorithm, Monte Carlo-BFGS algorithm, mesh-BFGS algorithm. The computational performance of the five algorithms is compared, and the numerical results make us question the high efficiency of the chaos optimization algorithms claimed in some references. It is concluded that the efficiency of the hybrid optimization algorithms is influenced by the statistical property of chaotic/stochastic sequences generated from chaotic/stochastic algorithms, and the location of the global optimum of nonlinear functions. In addition, it is inappropriate to advocate the high efficiency of the global optimization algorithms only depending on several numerical examples of low-dimensional functions

  9. Targeting the intrinsically disordered structural ensemble of α-synuclein by small molecules as a potential therapeutic strategy for Parkinson's disease.

    Directory of Open Access Journals (Sweden)

    Gergely Tóth

    Full Text Available The misfolding of intrinsically disordered proteins such as α-synuclein, tau and the Aβ peptide has been associated with many highly debilitating neurodegenerative syndromes including Parkinson's and Alzheimer's diseases. Therapeutic targeting of the monomeric state of such intrinsically disordered proteins by small molecules has, however, been a major challenge because of their heterogeneous conformational properties. We show here that a combination of computational and experimental techniques has led to the identification of a drug-like phenyl-sulfonamide compound (ELN484228, that targets α-synuclein, a key protein in Parkinson's disease. We found that this compound has substantial biological activity in cellular models of α-synuclein-mediated dysfunction, including rescue of α-synuclein-induced disruption of vesicle trafficking and dopaminergic neuronal loss and neurite retraction most likely by reducing the amount of α-synuclein targeted to sites of vesicle mobilization such as the synapse in neurons or the site of bead engulfment in microglial cells. These results indicate that targeting α-synuclein by small molecules represents a promising approach to the development of therapeutic treatments of Parkinson's disease and related conditions.

  10. 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.

  11. 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

  12. Philosophical perspectives on quantum chaos: Models and interpretations

    Science.gov (United States)

    Bokulich, Alisa Nicole

    2001-09-01

    The problem of quantum chaos is a special case of the larger problem of understanding how the classical world emerges from quantum mechanics. While we have learned that chaos is pervasive in classical systems, it appears to be almost entirely absent in quantum systems. The aim of this dissertation is to determine what implications the interpretation of quantum mechanics has for attempts to explain the emergence of classical chaos. There are three interpretations of quantum mechanics that have set out programs for solving the problem of quantum chaos: the standard interpretation, the statistical interpretation, and the deBroglie-Bohm causal interpretation. One of the main conclusions of this dissertation is that an interpretation alone is insufficient for solving the problem of quantum chaos and that the phenomenon of decoherence must be taken into account. Although a completely satisfactory solution of the problem of quantum chaos is still outstanding, I argue that the deBroglie-Bohm interpretation with the help of decoherence outlines the most promising research program to pursue. In addition to making a contribution to the debate in the philosophy of physics concerning the interpretation of quantum mechanics, this dissertation reveals two important methodological lessons for the philosophy of science. First, issues of reductionism and intertheoretic relations cannot be divorced from questions concerning the interpretation of the theories involved. Not only is the exploration of intertheoretic relations a central part of the articulation and interpretation of an individual theory, but the very terms used to discuss intertheoretic relations, such as `state' and `classical limit', are themselves defined by particular interpretations of the theory. The second lesson that emerges is that, when it comes to characterizing the relationship between classical chaos and quantum mechanics, the traditional approaches to intertheoretic relations, namely reductionism and

  13. True quantum chaos? An instructive example

    International Nuclear Information System (INIS)

    Berry, M.V.

    1992-01-01

    Any chaotic classical system can be transformed into a quantum system that preserves the chaos, because the classical Liouville equation involving 2Ν phase-space variables q ,p has the form of a 'Schroedinger equation' with 'coordinates' Q=[q,p]. The feature of this quantum system that allows chaos to persist is linarity of the Hamiltonian' in the 2Ν 'momentum' operators conjugate to Q. (orig.)

  14. A Fragment-Based Method of Creating Small-Molecule Libraries to Target the Aggregation of Intrinsically Disordered Proteins.

    Science.gov (United States)

    Joshi, Priyanka; Chia, Sean; Habchi, Johnny; Knowles, Tuomas P J; Dobson, Christopher M; Vendruscolo, Michele

    2016-03-14

    The aggregation process of intrinsically disordered proteins (IDPs) has been associated with a wide range of neurodegenerative disorders, including Alzheimer's and Parkinson's diseases. Currently, however, no drug in clinical use targets IDP aggregation. To facilitate drug discovery programs in this important and challenging area, we describe a fragment-based approach of generating small-molecule libraries that target specific IDPs. The method is based on the use of molecular fragments extracted from compounds reported in the literature to inhibit of the aggregation of IDPs. These fragments are used to screen existing large generic libraries of small molecules to form smaller libraries specific for given IDPs. We illustrate this approach by describing three distinct small-molecule libraries to target, Aβ, tau, and α-synuclein, which are three IDPs implicated in Alzheimer's and Parkinson's diseases. The strategy described here offers novel opportunities for the identification of effective molecular scaffolds for drug discovery for neurodegenerative disorders and to provide insights into the mechanism of small-molecule binding to IDPs.

  15. Discrete chaos with applications in science and engineering

    CERN Document Server

    Elaydi, Saber N

    2007-01-01

    PREFACE FOREWORD The Stability of One-Dimensional Maps Introduction Maps vs. Difference Equations Maps vs. Differential Equations Linear Maps/Difference Equations Fixed (Equilibrium) Points Graphical Iteration and Stability Criteria for Stability Periodic Points and Their Stability The Period-Doubling Route to Chaos Applications Attraction and Bifurcation Introduction Basin of Attraction of Fixed Points Basin of Attraction of Periodic Orbits Singer's Theorem Bifurcation Sharkovsky's Theorem The Lorenz Map Period-Doubling in the Real World Poincaré Section/Map Appendix Chaos in One Dimension Introduction Density of the Set of Periodic Points Transitivity Sensitive Dependence Definition of Chaos Cantor Sets Symbolic Dynamics Conjugacy Other Notions of Chaos Rössler's Attractor Saturn's Rings Stability of Two-Dimensional Maps Linear Maps vs. Linear Systems Computing An Fundamental Set of Solutions Second-Order Difference Equations Phase Space ...

  16. Random matrices and chaos in nuclear physics: Nuclear structure

    International Nuclear Information System (INIS)

    Weidenmueller, H. A.; Mitchell, G. E.

    2009-01-01

    Evidence for the applicability of random-matrix theory to nuclear spectra is reviewed. In analogy to systems with few degrees of freedom, one speaks of chaos (more accurately, quantum chaos) in nuclei whenever random-matrix predictions are fulfilled. An introduction into the basic concepts of random-matrix theory is followed by a survey over the extant experimental information on spectral fluctuations, including a discussion of the violation of a symmetry or invariance property. Chaos in nuclear models is discussed for the spherical shell model, for the deformed shell model, and for the interacting boson model. Evidence for chaos also comes from random-matrix ensembles patterned after the shell model such as the embedded two-body ensemble, the two-body random ensemble, and the constrained ensembles. All this evidence points to the fact that chaos is a generic property of nuclear spectra, except for the ground-state regions of strongly deformed nuclei.

  17. Gullies of Gorgonus Chaos

    Science.gov (United States)

    2002-01-01

    (Released 11 June 2002) The Science This fractured surface belongs to a portion of a region called Gorgonum Chaos located in the southern hemisphere of Mars. Gorgonum Chaos is named after the Gorgons in ancient Greek mythology. The Gorgons were monstrous sisters with snakes for hair, tusks like boars and lolling tongues who lived in caves. As it turns out this is indeed a fitting name for this region of Mars because it contains a high density of gullies that 'snake' their way down the walls of the troughs located in this region of chaos. Upon closer examination one finds that these gullies and alluvial deposits, initially discovered by Mars Global Surveyor, are visible on the trough walls (best seen near the bottom of the image). These gullies appear to emanate from a specific layer in the walls. The gullies have been proposed to have formed by the subsurface release of water. The Story This fractured, almost spooky-looking surface belongs to a region called Gorgonum Chaos in the southern hemisphere of Mars. Chaos is a term used for regions of Mars with distinctive areas of broken terrain like the one seen above. This area of Martian chaos is named after the Gorgons in ancient Greek mythology. The Gorgons were monstrous sisters with snakes for hair, tusks like boars, and lolling tongues, who lived in caves. The Gorgons, including famous sister Medusa, could turn a person to stone, and their writhing, snakelike locks cause revulsion to this day. Given the afflicted nature of this contorted terrain, with all of its twisted, branching channels and hard, stony-looking hills in the top half of the image, this is indeed a fitting name for this region of Mars. The name also has great appeal, because the area contains a high density of gullies that 'snake' their way down the walls of the troughs located in this region of Martian chaos. Gullies are trenches cut into the land as accelerated streams of water (or another liquid) erode the surface. To see these, click on the

  18. Some remarks on chaos in topological dynamics

    Directory of Open Access Journals (Sweden)

    Huoyung Wang

    2011-10-01

    Full Text Available Bau-Sen Du introduced a notion of chaos which is stronger than Li-Yorke sensitivity. A TDS (X, f is called chaotic if there is a positive e such that for any x and any nonempty open set V of X there is a point y in V such that the pair (x, y is proximal but not e-asymptotic. In this article, we show that a TDS (T, f is transitive but not mixing if and only if (T, f is Li-Yorke sensitive but not chaotic, where T is a tree. Moreover, we compare such chaos with other notions of chaos.

  19. Quantum chaos induced by nonadiabatic coupling in wave-packet dynamics

    International Nuclear Information System (INIS)

    Higuchi, Hisashi; Takatsuka, Kazuo

    2002-01-01

    The effect of nonadiabatic coupling due to breakdown of the Born-Oppenheimer approximation on chaos is investigated. A couple of measures (indicators) that detect the extent of chaos in wave-packet dynamics on coupled potential functions are devised. Using them, we show that chaos is indeed induced by a nonadiabatic coupling in individual time-dependent wave-packet dynamics. This chaos is genuinely of quantum nature, since it arises from bifurcation and merging of a wave packet at the quasicrossing region of two coupled potential functions

  20. 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.

  1. Chaos control using sliding-mode theory

    International Nuclear Information System (INIS)

    Nazzal, Jamal M.; Natsheh, Ammar N.

    2007-01-01

    Chaos control means to design a controller that is able to mitigating or eliminating the chaos behavior of nonlinear systems that experiencing such phenomenon. In this paper, a nonlinear Sliding-Mode Controller (SMC) is presented. Two nonlinear chaotic systems are chosen to be our case study in this paper, the well known Chua's circuit and Lorenz system. The study shows the effectiveness of the designed nonlinear Sliding-Mode Controller

  2. Polynomiography and Chaos

    Science.gov (United States)

    Kalantari, Bahman

    Polynomiography is the algorithmic visualization of iterative systems for computing roots of a complex polynomial. It is well known that iterations of a rational function in the complex plane result in chaotic behavior near its Julia set. In one scheme of computing polynomiography for a given polynomial p(z), we select an individual member from the Basic Family, an infinite fundamental family of rational iteration functions that in particular include Newton's. Polynomiography is an excellent means for observing, understanding, and comparing chaotic behavior for variety of iterative systems. Other iterative schemes in polynomiography are possible and result in chaotic behavior of different kinds. In another scheme, the Basic Family is collectively applied to p(z) and the iterates for any seed in the Voronoi cell of a root converge to that root. Polynomiography reveals chaotic behavior of another kind near the boundary of the Voronoi diagram of the roots. We also describe a novel Newton-Ellipsoid iterative system with its own chaos and exhibit images demonstrating polynomiographies of chaotic behavior of different kinds. Finally, we consider chaos for the more general case of polynomiography of complex analytic functions. On the one hand polynomiography is a powerful medium capable of demonstrating chaos in different forms, it is educationally instructive to students and researchers, also it gives rise to numerous research problems. On the other hand, it is a medium resulting in images with enormous aesthetic appeal to general audiences.

  3. Collision analysis of one kind of chaos-based hash function

    International Nuclear Information System (INIS)

    Xiao Di; Peng Wenbing; Liao Xiaofeng; Xiang Tao

    2010-01-01

    In the last decade, various chaos-based hash functions have been proposed. Nevertheless, the corresponding analyses of them lag far behind. In this Letter, we firstly take a chaos-based hash function proposed very recently in Amin, Faragallah and Abd El-Latif (2009) as a sample to analyze its computational collision problem, and then generalize the construction method of one kind of chaos-based hash function and summarize some attentions to avoid the collision problem. It is beneficial to the hash function design based on chaos in the future.

  4. Congenital high airway obstruction syndrome (CHAOS) associated with cervical myelomeningocele.

    Science.gov (United States)

    Adin, Mehmet Emin

    2017-10-01

    Congenital high airway obstruction syndrome (CHAOS) is a rare and potentially fatal entity resulting from complete or near complete developmental airway obstruction. Although most reported cases of CHAOS are sporadic, the condition may also be associated with certain syndromes and a variety of cervical masses. Meningocele and myelomeningocele have not yet been reported in association with CHAOS. We describe the typical constellation of sonographic findings in a case of early diagnosis of CHAOS associated with cervical myelomeningocele. © 2016 Wiley Periodicals, Inc. J Clin Ultrasound 45:507-510, 2017. © 2016 Wiley Periodicals, Inc.

  5. Chaos analysis and chaotic EMI suppression of DC-DC converters

    CERN Document Server

    Zhang, Bo

    2014-01-01

    Introduces chaos theory, its analytical methods and the means to apply chaos to the switching power supply design DC-DC converters are typical switching systems which have plenty of nonlinear behaviors, such as bifurcation and chaos. The nonlinear behaviors of DC-DC converters have been studied heavily over the past 20 years, yet researchers are still unsure of the practical application of bifurcations and chaos in switching converters. The electromagnetic interference (EMI), which resulted from the high rates of changes of voltage and current, has become a major design criterion in DC-DC co

  6. Colloquium: Random matrices and chaos in nuclear spectra

    International Nuclear Information System (INIS)

    Papenbrock, T.; Weidenmueller, H. A.

    2007-01-01

    Chaos occurs in quantum systems if the statistical properties of the eigenvalue spectrum coincide with predictions of random-matrix theory. Chaos is a typical feature of atomic nuclei and other self-bound Fermi systems. How can the existence of chaos be reconciled with the known dynamical features of spherical nuclei? Such nuclei are described by the shell model (a mean-field theory) plus a residual interaction. The question is answered using a statistical approach (the two-body random ensemble): The matrix elements of the residual interaction are taken to be random variables. Chaos is shown to be a generic feature of the ensemble and some of its properties are displayed, emphasizing those which differ from standard random-matrix theory. In particular, the existence of correlations among spectra carrying different quantum numbers is demonstrated. These are subject to experimental verification

  7. Effects of maturation and acidosis on the chaos-like complexity of the neural respiratory output in the isolated brainstem of the tadpole, Rana esculenta.

    Science.gov (United States)

    Straus, Christian; Samara, Ziyad; Fiamma, Marie-Noëlle; Bautin, Nathalie; Ranohavimparany, Anja; Le Coz, Patrick; Golmard, Jean-Louis; Darré, Pierre; Zelter, Marc; Poon, Chi-Sang; Similowski, Thomas

    2011-05-01

    Human ventilation at rest exhibits mathematical chaos-like complexity that can be described as long-term unpredictability mediated (in whole or in part) by some low-dimensional nonlinear deterministic process. Although various physiological and pathological situations can affect respiratory complexity, the underlying mechanisms remain incompletely elucidated. If such chaos-like complexity is an intrinsic property of central respiratory generators, it should appear or increase when these structures mature or are stimulated. To test this hypothesis, we employed the isolated tadpole brainstem model [Rana (Pelophylax) esculenta] and recorded the neural respiratory output (buccal and lung rhythms) of pre- (n = 8) and postmetamorphic tadpoles (n = 8), at physiologic (7.8) and acidic pH (7.4). We analyzed the root mean square of the cranial nerve V or VII neurograms. Development and acidosis had no effect on buccal period. Lung frequency increased with development (P acidosis, but in postmetamorphic tadpoles only (P respiratory central rhythm generator accounts for ventilatory chaos-like complexity, especially in the postmetamorphic stage and at low pH. According to the ventilatory generators homology theory, this may also be the case in mammals.

  8. Bifurcation and chaos in neural excitable system

    International Nuclear Information System (INIS)

    Jing Zhujun; Yang Jianping; Feng Wei

    2006-01-01

    In this paper, we investigate the dynamical behaviors of neural excitable system without periodic external current (proposed by Chialvo [Generic excitable dynamics on a two-dimensional map. Chaos, Solitons and Fractals 1995;5(3-4):461-79] and with periodic external current as system's parameters vary. The existence and stability of three fixed points, bifurcation of fixed points, the conditions of existences of fold bifurcation, flip bifurcation and Hopf bifurcation are derived by using bifurcation theory and center manifold theorem. The chaotic existence in the sense of Marotto's definition of chaos is proved. We then give the numerical simulated results (using bifurcation diagrams, computations of Maximum Lyapunov exponent and phase portraits), which not only show the consistence with the analytic results but also display new and interesting dynamical behaviors, including the complete period-doubling and inverse period-doubling bifurcation, symmetry period-doubling bifurcations of period-3 orbit, simultaneous occurrence of two different routes (invariant cycle and period-doubling bifurcations) to chaos for a given bifurcation parameter, sudden disappearance of chaos at one critical point, a great abundance of period windows (period 2 to 10, 12, 19, 20 orbits, and so on) in transient chaotic regions with interior crises, strange chaotic attractors and strange non-chaotic attractor. In particular, the parameter k plays a important role in the system, which can leave the chaotic behavior or the quasi-periodic behavior to period-1 orbit as k varies, and it can be considered as an control strategy of chaos by adjusting the parameter k. Combining the existing results in [Generic excitable dynamics on a two-dimensional map. Chaos, Solitons and Fractals 1995;5(3-4):461-79] with the new results reported in this paper, a more complete description of the system is now obtained

  9. Hamiltonian Chaos and Fractional Dynamics

    International Nuclear Information System (INIS)

    Combescure, M

    2005-01-01

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

  10. Chaos in nuclei: Theory and experiment

    Science.gov (United States)

    Muñoz, L.; Molina, R. A.; Gómez, J. M. G.

    2018-05-01

    During the last three decades the quest for chaos in nuclei has been quite intensive, both with theoretical calculations using nuclear models and with detailed analyses of experimental data. In this paper we outline the concept and characteristics of quantum chaos in two different approaches, the random matrix theory fluctuations and the time series fluctuations. Then we discuss the theoretical and experimental evidence of chaos in nuclei. Theoretical calculations, especially shell-model calculations, have shown a strongly chaotic behavior of bound states in regions of high level density. The analysis of experimental data has shown a strongly chaotic behavior of nuclear resonances just above the one-nucleon emission threshold. For bound states, combining experimental data of a large number of nuclei, a tendency towards chaotic motion is observed in spherical nuclei, while deformed nuclei exhibit a more regular behavior associated to the collective motion. On the other hand, it had never been possible to observe chaos in the experimental bound energy levels of any single nucleus. However, the complete experimental spectrum of the first 151 states up to excitation energies of 6.20 MeV in the 208Pb nucleus have been recently identified and the analysis of its spectral fluctuations clearly shows the existence of chaotic motion.

  11. Stochastic chaos in a Duffing oscillator and its control

    International Nuclear Information System (INIS)

    Wu Cunli; Lei Youming; Fang Tong

    2006-01-01

    Stochastic chaos discussed here means a kind of chaotic responses in a Duffing oscillator with bounded random parameters under harmonic excitations. A system with random parameters is usually called a stochastic system. The modifier 'stochastic' here implies dependent on some random parameter. As the system itself is stochastic, so is the response, even under harmonic excitations alone. In this paper stochastic chaos and its control are verified by the top Lyapunov exponent of the system. A non-feedback control strategy is adopted here by adding an adjustable noisy phase to the harmonic excitation, so that the control can be realized by adjusting the noise level. It is found that by this control strategy stochastic chaos can be tamed down to the small neighborhood of a periodic trajectory or an equilibrium state. In the analysis the stochastic Duffing oscillator is first transformed into an equivalent deterministic nonlinear system by the Gegenbauer polynomial approximation, so that the problem of controlling stochastic chaos can be reduced into the problem of controlling deterministic chaos in the equivalent system. Then the top Lyapunov exponent of the equivalent system is obtained by Wolf's method to examine the chaotic behavior of the response. Numerical simulations show that the random phase control strategy is an effective way to control stochastic chaos

  12. Handbook of Chaos Control

    CERN Document Server

    Schuster, H G

    2008-01-01

    This long-awaited revised second edition of the standard reference on the subject has been considerably expanded to include such recent developments as novel control schemes, control of chaotic space-time patterns, control of noisy nonlinear systems, and communication with chaos, as well as promising new directions in research. The contributions from leading international scientists active in the field provide a comprehensive overview of our current level of knowledge on chaos control and its applications in physics, chemistry, biology, medicine, and engineering. In addition, they show the overlap with the traditional field of control theory in the engineering community.An interdisciplinary approach of interest to scientists and engineers working in a number of areas

  13. Chaos Theory as a Model for Managing Issues and Crises.

    Science.gov (United States)

    Murphy, Priscilla

    1996-01-01

    Uses chaos theory to model public relations situations in which the salient feature is volatility of public perceptions. Discusses the premises of chaos theory and applies them to issues management, the evolution of interest groups, crises, and rumors. Concludes that chaos theory is useful as an analogy to structure image problems and to raise…

  14. 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…

  15. Chaos in the fractional order Chen system and its control

    International Nuclear Information System (INIS)

    Li Chunguang; Chen Guanrong

    2004-01-01

    In this letter, we study the chaotic behaviors in the fractional order Chen system. We found that chaos exists in the fractional order Chen system with order less than 3. The lowest order we found to have chaos in this system is 2.1. Linear feedback control of chaos in this system is also studied

  16. The Nature (and Nurture) of Children's Perceptions of Family Chaos

    Science.gov (United States)

    Hanscombe, Ken B.; Haworth, Claire M. A.; Davis, Oliver S. P.; Jaffee, Sara R.; Plomin, Robert

    2010-01-01

    Chaos in the home is a key environment in cognitive and behavioural development. However, we show that children's experience of home chaos is partly genetically mediated. We assessed children's perceptions of household chaos at ages 9 and 12 in 2337 pairs of twins. Using child-specific reports allowed us to use structural equation modelling to…

  17. Experimental study of chaos synchronization in the Belousov-Zhabotinsky chemical system

    International Nuclear Information System (INIS)

    Li Yanni; Chen Lan; Cai Zunsheng; Zhao Xuezhuang

    2004-01-01

    Employing self-adaptive parameter regulation scheme, chaos synchronization in the Belousov-Zhabotinsky-CSTR chemical system has been studied experimentally. By optimizing the combination of regulation parameters, the trend of chaos synchronization is observed and the prediction of chaos synchronization from numerical simulation is thus verified by the experiment. In addition, the difference of sensitivity to noise with the mass coupling scheme and the self-adaptive parameter regulation scheme in chaos synchronization has also been discussed

  18. Scaling properties of localized quantum chaos

    International Nuclear Information System (INIS)

    Izrailev, F.M.

    1991-01-01

    Statistical properties of spectra and eigenfunctions are studied for the model of quantum chaos in the presence of dynamical localization. The main attention is paid to the scaling properties of localization length and level spacing distribution in the intermediate region between Poissonian and Wigner-Dyson statistics. It is shown that main features of such localized quantum chaos are well described by the introduced ensemble of band random matrices. 28 refs.; 7 figs

  19. Individual chaos implies collective chaos for weakly mixing discrete dynamical systems

    International Nuclear Information System (INIS)

    Liao Gongfu; Ma Xianfeng; Wang Lidong

    2007-01-01

    Let X be a metric space (X,f) a discrete dynamical system, where f:X->X is a continuous function. Let f-bar denote the natural extension of f to the space of all non-empty compact subsets of X endowed with Hausdorff metric induced by d. In this paper we investigate some dynamical properties of f and f-bar . It is proved that f is weakly mixing (mixing) if and only if f-bar is weakly mixing (mixing, respectively). From this, we deduce that weak-mixing of f implies transitivity of f-bar , further, if f is mixing or weakly mixing, then chaoticity of f (individual chaos) implies chaoticity of f-bar (collective chaos) and if X is a closed interval then f-bar is chaotic (in the sense of Devaney) if and only if f is weakly mixing

  20. Chaos in high-power high-frequency gyrotrons

    International Nuclear Information System (INIS)

    Airila, M.

    2004-01-01

    Gyrotron interaction is a complex nonlinear dynamical process, which may turn chaotic in certain circumstances. The emergence of chaos renders dynamical systems unpredictable and causes bandwidth broadening of signals. Such effects would jeopardize the prospect of advanced gyrotrons in fusion. Therefore, it is important to be aware of the possibility of chaos in gyrotrons. There are three different chaos scenarios closely related to the development of high-power gyrotrons: First, the onset of chaos in electron trajectories would lead to difficulties in the design and efficient operation of depressed potential collectors, which are used for efficiency enhancement. Second, the radio-frequency signal could turn chaotic, decreasing the output power and the spectral purity of the output signal. As a result, mode conversion, transmission, and absorption efficiencies would be reduced. Third, spatio-temporal chaos in the resonator field structure can set a limit for the use of large-diameter interaction cavities and high-order TE modes (large azimuthal index) allowing higher generated power. In this thesis, the issues above are addressed with numerical modeling. It is found that chaos in electron residual energies is practically absent in the parameter region corresponding to high efficiency. Accordingly, depressed collectors are a feasible solution also in advanced high-power gyrotrons. A new method is presented for straightforward numerical solution of the one-dimensional self-consistent time-dependent gyrotron equations, and the method is generalized to two dimensions. In 1D, a chart of gyrotron oscillations is calculated. It is shown that the regions of stationary oscillations, automodulation, and chaos have a complicated topology in the plane of generalized gyrotron variables. The threshold current for chaotic oscillations exceeds typical operating currents by a factor of ten. However, reflection of the output signal may significantly lower the threshold. 2D

  1. Calculating topological entropy for transient chaos with an application to communicating with chaos

    International Nuclear Information System (INIS)

    Jacobs, J.; Ott, E.; Hunt, B.R.

    1998-01-01

    Recent work on communicating with chaos provides a practical motivation for being able to determine numerically the topological entropy for chaotic invariant sets. In this paper we discuss numerical methods for evaluating topological entropy. To assess the accuracy and convergence of the methods, we test them in situations where the topological entropy is known independently. We also discuss the entropy of invariant chaotic saddles formed by those points in a given attractor that never visit some forbidden 'gap' region. Such gaps have been proposed as a means of providing noise immunity in schemes for communication with chaos, and we discuss the dependence of the topological entropy on the size of the gap. copyright 1998 The American Physical Society

  2. The Chaos of Katrina

    National Research Council Canada - National Science Library

    Morris, Jr, Gerald W

    2007-01-01

    .... The study investigates whether chaos theory, part of complexity science, can extract information from Katrina contracting data to help managers make better logistics decisions during disaster relief operations...

  3. Generic superweak chaos induced by Hall effect

    Science.gov (United States)

    Ben-Harush, Moti; Dana, Itzhack

    2016-05-01

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

  4. Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder.

    Science.gov (United States)

    Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

    2018-04-01

    Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC-vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder.

  5. Multimodal Investigation of Network Level Effects Using Intrinsic Functional Connectivity, Anatomical Covariance, and Structure-to-Function Correlations in Unmedicated Major Depressive Disorder

    Science.gov (United States)

    Scheinost, Dustin; Holmes, Sophie E; DellaGioia, Nicole; Schleifer, Charlie; Matuskey, David; Abdallah, Chadi G; Hampson, Michelle; Krystal, John H; Anticevic, Alan; Esterlis, Irina

    2018-01-01

    Converging evidence suggests that major depressive disorder (MDD) affects multiple large-scale brain networks. Analyses of the correlation or covariance of regional brain structure and function applied to structural and functional MRI data may provide insights into systems-level organization and structure-to-function correlations in the brain in MDD. This study applied tensor-based morphometry and intrinsic connectivity distribution to identify regions of altered volume and intrinsic functional connectivity in data from unmedicated individuals with MDD (n=17) and healthy comparison participants (HC, n=20). These regions were then used as seeds for exploratory anatomical covariance and connectivity analyses. Reduction in volume in the anterior cingulate cortex (ACC) and lower structural covariance between the ACC and the cerebellum were observed in the MDD group. Additionally, individuals with MDD had significantly lower whole-brain intrinsic functional connectivity in the medial prefrontal cortex (mPFC). This mPFC region showed altered connectivity to the ventral lateral PFC (vlPFC) and local circuitry in MDD. Global connectivity in the ACC was negatively correlated with reported depressive symptomatology. The mPFC–vlPFC connectivity was positively correlated with depressive symptoms. Finally, we observed increased structure-to-function correlation in the PFC/ACC in the MDD group. Although across all analysis methods and modalities alterations in the PFC/ACC were a common finding, each modality and method detected alterations in subregions belonging to distinct large-scale brain networks. These exploratory results support the hypothesis that MDD is a systems level disorder affecting multiple brain networks located in the PFC and provide new insights into the pathophysiology of this disorder. PMID:28944772

  6. Generalized Statistical Mechanics at the Onset of Chaos

    Directory of Open Access Journals (Sweden)

    Alberto Robledo

    2013-11-01

    Full Text Available Transitions to chaos in archetypal low-dimensional nonlinear maps offer real and precise model systems in which to assess proposed generalizations of statistical mechanics. The known association of chaotic dynamics with the structure of Boltzmann–Gibbs (BG statistical mechanics has suggested the potential verification of these generalizations at the onset of chaos, when the only Lyapunov exponent vanishes and ergodic and mixing properties cease to hold. There are three well-known routes to chaos in these deterministic dissipative systems, period-doubling, quasi-periodicity and intermittency, which provide the setting in which to explore the limit of validity of the standard BG structure. It has been shown that there is a rich and intricate behavior for both the dynamics within and towards the attractors at the onset of chaos and that these two kinds of properties are linked via generalized statistical-mechanical expressions. Amongst the topics presented are: (i permanently growing sensitivity fluctuations and their infinite family of generalized Pesin identities; (ii the emergence of statistical-mechanical structures in the dynamics along the routes to chaos; (iii dynamical hierarchies with modular organization; and (iv limit distributions of sums of deterministic variables. The occurrence of generalized entropy properties in condensed-matter physical systems is illustrated by considering critical fluctuations, localization transition and glass formation. We complete our presentation with the description of the manifestations of the dynamics at the transitions to chaos in various kinds of complex systems, such as, frequency and size rank distributions and complex network images of time series. We discuss the results.

  7. Design of High-Security USB Flash Drives Based on Chaos Authentication

    Directory of Open Access Journals (Sweden)

    Teh-Lu Liao

    2018-05-01

    Full Text Available This paper aims to propose a novel design of high-security USB flash drives with the chaos authentication. A chaos authentication approach with the non-linear encryption and decryption function design is newly proposed and realized based on the controller design of chaos synchronization. To complete the design of high-security USB flash drives, first, we introduce six parameters into the original Henon map to adjust and obtain richer chaotic state responses. Then a discrete sliding mode scheme is proposed to solve the synchronization problem of discrete hyperchaotic Henon maps. The proposed sliding mode controller can ensure the synchronization of the master-slave Henon maps. The selection of the switching surface and the existence of the sliding motion are also addressed. Finally, the obtained results are applied to design a new high-security USB flash drive with chaos authentication. We built discrete hyperchaotic Henon maps in the smartphone (master and microcontroller (slave, respectively. The Bluetooth module is used to communicate between the master and the slave to achieve chaos synchronization such that the same random and dynamical chaos signal can be simultaneously obtained at both the USB flash drive and smartphone, and pass the chaos authentication. When users need to access data in the flash drive, they can easily enable the encryption APP in the smartphone (master for chaos authentication. After completing the chaos synchronization and authentication, the ARM-based microcontroller allows the computer to access the data in the high-security USB flash drive.

  8. Chaos: A Topic for Interdisciplinary Education in Physics

    Science.gov (United States)

    Bae, Saebyok

    2009-01-01

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

  9. Controlling chaos faster

    International Nuclear Information System (INIS)

    Bick, Christian; Kolodziejski, Christoph; Timme, Marc

    2014-01-01

    Predictive feedback control is an easy-to-implement method to stabilize unknown unstable periodic orbits in chaotic dynamical systems. Predictive feedback control is severely limited because asymptotic convergence speed decreases with stronger instabilities which in turn are typical for larger target periods, rendering it harder to effectively stabilize periodic orbits of large period. Here, we study stalled chaos control, where the application of control is stalled to make use of the chaotic, uncontrolled dynamics, and introduce an adaptation paradigm to overcome this limitation and speed up convergence. This modified control scheme is not only capable of stabilizing more periodic orbits than the original predictive feedback control but also speeds up convergence for typical chaotic maps, as illustrated in both theory and application. The proposed adaptation scheme provides a way to tune parameters online, yielding a broadly applicable, fast chaos control that converges reliably, even for periodic orbits of large period

  10. Fascination of chaos

    International Nuclear Information System (INIS)

    Loskutov, Alexander

    2010-01-01

    This review introduces most of the concepts used in the study of chaotic phenomena in nonlinear systems and has as its objective to summarize the current understanding of results from the theory of chaotic dynamical systems and to describe the original ideas underlying the study of deterministic chaos. The presentation relies on informal analysis, with abstract mathematical ideas visualized geometrically or by examples from physics. Hyperbolic dynamics, homoclinic trajectories and tangencies, wild hyperbolic sets, and different types of attractors which appear in dynamical systems are considered. The key aspects of ergodic theory are discussed, and the basic statistical properties of chaotic dynamical systems are described. The fundamental difference between stochastic dynamics and deterministic chaos is explained. The review concludes with an investigation of the possibility of studying complex systems on the basis of the analysis of registered signals, i.e. the generated time series. (reviews of topical problems)

  11. Controlling chaos faster.

    Science.gov (United States)

    Bick, Christian; Kolodziejski, Christoph; Timme, Marc

    2014-09-01

    Predictive feedback control is an easy-to-implement method to stabilize unknown unstable periodic orbits in chaotic dynamical systems. Predictive feedback control is severely limited because asymptotic convergence speed decreases with stronger instabilities which in turn are typical for larger target periods, rendering it harder to effectively stabilize periodic orbits of large period. Here, we study stalled chaos control, where the application of control is stalled to make use of the chaotic, uncontrolled dynamics, and introduce an adaptation paradigm to overcome this limitation and speed up convergence. This modified control scheme is not only capable of stabilizing more periodic orbits than the original predictive feedback control but also speeds up convergence for typical chaotic maps, as illustrated in both theory and application. The proposed adaptation scheme provides a way to tune parameters online, yielding a broadly applicable, fast chaos control that converges reliably, even for periodic orbits of large period.

  12. Controlling chaos faster

    Energy Technology Data Exchange (ETDEWEB)

    Bick, Christian [Network Dynamics, Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen (Germany); Bernstein Center for Computational Neuroscience (BCCN), 37077 Göttingen (Germany); Institute for Mathematics, Georg–August–Universität Göttingen, 37073 Göttingen (Germany); Kolodziejski, Christoph [Network Dynamics, Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen (Germany); III. Physical Institute—Biophysics, Georg–August–Universität Göttingen, 37077 Göttingen (Germany); Timme, Marc [Network Dynamics, Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen (Germany); Institute for Nonlinear Dynamics, Georg–August–Universität Göttingen, 37077 Göttingen (Germany)

    2014-09-01

    Predictive feedback control is an easy-to-implement method to stabilize unknown unstable periodic orbits in chaotic dynamical systems. Predictive feedback control is severely limited because asymptotic convergence speed decreases with stronger instabilities which in turn are typical for larger target periods, rendering it harder to effectively stabilize periodic orbits of large period. Here, we study stalled chaos control, where the application of control is stalled to make use of the chaotic, uncontrolled dynamics, and introduce an adaptation paradigm to overcome this limitation and speed up convergence. This modified control scheme is not only capable of stabilizing more periodic orbits than the original predictive feedback control but also speeds up convergence for typical chaotic maps, as illustrated in both theory and application. The proposed adaptation scheme provides a way to tune parameters online, yielding a broadly applicable, fast chaos control that converges reliably, even for periodic orbits of large period.

  13. Elimination of spiral chaos by periodic force for the Aliev-Panfilov model

    OpenAIRE

    Sakaguchi, Hidetsugu; Fujimoto, Takefumi

    2003-01-01

    Spiral chaos appears in the two dimensional Aliev-Panfilov model. The generation mechanism of the spiral chaos is related to the breathing instability of pulse trains. The spiral chaos can be eliminated by applying periodic force uniformly. The elimination of spiral chaos is most effective, when the frequency of the periodic force is close to that of the breathing motion.

  14. Deterministic chaos in the processor load

    International Nuclear Information System (INIS)

    Halbiniak, Zbigniew; Jozwiak, Ireneusz J.

    2007-01-01

    In this article we present the results of research whose purpose was to identify the phenomenon of deterministic chaos in the processor load. We analysed the time series of the processor load during efficiency tests of database software. Our research was done on a Sparc Alpha processor working on the UNIX Sun Solaris 5.7 operating system. The conducted analyses proved the presence of the deterministic chaos phenomenon in the processor load in this particular case

  15. Digital Communication Devices Based on Nonlinear Dynamics and Chaos

    National Research Council Canada - National Science Library

    Larson, Lawrence

    2003-01-01

    The final report of the ARO MURI "Digital Communications Based on Chaos and Nonlinear Dynamics" contains research results in the areas of chaos and nonlinear dynamics applied to wireless and optical communications...

  16. Household chaos, sociodemographic risk, coparenting, and parent-infant relations during infants' first year.

    Science.gov (United States)

    Whitesell, Corey J; Teti, Douglas M; Crosby, Brian; Kim, Bo-Ram

    2015-04-01

    Household chaos is a construct often overlooked in studies of human development, despite its theoretical links with the integrity of individual well-being, family processes, and child development. The present longitudinal study examined relations between household chaos and well-established correlates of chaos (sociodemographic risk, major life events, and personal distress) and several constructs that, to date, are theoretically linked with chaos but never before assessed as correlates (quality of coparenting and emotional availability with infants at bedtime). In addressing this aim, we introduce a new measure of household chaos (the Descriptive In-home Survey of Chaos--Observer ReporteD, or DISCORD), wholly reliant on independent observer report, which draws from household chaos theory and prior empirical work but extends the measurement of chaos to include information about families' compliance with a home visiting protocol. Household chaos was significantly associated with socioeconomic risk, negative life events, less favorable coparenting, and less emotionally available bedtime parenting, but not with personal distress. These findings emphasize the need to examine household chaos as a direct and indirect influence on child and family outcomes, as a moderator of intervention attempts to improving parenting and child development, and as a target of intervention in its own right. (c) 2015 APA, all rights reserved).

  17. Chaos and fractals. Applications to nuclear engineering

    International Nuclear Information System (INIS)

    Clausse, A.; Delmastro, D.F.

    1990-01-01

    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) [es

  18. Chaos and order in models of black hole pairs

    International Nuclear Information System (INIS)

    Levin, Janna

    2006-01-01

    Chaos in the orbits of black hole pairs has by now been confirmed by several independent groups. While the chaotic behavior of binary black hole orbits is no longer argued, it remains difficult to quantify the importance of chaos to the evolutionary dynamics of a pair of comparable mass black holes. None of our existing approximations are robust enough to offer convincing quantitative conclusions in the most highly nonlinear regime. It is intriguing to note that, in three different approximations to a black hole pair built of a spinning black hole and a nonspinning companion, two approximations exhibit chaos and one approximation does not. The fully relativistic scenario of a spinning test mass around a Schwarzschild black hole shows chaos, as does the post-Newtonian Lagrangian approximation. However, the approximately equivalent post-Newtonian Hamiltonian approximation does not show chaos when only one body spins. It is well known in dynamical systems theory that one system can be regular while an approximately related system is chaotic, so there is no formal conflict. However, the physical question remains: Is there chaos for comparable mass binaries when only one object spins? We are unable to answer this question given the poor convergence of the post-Newtonian approximation to the fully relativistic system. A resolution awaits better approximations that can be trusted in the highly nonlinear regime

  19. Generating intrinsically disordered protein conformational ensembles from a Markov chain

    Science.gov (United States)

    Cukier, Robert I.

    2018-03-01

    Intrinsically disordered proteins (IDPs) sample a diverse conformational space. They are important to signaling and regulatory pathways in cells. An entropy penalty must be payed when an IDP becomes ordered upon interaction with another protein or a ligand. Thus, the degree of conformational disorder of an IDP is of interest. We create a dichotomic Markov model that can explore entropic features of an IDP. The Markov condition introduces local (neighbor residues in a protein sequence) rotamer dependences that arise from van der Waals and other chemical constraints. A protein sequence of length N is characterized by its (information) entropy and mutual information, MIMC, the latter providing a measure of the dependence among the random variables describing the rotamer probabilities of the residues that comprise the sequence. For a Markov chain, the MIMC is proportional to the pair mutual information MI which depends on the singlet and pair probabilities of neighbor residue rotamer sampling. All 2N sequence states are generated, along with their probabilities, and contrasted with the probabilities under the assumption of independent residues. An efficient method to generate realizations of the chain is also provided. The chain entropy, MIMC, and state probabilities provide the ingredients to distinguish different scenarios using the terminologies: MoRF (molecular recognition feature), not-MoRF, and not-IDP. A MoRF corresponds to large entropy and large MIMC (strong dependence among the residues' rotamer sampling), a not-MoRF corresponds to large entropy but small MIMC, and not-IDP corresponds to low entropy irrespective of the MIMC. We show that MorFs are most appropriate as descriptors of IDPs. They provide a reasonable number of high-population states that reflect the dependences between neighbor residues, thus classifying them as IDPs, yet without very large entropy that might lead to a too high entropy penalty.

  20. Learning to learn - intrinsic plasticity as a metaplasticity mechanism for memory formation.

    Science.gov (United States)

    Sehgal, Megha; Song, Chenghui; Ehlers, Vanessa L; Moyer, James R

    2013-10-01

    "Use it or lose it" is a popular adage often associated with use-dependent enhancement of cognitive abilities. Much research has focused on understanding exactly how the brain changes as a function of experience. Such experience-dependent plasticity involves both structural and functional alterations that contribute to adaptive behaviors, such as learning and memory, as well as maladaptive behaviors, including anxiety disorders, phobias, and posttraumatic stress disorder. With the advancing age of our population, understanding how use-dependent plasticity changes across the lifespan may also help to promote healthy brain aging. A common misconception is that such experience-dependent plasticity (e.g., associative learning) is synonymous with synaptic plasticity. Other forms of plasticity also play a critical role in shaping adaptive changes within the nervous system, including intrinsic plasticity - a change in the intrinsic excitability of a neuron. Intrinsic plasticity can result from a change in the number, distribution or activity of various ion channels located throughout the neuron. Here, we review evidence that intrinsic plasticity is an important and evolutionarily conserved neural correlate of learning. Intrinsic plasticity acts as a metaplasticity mechanism by lowering the threshold for synaptic changes. Thus, learning-related intrinsic changes can facilitate future synaptic plasticity and learning. Such intrinsic changes can impact the allocation of a memory trace within a brain structure, and when compromised, can contribute to cognitive decline during the aging process. This unique role of intrinsic excitability can provide insight into how memories are formed and, more interestingly, how neurons that participate in a memory trace are selected. Most importantly, modulation of intrinsic excitability can allow for regulation of learning ability - this can prevent or provide treatment for cognitive decline not only in patients with clinical disorders but

  1. Chaotic operation and chaos control of travelling wave ultrasonic motor.

    Science.gov (United States)

    Shi, Jingzhuo; Zhao, Fujie; Shen, Xiaoxi; Wang, Xiaojie

    2013-08-01

    The travelling wave ultrasonic motor, which is a nonlinear dynamic system, has complex chaotic phenomenon with some certain choices of system parameters and external inputs, and its chaotic characteristics have not been studied until now. In this paper, the preliminary study of the chaos phenomenon in ultrasonic motor driving system has been done. The experiment of speed closed-loop control is designed to obtain several groups of time sampling data sequence of the amplitude of driving voltage, and phase-space reconstruction is used to analyze the chaos characteristics of these time sequences. The largest Lyapunov index is calculated and the result is positive, which shows that the travelling wave ultrasonic motor has chaotic characteristics in a certain working condition Then, the nonlinear characteristics of travelling wave ultrasonic motor are analyzed which includes Lyapunov exponent map, the bifurcation diagram and the locus of voltage relative to speed based on the nonlinear chaos model of a travelling wave ultrasonic motor. After that, two kinds of adaptive delay feedback controllers are designed in this paper to control and suppress chaos in USM speed control system. Simulation results show that the method can control unstable periodic orbits, suppress chaos in USM control system. Proportion-delayed feedback controller was designed following and arithmetic of fuzzy logic was used to adaptively adjust the delay time online. Simulation results show that this method could fast and effectively change the chaos movement into periodic or fixed-point movement and make the system enter into stable state from chaos state. Finally the chaos behavior was controlled. Copyright © 2013 Elsevier B.V. All rights reserved.

  2. 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 broadcasts 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...

  3. Engineering Aromatic-Aromatic Interactions To Nucleate Folding in Intrinsically Disordered Regions of Proteins.

    Science.gov (United States)

    Balakrishnan, Swati; Sarma, Siddhartha P

    2017-08-22

    Aromatic interactions are an important force in protein folding as they combine the stability of a hydrophobic interaction with the selectivity of a hydrogen bond. Much of our understanding of aromatic interactions comes from "bioinformatics" based analyses of protein structures and from the contribution of these interactions to stabilizing secondary structure motifs in model peptides. In this study, the structural consequences of aromatic interactions on protein folding have been explored in engineered mutants of the molten globule protein apo-cytochrome b 5 . Structural changes from disorder to order due to aromatic interactions in two variants of the protein, viz., WF-cytb5 and FF-cytb5, result in significant long-range secondary and tertiary structure. The results show that 54 and 52% of the residues in WF-cytb5 and FF-cytb5, respectively, occupy ordered regions versus 26% in apo-cytochrome b 5 . The interactions between the aromatic groups are offset-stacked and edge-to-face for the Trp-Phe and Phe-Phe mutants, respectively. Urea denaturation studies indicate that both mutants have a C m higher than that of apo-cytochrome b 5 and are more stable to chaotropic agents than apo-cytochrome b 5 . The introduction of these aromatic residues also results in "trimer" interactions with existing aromatic groups, reaffirming the selectivity of the aromatic interactions. These studies provide insights into the aromatic interactions that drive disorder-to-order transitions in intrinsically disordered regions of proteins and will aid in de novo protein design beyond small peptide scaffolds.

  4. Does chaos theory have major implications for philosophy of medicine?

    Science.gov (United States)

    Holm, S

    2002-12-01

    In the literature it is sometimes claimed that chaos theory, non-linear dynamics, and the theory of fractals have major implications for philosophy of medicine, especially for our analysis of the concept of disease and the concept of causation. This paper gives a brief introduction to the concepts underlying chaos theory and non-linear dynamics. It is then shown that chaos theory has only very minimal implications for the analysis of the concept of disease and the concept of causation, mainly because the mathematics of chaotic processes entail that these processes are fully deterministic. The practical unpredictability of chaotic processes, caused by their extreme sensitivity to initial conditions, may raise practical problems in diagnosis, prognosis, and treatment, but it raises no major theoretical problems. The relation between chaos theory and the problem of free will is discussed, and it is shown that chaos theory may remove the problem of predictability of decisions, but does not solve the problem of free will. Chaos theory may thus be very important for our understanding of physiological processes, and specific disease entities, without having any major implications for philosophy of medicine.

  5. Biologically inspired rate control of chaos.

    Science.gov (United States)

    Olde Scheper, Tjeerd V

    2017-10-01

    The overall intention of chaotic control is to eliminate chaos and to force the system to become stable in the classical sense. In this paper, I demonstrate a more subtle method that does not eliminate all traces of chaotic behaviour; yet it consistently, and reliably, can provide control as intended. The Rate Control of Chaos (RCC) method is derived from metabolic control processes and has several remarkable properties. RCC can control complex systems continuously, and unsupervised, it can also maintain control across bifurcations, and in the presence of significant systemic noise. Specifically, I show that RCC can control a typical set of chaotic models, including the 3 and 4 dimensional chaotic Lorenz systems, in all modes. Furthermore, it is capable of controlling spatiotemporal chaos without supervision and maintains control of the system across bifurcations. This property of RCC allows a dynamic system to operate in parameter spaces that are difficult to control otherwise. This may be particularly interesting for the control of forced systems or dynamic systems that are chaotically perturbed. These control properties of RCC are applicable to a range of dynamic systems, thereby appearing to have far-reaching effects beyond just controlling chaos. RCC may also point to the existence of a biochemical control function of an enzyme, to stabilise the dynamics of the reaction cascade.

  6. Quantum manifestations of chaos

    International Nuclear Information System (INIS)

    Borondo, F.; Benito, R.M.

    1998-01-01

    The correspondence between classical and quantum mechanics is considered both in the regular and chaotic regimes, and the main results regarding the quantum manifestations of chaos are reviewed. (Author) 16 refs

  7. Nonlinear dynamics and chaos in a fractional-order financial system

    International Nuclear Information System (INIS)

    Chen Weiching

    2008-01-01

    This study examines the two most attractive characteristics, memory and chaos, in simulations of financial systems. A fractional-order financial system is proposed in this study. It is a generalization of a dynamic financial model recently reported in the literature. The fractional-order financial system displays many interesting dynamic behaviors, such as fixed points, periodic motions, and chaotic motions. It has been found that chaos exists in fractional-order financial systems with orders less than 3. In this study, the lowest order at which this system yielded chaos was 2.35. Period doubling and intermittency routes to chaos in the fractional-order financial system were found

  8. Chaos synchronization of a new chaotic system via nonlinear control

    International Nuclear Information System (INIS)

    Zhang Qunjiao; Lu Junan

    2008-01-01

    This paper investigates chaos synchronization of a new chaotic system [Lue J, Chen G, Cheng D. A new chaotic system and beyond: the generalized Lorenz-like system. Int J Bifurcat Chaos 2004;14:1507-37]. Two kinds of novel nonlinear controllers are designed based on the Lyapunov stability theory. It can be viewed as an improvement to the existing results of reference [Park JH. Chaos synchronization of a chaotic system via nonlinear control. Chaos, Solitons and Fractals 2005;25:579-84] because we use less controllers but realize a global and exponential asymptotical synchronization. Numerical simulations are provided to show the effectiveness and advantage of this method

  9. Chaos in charged AdS black hole extended phase space

    Science.gov (United States)

    Chabab, M.; El Moumni, H.; Iraoui, S.; Masmar, K.; Zhizeh, S.

    2018-06-01

    We present an analytical study of chaos in a charged black hole in the extended phase space in the context of the Poincare-Melnikov theory. Along with some background on dynamical systems, we compute the relevant Melnikov function and find its zeros. Then we analyse these zeros either to identify the temporal chaos in the spinodal region, or to observe spatial chaos in the small/large black hole equilibrium configuration. As a byproduct, we derive a constraint on the Black hole' charge required to produce chaotic behaviour. To the best of our knowledge, this is the first endeavour to understand the correlation between chaos and phase picture in black holes.

  10. 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.

  11. 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.

  12. No Association between Cortical Gyrification or Intrinsic Curvature and Attention-deficit/Hyperactivity Disorder in Adolescents and Young Adults

    Directory of Open Access Journals (Sweden)

    Natalie J. Forde

    2017-04-01

    Full Text Available Magnetic resonance imaging (MRI studies have highlighted subcortical, cortical, and structural connectivity abnormalities associated with attention-deficit/hyperactivity disorder (ADHD. Gyrification investigations of the cortex have been inconsistent and largely negative, potentially due to a lack of sensitivity of the previously used morphological parameters. The innovative approach of applying intrinsic curvature analysis, which is predictive of gyrification pattern, to the cortical surface applied herein allowed us greater sensitivity to determine whether the structural connectivity abnormalities thus far identified at a centimeter scale also occur at a millimeter scale within the cortical surface. This could help identify neurodevelopmental processes that contribute to ADHD. Structural MRI datasets from the NeuroIMAGE project were used [n = 306 ADHD, n = 164 controls, and n = 148 healthy siblings of individuals with ADHD (age in years, mean(sd; 17.2 (3.4, 16.8 (3.2, and 17.7 (3.8, respectively]. Reconstructions of the cortical surfaces were computed with FreeSurfer. Intrinsic curvature (taken as a marker of millimeter-scale surface connectivity and local gyrification index were calculated for each point on the surface (vertex with Caret and FreeSurfer, respectively. Intrinsic curvature skew and mean local gyrification index were extracted per region; frontal, parietal, temporal, occipital, cingulate, and insula. A generalized additive model was used to compare the trajectory of these measures between groups over age, with sex, scanner site, total surface area of hemisphere, and familiality accounted for. After correcting for sex, scanner site, and total surface area no group differences were found in the developmental trajectory of intrinsic curvature or local gyrification index. Despite the increased sensitivity of intrinsic curvature, compared to gyrification measures, to subtle morphological abnormalities of the cortical surface we found

  13. 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

    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....

  14. Chaos and Christianity: A Response to Butz and a Biblical Alternative.

    Science.gov (United States)

    Watts, Richard E.; Trusty, Jerry

    1997-01-01

    M.R. Butz's position regarding chaos theory and Christianity is reviewed. The compatibility of biblical theology and the sciences is discussed. Parallels between chaos theory and the philosophical perspective of Soren Kierkegaard are explored. A biblical model is offered for counselors in assisting Christian clients in embracing chaos. (Author/EMK)

  15. Metadata in CHAOS

    DEFF Research Database (Denmark)

    Lykke, Marianne; Skov, Mette; Lund, Haakon

    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...

  16. Effect of smoothing on robust chaos.

    Science.gov (United States)

    Deshpande, Amogh; Chen, Qingfei; Wang, Yan; Lai, Ying-Cheng; Do, Younghae

    2010-08-01

    In piecewise-smooth dynamical systems, situations can arise where the asymptotic attractors of the system in an open parameter interval are all chaotic (e.g., no periodic windows). This is the phenomenon of robust chaos. Previous works have established that robust chaos can occur through the mechanism of border-collision bifurcation, where border is the phase-space region where discontinuities in the derivatives of the dynamical equations occur. We investigate the effect of smoothing on robust chaos and find that periodic windows can arise when a small amount of smoothness is present. We introduce a parameter of smoothing and find that the measure of the periodic windows in the parameter space scales linearly with the parameter, regardless of the details of the smoothing function. Numerical support and a heuristic theory are provided to establish the scaling relation. Experimental evidence of periodic windows in a supposedly piecewise linear dynamical system, which has been implemented as an electronic circuit, is also provided.

  17. 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...

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

    International Nuclear Information System (INIS)

    Amin, Mohamed; Faragallah, Osama S.; Abd El-Latif, Ahmed A.

    2009-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Amin, Mohamed [Dept. of Mathematics and Computer Science, Faculty of Science, Menoufia University, Shebin El-Koom 32511 (Egypt)], E-mail: mamin04@yahoo.com; Faragallah, Osama S. [Dept. of Computer Science and Engineering, Faculty of Electronic Engineering, Menoufia University, Menouf 32952 (Egypt)], E-mail: osam_sal@yahoo.com; Abd El-Latif, Ahmed A. [Dept. of Mathematics and Computer Science, Faculty of Science, Menoufia University, Shebin El-Koom 32511 (Egypt)], E-mail: ahmed_rahiem@yahoo.com

    2009-10-30

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

  20. Detergent-induced aggregation of an amyloidogenic intrinsically ...

    Indian Academy of Sciences (India)

    Shruti Arya

    2017-11-02

    Nov 2, 2017 ... the effect of a well-known anionic lipid mimetic, sodium dodecyl sulfate (SDS), on the aggregation ... for the fabrication of nano-structures for a wide variety ...... M 2014 Classification of intrinsically disordered regions.

  1. Chaos and the (un)predictability of evolution in a changing environment.

    Science.gov (United States)

    Rego-Costa, Artur; Débarre, Florence; Chevin, Luis-Miguel

    2018-02-01

    Among the factors that may reduce the predictability of evolution, chaos, characterized by a strong dependence on initial conditions, has received much less attention than randomness due to genetic drift or environmental stochasticity. It was recently shown that chaos in phenotypic evolution arises commonly under frequency-dependent selection caused by competitive interactions mediated by many traits. This result has been used to argue that chaos should often make evolutionary dynamics unpredictable. However, populations also evolve largely in response to external changing environments, and such environmental forcing is likely to influence the outcome of evolution in systems prone to chaos. We investigate how a changing environment causing oscillations of an optimal phenotype interacts with the internal dynamics of an eco-evolutionary system that would be chaotic in a constant environment. We show that strong environmental forcing can improve the predictability of evolution by reducing the probability of chaos arising, and by dampening the magnitude of chaotic oscillations. In contrast, weak forcing can increase the probability of chaos, but it also causes evolutionary trajectories to track the environment more closely. Overall, our results indicate that, although chaos may occur in evolution, it does not necessarily undermine its predictability. © 2017 The Author(s). Evolution © 2017 The Society for the Study of Evolution.

  2. Chaos-induced resonant effects and its control

    International Nuclear Information System (INIS)

    Zambrano, Samuel; Casado, Jose M.; Sanjuan, Miguel A.F.

    2007-01-01

    This Letter shows that a suitable chaotic signal can induce resonant effects analogous to those observed in presence of noise in a bistable system under periodic forcing. By constructing groups of chaotic and random perturbations with similar one-time statistics we show that in some cases chaos and noise induce indistinguishable resonant effects. This reinforces the conjecture by which in some situations where noise is supposed to play a key role maybe chaos is the key ingredient. Here we also show that the presence of a chaotic signal as the perturbation leading to a resonance opens new control perspectives based on our ability to stabilize chaos in different periodic orbits. A discussion of the possible implications of these facts is also presented at the end of the Letter

  3. Modified projective synchronization with complex scaling factors of uncertain real chaos and complex chaos

    International Nuclear Information System (INIS)

    Zhang Fang-Fang; Liu Shu-Tang; Yu Wei-Yong

    2013-01-01

    To increase the variety and security of communication, we present the definitions of modified projective synchronization with complex scaling factors (CMPS) of real chaotic systems and complex chaotic systems, where complex scaling factors establish a link between real chaos and complex chaos. Considering all situations of unknown parameters and pseudo-gradient condition, we design adaptive CMPS schemes based on the speed-gradient method for the real drive chaotic system and complex response chaotic system and for the complex drive chaotic system and the real response chaotic system, respectively. The convergence factors and dynamical control strength are added to regulate the convergence speed and increase robustness. Numerical simulations verify the feasibility and effectiveness of the presented schemes. (general)

  4. Some new surprises in chaos.

    Science.gov (United States)

    Bunimovich, Leonid A; Vela-Arevalo, Luz V

    2015-09-01

    "Chaos is found in greatest abundance wherever order is being sought.It always defeats order, because it is better organized"Terry PratchettA 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.

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

    Science.gov (United States)

    Akhmet, Marat; Rafatov, Ismail; Fen, Mehmet Onur

    2014-12-01

    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).].

  6. "I Had Seen Order and Chaos, but Had Thought They Were Different." The Challenges of the Chaos Theory for Career Development

    Science.gov (United States)

    Pryor, Robert; Bright, Jim

    2004-01-01

    This paper highlights five challenges to the accepted wisdom in career development theory and practice. It presents the chaos theory of careers and argues that the chaos theory provides a more complete and authentic account of human behaviour. The paper argues that positivism, reductionism and assumptions of linearity are inappropriate for…

  7. Applying Chaos Theory to Lesson Planning and Delivery

    Science.gov (United States)

    Cvetek, Slavko

    2008-01-01

    In this article, some of the ways in which thinking about chaos theory can help teachers and student-teachers to accept uncertainty and randomness as natural conditions in the classroom are considered. Building on some key features of complex systems commonly attributed to chaos theory (e.g. complexity, nonlinearity, sensitivity to initial…

  8. The Chaos Theory of Careers: A User's Guide

    Science.gov (United States)

    Bright, Jim E. H.; Pryor, Robert G. L.

    2005-01-01

    The purpose of this article is to set out the key elements of the Chaos Theory of Careers. The complexity of influences on career development presents a significant challenge to traditional predictive models of career counseling. Chaos theory can provide a more appropriate description of career behavior, and the theory can be applied with clients…

  9. Detecting Chaos from Agricultural Product Price Time Series

    Directory of Open Access Journals (Sweden)

    Xin Su

    2014-12-01

    Full Text Available Analysis of the characteristics of agricultural product price volatility and trend forecasting are necessary to formulate and implement agricultural price control policies. Taking wholesale cabbage prices as an example, a multiple test methodology has been adopted to identify the nonlinearity, fractality, and chaos of the data. The approaches used include the R/S analysis, the BDS test, the power spectra, the recurrence plot, the largest Lyapunov exponent, the Kolmogorov entropy, and the correlation dimension. The results show that there is chaos in agricultural wholesale price data, which provides a good theoretical basis for selecting reasonable forecasting models as prediction techniques based on chaos theory can be applied to forecasting agricultural prices.

  10. Chaos, strange attractors, and fractal basin boundaries

    International Nuclear Information System (INIS)

    Grebogi, C.

    1989-01-01

    Even simple mathematical models of physical systems are often observed to exhibit rather complex time evolution. Upon observation, one often has the feeling that such complex time evolutions could, for most practical purposes, be best characterized by statistical properties rather than by detailed knowledge of the exact process. In such situations, the time evolution is often labeled chaotic or turbulent. The study of chaotic dynamics has recently undergone explosive growth. Motivation for this comes partly from the fact that chaotic dynamics is being found to be of fundamental importance in many branches of science and engineering. Examples illustrating the wide-ranging applications of chaotic dynamics to scientific and engineering problems are the following: fluid dynamics, biology, ecology, meteorology, optics, electronics, mechanical engineerings, physiology, economics, chemistry, accelerator technology, thermonuclear fusion, celestial mechanics, and oceanography. The common element in all of the above topics is that they involve nonlinearity in some way. Indeed chaos is expected to be common whenever nonlinearity plays a role. Since nonlinearity is inherent in so much of science and engineering, an understanding of chaos is essential. Given the varied nature of applications where chaos is important, it is natural that researchers in a broad range of fields have become interested in and have contributed to recent developments in chaos

  11. Chaos theory: A fascinating concept for oncologists

    International Nuclear Information System (INIS)

    Denis, F.; Letellier, C.

    2012-01-01

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

  12. Chaos synchronization of coupled hyperchaotic system

    International Nuclear Information System (INIS)

    Yang Lixin; Chu Yandong; Zhang Jiangang; Li Xianfeng

    2009-01-01

    Chaos synchronization, as an important topic, has become an active research subject in nonlinear science. Over the past two decades, chaos synchronization between nonlinear systems has been extensively studied, and many types of synchronization have been announced. This paper introduces synchronization of coupled hyperchaotic system, based on the Lapunov stability theory, asymptotic stability of the system is guaranteed by means of Lapunov function. The numerical simulation was provided in order to show the effectiveness of this method for the synchronization of the chaotic hyperchaotic Chen system and Rossler system.

  13. Polynomial chaos functions and stochastic differential equations

    International Nuclear Information System (INIS)

    Williams, M.M.R.

    2006-01-01

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

  14. Learning to learn – intrinsic plasticity as a metaplasticity mechanism for memory formation

    Science.gov (United States)

    Sehgal, Megha; Song, Chenghui; Ehlers, Vanessa L.; Moyer, James R.

    2013-01-01

    “Use it or lose it” is a popular adage often associated with use-dependent enhancement of cognitive abilities. Much research has focused on understanding exactly how the brain changes as a function of experience. Such experience-dependent plasticity involves both structural and functional alterations that contribute to adaptive behaviors, such as learning and memory, as well as maladaptive behaviors, including anxiety disorders, phobias, and posttraumatic stress disorder. With the advancing age of our population, understanding how use-dependent plasticity changes across the lifespan may also help to promote healthy brain aging. A common misconception is that such experience-dependent plasticity (e.g., associative learning) is synonymous with synaptic plasticity. Other forms of plasticity also play a critical role in shaping adaptive changes within the nervous system, including intrinsic plasticity – a change in the intrinsic excitability of a neuron. Intrinsic plasticity can result from a change in the number, distribution or activity of various ion channels located throughout the neuron. Here, we review evidence that intrinsic plasticity is an important and evolutionarily conserved neural correlate of learning. Intrinsic plasticity acts as a metaplasticity mechanism by lowering the threshold for synaptic changes. Thus, learning-related intrinsic changes can facilitate future synaptic plasticity and learning. Such intrinsic changes can impact the allocation of a memory trace within a brain structure, and when compromised, can contribute to cognitive decline during the aging process. This unique role of intrinsic excitability can provide insight into how memories are formed and, more interestingly, how neurons that participate in a memory trace are selected. Most importantly, modulation of intrinsic excitability can allow for regulation of learning ability – this can prevent or provide treatment for cognitive decline not only in patients with clinical

  15. Light Management in Optoelectronic Devices with Disordered and Chaotic Structures

    KAUST Repository

    Khan, Yasser

    2012-07-01

    With experimental realization, energy harvesting capabilities of chaotic microstructures were explored. Incident photons falling into chaotic trajectories resulted in energy buildup for certain frequencies. As a consequence, many fold enhancement in light trapping was observed. These ellipsoid like chaotic microstructures demonstrated 25% enhancement in light trapping at 450nm excitation and 15% enhancement at 550nm excitation. Optimization of these structures can drive novel chaos-assisted energy harvesting systems. In subsequent sections of the thesis, prospect of broadband light extraction from white light emitting diodes were investigated, which is an unchallenged but quintessential problem in solid-state lighting. Size dependent scattering allows microstructures to interact strongly with narrow-band light. If disorder is introduced in spread and sizes of microstructures, broadband light extraction is possible. A novel scheme with Voronoi tessellation to quantify disorder in physical systems was also introduced, and a link between voronoi disorder and state disorder of statistical mechanics was established. Overall, in this thesis some nascent concepts regarding disorder and chaos were investigated to efficiently manage electromagnetic waves in optoelectronic devices.

  16. Digested disorder

    Science.gov (United States)

    DeForte, Shelly; Reddy, Krishna D; Uversky, Vladimir N

    2013-01-01

    The current literature on intrinsically disordered proteins is overwhelming. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a series of reader’s digest type articles objectively representing the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the period of April, May, and June of 2013. The papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings. PMID:28516028

  17. Fast hydrogen exchange affects {sup 15}N relaxation measurements in intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Seho; Wu, Kuen-Phon; Baum, Jean, E-mail: jean.baum@rutgers.edu [Rutgers University, Department of Chemistry and Chemical Biology (United States)

    2013-03-15

    Unprotected amide protons can undergo fast hydrogen exchange (HX) with protons from the solvent. Generally, NMR experiments using the out-and-back coherence transfer with amide proton detection are affected by fast HX and result in reduced signal intensity. When one of these experiments, {sup 1}H-{sup 15}N HSQC, is used to measure the {sup 15}N transverse relaxation rate (R{sub 2}), the measured R{sub 2} rate is convoluted with the HX rate (k{sub HX}) and has higher apparent R{sub 2} values. Since the {sup 15}N R{sub 2} measurement is important for analyzing protein backbone dynamics, the HX effect on the R{sub 2} measurement is investigated and described here by multi-exponential signal decay. We demonstrate these effects by performing {sup 15}N R{sub 2}{sup CPMG} experiments on {alpha}-synuclein, an intrinsically disordered protein, in which the amide protons are exposed to solvent. We show that the HX effect on R{sub 2}{sup CPMG} can be extracted by the derived equation. In conclusion, the HX effect may be pulse sequence specific and results from various sources including the J coupling evolution, the change of steady state water proton magnetization, and the D{sub 2}O content in the sample. To avoid the HX effect on the analysis of relaxation data of unprotected amides, it is suggested that NMR experimental conditions insensitive to the HX should be considered or that intrinsic R{sub 2}{sup CPMG} values be obtained by methods described herein.

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

    International Nuclear Information System (INIS)

    Akhmet, Marat; Fen, Mehmet Onur; Rafatov, Ismail

    2014-01-01

    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).

  19. Switching control of linear systems for generating chaos

    International Nuclear Information System (INIS)

    Liu Xinzhi; Teo, Kok-Lay; Zhang Hongtao; Chen Guanrong

    2006-01-01

    In this paper, a new switching method is developed, which can be applied to generating different types of chaos or chaos-like dynamics from two or more linear systems. A numerical simulation is given to illustrate the generated chaotic dynamic behavior of the systems with some variable parameters. Finally, a circuit is built to realize various chaotic dynamical behaviors

  20. Neural chaos and schizophrenia

    Czech Academy of Sciences Publication Activity Database

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

    2007-01-01

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

  1. Chaos control of Chen chaotic dynamical system

    International Nuclear Information System (INIS)

    Yassen, M.T.

    2003-01-01

    This paper is devoted to study the problem of controlling chaos in Chen chaotic dynamical system. Two different methods of control, feedback and nonfeedback methods are used to suppress chaos to unstable equilibria or unstable periodic orbits (UPO). The Lyapunov direct method and Routh-Hurwitz criteria are used to study the conditions of the asymptotic stability of the steady states of the controlled system. Numerical simulations are presented to show these results

  2. Topographic variations in chaos on Europa: Implications for diapiric formation

    Science.gov (United States)

    Schenk, Paul M.; Pappalardo, Robert T.

    2004-01-01

    Disrupted terrain, or chaos, on Europa, might have formed through melting of a floating ice shell from a subsurface ocean [Cam et al., 1998; Greenberg et al., 19991, or breakup by diapirs rising from the warm lower portion of the ice shell [Head and Pappalardo, 1999; Collins et al., 20001. Each model makes specific and testable predictions for topographic expression within chaos and relative to surrounding terrains on local and regional scales. High-resolution stereo-controlled photoclinometric topography indicates that chaos topography, including the archetypal Conamara Chaos region, is uneven and commonly higher than surrounding plains by up to 250 m. Elevated and undulating topography is more consistent with diapiric uplift of deep material in a relatively thick ice shell, rather than melt-through and refreezing of regionally or globally thin ice by a subsurface ocean. Vertical and horizontal scales of topographic doming in Conamara Chaos are consistent with a total ice shell thickness >15 km. Contact between Europa's ocean and surface may most likely be indirectly via diapirism or convection.

  3. Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics.

    Science.gov (United States)

    Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

    2016-10-17

    Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law.

  4. Synchronization and suppression of chaos in non-locally coupled ...

    Indian Academy of Sciences (India)

    Coupled map lattices have been intensively investigated as models to understand many spatiotemporal phenomena observed in extended system, and consequently spatiotemporal chaos. We used the complex order parameter to quantify chaos synchronization for a one-dimensional chain of coupled logistic maps with a ...

  5. A new type of cascading synchronization for halo-chaos and its potential for communication applications

    International Nuclear Information System (INIS)

    Fang Jinqing; Yu Xinghuo

    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

  6. Controlling Mackey-Glass chaos

    Science.gov (United States)

    Kiss, Gábor; Röst, Gergely

    2017-11-01

    The Mackey-Glass equation is the representative example of delay induced chaotic behavior. Here, we propose various control mechanisms so that otherwise erratic solutions are forced to converge to the positive equilibrium or to a periodic orbit oscillating around that equilibrium. We take advantage of some recent results of the delay differential literature, when a sufficiently large domain of the phase space has been shown to be attractive and invariant, where the system is governed by monotone delayed feedback and chaos is not possible due to some Poincaré-Bendixson type results. We systematically investigate what control mechanisms are suitable to drive the system into such a situation and prove that constant perturbation, proportional feedback control, Pyragas control, and state dependent delay control can all be efficient to control Mackey-Glass chaos with properly chosen control parameters.

  7. Chaos in quantum channels

    Energy Technology Data Exchange (ETDEWEB)

    Hosur, Pavan; Qi, Xiao-Liang [Department of Physics, Stanford University,476 Lomita Mall, Stanford, California 94305 (United States); Roberts, Daniel A. [Center for Theoretical Physics and Department of Physics, Massachusetts Institute of Technology,77 Massachusetts Ave, Cambridge, Massachusetts 02139 (United States); Yoshida, Beni [Perimeter Institute for Theoretical Physics,31 Caroline Street North, Waterloo, Ontario N2L 2Y5 (Canada); Walter Burke Institute for Theoretical Physics, California Institute of Technology,1200 E California Blvd, Pasadena CA 91125 (United States)

    2016-02-01

    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.

  8. Controlling Mackey-Glass chaos.

    Science.gov (United States)

    Kiss, Gábor; Röst, Gergely

    2017-11-01

    The Mackey-Glass equation is the representative example of delay induced chaotic behavior. Here, we propose various control mechanisms so that otherwise erratic solutions are forced to converge to the positive equilibrium or to a periodic orbit oscillating around that equilibrium. We take advantage of some recent results of the delay differential literature, when a sufficiently large domain of the phase space has been shown to be attractive and invariant, where the system is governed by monotone delayed feedback and chaos is not possible due to some Poincaré-Bendixson type results. We systematically investigate what control mechanisms are suitable to drive the system into such a situation and prove that constant perturbation, proportional feedback control, Pyragas control, and state dependent delay control can all be efficient to control Mackey-Glass chaos with properly chosen control parameters.

  9. Spatiotemporal chaos from bursting dynamics

    International Nuclear Information System (INIS)

    Berenstein, Igal; De Decker, Yannick

    2015-01-01

    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

  10. A quantum correction to chaos

    International Nuclear Information System (INIS)

    Fitzpatrick, A. Liam; Kaplan, Jared

    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 λ_L, which is a diagnostic for the early onset of chaos, receives 1/c corrections that may be interpreted as λ_L=((2π)/β)(1+(12/c)). 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 λ_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.

  11. Controlling the optical field chaos in storage ring free-electron lasers

    International Nuclear Information System (INIS)

    Wang Wenjie

    1995-01-01

    The controlling of optical field chaos in a storage ring free-electron laser oscillator is discussed by using a phenomenal model. A novel method (which is called the 'beating method') of controlling chaos in a nonlinear dynamical system described by non-autonomous ordinary differential equations was developed. The result of theoretical analysis and numerical simulation shows that the optical field chaos in a storage ring free-electron laser oscillator can be suppressed and a periodic laser intensity can be obtained when a weak periodic control field is added to the optical cavity. The validity of this method of eliminating chaos is confirmed by the fact that the leading Lyapunov characteristic exponent of the system changes from a positive real number to a negative one. A further research is carried out, and it is found that only when the period of the control field equals to an integral multiple of that of the gain modulation in the optical cavity can the optical field chaos be suppressed. This means that the 'beating method' of controlling chaos is a kind of resonant method. A way to determine the 'best beating position' in the phase trajectory has also been obtained

  12. Controlling chaos in the current-driven ion acoustic instability

    International Nuclear Information System (INIS)

    Fukuyama, T.; Taniguchi, K.; Kawai, Y.

    2002-01-01

    Control of intermittent chaos caused by the current-driven ion acoustic instability is attempted and the controlling mechanism is investigated. When a small negative dc voltage is applied to the chaotic system as a perturbation, the system changes from a chaotic state to a periodic state while maintaining the instability, indicating that the chaotic state caused by the ion acoustic instability is well controlled by applying a small negative dc voltage. A hysteresis structure is observed on the V-I curve of the mesh grid to which the negative dc voltage to control is applied. Furthermore, when a negative dc voltage is applied to the state which shows a laminar structure existing under same experimental conditions, the system becomes chaotic via a bifurcation. Driven-chaos is excited when a negative dc voltage is applied to the laminar state. Applying a small negative dc voltage leads to controlling intermittent chaos while exciting driven-chaos

  13. Chaos Modelling with Computers

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 1; Issue 5. Chaos Modelling with Computers Unpredicatable Behaviour of Deterministic Systems. Balakrishnan Ramasamy T S K V Iyer. General Article Volume 1 Issue 5 May 1996 pp 29-39 ...

  14. THEORY OF SECULAR CHAOS AND MERCURY'S ORBIT

    International Nuclear Information System (INIS)

    Lithwick, Yoram; Wu Yanqin

    2011-01-01

    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.

  15. Classical and quantum chaos in a circular billiard with a straight cut

    International Nuclear Information System (INIS)

    Ree, S.; Reichl, L.E.

    1999-01-01

    We study classical and quantum dynamics of a particle in a circular billiard with a straight cut. Classically, this system can be integrable, nonintegrable with soft chaos, or nonintegrable with hard chaos as we vary the size of the cut. We plot Poincaracute e surfaces of section to study chaos. Quantum mechanically, we look at Husimi plots, and also use the quantum web, the technique primarily used in spin systems so far, to try to see differences in quantum manifestations of soft and hard chaos. copyright 1999 The American Physical Society

  16. Chaos induced by quantum effect due to breakdown of the Born-Oppenheimer adiabaticity

    International Nuclear Information System (INIS)

    Fujisaki, Hiroshi; Takatsuka, Kazuo

    2001-01-01

    Chaos in the multimode nonadiabatic system constructed by Heller [J. Chem. Phys. >92, 1718 (1990)], which consists of two diabatic two-dimensional harmonic potentials with the Condon coupling, is studied. A thorough investigation is carried out by scanning the magnitudes of the Condon coupling and the Duschinsky angle. To elucidate mechanisms that can cause chaos in this quantum system, the statistical properties of the energy levels and eigenfunctions of the system are investigated. We find an evidence in terms of the nearest-neighbor spacing distribution of energy levels and other measures that a certain class of chaos is purely induced by the nonadiabatic interaction due to breakdown of the Born-Oppenheimer approximation. Since the nonadiabatic transition can induce repeated bifurcation and merging of a wave packet around the region of quasicrossing between two potential surfaces, and since this interaction does not have a counterpart in the lower adiabatic system, the present chaos deserves being called 'nonadiabatic chaos.' Another type of chaos in a nonadiabatic system was previously identified [D. M. Leitner et al., J. Chem. Phys. >104, 434 (1996)] that reflects the inherent chaos of a corresponding adiabatic potential. We present a comparative study to establish the similarity and difference between these kinds of chaos

  17. 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.

  18. Chaos controlling problems for circuit systems with Josephson junction

    International Nuclear Information System (INIS)

    Gou, X-F; Wang, X; Xie, J-L

    2008-01-01

    The complex dynamical characters of the Josephson junction circuit system are studied and the tunnel effect is considered. The dynamical equation of the system is established. The route from periodic motion to chaos is illustrated using bifurcation diagram. An adscititious coupling controller is constructed to control the chaos

  19. Topological chaos of the spatial prisoner's dilemma game on regular networks.

    Science.gov (United States)

    Jin, Weifeng; Chen, Fangyue

    2016-02-21

    The spatial version of evolutionary prisoner's dilemma on infinitely large regular lattice with purely deterministic strategies and no memories among players is investigated in this paper. Based on the statistical inferences, it is pertinent to confirm that the frequency of cooperation for characterizing its macroscopic behaviors is very sensitive to the initial conditions, which is the most practically significant property of chaos. Its intrinsic complexity is then justified on firm ground from the theory of symbolic dynamics; that is, this game is topologically mixing and possesses positive topological entropy on its subsystems. It is demonstrated therefore that its frequency of cooperation could not be adopted by simply averaging over several steps after the game reaches the equilibrium state. Furthermore, the chaotically changing spatial patterns via empirical observations can be defined and justified in view of symbolic dynamics. It is worth mentioning that the procedure proposed in this work is also applicable to other deterministic spatial evolutionary games therein. Copyright © 2015 Elsevier Ltd. All rights reserved.

  20. Digested disorder

    Science.gov (United States)

    Reddy, Krishna D; DeForte, Shelly; Uversky, Vladimir N

    2014-01-01

    The current literature on intrinsically disordered proteins grows fast. To keep interested readers up to speed with this literature, we continue a “Digested Disorder” project and represent a new issue of reader’s digest of the research papers and reviews on intrinsically disordered proteins. The only 2 criteria for inclusion in this digest are the publication date (a paper should be published within the covered time frame) and topic (a paper should be dedicated to any aspect of protein intrinsic disorder). The current digest issue covers papers published during the third quarter of 2013; i.e., during the period of June, July, and September of 2013. Similar to previous issues, the papers are grouped hierarchically by topics they cover, and for each of the included paper a short description is given on its major findings. PMID:28232877

  1. Programming molecular self-assembly of intrinsically disordered proteins containing sequences of low complexity

    Science.gov (United States)

    Simon, Joseph R.; Carroll, Nick J.; Rubinstein, Michael; Chilkoti, Ashutosh; López, Gabriel P.

    2017-06-01

    Dynamic protein-rich intracellular structures that contain phase-separated intrinsically disordered proteins (IDPs) composed of sequences of low complexity (SLC) have been shown to serve a variety of important cellular functions, which include signalling, compartmentalization and stabilization. However, our understanding of these structures and our ability to synthesize models of them have been limited. We present design rules for IDPs possessing SLCs that phase separate into diverse assemblies within droplet microenvironments. Using theoretical analyses, we interpret the phase behaviour of archetypal IDP sequences and demonstrate the rational design of a vast library of multicomponent protein-rich structures that ranges from uniform nano-, meso- and microscale puncta (distinct protein droplets) to multilayered orthogonally phase-separated granular structures. The ability to predict and program IDP-rich assemblies in this fashion offers new insights into (1) genetic-to-molecular-to-macroscale relationships that encode hierarchical IDP assemblies, (2) design rules of such assemblies in cell biology and (3) molecular-level engineering of self-assembled recombinant IDP-rich materials.

  2. How does the Xenopus laevis embryonic cell cycle avoid spatial chaos?

    Science.gov (United States)

    Gelens, Lendert; Huang, Kerwyn Casey; Ferrell, James E.

    2015-01-01

    Summary Theoretical studies have shown that a deterministic biochemical oscillator can become chaotic when operating over a sufficiently large volume, and have suggested that the Xenopus laevis cell cycle oscillator operates close to such a chaotic regime. To experimentally test this hypothesis, we decreased the speed of the post-fertilization calcium wave, which had been predicted to generate chaos. However, cell divisions were found to develop normally and eggs developed into normal tadpoles. Motivated by these experiments, we carried out modeling studies to understand the prerequisites for the predicted spatial chaos. We showed that this type of spatial chaos requires oscillatory reaction dynamics with short pulse duration, and postulated that the mitotic exit in Xenopus laevis is likely slow enough to avoid chaos. In systems with shorter pulses, chaos may be an important hazard, as in cardiac arrhythmias, or a useful feature, as in the pigmentation of certain mollusk shells. PMID:26212326

  3. Specifying the Links Between Household Chaos and Preschool Children’s Development

    Science.gov (United States)

    Martin, Anne; Razza, Rachel; Brooks-Gunn, Jeanne

    2011-01-01

    Household chaos has been linked to poorer cognitive, behavioral, and self-regulatory outcomes in young children, but the mechanisms responsible remain largely unknown. Using a diverse sample of families in Chicago, the present study tests for the independent contributions made by five indicators of household chaos: noise, crowding, family instability, lack of routine, and television usually on. Chaos was measured at age 2; outcomes measured at age 5 tap receptive vocabulary, attention and behavior problems, and effortful control. Results show that controlling for all other measures of chaos, children with a lack of routine scored lower on receptive vocabulary and delayed gratification, while children whose television was generally on scored higher on aggression and attention problems. The provision of learning materials mediated a small part of the association between television and receptive vocabulary. Family instability, crowding, and noise did not predict any outcomes once other measures of chaos were controlled. PMID:22919120

  4. [Chaos theory: a fascinating concept for oncologists].

    Science.gov (United States)

    Denis, F; Letellier, C

    2012-05-01

    The oncologist is confronted daily by questions related to the fact that any patient presents a specific evolution for his cancer: he is challenged by very different, unexpected and often unpredictable outcomes, in some of his patients. The mathematical approach used today to describe this evolution has recourse to statistics and probability laws: such an approach does not ultimately apply to one particular patient, but to a given more or less heterogeneous population. This approach therefore poorly characterizes the dynamics of this disease and does not allow to state whether a patient is cured, to predict if he will relapse and when this could occur, and in what form, nor to predict the response to treatment and, in particular, to radiation therapy. Chaos theory, not well known by oncologists, could allow a better understanding of these issues. Developed to investigate complex systems producing behaviours that cannot be predicted due to a great sensitivity to initial conditions, chaos theory is rich of suitable concepts for a new approach of cancer dynamics. This article is three-fold: to provide a brief introduction to chaos theory, to clarify the main connecting points between chaos and carcinogenesis and to point out few promising research perspectives, especially in radiotherapy. Copyright © 2012 Société française de radiothérapie oncologique (SFRO). Published by Elsevier SAS. All rights reserved.

  5. Complex Modified Hybrid Projective Synchronization of Different Dimensional Fractional-Order Complex Chaos and Real Hyper-Chaos

    Directory of Open Access Journals (Sweden)

    Jian Liu

    2014-11-01

    Full Text Available This paper introduces a type of modified hybrid projective synchronization with complex transformationmatrix (CMHPS for different dimensional fractional-order complex chaos and fractional-order real hyper-chaos. The transformationmatrix in this type of chaotic synchronization is a non-square matrix, and its elements are complex numbers. Based on the stability theory of fractional-order systems, by employing the feedback control technique, necessary and sufficient criteria on CMHPS are derived. Furthermore, CMHPS between fractional-order real hyper-chaotic Rössler system and other two different dimensional fractional-order complex Lorenz-like chaotic systems is provided as two examples to discuss reduced order and increased order synchronization, respectively.

  6. Chaos on hyperspace

    Czech Academy of Sciences Publication Activity Database

    Beran, Zdeněk; Čelikovský, Sergej

    2013-01-01

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

  7. Chaos Theory and Its Application to Education: Mehmet Akif Ersoy University Case

    Science.gov (United States)

    Akmansoy, Vesile; Kartal, Sadik

    2014-01-01

    Discussions have arisen regarding the application of the new paradigms of chaos theory to social sciences as compared to physical sciences. This study examines what role chaos theory has within the education process and what effect it has by describing the views of university faculty regarding chaos and education. The participants in this study…

  8. Error function attack of chaos synchronization based encryption schemes.

    Science.gov (United States)

    Wang, Xingang; Zhan, Meng; Lai, C-H; Gang, Hu

    2004-03-01

    Different chaos synchronization based encryption schemes are reviewed and compared from the practical point of view. As an efficient cryptanalysis tool for chaos encryption, a proposal based on the error function attack is presented systematically and used to evaluate system security. We define a quantitative measure (quality factor) of the effective applicability of a chaos encryption scheme, which takes into account the security, the encryption speed, and the robustness against channel noise. A comparison is made of several encryption schemes and it is found that a scheme based on one-way coupled chaotic map lattices performs outstandingly well, as judged from quality factor. Copyright 2004 American Institute of Physics.

  9. Transient chaos - a resolution of breakdown of quantum-classical correspondence in optomechanics

    Science.gov (United States)

    Wang, Guanglei; Lai, Ying-Cheng; Grebogi, Celso

    2016-01-01

    Recently, the phenomenon of quantum-classical correspondence breakdown was uncovered in optomechanics, where in the classical regime the system exhibits chaos but in the corresponding quantum regime the motion is regular - there appears to be no signature of classical chaos whatsoever in the corresponding quantum system, generating a paradox. We find that transient chaos, besides being a physically meaningful phenomenon by itself, provides a resolution. Using the method of quantum state diffusion to simulate the system dynamics subject to continuous homodyne detection, we uncover transient chaos associated with quantum trajectories. The transient behavior is consistent with chaos in the classical limit, while the long term evolution of the quantum system is regular. Transient chaos thus serves as a bridge for the quantum-classical transition (QCT). Strikingly, as the system transitions from the quantum to the classical regime, the average chaotic transient lifetime increases dramatically (faster than the Ehrenfest time characterizing the QCT for isolated quantum systems). We develop a physical theory to explain the scaling law. PMID:27748418

  10. Relations between distributional, Li-Yorke and ω chaos

    International Nuclear Information System (INIS)

    Guirao, Juan Luis Garcia; Lampart, Marek

    2006-01-01

    The forcing relations between notions of distributional, Li-Yorke and ω 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 ω chaotic, not distributionally chaotic and has zero topological entropy

  11. Chaos and the classical limit of quantum systems

    Energy Technology Data Exchange (ETDEWEB)

    Hogg, T; Huberman, B A [Xerox Palo Alto Research Center, CA (USA)

    1984-10-01

    The authors discuss the question of whether experiments can be designed to test the existence of quantum chaos. In particular, they show that high energies are not sufficient to guarantee that an initially localized wave packet will behave classically for long times. Computer simulations illustrating these ideas are presented and the question whether experiments can be designed to observe quantum chaos is commented on.

  12. 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.

  13. The Application of Chaos Theory to the Career-Plateaued Worker.

    Science.gov (United States)

    Duffy, Jean Ann

    2000-01-01

    Applies some of the principles of chaos theory to career-plateaued workers on the basis of a case study. Concludes that chaos theory provides career practitioners a useful application for working with this type of client. (Author/JDM)

  14. Defects and spatiotemporal disorder in a pattern of falling liquid columns

    Science.gov (United States)

    Brunet, Philippe; Limat, Laurent

    2004-10-01

    Disordered regimes of a one-dimensional pattern of liquid columns hanging below an overflowing circular dish are investigated experimentally. The interaction of two basic dynamical modes (oscillations and drift) combined with the occurrence of defects (birth of new columns, disappearances by coalescences of two columns) leads to spatiotemporal chaos. When the flow rate is progressively increased, a continuous transition between transient and permanent chaos is pointed into evidence. We introduce the rate of defects as the sole relevant quantity to quantify this “turbulence” without ambiguity. Statistics on both transient and endlessly chaotic regimes enable to define a critical flow rate around which exponents are extracted. Comparisons are drawn with other interfacial pattern-forming systems, where transition towards chaos follows similar steps. Qualitatively, careful examinations of the global dynamics show that the contamination processes are nonlocal and involve the propagation of blocks of elementary laminar states (such as propagative domains or local oscillations), emitted near the defects, which turn out to be essential ingredients of this self-sustained disorder.

  15. A quantum correction to chaos

    Energy Technology Data Exchange (ETDEWEB)

    Fitzpatrick, A. Liam [Department of Physics, Boston University,590 Commonwealth Avenue, Boston, MA 02215 (United States); Kaplan, Jared [Department of Physics and Astronomy, Johns Hopkins University,3400 N. Charles St, Baltimore, MD 21218 (United States)

    2016-05-12

    We use results on Virasoro conformal blocks to study chaotic dynamics in CFT{sub 2} at large central charge c. The Lyapunov exponent λ{sub L}, which is a diagnostic for the early onset of chaos, receives 1/c corrections that may be interpreted as λ{sub L}=((2π)/β)(1+(12/c)). 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 λ{sub L} that emerges at large c, focusing on CFT{sub 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.

  16. On the definition of 'chaos'

    International Nuclear Information System (INIS)

    Kolesov, Andrei Yu; Rozov, Nikolai Kh

    2009-01-01

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

  17. 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...

  18. Many-Body Quantum Chaos and Entanglement in a Quantum Ratchet

    Science.gov (United States)

    Valdez, Marc Andrew; Shchedrin, Gavriil; Heimsoth, Martin; Creffield, Charles E.; Sols, Fernando; Carr, Lincoln D.

    2018-06-01

    We uncover signatures of quantum chaos in the many-body dynamics of a Bose-Einstein condensate-based quantum ratchet in a toroidal trap. We propose measures including entanglement, condensate depletion, and spreading over a fixed basis in many-body Hilbert space, which quantitatively identify the region in which quantum chaotic many-body dynamics occurs, where random matrix theory is limited or inaccessible. With these tools, we show that many-body quantum chaos is neither highly entangled nor delocalized in the Hilbert space, contrary to conventionally expected signatures of quantum chaos.

  19. Improved particle swarm optimization combined with chaos

    International Nuclear Information System (INIS)

    Liu Bo; Wang Ling; Jin Yihui; Tang Fang; Huang Dexian

    2005-01-01

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

  20. Entanglement as a signature of quantum chaos.

    Science.gov (United States)

    Wang, Xiaoguang; Ghose, Shohini; Sanders, Barry C; Hu, Bambi

    2004-01-01

    We explore the dynamics of entanglement in classically chaotic systems by considering a multiqubit system that behaves collectively as a spin system obeying the dynamics of the quantum kicked top. In the classical limit, the kicked top exhibits both regular and chaotic dynamics depending on the strength of the chaoticity parameter kappa in the Hamiltonian. We show that the entanglement of the multiqubit system, considered for both the bipartite and the pairwise entanglement, yields a signature of quantum chaos. Whereas bipartite entanglement is enhanced in the chaotic region, pairwise entanglement is suppressed. Furthermore, we define a time-averaged entangling power and show that this entangling power changes markedly as kappa moves the system from being predominantly regular to being predominantly chaotic, thus sharply identifying the edge of chaos. When this entangling power is averaged over all states, it yields a signature of global chaos. The qualitative behavior of this global entangling power is similar to that of the classical Lyapunov exponent.

  1. 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.

  2. Dynamics and chaos control of gyrostat satellite

    International Nuclear Information System (INIS)

    Aslanov, Vladimir; Yudintsev, Vadim

    2012-01-01

    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.

  3. Controlling chaos and synchronization for new chaotic system using linear feedback control

    International Nuclear Information System (INIS)

    Yassen, M.T.

    2005-01-01

    This paper is devoted to study the problem of controlling chaos for new chaotic dynamical system (four-scroll dynamical system). Linear feedback control is used to suppress chaos to unstable equilibria and to achieve chaos synchronization of two identical four-scroll systems. Routh-Hurwitz criteria is used to study the conditions of the asymptotic stability of the equilibrium points of the controlled system. The sufficient conditions for achieving synchronization of two identical four-scroll systems are derived by using Lyapunov stability theorem. Numerical simulations are presented to demonstrate the effectiveness of the proposed chaos control and synchronization schemes

  4. Multi-scaled explorations of binding-induced folding of intrinsically disordered protein inhibitor IA3 to its target enzyme.

    Directory of Open Access Journals (Sweden)

    Jin Wang

    2011-04-01

    Full Text Available Biomolecular function is realized by recognition, and increasing evidence shows that recognition is determined not only by structure but also by flexibility and dynamics. We explored a biomolecular recognition process that involves a major conformational change - protein folding. In particular, we explore the binding-induced folding of IA3, an intrinsically disordered protein that blocks the active site cleft of the yeast aspartic proteinase saccharopepsin (YPrA by folding its own N-terminal residues into an amphipathic alpha helix. We developed a multi-scaled approach that explores the underlying mechanism by combining structure-based molecular dynamics simulations at the residue level with a stochastic path method at the atomic level. Both the free energy profile and the associated kinetic paths reveal a common scheme whereby IA3 binds to its target enzyme prior to folding itself into a helix. This theoretical result is consistent with recent time-resolved experiments. Furthermore, exploration of the detailed trajectories reveals the important roles of non-native interactions in the initial binding that occurs prior to IA3 folding. In contrast to the common view that non-native interactions contribute only to the roughness of landscapes and impede binding, the non-native interactions here facilitate binding by reducing significantly the entropic search space in the landscape. The information gained from multi-scaled simulations of the folding of this intrinsically disordered protein in the presence of its binding target may prove useful in the design of novel inhibitors of aspartic proteinases.

  5. Intermittency route to chaos in a biochemical system.

    Science.gov (United States)

    De la Fuente, I M; Martinez, L; Veguillas, J

    1996-01-01

    The numerical analysis of a glycolytic model performed through the construction of a system of three differential-delay equations reveals a phenomenon of intermittency route to chaos. In our biochemical system, the consideration of delay time variations under constant input flux as well as frequency variations of the periodic substrate input flux allows us, in both cases, to observe a type of transition to chaos different from the 'Feigenbaum route'.

  6. Chaos synchronization of the fractional-order Chen's system

    International Nuclear Information System (INIS)

    Zhu Hao; Zhou Shangbo; He Zhongshi

    2009-01-01

    In this paper, based on the stability theorem of linear fractional systems, a necessary condition is given to check the chaos synchronization of fractional systems with incommensurate order. Chaos synchronization is studied by utilizing the Pecora-Carroll (PC) method and the coupling method. The necessary condition can also be used as a tool to confirm results of a numerical simulation. Numerical simulation results show the effectiveness of the necessary condition.

  7. Aram Chaos Rocks

    Science.gov (United States)

    2005-01-01

    8 September 2005 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows outcrops of light-toned, sedimentary rock among darker-toned mesas in Aram Chaos. Dark, windblown megaripples -- large ripples -- are also present at this location. Location near: 3.0oN, 21.6oW Image width: width: 3 km (1.9 mi) Illumination from: lower left Season: Northern Autumn

  8. Chaos and Structures in Nonlinear Plasmas

    Science.gov (United States)

    Chen, James

    In recent decades, the concepts and applications of chaos, complexity, and nonlinear dynamics have profoundly influenced scientific as well as literary thinking. Some aspects of these concepts are used in almost all of the geophysical disciplines. Chaos and Structures in Nonlinear Plasmas, written by two respected plasma physicists, focuses on nonlinear phenomena in laboratory and space plasmas, which are rich in nonlinear and complex collective effects. Chaos is treated only insofar as it relates to some aspects of nonlinear plasma physics.At the outset, the authors note that plasma physics research has made fundamental contributions to modern nonlinear sciences. For example, the Poincare surface of section technique was extensively used in studies of stochastic field lines in magnetically confined plasmas and turbulence. More generally, nonlinearity in plasma waves and wave-wave and wave-particle interactions critically determines the propagation of energy through a plasma medium. The book also makes it clear that the importance of understanding nonlinear waves goes beyond plasma physics, extending to such diverse fields as solid state physics, fluid dynamics, atmospheric physics, and optics. In space physics, non-linear plasma physics is essential for interpreting in situ as well as remote-sensing data.

  9. Chaos, dynamical structure and climate variability

    Energy Technology Data Exchange (ETDEWEB)

    Stewart, H.B. [Brookhaven National Lab., Upton, NY (United States). Dept. of Applied Science

    1995-09-01

    Deterministic chaos in dynamical systems offers a new paradigm for understanding irregular fluctuations. Techniques for identifying deterministic chaos from observed data, without recourse to mathematical models, are being developed. Powerful methods exist for reconstructing multidimensional phase space from an observed time series of a single scalar variable; these methods are invaluable when only a single scalar record of the dynamics is available. However, in some applications multiple concurrent time series may be available for consideration as phase space coordinates. Here the authors propose some basic analytical tools for such multichannel time series data, and illustrate them by applications to a simple synthetic model of chaos, to a low-order model of atmospheric circulation, and to two high-resolution paleoclimate proxy data series. The atmospheric circulation model, originally proposed by Lorenz, has 27 principal unknowns; they establish that the chaotic attractor can be embedded in a subspace of eight dimensions by exhibiting a specific subset of eight unknowns which pass multichannel tests for false nearest neighbors. They also show that one of the principal unknowns in the 27-variable model--the global mean sea surface temperature--is of no discernible usefulness in making short-term forecasts.

  10. Chaos and its control in an impulsive differential system

    International Nuclear Information System (INIS)

    Jiang Guirong; Lu Qishao; Qian Linning

    2007-01-01

    In this paper, the existence of chaos and its control in an autonomous impulsive differential system are discussed both theoretically and numerically. The existence of a snap-back repeller, as well as the chaos in the sense of Li-Yorke, is proved based on the qualitative analysis using the Poincare map and the Lambert W-function. Moreover, the existence of the period-3 periodic window embedded in the chaotic region is also demonstrated. An algorithm of chaos control to stabilize the unstable periodic solutions is proposed. Detailed numerical results of chaotic attractors and stabilization of unstable periodic orbits by the impulsive effects, which are illustrated by an example, are in good agreement with the theoretical analysis

  11. 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...

  12. 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.

  13. Suppression of chaos at slow variables by rapidly mixing fast dynamics

    Science.gov (United States)

    Abramov, R.

    2012-04-01

    One of the key questions about chaotic multiscale systems is how the fast dynamics affects chaos at the slow variables, and, therefore, impacts uncertainty and predictability of the slow dynamics. Here we demonstrate that the linear slow-fast coupling with the total energy conservation property promotes the suppression of chaos at the slow variables through the rapid mixing at the fast variables, both theoretically and through numerical simulations. A suitable mathematical framework is developed, connecting the slow dynamics on the tangent subspaces to the infinite-time linear response of the mean state to a constant external forcing at the fast variables. Additionally, it is shown that the uncoupled dynamics for the slow variables may remain chaotic while the complete multiscale system loses chaos and becomes completely predictable at the slow variables through increasing chaos and turbulence at the fast variables. This result contradicts the common sense intuition, where, naturally, one would think that coupling a slow weakly chaotic system with another much faster and much stronger mixing system would result in general increase of chaos at the slow variables.

  14. Quantum chaos: entropy signatures

    International Nuclear Information System (INIS)

    Miller, P.A.; Sarkar, S.; Zarum, R.

    1998-01-01

    A definition of quantum chaos is given in terms of entropy production rates for a quantum system coupled weakly to a reservoir. This allows the treatment of classical and quantum chaos on the same footing. In the quantum theory the entropy considered is the von Neumann entropy and in classical systems it is the Gibbs entropy. The rate of change of the coarse-grained Gibbs entropy of the classical system with time is given by the Kolmogorov-Sinai (KS) entropy. The relation between KS entropy and the rate of change of von Neumann entropy is investigated for the kicked rotator. For a system which is classically chaotic there is a linear relationship between these two entropies. Moreover it is possible to construct contour plots for the local KS entropy and compare it with the corresponding plots for the rate of change of von Neumann entropy. The quantitative and qualitative similarities of these plots are discussed for the standard map (kicked rotor) and the generalised cat maps. (author)

  15. 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...

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

    International Nuclear Information System (INIS)

    Zhang, G; Yang, S-Z; He, L-F

    2008-01-01

    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

  17. Parrondo’s paradox for chaos control and anticontrol of fractional-order systems

    International Nuclear Information System (INIS)

    Danca, Marius-F; Tang, Wallace K S

    2016-01-01

    We present the generalized forms of Parrondo’s paradox existing in fractional-order nonlinear systems. The generalization is implemented by applying a parameter switching (PS) algorithm to the corresponding initial value problems associated with the fractional-order nonlinear systems. The PS algorithm switches a system parameter within a specific set of N ≥ 2 values when solving the system with some numerical integration method. It is proven that any attractor of the concerned system can be approximated numerically. By replacing the words “winning” and “loosing” in the classical Parrondo’s paradox with “order” and “chaos', respectively, the PS algorithm leads to the generalized Parrondo’s paradox: chaos 1 + chaos 2 + ··· + chaos N = order and order 1 + order 2 + ··· + order N = chaos. Finally, the concept is well demonstrated with the results based on the fractional-order Chen system. (paper)

  18. Intrinsic intensity fluctuations in random lasers

    International Nuclear Information System (INIS)

    Molen, Karen L. van der; Mosk, Allard P.; Lagendijk, Ad

    2006-01-01

    We present a quantitative experimental and theoretical study of intensity fluctuations in the emitted light of a random laser that has different realizations of disorder for every pump pulse. A model that clarifies these intrinsic fluctuations is developed. We describe the output versus input power graphs of the random laser with an effective spontaneous emission factor (β factor)

  19. The intrinsically disordered structural platform of the plant defence hub protein RPM1-interacting protein 4 provides insights into its mode of action in the host-pathogen interface and evolution of the nitrate-induced domain protein family.

    Science.gov (United States)

    Sun, Xiaolin; Greenwood, David R; Templeton, Matthew D; Libich, David S; McGhie, Tony K; Xue, Bin; Yoon, Minsoo; Cui, Wei; Kirk, Christopher A; Jones, William T; Uversky, Vladimir N; Rikkerink, Erik H A

    2014-09-01

    Arabidopsis thaliana (At) RPM1-interacting protein 4 (RIN4), targeted by many defence-suppressing bacterial type III effectors and monitored by several resistance proteins, regulates plant immune responses to pathogen-associated molecular patterns and type III effectors. Little is known about the overall protein structure of AtRIN4, especially in its unbound form, and the relevance of structure to its diverse biological functions. AtRIN4 contains two nitrate-induced (NOI) domains and is a member of the NOI family. Using experimental and bioinformatic approaches, we demonstrate that the unbound AtRIN4 is intrinsically disordered under physiological conditions. The intrinsically disordered polypeptide chain of AtRIN4 is interspersed with molecular recognition features (MoRFs) and anchor-identified long-binding regions, potentially allowing it to undergo disorder-to-order transitions upon binding to partner(s). A poly-l-proline II structure, often responsible for protein recognition, is also identified in AtRIN4. By performing bioinformatics analyses on RIN4 homologues from different plant species and the NOI proteins from Arabidopsis, we infer the conservation of intrinsic disorder, MoRFs and long-binding regions of AtRIN4 in other plant species and the NOI family. Intrinsic disorder and MoRFs could provide RIN4 proteins with the binding promiscuity and plasticity required to act as hubs in a pivotal position within plant defence signalling cascades. © 2014 FEBS.

  20. A history of chaos theory.

    Science.gov (United States)

    Oestreicher, Christian

    2007-01-01

    Whether every effect can be precisely linked to a given cause or to a list of causes has been a matter of debate for centuries, particularly during the 17th century, when astronomers became capable of predicting the trajectories of planets. Recent mathematical models applied to physics have included the idea that given phenomena cannot be predicted precisely, although they can be predicted to some extent, in line with the chaos theory. Concepts such as deterministic models, sensitivity to initial conditions, strange attractors, and fractal dimensions are inherent to the development of this theory A few situations involving normal or abnormal endogenous rhythms in biology have been analyzed following the principles of chaos theory. This is particularly the case with cardiac arrhythmias, but less so with biological clocks and circadian rhythms.

  1. Magnetic field induced dynamical chaos.

    Science.gov (United States)

    Ray, Somrita; Baura, Alendu; Bag, Bidhan Chandra

    2013-12-01

    In this article, we have studied the dynamics of a particle having charge in the presence of a magnetic field. The motion of the particle is confined in the x-y plane under a two dimensional nonlinear potential. We have shown that constant magnetic field induced dynamical chaos is possible even for a force which is derived from a simple potential. For a given strength of the magnetic field, initial position, and velocity of the particle, the dynamics may be regular, but it may become chaotic when the field is time dependent. Chaotic dynamics is very often if the field is time dependent. Origin of chaos has been explored using the Hamiltonian function of the dynamics in terms of action and angle variables. Applicability of the present study has been discussed with a few examples.

  2. A history of chaos theory

    Science.gov (United States)

    Oestreicher, Christian

    2007-01-01

    Whether every effect can be precisely linked to a given cause or to a list of causes has been a matter of debate for centuries, particularly during the 17th century when astronomers became capable of predicting the trajectories of planets. Recent mathematical models applied to physics have included the idea that given phenomena cannot be predicted precisely although they can be predicted to some extent in line with the chaos theory Concepts such as deterministic models, sensitivity to initial conditions, strange attractors, and fractal dimensions are inherent to the development of this theory, A few situations involving normal or abnormal endogenous rhythms in biology have been analyzed following the principles of chaos theory This is particularly the case with cardiac arrhythmias, but less so with biological clocks and circadian rhythms. PMID:17969865

  3. Next-order spin-orbit contributions to chaos in compact binaries

    International Nuclear Information System (INIS)

    Wang Yuzhao; Wu Xin

    2011-01-01

    This paper is mainly devoted to numerically investigating the effects of the next-order spin-orbit interactions including the 2.5 post-Newtonian order term of the equations of motion and the second post-Newtonian order terms of the spin precession equations on chaos in the conservative Lagrangian dynamics of a spinning compact binary system. It is shown sufficiently through individual orbit simulations, the dependence of the invariant fast Lyapunov indicators on the variations of initial spin angles and the phase space scans for chaos, that the next-order spin-orbit contributions do play an important role in the amplification of chaos.

  4. Chaos in an imperfectly premixed model combustor.

    Science.gov (United States)

    Kabiraj, Lipika; Saurabh, Aditya; Karimi, Nader; Sailor, Anna; Mastorakos, Epaminondas; Dowling, Ann P; Paschereit, Christian O

    2015-02-01

    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.

  5. Control and synchronization of chaos in nonlinear systems and prospects for application. Pt.1

    International Nuclear Information System (INIS)

    Fang Jinqing

    1996-01-01

    Main progress in one challenging subject of nonlinear science--control and synchronization of chaos in nonlinear systems are reviewed systematically, including recent advance in controlling and synchronizing hyperchaos. Current methods and principles of schemes of chaos control and synchronization are classified and summarized in detail. Potential prospects for application are commented both in theory and experiment. The whole review is divided into two parts. In the first one, subject on the mechanism and method of chaos control are analyzed and discussed extensively. In the second one, the synchronization of non-chaos, chaos, hyperchaos and their control and application are described. Main trends for development of the subject is mentioned. (101 refs.)

  6. 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.

  7. Chaos based on Riemannian geometric approach to Abelian-Higgs dynamical system

    International Nuclear Information System (INIS)

    Kawabe, Tetsuji

    2003-01-01

    Based on the Riemannian geometric approach, we study chaos of the Abelian-Higgs dynamical system derived from a classical field equation consisting of a spatially homogeneous Abelian gauge field and Higgs field. Using the global indicator of chaos formulated by the sectional curvature of the ambient manifold, we show that this approach brings the same qualitative and quantitative information about order and chaos as has been provided by the Lyapunov exponents in the conventional and phenomenological approach. We confirm that the mechanism of chaos is a parametric instability of the system. By analyzing a close relation between the sectional curvature and the Gaussian curvature, we point out that the Toda-Brumer criterion becomes a sufficient condition to the criterion based on this geometric approach as to the stability condition

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

    International Nuclear Information System (INIS)

    Zhang Xiaohong; Min Lequan

    2005-01-01

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

  9. Chaos Theory and James Joyce's "ulysses": Leopold Bloom as a Human COMPLEX@SYSTEM^

    Science.gov (United States)

    Mackey, Peter Francis

    1995-01-01

    These four ideas apply as much to our lives as to the life of Leopold Bloom: (1) A trivial decision can wholly change a life. (2) A chance encounter can dramatically alter life's course. (3) A contingent nexus exists between consciousness and environment. (4) A structure of meaning helps us interpret life's chaos. These ideas also relate to a contemporary science called by some "chaos theory." The connection between Ulysses and chaos theory enhances our understanding of Bloom's day; it also suggests that this novel may be about the real process of life itself. The first chapter explains how Joyce's own essays and comments to friends compel attention to the links between Ulysses and chaos theory. His scientific contemporaries anticipated chaos theory, and their ideas seem to have rubbed off on him. We see this in his sense of trivial things and chance, his modernistic organizational impulses, and the contingent nature of Bloom's experience. The second chapter studies what chaos theory and Joyce's ideas tell us about "Ithaca," the episode which particularly implicates our processes of interpreting this text as well as life itself as we face their chaos. The third chapter examines Bloom's close feel for the aboriginal world, a contingency that clarifies his vulnerability to trivial changes. The fourth chapter studies how Bloom's stream of consciousness unfolds--from his chance encounters with trivial things. Beneath this stream's seeming chaos, Bloom's distinct personality endures, similar to how Joyce's schemas give Ulysses an imbedded, underlying order. The fifth chapter examines how trivial perturbations, such as Lyons' misunderstanding about "Throwaway," produce small crises for Bloom, exacerbating his seeming impotence before his lonely "fate.". The final chapter analyzes Bloom's views that fate and chance dictate his life. His views provide an opportunity to explore the implications chaos theory has for our understanding of free will and determinism. Ultimately

  10. Parameter identification of chaos system based on unknown parameter observer

    International Nuclear Information System (INIS)

    Wang Shaoming; Luo Haigeng; Yue Chaoyuan; Liao Xiaoxin

    2008-01-01

    Parameter identification of chaos system based on unknown parameter observer is discussed generally. Based on the work of Guan et al. [X.P. Guan, H.P. Peng, L.X. Li, et al., Acta Phys. Sinica 50 (2001) 26], the design of unknown parameter observer is improved. The application of the improved approach is extended greatly. The works in some literatures [X.P. Guan, H.P. Peng, L.X. Li, et al., Acta Phys. Sinica 50 (2001) 26; J.H. Lue, S.C. Zhang, Phys. Lett. A 286 (2001) 148; X.Q. Wu, J.A. Lu, Chaos Solitons Fractals 18 (2003) 721; J. Liu, S.H. Chen, J. Xie, Chaos Solitons Fractals 19 (2004) 533] are only the special cases of our Corollaries 1 and 2. Some observers for Lue system and a new chaos system are designed to test our improved method, and simulations results demonstrate the effectiveness and feasibility of the improved approach

  11. Geometric and dynamic perspectives on phase-coherent and noncoherent chaos.

    Science.gov (United States)

    Zou, Yong; Donner, Reik V; Kurths, Jürgen

    2012-03-01

    Statistically distinguishing between phase-coherent and noncoherent chaotic dynamics from time series is a contemporary problem in nonlinear sciences. In this work, we propose different measures based on recurrence properties of recorded trajectories, which characterize the underlying systems from both geometric and dynamic viewpoints. The potentials of the individual measures for discriminating phase-coherent and noncoherent chaotic oscillations are discussed. A detailed numerical analysis is performed for the chaotic Rössler system, which displays both types of chaos as one control parameter is varied, and the Mackey-Glass system as an example of a time-delay system with noncoherent chaos. Our results demonstrate that especially geometric measures from recurrence network analysis are well suited for tracing transitions between spiral- and screw-type chaos, a common route from phase-coherent to noncoherent chaos also found in other nonlinear oscillators. A detailed explanation of the observed behavior in terms of attractor geometry is given.

  12. Mesoscopic chaos mediated by Drude electron-hole plasma in silicon optomechanical oscillators

    Science.gov (United States)

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

    2017-01-01

    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 generation of dynamical chaos in silicon-based monolithic optomechanical oscillators, enabled by the strong and coupled nonlinearities of two-photon absorption induced Drude electron–hole plasma. Deterministic chaotic oscillation is achieved, and statistical and entropic characterization quantifies the chaos complexity at 60 fJ intracavity energies. The correlation dimension D2 is determined at 1.67 for the chaotic attractor, along with a maximal Lyapunov exponent rate of about 2.94 times the fundamental optomechanical oscillation for fast adjacent trajectory divergence. Nonlinear dynamical maps demonstrate the subharmonics, bifurcations and stable regimes, along with distinct transitional routes into chaos. This provides a CMOS-compatible and scalable architecture for understanding complex dynamics on the mesoscopic scale. PMID:28598426

  13. Intrinsic Motivation as a Mediator of Relationships Between Symptoms and Functioning Among Individuals With Schizophrenia Spectrum Disorders in a Diverse Urban Community

    OpenAIRE

    Yamada, Ann-Marie; Lee, Karen K.; Dinh, Tam Q.; Barrio, Concepción; Brekke, John S.

    2010-01-01

    This study investigated intrinsic motivation as a mediator of the relationship between clinical symptoms and functioning. The mediation model was tested with a sample of 166 adults with schizophrenia spectrum disorders attending psychosocial rehabilitation programs in a diverse urban community. Ethnic minority status was examined as a moderator of the mediation model. Motivation was measured using items reflecting intrapsychic drive. Symptoms were assessed with the expanded Brief Psychiatric ...

  14. Onset of dynamical chaos in topologically massive gauge theories

    International Nuclear Information System (INIS)

    Giansanti, A.; Simic, P.D.

    1988-01-01

    The onset of dynamical chaos is studied numerically in (2+1)-dimensional non-Abelian field theory with the Chern-Simons topological term. In the limit of strong fields, slowly varying in space (spatially homogeneous fields), this theory is an analog to a system of three charged particles moving in a plane in an orthogonal magnetic field and under the influence of a quartic potential. The ''phase transition'' (order chaos) is observed within a narrow energy range. The threshold of the transition depends on the sign of the angular momentum of the field reflecting parity violation in the underlying field theory. The transition region is investigated in some detail and the hyperfine structure of order-chaos-order-... transitions is observed suggesting the necessity of probabilistic description

  15. Rank one chaos in a class of planar systems with heteroclinic cycle.

    Science.gov (United States)

    Chen, Fengjuan; Han, Maoan

    2009-12-01

    In this paper, we study rank one chaos in a class of planar systems with heteroclinic cycle. We first find a stable limit cycle inside the heteroclinic cycle. We then add an external periodic forcing to create rank one chaos. We follow a step-by-step procedure guided by the theory of rank one chaos to find experimental evidence of strange attractors with Sinai, Ruelle, and Bowen measures.

  16. Prediction of chaos in a Josephson junction by the Melnikov-function technique

    DEFF Research Database (Denmark)

    Bartuccelli, M.; Christiansen, Peter Leth; Pedersen, Niels Falsig

    1986-01-01

    The Melnikov function for prediction of Smale horseshoe chaos is applied to the rf-driven Josephson junction. Linear and quadratic damping resistors are considered. In the latter case the analytic solution including damping and dc bias is used to obtain an improved threshold curve for the onset...... of chaos. The prediction is compared to new computational solutions. The Melnikov technique provides a good, but slightly low, estimate of the chaos threshold....

  17. Fibrillation mechanism of a model intrinsically disordered protein revealed by 2D correlation deep UV resonance Raman spectroscopy.

    Science.gov (United States)

    Sikirzhytski, Vitali; Topilina, Natalya I; Takor, Gaius A; Higashiya, Seiichiro; Welch, John T; Uversky, Vladimir N; Lednev, Igor K

    2012-05-14

    Understanding of numerous biological functions of intrinsically disordered proteins (IDPs) is of significant interest to modern life science research. A large variety of serious debilitating diseases are associated with the malfunction of IDPs including neurodegenerative disorders and systemic amyloidosis. Here we report on the molecular mechanism of amyloid fibrillation of a model IDP (YE8) using 2D correlation deep UV resonance Raman spectroscopy. YE8 is a genetically engineered polypeptide, which is completely unordered at neutral pH yet exhibits all properties of a fibrillogenic protein at low pH. The very first step of the fibrillation process involves structural rearrangements of YE8 at the global structure level without the detectable appearance of secondary structural elements. The formation of β-sheet species follows the global structural changes and proceeds via the simultaneous formation of turns and β-strands. The kinetic mechanism revealed is an important new contribution to understanding of the general fibrillation mechanism proposed for IDP.

  18. Specifying the Links between Household Chaos and Preschool Children's Development

    Science.gov (United States)

    Martin, Anne; Razza, Rachel A.; Brooks-Gunn, Jeanne

    2012-01-01

    Household chaos has been linked to poorer cognitive, behavioural, and self-regulatory outcomes in young children, but the mechanisms responsible remain largely unknown. Using a diverse sample of families in Chicago, the present study tests for the independent contributions made by five indicators of household chaos: noise, crowding, family…

  19. Origin of chaos in 3-d Bohmian trajectories

    International Nuclear Information System (INIS)

    Tzemos, Athanasios C.; Contopoulos, George; Efthymiopoulos, Christos

    2016-01-01

    We study the 3-d Bohmian trajectories of a quantum system of three harmonic oscillators. We focus on the mechanism responsible for the generation of chaotic trajectories. We demonstrate the existence of a 3-d analogue of the mechanism found in earlier studies of 2-d systems [1,2], based on moving 2-d ‘nodal point–X-point complexes’. In the 3-d case, we observe a foliation of nodal point–X-point complexes, forming a ‘3-d structure of nodal and X-points’. Chaos is generated when the Bohmian trajectories are scattered at one or more close encounters with such a structure. - Highlights: • A mechanism for the emergence of 3-d Bohmian chaos is proposed. • We demonstrate the existence of a 3-d structure of nodal and X-points. • Chaos is generated when the trajectories are scattered by the X-points.

  20. Origin of chaos in 3-d Bohmian trajectories

    Energy Technology Data Exchange (ETDEWEB)

    Tzemos, Athanasios C., E-mail: thanasistzemos@gmail.com; Contopoulos, George, E-mail: gcontop@academyofathens.gr; Efthymiopoulos, Christos, E-mail: cefthim@academyofathens.gr

    2016-11-25

    We study the 3-d Bohmian trajectories of a quantum system of three harmonic oscillators. We focus on the mechanism responsible for the generation of chaotic trajectories. We demonstrate the existence of a 3-d analogue of the mechanism found in earlier studies of 2-d systems [1,2], based on moving 2-d ‘nodal point–X-point complexes’. In the 3-d case, we observe a foliation of nodal point–X-point complexes, forming a ‘3-d structure of nodal and X-points’. Chaos is generated when the Bohmian trajectories are scattered at one or more close encounters with such a structure. - Highlights: • A mechanism for the emergence of 3-d Bohmian chaos is proposed. • We demonstrate the existence of a 3-d structure of nodal and X-points. • Chaos is generated when the trajectories are scattered by the X-points.

  1. Communication with spatial periodic chaos synchronization

    International Nuclear Information System (INIS)

    Zhou, J.; Huang, H.B.; Qi, G.X.; Yang, P.; Xie, X.

    2005-01-01

    Based on the spatial periodic chaos synchronization in coupled ring and linear arrays, we proposed a random high-dimensional chaotic encryption scheme. The transmitter can choose hyperchaotic signals randomly from the ring at any different time and simultaneously transmit the information of chaotic oscillators in the ring to receiver through public channel, so that the message can be masked by different hyperchaotic signals in different time intervals during communication, and the receiver can decode the message based on chaos synchronization but the attacker does not know the random hyperchaotic dynamics and cannot decode the message. Furthermore, the high sensitivity to the symmetry of the coupling structure makes the attacker very difficult to obtain any useful message from the channel

  2. Kac-Moody algebras and controlled chaos

    International Nuclear Information System (INIS)

    Wesley, Daniel H

    2007-01-01

    Compactification can control chaotic Mixmaster behaviour in gravitational systems with p-form matter: we consider this in light of the connection between supergravity models and Kac-Moody algebras. We show that different compactifications define 'mutations' of the algebras associated with the noncompact theories. We list the algebras obtained in this way, and find novel examples of wall systems determined by Lorentzian (but not hyperbolic) algebras. Cosmological models with a smooth pre-big bang phase require that chaos is absent: we show that compactification alone cannot eliminate chaos in the simplest compactifications of the heterotic string on a Calabi-Yau, or M theory on a manifold of G 2 holonomy. (fast track communication)

  3. Two Isoforms of Yersinia pestis Plasminogen Activator Pla: Intraspecies Distribution, Intrinsic Disorder Propensity, and Contribution to Virulence.

    Science.gov (United States)

    Dentovskaya, Svetlana V; Platonov, Mikhail E; Svetoch, Tat'yana E; Kopylov, Pavel Kh; Kombarova, Tat'yana I; Ivanov, Sergey A; Shaikhutdinova, Rima Z; Kolombet, Lyubov' V; Chauhan, Sadhana; Ablamunits, Vitaly G; Motin, Vladimir L; Uversky, Vladimir N; Anisimov, Andrey P

    2016-01-01

    It has been shown previously that several endemic Y. pestis isolates with limited virulence contained the I259 isoform of the outer membrane protease Pla, while the epidemic highly virulent strains possessed only the T259 Pla isoform. Our sequence analysis of the pla gene from 118 Y. pestis subsp. microtus strains revealed that the I259 isoform was present exclusively in the endemic strains providing a convictive evidence of more ancestral origin of this isoform. Analysis of the effects of the I259T polymorphism on the intrinsic disorder propensity of Pla revealed that the I259T mutation slightly increases the intrinsic disorder propensity of the C-terminal tail of Pla and makes this protein slightly more prone for disorder-based protein-protein interactions, suggesting that the T259 Pla could be functionally more active than the I259 Pla. This assumption was proven experimentally by assessing the coagulase and fibrinolytic activities of the two Pla isoforms in human plasma, as well as in a direct fluorometric assay with the Pla peptide substrate. The virulence testing of Pla-negative or expressing the I259 and T259 Pla isoforms Y. pestis subsp. microtus and subsp. pestis strains did not reveal any significant difference in LD50 values and dose-dependent survival assays between them by using a subcutaneous route of challenge of mice and guinea pigs or intradermal challenge of mice. However, a significant decrease in time-to-death was observed in animals infected with the epidemic T259 Pla-producing strains as compared to the parent Pla-negative variants. Survival curves of the endemic I259 Pla+ strains fit between them, but significant difference in mean time to death post infection between the Pla-strains and their I259 Pla+ variants could be seen only in the isogenic set of subsp. pestis strains. These findings suggest an essential role for the outer membrane protease Pla evolution in Y. pestis bubonic infection exacerbation that is necessary for intensification

  4. Global chaos synchronization of three coupled nonlinear autonomous systems and a novel method of chaos encryption

    International Nuclear Information System (INIS)

    An Xinlei; Yu Jianning; Chu Yandong; Zhang Jiangang; Zhang Li

    2009-01-01

    In this paper, we discussed the fixed points and their linear stability of a new nonlinear autonomous system that introduced by J.C. Sprott. Based on Lyapunov stabilization theorem, a global chaos synchronization scheme of three coupled identical systems is investigated. By choosing proper coupling parameters, the states of all the three systems can be synchronized. Then this method was applied to secure communication through chaotic masking, used three coupled identical systems, propose a novel method of chaos encryption, after encrypting in the previous two transmitters, information signal can be recovered exactly at the receiver end. Simulation results show that the method can realize monotonous synchronization. Further more, the information signal can be recovered undistorted when applying this method to secure communication.

  5. SECULAR CHAOS AND THE PRODUCTION OF HOT JUPITERS

    International Nuclear Information System (INIS)

    Wu Yanqin; Lithwick, Yoram

    2011-01-01

    In a planetary system with two or more well-spaced, eccentric, inclined planets, secular interactions may lead to chaos. The innermost planet may gradually become very eccentric and/or inclined as a result of the secular degrees of freedom drifting toward equipartition of angular momentum deficit. Secular chaos is known to be responsible for the eventual destabilization of Mercury in our own solar system. Here we focus on systems with three giant planets. We characterize the secular chaos and demonstrate the criterion for it to occur, but leave a detailed understanding of secular chaos to a companion paper. After an extended period of eccentricity diffusion, the inner planet's pericenter can approach the star to within a few stellar radii. Strong tidal interactions and ensuing tidal dissipation extract orbital energy from the planet and pull it inward, creating a hot Jupiter. In contrast to other proposed channels for the production of hot Jupiters, such a scenario (which we term 'secular migration') explains a range of observations: the pile-up of hot Jupiters at 3 day orbital periods, the fact that hot Jupiters are in general less massive than other radial velocity planets, that they may have misaligned inclinations with respect to stellar spin, and that they have few easily detectable companions (but may have giant companions in distant orbits). Secular migration can also explain close-in planets as low in mass as Neptune; and an aborted secular migration can explain the 'warm Jupiters' at intermediate distances. In addition, the frequency of hot Jupiters formed via secular migration increases with stellar age. We further suggest that secular chaos may be responsible for the observed eccentricities of giant planets at larger distances and that these planets could exhibit significant spin-orbit misalignment.

  6. Large-scale analysis of intrinsic disorder flavors and associated functions in the protein sequence universe.

    Science.gov (United States)

    Necci, Marco; Piovesan, Damiano; Tosatto, Silvio C E

    2016-12-01

    Intrinsic disorder (ID) in proteins has been extensively described for the last decade; a large-scale classification of ID in proteins is mostly missing. Here, we provide an extensive analysis of ID in the protein universe on the UniProt database derived from sequence-based predictions in MobiDB. Almost half the sequences contain an ID region of at least five residues. About 9% of proteins have a long ID region of over 20 residues which are more abundant in Eukaryotic organisms and most frequently cover less than 20% of the sequence. A small subset of about 67,000 (out of over 80 million) proteins is fully disordered and mostly found in Viruses. Most proteins have only one ID, with short ID evenly distributed along the sequence and long ID overrepresented in the center. The charged residue composition of Das and Pappu was used to classify ID proteins by structural propensities and corresponding functional enrichment. Swollen Coils seem to be used mainly as structural components and in biosynthesis in both Prokaryotes and Eukaryotes. In Bacteria, they are confined in the nucleoid and in Viruses provide DNA binding function. Coils & Hairpins seem to be specialized in ribosome binding and methylation activities. Globules & Tadpoles bind antigens in Eukaryotes but are involved in killing other organisms and cytolysis in Bacteria. The Undefined class is used by Bacteria to bind toxic substances and mediate transport and movement between and within organisms in Viruses. Fully disordered proteins behave similarly, but are enriched for glycine residues and extracellular structures. © 2016 The Protein Society.

  7. Socioeconomic Risk Moderates the Link between Household Chaos and Maternal Executive Function

    Science.gov (United States)

    Deater-Deckard, Kirby; Chen, Nan; Wang, Zhe; Bell, Martha Ann

    2012-01-01

    We examined the link between household chaos (i.e., noise, clutter, disarray, lack of routines) and maternal executive function (i.e., effortful regulation of attention and memory), and whether it varied as a function of socioeconomic risk (i.e., single parenthood, lower mother and father educational attainment, housing situation, and father unemployment). We hypothesized that: 1) higher levels of household chaos would be linked with poorer maternal executive function, even when controlling for other measures of cognitive functioning (e.g., verbal ability), and 2) this link would be strongest in the most socioeconomically distressed or lowest-socioeconomic status households. The diverse sample included 153 mothers from urban and rural areas who completed a questionnaire and a battery of cognitive executive function tasks and a verbal ability task in the laboratory. Results were mixed for hypothesis 1, and consistent with hypothesis 2. Two-thirds of the variance overlapped between household chaos and maternal executive function, but only in families with high levels of socioeconomic risk. This pattern was not found for chaos and maternal verbal ability, suggesting that the potentially deleterious effects of household chaos may be specific to maternal executive function. The findings implicate household chaos as a powerful statistical predictor of maternal executive function in socioeconomically distressed contexts. PMID:22563703

  8. Mapping multivalency and differential affinities within large intrinsically disordered protein complexes with segmental motion analysis.

    Science.gov (United States)

    Milles, Sigrid; Lemke, Edward A

    2014-07-07

    Intrinsically disordered proteins (IDPs) can bind to multiple interaction partners. Numerous binding regions in the IDP that act in concert through complex cooperative effects facilitate such interactions, but complicate studying IDP complexes. To address this challenge we developed a combined fluorescence correlation and time-resolved polarization spectroscopy approach to study the binding properties of the IDP nucleoporin153 (Nup153) to nuclear transport receptors (NTRs). The detection of segmental backbone mobility of Nup153 within the unperturbed complex provided a readout of local, region-specific binding properties that are usually masked in measurements of the whole IDP. The binding affinities of functionally and structurally diverse NTRs to distinct regions of Nup153 can differ by orders of magnitudes-a result with implications for the diversity of transport routes in nucleocytoplasmic transport. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Controlling chaos (OGY) implemented on a reconstructed ecological two-dimensional map

    International Nuclear Information System (INIS)

    Sakai, Kenshi; Noguchi, Yuko

    2009-01-01

    We numerically demonstrate a way to stabilize an unstable equilibrium in the ecological dynamics reconstructed from real-world time series data, namely, alternate bearing of citrus trees. The reconstruction of deterministic dynamics from short and noisy ecological time series has been a crucial issue since May's historical work [May RM. Biological populations with nonoverlapping generations: stable points, stable cycles and chaos. Science 1974;186:645-7; Hassell MP, Lawton JH, May RM. Patterns of dynamical behavior in single species populations. J Anim Ecol 1976;45:471-86]. Response surface methodology, followed by the differential equation approach is recognized as a promising method of reconstruction [Turchin P. Rarity of density dependence or population with lags? Nature 1990;344:660-3; Turchin P, Taylor AD. Complex dynamics in ecological time series. Ecology 1992;73:289-305; Ellner S, Turchin P. Chaos in a noisy world: new method and evidence from time series analysis. Am Nat 1995;145(3):343-75; Turchin P, Ellner S. Living on the edge of chaos: population dynamics of fennoscandian voles. Ecology 2000;8(11):3116]. Here, the reconstructed ecological dynamics was described by a two-dimensional map derived from the response surface created by the data. The response surface created was experimentally validated in four one-year forward predictions in 2001, 2002, 2003 and 2004. Controlling chaos is very important when applying chaos theory to solving real-world problems. The OGY method is the first and most popular methodology for controlling chaos and can be used as an algorithm to stabilize an unstable fixed point by putting the state on a stable manifold [Ott E, Grebogi C, York JA. Controlling chaos. Phys Rev Lett 1990;64:1996-9]. We applied the OGY method to our reconstructed two-dimensional map and as a result were able to control alternate bearing in numerical simulations.

  10. Chaos in reversed-field-pinch plasma simulation and experiment

    International Nuclear Information System (INIS)

    Watts, C.; Newman, D.E.; Sprott, J.C.

    1994-01-01

    We investigate the possibility that chaos and simple determinism are governing the dynamics of reversed-field-pinch (RFP) plasmas using data from both numerical simulations and experiment. A large repertoire of nonlinear-analysis techniques is used to identify low-dimensional chaos. These tools include phase portraits and Poincare sections, correlation dimension, the spectrum of Lyapunov exponents, and short-term predictability. In addition, nonlinear-noise-reduction techniques are applied to the experimental data in an attempt to extract any underlying deterministic dynamics. Two model systems are used to simulate the plasma dynamics. These are the DEBS computer code, which models global RFP dynamics, and the dissipative trapped-electron-mode model, which models drift-wave turbulence. Data from both simulations show strong indications of low-dimensional chaos and simple determinism. Experimental data were obtained from the Madison Symmetric Torus RFP and consist of a wide array of both global and local diagnostic signals. None of the signals shows any indication of low-dimensional chaos or other simple determinism. Moreover, most of the analysis tools indicate that the experimental system is very high dimensional with properties similar to noise. Nonlinear noise reduction is unsuccessful at extracting an underlying deterministic system

  11. 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.

  12. Structural properties of the intrinsically disordered, multiple calcium ion-binding otolith matrix macromolecule-64 (OMM-64).

    Science.gov (United States)

    Poznar, Monika; Hołubowicz, Rafał; Wojtas, Magdalena; Gapiński, Jacek; Banachowicz, Ewa; Patkowski, Adam; Ożyhar, Andrzej; Dobryszycki, Piotr

    2017-11-01

    Fish otoliths are calcium carbonate biominerals that are involved in hearing and balance sensing. An organic matrix plays a crucial role in their formation. Otolith matrix macromolecule-64 (OMM-64) is a highly acidic, calcium-binding protein (CBP) found in rainbow trout otoliths. It is a component of high-molecular-weight aggregates, which influence the size, shape and polymorph of calcium carbonate in vitro. In this study, a protocol for the efficient expression and purification of OMM-64 was developed. For the first time, the complete structural characteristics of OMM-64 were described. Various biophysical methods were combined to show that OMM-64 occurs as an intrinsically disordered monomer. Under denaturing conditions (pH, temperature) OMM-64 exhibits folding propensity. It was determined that OMM-64 binds approximately 61 calcium ions with millimolar affinity. The folding-unfolding experiments showed that calcium ions induced the collapse of OMM-64. The effect of other counter ions present in trout endolymph on OMM-64 conformational changes was studied. The significance of disordered properties of OMM-64 and the possible function of this protein is discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

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

    International Nuclear Information System (INIS)

    Medvinsky, Alexander B.; Rusakov, Alexey V.

    2011-01-01

    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

  14. 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

  15. Dynamical chaos: systems of classical mechanics

    International Nuclear Information System (INIS)

    Loskutov, A Yu

    2007-01-01

    This article is a methodological manual for those who are interested in chaotic dynamics. An exposition is given on the foundations of the theory of deterministic chaos that originates in classical mechanics systems. Fundamental results obtained in this area are presented, such as elements of the theory of nonlinear resonance and the Kolmogorov-Arnol'd-Moser theory, the Poincare-Birkhoff fixed-point theorem, and the Mel'nikov method. Particular attention is given to the analysis of the phenomena underlying the self-similarity and nature of chaos: splitting of separatrices and homoclinic and heteroclinic tangles. Important properties of chaotic systems - unpredictability, irreversibility, and decay of temporal correlations - are described. Models of classical statistical mechanics with chaotic properties, which have become popular in recent years - billiards with oscillating boundaries - are considered. It is shown that if a billiard has the property of well-developed chaos, then perturbations of its boundaries result in Fermi acceleration. But in nearly-integrable billiard systems, excitations of the boundaries lead to a new phenomenon in the ensemble of particles, separation of particles in accordance their velocities. If the initial velocity of the particles exceeds a certain critical value characteristic of the given billiard geometry, the particles accelerate; otherwise, they decelerate. (methodological notes)

  16. Transient chaos in a globally coupled system of nearly conservative Hamiltonian Duffing oscillators

    International Nuclear Information System (INIS)

    Sabarathinam, S.; Thamilmaran, K.

    2015-01-01

    Highlights: •We have examined transient chaos in globally coupled oscillators. •We analyze transient chaos using new techniques. •We give experimental confirmation of transient chaos. -- Abstract: In this work, transient chaos in a ring and globally coupled system of nearly conservative Hamiltonian Duffing oscillators is reported. The networks are formed by coupling of three, four and six Duffing oscillators. The nearly conservative Hamiltonian nature of the coupled system is proved by stability analysis. The transient phenomenon is confirmed through various numerical investigations such as recurrence analysis, 0–1 test and Finite Time Lyapunov Exponents. Further, the effect of damping and the average transient lifetime of three, four and six coupled schemes for randomly generated initial conditions have been analyzed. The experimental confirmation of transient chaos in an illustrative system of three ringly coupled Duffing oscillators is also presented

  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 as the hub of systems dynamics. The part I-The attitude control of spacecraft by involving in the heteroclinic chaos

    Science.gov (United States)

    Doroshin, Anton V.

    2018-06-01

    In this work the chaos in dynamical systems is considered as a positive aspect of dynamical behavior which can be applied to change systems dynamical parameters and, moreover, to change systems qualitative properties. From this point of view, the chaos can be characterized as a hub for the system dynamical regimes, because it allows to interconnect separated zones of the phase space of the system, and to fulfill the jump into the desirable phase space zone. The concretized aim of this part of the research is to focus on developing the attitude control method for magnetized gyrostat-satellites, which uses the passage through the intentionally generated heteroclinic chaos. The attitude dynamics of the satellite/spacecraft in this case represents the series of transitions from the initial dynamical regime into the chaotic heteroclinic regime with the subsequent exit to the final target dynamical regime with desirable parameters of the attitude dynamics.

  19. Self-generation and management of spin-electromagnetic wave solitons and chaos

    International Nuclear Information System (INIS)

    Ustinov, Alexey B.; Kondrashov, Alexandr V.; Nikitin, Andrey A.; Kalinikos, Boris A.

    2014-01-01

    Self-generation of microwave spin-electromagnetic wave envelope solitons and chaos has been observed and studied. For the investigation, we used a feedback active ring oscillator based on artificial multiferroic, which served as a nonlinear waveguide. We show that by increasing the wave amplification in the feedback ring circuit, a transition from monochromatic auto-generation to soliton train waveform and then to dynamical chaos occurs in accordance with the Ruelle-Takens scenario. Management of spin-electromagnetic-wave solitons and chaos parameters by both dielectric permittivity and magnetic permeability of the multiferroic waveguiding structure is demonstrated.

  20. Bifurcation and chaos response of a cracked rotor with random disturbance

    Science.gov (United States)

    Leng, Xiaolei; Meng, Guang; Zhang, Tao; Fang, Tong

    2007-01-01

    The Monte-Carlo method is used to investigate the bifurcation and chaos characteristics of a cracked rotor with a white noise process as its random disturbance. Special attention is paid to the influence of the stiffness change ratio and the rotating speed ratio on the bifurcation and chaos response of the system. Numerical simulations show that the affect of the random disturbance is significant as the undisturbed response of the cracked rotor system is a quasi-periodic or chaos one, and such affect is smaller as the undisturbed response is a periodic one.