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Sample records for chaos intrinsically disordered

  1. Intrinsically Disordered Energy Landscapes

    Science.gov (United States)

    Chebaro, Yassmine; Ballard, Andrew J.; Chakraborty, Debayan; Wales, David J.

    2015-05-01

    Analysis of an intrinsically disordered protein (IDP) reveals an underlying multifunnel structure for the energy landscape. We suggest that such ‘intrinsically disordered’ landscapes, with a number of very different competing low-energy structures, are likely to characterise IDPs, and provide a useful way to address their properties. In particular, IDPs are present in many cellular protein interaction networks, and several questions arise regarding how they bind to partners. Are conformations resembling the bound structure selected for binding, or does further folding occur on binding the partner in a induced-fit fashion? We focus on the p53 upregulated modulator of apoptosis (PUMA) protein, which adopts an -helical conformation when bound to its partner, and is involved in the activation of apoptosis. Recent experimental evidence shows that folding is not necessary for binding, and supports an induced-fit mechanism. Using a variety of computational approaches we deduce the molecular mechanism behind the instability of the PUMA peptide as a helix in isolation. We find significant barriers between partially folded states and the helix. Our results show that the favoured conformations are molten-globule like, stabilised by charged and hydrophobic contacts, with structures resembling the bound state relatively unpopulated in equilibrium.

  2. Unusual biophysics of intrinsically disordered proteins.

    Science.gov (United States)

    Uversky, Vladimir N

    2013-05-01

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

  3. Intrinsically localized chaos in discrete nonlinear extended systems

    CERN Document Server

    Martínez, P J; Falo, F; Mazo, J J

    1999-01-01

    The phenomenon of intrinsic localization in discrete nonlinear extended systems, i.e. the (generic) existence of discrete breathers, is shown to be not restricted to periodic solutions but it also extends to more complex (chaotic) dynamical behaviour. We illustrate this with two different forced and damped systems exhibiting this type of solutions: In an anisotropic Josephson junction ladder, we obtain intrinsically localized chaotic solutions by following periodic rotobreather solutions through a cascade of period-doubling bifurcations. In an array of forced and damped van der Pol oscillators, they are obtained by numerical continuation (path-following) methods from the uncoupled limit, where its existence is trivially ascertained, following the ideas of the anticontinuum limit.

  4. Structure and intrinsic disorder in protein autoinhibition.

    Science.gov (United States)

    Trudeau, Travis; Nassar, Roy; Cumberworth, Alexander; Wong, Eric T C; Woollard, Geoffrey; Gsponer, Jörg

    2013-03-05

    Autoinhibition plays a significant role in the regulation of many proteins. By analyzing autoinhibited proteins, we demonstrate that these proteins are enriched in intrinsic disorder because of the properties of their inhibitory modules (IMs). A comparison of autoinhibited proteins with structured and intrinsically disordered IMs revealed that in the latter group (1) multiple phosphorylation sites are highly abundant; (2) splice variants occur in greater number than in their structured cousins; and (3) activation is often associated with changes in secondary structure in the IM. Analyses of families of autoinhibited proteins revealed that the levels of disorder in IMs can vary significantly throughout homologous proteins, whereas residues located at the interfaces between the IMs and inhibited domains are conserved. Our findings suggest that intrinsically disordered IMs provide advantages over structured ones that are likely to be exploited in the fine-tuning of the equilibrium between active and inactive states of autoinhibited proteins.

  5. 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…

  6. Spatiotemporal chaos in capacitively coupled intrinsic Josephson junction arrays and control by a shunted LCR series resonance circuit

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, T G; Yan, S L; Fang, L; He, M; Zhao, X J [Department of Electronics, Nankai University, Tianjin 300071 (China)], E-mail: zhoutg@nankai.edu.cn

    2009-05-15

    The dynamics of capacitively coupled intrinsic Josephson junction arrays with a McCumber parameter {beta}{sub c}<1 driven by a dc current are investigated by using numerical simulations. For the first time, spatiotemporal chaotic behaviors are found. Analysis of the dynamics of individual junctions shows that the chaos is caused by the strong diffusive coupling between the junctions in the array. The chaotic regions of different parameters are also presented, from which the conditions for chaos are deduced. The properties of the array shunted by an LCR series resonance circuit are also investigated. The results show that the spatiotemporal chaos can be effectively controlled by the shunted LCR circuit. This presents a new spatiotemporal chaos control method.

  7. Intrinsically disordered proteins drive membrane curvature

    Science.gov (United States)

    Busch, David J.; Houser, Justin R.; Hayden, Carl C.; Sherman, Michael B.; Lafer, Eileen M.; Stachowiak, Jeanne C.

    2015-07-01

    Assembly of highly curved membrane structures is essential to cellular physiology. The prevailing view has been that proteins with curvature-promoting structural motifs, such as wedge-like amphipathic helices and crescent-shaped BAR domains, are required for bending membranes. Here we report that intrinsically disordered domains of the endocytic adaptor proteins, Epsin1 and AP180 are highly potent drivers of membrane curvature. This result is unexpected since intrinsically disordered domains lack a well-defined three-dimensional structure. However, in vitro measurements of membrane curvature and protein diffusivity demonstrate that the large hydrodynamic radii of these domains generate steric pressure that drives membrane bending. When disordered adaptor domains are expressed as transmembrane cargo in mammalian cells, they are excluded from clathrin-coated pits. We propose that a balance of steric pressure on the two surfaces of the membrane drives this exclusion. These results provide quantitative evidence for the influence of steric pressure on the content and assembly of curved cellular membrane structures.

  8. Chaos

    OpenAIRE

    2012-01-01

    In certain two-dimensional time-dependent flows, the braiding of periodic orbits provides a way to analyze chaos in the system through application of the Thurston-Nielsen classification theorem (TNCT). We expand upon earlier work that introduced the application of the TNCT to braiding of almost-cyclic sets, which are individual components of almost-invariant sets [Stremler et al., "Topological chaos and periodic braiding of almost-cyclic sets," Phys. Rev. Lett. 106, 114101 (2011)]. In this co...

  9. Intrinsically disordered proteins: structural and functional dynamics

    Directory of Open Access Journals (Sweden)

    Wallin S

    2017-02-01

    Full Text Available Stefan Wallin Department of Physics and Physical Oceanography, Memorial University of Newfoundland, St. John’s, NL, Canada Abstract: The classical view holds that proteins fold into essentially unique three-dimensional structures before becoming biologically active. However, studies over the last several years have provided broad and convincing evidence that some proteins do not adopt a single structure and yet are fully functional. These intrinsically disordered proteins (IDPs have been found to be highly prevalent in many genomes, including human, and play key roles in central cellular processes, such as regulation of transcription and translation, cell cycle, and cell signaling. Moreover, IDPs are overrepresented among proteins implicated in disease, including various cancers and neurodegenerative disorders. Intense efforts, by using both experimental and computational approaches, are consequently under way to uncover the molecular mechanisms that underpin the roles of IDPs in biology and disease. This review provides an introduction to the general biophysical properties of IDPs and discusses some of the recent emerging areas in IDP research, including the roles of IDPs in allosteric regulation, regulatory unfolding, and formation of intracellular membrane-less organelles. In addition, recent attempts at therapeutic targeting of IDPs by small molecules, noting in particular that IDPs represent a potentially important source of new drug targets in light of their central role in protein–protein interaction networks, are also reviewed. Keywords: natively unfolded proteins, unstructured proteins, protein folding, protein–protein interaction, cell regulation, signaling, drug development, inhibitors

  10. Intrinsically disordered regions in autophagy proteins.

    Science.gov (United States)

    Mei, Yang; Su, Minfei; Soni, Gaurav; Salem, Saeed; Colbert, Christopher L; Sinha, Sangita C

    2014-04-01

    Autophagy is an essential eukaryotic pathway required for cellular homeostasis. Numerous key autophagy effectors and regulators have been identified, but the mechanism by which they carry out their function in autophagy is not fully understood. Our rigorous bioinformatic analysis shows that the majority of key human autophagy proteins include intrinsically disordered regions (IDRs), which are sequences lacking stable secondary and tertiary structure; suggesting that IDRs play an important, yet hitherto uninvestigated, role in autophagy. Available crystal structures corroborate the absence of structure in some of these predicted IDRs. Regions of orthologs equivalent to the IDRs predicted in the human autophagy proteins are poorly conserved, indicating that these regions may have diverse functions in different homologs. We also show that IDRs predicted in human proteins contain several regions predicted to facilitate protein-protein interactions, and delineate the network of proteins that interact with each predicted IDR-containing autophagy protein, suggesting that many of these interactions may involve IDRs. Lastly, we experimentally show that a BCL2 homology 3 domain (BH3D), within the key autophagy effector BECN1 is an IDR. This BH3D undergoes a dramatic conformational change from coil to α-helix upon binding to BCL2s, with the C-terminal half of this BH3D constituting a binding motif, which serves to anchor the interaction of the BH3D to BCL2s. The information presented here will help inform future in-depth investigations of the biological role and mechanism of IDRs in autophagy proteins.

  11. 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.

  12. Influence of Sequence Changes and Environment on Intrinsically Disordered Proteins

    OpenAIRE

    Amrita Mohan; Uversky, Vladimir N.; Predrag Radivojac

    2009-01-01

    Author Summary Intrinsically disordered proteins, proteins that exist as conformational ensembles without time-invariant residue positions, have emerged as an important and common class of proteins in all kingdoms of life. Disordered proteins are characterized by distinct amino acid preferences, distinct mechanisms of binding, distinct substitution patterns and rates of evolution, and functional roles predominantly related to signaling and regulation. In recent years, disordered proteins have...

  13. Prediction of intrinsic disorder in proteins using MFDp2.

    Science.gov (United States)

    Mizianty, Marcin J; Uversky, Vladimir; Kurgan, Lukasz

    2014-01-01

    Intrinsically disordered proteins (IDPs) are either entirely disordered or contain disordered regions in their native state. IDPs were found to be abundant across all kingdoms of life, particularly in eukaryotes, and are implicated in numerous cellular processes. Experimental annotation of disorder lags behind the rapidly growing sizes of the protein databases and thus computational methods are used to close this gap and to investigate the disorder. MFDp2 is a novel webserver for accurate sequence-based prediction of protein disorder which also outputs well-described sequence-derived information that allows profiling the predicted disorder. We conveniently visualize sequence conservation, predicted secondary structure, relative solvent accessibility, and alignments to chains with annotated disorder. The webserver allows predictions for multiple proteins at the same time, includes help pages and tutorial, and the results can be downloaded as text-based (parsable) file. MFDp2 is freely available at http://biomine.ece.ualberta.ca/MFDp2/.

  14. Electronegativity and intrinsic disorder of preeclampsia-related proteins.

    Science.gov (United States)

    Polanco, Carlos; Castañón-González, Jorge Alberto; Uversky, Vladimir N; Buhse, Thomas; Samaniego Mendoza, José Lino; Calva, Juan J

    2017-01-01

    Preeclampsia, hemorrhage, and infection are the leading causes of maternal death in underdeveloped countries. Since several proteins associated with preeclampsia are known, we conducted a computational study which evaluated the commonness and potential functionality of intrinsic disorder of these proteins and also made an attempt to characterize their origin. The origin of the preeclampsia-related proteins was assessed with a supervised technique, a Polarity Index Method (PIM), which evaluates the electronegativity of proteins based solely on their sequence. The commonness of intrinsic disorder was evaluated using several disorder predictors from the PONDR family, the charge-hydropathy plot (CH-plot) and cumulative distribution function (CDF) analyses, and using the MobiDB web-based tool, whereas potential functionality of intrinsic disorder was studied with the D2P2 resource and ANCHOR predictor of disorder-based binding sites, and the STRING tool was used to build the interactivity networks of the preeclampsia-related proteins. Peculiarities of the PIM-derived polar profile of the group of preeclampsia-related proteins were then compared with profiles of a group of lipoproteins, antimicrobial peptides, angiogenesis-related proteins, and the intrinsically disordered proteins. Our results showed a high graphical correlation between preeclampsia proteins, lipoproteins, and the angiogenesis proteins. We also showed that many preeclampsia-related proteins contain numerous functional disordered regions. Therefore, these bioinformatics results led us to assume that the preeclampsia proteins are highly associated with the lipoproteins group, and that some preeclampsia-related proteins contain significant amounts of functional disorders.

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

    DEFF Research Database (Denmark)

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

    2014-01-01

    Many intrinsically disordered proteins fold upon binding to other macromolecules. The secondary structure present in the well-ordered complex is often formed transiently in the unbound state. The consequence of such transient structure for the binding process is, however, not clear. The activatio...

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

    Indian Academy of Sciences (India)

    Prabhakar Pradhan; S Sridhar

    2002-02-01

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

  17. 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...

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

    Science.gov (United States)

    Konrat, Robert

    2014-01-01

    Intrinsically disordered proteins (IDPs) are characterized by substantial conformational plasticity. Given their inherent structural flexibility X-ray crystallography is not applicable to study these proteins. In contrast, NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This article will summarize key advances in basic physical-chemistry and NMR methodology, outline their limitations and envision future R&D directions. PMID:24656082

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

    Science.gov (United States)

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

    2016-01-01

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

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

    DEFF Research Database (Denmark)

    Kragelund, Birthe Brandt; Schenstrøm, Signe Marie; Rebula, Caio A.;

    2016-01-01

    DSS1/Sem1 is a versatile intrinsically disordered protein. Besides being a bona fide subunit of the 26S proteasome, DSS1 associates with other protein complexes, including BRCA2-RPA, involved in homologous recombination; the Csn12-Thp3 complex, involved in RNA splicing; the integrator, involved...... in transcription; and the TREX-2 complex, involved in nuclear export of mRNA and transcription elongation. As a subunit of the proteasome, DSS1 functions both in complex assembly and possibly as a ubiquitin receptor. Here, we summarise structural and functional aspects of DSS1/Sem1 with particular emphasis on its...... multifunctional and disordered properties. We suggest that DSS1/Sem1 can act as a polyanionic adhesive to prevent nonproductive interactions during construction of protein assemblies, uniquely employing different structures when associating with the diverse multisubunit complexes....

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

    Directory of Open Access Journals (Sweden)

    Robert Tsanev

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

  2. Tardigrades Use Intrinsically Disordered Proteins to Survive Desiccation.

    Science.gov (United States)

    Boothby, Thomas C; Tapia, Hugo; Brozena, Alexandra H; Piszkiewicz, Samantha; Smith, Austin E; Giovannini, Ilaria; Rebecchi, Lorena; Pielak, Gary J; Koshland, Doug; Goldstein, Bob

    2017-03-16

    Tardigrades are microscopic animals that survive a remarkable array of stresses, including desiccation. How tardigrades survive desiccation has remained a mystery for more than 250 years. Trehalose, a disaccharide essential for several organisms to survive drying, is detected at low levels or not at all in some tardigrade species, indicating that tardigrades possess potentially novel mechanisms for surviving desiccation. Here we show that tardigrade-specific intrinsically disordered proteins (TDPs) are essential for desiccation tolerance. TDP genes are constitutively expressed at high levels or induced during desiccation in multiple tardigrade species. TDPs are required for tardigrade desiccation tolerance, and these genes are sufficient to increase desiccation tolerance when expressed in heterologous systems. TDPs form non-crystalline amorphous solids (vitrify) upon desiccation, and this vitrified state mirrors their protective capabilities. Our study identifies TDPs as functional mediators of tardigrade desiccation tolerance, expanding our knowledge of the roles and diversity of disordered proteins involved in stress tolerance.

  3. Structural Characterization of Intrinsically Disordered Proteins by NMR Spectroscopy

    Directory of Open Access Journals (Sweden)

    Peter Tompa

    2013-09-01

    Full Text Available Recent advances in NMR methodology and techniques allow the structural investigation of biomolecules of increasing size with atomic resolution. NMR spectroscopy is especially well-suited for the study of intrinsically disordered proteins (IDPs and intrinsically disordered regions (IDRs which are in general highly flexible and do not have a well-defined secondary or tertiary structure under functional conditions. In the last decade, the important role of IDPs in many essential cellular processes has become more evident as the lack of a stable tertiary structure of many protagonists in signal transduction, transcription regulation and cell-cycle regulation has been discovered. The growing demand for structural data of IDPs required the development and adaption of methods such as 13C-direct detected experiments, paramagnetic relaxation enhancements (PREs or residual dipolar couplings (RDCs for the study of ‘unstructured’ molecules in vitro and in-cell. The information obtained by NMR can be processed with novel computational tools to generate conformational ensembles that visualize the conformations IDPs sample under functional conditions. Here, we address NMR experiments and strategies that enable the generation of detailed structural models of IDPs.

  4. Topology-based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions.

    Science.gov (United States)

    Ganguly, Debabani; Chen, Jianhan

    2011-04-01

    Coupled binding and folding is frequently involved in specific recognition of so-called intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a lack of stable tertiary fold for function. Here, we exploit topology-based Gō-like modeling as an effective tool for the mechanism of IDP recognition within the theoretical framework of minimally frustrated energy landscape. Importantly, substantial differences exist between IDPs and globular proteins in both amino acid sequence and binding interface characteristics. We demonstrate that established Gō-like models designed for folded proteins tend to over-estimate the level of residual structures in unbound IDPs, whereas under-estimating the strength of intermolecular interactions. Such systematic biases have important consequences in the predicted mechanism of interaction. A strategy is proposed to recalibrate topology-derived models to balance intrinsic folding propensities and intermolecular interactions, based on experimental knowledge of the overall residual structure level and binding affinity. Applied to pKID/KIX, the calibrated Gō-like model predicts a dominant multistep sequential pathway for binding-induced folding of pKID that is initiated by KIX binding via the C-terminus in disordered conformations, followed by binding and folding of the rest of C-terminal helix and finally the N-terminal helix. This novel mechanism is consistent with key observations derived from a recent NMR titration and relaxation dispersion study and provides a molecular-level interpretation of kinetic rates derived from dispersion curve analysis. These case studies provide important insight into the applicability and potential pitfalls of topology-based modeling for studying IDP folding and interaction in general.

  5. 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.

  6. Disorder Chaos in the Sherrington-Kirkpatrick Model with External Field

    CERN Document Server

    Chen, Wei-Kuo

    2011-01-01

    Consider a spin system obtained by coupling two distinct Sherrington-Kirkpatrick (SK) models with the same temperature and external field whose Hamiltonians are correlated. The disorder chaos conjecture for the SK model states that the overlap under the corresponding Gibbs measure is essentially concentrated at a single value. In the absence of external field, this statement was first confirmed by Chatterjee. In the present paper, using Guerra's replica symmetry-breaking bound, we prove that the SK model is also chaotic in the presence of external field and the position of the overlap is determined by an equation related to Guerra's bound and the Parisi measure.

  7. Phenotypic plasticity in prostate cancer: role of intrinsically disordered proteins.

    Science.gov (United States)

    Mooney, Steven M; Jolly, Mohit Kumar; Levine, Herbert; Kulkarni, Prakash

    2016-01-01

    A striking characteristic of cancer cells is their remarkable phenotypic plasticity, which is the ability to switch states or phenotypes in response to environmental fluctuations. Phenotypic changes such as a partial or complete epithelial to mesenchymal transition (EMT) that play important roles in their survival and proliferation, and development of resistance to therapeutic treatments, are widely believed to arise due to somatic mutations in the genome. However, there is a growing concern that such a deterministic view is not entirely consistent with multiple lines of evidence, which indicate that stochasticity may also play an important role in driving phenotypic plasticity. Here, we discuss how stochasticity in protein interaction networks (PINs) may play a key role in determining phenotypic plasticity in prostate cancer (PCa). Specifically, we point out that the key players driving transitions among different phenotypes (epithelial, mesenchymal, and hybrid epithelial/mesenchymal), including ZEB1, SNAI1, OVOL1, and OVOL2, are intrinsically disordered proteins (IDPs) and discuss how plasticity at the molecular level may contribute to stochasticity in phenotypic switching by rewiring PINs. We conclude by suggesting that targeting IDPs implicated in EMT in PCa may be a new strategy to gain additional insights and develop novel treatments for this disease, which is the most common form of cancer in adult men.

  8. 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.

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

    Science.gov (United States)

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

    2016-01-18

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

  10. Stochastic Chaos with Its Control and Synchronization

    Institute of Scientific and Technical Information of China (English)

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

    2008-01-01

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

  11. Orderly order in protein intrinsic disorder distribution: disorder in 3500 proteomes from viruses and the three domains of life.

    Science.gov (United States)

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

    2012-01-01

    Intrinsically disordered proteins and intrinsically disordered protein regions are highly abundant in nature. However, the quantitative and qualitative measures of protein intrinsic disorder in species with known genomes are still not available. Furthermore, although the correlation between high fraction of disordered residues and advanced species has been reported, the details of this correlation and the connection between the disorder content and proteome complexity have not been reported as of yet. To fill this gap, we analysed entire proteomes of 3484 species from three domains of life (archaea, bacteria and eukaryotes) and from viruses. Our analysis revealed that the evolution process is characterized by distinctive patterns of changes in the protein intrinsic disorder content. We are showing here that viruses are characterized by the widest spread of the proteome disorder content (the percentage of disordered residues ranges from 7.3% in human coronavirus NL63 to 77.3% in Avian carcinoma virus). For several organisms, a clear correlation is seen between their disorder contents and habitats. In multicellular eukaryotes, there is a weak correlation between the complexity of an organism (evaluated as a number of different cell types) and its overall disorder content. For both the prokaryotes and eukaryotes, the disorder content is generally independent of the proteome size. However, disorder shows a sharp increase associated with the transition from prokaryotic to eukaryotic cells. This suggests that the increased disorder content in eukaryotic proteomes might be used by nature to deal with the increased cell complexity due to the appearance of the various cellular compartments.

  12. 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.

  13. Physical white chaos generation

    CERN Document Server

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

    2014-01-01

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

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

    NARCIS (Netherlands)

    Ebisch, Sjoerd J. H.; Aleman, Andre

    2016-01-01

    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 ev

  15. Protein intrinsic disorder and network connectivity. The case of 14-3-3 proteins.

    Directory of Open Access Journals (Sweden)

    Marina eUhart

    2014-02-01

    Full Text Available The understanding of networks is a common goal of an unprecedented array oftraditional disciplines. One of the network properties most influenced by thestructural contents of its nodes is the inter-connectivity. Recent studies in whichstructural information was included into the topological analysis of proteinnetworks revealed that the content of intrinsic disorder in the nodes couldmodulate the network topology, rewire networks and change their inter-connectivity, which is defined by its clustering coefficient. Here, we review therole of intrinsic disorder present in the partners of the highly conserved 14-3-3protein family on its interaction networks. The 14-3-3s are phospho-serine/threonine binding proteins that have strong influence in the regulation ofmetabolism and signal transduction networks. Intrinsic disorder increases theclustering coefficients, namely the inter-connectivity of the nodes within each14-3-3 paralog networks. We also review two new ideas to measure intrinsicdisorder independently of the primary sequence of proteins, a thermodynamicmodel and a method that uses protein structures and their solventenvironment. This new methods could be useful to explain unsolved questionsabout versatility and fixation of intrinsic disorder through evolution. Therelation between the intrinsic disorder and network topologies could be aninteresting model to investigate new implicitness of the graph theory intobiology.

  16. Intrinsic Disorder in Male Sex Determination: Disorderedness of Proteins from the Sry Transcriptional Network.

    Science.gov (United States)

    Merone, Jean; Nwogu, Onyekahi; Redington, Jennifer M; Uversky, Vladimir N

    2016-10-28

    Sex differentiation is a complex process where sexually indifferent embryo progressively acquires male or female characteristics via tightly controlled, perfectly timed, and sophisticatedly intertwined chain of events. This process is controlled and regulated by a set of specific proteins, with one of the first steps in sex differentiation being the activation of the Y-chromosomal Sry gene (sex-determining region Y) in males that acts as a switch from undifferentiated gonad somatic cells to testis development. There are several key players in this process, which constitute the Sry transcriptional network, and collective action of which governs testis determination. Although it is accepted now that many proteins engaged in signal transduction as well as regulation and control of various biological processes are intrinsically disordered (i.e., do not have unique structure and remain unstructured, or incompletely structured, under physiological conditions), the roles and profusion of intrinsic disorder in proteins involved in the male sex determination have not been accessed as of yet. The goal of this study is to cover this gap by analyzing some key players of the Sry transcriptional network. To this end, we employed a broad set of computational tools for intrinsic disorder analysis and conducted intensive literature search in order to gain information on the structural peculiarities of the Sry network-related proteins, their intrinsic disorder predispositions, and the roles of intrinsic disorder in their functions.

  17. High-throughput characterization of intrinsic disorder in proteins from the Protein Structure Initiative.

    Science.gov (United States)

    Johnson, Derrick E; Xue, Bin; Sickmeier, Megan D; Meng, Jingwei; Cortese, Marc S; Oldfield, Christopher J; Le Gall, Tanguy; Dunker, A Keith; Uversky, Vladimir N

    2012-10-01

    The identification of intrinsically disordered proteins (IDPs) among the targets that fail to form satisfactory crystal structures in the Protein Structure Initiative represents a key to reducing the costs and time for determining three-dimensional structures of proteins. To help in this endeavor, several Protein Structure Initiative Centers were asked to send samples of both crystallizable proteins and proteins that failed to crystallize. The abundance of intrinsic disorder in these proteins was evaluated via computational analysis using predictors of natural disordered regions (PONDR®) and the potential cleavage sites and corresponding fragments were determined. Then, the target proteins were analyzed for intrinsic disorder by their resistance to limited proteolysis. The rates of tryptic digestion of sample target proteins were compared to those of lysozyme/myoglobin, apomyoglobin, and α-casein as standards of ordered, partially disordered and completely disordered proteins, respectively. At the next stage, the protein samples were subjected to both far-UV and near-UV circular dichroism (CD) analysis. For most of the samples, a good agreement between CD data, predictions of disorder and the rates of limited tryptic digestion was established. Further experimentation is being performed on a smaller subset of these samples in order to obtain more detailed information on the ordered/disordered nature of the proteins.

  18. Intramolecular Three-Colour Single Pair FRET of Intrinsically Disordered Proteins with Increased Dynamic Range

    Science.gov (United States)

    Milles, Sigrid; Koehler, Christine; Gambin, Yann

    2012-01-01

    Single molecule observation of fluorescence resonance energy transfer can be used to provide insights 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. PMID:22739670

  19. Intrinsically disordered tau protein in Alzheimer's tangles: a coincidence or a rule?

    Science.gov (United States)

    Skrabana, R; Skrabanova, M; Csokova, N; Sevcik, J; Novak, M

    2006-01-01

    Tau protein, the major constituent of neurofibrillary tangles in Alzheimer's disease (AD) and related tauopathies, is classified as intrinsically disordered protein (IDP). IDPs in contrast to globular proteins contain high proportion of polar and charged amino acids in their sequence, which results in the absence of a well-defined three-dimensional structure of the free protein. Structural flexibility of IDPs is required to perform their important role in many cellular processes. In the course of tauopathies, highly soluble disordered tau protein acquires rigid fold and forms highly insoluble filaments. Beneficial intrinsic disorder transforms into a fatal order: is it a coincidence, or is there an underlying reason for preferential IDPs assembly? In this review we present the structural characteristics of tau protein filamentous lesions in AD and discuss the tendency of IDPs to assembly and to form amyloid deposits (Ref: 65).

  20. 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.

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

    Science.gov (United States)

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

    2016-02-01

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

  2. Compartmentalization and Functionality of Nuclear Disorder: Intrinsic Disorder and Protein-Protein Interactions in Intra-Nuclear Compartments

    Directory of Open Access Journals (Sweden)

    Fanchi Meng

    2015-12-01

    Full Text Available The cell nucleus contains a number of membrane-less organelles or intra-nuclear compartments. These compartments are dynamic structures representing liquid-droplet phases which are only slightly denser than the bulk intra-nuclear fluid. They possess different functions, have diverse morphologies, and are typically composed of RNA (or, in some cases, DNA and proteins. We analyzed 3005 mouse proteins localized in specific intra-nuclear organelles, such as nucleolus, chromatin, Cajal bodies, nuclear speckles, promyelocytic leukemia (PML nuclear bodies, nuclear lamina, nuclear pores, and perinuclear compartment and compared them with ~29,863 non-nuclear proteins from mouse proteome. Our analysis revealed that intrinsic disorder is enriched in the majority of intra-nuclear compartments, except for the nuclear pore and lamina. These compartments are depleted in proteins that lack disordered domains and enriched in proteins that have multiple disordered domains. Moonlighting proteins found in multiple intra-nuclear compartments are more likely to have multiple disordered domains. Protein-protein interaction networks in the intra-nuclear compartments are denser and include more hubs compared to the non-nuclear proteins. Hubs in the intra-nuclear compartments (except for the nuclear pore are enriched in disorder compared with non-nuclear hubs and non-nuclear proteins. Therefore, our work provides support to the idea of the functional importance of intrinsic disorder in the cell nucleus and shows that many proteins associated with sub-nuclear organelles in nuclei of mouse cells are enriched in disorder. This high level of disorder in the mouse nuclear proteins defines their ability to serve as very promiscuous binders, possessing both large quantities of potential disorder-based interaction sites and the ability of a single such site to be involved in a large number of interactions.

  3. 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.

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

    Science.gov (United States)

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

    2015-01-01

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

  5. Expression, fermentation and purification of a predicted intrinsically disordered region of the transcription factor, NFAT5.

    Science.gov (United States)

    DuMond, Jenna F; He, Yi; Burg, Maurice B; Ferraris, Joan D

    2015-11-01

    Hypertonicity stimulates Nuclear Factor of Activated T-cells 5 (NFAT5) nuclear localization and transactivating activity. Many transcription factors are known to contain intrinsically disordered regions (IDRs) which become more structured with local environmental changes such as osmolality, temperature and tonicity. The transactivating domain of NFAT5 is predicted to be intrinsically disordered under normal tonicity, and under high NaCl, the activity of this domain is increased. To study the binding of co-regulatory proteins at IDRs a cDNA construct expressing the NFAT5 TAD was created and transformed into Escherichia coli cells. Transformed E. coli cells were mass produced by fermentation and extracted by cell lysis to release the NFAT5 TAD. The NFAT5 TAD was subsequently purified using a His-tag column, cation exchange chromatography as well as hydrophobic interaction chromatography and then characterized by mass spectrometry (MS).

  6. 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

  7. Multifarious roles of intrinsic disorder in proteins illustrate its broad impact on plant biology.

    Science.gov (United States)

    Sun, Xiaolin; Rikkerink, Erik H A; Jones, William T; Uversky, Vladimir N

    2013-01-01

    Intrinsically disordered proteins (IDPs) are highly abundant in eukaryotic proteomes. Plant IDPs play critical roles in plant biology and often act as integrators of signals from multiple plant regulatory and environmental inputs. Binding promiscuity and plasticity allow IDPs to interact with multiple partners in protein interaction networks and provide important functional advantages in molecular recognition through transient protein-protein interactions. Short interaction-prone segments within IDPs, termed molecular recognition features, represent potential binding sites that can undergo disorder-to-order transition upon binding to their partners. In this review, we summarize the evidence for the importance of IDPs in plant biology and evaluate the functions associated with intrinsic disorder in five different types of plant protein families experimentally confirmed as IDPs. Functional studies of these proteins illustrate the broad impact of disorder on many areas of plant biology, including abiotic stress, transcriptional regulation, light perception, and development. Based on the roles of disorder in the protein-protein interactions, we propose various modes of action for plant IDPs that may provide insight for future experimental approaches aimed at understanding the molecular basis of protein function within important plant pathways.

  8. 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.

  9. Amygdala-based intrinsic functional connectivity and anxiety disorders in adolescents and young adults.

    Science.gov (United States)

    Toazza, Rudineia; Franco, Alexandre Rosa; Buchweitz, Augusto; Molle, Roberta Dalle; Rodrigues, Danitsa Marcos; Reis, Roberta Sena; Mucellini, Amanda Brondani; Esper, Nathalia Bianchini; Aguzzoli, Cristiano; Silveira, Patrícia Pelufo; Salum, Giovanni Abrahão; Manfro, Gisele Gus

    2016-11-30

    Anxiety disorders (AD) are the most prevalent group of psychiatric disorders in adolescents and young adults. Nevertheless, the pathophysiology of anxiety disorders is still poorly understood. This study investigated differences in the functional connectivity of intrinsic amygdala-based networks of participants with and without AD. Resting state fMRI data were obtained from 18 participants with an AD and 19 healthy comparison individuals. Psychiatric diagnosis was assessed using standardized structured interviews. The comparison between groups was carried out using functional connectivity maps from six seed regions defined using probabilistic maps bilaterally within the amygdala (basolateral, superficial and centromedial amygdala). We found significant between-group differences in five clusters, which showed aberrant functional connectivity with the left basolateral amygdala: right precentral gyrus, right cingulate gyrus, bilateral precuneus, and right superior frontal gyrus in subjects with AD as compared with the comparison subjects. For the comparison subjects, the correlations between the amygdala and the five clusters were either non-significant, or negative. The present study suggests there is an intrinsic disruption in the communication between left basolateral amygdala and a network of brain regions involved with emotion regulation, and with the default mode network in adolescents and young adults with anxiety disorders.

  10. 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.

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

    CERN Document Server

    Cordeiro, Tiago; Urbanek, Annika; Estaña, Alejandro; Cortés, Juan; Sibille, Nathalie; Bernadó, Pau

    2016-01-01

    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 application of traditional structural approaches, and new tools and concepts are being developed to address the challenges they pose. Small-Angle Scattering (SAS) is a structural biology technique that probes the size and shape of disordered proteins and their complexes with other biomolecules. The low-resolution nature of SAS can be compensated with specially designed computational tools and its combined interpretation with complementary structural information. In this review, we describe recent advances in the application of SAS to disordered proteins and highly flexible complexes and discuss current challenges.

  12. Chaos control of cardiac arrhythmias.

    Science.gov (United States)

    Garfinkel, A; Weiss, J N; Ditto, W L; Spano, M L

    1995-01-01

    Chaos theory has shown that many disordered and erratic phenomena are in fact deterministic, and can be understood causally and controlled. The prospect that cardiac arrhythmias might be instances of deterministic chaos is therefore intriguing. We used a recently developed method of chaos control to stabilize a ouabain-induced arrhythmia in rabbit ventricular tissue in vitro. Extension of these results to clinically significant arrhythmias such as fibrillation will require overcoming the additional obstacles of spatiotemporal complexity.

  13. Intrinsic Disorder in Transmembrane Proteins: Roles in Signaling and Topology Prediction.

    Directory of Open Access Journals (Sweden)

    Jérôme Bürgi

    Full Text Available Intrinsically disordered regions (IDRs are peculiar stretches of amino acids that lack stable conformations in solution. Intrinsic Disorder containing Proteins (IDP are defined by the presence of at least one large IDR and have been linked to multiple cellular processes including cell signaling, DNA binding and cancer. Here we used computational analyses and publicly available databases to deepen insight into the prevalence and function of IDRs specifically in transmembrane proteins, which are somewhat neglected in most studies. We found that 50% of transmembrane proteins have at least one IDR of 30 amino acids or more. Interestingly, these domains preferentially localize to the cytoplasmic side especially of multi-pass transmembrane proteins, suggesting that disorder prediction could increase the confidence of topology prediction algorithms. This was supported by the successful prediction of the topology of the uncharacterized multi-pass transmembrane protein TMEM117, as confirmed experimentally. Pathway analysis indicated that IDPs are enriched in cell projection and axons and appear to play an important role in cell adhesion, signaling and ion binding. In addition, we found that IDP are enriched in phosphorylation sites, a crucial post translational modification in signal transduction, when compared to fully ordered proteins and to be implicated in more protein-protein interaction events. Accordingly, IDPs were highly enriched in short protein binding regions called Molecular Recognition Features (MoRFs. Altogether our analyses strongly support the notion that the transmembrane IDPs act as hubs in cellular signal events.

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

    Science.gov (United States)

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

    2015-11-01

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

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

    Science.gov (United States)

    Mao, Hsuan-Han Alberto

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

  16. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins.

    Science.gov (United States)

    Schuler, Benjamin; Soranno, Andrea; Hofmann, Hagen; Nettels, Daniel

    2016-07-05

    The properties of unfolded proteins have long been of interest because of their importance to the protein folding process. Recently, the surprising prevalence of unstructured regions or entirely disordered proteins under physiological conditions has led to the realization that such intrinsically disordered proteins can be functional even in the absence of a folded structure. However, owing to their broad conformational distributions, many of the properties of unstructured proteins are difficult to describe with the established concepts of structural biology. We have thus seen a reemergence of polymer physics as a versatile framework for understanding their structure and dynamics. An important driving force for these developments has been single-molecule spectroscopy, as it allows structural heterogeneity, intramolecular distance distributions, and dynamics to be quantified over a wide range of timescales and solution conditions. Polymer concepts provide an important basis for relating the physical properties of unstructured proteins to folding and function.

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

    Directory of Open Access Journals (Sweden)

    Rajamannar eRamasubbu

    2014-02-01

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

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

    Science.gov (United States)

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

    2015-01-01

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

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

    Science.gov (United States)

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

    2015-08-11

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

  20. 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/.

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

    Directory of Open Access Journals (Sweden)

    Andrew J Guy

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

  2. Identification of a Drug Targeting an Intrinsically Disordered Protein Involved in Pancreatic Adenocarcinoma

    Science.gov (United States)

    Neira, José L.; Bintz, Jennifer; Arruebo, María; Rizzuti, Bruno; Bonacci, Thomas; Vega, Sonia; Lanas, Angel; Velázquez-Campoy, Adrián; Iovanna, Juan L.; Abián, Olga

    2017-01-01

    Intrinsically disordered proteins (IDPs) are prevalent in eukaryotes, performing signaling and regulatory functions. Often associated with human diseases, they constitute drug-development targets. NUPR1 is a multifunctional IDP, over-expressed and involved in pancreatic ductal adenocarcinoma (PDAC) development. By screening 1120 FDA-approved compounds, fifteen candidates were selected, and their interactions with NUPR1 were characterized by experimental and simulation techniques. The protein remained disordered upon binding to all fifteen candidates. These compounds were tested in PDAC-derived cell-based assays, and all induced cell-growth arrest and senescence, reduced cell migration, and decreased chemoresistance, mimicking NUPR1-deficiency. The most effective compound completely arrested tumor development in vivo on xenografted PDAC-derived cells in mice. Besides reporting the discovery of a compound targeting an intact IDP and specifically active against PDAC, our study proves the possibility to target the ‘fuzzy’ interface of a protein that remains disordered upon binding to its natural biological partners or to selected drugs.

  3. 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.

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

    Science.gov (United States)

    Peng, Zhenling; Kurgan, Lukasz

    2015-10-15

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

  5. 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.

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

    Science.gov (United States)

    Nielsen, Jakob T; Mulder, Frans A A

    2016-01-01

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

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

    Science.gov (United States)

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

    2016-02-01

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

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

    Science.gov (United States)

    Quiroz, Felipe García; Chilkoti, Ashutosh

    2015-11-01

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

  9. Electrospray ionization-mass spectrometry conformational analysis of isolated domains of an intrinsically disordered protein.

    Science.gov (United States)

    Testa, Lorenzo; Brocca, Stefania; Samalikova, Maria; Santambrogio, Carlo; Alberghina, Lilia; Grandori, Rita

    2011-01-01

    The highly dynamic and heterogeneous molecular ensembles characterizing intrinsically disordered proteins (IDP) in solution pose major challenges to the conventional methods for structural analysis. Electrospray ionization-mass spectrometry (ESI-MS) allows direct detection of distinct conformational components, effectively capturing also partially folded and short-lived states. We report the description of two complementary fragments (1-186 and 187-284) of the IDP Sic1, a cyclin-dependent protein kinase inhibitor of yeast Saccharomyces cerevisiae. Structural heterogeneity is noted in both cases, but the two fragments reveal slightly different conformational properties. The results are consistent with previously reported differences between the two protein moieties and corroborate the feasibility of IDP conformational analysis by ESI-MS.

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

    Science.gov (United States)

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

    2012-01-01

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

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

    Science.gov (United States)

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

    2014-10-02

    Molecular recognition by intrinsically disordered proteins (IDPs) plays a central role in many critical cellular processes. Toward achieving detailed mechanistic understanding of IDP-target interactions, here we employ the "Hamiltonian mapping" methodology, which is rooted in the weighted histogram analysis method (WHAM), for the fast and efficient calibration of structure-based models in studies of IDPs. By performing reference simulations on a given Hamiltonian, we illustrate for two model IDPs how this method can extrapolate thermodynamic behavior under a range of modified Hamiltonians, in this case representing changes in the binding affinity (Kd) of the system. Given sufficient conformational sampling in a single trajectory, Hamiltonian mapping accurately reproduces Kd values from direct simulation. This method may be generally applied to systems beyond IDPs in force field optimization and in describing changes in thermodynamic behavior as a function of external conditions for connection with experiment.

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

    Science.gov (United States)

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

    2015-06-01

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

  13. 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.

  14. 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.

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

    Science.gov (United States)

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

    2014-01-01

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

  16. Ordered water within the collapsed globules of an amyloidogenic intrinsically disordered protein.

    Science.gov (United States)

    Arya, Shruti; Mukhopadhyay, Samrat

    2014-08-07

    Intrinsically disordered proteins (IDPs) confront the traditional sequence-structure-function paradigm and are associated with important functions and amyloid disorders. Water molecules residing in the vicinity of the polypeptide chain play potentially important roles in directing the course of binding-induced folding and amyloid aggregation of IDP. Here we characterized the nature of water molecules entrapped within the collapsed globules of an amyloidogenic IDP, namely, κ-casein. These globules can undergo further compaction in the presence of an anionic detergent that is capable of diminishing the intrachain repulsion from the positively charged glutamine/asparagine-rich amyloidogenic N-terminal domain comprising 100 residues. Using time-resolved fluorescence spectroscopy, we estimated the longer component of the solvation time to be ∼1.4 ns, which is 3 orders of magnitude slower than that in bulk water and more than an order of magnitude slower than the "biological water" present at the protein surface. Profoundly restrained water within the collapsed IDP globules resembles the ordered water cluster found under nanoconfinement. We suggest that the association of these globules would result in the release of ordered water molecules into the bulk milieu causing an entropic gain that would eventually drive the formation of the key (obligatory) oligomeric intermediates on the pathway to amyloids via nucleation-dependent polymerization.

  17. 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/.

  18. 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.

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

    Directory of Open Access Journals (Sweden)

    Elio A Cino

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

  20. An intrinsically disordered protein, CP12: jack of all trades and master of the Calvin cycle.

    Science.gov (United States)

    Gontero, Brigitte; Maberly, Stephen C

    2012-10-01

    Many proteins contain disordered regions under physiological conditions and lack specific three-dimensional structure. These are referred to as IDPs (intrinsically disordered proteins). CP12 is a chloroplast protein of approximately 80 amino acids and has a molecular mass of approximately 8.2-8.5 kDa. It is enriched in charged amino acids and has a small number of hydrophobic residues. It has a high proportion of disorder-promoting residues, but has at least two (often four) cysteine residues forming one (or two) disulfide bridge(s) under oxidizing conditions that confers some order. However, CP12 behaves like an IDP. It appears to be universally distributed in oxygenic photosynthetic organisms and has recently been detected in a cyanophage. The best studied role of CP12 is its regulation of the Calvin cycle responsible for CO2 assimilation. Oxidized CP12 forms a supramolecular complex with two key Calvin cycle enzymes, GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and PRK (phosphoribulokinase), down-regulating their activity. Association-dissociation of this complex, induced by the redox state of CP12, allows the Calvin cycle to be inactive in the dark and active in the light. CP12 is promiscuous and interacts with other enzymes such as aldolase and malate dehydrogenase. It also plays other roles in plant metabolism such as protecting GAPDH from inactivation and scavenging metal ions such as copper and nickel, and it is also linked to stress responses. Thus CP12 seems to be involved in many functions in photosynthetic cells and behaves like a jack of all trades as well as being a master of the Calvin cycle.

  1. 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.

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

    DEFF Research Database (Denmark)

    Nielsen, Jakob T; Mulder, Frans A A

    2016-01-01

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

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

    Science.gov (United States)

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

    2012-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Adrian Velazquez-Campoy

    2013-06-01

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

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

    Science.gov (United States)

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

    2014-12-01

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

  6. Coupled folding and binding kinetics in the intrinsically disordered peptide IA3

    Science.gov (United States)

    Narayanan, Ranjani; Ganesh, Omjoy; Edison, Arthur; Hagen, Stephen

    2008-03-01

    IA3 is an intrinsically disordered 68 residue peptide and is an endogenous inhibitor of yeast proteinase A (YPrA). X-ray crystallography of the IA3.YPrA complex [Li et al, Nat. Struct. Biol. (7), 113-117 (2000)] indicates that the N-terminus of IA3 adopts an alpha-helical fold when it is bound to the YPrA active site. We have used equilibrium circular dichroism and multi-wavelength, nanosecond time-resolved laser temperature-jump spectroscopy to study the coupled folding and binding interaction of IA3 with YPrA. Our initial measurements of the rate of helix formation in free IA3 indicate mono-exponential folding kinetics that extrapolate to kF˜ 10^5/s at room temperature in aqueous solutions. By comparing this rate to the kinetics we observe for IA3 interacting with YPrA, we can assess possible mechanisms for the coupled folding and binding of IA3.

  7. 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.

  8. Role of intrinsic disorder in the structural phase transition of magnetoelectric EuTiO3

    Science.gov (United States)

    Allieta, Mattia; Scavini, Marco; Spalek, Leszek J.; Scagnoli, Valerio; Walker, Helen C.; Panagopoulos, Christos; Saxena, Siddharth S.; Katsufuji, Takuro; Mazzoli, Claudio

    2012-05-01

    Up to now, the crystallographic structure of the magnetoelectric perovskite EuTiO3 has been considered to remain cubic down to low temperature. Here we present high-resolution synchrotron x-ray powder-diffraction data showing the existence of a structural phase transition, from cubic Pm-3m to tetragonal I4/mcm, involving TiO6 octahedra tilting, in analogy to the case of SrTiO3. The temperature evolution of the tilting angle and of the full width at half maximum of the (200) cubic reflection family indicate a critical temperature Tc = 235 K. This critical temperature is well below the recent anomaly reported by specific-heat measurement at TA ˜ 282 K. By performing atomic pair distribution function analysis on diffraction data, we provide evidence of a mismatch between the local (short-range) and the average crystallographic structures in this material. Below the estimated Tc, the average model symmetry is fully compatible with the local environment distortion, but the former is characterized by a reduced value of the tilting angle compared to the latter. At T = 240 K, data show the presence of local octahedra tilting identical to the low-temperature one, while the average crystallographic structure remains cubic. On this basis, we propose that intrinsic lattice disorder is of fundamental importance in the understanding of EuTiO3 properties.

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

    Directory of Open Access Journals (Sweden)

    Shaolong Zhu

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

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

    Science.gov (United States)

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

    2016-04-15

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

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

    Directory of Open Access Journals (Sweden)

    James J Valdés

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

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

    Directory of Open Access Journals (Sweden)

    J Ramiro Lorenzo

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

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

    Science.gov (United States)

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

    1994-01-01

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

  14. Boolean Chaos

    OpenAIRE

    Zhang, Rui; Cavalcante, Hugo L. D. de S.; Gao, Zheng; Gauthier, Daniel J.; Socolar, Joshua E. S.; Adams, Matthew M.; Lathrop, Daniel P.

    2009-01-01

    We observe deterministic chaos in a simple network of electronic logic gates that are not regulated by a clocking signal. The resulting power spectrum is ultra-wide-band, extending from dc to beyond 2 GHz. The observed behavior is reproduced qualitatively using an autonomously updating Boolean model with signal propagation times that depend on the recent history of the gates and filtering of pulses of short duration, whose presence is confirmed experimentally. Electronic Boolean chaos may fin...

  15. Wireless communication with chaos.

    Science.gov (United States)

    Ren, Hai-Peng; Baptista, Murilo S; Grebogi, Celso

    2013-05-03

    The modern world fully relies on wireless communication. Because of intrinsic physical constraints of the wireless physical media (multipath, damping, and filtering), signals carrying information are strongly modified, preventing information from being transmitted with a high bit rate. We show that, though a chaotic signal is strongly modified by the wireless physical media, its Lyapunov exponents remain unaltered, suggesting that the information transmitted is not modified by the channel. For some particular chaotic signals, we have indeed proved that the dynamic description of both the transmitted and the received signals is identical and shown that the capacity of the chaos-based wireless channel is unaffected by the multipath propagation of the physical media. These physical properties of chaotic signals warrant an effective chaos-based wireless communication system.

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

    Directory of Open Access Journals (Sweden)

    Eric T C Wong

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

  17. A Set of Efficient nD NMR Protocols for Resonance Assignments of Intrinsically Disordered Proteins.

    Science.gov (United States)

    Wiedemann, Christoph; Bellstedt, Peter; Häfner, Sabine; Herbst, Christian; Bordusa, Frank; Görlach, Matthias; Ohlenschläger, Oliver; Ramachandran, Ramadurai

    2016-07-04

    The RF pulse scheme RN[N-CA HEHAHA]NH, which provides a convenient approach to the acquisition of different multidimensional chemical shift correlation NMR spectra leading to backbone resonance assignments, including those of the proline residues of intrinsically disordered proteins (IDPs), is experimentally demonstrated. Depending on the type of correlation data required, the method involves the generation of in-phase ((15) N)(x) magnetisation via different magnetisation transfer pathways such as H→N→CO→N, HA→CA→CO→N, H→N→CA→N and H→CA→N, the subsequent application of (15) N-(13) C(α) heteronuclear Hartmann-Hahn mixing over a period of ≈100 ms, chemical-shift labelling of relevant nuclei before and after the heteronuclear mixing step and amide proton detection in the acquisition dimension. It makes use of the favourable relaxation properties of IDPs and the presence of (1) JCαN and (2) JCαN couplings to achieve efficient correlation of the backbone resonances of each amino acid residue "i" with the backbone amide resonances of residues "i-1" and "i+1". It can be implemented in a straightforward way through simple modifications of the RF pulse schemes commonly employed in protein NMR studies. The efficacy of the approach is demonstrated using a uniformly ((15) N,(13) C) labelled sample of α-synuclein. The different possibilities for obtaining the amino-acid-type information, simultaneously with the connectivity data between the backbone resonances of sequentially neighbouring residues, have also been outlined.

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

    Science.gov (United States)

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

    2015-01-01

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

  19. Tyrosinase degradation is prevented when EDEM1 lacks the intrinsically disordered region.

    Directory of Open Access Journals (Sweden)

    Marioara B Marin

    Full Text Available EDEM1 is a mannosidase-like protein that recruits misfolded glycoproteins from the calnexin/calreticulin folding cycle to downstream endoplasmic reticulum associated degradation (ERAD pathway. Here, we investigate the role of EDEM1 in the processing of tyrosinase, a tumour antigen overexpressed in melanoma cells. First, we analyzed and modeled EDEM1 major domains. The homology model raised on the crystal structures of human and Saccharomyces cerevisiae ER class I α1,2-mannosidases reveals that the major mannosidase domain located between aminoacids 121-598 fits with high accuracy. We have further identified an N-terminal region located between aminoacids 40-119, predicted to be intrinsically disordered (ID and susceptible to adopt multiple conformations, hence facilitating protein-protein interactions. To investigate these two domains we have constructed an EDEM1 deletion mutant lacking the ID region and a triple mutant disrupting the glycan-binding domain and analyzed their association with tyrosinase. Tyrosinase is a glycoprotein partly degraded endogenously by ERAD and the ubiquitin proteasomal system. We found that the degradation of wild type and misfolded tyrosinase was enhanced when EDEM1 was overexpressed. Glycosylated and non-glycosylated mutants co-immunoprecipitated with EDEM1 even in the absence of its intact mannosidase-like domain, but not when the ID region was deleted. In contrast, calnexin and SEL 1L associated with the deletion mutant. Our data suggest that the ID region identified in the N-terminal end of EDEM1 is involved in the binding of glycosylated and non-glycosylated misfolded proteins. Accelerating tyrosinase degradation by EDEM1 overexpression may lead to an efficient antigen presentation and enhanced elimination of melanoma cells.

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

    Science.gov (United States)

    Wong, Eric T C; Na, Dokyun; Gsponer, Jörg

    2013-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Raúl Esteban Ithuralde

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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

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

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

    Science.gov (United States)

    Franz, S.

    2004-10-01

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

  4. Robust Chaos

    CERN Document Server

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

    1998-01-01

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

  5. Thermal compaction of the intrinsically disordered protein tau: entropic, structural, and hydrophobic factors.

    Science.gov (United States)

    Battisti, Anna; Ciasca, Gabriele; Grottesi, Alessandro; Tenenbaum, Alexander

    2017-03-28

    Globular denatured proteins have structural properties similar to those of random coils. Experiments on denatured proteins have shown that when the temperature is increased thermal compaction may take place, resulting in a reduction of their radius of gyration Rg to range between 5% and 35% of its initial value. This phenomenon has been attributed to various causes, namely entropic, hydrophobic, and structural factors. The intrinsically disordered protein tau, which helps in nucleating and stabilizing microtubules in the axons of the neurons, also undergoes a relevant compaction process: when its temperature is increased from 293 K to 333 K its gyration radius decreases by 18%. We have performed an atomistic simulation of this molecule, at the lowest and highest temperatures of the mentioned interval, using both standard molecular dynamics and metadynamics, in parallel with small-angle X-ray scattering experiments. Using the fit of the experimental data and a genetic algorithm to select the most probable configurations among those produced in both atomistic simulations (standard MD and metadynamics), we were able to compute relevant changes, related to the temperature increase, in the average angles between residues, in the transient secondary structures, in the solvent accessible surface area, and in the number of intramolecular H-bonds. The analysis of the data showed how to decompose the compaction phenomenon into three contributions. An estimate of the entropic contribution to the compaction was obtained using the changes in the mean values of the angles between contiguous residues. The computation of the solvent accessible surface at the two temperatures allowed an estimation of the second factor contributing to the compaction, namely the increase in the hydrophobic interaction. We also measured the change in the average number of residues temporarily being in α-helices, 3-helices, PP II helices, β-sheets and β-turns. Those changes in the secondary

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

    Directory of Open Access Journals (Sweden)

    Smaldone G

    2013-07-01

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

  7. Discrete Chaos

    CERN Document Server

    Waelbroeck, H

    1999-01-01

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

  8. Temperature-dependent structural changes in intrinsically disordered proteins: formation of alpha-helices or loss of polyproline II?

    DEFF Research Database (Denmark)

    Kjærgaard, Magnus; Nørholm, Ann-Beth; Hendus-Altenburger, Ruth;

    2010-01-01

    temperature, which most likely reflects formation of transient alpha-helices or loss of polyproline II (PPII) content. Using three IDPs, ACTR, NHE1, and Spd1, we show that the temperature-induced structural change is common among IDPs and is accompanied by a contraction of the conformational ensemble......Structural characterization of intrinsically disordered proteins (IDPs) is mandatory for deciphering their potential unique physical and biological properties. A large number of circular dichroism (CD) studies have demonstrated that a structural change takes place in IDPs with increasing....... This phenomenon was explored at residue resolution by multidimensional NMR spectroscopy. Intrinsic chemical shift referencing allowed us to identify regions of transiently formed helices and their temperature-dependent changes in helicity. All helical regions were found to lose rather than gain helical structures...

  9. Characterising intra- and inter-intrinsic network synchrony in combat-related post-traumatic stress disorder.

    Science.gov (United States)

    Dunkley, Benjamin T; Doesburg, Sam M; Jetly, Rakesh; Sedge, Paul A; Pang, Elizabeth W; Taylor, Margot J

    2015-11-30

    Soldiers with post-traumatic stress disorder (PTSD) exhibit elevated gamma-band synchrony in left fronto-temporal cortex, and connectivity measures in these regions correlate with comorbidities and PTSD severity, which suggests increased gamma synchrony is related to symptomology. However, little is known about the role of intrinsic, phase-synchronised networks in the disorder. Using magnetoencephalography (MEG), we characterised spectral connectivity in the default-mode, salience, visual, and attention networks during resting-state in a PTSD population and a trauma-exposed control group. Intrinsic network connectivity was examined in canonical frequency bands. We observed increased inter-network synchronisation in the PTSD group compared with controls in the gamma (30-80 Hz) and high-gamma range (80-150 Hz). Analyses of connectivity and symptomology revealed that PTSD severity was positively associated with beta synchrony in the ventral-attention-to-salience networks, and gamma synchrony within the salience network, but also negatively correlated with beta synchrony within the visual network. These novel results show that frequency-specific, network-level atypicalities may reflect trauma-related alterations of ongoing functional connectivity, and correlations of beta synchrony in attentional-to-salience and visual networks with PTSD severity suggest complicated network interactions mediate symptoms. These results contribute to accumulating evidence that PTSD is a complicated network-based disorder expressed as altered neural interactions.

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

    Science.gov (United States)

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

    2013-01-01

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

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

    Science.gov (United States)

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

    2014-06-01

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

  12. 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.

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

    Directory of Open Access Journals (Sweden)

    Satoshi Fukuchi

    2010-12-01

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

  14. Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family.

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    Jianhui Song

    Full Text Available Molecular recognition by intrinsically disordered proteins (IDPs commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs.

  15. Polycation-π interactions are a driving force for molecular recognition by an intrinsically disordered oncoprotein family.

    Science.gov (United States)

    Song, Jianhui; Ng, Sheung Chun; Tompa, Peter; Lee, Kevin A W; Chan, Hue Sun

    2013-01-01

    Molecular recognition by intrinsically disordered proteins (IDPs) commonly involves specific localized contacts and target-induced disorder to order transitions. However, some IDPs remain disordered in the bound state, a phenomenon coined "fuzziness", often characterized by IDP polyvalency, sequence-insensitivity and a dynamic ensemble of disordered bound-state conformations. Besides the above general features, specific biophysical models for fuzzy interactions are mostly lacking. The transcriptional activation domain of the Ewing's Sarcoma oncoprotein family (EAD) is an IDP that exhibits many features of fuzziness, with multiple EAD aromatic side chains driving molecular recognition. Considering the prevalent role of cation-π interactions at various protein-protein interfaces, we hypothesized that EAD-target binding involves polycation- π contacts between a disordered EAD and basic residues on the target. Herein we evaluated the polycation-π hypothesis via functional and theoretical interrogation of EAD variants. The experimental effects of a range of EAD sequence variations, including aromatic number, aromatic density and charge perturbations, all support the cation-π model. Moreover, the activity trends observed are well captured by a coarse-grained EAD chain model and a corresponding analytical model based on interaction between EAD aromatics and surface cations of a generic globular target. EAD-target binding, in the context of pathological Ewing's Sarcoma oncoproteins, is thus seen to be driven by a balance between EAD conformational entropy and favorable EAD-target cation-π contacts. Such a highly versatile mode of molecular recognition offers a general conceptual framework for promiscuous target recognition by polyvalent IDPs.

  16. Alterations of Intrinsic Brain Connectivity Patterns in Depression and Bipolar Disorders: A Critical Assessment of Magnetoencephalography-Based Evidence

    Science.gov (United States)

    Alamian, Golnoush; Hincapié, Ana-Sofía; Combrisson, Etienne; Thiery, Thomas; Martel, Véronique; Althukov, Dmitrii; Jerbi, Karim

    2017-01-01

    Despite being the object of a thriving field of clinical research, the investigation of intrinsic brain network alterations in psychiatric illnesses is still in its early days. Because the pathological alterations are predominantly probed using functional magnetic resonance imaging (fMRI), many questions about the electrophysiological bases of resting-state alterations in psychiatric disorders, particularly among mood disorder patients, remain unanswered. Alongside important research using electroencephalography (EEG), the specific recent contributions and future promise of magnetoencephalography (MEG) in this field are not fully recognized and valued. Here, we provide a critical review of recent findings from MEG resting-state connectivity within major depressive disorder (MDD) and bipolar disorder (BD). The clinical MEG resting-state results are compared with those previously reported with fMRI and EEG. Taken together, MEG appears to be a promising but still critically underexploited technique to unravel the neurophysiological mechanisms that mediate abnormal (both hyper- and hypo-) connectivity patterns involved in MDD and BD. In particular, a major strength of MEG is its ability to provide source-space estimations of neuromagnetic long-range rhythmic synchronization at various frequencies (i.e., oscillatory coupling). The reviewed literature highlights the relevance of probing local and interregional rhythmic synchronization to explore the pathophysiological underpinnings of each disorder. However, before we can fully take advantage of MEG connectivity analyses in psychiatry, several limitations inherent to MEG connectivity analyses need to be understood and taken into account. Thus, we also discuss current methodological challenges and outline paths for future research. MEG resting-state studies provide an important window onto perturbed spontaneous oscillatory brain networks and hence supply an important complement to fMRI-based resting-state measurements in

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    disordered proteins at DNA break sites. Demixing, which relies on electrostatic interactions between positively charged RGG repeats and negatively charged PAR, is amplified by aggregation-prone prion-like domains, and orchestrates the earliest cellular responses to DNA breakage. We propose that PAR...

  18. 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.

  19. Prediction of Intrinsic Disorder in MERS-CoV/HCoV-EMC Supports a High Oral-Fecal Transmission.

    Science.gov (United States)

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

    2013-11-13

    A novel coronavirus, MERS-CoV (NCoV, HCoV-EMC/2012), originating from the Middle-East, has been discovered. Incoming data reveal that the virus is highly virulent to humans. A model that categorizes coronaviuses according to the hardness of their shells was developed before the discovery of MERS-CoV. Using protein intrinsic disorder prediction, coronaviruses were categorized into three groups that can be linked to the levels of oral-fecal and respiratory transmission regardless of genetic proximity. Using this model, MERS-CoV is placed into disorder group C, which consists of coronaviruses that have relatively hard inner and outer shells. The members of this group are likely to persist in the environment for a longer period of time and possess the highest oral-fecal components but relatively low respiratory transmission components. Oral-urine and saliva transmission are also highly possible since both require harder protective shells. Results show that disorder prediction can be used as a tool that suggests clues to look for in further epidemiological investigations.

  20. Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.

    Science.gov (United States)

    Mittal, Anuradha; Lyle, Nicholas; Harmon, Tyler S; Pappu, Rohit V

    2014-08-12

    There is growing interest in the topic of intrinsically disordered proteins (IDPs). Atomistic Metropolis Monte Carlo (MMC) simulations based on novel implicit solvation models have yielded useful insights regarding sequence-ensemble relationships for IDPs modeled as autonomous units. However, a majority of naturally occurring IDPs are tethered to ordered domains. Tethering introduces additional energy scales and this creates the challenge of broken ergodicity for standard MMC sampling or molecular dynamics that cannot be readily alleviated by using generalized tempering methods. We have designed, deployed, and tested our adaptation of the Nested Markov Chain Monte Carlo sampling algorithm. We refer to our adaptation as Hamiltonian Switch Metropolis Monte Carlo (HS-MMC) sampling. In this method, transitions out of energetic traps are enabled by the introduction of an auxiliary Markov chain that draws conformations for the disordered region from a Boltzmann distribution that is governed by an alternative potential function that only includes short-range steric repulsions and conformational restraints on the ordered domain. We show using multiple, independent runs that the HS-MMC method yields conformational distributions that have similar and reproducible statistical properties, which is in direct contrast to standard MMC for equivalent amounts of sampling. The method is efficient and can be deployed for simulations of a range of biologically relevant disordered regions that are tethered to ordered domains.

  1. Relation of Origins of Primitive Chaos

    CERN Document Server

    Ogasawara, Yoshihito

    2014-01-01

    A new concept, primitive chaos, was proposed, as a concept closely related to the fundamental problems of sciences themselves such as determinism, causality, free will, predictability, and time asymmetry [{\\em J. Phys. Soc. Jpn.} {\\bf 2014}, {\\em 83}, 1401]. This concept is literally a primitive chaos in such a sense that it leads to the characteristic properties of the conventional chaos under natural conditions. Then, two contrast concepts, nondegenerate Peano continuum and Cantor set, are known as the origins of the primitive chaos. In this study, the relation of these origins is investigated with the aid of a mathematical method, topology. Then, we can see the emergence of interesting concepts such as the relation of whole and part, and coarse graining, which imply the essence of our intrinsic recognition for phenomena.

  2. Application of the maximum entropy principle to determine ensembles of intrinsically disordered proteins from residual dipolar couplings.

    Science.gov (United States)

    Sanchez-Martinez, M; Crehuet, R

    2014-12-21

    We present a method based on the maximum entropy principle that can re-weight an ensemble of protein structures based on data from residual dipolar couplings (RDCs). The RDCs of intrinsically disordered proteins (IDPs) provide information on the secondary structure elements present in an ensemble; however even two sets of RDCs are not enough to fully determine the distribution of conformations, and the force field used to generate the structures has a pervasive influence on the refined ensemble. Two physics-based coarse-grained force fields, Profasi and Campari, are able to predict the secondary structure elements present in an IDP, but even after including the RDC data, the re-weighted ensembles differ between both force fields. Thus the spread of IDP ensembles highlights the need for better force fields. We distribute our algorithm in an open-source Python code.

  3. Intrinsic disorder of the bacterial cell division protein ZipA: coil-to-brush conformational transition.

    Science.gov (United States)

    López-Montero, Iván; López-Navajas, Pilar; Mingorance, Jesús; Rivas, Germán; Vélez, Marisela; Vicente, Miguel; Monroy, Francisco

    2013-08-01

    The full-length ZipA protein from Escherichia coli, one of the essential elements of the cell division machinery, was studied in a surface model built as adsorbed monolayers. The interplay between lateral packing and molecular conformation was probed using a combined methodology based on the scaling analysis of the surface pressure isotherms and ellipsometry measurements of the monolayer thickness. The observed behavior is compatible with the one expected for an intrinsically disordered and highly flexible protein that is preferentially structured in a random coil conformation. At low grafting densities, ZipA coils organize in a mushroom-like regime, whereas a coil-to-brush transition occurs on increasing lateral packing. The structural results suggest a functional scenario in which ZipA acts as a flexible tether anchoring bacterial proto-ring elements to the membrane during the earlier stages of division.

  4. Intrinsic Functional Connectivity in Attention-Deficit/Hyperactivity Disorder: A Science in Development.

    Science.gov (United States)

    Castellanos, F Xavier; Aoki, Yuta

    2016-05-01

    Functional magnetic resonance imaging (fMRI) without an explicit task, i.e., resting state fMRI, of individuals with Attention-Deficit/Hyperactivity Disorder (ADHD) is growing rapidly. Early studies were unaware of the vulnerability of this method to even minor degrees of head motion, a major concern in the field. Recent efforts are implementing various strategies to address this source of artifact along with a growing set of analytical tools. Availability of the ADHD-200 Consortium dataset, a large-scale multi-site repository, is facilitating increasingly sophisticated approaches. In parallel, investigators are beginning to explicitly test the replicability of published findings. In this narrative review, we sketch out broad, overarching hypotheses being entertained while noting methodological uncertainties. Current hypotheses implicate the interplay of default, cognitive control (frontoparietal) and attention (dorsal, ventral, salience) networks in ADHD; functional connectivities of reward-related and amygdala-related circuits are also supported as substrates for dimensional aspects of ADHD. Before these can be further specified and definitively tested, we assert the field must take on the challenge of mapping the "topography" of the analytical space, i.e., determining the sensitivities of results to variations in acquisition, analysis, demographic and phenotypic parameters. Doing so with openly available datasets will provide the needed foundation for delineating typical and atypical developmental trajectories of brain structure and function in neurodevelopmental disorders including ADHD when applied to large-scale multi-site prospective longitudinal studies such as the forthcoming Adolescent Brain Cognitive Development study.

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

    Science.gov (United States)

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

    2014-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Alexey V Uversky

    2013-09-01

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

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

    Directory of Open Access Journals (Sweden)

    Susana Barrera-Vilarmau

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

  8. Chaos and confusion in DSM-5 diagnosis of Internet Gaming Disorder: Issues, concerns, and recommendations for clarity in the field.

    Science.gov (United States)

    Kuss, Daria J; Griffiths, Mark D; Pontes, Halley M

    2016-09-07

    Background The umbrella term "Internet addiction" has been criticized for its lack of specificity given the heterogeneity of potentially problematic behaviors that can be engaged in online as well as different underlying etiological mechanisms. This has led to the naming of specific online addictions, the most notable being Internet Gaming Disorder (IGD). Methods Using the contemporary literature concerning IGD and cognate topics, issues and concerns relating to the concept of IGD are examined. Results Internet addiction and IGD are not the same, and distinguishing between the two is conceptually meaningful. Similarly, the diagnosis of IGD as proposed in the appendix of the latest (fifth) edition of the Diagnostic and Statistical Manual of Mental Disorders (DSM-5) remains vague regarding whether or not games need to be engaged in online, stating that IGD typically involves specific Internet games, but can also include offline games, adding to the lack of clarity. A number of authors have voiced concerns regarding the viability of including the word "Internet" in IGD, and instead proposed to use the term "video gaming disorder" or simply "gaming disorder," suggesting addiction to video gaming can also occur offline. Conclusion The DSM-5 has caused more confusion than clarity regarding the disorder, reflected by researchers in the field contesting a supposedly reached consensus for IGD diagnosis.

  9. P150glued-associated disorders are caused by activation of intrinsic apoptotic pathway.

    Directory of Open Access Journals (Sweden)

    Kei-Ichi Ishikawa

    Full Text Available Mutations in p150glued cause hereditary motor neuropathy with vocal cord paralysis (HMN7B and Perry syndrome (PS. Here we show that both overexpression of p150glued mutants and knockdown of endogenous p150glued induce apoptosis. Overexpression of a p150glued plasmid containing either a HMN7B or PS mutation resulted in cytoplasmic p150glued-positive aggregates and was associated with cell death. Cells containing mutant p150glued aggregates underwent apoptosis that was characterized by an increase in cleaved caspase-3- or Annexin V-positive cells and was attenuated by both zVAD-fmk (a pan-caspase inhibitor application and caspase-3 siRNA knockdown. In addition, overexpression of mutant p150glued decreased mitochondrial membrane potentials and increased levels of translocase of the mitochondrial outer membrane (Tom20 protein, indicating accumulation of damaged mitochondria. Importantly, siRNA knockdown of endogenous p150glued independently induced apoptosis via caspase-8 activation and was not associated with mitochondrial morphological changes. Simultaneous knockdown of endogenous p150glued and overexpression of mutant p150glued had additive apoptosis induction effects. These findings suggest that both p150glued gain-of-toxic-function and loss-of-physiological-function can cause apoptosis and may underlie the pathogenesis of p150glued-associated disorders.

  10. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

    Directory of Open Access Journals (Sweden)

    Matteo eLambrughi

    2012-11-01

    Full Text Available Cyclin-dependent kinase inhibitors (CKIs are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs, which lack a well-defined and organized three-dimensional structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs and collapsed conformations. These structural features can be relevant to protein function in vivo.The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models of the compact conformations of the Sic1 kinase-inhibitory domain (KID by all-atom molecular-dynamics simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of hub residues and electrostatic interactions which are likely to be involved in the stabilization of globular states.

  11. Altered cerebellar functional connectivity with intrinsic connectivity networks in adults with major depressive disorder.

    Directory of Open Access Journals (Sweden)

    Li Liu

    Full Text Available BACKGROUND: Numerous studies have demonstrated the higher-order functions of the cerebellum, including emotion regulation and cognitive processing, and have indicated that the cerebellum should therefore be included in the pathophysiological models of major depressive disorder. The aim of this study was to compare the resting-state functional connectivity of the cerebellum in adults with major depression and healthy controls. METHODS: Twenty adults with major depression and 20 gender-, age-, and education-matched controls were investigated using seed-based resting-state functional connectivity magnetic resonance imaging. RESULTS: Compared with the controls, depressed patients showed significantly increased functional connectivity between the cerebellum and the temporal poles. However, significantly reduced cerebellar functional connectivity was observed in the patient group in relation to both the default-mode network, mainly including the ventromedial prefrontal cortex and the posterior cingulate cortex/precuneus, and the executive control network, mainly including the superior frontal cortex and orbitofrontal cortex. Moreover, the Hamilton Depression Rating Scale score was negatively correlated with the functional connectivity between the bilateral Lobule VIIb and the right superior frontal gyrus in depressed patients. CONCLUSIONS: This study demonstrated increased cerebellar coupling with the temporal poles and reduced coupling with the regions in the default-mode and executive control networks in adults with major depression. These differences between patients and controls could be associated with the emotional disturbances and cognitive control function deficits that accompany major depression. Aberrant cerebellar connectivity during major depression may also imply a substantial role for the cerebellum in the pathophysiological models of depression.

  12. Temperature chaos and quenched heterogeneities

    Science.gov (United States)

    Barucca, Paolo; Parisi, Giorgio; Rizzo, Tommaso

    2014-03-01

    We present a treatable generalization of the Sherrington-Kirkpatrick (SK) model which introduces correlations in the elements of the coupling matrix through multiplicative disorder on the single variables and investigate the consequences on the phase diagram. We define a generalized qEA parameter and test the structural stability of the SK results in this correlated case evaluating the de Almeida-Thouless line of the model. As a main result we demonstrate the increase of temperature chaos effects due to heterogeneities.

  13. Some chaotic features of intrinsically coupled Josephson junctions

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-08-15

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

  14. The Effect of Intrinsic Disorder and Self-association on the Translational Diffusion of Proteins: the Case of α-Casein.

    Science.gov (United States)

    Melnikova, Daria L; Skirda, Vladimir Dmitrievich; Nesmelova, Irina V

    2017-03-27

    Translational diffusion is the major mode of macromolecular transport in leaving organisms and therefore it is vital to many biological and biotechnological processes. Although translational diffusion of proteins has received considerable theoretical and experimental scrutiny, much of that attention has been directed towards the description of globular proteins. The translational diffusion of intrinsically disordered proteins (IDPs), however, is much less studied. Here, we use a pulsed-gradient nuclear magnetic resonance technique (PFG NMR) to investigate the translational diffusion of a disordered protein in a wide range of concentrations using α-casein that belongs to the class of natively disordered proteins as an example.

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

    Science.gov (United States)

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

    2015-11-01

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

  16. Chaos and confusion in DSM-5 diagnosis of Internet Gaming Disorder: issues, concerns, and recommendations for clarity in the field

    OpenAIRE

    2016-01-01

    Background:\\ud The umbrella term "Internet addiction" has been criticized for its lack of specificity given the heterogeneity of potentially problematic behaviors that can be engaged in online as well as different underlying etiological mechanisms. This has led to the naming of specific online addictions, the most notable being Internet Gaming Disorder (IGD).\\ud \\ud Methods:\\ud Using the contemporary literature concerning IGD and cognate topics, issues and concerns relating to the concept of ...

  17. Structural analysis of the complex between calmodulin and full-length myelin basic protein, an intrinsically disordered molecule.

    Science.gov (United States)

    Majava, Viivi; Wang, Chaozhan; Myllykoski, Matti; Kangas, Salla M; Kang, Sung Ung; Hayashi, Nobuhiro; Baumgärtel, Peter; Heape, Anthony M; Lubec, Gert; Kursula, Petri

    2010-06-01

    Myelin basic protein (MBP) is present between the cytoplasmic leaflets of the compact myelin membrane in both the peripheral and central nervous systems, and characterized to be intrinsically disordered in solution. One of the best-characterized protein ligands for MBP is calmodulin (CaM), a highly acidic calcium sensor. We pulled down MBP from human brain white matter as the major calcium-dependent CaM-binding protein. We then used full-length brain MBP, and a peptide from rodent MBP, to structurally characterize the MBP-CaM complex in solution by small-angle X-ray scattering, NMR spectroscopy, synchrotron radiation circular dichroism spectroscopy, and size exclusion chromatography. We determined 3D structures for the full-length protein-protein complex at different stoichiometries and detect ligand-induced folding of MBP. We also obtained thermodynamic data for the two CaM-binding sites of MBP, indicating that CaM does not collapse upon binding to MBP, and show that CaM and MBP colocalize in myelin sheaths. In addition, we analyzed the post-translational modifications of rat brain MBP, identifying a novel MBP modification, glucosylation. Our results provide a detailed picture of the MBP-CaM interaction, including a 3D model of the complex between full-length proteins.

  18. Anchoring Intrinsically Disordered Proteins to Multiple Targets: Lessons from N-Terminus of the p53 Protein

    Directory of Open Access Journals (Sweden)

    Yongqi Huang

    2011-02-01

    Full Text Available Anchor residues, which are deeply buried upon binding, play an important role in protein–protein interactions by providing recognition specificity and facilitating the binding kinetics. Up to now, studies on anchor residues have been focused mainly on ordered proteins. In this study, we investigated anchor residues in intrinsically disordered proteins (IDPs which are flexible in the free state. We identified the anchor residues of the N-terminus of the p53 protein (Glu17–Asn29, abbreviated as p53N which are involved in binding with two different targets (MDM2 and Taz2, and analyzed their side chain conformations in the unbound states. The anchor residues in the unbound p53N were found to frequently sample conformations similar to those observed in the bound complexes (i.e., Phe19, Trp23, and Leu26 in the p53N-MDM2 complex, and Leu22 in the p53N-Taz2 complex. We argue that the bound-like conformations of the anchor residues in the unbound state are important for controlling the specific interactions between IDPs and their targets. Further, we propose a mechanism to account for the binding promiscuity of IDPs in terms of anchor residues and molecular recognition features (MoRFs.

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

    KAUST Repository

    Hameed, Umar Farook Shahul

    2014-05-09

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

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

    Science.gov (United States)

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

    2016-01-01

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

  1. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

    Science.gov (United States)

    Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

    2017-01-01

    Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

  2. Are Charge-State Distributions a Reliable Tool Describing Molecular Ensembles of Intrinsically Disordered Proteins by Native MS?

    Science.gov (United States)

    Natalello, Antonino; Santambrogio, Carlo; Grandori, Rita

    2016-10-01

    Native mass spectrometry (MS) has become a central tool of structural proteomics, but its applicability to the peculiar class of intrinsically disordered proteins (IDPs) is still object of debate. IDPs lack an ordered tridimensional structure and are characterized by high conformational plasticity. Since they represent valuable targets for cancer and neurodegeneration research, there is an urgent need of methodological advances for description of the conformational ensembles populated by these proteins in solution. However, structural rearrangements during electrospray-ionization (ESI) or after the transfer to the gas phase could affect data obtained by native ESI-MS. In particular, charge-state distributions (CSDs) are affected by protein conformation inside ESI droplets, while ion mobility (IM) reflects protein conformation in the gas phase. This review focuses on the available evidence relating IDP solution ensembles with CSDs, trying to summarize cases of apparent consistency or discrepancy. The protein-specificity of ionization patterns and their responses to ligands and buffer conditions suggests that CSDs are imprinted to protein structural features also in the case of IDPs. Nevertheless, it seems that these proteins are more easily affected by electrospray conditions, leading in some cases to rearrangements of the conformational ensembles.

  3. Chaos Control in Mechanical Systems

    Directory of Open Access Journals (Sweden)

    Marcelo A. Savi

    2006-01-01

    Full Text Available Chaos has an intrinsically richness related to its structure and, because of that, there are benefits for a natural system of adopting chaotic regimes with their wide range of potential behaviors. Under this condition, the system may quickly react to some new situation, changing conditions and their response. Therefore, chaos and many regulatory mechanisms control the dynamics of living systems, conferring a great flexibility to the system. Inspired by nature, the idea that chaotic behavior may be controlled by small perturbations of some physical parameter is making this kind of behavior to be desirable in different applications. Mechanical systems constitute a class of system where it is possible to exploit these ideas. Chaos control usually involves two steps. In the first, unstable periodic orbits (UPOs that are embedded in the chaotic set are identified. After that, a control technique is employed in order to stabilize a desirable orbit. This contribution employs the close-return method to identify UPOs and a semi-continuous control method, which is built up on the OGY method, to stabilize some desirable UPO. As an application to a mechanical system, a nonlinear pendulum is considered and, based on parameters obtained from an experimental setup, analyses are carried out. Signals are generated by numerical integration of the mathematical model and two different situations are treated. Firstly, it is assumed that all state variables are available. After that, the analysis is done from scalar time series and therefore, it is important to evaluate the effect of state space reconstruction. Delay coordinates method and extended state observers are employed with this aim. Results show situations where these techniques may be used to control chaos in mechanical systems.

  4. Impact of Hydrostatic Pressure on an Intrinsically Disordered Protein: A High-Pressure NMR Study of α-Synuclein [a

    Science.gov (United States)

    Roche, Julien; Ying, Jinfa; Maltsev, Alexander S.

    2013-01-01

    The impact of pressure on the backbone 15N, 1H and 13C chemical shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range spanning from 1–2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in short model peptides. In particular, the non-linear pressure response of the 1HN chemical shifts, which commonly is associated with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of 1HN chemical shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anti-correlated with its temperature dependence. The pressure dependence of 13C chemical shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in 3JHN-Hα by 0.22 ± 0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient ca 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar. PMID:23813793

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-05-15

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

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

    Science.gov (United States)

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

    2012-01-01

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

  7. Impact of hydrostatic pressure on an intrinsically disordered protein: a high-pressure NMR study of α-synuclein.

    Science.gov (United States)

    Roche, Julien; Ying, Jinfa; Maltsev, Alexander S; Bax, Ad

    2013-09-23

    The impact of pressure on the backbone (15) N, (1) H and (13) C chemical shifts in N-terminally acetylated α-synuclein has been evaluated over a pressure range 1-2500 bar. Even while the chemical shifts fall very close to random coil values, as expected for an intrinsically disordered protein, substantial deviations in the pressure dependence of the chemical shifts are seen relative to those in short model peptides. In particular, the nonlinear pressure response of the (1) H(N) chemical shifts, which commonly is associated with the presence of low-lying "excited states", is much larger in α-synuclein than in model peptides. The linear pressure response of (1) H(N) chemical shift, commonly linked to H-bond length change, correlates well with those in short model peptides, and is found to be anticorrelated with its temperature dependence. The pressure dependence of (13) C chemical shifts shows remarkably large variations, even when accounting for residue type, and do not point to a clear shift in population between different regions of the Ramachandran map. However, a nearly universal decrease in (3) JHN-Hα by 0.22 ± 0.05 Hz suggests a slight increase in population of the polyproline II region at 2500 bar. The first six residues of N-terminally acetylated synuclein show a transient of approximately 15% population of α-helix, which slightly diminishes at 2500 bar. The backbone dynamics of the protein is not visibly affected beyond the effect of slight increase in water viscosity at 2500 bar.

  8. A J-modulated protonless NMR experiment characterizes the conformational ensemble of the intrinsically disordered protein WIP.

    Science.gov (United States)

    Rozentur-Shkop, Eva; Goobes, Gil; Chill, Jordan H

    2016-12-01

    Intrinsically disordered proteins (IDPs) are multi-conformational polypeptides that lack a single stable three-dimensional structure. It has become increasingly clear that the versatile IDPs play key roles in a multitude of biological processes, and, given their flexible nature, NMR is a leading method to investigate IDP behavior on the molecular level. Here we present an IDP-tailored J-modulated experiment designed to monitor changes in the conformational ensemble characteristic of IDPs by accurately measuring backbone one- and two-bond J((15)N,(13)Cα) couplings. This concept was realized using a unidirectional (H)NCO (13)C-detected experiment suitable for poor spectral dispersion and optimized for maximum coverage of amino acid types. To demonstrate the utility of this approach we applied it to the disordered actin-binding N-terminal domain of WASp interacting protein (WIP), a ubiquitous key modulator of cytoskeletal changes in a range of biological systems. One- and two-bond J((15)N,(13)Cα) couplings were acquired for WIP residues 2-65 at various temperatures, and in denaturing and crowding environments. Under native conditions fitted J-couplings identified in the WIP conformational ensemble a propensity for extended conformation at residues 16-23 and 45-60, and a helical tendency at residues 28-42. These findings are consistent with a previous study of the based upon chemical shift and RDC data and confirm that the WIP(2-65) conformational ensemble is biased towards the structure assumed by this fragment in its actin-bound form. The effects of environmental changes upon this ensemble were readily apparent in the J-coupling data, which reflected a significant decrease in structural propensity at higher temperatures, in the presence of 8 M urea, and under the influence of a bacterial cell lysate. The latter suggests that crowding can cause protein unfolding through protein-protein interactions that stabilize the unfolded state. We conclude that J-couplings are

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-11-01

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

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

    Science.gov (United States)

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

    2012-11-01

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

  11. 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.

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

    Science.gov (United States)

    Dyson, H Jane; Wright, Peter E

    2016-03-25

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

  13. 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.

  14. Quantum Chaos and Statistical Mechanics

    OpenAIRE

    Srednicki, Mark

    1994-01-01

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

  15. Cosmology, Epistemology and Chaos

    Science.gov (United States)

    Unno, Wasaburo

    1992-03-01

    We may consider the following three fundamental epistemological questions concerning cosmology. Can cosmology at last understand the origin of the universe? Can computers at last create? Can life be formed at last synthetically? These questions are in some sense related to the liar paradox containing the self-reference and, therefore, may not be answered by recursive processes in finite time. There are, however, various implications such that the chaos may break the trap of the self- reference paradox. In other words, Goedel's incompleteness theorem would not apply to chaos, even if the chaos can be generated by recursive processes. Internal relations among cosmology, epistemology and chaos must be investigated in greater detail

  16. Applied Chaos Control

    Science.gov (United States)

    Spano, Mark

    1997-04-01

    The publication by Ott, Grebogi and Yorke(E. Ott, C. Grebogi and J. A. Yorke, Phys. Rev. Lett. 64, 1196 (1990).) of their theory of chaos control in 1990 led to an explosion of experimental work applying their theory to mechanical systems and electronic circuits, lasers and chemical reactors, and heart and brain tissue, to name only a few. In this talk the basics of chaos control as implemented in a simple mechanical system will be described, as well as extensions of the method to biological applications. Finally, current advances in the field, including the maintenance of chaos and the control of high dimensional chaos, will be discussed.

  17. Molecular Basis for Structural Heterogeneity of an Intrinsically Disordered Protein Bound to a Partner by Combined ESI-IM-MS and Modeling

    Science.gov (United States)

    D'Urzo, Annalisa; Konijnenberg, Albert; Rossetti, Giulia; Habchi, Johnny; Li, Jinyu; Carloni, Paolo; Sobott, Frank; Longhi, Sonia; Grandori, Rita

    2015-03-01

    Intrinsically disordered proteins (IDPs) form biologically active complexes that can retain a high degree of conformational disorder, escaping structural characterization by conventional approaches. An example is offered by the complex between the intrinsically disordered NTAIL domain and the phosphoprotein X domain (PXD) from measles virus (MeV). Here, distinct conformers of the complex are detected by electrospray ionization-mass spectrometry (ESI-MS) and ion mobility (IM) techniques yielding estimates for the solvent-accessible surface area (SASA) in solution and the average collision cross-section (CCS) in the gas phase. Computational modeling of the complex in solution, based on experimental constraints, provides atomic-resolution structural models featuring different levels of compactness. The resulting models indicate high structural heterogeneity. The intermolecular interactions are predominantly hydrophobic, not only in the ordered core of the complex, but also in the dynamic, disordered regions. Electrostatic interactions become involved in the more compact states. This system represents an illustrative example of a hydrophobic complex that could be directly detected in the gas phase by native mass spectrometry. This work represents the first attempt to modeling the entire NTAIL domain bound to PXD at atomic resolution.

  18. 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.

  19. 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

  20. A bound on chaos

    CERN Document Server

    Maldacena, Juan; Stanford, Douglas

    2015-01-01

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

  1. Spirals, chaos, and new mechanisms of wave propagation.

    Science.gov (United States)

    Chen, P S; Garfinkel, A; Weiss, J N; Karagueuzian, H S

    1997-02-01

    The chaos theory is based on the idea that phenomena that appear disordered and random may actually be produced by relatively simple deterministic mechanisms. The disordered (aperiodic) activation that characterizes a chaotic motion is reached through one of a few well-defined paths that are characteristic of nonlinear dynamical systems. Our group has been studying VF using computerized mapping techniques. We found that in electrically induced VF, reentrant wavefronts (spiral waves) are present both in the initial tachysystolic stage (resembling VT) and the later tremulous incoordination stage (true VF). The electrophysiological characteristics associated with the transition from VT to VF is compatible with the quasiperiodic route to chaos as described in the Ruelle-Takens theorem. We propose that specific restitution of action potential duration (APD) and conduction velocity properties can cause a spiral wave (the primary oscillator) to develop additional oscillatory modes that lead to spiral meander and breakup. When spiral waves begin to meander and are modulated by other oscillatory processes, the periodic activity is replaced by unstable quasiperiodic oscillation, which then undergoes transition to chaos, signaling the onset of VF. We conclude that VF is a form of deterministic chaos. The development of VF is compatible with quasiperiodic transition to chaos. These results indicate that both the prediction and the control of fibrillation are possible based on the chaos theory and with the advent of chaos control algorithms.

  2. Importance of electrostatic interactions in the association of intrinsically disordered histone chaperone Chz1 and histone H2A.Z-H2B.

    Directory of Open Access Journals (Sweden)

    Xiakun Chu

    Full Text Available Histone chaperones facilitate assembly and disassembly of nucleosomes. Understanding the process of how histone chaperones associate and dissociate from the histones can help clarify their roles in chromosome metabolism. Some histone chaperones are intrinsically disordered proteins (IDPs. Recent studies of IDPs revealed that the recognition of the biomolecules is realized by the flexibility and dynamics, challenging the century-old structure-function paradigm. Here we investigate the binding between intrinsically disordered chaperone Chz1 and histone variant H2A.Z-H2B by developing a structure-based coarse-grained model, in which Debye-Hückel model is implemented for describing electrostatic interactions due to highly charged characteristic of Chz1 and H2A.Z-H2B. We find that major structural changes of Chz1 only occur after the rate-limiting electrostatic dominant transition state and Chz1 undergoes folding coupled binding through two parallel pathways. Interestingly, although the electrostatic interactions stabilize bound complex and facilitate the recognition at first stage, the rate for formation of the complex is not always accelerated due to slow escape of conformations with non-native electrostatic interactions at low salt concentrations. Our studies provide an ionic-strength-controlled binding/folding mechanism, leading to a cooperative mechanism of "local collapse or trapping" and "fly-casting" together and a new understanding of the roles of electrostatic interactions in IDPs' binding.

  3. Chaos Rules Revisited

    Directory of Open Access Journals (Sweden)

    David Murphy

    2011-11-01

    Full Text Available About 20 years ago, while lost in the midst of my PhD research, I mused over proposed titles for my thesis. I was pretty pleased with myself when I 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. I used the then-emerging theories of chaos and complexity to underpin my analysis. So it was with more than a little excitement that I read the call for contributions to this special issue of IRRODL. What follows is a walk-through of my thesis with an emphasis on the contribution of chaos and complexity theory.

  4. 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.

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

    Science.gov (United States)

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

    2017-01-01

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

  6. Fractal Patterns and Chaos Games

    Science.gov (United States)

    Devaney, Robert L.

    2004-01-01

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

  7. Frozen spatial chaos induced by boundaries

    CERN Document Server

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

    1999-01-01

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

  8. Introducing chaos a graphic guide

    CERN Document Server

    Sardar, Ziauddin; Abrams, Iwona

    2014-01-01

    Explains how chaos makes its presence felt in many varieties of event, from the fluctuation of animal populations to the ups and downs of the stock market. This book also examines the roots of chaos in modern mathematics and physics, and explores the relationship between chaos and complexity.

  9. Ordered self-assembly mechanism of a spherical oncoprotein oligomer triggered by zinc removal and stabilized by an intrinsically disordered domain.

    Directory of Open Access Journals (Sweden)

    Clara Smal

    Full Text Available BACKGROUND: Self-assembly is a common theme in proteins of unrelated sequences or functions. The human papillomavirus E7 oncoprotein is an extended dimer with an intrinsically disordered domain, that can form large spherical oligomers. These are the major species in the cytosol of HPV transformed and cancerous cells. E7 binds to a large number of targets, some of which lead to cell transformation. Thus, the assembly process not only is of biological relevance, but represents a model system to investigate a widely distributed mechanism. METHODOLOGY/PRINCIPAL FINDINGS: Using various techniques, we monitored changes in secondary, tertiary and quaternary structure in a time course manner. By applying a robust kinetic model developed by Zlotnik, we determined the slow formation of a monomeric "Z-nucleus" after zinc removal, followed by an elongation phase consisting of sequential second-order events whereby one monomer is added at a time. This elongation process takes place at a strikingly slow overall average rate of one monomer added every 28 seconds at 20 µM protein concentration, strongly suggesting either a rearrangement of the growing complex after binding of each monomer or the existence of a "conformation editing" mechanism through which the monomer binds and releases until the appropriate conformation is adopted. The oligomerization determinant lies within its small 5 kDa C-terminal globular domain and, remarkably, the E7 N-terminal intrinsically disordered domain stabilizes the oligomer, preventing an insoluble amyloid route. CONCLUSION: We described a controlled ordered mechanism with features in common with soluble amyloid precursors, chaperones, and other spherical oligomers, thus sharing determining factors for symmetry, size and shape. In addition, such a controlled and discrete polymerization reaction provides a valuable tool for nanotechnological applications. Finally, its increased immunogenicity related to its supramolecular

  10. A novel intrinsically disordered outer membrane lipoprotein of Aggregatibacter actinomycetemcomitans binds various cytokines and plays a role in biofilm response to interleukin-1β and interleukin-8.

    Science.gov (United States)

    Ahlstrand, Tuuli; Tuominen, Heidi; Beklen, Arzu; Torittu, Annamari; Oscarsson, Jan; Sormunen, Raija; Pöllänen, Marja T; Permi, Perttu; Ihalin, Riikka

    2017-02-17

    Intrinsically disordered proteins (IDPs) do not have a well-defined and stable 3-dimensional fold. Some IDPs can function as either transient or permanent binders of other proteins and may interact with an array of ligands by adopting different conformations. A novel outer membrane lipoprotein, bacterial interleukin receptor I (BilRI) of the opportunistic oral pathogen Aggregatibacter actinomycetemcomitans binds a key gatekeeper proinflammatory cytokine interleukin (IL)-1β. Because the amino acid sequence of the novel lipoprotein resembles that of fibrinogen binder A of Haemophilus ducreyi, BilRI could have the potential to bind other proteins, such as host matrix proteins. However, from the tested host matrix proteins, BilRI interacted with neither collagen nor fibrinogen. Instead, the recombinant non-lipidated BilRI, which was intrinsically disordered, bound various pro/anti-inflammatory cytokines, such as IL-8, tumor necrosis factor (TNF)-α, interferon (IFN)-γ and IL-10. Moreover, BilRI played a role in the in vitro sensing of IL-1β and IL-8 because low concentrations of cytokines did not decrease the amount of extracellular DNA in the matrix of bilRI(-) mutant biofilm as they did in the matrix of wild-type biofilm when the biofilms were exposed to recombinant cytokines for 22 hours. BilRI played a role in the internalization of IL-1β in the gingival model system but did not affect either IL-8 or IL-6 uptake. However, bilRI deletion did not entirely prevent IL-1β internalization, and the binding of cytokines to BilRI was relatively weak. Thus, BilRI might sequester cytokines on the surface of A. actinomycetemcomitans to facilitate the internalization process in low local cytokine concentrations.

  11. Spatiotemporal Chaos in Large Systems The Scaling of Complexity with Size

    CERN Document Server

    Greenside, H S

    1996-01-01

    The dynamics of a nonequilibrium system can become complex because the system has many components (e.g., a human brain), because the system is strongly driven from equilibrium (e.g., large Reynolds-number flows), or because the system becomes large compared to certain intrinsic length scales. Recent experimental and theoretical work is reviewed that addresses this last route to complexity. In the idealized case of a sufficiently large, nontransient, homogeneous, and chaotic system, the fractal dimension D becomes proportional to the system's volume V which defines the regime of extensive chaos. The extensivity of the fractal dimension suggests a new way to characterize correlations in high-dimensional systems in terms of an intensive dimension correlation length $\\xi_\\delta$. Recent calculations at Duke University show that $\\xi_\\delta$ is a length scale smaller than and independent of some commonly used measures of disorder such as the two-point and mutual-information correlation lengths. Identifying the bas...

  12. Dissipative structures and chaos

    CERN Document Server

    Mori, Hazime

    1998-01-01

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

  13. Chaos Induced by Quantization

    CERN Document Server

    Shigehara, T; Mishima, T; Cheon, T; Shigehara, Takaomi; Mizoguchi, Hiroshi; Mishima, Taketoshi; Cheon, Taksu

    1998-01-01

    In this paper, we show that two-dimensional billiards with point interactions inside exhibit a chaotic nature in the microscopic world, although their classical counterpart is non-chaotic. After deriving the transition matrix of the system by using the self-adjoint extension theory of functional analysis, we deduce the general condition for the appearance of chaos. The prediction is confirmed by numerically examining the statistical properties of energy spectrum of rectangular billiards with multiple point interactions inside. The dependence of the level statistics on the strength as well as the number of the scatterers is displayed. KEYWORDS: wave chaos, quantum mechanics, pseudointegrable billiard, point interaction, functional analysis

  14. A Description of Quantum Chaos

    CERN Document Server

    Inoue, K; Ohya, M; Inoue, Kei; Kossakowski, Andrzej; Ohya, Masanori

    2004-01-01

    A measure describing the chaos of a dynamics was introduced by two complexities in information dynamics, and it is called the chaos degree. In particular, the entropic chaos degree has been used to characterized several dynamical maps such that logistis, Baker's, Tinckerbel's in classical or quantum systems. In this paper, we give a new treatment of quantum chaos by defining the entropic chaos degree for quantum transition dynamics, and we prove that every non-chaotic quantum dynamics, e.g., dissipative dynamics, has zero chaos degree. A quantum spin 1/2 system is studied by our chaos degree, and it is shown that this degree well describes the chaotic behavior of the spin system.

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

    Science.gov (United States)

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

    2014-07-29

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

  16. A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein

    Science.gov (United States)

    Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

    2014-01-01

    α-Synuclein is an intrinsically disordered protein of 140 residues that switches to an α-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential HN–Hα and HN–HN NOEs, values for 3JHNHα, 1JHαCα, 2JCαN, and 1JCαN, as well as chemical shifts of 15N, 13Cα, and 13C′ nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20–30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone β region (20–40%) than seen in the database. A generally lower population of the αR region (10–20%) is found. Analysis of 1H–1H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein. PMID:24976112

  17. A maximum entropy approach to the study of residue-specific backbone angle distributions in α-synuclein, an intrinsically disordered protein.

    Science.gov (United States)

    Mantsyzov, Alexey B; Maltsev, Alexander S; Ying, Jinfa; Shen, Yang; Hummer, Gerhard; Bax, Ad

    2014-09-01

    α-Synuclein is an intrinsically disordered protein of 140 residues that switches to an α-helical conformation upon binding phospholipid membranes. We characterize its residue-specific backbone structure in free solution with a novel maximum entropy procedure that integrates an extensive set of NMR data. These data include intraresidue and sequential H(N) − H(α) and H(N) − H(N) NOEs, values for (3) JHNHα, (1) JHαCα, (2) JCαN, and (1) JCαN, as well as chemical shifts of (15)N, (13)C(α), and (13)C' nuclei, which are sensitive to backbone torsion angles. Distributions of these torsion angles were identified that yield best agreement to the experimental data, while using an entropy term to minimize the deviation from statistical distributions seen in a large protein coil library. Results indicate that although at the individual residue level considerable deviations from the coil library distribution are seen, on average the fitted distributions agree fairly well with this library, yielding a moderate population (20-30%) of the PPII region and a somewhat higher population of the potentially aggregation-prone β region (20-40%) than seen in the database. A generally lower population of the αR region (10-20%) is found. Analysis of (1)H − (1)H NOE data required consideration of the considerable backbone diffusion anisotropy of a disordered protein.

  18. Inverse anticipating chaos synchronization.

    Science.gov (United States)

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

    2002-07-01

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

  19. Morphogenesis of Chaos

    CERN Document Server

    Akhmet, Marat

    2012-01-01

    Morphogenesis, as it is understood in a wide sense by Ren\\'e Thom, is considered for various types of chaos. That is, those, obtained by period-doubling cascade, Devaney's and Li-Yorke chaos. Moreover, in discussion form we consider inheritance of intermittency, the double-scroll Chua's attractor and quasiperiodical motions as a possible skeleton of a chaotic attractor. To make our introduction of the paper more clear, we have to say that one may consider other various accompanying concepts of chaos such that a structure of the chaotic attractor, its fractal dimension, form of the bifurcation diagram, the spectra of Lyapunov exponents, etc. We make comparison of the main concept of our paper with Turing's morphogenesis and John von Neumann automata, considering that this may be not only formal one, but will give ideas for the chaos development in the morphogenesis of Turing and for self-replicating machines. To provide rigorous study of the subject, we introduce new definitions such as chaotic sets of functio...

  20. 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.

  1. Chaos induced by coupling between Josephson junctions

    Science.gov (United States)

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

    2015-02-01

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

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

    Directory of Open Access Journals (Sweden)

    Kaare eBjerregaard-Andersen

    2013-11-01

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

  3. Converting transient chaos into sustained chaos by feedback control

    Science.gov (United States)

    Lai, Ying-Cheng; Grebogi, Celso

    1994-02-01

    A boundary crisis is a catastrophic event in which a chaotic attractor is suddenly destroyed, leaving a nonattracting chaotic saddle in its place in the phase space. Based on the controlling-chaos idea [E. Ott, C. Grebogi, and J. A. Yorke, Phys. Rev. Lett. 64, 1196 (1990)], we present a method for stabilizing chaotic trajectories on the chaotic saddle by applying only small parameter perturbations. This strategy enables us to convert transient chaos into sustained chaos, thereby restoring attracting chaotic motion.

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

    Institute of Scientific and Technical Information of China (English)

    邹恩; 李祥飞; 张泰山

    2004-01-01

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

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

    Science.gov (United States)

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

    2015-01-15

    Protein ID (intrinsic disorder) plays a significant, yet relatively unexplored role in transcription factors (TFs). In the present paper, analysis of the transcription regulatory domains (TRDs) of six phylogenetically representative, plant-specific NAC [no apical meristem, ATAF (Arabidopsis transcription activation factor), cup-shaped cotyledon] TFs shows that the domains are present in similar average pre-molten or molten globule-like states, but have different patterns of order/disorder and MoRFs (molecular recognition features). ANAC046 (Arabidopsis NAC 046) was selected for further studies because of its simple MoRF pattern and its ability to interact with RCD1 (radical-induced cell death 1). Experiments in yeast and thermodynamic characterization suggest that its single MoRF region is sufficient for both transcriptional activation and interaction with RCD1. The remainder of the large regulatory domain is unlikely to contribute to the interaction, since the domain and truncations thereof have similar affinities for RCD1, which are also similar for ANAC013-RCD1 interactions. However, different enthalpic and entropic contributions to binding were revealed for ANAC046 and ANAC013, suggestive of differences in binding mechanisms. Although substitution of both hydrophobic and acidic residues of the ANAC046 MoRF region abolished binding, substitution of other residues, even with α-helix-breaking proline, was less disruptive. Together, the biophysical analyses suggest that RCD1-ANAC046 complex formation does not involve folding-upon-binding, but rather fuzziness or an unknown structure in ANAC046. We suggest that the ANAC046 regulatory domain functions as an entropic chain with a terminal hot spot interacting with RCD1. RCD1, a cellular hub, may be able to interact with many different TFs by exploiting their ID-based flexibility, as demonstrated for its interactions with ANAC046 and ANAC013.

  6. 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.

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

    Science.gov (United States)

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

    2008-01-01

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

  8. Deuterium isotope shifts for backbone ¹H, ¹⁵N and ¹³C nuclei in intrinsically disordered protein α-synuclein.

    Science.gov (United States)

    Maltsev, Alexander S; Ying, Jinfa; Bax, Ad

    2012-10-01

    Intrinsically disordered proteins (IDPs) are abundant in nature and characterization of their potential structural propensities remains a widely pursued but challenging task. Analysis of NMR secondary chemical shifts plays an important role in such studies, but the output of such analyses depends on the accuracy of reference random coil chemical shifts. Although uniform perdeuteration of IDPs can dramatically increase spectral resolution, a feature particularly important for the poorly dispersed IDP spectra, the impact of deuterium isotope shifts on random coil values has not yet been fully characterized. Very precise (2)H isotope shift measurements for (13)C(α), (13)C(β), (13)C', (15)N, and (1)H(N) have been obtained by using a mixed sample of protonated and uniformly perdeuterated α-synuclein, a protein with chemical shifts exceptionally close to random coil values. Decomposition of these isotope shifts into one-bond, two-bond and three-bond effects as well as intra- and sequential residue contributions shows that such an analysis, which ignores conformational dependence, is meaningful but does not fully describe the total isotope shift to within the precision of the measurements. Random coil (2)H isotope shifts provide an important starting point for analysis of such shifts in structural terms in folded proteins, where they are known to depend strongly on local geometry.

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

    Science.gov (United States)

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

    2016-09-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-07-18

    Highlights: • W- and D-Band line shapes are sensitive to motions in the 0.1–2 ns time regime. • These frequencies effectively report on conformational dynamics of IDPs. • W-band spectra reflecting helical formation in IA{sub 3} is experimentally demonstrated. - Abstract: Site-directed spin labeling (SDSL) electron paramagnetic resonance (EPR) spectroscopy is a powerful tool for characterizing conformational sampling and dynamics in biological macromolecules. Here we demonstrate that nitroxide spectra collected at frequencies higher than X-band (∼9.5 GHz) have sensitivity to the timescale of motion sampled by highly dynamic intrinsically disordered proteins (IDPs). The 68 amino acid protein IA{sub 3}, was spin-labeled at two distinct sites and a comparison of X-band, Q-band (35 GHz) and W-band (95 GHz) spectra are shown for this protein as it undergoes the helical transition chemically induced by tri-fluoroethanol. Experimental spectra at W-band showed pronounced line shape dispersion corresponding to a change in correlation time from ∼0.3 ns (unstructured) to ∼0.6 ns (α-helical) as indicated by comparison with simulations. Experimental and simulated spectra at X- and Q-bands showed minimal dispersion over this range, illustrating the utility of SDSL EPR at higher frequencies for characterizing structural transitions and dynamics in IDPs.

  11. Familial Alzheimer A2 V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer.

    Science.gov (United States)

    Nguyen, Phuong H; Tarus, Bogdan; Derreumaux, Philippe

    2014-01-16

    The self-assembly of the amyloid-β (Aβ) peptide of 39-43 amino acids into senile plaques is one hallmark of Alzheimer's disease (AD) pathology. While A2 V carriers remain healthy in the heterozygous state, they suffer from early onset AD in the homozygous state. As a first toward understanding the impact of A2 V on Aβ at its earlier stage, we characterized the equilibrium ensemble of the Aβ1-28 wild type and Aβ1-28 A2 V monomers by means of extensive atomistic replica exchange molecular dynamics simulations. While global conformational properties such as the radius of gyration and the average secondary structure content of the whole peptides are very similar, the population of β-hairpins is increased by a factor of 4 in A2 V, and this may explain the enhanced Aβ1-40 A2 V aggregation kinetics with respect to Aβ1-40 wild type. Both peptides display a non-negligible population of extended metastable conformations differing however in their atomic details that represent ideal seeds for polymerization. Remarkably, upon A2 V mutation, the intrinsic disorder of Aβ1-28 monomer is reduced by a factor of 2, and the free energy landscape is completely different. This difference in the conformational ensembles of the two peptides may explain in part why the mixture of the Aβ40 WT and A2 V peptides protects against AD.

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

    Directory of Open Access Journals (Sweden)

    Karyna eRosario

    2015-07-01

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

  13. 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

  14. 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...

  15. Arithmetic quantum chaos

    CERN Document Server

    Marklof, J

    2005-01-01

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

  16. Chaos in quantum channels

    CERN Document Server

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

    2015-01-01

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

  17. 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.

  18. Noise tolerant spatiotemporal chaos computing

    Energy Technology Data Exchange (ETDEWEB)

    Kia, Behnam; Kia, Sarvenaz; Ditto, William L. [Department of Physics and Astronomy, University of Hawaii at Manoa, Honolulu, Hawaii 96822 (United States); Lindner, John F. [Physics Department, The College of Wooster, Wooster, Ohio 44691 (United States); Sinha, Sudeshna [Indian Institute of Science Education and Research (IISER), Mohali, Punjab 140306 (India)

    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.

  19. 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.

  20. Tailoring wavelets for chaos control.

    Science.gov (United States)

    Wei, G W; Zhan, Meng; Lai, C-H

    2002-12-31

    Chaos is a class of ubiquitous phenomena and controlling chaos is of great interest and importance. In this Letter, we introduce wavelet controlled dynamics as a new paradigm of dynamical control. We find that by modifying a tiny fraction of the wavelet subspaces of a coupling matrix, we could dramatically enhance the transverse stability of the synchronous manifold of a chaotic system. Wavelet controlled Hopf bifurcation from chaos is observed. Our approach provides a robust strategy for controlling chaos and other dynamical systems in nature.

  1. Galaxies and chaos

    CERN Document Server

    Voglis, Nikos

    2003-01-01

    Galaxies and Chaos examines the application of tools developed for Nonlinear Dynamical Systems to Galactic Dynamics and Galaxy Formation, as well as to related issues in Celestial Mechanics. The contributions collected in this volume have emerged from selected presentations at a workshop on this topic and key chapters have been suitably expanded in order to be accessible to nonspecialist researchers and postgraduate students wishing to enter this exciting field of research.

  2. SPICE and Chaos

    DEFF Research Database (Denmark)

    Lindberg, Erik

    1996-01-01

    Can we believe in the results of our circuit simulators ? Is it possible to distinguish between results due to numerical chaos and resultsdue to the eventual chaotic nature of our modelsof physical systems ?. Three experiments with SPICE are presented: (1) A "stable" active RCcircuit with poles i...... in the models of the circuits to be analyzed. If trimmed properly SPICE normally gives the correct result....

  3. 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...

  4. Failure of chaos control

    Science.gov (United States)

    van De Water W; de Weger J

    2000-11-01

    We study the control of chaos in an experiment on a parametrically excited pendulum whose excitation mechanism is not perfect. This imperfection leads to a weakly excited degree of freedom with an associated small eigenvalue. Although the state of the pendulum could be characterized well and although the perturbation is weak, we fail to control chaos. From a numerical model we learn that the small eigenvalue cannot be ignored when attempting control. However, the estimate of this eigenvalue from an (experimental) time series is elusive. The reason is that points in an experimental time series are distributed according to the natural measure. It is this extremely uneven distribution of points that thwarts attempts to measure eigenvalues that are very different. Another consequence of the phase-space distribution of points for control is the occurrence of logarithmic-oscillations in the waiting time before control can be attempted. We come to the conclusion that chaos needs to be destroyed before the information needed for its control can be obtained.

  5. Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium.

    Science.gov (United States)

    Stern, S; Santos, R; Marchetto, M C; Mendes, A P D; Rouleau, G A; Biesmans, S; Wang, Q-W; Yao, J; Charnay, P; Bang, A G; Alda, M; Gage, F H

    2017-02-28

    Bipolar disorder (BD) is a progressive psychiatric disorder with more than 3% prevalence worldwide. Affected individuals experience recurrent episodes of depression and mania, disrupting normal life and increasing the risk of suicide greatly. The complexity and genetic heterogeneity of psychiatric disorders have challenged the development of animal and cellular models. We recently reported that hippocampal dentate gyrus (DG) neurons differentiated from induced pluripotent stem cell (iPSC)-derived fibroblasts of BD patients are electrophysiologically hyperexcitable. Here we used iPSCs derived from Epstein-Barr virus-immortalized B-lymphocytes to verify that the hyperexcitability of DG-like neurons is reproduced in this different cohort of patients and cells. Lymphocytes are readily available for research with a large number of banked lines with associated patient clinical description. We used whole-cell patch-clamp recordings of over 460 neurons to characterize neurons derived from control individuals and BD patients. Extensive functional analysis showed that intrinsic cell parameters are very different between the two groups of BD neurons, those derived from lithium (Li)-responsive (LR) patients and those derived from Li-non-responsive (NR) patients, which led us to partition our BD neurons into two sub-populations of cells and suggested two different subdisorders. Training a Naïve Bayes classifier with the electrophysiological features of patients whose responses to Li are known allows for accurate classification with more than 92% success rate for a new patient whose response to Li is unknown. Despite their very different functional profiles, both populations of neurons share a large, fast after-hyperpolarization (AHP). We therefore suggest that the large, fast AHP is a key feature of BD and a main contributor to the fast, sustained spiking abilities of BD neurons. Confirming our previous report with fibroblast-derived DG neurons, chronic Li treatment reduced

  6. 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…

  7. 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.

  8. Quantum chaos in the nuclear collective model. II. Peres lattices.

    Science.gov (United States)

    Stránský, Pavel; Hruska, Petr; Cejnar, Pavel

    2009-06-01

    This is a continuation of our paper [Phys. Rev. E 79, 046202 (2009)] devoted to signatures of quantum chaos in the geometric collective model of atomic nuclei. We apply the method by Peres to study ordered and disordered patterns in quantum spectra drawn as lattices in the plane of energy vs average of a chosen observable. Good qualitative agreement with standard measures of chaos is manifested. The method provides an efficient tool for studying structural changes in eigenstates across quantum spectra of general systems.

  9. 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.

  10. Controlling Beam Halo-Chaos

    Institute of Scientific and Technical Information of China (English)

    方锦清; 罗晓曙; 陈关荣; 翁甲强

    2001-01-01

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

  11. Multiple structural states exist throughout the helical nucleation sequence of the intrinsically disordered protein stathmin, as reported by electron paramagnetic resonance spectroscopy.

    Science.gov (United States)

    Chui, Ashley J; López, Carlos J; Brooks, Evan K; Chua, Katherina C; Doupey, Tonia G; Foltz, Gretchen N; Kamel, Joseph G; Larrosa, Estefania; Sadiki, Amissi; Bridges, Michael D

    2015-03-10

    The intrinsically disordered protein (IDP) stathmin plays an important regulatory role in cytoskeletal maintenance through its helical binding to tubulin and microtubules. However, it lacks a stable fold in the absence of its binding partner. Although stathmin has been a focus of research over the past two decades, the solution-phase conformational dynamics of this IDP are poorly understood. It has been reported that stathmin is purely monomeric in solution and that it bears a short helical region of persistent foldedness, which may act to nucleate helical folding in the C-terminal direction. Here we report a comprehensive study of the structural equilibria local to this region in stathmin that contradicts these two claims. Using the technique of electron paramagnetic resonance (EPR) spectroscopy on spin-labeled stathmin mutants in the solution-phase and when immobilized on Sepharose solid support, we show that all sites in the helical nucleation region of stathmin exhibit multiple spectral components that correspond to dynamic states of differing mobilities and stabilities. Importantly, a state with relatively low mobility dominates each spectrum with an average population greater than 50%, which we suggest corresponds to an oligomerized state of the protein. This is in contrast to a less populated, more mobile state, which likely represents a helically folded monomeric state of stathmin, and a highly mobile state, which we propose is the random coil conformer of the protein. Our interpretation of the EPR data is confirmed by further characterization of the protein using the techniques of native and SDS PAGE, gel filtration chromatography, and multiangle and dynamic light scattering, all of which show the presence of oligomeric stathmin in solution. Collectively, these data suggest that stathmin exists in a diverse equilibrium of states throughout the purported helical nucleation region and that this IDP exhibits a propensity toward oligomerization.

  12. An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4-DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex.

    Science.gov (United States)

    Hammel, Michal; Yu, Yaping; Radhakrishnan, Sarvan K; Chokshi, Chirayu; Tsai, Miaw-Sheue; Matsumoto, Yoshihiro; Kuzdovich, Monica; Remesh, Soumya G; Fang, Shujuan; Tomkinson, Alan E; Lees-Miller, Susan P; Tainer, John A

    2016-12-30

    DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). Yet, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcs (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.

  13. Structural and functional insights into the regulation mechanism of CK2 by IP6 and the intrinsically disordered protein Nopp140.

    Science.gov (United States)

    Lee, Won-Kyu; Son, Sang Hyeon; Jin, Bong-Suk; Na, Jung-Hyun; Kim, Soo-Youl; Kim, Kook-Han; Kim, Eunice Eunkyeong; Yu, Yeon Gyu; Lee, Hyung Ho

    2013-11-26

    Protein kinase CK2 is a ubiquitous kinase that can phosphorylate hundreds of cellular proteins and plays important roles in cell growth and development. Deregulation of CK2 is related to a variety of human cancers, and CK2 is regarded as a suppressor of apoptosis; therefore, it is a target of anticancer therapy. Nucleolar phosphoprotein 140 (Nopp140), which is an intrinsically disordered protein, interacts with CK2 and inhibits the latter's catalytic activity in vitro. Interestingly, the catalytic activity of CK2 is recovered in the presence of d-myo-inositol 1,2,3,4,5,6-hexakisphosphate (IP6). IP6 is widely distributed in animal cells, but the molecular mechanisms that govern its cellular functions in animal cells have not been completely elucidated. In this study, the crystal structure of CK2 in complex with IP6 showed that the lysine-rich cluster of CK2 plays an important role in binding to IP6. The biochemical experiments revealed that a Nopp140 fragment (residues 568-596) and IP6 competitively bind to the catalytic subunit of CK2 (CK2α), and phospho-Ser574 of Nopp140 significantly enhances its interaction with CK2α. Substitutions of K74E, K76E, and K77E in CK2α significantly reduced the interactions of CK2α with both IP6 and the Nopp140-derived peptide. Our study gives an insight into the regulation of CK2. In particular, our work suggests that CK2 activity is inhibited by Nopp140 and reactivated by IP6 by competitive binding at the substrate recognition site of CK2.

  14. Fingerprints of Chaos

    CERN Document Server

    Baran, V; Baran, Virgil; Bonasera, Aldo

    1998-01-01

    The asymptotic distance between trajectories $d_{\\infty}$, is studied in detail to characterize the occurrence of chaos. We show that this quantity is quite distinct and complementary to the Lyapunov exponents, and it allows for a quantitave estimate for the folding mechanism which keeps the motion bounded in phase space. We study the behaviour of $d_{\\infty}$ in simple unidimensional maps. Near a critical point $d_{\\infty}$ has a power law dependence on the control parameter. Furthermore, at variance with the Lyapunov exponents, it shows jumps when there are sudden changes on the available phase-space.

  15. Quantum bouncer with chaos

    Science.gov (United States)

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

    1993-02-01

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

  16. Landslide in Aureum Chaos

    Science.gov (United States)

    2004-01-01

    15 May 2004 This Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows the results of a small landslide off of a hillslope in the Aureum Chaos region of Mars. Mass movement occurred from right (the slope) to left (the lobate feature pointed left). Small dark dots in the landslide area are large boulders. This feature is located near 2.6oS, 24.5oW. This picture covers an area approximately 3 km (1.9 mi) across and is illuminated by sunlight from the left/upper left.

  17. Nonhyperbolic homoclinic chaos

    CERN Document Server

    Cicogna, G

    1999-01-01

    Homoclinic chaos is usually examined with the hypothesis of hyperbolicity of the critical point. We consider here, following a (suitably adjusted) classical analytic method, the case of non-hyperbolic points and show that, under a Melnikov-type condition plus an additional assumption, the negatively and positively asymptotic sets persist under periodic perturbations, together with their infinitely many intersections on the Poincaré section. We also examine, by means of essentially the same procedure, the case of (heteroclinic) orbits tending to the infinity; this case includes in particular the classical Sitnikov 3--body problem.

  18. 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.

  19. Chaos a very short introduction

    CERN Document Server

    Smith, Leonard

    2007-01-01

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

  20. Stalling chaos control accelerates convergence

    Science.gov (United States)

    Bick, Christian; Kolodziejski, Christoph; Timme, Marc

    2013-06-01

    Since chaos control has found its way into many applications, the development of fast, easy-to-implement and universally applicable chaos control methods is of crucial importance. Predictive feedback control has been widely applied but suffers from a speed limit imposed by highly unstable periodic orbits. We show that this limit can be overcome by stalling the control, thereby taking advantage of the stable directions of the uncontrolled chaotic map. This analytical finding is confirmed by numerical simulations, giving a chaos-control method that is capable of successfully stabilizing periodic orbits of high period.

  1. A Chaos Conveyor Belt

    Science.gov (United States)

    Schmidt, Britney E.

    2013-10-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2000-07-01

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

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

    Science.gov (United States)

    Melker, Alexander I.

    2007-04-01

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

  4. Chaos and complexity by design

    CERN Document Server

    Roberts, Daniel A

    2016-01-01

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

  5. The Chaos Within Sudoku

    CERN Document Server

    Ercsey-Ravasz, Maria

    2012-01-01

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

  6. Chaos and language.

    Science.gov (United States)

    Mitchener, W Garrett; Nowak, Martin A

    2004-04-01

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

  7. Partially predictable chaos

    CERN Document Server

    Wernecke, Hendrik; Gros, Claudius

    2016-01-01

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

  8. Boundary condition may change chaos

    Energy Technology Data Exchange (ETDEWEB)

    Itoh, Sanae-I.; Yagi, Masatoshi [Kyushu Univ., RIAM, Kasuga, Fukuoka (Japan); Kawai, Yoshinobu [Kyushu Univ., Interdisciplinary Graduate School of Engineering Sciences, Kasuga, Fukuoka (Japan)

    2001-07-01

    Role of boundary condition for the appearance of chaos is examined. Imposition of the boundary condition is interpreted as the reduction of the system size L. For a demonstration, Rayleigh-Benard instability is considered and the shell model analysis is applied. It is shown that the reduction of L reduces the number of positive Lyapunov exponent of the system, hence opens the route from the turbulence, to the chaos and to the limit cycle/fixed point. (author)

  9. Stochastic Estimation via Polynomial Chaos

    Science.gov (United States)

    2015-10-01

    TΨ is a vector with P+1 elements. With these dimensions, (29) is solvable by standard numerical linear algebra techniques. The specific matrix...initial conditions for partial differential equations. Here, the elementary theory of the polynomial chaos is presented followed by the details of a...the elementary theory of the polynomial chaos is presented followed by the details of a number of example calculations where the statistical mean and

  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. Utilizing nonlinearity of transistors for reconfigurable chaos computation

    Science.gov (United States)

    Ditto, William; Kia, Behnam

    2014-03-01

    A VLSI circuit design for chaos computing is presented that exploits the intrinsic nonlinearity of transistors to implement a novel approach for conventional and chaotic computing circuit design. In conventional digital circuit design and implementation, transistors are simply switched on or off. We argue that by using the full range of nonlinear dynamics of transistors, we can design and build more efficient computational elements and logic blocks. Furthermore, the nonlinearity of these transistor circuits can be used to program the logic block to implement different types of computational elements that can be reconfigured. Because the intrinsic nonlinear dynamics of the transistors are utilized the resulting circuits typically require fewer transistors compared to conventional digital circuits as we exploit the intrinsic nonlinearity of the transistors to realize computations. This work was done with support from ONR grant N00014-12-1-0026 and from an ONR STTR and First Pass Engineering.

  12. ORDER IN THE CHAOS IN SPORTS ORGANIZATIONS

    Directory of Open Access Journals (Sweden)

    Mehran Azarian

    2014-07-01

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

  13. 4D Non-uniformly sampled HCBCACON and {sup 1}J(NC{sup {alpha}})-selective HCBCANCO experiments for the sequential assignment and chemical shift analysis of intrinsically disordered proteins

    Energy Technology Data Exchange (ETDEWEB)

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

    2012-06-15

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

  14. Quantum chaos and holographic tensor models

    Science.gov (United States)

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

    2017-03-01

    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.

  15. 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.

  16. Chaos of chiral condensate

    CERN Document Server

    Hashimoto, Koji; Yoshida, Kentaroh

    2016-01-01

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

  17. String Cosmology and Chaos

    CERN Document Server

    Barrow, John D; Barrow, John D.; Dabrowski, Mariusz P.

    1998-01-01

    We investigate Bianchi type IX ''Mixmaster'' universes within the framework of the low-energy tree-level effective action for string theory, which (when the ''stringy'' 2-form axion potential vanishes) is formally the same as the Brans-Dicke action with $\\omega =-1$. We show that, unlike the case of general relativity in vacuum, there is no Mixmaster chaos in these string cosmologies. In the Einstein frame an infinite sequence of chaotic oscillations of the scale factors on approach to the initial singularity is impossible, as it was in general relativistic Mixmaster universes in the presence of stiff -fluid matter (or a massless scalar field). A finite sequence of oscillations of the scale factors approximated by Kasner metrics is possible, but it always ceases when all expansion rates become positive. In the string frame the evolution through Kasner epochs changes to a new form which reflects the duality symmetry of the theory. Again, we show that chaotic oscillations must end after a finite time. The need ...

  18. Stickiness in Chaos

    CERN Document Server

    Contopoulos, George

    2008-01-01

    We distinguish two types of stickiness in systems of two degrees of freedom (a) stickiness around an island of stability and (b) stickiness in chaos, along the unstable asymptotic curves of unstable periodic orbits. We studied these effects in the standard map with a rather large nonlinearity K=5, and we emphasized the role of the asymptotic curves U, S from the central orbit O and the asymptotic curves U+U-S+S- from the simplest unstable orbit around the island O1. We calculated the escape times (initial stickiness times) for many initial points outside but close to the island O1. The lines that separate the regions of the fast from the slow escape time follow the shape of the asymptotic curves S+,S-. We explained this phenomenon by noting that lines close to S+ on its inner side (closer to O1) approach a point of the orbit 4/9, say P1, and then follow the oscillations of the asymptotic curve U+, and escape after a rather long time, while the curves outside S+ after their approach to P1 follow the shape of t...

  19. Chaos theory for the biomedical engineer.

    Science.gov (United States)

    Eberhart, R C

    1989-01-01

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

  20. On CFT and quantum chaos

    Science.gov (United States)

    Turiaci, Gustavo J.; Verlinde, Herman

    2016-12-01

    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.

  1. On CFT and Quantum Chaos

    CERN Document Server

    Turiaci, Gustavo

    2016-01-01

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

  2. The information geometry of chaos

    Science.gov (United States)

    Cafaro, Carlo

    2008-10-01

    In this Thesis, we propose a new theoretical information-geometric framework (IGAC, Information Geometrodynamical Approach to Chaos) suitable to characterize chaotic dynamical behavior of arbitrary complex systems. First, the problem being investigated is defined; its motivation and relevance are discussed. The basic tools of information physics and the relevant mathematical tools employed in this work are introduced. The basic aspects of Entropic Dynamics (ED) are reviewed. ED is an information-constrained dynamics developed by Ariel Caticha to investigate the possibility that laws of physics---either classical or quantum---may emerge as macroscopic manifestations of underlying microscopic statistical structures. ED is of primary importance in our IGAC. The notion of chaos in classical and quantum physics is introduced. Special focus is devoted to the conventional Riemannian geometrodynamical approach to chaos (Jacobi geometrodynamics) and to the Zurek-Paz quantum chaos criterion of linear entropy growth. After presenting this background material, we show that the ED formalism is not purely an abstract mathematical framework, but is indeed a general theoretical scheme from which conventional Newtonian dynamics is obtained as a special limiting case. The major elements of our IGAC and the novel notion of information geometrodynamical entropy (IGE) are introduced by studying two "toy models". To illustrate the potential power of our IGAC, one application is presented. An information-geometric analogue of the Zurek-Paz quantum chaos criterion of linear entropy growth is suggested. Finally, concluding remarks emphasizing strengths and weak points of our approach are presented and possible further research directions are addressed. At this stage of its development, IGAC remains an ambitious unifying information-geometric theoretical construct for the study of chaotic dynamics with several unsolved problems. However, based on our recent findings, we believe it already

  3. Distributed chaos and isotropic turbulence

    CERN Document Server

    Bershadskii, A

    2015-01-01

    Power spectrum of the distributed chaos can be represented by a weighted superposition of the exponential functions which is converged to a stretched exponential $\\exp-(k/k_{\\beta})^{\\beta }$. An asymptotic theory has been developed in order to estimate the value of $\\beta$ for the isotropic turbulence. This value has been found to be $\\beta =3/4$. Excellent agreement has been established between this theory and the data of direct numerical simulations not only for the velocity field but also for the passive scalar and energy dissipation fields. One can conclude that the isotropic turbulence emerges from the distributed chaos.

  4. Enhancing chaoticity of spatiotemporal chaos.

    Science.gov (United States)

    Li, Xiaowen; Zhang, Heqiao; Xue, Yu; Hu, Gang

    2005-01-01

    In some practical situations strong chaos is needed. This introduces the task of chaos control with enhancing chaoticity rather than suppressing chaoticity. In this paper a simple method of linear amplifications incorporating modulo operations is suggested to make spatiotemporal systems, which may be originally chaotic or nonchaotic, strongly chaotic. Specifically, this control can eliminate periodic windows, increase the values and the number of positive Lyapunov exponents, make the probability distributions of the output chaotic sequences more homogeneous, and reduce the correlations of chaotic outputs for different times and different space units. The applicability of the method to practical tasks, in particular to random number generators and secure communications, is briefly discussed.

  5. Controlling chaos with simple limiters

    Science.gov (United States)

    Corron; Pethel; Hopper

    2000-04-24

    New experimental results demonstrate that chaos control can be accomplished using controllers that are very simple relative to the system being controlled. Chaotic dynamics in a driven pendulum and a double scroll circuit are controlled using an adjustable, passive limiter-a weight for the pendulum and a diode for the circuit. For both experiments, multiple unstable periodic orbits are selectively controlled using minimal perturbations. These physical examples suggest that chaos control can be practically applied to a much wider array of important problems than initially thought possible.

  6. Is chaos good for learning?

    Science.gov (United States)

    Sprott, J C

    2013-04-01

    This paper demonstrates that an artificial neural network training on time-series data from the logistic map at the onset of chaos trains more effectively when it is weakly chaotic. This suggests that a modest amount of chaos in the brain in addition to the ever present random noise might be beneficial for learning. In such a case, human subjects might exhibit an increased Lyapunov exponent in their EEG recordings during the performance of creative tasks, suggesting a possible line of future research.

  7. Universal quantification for deterministic chaos in dynamical systems

    CERN Document Server

    Selvam, A M

    1993-01-01

    A cell dynamical system model for deterministic chaos enables precise quantification of the round-off error growth,i.e., deterministic chaos in digital computer realizations of mathematical models of continuum dynamical systems. The model predicts the following: (a) The phase space trajectory (strange attractor) when resolved as a function of the computer accuracy has intrinsic logarithmic spiral curvature with the quasiperiodic Penrose tiling pattern for the internal structure. (b) The universal constant for deterministic chaos is identified as the steady-state fractional round-off error k for each computational step and is equal to 1 /sqr(tau) (=0.382) where tau is the golden mean. (c) The Feigenbaum's universal constants a and d are functions of k and, further, the expression 2(a**2) = (pie)*d quantifies the steady-state ordered emergence of the fractal geometry of the strange attractor. (d) The power spectra of chaotic dynamical systems follow the universal and unique inverse power law form of the statist...

  8. Deterministic polarization chaos from a laser diode

    CERN Document Server

    Virte, Martin; Thienpont, Hugo; Sciamanna, Marc

    2014-01-01

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

  9. Chaos Behaviour of Molecular Orbit

    Institute of Scientific and Technical Information of China (English)

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

    2007-01-01

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

  10. Distributed chaos in turbulent wakes

    CERN Document Server

    Bershadskii, A

    2016-01-01

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

  11. Pioneer Women in Chaos Theory

    CERN Document Server

    Wang, Frank Y

    2009-01-01

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

  12. Chaos in the Solar System

    CERN Document Server

    Lecar, M; Holman, M; Murray, N

    2002-01-01

    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-period'' 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 10^{12} 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 10^9 times the age of the solar ...

  13. 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.

  14. Does chaos assist localization or delocalization?

    Energy Technology Data Exchange (ETDEWEB)

    Tan, Jintao; Luo, Yunrong; Hai, Wenhua, E-mail: whhai2005@aliyun.com [Department of Physics and Key Laboratory of Low-dimensional Quantum Structures and Quantum Control of Ministry of Education, Hunan Normal University, Changsha 410081 (China); Lu, Gengbiao [Department of Physics and Electronic Science, Changsha University of Science and Technology, Changsha 410004 (China)

    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.

  15. Controlling neuronal noise using chaos control

    CERN Document Server

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

    1995-01-01

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

  16. 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...

  17. Robust chaos in smooth unimodal maps

    Science.gov (United States)

    Andrecut, M.; Ali, M. K.

    2001-08-01

    Robust chaos is defined by the absence of periodic windows and coexisting attractors in some neighborhood of the parameter space. It has been conjectured that robust chaos cannot occur in smooth systems [E. Barreto, B. Hunt, and C. Grebogi, Phys. Rev. Lett. 78, 4561 (1997); 80, 3049 (1998)]. Contrary to this conjecture, we describe a general procedure for generating robust chaos in smooth unimodal maps.

  18. How Can We Observe and Describe Chaos?

    CERN Document Server

    Kossakowski, A; Togawa, Y; Kossakowski, Andrzej; Ohya, Masanori; Togawa, Yosio

    2003-01-01

    We propose a new approach to define chaos in dynamical systems from the point of view of Information Dynamics. Observation of chaos in reality depends upon how to observe it, for instance, how to take the scale in space and time. Therefore it is natural to abandon taking several mathematical limiting procedures. We take account of them, and chaos degree previously introduced is redefined in this paper.

  19. Chaos in an enzyme reaction.

    Science.gov (United States)

    Olsen, L F; Degn, H

    1977-05-12

    Dynamic systems are usually thought to have either monotonic or periodic behaviour. Although the possibility of other types of behaviour has been recognised for many years, the existence of non-monotonic, non-periodic behaviour in dynamic systems has been firmly established only recently. It is termed chaotic behaviour. A review on the rapidly expanding literature on chaos in discrete model systems described by difference equations has been published by May. Rössler, on the other hand, has discussed a few published works on systems of differential equations with chaotic solutions, and he has proposed a three-component chemical model system which he argues has chaotic solutions [figure see text]. The argument is based on a theorem by Li and Yorke. Here we report the finding of chaotic behaviour as an experimental result in an enzyme system (peroxidase). Like Rössler we base our identification of chaos on the theorem by Li and Yorke.

  20. A Quantum Correction To Chaos

    CERN Document Server

    Fitzpatrick, A Liam

    2016-01-01

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

  1. 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

  2. Random Behaviour in Quantum Chaos

    CERN Document Server

    Garbaczewski, P

    2001-01-01

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

  3. Polynomial-Chaos-based Kriging

    OpenAIRE

    Schöbi, R; Sudret, B.; Wiart, J.

    2015-01-01

    International audience; Computer simulation has become the standard tool in many engineering fields for designing and optimizing systems, as well as for assessing their reliability. Optimization and uncertainty quantification problems typically require a large number of runs of the computational model at hand, which may not be feasible with high-fidelity models directly. Thus surrogate models (a.k.a metamodels) have been increasingly investigated in the last decade. Polynomial Chaos Expansion...

  4. Analysis of FBC deterministic chaos

    Energy Technology Data Exchange (ETDEWEB)

    Daw, C.S.

    1996-06-01

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

  5. Hamiltonian chaos and fractional dynamics

    CERN Document Server

    Zaslavsky, George M

    2008-01-01

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

  6. 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.

  7. The CHAOS-4 Geomagnetic Field Model

    DEFF Research Database (Denmark)

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

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

  8. Weak chaos in the asymmetric heavy top

    CERN Document Server

    Barrientos, M; Ranada, A F

    1995-01-01

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

  9. Radio lighting based on dynamic chaos generators

    CERN Document Server

    Dmitriev, Alexander; Gerasimov, Mark; Itskov, Vadim

    2016-01-01

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

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

    Science.gov (United States)

    Lindsay, Jean S.

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

  11. The CHAOS-4 geomagnetic field model

    DEFF Research Database (Denmark)

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

    2014-01-01

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

  12. Path and semimartingale properties of chaos processes

    DEFF Research Database (Denmark)

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

    2010-01-01

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

  13. Chaos in nonlinear oscillations controlling and synchronization

    CERN Document Server

    Lakshamanan, M

    1996-01-01

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

  14. 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 inter...

  15. 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...

  16. 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.

  17. 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...

  18. The ESC/E(Z) complex, an effector of response to ovarian steroids, manifests an intrinsic difference in cells from women with premenstrual dysphoric disorder.

    Science.gov (United States)

    Dubey, N; Hoffman, J F; Schuebel, K; Yuan, Q; Martinez, P E; Nieman, L K; Rubinow, D R; Schmidt, P J; Goldman, D

    2017-01-03

    Clinical evidence suggests that mood and behavioral symptoms in premenstrual dysphoric disorder (PMDD), a common, recently recognized, psychiatric condition among women, reflect abnormal responsivity to ovarian steroids. This differential sensitivity could be due to an unrecognized aspect of hormonal signaling or a difference in cellular response. In this study, lymphoblastoid cell line cultures (LCLs) from women with PMDD and asymptomatic controls were compared via whole-transcriptome sequencing (RNA-seq) during untreated (ovarian steroid-free) conditions and following hormone treatment. The women with PMDD manifested ovarian steroid-triggered behavioral sensitivity during a hormone suppression and addback clinical trial, and controls did not, leading us to hypothesize that women with PMDD might differ in their cellular response to ovarian steroids. In untreated LCLs, our results overall suggest a divergence between mRNA (for example, gene transcription) and protein (for example, RNA translation in proteins) for the same genes. Pathway analysis of the LCL transcriptome revealed, among others, over-expression of ESC/E(Z) complex genes (an ovarian steroid-regulated gene silencing complex) in untreated LCLs from women with PMDD, with more than half of these genes over-expressed as compared with the controls, and with significant effects for MTF2, PHF19 and SIRT1 (PMolecular Psychiatry advance online publication, 3 January 2017; doi:10.1038/mp.2016.229.

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

    Science.gov (United States)

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

    2011-07-01

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

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

    Science.gov (United States)

    Fraser, Suzanne; Moore, David

    2008-02-01

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

  1. Prediction based chaos control via a new neural network

    Energy Technology Data Exchange (ETDEWEB)

    Shen Liqun [School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin 150001 (China)], E-mail: liqunshen@gmail.com; Wang Mao [Space Control and Inertia Technology Research Center, Harbin Institute of Technology, Harbin 150001 (China); Liu Wanyu [School of Electrical Engineering and Automation, Harbin Institute of Technology, Harbin 150001 (China); Sun Guanghui [Space Control and Inertia Technology Research Center, Harbin Institute of Technology, Harbin 150001 (China)

    2008-11-17

    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.

  2. Some new surprises in chaos

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-09-15

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

  3. On the Mechanisms Behind Chaos

    DEFF Research Database (Denmark)

    Lindberg, Erik

    2006-01-01

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

  4. A Quantum Correction To Chaos

    OpenAIRE

    A. Fitzpatrick; 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 = 2 π β 1 + 12 c $$ {\\lambda}_L=\\frac{2\\pi }{\\beta}\\left(1+\\frac{12}{c}\\right) $$ . However, out of time order correlators receive other equally important 1 /c suppressed contributions that do not have such a simple interpretation. We revisit the proof ...

  5. Critical states of transient chaos

    CERN Document Server

    Kaufmann, Z; Szépfalusy, P

    1999-01-01

    One-dimensional maps exhibiting transient chaos and defined on two preimages of the unit interval [0,1] are investigated. It is shown that such maps have continuously many conditionally invariant measures $\\mu_{\\sigma}$ scaling at the fixed point at $x=0$ as $x^{\\sigma}$, but smooth elsewhere. Here $\\sigma$ should be smaller than a critical value $\\sigma_{c}$ that is related to the spectral properties of the Frobenius-Perron operator. The corresponding natural measures are proven to be entirely concentrated on the fixed point.

  6. Chaos control in duffing system

    Energy Technology Data Exchange (ETDEWEB)

    Wang Ruiqi [Department of Electrical Engineering and Electronics, Osaka Sangyo University, Nakagaito 3-1-1, Daito, Osaka 574-8530 (Japan); Deng Jin [Academy of Mathematics and System Sciences, Chinese Academy of Sciences, Beijing 100080 (China); Graduate School of the Chinese Academy of Sciences, Beijing 100039 (China); Jing Zhujun [Academy of Mathematics and System Sciences, Chinese Academy of Sciences, Beijing 100080 (China); Department of Mathematics, Hunan Normal University, Hunan, Changsha 410081 (China); E-mail: jingzj@math.ac.cn

    2006-01-01

    Analytical and numerical results concerning the inhibition of chaos in Duffing's equation with two weak forcing excitations are presented. We theoretically give parameter-space regions by using Melnikov's function, where chaotic states can be suppressed. The intervals of initial phase difference between the two excitations for which chaotic dynamics can be eliminated are given. Meanwhile, the influence of the phase difference on Lyapunov exponents for different frequencies is investigated. Numerical simulation results show the consistence with the theoretical analysis and the chaotic motions can be controlled to period-motions by adjusting parameter of suppressing excitation.

  7. Controlling Beam Halo-Chaos

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    In this work, we proposed the wavelet-based feedback controller is as follows: G = -g{fab(rrms)-fab(am)} (1)where the master wavelet function is in a simplified form(2)where a and b are scaling and translation constants, respectively. C is a selected constant. The main reason of using wavelet function for controller design is that it has strong nonlinearity and excellent localization property. It turns out that for halo-chaos control purpose, the translation b can be very small, so for simplicity one may let b = 0 . Our goal of control is rms→am, in this

  8. Global Optimal Trajectory in Chaos and NP-Hardness

    Science.gov (United States)

    Latorre, Vittorio; Gao, David Yang

    This paper presents an unconventional theory and method for solving general nonlinear dynamical systems. Instead of the direct iterative methods, the discretized nonlinear system is first formulated as a global optimization problem via the least squares method. A newly developed canonical duality theory shows that this nonconvex minimization problem can be solved deterministically in polynomial time if a global optimality condition is satisfied. The so-called pseudo-chaos produced by linear iterative methods are mainly due to the intrinsic numerical error accumulations. Otherwise, the global optimization problem could be NP-hard and the nonlinear system can be really chaotic. A conjecture is proposed, which reveals the connection between chaos in nonlinear dynamics and NP-hardness in computer science. The methodology and the conjecture are verified by applications to the well-known logistic equation, a forced memristive circuit and the Lorenz system. Computational results show that the canonical duality theory can be used to identify chaotic systems and to obtain realistic global optimal solutions in nonlinear dynamical systems. The method and results presented in this paper should bring some new insights into nonlinear dynamical systems and NP-hardness in computational complexity theory.

  9. Delay driven spatiotemporal chaos in single species population dynamics models.

    Science.gov (United States)

    Jankovic, Masha; Petrovskii, Sergei; Banerjee, Malay

    2016-08-01

    Questions surrounding the prevalence of complex population dynamics form one of the central themes in ecology. Limit cycles and spatiotemporal chaos are examples that have been widely recognised theoretically, although their importance and applicability to natural populations remains debatable. The ecological processes underlying such dynamics are thought to be numerous, though there seems to be consent as to delayed density dependence being one of the main driving forces. Indeed, time delay is a common feature of many ecological systems and can significantly influence population dynamics. In general, time delays may arise from inter- and intra-specific trophic interactions or population structure, however in the context of single species populations they are linked to more intrinsic biological phenomena such as gestation or resource regeneration. In this paper, we consider theoretically the spatiotemporal dynamics of a single species population using two different mathematical formulations. Firstly, we revisit the diffusive logistic equation in which the per capita growth is a function of some specified delayed argument. We then modify the model by incorporating a spatial convolution which results in a biologically more viable integro-differential model. Using the combination of analytical and numerical techniques, we investigate the effect of time delay on pattern formation. In particular, we show that for sufficiently large values of time delay the system's dynamics are indicative to spatiotemporal chaos. The chaotic dynamics arising in the wake of a travelling population front can be preceded by either a plateau corresponding to dynamical stabilisation of the unstable equilibrium or by periodic oscillations.

  10. An Experimental Investigation of Secure Communication With Chaos Masking

    CERN Document Server

    Dhar, Sourav

    2007-01-01

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

  11. Nonlinear Dynamics and Chaos: Applications in Atmospheric Sciences

    CERN Document Server

    Selvam, A M

    2010-01-01

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

  12. Markov transitions and the propagation of chaos

    Energy Technology Data Exchange (ETDEWEB)

    Gottlieb, Alexander David [Univ. of California, Berkeley, CA (United States)

    1998-12-01

    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 s how 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.

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

    Science.gov (United States)

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

    2016-06-01

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

  14. Efficient protocol for backbone and side-chain assignments of large, intrinsically disordered proteins: transient secondary structure analysis of 49.2 kDa microtubule associated protein 2c

    Energy Technology Data Exchange (ETDEWEB)

    Novacek, Jiri; Janda, Lubomir; Dopitova, Radka; Zidek, Lukas, E-mail: lzidek@chemi.muni.cz; Sklenar, Vladimir [Masaryk University, Faculty of Science, NCBR, and CEITEC (Czech Republic)

    2013-08-15

    Microtubule-associated proteins (MAPs) are abundantly present in axons and dendrites, and have been shown to play crucial role during the neuronal morphogenesis. The period of main dendritic outgrowth and synaptogenesis coincides with high expression levels of one of MAPs, the MAP2c, in rats. The MAP2c is a 49.2 kDa intrinsically disordered protein. To achieve an atomic resolution characterization of such a large protein, we have developed a protocol based on the acquisition of two five-dimensional {sup 13}C-directly detected NMR experiments. Our previously published 5D CACONCACO experiment (Novacek et al. in J Biomol NMR 50(1):1-11, 2011) provides the sequential assignment of the backbone resonances, which is not interrupted by the presence of the proline residues in the amino acid sequence. A novel 5D HC(CC-TOCSY)CACON experiment facilitates the assignment of the aliphatic side chain resonances. To streamline the data analysis, we have developed a semi-automated procedure for signal assignments. The obtained data provides the first atomic resolution insight into the conformational state of MAP2c and constitutes a model for further functional studies of MAPs.

  15. Chaos dynamic characteristics during mine fires

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

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

  16. Physics and Applications of Laser Diode Chaos

    CERN Document Server

    Sciamanna, Marc

    2015-01-01

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

  17. 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...

  18. 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

  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. Chaos from simple models to complex systems

    CERN Document Server

    Cencini, Massimo; Vulpiani, Angelo

    2010-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

    瞿玮; 覃园园

    2005-01-01

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

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

    Science.gov (United States)

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

    2014-11-01

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

  3. 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...

  4. Superfluid (quantum) turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

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

  5. Optimized chaos control with simple limiters.

    Science.gov (United States)

    Wagner, C; Stoop, R

    2001-01-01

    We present an elementary derivation of chaos control with simple limiters using the logistic map and the Henon map as examples. This derivation provides conditions for optimal stabilization of unstable periodic orbits of a chaotic attractor.

  6. A simple method of chaos control

    CERN Document Server

    Shahverdiev, E M

    1998-01-01

    A simple method to perform chaos control without the need of complex numerical and analytical calculations is proposed. The method works for dynamical systems with bounded solutions and in the trivial case of constant Jacobians.

  7. Compressive Sensing with Optical Chaos

    Science.gov (United States)

    Rontani, D.; Choi, D.; Chang, C.-Y.; Locquet, A.; Citrin, D. S.

    2016-12-01

    Compressive sensing (CS) is a technique to sample a sparse signal below the Nyquist-Shannon limit, yet still enabling its reconstruction. As such, CS permits an extremely parsimonious way to store and transmit large and important classes of signals and images that would be far more data intensive should they be sampled following the prescription of the Nyquist-Shannon theorem. CS has found applications as diverse as seismology and biomedical imaging. In this work, we use actual optical signals generated from temporal intensity chaos from external-cavity semiconductor lasers (ECSL) to construct the sensing matrix that is employed to compress a sparse signal. The chaotic time series produced having their relevant dynamics on the 100 ps timescale, our results open the way to ultrahigh-speed compression of sparse signals.

  8. Detecting chaos from time series

    Science.gov (United States)

    Xiaofeng, Gong; Lai, C. H.

    2000-02-01

    In this paper, an entirely data-based method to detect chaos from the time series is developed by introducing icons/Journals/Common/epsilon" ALT="epsilon" ALIGN="TOP"/> p -neighbour points (the p -steps icons/Journals/Common/epsilon" ALT="epsilon" ALIGN="TOP"/> -neighbour points). We demonstrate that for deterministic chaotic systems, there exists a linear relationship between the logarithm of the average number of icons/Journals/Common/epsilon" ALT="epsilon" ALIGN="TOP"/> p -neighbour points, lnn p ,icons/Journals/Common/epsilon" ALT="epsilon" ALIGN="TOP"/> , and the time step, p . The coefficient can be related to the KS entropy of the system. The effects of the embedding dimension and noise are also discussed.

  9. Chaos, Fractals and Their Applications

    Science.gov (United States)

    Thompson, J. Michael T.

    2016-12-01

    This paper gives an up-to-date account of chaos and fractals, in a popular pictorial style for the general scientific reader. A brief historical account covers the development of the subject from Newton’s laws of motion to the astronomy of Poincaré and the weather forecasting of Lorenz. Emphasis is given to the important underlying concepts, embracing the fractal properties of coastlines and the logistics of population dynamics. A wide variety of applications include: NASA’s discovery and use of zero-fuel chaotic “superhighways” between the planets; erratic chaotic solutions generated by Euler’s method in mathematics; atomic force microscopy; spontaneous pattern formation in chemical and biological systems; impact mechanics in offshore engineering and the chatter of cutting tools; controlling chaotic heartbeats. Reference is made to a number of interactive simulations and movies accessible on the web.

  10. Control of collective network chaos

    Energy Technology Data Exchange (ETDEWEB)

    Wagemakers, Alexandre, E-mail: alexandre.wagemakers@urjc.es; Sanjuán, Miguel A. F., E-mail: miguel.sanjuan@urjc.es [Departamento de Física, Universidad Rey Juan Carlos, Tulipán s/n, 28933 Móstoles, Madrid (Spain); Barreto, Ernest, E-mail: ebarreto@gmu.edu; So, Paul, E-mail: paso@gmu.edu [School of Physics, Astronomy, and Computational Sciences and The Krasnow Institute for Advanced Study, George Mason University, Fairfax, Virginia 22030 (United States)

    2014-06-01

    Under certain conditions, the collective behavior of a large globally-coupled heterogeneous network of coupled oscillators, as quantified by the macroscopic mean field or order parameter, can exhibit low-dimensional chaotic behavior. Recent advances describe how a small set of “reduced” ordinary differential equations can be derived that captures this mean field behavior. Here, we show that chaos control algorithms designed using the reduced equations can be successfully applied to imperfect realizations of the full network. To systematically study the effectiveness of this technique, we measure the quality of control as we relax conditions that are required for the strict accuracy of the reduced equations, and hence, the controller. Although the effects are network-dependent, we show that the method is effective for surprisingly small networks, for modest departures from global coupling, and even with mild inaccuracy in the estimate of network heterogeneity.

  11. Control of collective network chaos

    Science.gov (United States)

    Wagemakers, Alexandre; Barreto, Ernest; Sanjuán, Miguel A. F.; So, Paul

    2014-06-01

    Under certain conditions, the collective behavior of a large globally-coupled heterogeneous network of coupled oscillators, as quantified by the macroscopic mean field or order parameter, can exhibit low-dimensional chaotic behavior. Recent advances describe how a small set of "reduced" ordinary differential equations can be derived that captures this mean field behavior. Here, we show that chaos control algorithms designed using the reduced equations can be successfully applied to imperfect realizations of the full network. To systematically study the effectiveness of this technique, we measure the quality of control as we relax conditions that are required for the strict accuracy of the reduced equations, and hence, the controller. Although the effects are network-dependent, we show that the method is effective for surprisingly small networks, for modest departures from global coupling, and even with mild inaccuracy in the estimate of network heterogeneity.

  12. Chaos on the conveyor belt

    CERN Document Server

    Sándor, Bulcsú; Tél, Tamás; Néda, Zoltán

    2013-01-01

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

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

    Science.gov (United States)

    Ornstein, D S

    1989-01-13

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

  14. Intrinsic-Density Functionals

    CERN Document Server

    Engel, J

    2006-01-01

    The Hohenberg-Kohn theorem and Kohn-Sham procedure are extended to functionals of the localized intrinsic density of a self-bound system such as a nucleus. After defining the intrinsic-density functional, we modify the usual Kohn-Sham procedure slightly to evaluate the mean-field approximation to the functional, and carefully describe the construction of the leading corrections for a system of fermions in one dimension with a spin-degeneracy equal to the number of particles N. Despite the fact that the corrections are complicated and nonlocal, we are able to construct a local Skyrme-like intrinsic-density functional that, while different from the exact functional, shares with it a minimum value equal to the exact ground-state energy at the exact ground-state intrinsic density, to next-to-leading order in 1/N. We briefly discuss implications for real Skyrme functionals.

  15. Terminal chaos for information processing in neurodynamics.

    Science.gov (United States)

    Zak, M

    1991-01-01

    New nonlinear phenomenon-terminal chaos caused by failure of the Lipschitz condition at equilibrium points of dynamical systems is introduced. It is shown that terminal chaos has a well organized probabilistic structure which can be predicted and controlled. This gives an opportunity to exploit this phenomenon for information processing. It appears that chaotic states of neurons activity are associated with higher level of cognitive processes such as generalization and abstraction.

  16. How Did You Get into Chaos?

    Science.gov (United States)

    Thiel, Marco; Kurths, Jürgen; Romano, M. Carmen; Moura, Alessandro; Károlyi, György

    In the celebratory dinner honouring Celso Grebogi's 60th birthday, a number of scientists in the area of chaos were asked by James Yorke to tell the tale about how they got involved in the field. Since all the participants have played crucial roles in the development of the subject, their stories give unique insights into the historical development of dynamical systems and chaos. We have transcribed their tales here.

  17. Detecting nonlinearity and chaos in epidemic data

    Energy Technology Data Exchange (ETDEWEB)

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

    1993-08-01

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

  18. Chaos control using sliding-mode theory

    Energy Technology Data Exchange (ETDEWEB)

    Nazzal, Jamal M. [Faculty of Engineering, Al-Ahliyya Amman University, Post Code 19328 Amman (Jordan)]. E-mail: jnazzal@ammanu.edu.jo; Natsheh, Ammar N. [Faculty of Engineering, Al-Ahliyya Amman University, Post Code 19328 Amman (Jordan)

    2007-07-15

    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.

  19. Chaos control in traffic flow models

    CERN Document Server

    Shahverdiev, E M; Shahverdiev, Elman Mohammed; Tadaki, Shin-ichi

    1998-01-01

    Chaos control in some of the one- and two-dimensional traffic flow dynamical models in the mean field theory is studied.One dimensional model is investigated taking into account the effect of random delay. Two dimensional model takes into account the effects of overpasses, symmetric distribution of cars and blockages of cars moving in the same direction. Chaos synchronization is performed within both replica and nonreplica approaches, and using parameter perturbation method.

  20. Chaos and Quantumlike Mechanics in Atmospheric Flows A Superstring Theory for Supergravity

    CERN Document Server

    Selvam, A M

    1997-01-01

    The author has identified quantumlike mechanics in atmospheric flows with intrinsic nonlocal space-time connections manifested as the selfsimilar fractal geometry to the global cloud cover pattern concomitant with inverse power law form for power spectra of temporal fluctuations. Such long-range spatiotemporal correlations are generic to dynamical systems in nature and are recently identified as signatures of selforganized criticality, a field of study belonging to the newly emerging discipline of nonlinear dynamics and chaos. The author has presented a universal thory of chaos which postulates that spatial integration of enclosed small scale fluctuations result in the generation of a hierarchical scale invariant eddy continuum(network) with ordered two-way energy flow between the scales. The model concepts lead to the following results. (1) The eddy energy spectrum follows normal distribution characteristics,i.e.,the square of the eddy amplitude represents the probability density,a result which is observed i...

  1. Cantorian Fractal Patterns, Quantum-Like Chaos and Prime Numbers in Atmospheric Flows

    CERN Document Server

    Selvam, A M; Fadnavis, Suvarna

    1998-01-01

    Atmospheric flows exhibit cantorian fractal space-time fluctuations signifying long-range spatiotemporal correlations. A recently developed cell dynamical system model shows that such non-local connections are intrinsic to quantum-like chaos governing flow dynamics. The dynamical evolution of fractal structures can be quantified in terms of ordered energy flow described by mathematical functions which occur in the field of number theory. The quantum-like chaos in atmospheric flows can be quantified in terms of the following mathematical functions / concepts: (1) The fractal structure of the flow pattern is resolved into an overall logarithmic spiral trajectory with the quasiperiodic Penrose tiling pattern for the internal structure and is equivalent to a hierarchy of vortices. The incorporation of Fibonacci mathematical series, representative of ramified bifurcations, indicates ordered growth of fractal patterns. (2) The steady state emergence of progressively larger fractal structures incorporates unique pri...

  2. Chaos control applied to piezoelectric vibration-based energy harvesting systems

    Science.gov (United States)

    Barbosa, W. O. V.; De Paula, A. S.; Savi, M. A.; Inman, D. J.

    2015-11-01

    Chaotic behavior presents intrinsic richness due to the existence of an infinity number of unstable periodic orbits (UPOs). The possibility of stabilizing these periodic patterns with a small amount of energy makes this kind of response interesting to various dynamical systems. Energy harvesting has as a goal the use of available mechanical energy by promoting a conversion into electrical energy. The combination of these two approaches may establish autonomous systems where available environmental mechanical energy can be employed for control purposes. Two different goals can be defined as priority, allowing a change between them: vibration reduction and energy harvesting enhancement. This work deals with the use of harvested energy to perform chaos control. Both control actuation and energy harvesting are induced employing piezoelectric materials, in a simultaneous way. A bistable piezomagnetoelastic structure subjected to harmonic excitations is investigated as a case study. Numerical simulations show situations where it is possible to perform chaos control using only the energy generated by the harvesting system.

  3. Relationship of a chaos equation to Piaget's developmental theory and selective attention deficits

    Directory of Open Access Journals (Sweden)

    Yanagisawa, H.

    2016-06-01

    Full Text Available Piaget's theory provides a typical example of a relationship between human development and chaos theory. Here, Piaget's developmental theory and selective attention deficits are compared with a chaos equation. Continuous covariation is a necessary condition to equilibrium and the chaos phenomenon, and equilibrium is the converged solution in a chaos equation. Each convergence and non-convergence is a fixed and a chaotic state. In many chaos equations, there are two kinds of variables that change or do not change each site beyond the Feigenbaum point. Two types of developmental disorders are assumed. One is low speed in judging convergence or nonconvergence. The other is low-speed change after a person's own judgment. In the former, a person cannot sense a difference between a converging point and his present state. Because he/she cannot understand others' emotions, he/she will continue with his/her experience with no convergence . Therefore, he/she cannot request help, and it might be thought that he/she can wait. This type is equivalent to Asperger's syndrome. In the latter, a person senses a difference. Because the person strictly feels the difference between a fixed point and his/her present state, he/she cannot wait for convergence. Therefore, he can request help. His present ate might be anger, and this type is equivalent to ADHD. In the former, a wide chaotic state narrows with experience. Piaget's developmental theory might be that humans have the ability to change each state. Chaos theory shows "Selective attention deficits with autism" as two different patterns in non-convergence or convergence.

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-10-15

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

  5. CHAOS III: Gas-Phase Abundances in NGC5457

    CERN Document Server

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

    2016-01-01

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

  6. 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.

  7. Lorentz invariant intrinsic decoherence

    CERN Document Server

    Milburn, G J

    2003-01-01

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

  8. 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.

  9. Chaos in Black holes Surrounded by Electromagnetic Fields

    OpenAIRE

    Santoprete, Manuele; Cicogna, Giampaolo

    2001-01-01

    In this paper we prove the occurence of chaos for charged particles moving around a Schwarzshild black hole, perturbed by uniform electric and magnetic fields. The appearance of chaos is studied resorting to the Poincare'-Melnikov method.

  10. Intrinsic Time Quantum Geometrodynamics

    CERN Document Server

    Ita, Eyo Eyo; Yu, Hoi-Lai

    2015-01-01

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

  11. Some Remarks on Distributional Chaos for Linear Operators

    Institute of Scientific and Technical Information of China (English)

    TIAN GENG; Hou BING-ZHE; Ji You-qing

    2011-01-01

    In this paper,we consider some properties for bounded linear operators concerning distributional chaos.Norm-unimodality of bounded linear operators implies distributional chaos.Some properties such as similarity and spectra description for norm-unimodal operators are considered.The existence of distributional chaos in nest algebra is also proved.In addition,we obtain a sufficient and necessary condition of distributional chaos for a class of operators,which contains unilateral backward weighted shift operators.

  12. 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.

  13. Controlling Beam Halo-chaos Using a Special Nonlinear Method

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    Beam halo-chaos in high-current accelerators has become a key concerned issue because it can cause excessive radioactivity from the accelerators therefore significantly limits their applications in industry,medicine, and national defense. Some general engineering methods for chaos control have been developedin recent years, but they generally are unsuccessful for beam halo-chaos suppression due to manytechnical constraints. Beam halo-chaos is essentially a spatotemporal chaotic motion within a high power

  14. Regularly timed events amid chaos

    Science.gov (United States)

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

    2015-11-01

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

  15. Target-oriented chaos control

    Energy Technology Data Exchange (ETDEWEB)

    Dattani, Justine [Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Bath BA2 7AY (United Kingdom); Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge CB3 0WA (United Kingdom); Blake, Jack C.H. [Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Bath BA2 7AY (United Kingdom); Hilker, Frank M., E-mail: f.hilker@bath.ac.uk [Centre for Mathematical Biology, Department of Mathematical Sciences, University of Bath, Bath BA2 7AY (United Kingdom)

    2011-10-31

    Designing intervention methods to control chaotic behavior in dynamical systems remains a challenging problem, in particular for systems that are difficult to access or to measure. We propose a simple, intuitive technique that modifies the values of the state variables directly toward a certain target. The intervention takes into account the difference to the target value, and is a combination of traditional proportional feedback and constant feedback methods. It proves particularly useful when the target corresponds to the equilibrium of the uncontrolled system, and is available or can be estimated from expert knowledge (e.g. in biology and economy). -- Highlights: → We propose a chaos control method that forces the system to a certain target. → The intervention takes into account the difference to the target value. → It can be seen as a combination of proportional and constant feedback methods. → The method is very robust and highly efficient in the long-term. → It is particularly applicable when suitable target values are known or available.

  16. 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 κ^{2} 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.

  17. 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?

  18. 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…

  19. Chaos control and synchronization in a fractional neuron network system

    Energy Technology Data Exchange (ETDEWEB)

    Zhou Shangbo [Computer Department of Chongqing University, Chongqing 400044 (China); Li Hua [Department of Mathematics and Computer Science, University of Lethbridge, T1K 3M4 (Canada)], E-mail: hua.li@uleth.ca; Zhu Zhengzhou [Computer Department of Chongqing University, Chongqing 400044 (China)

    2008-05-15

    In this paper, an algorithm of numerical solution for fractional differential equations is presented. Chaos in a neuron network system is also illustrated. Moreover, chaos feedback control and synchronization systems are constructed. The study and experiment indicate that the chaos in fractional order neuron networks could be controlled and synchronized.

  20. Predicting Intrinsic Motivation

    Science.gov (United States)

    Martens, Rob; Kirschner, Paul A.

    2004-01-01

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

  1. Controlling chaos in ecology: from deterministic to individual-based models.

    Science.gov (United States)

    Solé, R V; Gamarra, J G; Ginovart, M; López, D

    1999-11-01

    The possibility of chaos control in biological systems has been stimulated by recent advances in the study of heart and brain tissue dynamics. More recently, some authors have conjectured that such a method might be applied to population dynamics and even play a nontrivial evolutionary role in ecology. In this paper we explore this idea by means of both mathematical and individual-based simulation models. Because of the intrinsic noise linked to individual behavior, controlling a noisy system becomes more difficult but, as shown here, it is a feasible task allowed to be experimentally tested.

  2. 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.

  3. 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.  

  4. Avoiding Quantum Chaos in Quantum Computation

    CERN Document Server

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

    2001-01-01

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

  5. Nonlinear Physics Integrability, Chaos and Beyond

    CERN Document Server

    Lakshmanan, M

    1997-01-01

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

  6. Nonlinear Dynamics and Chaos: Advances and Perspectives

    CERN Document Server

    Thiel, Marco; Romano, M. Carmen; Károlyi, György; Moura, Alessandro

    2010-01-01

    This book is a collection of contributions on various aspects of active frontier research in the field of dynamical systems and chaos. Each chapter examines a specific research topic and, in addition to reviewing recent results, also discusses future perspectives. The result is an invaluable snapshot of the state of the field by some of its most important researchers. The first contribution in this book, "How did you get into Chaos?", is actually a collection of personal accounts by a number of distinguished scientists on how they entered the field of chaos and dynamical systems, featuring comments and recollections by James Yorke, Harry Swinney, Floris Takens, Peter Grassberger, Edward Ott, Lou Pecora, Itamar Procaccia, Michael Berry, Giulio Casati, Valentin Afraimovich, Robert MacKay, and last but not least, Celso Grebogi, to whom this volume is dedicated.

  7. 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...

  8. Ventilatory chaos is impaired in carotid atherosclerosis.

    Directory of Open Access Journals (Sweden)

    Laurence Mangin

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

  9. Distributed chaos and inertial ranges in turbulence

    CERN Document Server

    Bershadskii, A

    2016-01-01

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

  10. Chaos in an imperfectly premixed model combustor

    Energy Technology Data Exchange (ETDEWEB)

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

    2015-02-15

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

  11. Quantum chaos on a critical Fermi surface

    CERN Document Server

    Patel, Aavishkar A

    2016-01-01

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

  12. Atoms in static fields Chaos or Diffraction?

    CERN Document Server

    Dando, P A

    1998-01-01

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

  13. SENSITIVE ERROR ANALYSIS OF CHAOS SYNCHRONIZATION

    Institute of Scientific and Technical Information of China (English)

    HUANG XIAN-GAO; XU JIAN-XUE; HUANG WEI; L(U) ZE-JUN

    2001-01-01

    We study the synchronizing sensitive errors of chaotic systems for adding other signals to the synchronizing signal.Based on the model of the Henon map masking, we examine the cause of the sensitive errors of chaos synchronization.The modulation ratio and the mean square error are defined to measure the synchronizing sensitive errors by quality.Numerical simulation results of the synchronizing sensitive errors are given for masking direct current, sinusoidal and speech signals, separately. Finally, we give the mean square error curves of chaos synchronizing sensitivity and threedimensional phase plots of the drive system and the response system for masking the three kinds of signals.

  14. USING OPTIMAL FEEDBACK CONTROL FOR CHAOS TARGETING

    Institute of Scientific and Technical Information of China (English)

    PENG ZHAO-WANG; ZHONG TING-XIU

    2000-01-01

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

  15. Experimental realization of chaos control by thresholding.

    Science.gov (United States)

    Murali, K; Sinha, Sudeshna

    2003-07-01

    We report the experimental verification of thresholding as a versatile tool for efficient and flexible chaos control. The strategy here simply involves monitoring a single state variable and resetting it when it exceeds a threshold. We demonstrate the success of the technique in rapidly controlling different chaotic electrical circuits, including a hyperchaotic circuit, onto stable fixed points and limit cycles of different periods, by thresholding just one variable. The simplicity of this controller entailing no run-time computation, and the ease and rapidity of switching between different targets it offers, suggests a potent tool for chaos based applications.

  16. Investigation on evolutionary optimization of chaos control

    Energy Technology Data Exchange (ETDEWEB)

    Zelinka, Ivan [Faculty of Applied Informatics, Tomas Bata University in Zli' n, Nad Stranemi 4511, 762 72 Zli' n (Czech Republic)], E-mail: zelinka@fai.utb.cz; Senkerik, Roman [Faculty of Applied Informatics, Tomas Bata University in Zli' n, Nad Stranemi 4511, 762 72 Zli' n (Czech Republic)], E-mail: senkerik@fai.utb.cz; Navratil, Eduard [Faculty of Applied Informatics, Tomas Bata University in Zli' n, Nad Stranemi 4511, 762 72 Zli' n (Czech Republic)], E-mail: enavratil@fai.utb.cz

    2009-04-15

    This work deals with an investigation on optimization of the feedback control of chaos based on the use of evolutionary algorithms. The main objective is to show that evolutionary algorithms are capable of optimization of chaos control. As models of deterministic chaotic systems, one-dimensional Logistic equation and two-dimensional Henon map were used. The optimizations were realized in several ways, each one for another set of parameters of evolution algorithms or separate cost functions. The evolutionary algorithm SOMA (self-organizing migrating algorithm) was used in four versions. For each version simulations were repeated several times to show and check for robustness of the applied method.

  17. Quantum dynamical entropies in discrete classical chaos

    Energy Technology Data Exchange (ETDEWEB)

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

    2004-01-09

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

  18. Dynamic system uncertainty propagation using polynomial chaos

    Institute of Scientific and Technical Information of China (English)

    Xiong Fenfen; Chen Shishi; Xiong Ying

    2014-01-01

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

  19. Chaos in Practice: Techniques for Career Counsellors

    Science.gov (United States)

    Pryor, Robert G. L.; Bright, Jim

    2005-01-01

    The chaos theory of careers emphasises continual change, the centrality and importance of chance events, the potential of minor events to have disproportionately large impacts on subsequent events, and the capacity for dramatic phase shifts in career behaviour. This approach challenges traditional approaches to career counselling, assumptions…

  20. Teaching Chaos to Art College Students

    Science.gov (United States)

    Blum, Ben

    2001-03-01

    This is a report of the author's teaching the basic concepts of chaos to students at Massachusetts College of Art. In order to bypass the students' aversion to mathematics stemming from earlier difficult experiences with mathematics, the course started with some symbolism which was totally unfamiliar to them: a Boolean system based on Brown's Laws of Form. This was then used to develop the mathematical ideas of duality and self-reference. After that was a general survey of the various areas of mathematics using Guillen's Bridges to Infinity. Chaos was then introduced using Gleick's Chaos, which provides a very engaging narrative, along with an introduction to the basic ideas. Two different strategies were used to introduce the mathematical ideas. First, making use of the students' visual orientation, sensitive dependence on initial conditions, fractional dimension, fractals, the Koch snowflake, self-similiarity, and statistical self-similiarity were covered pictorially. Second, so that the students could get a real feeling for the mathematics of chaos, they individually worked out a recurrence equation with varying seeds, using a hand-held calculator.

  1. Chaos in the Belousov-Zhabotinsky reaction

    Science.gov (United States)

    Field, Richard J.

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

  2. A Framework for Chaos Theory Career Counselling

    Science.gov (United States)

    Pryor, Robert G. L.

    2010-01-01

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

  3. From Cool Cash to Coded Chaos

    DEFF Research Database (Denmark)

    Rennison, Betina Wolfgang

    of management differently. In this chaos of codes the managerial challenge is to take a second order position in order to strategically manage the communication that manages management itself. Key words: Management; personnel management; human-relations; pay-system; communication; system-theory; discursive...

  4. Spatio-temporal chaos : A solvable model

    NARCIS (Netherlands)

    Diks, C; Takens, F; DeGoede, J

    1997-01-01

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

  5. Chaos and fractals an elementary introduction

    CERN Document Server

    Feldman, David P

    2012-01-01

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

  6. Dynamic system uncertainty propagation using polynomial chaos

    Directory of Open Access Journals (Sweden)

    Xiong Fenfen

    2014-10-01

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

  7. Chaos in a Bose-Einstein condensate

    Institute of Scientific and Technical Information of China (English)

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

    2010-01-01

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

  8. 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.

  9. Control and synchronization of spatiotemporal chaos.

    Science.gov (United States)

    Ahlborn, Alexander; Parlitz, Ulrich

    2008-01-01

    Chaos control methods for the Ginzburg-Landau equation are presented using homogeneously, inhomogeneously, and locally applied multiple delayed feedback signals. In particular, it is shown that a small number of control cells is sufficient for stabilizing plane waves or for trapping spiral waves, and that successful control is closely connected to synchronization of the dynamics in regions close to the control cells.

  10. Many-body chaos at weak coupling

    Science.gov (United States)

    Stanford, Douglas

    2016-10-01

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

  11. Chaos: A Very Short Introduction

    Energy Technology Data Exchange (ETDEWEB)

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

    2007-07-20

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

  12. 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

  13. Intrinsic Depletion or Not

    DEFF Research Database (Denmark)

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

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

  14. Controlling halo-chaos via wavelet-based feedback

    Directory of Open Access Journals (Sweden)

    Jin-Qing Fang

    2002-01-01

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

  15. Chaos and dynamics of spinning particles in Kerr spacetime

    CERN Document Server

    Han, Wen-Biao

    2010-01-01

    We study chaos dynamics of spinning particles in Kerr spacetime of rotating black holes use the Papapetrou equations by numerical integration. Because of spin, this system exists many chaos solutions, and exhibits some exceptional dynamic character. We investigate the relations between the orbits chaos and the spin magnitude S, pericenter, polar angle and Kerr rotation parameter a by means of a kind of brand new Fast Lyapulov Indicator (FLI) which is defined in general relativity. The classical definition of Lyapulov exponent (LE) perhaps fails in curve spacetime. And we emphasize that the Poincar\\'e sections cannot be used to detect chaos for this case. Via calculations, some new interesting conclusions are found: though chaos is easier to emerge with bigger S, but not always depends on S monotonically; the Kerr parameter a has a contrary action on the chaos occurrence. Furthermore, the spin of particles can destroy the symmetry of the orbits about the equatorial plane. And for some special initial condition...

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

    Science.gov (United States)

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

    2016-06-01

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

  17. 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...

  18. Quantum simulation of disordered systems with cold atoms

    Science.gov (United States)

    Garreau, Jean-Claude

    2017-01-01

    This paper reviews the physics of quantum disorder in relation with a series of experiments using laser-cooled atoms exposed to "kicks" of a standing wave, realizing a paradigmatic model of quantum chaos, the kicked rotor. This dynamical system can be mapped onto a tight-binding Hamiltonian with pseudo-disorder, formally equivalent to the Anderson model of quantum disorder, with quantum chaos playing the role of disorder. This provides a very good quantum simulator for the Anderson physics. xml:lang="fr"

  19. Gaussian Intrinsic Entanglement

    Science.gov (United States)

    Mišta, Ladislav; Tatham, Richard

    2016-12-01

    We introduce a cryptographically motivated quantifier of entanglement in bipartite Gaussian systems called Gaussian intrinsic entanglement (GIE). The GIE is defined as the optimized mutual information of a Gaussian distribution of outcomes of measurements on parts of a system, conditioned on the outcomes of a measurement on a purifying subsystem. We show that GIE vanishes only on separable states and exhibits monotonicity under Gaussian local trace-preserving operations and classical communication. In the two-mode case, we compute GIE for all pure states as well as for several important classes of symmetric and asymmetric mixed states. Surprisingly, in all of these cases, GIE is equal to Gaussian Rényi-2 entanglement. As GIE is operationally associated with the secret-key agreement protocol and can be computed for several important classes of states, it offers a compromise between computable and physically meaningful entanglement quantifiers.

  20. Intrinsic Time Quantum Gravity

    CERN Document Server

    Yu, Hoi Lai

    2016-01-01

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

  1. Control of Beam Halo-Chaos by Soliton

    Institute of Scientific and Technical Information of China (English)

    BAI Long; WENG Jia-Qiang; FANG Jin-Qing

    2005-01-01

    @@ The Kapchinsky-Vladimirsky beam through an alternating-gradient quadrupole magnetic field is studied using the particle-core model. The beam halo-chaos is found, and the soliton controller is proposed based on the mechanism of halo formation and strategy of controlling halo-chaos. We perform a multiparticle simulation to control the halo by soliton controller, and find that the halo-chaos and its regeneration can be eliminated. It is shown that our control method is effective.

  2. Testing for deterministic monetary chaos: Metric and topological diagnostics

    Energy Technology Data Exchange (ETDEWEB)

    Barkoulas, John T. [Department of Finance and Quantitative Analysis, Georgia Southern University, Statesboro, GA 30460 (United States)], E-mail: jbarkoul@georgiasouthern.edu

    2008-11-15

    The evidence of deterministic chaos in monetary aggregates tends to be contradictory in the literature. We revisit the issue of monetary chaos by applying tools based on both the metric (correlation dimension and Lyapunov exponents) and topological (recurrence plots) approaches to chaos. For simple-sum and divisia monetary aggregates over an expanded sample period, the empirical evidence from both approaches is negative for monetary chaotic dynamics.

  3. Quantum Chaos in Physical Systems: from Super Conductors to Quarks

    OpenAIRE

    Bittner, Elmar; Markum, Harald; Pullirsch, Rainer

    2001-01-01

    This article is the written version of a talk delivered at the Bexbach Colloquium of Science 2000 and starts with an introduction into quantum chaos and its relationship to classical chaos. The Bohigas-Giannoni-Schmit conjecture is formulated and evaluated within random-matrix theory. Several examples of physical systems exhibiting quantum chaos ranging from nuclear to solid state physics are presented. The presentation concludes with recent research work on quantum chromodynamics and the qua...

  4. Measurement induced chaos with entangled states

    CERN Document Server

    Kiss, T; Tóth, L D; Gábris, A; Jex, I; Alber, G

    2011-01-01

    Quantum control, in a broad sense, may include measurement of quantum systems and, as a feed back operation, selection from an ensemble conditioned on the measurements. The resulting dynamics can be nonlinear and, if applied iteratively, can lead to true chaos in a quantum system. We consider the dynamics of an ensemble of two qubit systems subjected to measurement and conditional selection. We prove that the iterative dynamics leads to true chaos in the entanglement of the qubits. A class of special initial states exhibits high sensitivity to the initial conditions. In the parameter space of the special initial states we identify two types of islands: one converging to a separable state, while the other being asymptotically completely entangled. The islands form a fractal like structure. Adding noise to the initial state introduces a further stable asymptotic cycle.

  5. Tuning quantum measurements to control chaos

    Science.gov (United States)

    Eastman, Jessica K.; Hope, Joseph J.; Carvalho, André R. R.

    2017-01-01

    Environment-induced decoherence has long been recognised as being of crucial importance in the study of chaos in quantum systems. In particular, the exact form and strength of the system-environment interaction play a major role in the quantum-to-classical transition of chaotic systems. In this work we focus on the effect of varying monitoring strategies, i.e. for a given decoherence model and a fixed environmental coupling, there is still freedom on how to monitor a quantum system. We show here that there is a region between the deep quantum regime and the classical limit where the choice of the monitoring parameter allows one to control the complex behaviour of the system, leading to either the emergence or suppression of chaos. Our work shows that this is a result from the interplay between quantum interference effects induced by the nonlinear dynamics and the effectiveness of the decoherence for different measurement schemes. PMID:28317933

  6. An exploration of dynamical systems and chaos

    CERN Document Server

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

    2015-01-01

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

  7. Chaos in effective classical and quantum dynamics

    CERN Document Server

    Casetti, L; Modugno, M; Casetti, Lapo; Gatto, Raoul; Modugno, Michele

    1998-01-01

    We investigate the dynamics of classical and quantum N-component phi^4 oscillators in presence of an external field. In the large N limit the effective dynamics is described by two-degree-of-freedom classical Hamiltonian systems. In the classical model we observe chaotic orbits for any value of the external field, while in the quantum case chaos is strongly suppressed. A simple explanation of this behaviour is found in the change in the structure of the orbits induced by quantum corrections. Consistently with Heisenberg's principle, quantum fluctuations are forced away from zero, removing in the effective quantum dynamics a hyperbolic fixed point that is a major source of chaos in the classical model.

  8. Quantum chaos in QCD and hadrons

    CERN Document Server

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

    2005-01-01

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

  9. Buoyancy driven turbulence and distributed chaos

    CERN Document Server

    Bershadskii, A

    2016-01-01

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

  10. Migraine--new perspectives from chaos theory.

    Science.gov (United States)

    Kernick, D

    2005-08-01

    Converging from a number of disciplines, non-linear systems theory and in particular chaos theory offer new descriptive and prescriptive insights into physiological systems. This paper briefly reviews an approach to physiological systems from these perspectives and outlines how these concepts can be applied to the study of migraine. It suggests a wide range of potential applications including new approaches to classification, treatment and pathophysiological mechanisms. A hypothesis is developed that suggests that dysfunctional consequences can result from a mismatch between the complexity of the environment and the system that is seeking to regulate it and that the migraine phenomenon is caused by an incongruity between the complexity of mid brain sensory integration and cortical control networks. Chaos theory offers a new approach to the study of migraine that complements existing frameworks but may more accurately reflect underlying physiological mechanisms.

  11. Chaos theory perspective for industry clusters development

    Science.gov (United States)

    Yu, Haiying; Jiang, Minghui; Li, Chengzhang

    2016-03-01

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

  12. Kac-Moody Algebras and Controlled Chaos

    CERN Document Server

    Wesley, D H

    2007-01-01

    Compactification can control chaotic Mixmaster behavior 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 hyperbolic (but not strictly 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.

  13. Chaos in hydrodynamic BL Herculis models

    CERN Document Server

    Smolec, R

    2014-01-01

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

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

    OpenAIRE

    Kröger, H.

    2003-01-01

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

  15. 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.

  16. Complex motions and chaos in nonlinear systems

    CERN Document Server

    Machado, José; Zhang, Jiazhong

    2016-01-01

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

  17. Computer Auxiliary Analysis for Stochasticity of Chaos

    Institute of Scientific and Technical Information of China (English)

    ZHAOGeng; FANGJin-qing

    2003-01-01

    In this work, we propose a mathematics-physical statistic analytical method for stochastic process of chaos, based on stochastic test via combination measurement of Monobit and Runs. Computer auxiliary analysis shows that it is of stochasticity for stochastic number produced from the chaotic circuit. Our software is written by VB and C++, the later can be tested by the former, and at the same time it is verified by stochastic number produced by the computer. So the data treatment results are reliable.

  18. Chaos in a topologically transitive system

    Institute of Scientific and Technical Information of China (English)

    XIONG; Jincheng

    2005-01-01

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

  19. Chaos: Understanding and Controlling Laser Instability

    Science.gov (United States)

    Blass, William E.

    1997-01-01

    In order to characterize the behavior of tunable diode lasers (TDL), the first step in the project involved the redesign of the TDL system here at the University of Tennessee Molecular Systems Laboratory (UTMSL). Having made these changes it was next necessary to optimize the new optical system. This involved the fine adjustments to the optical components, particularly in the monochromator, to minimize the aberrations of coma and astigmatism and to assure that the energy from the beam is focused properly on the detector element. The next step involved the taking of preliminary data. We were then ready for the analysis of the preliminary data. This required the development of computer programs that use mathematical techniques to look for signatures of chaos. Commercial programs were also employed. We discovered some indication of high dimensional chaos, but were hampered by the low sample rate of 200 KSPS (kilosamples/sec) and even more by our sample size of 1024 (1K) data points. These limitations were expected and we added a high speed data acquisition board. We incorporated into the system a computer with a 40 MSPS (million samples/sec) data acquisition board. This board can also capture 64K of data points so that were then able to perform the more accurate tests for chaos. The results were dramatic and compelling, we had demonstrated that the lead salt diode laser had a chaotic frequency output. Having identified the chaotic character in our TDL data, we proceeded to stage two as outlined in our original proposal. This required the use of an Occasional Proportional Feedback (OPF) controller to facilitate the control and stabilization of the TDL system output. The controller was designed and fabricated at GSFC and debugged in our laboratories. After some trial and error efforts, we achieved chaos control of the frequency emissions of the laser. The two publications appended to this introduction detail the entire project and its results.

  20. Optimal chaos control through reinforcement learning.

    Science.gov (United States)

    Gadaleta, Sabino; Dangelmayr, Gerhard

    1999-09-01

    A general purpose chaos control algorithm based on reinforcement learning is introduced and applied to the stabilization of unstable periodic orbits in various chaotic systems and to the targeting problem. The algorithm does not require any information about the dynamical system nor about the location of periodic orbits. Numerical tests demonstrate good and fast performance under noisy and nonstationary conditions. (c) 1999 American Institute of Physics.

  1. Chaos control of parametric driven Duffing oscillators

    Energy Technology Data Exchange (ETDEWEB)

    Jin, Leisheng; Mei, Jie; Li, Lijie, E-mail: L.Li@swansea.ac.uk [College of Engineering, Swansea University, Swansea SA2 8PP (United Kingdom)

    2014-03-31

    Duffing resonators are typical dynamic systems, which can exhibit chaotic oscillations, subject to certain driving conditions. Chaotic oscillations of resonating systems with negative and positive spring constants are identified to investigate in this paper. Parametric driver imposed on these two systems affects nonlinear behaviours, which has been theoretically analyzed with regard to variation of driving parameters (frequency, amplitude). Systematic calculations have been performed for these two systems driven by parametric pumps to unveil the controllability of chaos.

  2. Chaos control of parametric driven Duffing oscillators

    Science.gov (United States)

    Jin, Leisheng; Mei, Jie; Li, Lijie

    2014-03-01

    Duffing resonators are typical dynamic systems, which can exhibit chaotic oscillations, subject to certain driving conditions. Chaotic oscillations of resonating systems with negative and positive spring constants are identified to investigate in this paper. Parametric driver imposed on these two systems affects nonlinear behaviours, which has been theoretically analyzed with regard to variation of driving parameters (frequency, amplitude). Systematic calculations have been performed for these two systems driven by parametric pumps to unveil the controllability of chaos.

  3. Reducing or enhancing chaos using periodic orbits.

    Science.gov (United States)

    Bachelard, R; Chandre, C; Leoncini, X

    2006-06-01

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

  4. Chaos in free electron laser oscillators

    Energy Technology Data Exchange (ETDEWEB)

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

    2009-07-01

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

  5. Chaos synchronization based on a continuous chaos control method in semiconductor lasers with optical feedback.

    Science.gov (United States)

    Murakami, A; Ohtsubo, J

    2001-06-01

    Chaos synchronization using a continuous chaos control method was studied in two identical chaotic laser systems consisting of semiconductor lasers and optical feedback from an external mirror. Numerical calculations for rate equations indicate that the stability of chaos synchronization depends significantly on the external mirror position. We performed a linear stability analysis for the rate equations. Our results show that the stability of the synchronization is much influenced by the mode interaction between the relaxation oscillation frequency of the semiconductor laser and the external cavity frequency. Due to this interaction, an intensive mode competition between the two frequencies destroys the synchronization, but stable synchronization can be achieved when the mode competition is very weak.

  6. 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

  7. Bifurcations and Chaos in Duffing Equation

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

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

  8. Chaos in Chiral Condensates in Gauge Theories

    Science.gov (United States)

    Hashimoto, Koji; Murata, Keiju; Yoshida, Kentaroh

    2016-12-01

    Assigning a chaos index for dynamics of generic quantum field theories is a challenging problem because the notion of a Lyapunov exponent, which is useful for singling out chaotic behavior, works only in classical systems. We address the issue by using the AdS /CFT correspondence, as the large Nc limit provides a classicalization (other than the standard ℏ→0 ) while keeping nontrivial quantum condensation. We demonstrate the chaos in the dynamics of quantum gauge theories: The time evolution of homogeneous quark condensates ⟨q ¯q ⟩ and ⟨q ¯γ5q ⟩ in an N =2 supersymmetric QCD with the S U (Nc) gauge group at large Nc and at a large 't Hooft coupling λ ≡NcgYM2 exhibits a positive Lyapunov exponent. The chaos dominates the phase space for energy density E ≳(6 ×1 02)×mq4(Nc/λ2), where mq is the quark mass. We evaluate the largest Lyapunov exponent as a function of (Nc,λ ,E ) and find that the N =2 supersymmetric QCD is more chaotic for smaller Nc.

  9. Chaos driven by interfering memory

    CERN Document Server

    Perrard, Stéphane; Fort, Emmanuel; Couder, Yves

    2016-01-01

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

  10. Disorder chaos and multiple valleys in spin glasses

    CERN Document Server

    Chatterjee, Sourav

    2009-01-01

    We prove that the Sherrington-Kirkpatrick model of spin glasses is chaotic under small perturbations of the couplings at any temperature in the absence of an external field. The result is proved for two kinds of perturbations: (a) distorting the couplings via Ornstein-Uhlenbeck flows, and (b) replacing a small fraction of the couplings by independent copies. We further prove that the S-K model exhibits multiple valleys in its energy landscape, i.e. there are many states with near-minimal energy that are mutually nearly orthogonal. We show that the variance of the free energy of the S-K model is unusually small at any temperature. (By `unusually small' we mean that it is much smaller than the number of sites; in other words, it beats the classical Gaussian concentration inequality, a phenomenon that we call `superconcentration'.) We prove that the bond overlap in the Edwards-Anderson model of spin glasses is not chaotic under perturbations of the couplings, even large perturbations. Lastly, we obtain sharp low...

  11. Intrinsic Angular Momentum of Light.

    Science.gov (United States)

    Santarelli, Vincent

    1979-01-01

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

  12. Using a quantum computer to investigate quantum chaos

    OpenAIRE

    Schack, Ruediger

    1997-01-01

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

  13. 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…

  14. Major open problems in chaos theory and nonlinear dynamics

    CERN Document Server

    Li, Y Charles

    2013-01-01

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

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

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

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

    Science.gov (United States)

    Lindsay, Jean S.

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

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

    Science.gov (United States)

    Procaccia, Itamar

    1988-06-01

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

  18. Experimental Control of Instabilities and Chaos in Fast Dynamical Systems

    Science.gov (United States)

    1997-06-01

    is short (- 10 cm) [153]-[155]; these studies have more recently been considered from the chaos control viewpoint [42]. The apparatus required to...13] Christini, David J., and James A. Collins. Controlling Nonchaotic Neuronal Noise Using Chaos Control Techniques. Phys. Rev. Lett. 75:2782-2785

  19. Time generated by intrinsic observers

    CERN Document Server

    Svozil, Karl

    2009-01-01

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

  20. The role of intrinsically unstructured proteins in neurodegenerative diseases.

    Directory of Open Access Journals (Sweden)

    Swasti Raychaudhuri

    Full Text Available The number and importance of intrinsically disordered proteins (IUP, known to be involved in various human disorders, are growing rapidly. To test for the generalized implications of intrinsic disorders in proteins involved in Neurodegenerative diseases, disorder prediction tools have been applied to three datasets comprising of proteins involved in Huntington Disease (HD, Parkinson's disease (PD, Alzheimer's disease (AD. Results show, in general, proteins in disease datasets possess significantly enhanced intrinsic unstructuredness. Most of these disordered proteins in the disease datasets are found to be involved in neuronal activities, signal transduction, apoptosis, intracellular traffic, cell differentiation etc. Also these proteins are found to have more number of interactors and hence as the proportion of disorderedness (i.e., the length of the unfolded stretch increased, the size of the interaction network simultaneously increased. All these observations reflect that, "Moonlighting" i.e. the contextual acquisition of different structural conformations (transient, eventually may allow these disordered proteins to act as network "hubs" and thus they may have crucial influences in the pathogenecity of neurodegenerative diseases.

  1. 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.

  2. $\\mathcal{PT}$-Symmetry-Breaking Chaos in Optomechanics

    CERN Document Server

    Lü, Xin-You; Ma, Jin-Yong; Wu, Ying

    2015-01-01

    We demonstrate a $\\mathcal{PT}$-symmetry-breaking chaos in optomechanical system (OMS), which features an ultralow driving threshold. In principle, this chaos will emerge once a driving laser is applied to the cavity mode and lasts for a period of time. The driving strength is inversely proportional to the starting time of chaos. This originally comes from the dynamical enhancement of nonlinearity by field localization in $\\mathcal{PT}$-symmetry-breaking phase ($\\mathcal{PT}$BP). Moreover, this chaos is switchable by tuning the system parameters so that a $\\mathcal{PT}$-symmetry phase transition occurs. This work may fundamentally broaden the regimes of cavity optomechanics and nonlinear optics. It offers the prospect of exploring ultralow-power-laser triggered chaos and its potential applications in secret communication.

  3. Erbium - doped fiber laser systems: Routes to chaos

    Directory of Open Access Journals (Sweden)

    Rubežić Vesna

    2014-01-01

    Full Text Available Erbium-doped fiber laser systems exhibit a large variety of complex dynamical behaviors, bifurcations and attractors. In this paper, the chaotic behavior which can be achieved under certain conditions in a laser system with erbium-doped fiber, is discussed. The chaos in this system occurs through several standard scenarios. In this paper, the simulation sequence of quasiperiodic, intermittent and period-doubling scenario transitions to chaos is shown. Quasiperiodic and intermittent transitions to chaos are shown on the example system with a single ring. The electro-optical modulator was applied to the system for modulating the loss in the cavity. We used the sinusoidal and rectangular signals for modulation. Generation of chaos is achieved by changing the parameters of signal for modulation. Period-doubling transition to chaos is illustrated in a system with two rings. Simulation results are shown in the time domain and phase space.

  4. Dynamical chaos in chip-scale optomechanical oscillators

    CERN Document Server

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

    2016-01-01

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

  5. Population Floors and the Persistence of Chaos in Ecological Models.

    Science.gov (United States)

    Ruxton; Rohani

    1998-06-01

    Chaotic dynamics have been observed in a wide range of population models. Here we describe the effects of perturbing several of these models so as to introduce a non-zero minimum population size. This perturbation generally reduces the likelihood of observing chaos, in both discrete and continuous time models. The extent of this effect depends on whether chaos is generated through period-doubling, quasiperiodicity, or intermittence. Chaos reached via the quasiperiodic route is more robust against the perturbation than period-doubling chaos, whilst the inclusion of a population floor in a model exhibiting intermittent chaos may increase the frequency of population bursts although these become non-chaotic. Copyright 1998 Academic Press.

  6. Chaos and Correlated Avalanches in Excitatory Neural Networks with Synaptic Plasticity

    Science.gov (United States)

    Pittorino, Fabrizio; Ibáñez-Berganza, Miguel; di Volo, Matteo; Vezzani, Alessandro; Burioni, Raffaella

    2017-03-01

    A collective chaotic phase with power law scaling of activity events is observed in a disordered mean field network of purely excitatory leaky integrate-and-fire neurons with short-term synaptic plasticity. The dynamical phase diagram exhibits two transitions from quasisynchronous and asynchronous regimes to the nontrivial, collective, bursty regime with avalanches. In the homogeneous case without disorder, the system synchronizes and the bursty behavior is reflected into a period doubling transition to chaos for a two dimensional discrete map. Numerical simulations show that the bursty chaotic phase with avalanches exhibits a spontaneous emergence of persistent time correlations and enhanced Kolmogorov complexity. Our analysis reveals a mechanism for the generation of irregular avalanches that emerges from the combination of disorder and deterministic underlying chaotic dynamics.

  7. Associations of personality with intrinsic motivation in schizophrenia.

    Science.gov (United States)

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

    2013-06-30

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

  8. Intramolecular quantum chaos in doped helium nanodroplets

    Science.gov (United States)

    Polyakova, E.; Stolyarov, D.; Zhang, X.; Kresin, V. V.; Wittig, C.

    2003-07-01

    A mass spectrometric depletion spectrum (17 700-18 300 cm -1) is reported for NO 2 in superfluid (0.37 K) helium nanodroplets. Gas phase NO 2 is believed to be vibronically chaotic at these energies. Transitions are broadened and blue-shifted relative to their gas phase counterparts. The spectrum is fitted reasonably well by setting all of the widths and shifts equal to 7 cm -1. Modest dispersions (i.e., 90% lie within 2 cm -1 of the central values) are consistent with quantum chaos in NO 2. Relaxation is dominated by interactions of NO 2 with its non-superfluid helium nearest neighbors.

  9. Conduction at the onset of chaos

    Science.gov (United States)

    Baldovin, Fulvio

    2017-02-01

    After a general discussion of the thermodynamics of conductive processes, we introduce specific observables enabling the connection of the diffusive transport properties with the microscopic dynamics. We solve the case of Brownian particles, both analytically and numerically, and address then whether aspects of the classic Onsager's picture generalize to the non-local non-reversible dynamics described by logistic map iterates. While in the chaotic case numerical evidence of a monotonic relaxation is found, at the onset of chaos complex relaxation patterns emerge.

  10. Bose-Hubbard Hamiltonian: Quantum chaos approach

    Science.gov (United States)

    Kolovsky, Andrey R.

    2016-03-01

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

  11. River of kings [Mae Nam Chao Phraya

    Energy Technology Data Exchange (ETDEWEB)

    Mogg, R.

    1997-10-01

    Low rainfall and a growing demand for water have had profound effects on water supplies in Thailand`s Mae Nam Chao Phraya river basin. In particular, low water levels are causing problems at the Bhumibol and Sirikit dams, as rice farms are threatened. The work of a Government sponsored think-tank set up to coordinate water management in the region is describe. Strategies may include use of groundwater at peak demand, recycling waste water and improve technical efficiency to reduce distribution losses. Any such policy changes will inevitably have widespread political, economic and social consequences. (UK)

  12. Feigenbaum graphs at the onset of chaos

    Energy Technology Data Exchange (ETDEWEB)

    Luque, Bartolo; Lacasa, Lucas [Dept. Matemática Aplicada y Estadística, ETSI Aeronáuticos, Universidad Politécnica de Madrid (Spain); Robledo, Alberto, E-mail: robledo@fisica.unam.mx [Instituto de Física y Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México (Mexico)

    2012-11-01

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

  13. Effect of Chaos on Relativistic Quantum Tunneling

    Science.gov (United States)

    2012-06-01

    andAkis R., Phys. Rev. Lett., 103 (2009) 054101;Huang L., Lai Y.-C. and Grebogi C., Chaos, 21 (2011) 013102. [3] Novoselov K. S., Geim A. K., Morozov S. V...Feng R., Dai Z., Marchenkov A. N., Conrad E. H., First P. N. and de Heer W. A., J. Phys. Chem. B, 108 (2004) 19912; Novoselov K. S., Geim A. K., Morozov...P., Nature, 438 (2005) 201; Castro Neto A. H., Guinea F., Peres N. M. R., Novoselov K. S. and Geim A. K., Rev. Mod. Phys., 81 (2009) 109; Das Sarma S

  14. Chaos Synchronization in Two Coupled Duffing Oscillators

    Institute of Scientific and Technical Information of China (English)

    方见树; 荣曼生; 方焯; 刘小娟

    2001-01-01

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

  15. Quantum chaos and the black hole horizon

    CERN Document Server

    CERN. Geneva

    2016-01-01

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

  16. Self-organized chaos through polyhomeostatic optimization.

    Science.gov (United States)

    Markovic, D; Gros, Claudius

    2010-08-06

    The goal of polyhomeostatic control is to achieve a certain target distribution of behaviors, in contrast to homeostatic regulation, which aims at stabilizing a steady-state dynamical state. We consider polyhomeostasis for individual and networks of firing-rate neurons, adapting to achieve target distributions of firing rates maximizing information entropy. We show that any finite polyhomeostatic adaption rate destroys all attractors in Hopfield-like network setups, leading to intermittently bursting behavior and self-organized chaos. The importance of polyhomeostasis to adapting behavior in general is discussed.

  17. Importance of packing in spiral defect chaos

    Indian Academy of Sciences (India)

    Kapilanjan Krishna

    2008-04-01

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

  18. Polarization chaos in an optically pumped laser.

    Science.gov (United States)

    Serrat, C; Kul'minskii, A; Vilaseca, R; Corbalán, R

    1995-06-15

    We study the steady-state and dynamic behavior of an optically pumped J = 0 ? J = 1 ? J = 0 laser operating with an isotropic ring cavity and an axial magnetic field. The gain anisotropy induced by a linearly polarized pump-laser f ield leads, in the steady state, to locking of the two circularly polarized components of the laser field, which acquires a linear polarization parallel to that of the pump field. In the presence of laser intensity instabilities, however, locking does not occur, and polarization instabilities appear. For the f irst time to our knowledge, polarization chaos has been found in a laser system.

  19. Cryptography with chaos at the physical level

    Energy Technology Data Exchange (ETDEWEB)

    Machado, Romuel F. E-mail: romuelm@iceb.ufop.br; Baptista, Murilo S.; Grebogi, C

    2004-09-01

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

  20. Geometry in the large and hyperbolic chaos

    Energy Technology Data Exchange (ETDEWEB)

    Hasslacher, B.; Mainieri, R.

    1998-11-01

    This is the final report of a three-year, Laboratory Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). The authors calculated observables in strongly chaotic systems. This is difficult to do because of a lack of a workable orbit classification for such systems. This is due to global geometrical information from the original dynamical system being entangled in an unknown way throughout the orbit sequence. They used geometrical methods from modern mathematics and recent connections between global geometry and modern quantum field theory to study the natural geometrical objects belonging to hard chaos-hyperbolic manifolds.

  1. Time reversibility, computer simulation, and chaos

    CERN Document Server

    Hoover, William Graham

    1999-01-01

    A small army of physicists, chemists, mathematicians, and engineers has joined forces to attack a classic problem, the "reversibility paradox", with modern tools. This book describes their work from the perspective of computer simulation, emphasizing the author's approach to the problem of understanding the compatibility, and even inevitability, of the irreversible second law of thermodynamics with an underlying time-reversible mechanics. Computer simulation has made it possible to probe reversibility from a variety of directions and "chaos theory" or "nonlinear dynamics" has supplied a useful

  2. Delayed self-synchronization in homoclinic chaos

    Science.gov (United States)

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

    2002-04-01

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

  3. Wave Dynamical Chaos in Superconducting Microwave Cavities

    CERN Document Server

    Rehfeld, H; Dembowski, C; Gräf, H D; Hofferbert, R; Richter, A; Lengeler, Herbert

    1997-01-01

    During the last few years we have studied the chaotic behavior of special Euclidian geometries, so-called billiards, from the quantum or in more general sense "wave dynamical" point of view. Due to the equivalence between the stationary Schroedinger equation and the classical Helmholtz equation in the two-dimensional case (plain billiards), it is possible to simulate "quantum chaos" with the help of macroscopic, superconducting microwave cavities. Using this technique we investigated spectra of three billiards from the family of Pascal's Snails (Robnik-Billiards) with a different chaoticity in each case in order to test predictions of standard stochastical models for classical chaotic systems.

  4. A new optimization algorithm based on chaos

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

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

  5. Chaos in the BMN matrix model

    Science.gov (United States)

    Asano, Yuhma; Kawai, Daisuke; Yoshida, Kentaroh

    2015-06-01

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

  6. Chaos in the BMN matrix model

    CERN Document Server

    Asano, Yuhma; Yoshida, Kentaroh

    2015-01-01

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

  7. Using chaos to improve measurement precision

    Institute of Scientific and Technical Information of China (English)

    何斌; 杨灿军; 周银生; 陈鹰

    2002-01-01

    If the measuring signals wore input to the chaotic dynamic system as initial parameters, the system outputs might be in steady state, periodic state or chaos state. If the chaotic dynamic system outputs controlled in the periodic states, the periodic numbers would be changed most with the signals. Our novel method is to add chaotic dynamic vibration to the measurement or sensor system. The sensor sensitivity and precision of a measurement system would be improved with this method. Chaotic dynamics measurement algorithms are given and their sensitivity to parameters are analyzed in this paper. The effects of noises on the system are discussed,

  8. Using chaos to improve measurement precision

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    If the measuring signals were input to the chaotic dynamic system as initial parameters, the system outputs might be in steady state, periodic state or chaos state. If the chaotic dynamic system outputs controlled in the periodic states, the periodic numbers would be changed most with the signals. Our novel method is to add chaotic dynamic vibration to the measurement or sensor system.The sensor sensitivity and precision of a measurement system would be improved with this method. Chaotic dynamics measurement algorithms are given and their sensitivity to parameters are analyzed in this paper. The effects of noises on the system are discussed.

  9. Intrinsic time geometrodynamics: explicit examples

    CERN Document Server

    Lin, Huei-Chen

    2016-01-01

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

  10. Recent progress on intrinsic charm

    Science.gov (United States)

    Hobbs, T. J.

    2017-03-01

    Over the past ˜10 years, the topic of the nucleon's nonperturbative or intrinsic charm (IC) content has enjoyed something of a renaissance, largely motivated by theoretical developments involving quark modelers and PDF-fitters. In this talk I will briefly describe the importance of intrinsic charm to various issues in high-energy phenomenology, and survey recent progress in constraining its overall normalization and contribution to the momentum sum rule of the nucleon. I end with the conclusion that progress on the side of calculation has now placed the onus on experiment to unambiguously resolve the proton's intrinsic charm component.

  11. Electro-optic delay oscillator with nonlocal nonlinearity: Optical phase dynamics, chaos, and synchronization.

    Science.gov (United States)

    Lavrov, Roman; Peil, Michael; Jacquot, Maxime; Larger, Laurent; Udaltsov, Vladimir; Dudley, John

    2009-08-01

    We demonstrate experimentally how nonlinear optical phase dynamics can be generated with an electro-optic delay oscillator. The presented architecture consists of a linear phase modulator, followed by a delay line, and a differential phase-shift keying demodulator (DPSK-d). The latter represents the nonlinear element of the oscillator effecting a nonlinear transformation. This nonlinearity is considered as nonlocal in time since it is ruled by an intrinsic differential delay, which is significantly greater than the typical phase variations. To study the effect of this specific nonlinearity, we characterize the dynamics in terms of the dependence of the relevant feedback gain parameter. Our results reveal the occurrence of regular GHz oscillations (approximately half of the DPSK-d free spectral range), as well as a pronounced broadband phase-chaotic dynamics. Beyond this, the observed dynamical phenomena offer potential for applications in the field of microwave photonics and, in particular, for the realization of novel chaos communication systems. High quality and broadband phase-chaos synchronization is also reported with an emitter-receiver pair of the setup.

  12. Intrinsic motivation and learning dynamics

    CERN Document Server

    Zgonnikov, Arkady

    2013-01-01

    We investigate the effects of intrinsic motivation on the dynamics of learning processes. We construct a simple model of a single agent adapting to unknown environment. Performing a repeated choice between a number of initially unexplored alternatives, the agent gains rewards for each selected alternative and in doing so gradually comprehends the environment. In our model the agent choice is governed by two stimuli. The traditional extrinsic motive inclines the agent to maximize the cumulative payoff throughout the process, while the second, intrinsic one, biases the agent towards the novel options that she inherently likes. We show that the intrinsic motivation can induce an instability and periodic dynamics of the learning process which is always stationary in the case of selfish, rational agent. Interestingly, the opposite effect can arise as well: when the impact of intrinsic motivation on the agent choice is strong, the equiprobable choice equilibrium strategy becomes stable. Based on the presented resul...

  13. Equilibrium behavior of coarse-grained chaos

    Science.gov (United States)

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

    2015-03-01

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

  14. Chaos and structure of level densities

    Energy Technology Data Exchange (ETDEWEB)

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

    2008-01-01

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

  15. Rapid dynamical chaos in an exoplanetary system

    CERN Document Server

    Deck, Katherine M; Agol, Eric; Carter, Joshua A; Lissauer, Jack J; Ragozzine, Darin; Winn, Joshua N

    2012-01-01

    We report on the long-term dynamical evolution of the two-planet Kepler-36 system, which we studied through numerical integrations of initial conditions that are consistent with observations of the system. The orbits are chaotic with a Lyapunov time of only ~10 years. The chaos is a consequence of a particular set of orbital resonances, with the inner planet orbiting 34 times for every 29 orbits of the outer planet. The rapidity of the chaos is due to the interaction of the 29:34 resonance with the nearby first order 6:7 resonance, in contrast to the usual case in which secular terms in the Hamiltonian play a dominant role. Only one contiguous region of phase space, accounting for ~4.5% of the sample of initial conditions studied, corresponds to planetary orbits that do not show large scale orbital instabilities on the timescale of our integrations (~200 million years). The long-lived subset of the allowed initial conditions are those that satisfy the Hill stability criterion by the largest margin. Any succes...

  16. Order and chaos in soft condensed matter

    Indian Academy of Sciences (India)

    A K Sood; Rajesh Ganapathy

    2006-07-01

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

  17. Harmonic structures and intrinsic torsion

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

    2015-01-01

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

  18. Harmonic structures and intrinsic torsion

    DEFF Research Database (Denmark)

    Conti, Diego; Madsen, Thomas Bruun

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

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

    Institute of Scientific and Technical Information of China (English)

    Junhai MA; Yaqiang CUI; Lixia LIU

    2008-01-01

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

  20. Dynamical systems approach to one-dimensional spatiotemporal chaos: A cyclist's view

    Science.gov (United States)

    Lan, Yueheng

    We propose a dynamical systems approach to the study of weak turbulence (spatiotemporal chaos) based on the periodic orbit theory, emphasizing the role of recurrent patterns and coherent structures. After a brief review of the periodic orbit theory and its application to low-dimensional dynamics, we discuss its possible extension to study dynamics of spatially extended systems. The discussion is three-fold. First, we introduce a novel variational scheme for finding periodic orbits in high-dimensional systems. Second, we prove rigorously the existence of periodic structures (modulated amplitude waves) near the first instability of the complex Ginzburg-Landau equation, and check their role in pattern formation. Third, we present the extensive numerical exploration of the Kuramoto-Sivashinsky system in the chaotic regime: structure of the equilibrium solutions, our search for the shortest periodic orbits, description of the chaotic invariant set in terms of intrinsic coordinates and return maps on the Poincare section.

  1. 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.

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

    Institute of Scientific and Technical Information of China (English)

    JunhaiMa; BiaoRen; YanGao

    2004-01-01

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

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

    Energy Technology Data Exchange (ETDEWEB)

    Perc, Matjaz [Department of Physics, Faculty of Education, University of Maribor, Koroska cesta 160, SI-2000 Maribor (Slovenia)] e-mail: matjaz.perc@uni-mb.si; Marhl, Marko [Department of Physics, Faculty of Education, University of Maribor, Koroska cesta 160, SI-2000 Maribor (Slovenia)

    2006-01-01

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

  4. Decrease of cardiac chaos in congestive heart failure

    Science.gov (United States)

    Poon, Chi-Sang; Merrill, Christopher K.

    1997-10-01

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

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

    CERN Document Server

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

    2001-01-01

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

  6. Contributions of plasma physics to chaos and nonlinear dynamics

    Science.gov (United States)

    Escande, D. F.

    2016-11-01

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

  7. Evidence of low-dimensional chaos in magnetized plasma turbulence

    CERN Document Server

    Zivkovic, Tatjana

    2008-01-01

    We analyze probe data obtained from a toroidal magnetized plasma configuration suitable for studies of low-frequency gradient-driven instabilities. These instabilities give rise to field-aligned convection rolls analogous to Rayleigh-Benard cells in neutral fluids, and may theoretically develop similar routes to chaos. When using mean-field dimension analysis, we observe low dimensionality, but this could originate from either low-dimensional chaos, periodicity or quasi-periodicity. Therefore, we apply recurrence plot analysis as well as estimation of the largest Lyapunov exponent. These analyses provide evidence of low-dimensional chaos, in agreement with theoretical predictions.

  8. Diffusive Lorenz dynamics: Coherent structures and spatiotemporal chaos

    Institute of Scientific and Technical Information of China (English)

    YuehongQIAN; HudongCHEN; Da-HsuanFENG

    2000-01-01

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

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

    Directory of Open Access Journals (Sweden)

    Marcio Luiz Marietto

    2011-12-01

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

  10. New chaos-based encryption scheme for digital sequence

    Institute of Scientific and Technical Information of China (English)

    Zhang Zhengwei; Fan Yangyu; Zeng Li

    2007-01-01

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

  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. Controlling beam halo-chaos via backstepping design

    Institute of Scientific and Technical Information of China (English)

    Gao Yuan; Kong Feng

    2008-01-01

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

  13. 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.

  14. Theory of the nucleus as applied to quantum chaos

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-15

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

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

    Institute of Scientific and Technical Information of China (English)

    ZHANG Xiao-Hong; MIN Le-Quan

    2005-01-01

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

  16. Quasiperiodicity route to chaos in cardiac conduction model

    Science.gov (United States)

    Quiroz-Juárez, M. A.; Vázquez-Medina, R.; Ryzhii, E.; Ryzhii, M.; Aragón, J. L.

    2017-01-01

    It has been suggested that cardiac arrhythmias are instances of chaos. In particular that the ventricular fibrillation is a form of spatio-temporal chaos that arises from normal rhythm through a quasi-periodicity or Ruelle-Takens-Newhouse route to chaos. In this work, we modify the heterogeneous oscillator model of cardiac conduction system proposed in Ref. [Ryzhii E, Ryzhii M. A heterogeneous coupled oscillator model for simulation of ECG signals. Comput Meth Prog Bio 2014;117(1):40-49. doi:10.1016/j.cmpb.2014.04.009.], by including an ectopic pacemaker that stimulates the ventricular muscle to model arrhythmias. With this modification, the transition from normal rhythm to ventricular fibrillation is controlled by a single parameter. We show that this transition follows the so-called torus of quasi-periodic route to chaos, as verified by using numerical tools such as power spectrum and largest Lyapunov exponent.

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

    CERN Document Server

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

    2012-01-01

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

  18. Bifurcation of Periodic Orbits and Chaos in Duffing Equation

    Institute of Scientific and Technical Information of China (English)

    Mei-xiang Cai; Jian-ping Yang

    2006-01-01

    Duffing equation with fifth nonlinear-restoring force, one external forcing and a phase shift is investigated. The conditions of existences for primary resonance, second-order, third-order subharmonics, morder subharmonics and chaos are given by using second-averaging method, Melnikov methods and bifurcation theory. Numerical simulations including bifurcation diagrams, bifurcation surfaces, phase portraits, not only show the consistence with the theoretical analysis, but also exhibit the new dynamical behaviors. We show the onset of chaos, chaos suddenly disappearing to period orbit, one-band and double-band chaos, period-doubling bifurcations from period 1, 2, and 3 orbits, period-windows (period-2, 3 and 5) in chaotic regions.

  19. Chaos as a Source of Complexity and Diversity in Evolution

    CERN Document Server

    Kaneko, K

    1993-01-01

    The relevance of chaos to evolution is discussed in the context of the origin and maintenance of diversity and complexity. Evolution to the edge of chaos is demonstrated in an imitation game. As an origin of diversity, dynamic clustering of identical chaotic elements, globally coupled each to other, is briefly reviewed. The clustering is extended to nonlinear dynamics on hypercubic lattices, which enables us to construct a self-organizing genetic algorithm. A mechanism of maintenance of diversity, ``homeochaos", is given in an ecological system with interaction among many species. Homeochaos provides a dynamic stability sustained by high-dimensional weak chaos. A novel mechanism of cell differentiation is presented, based on dynamic clustering. Here, a new concept -- ``open chaos" -- is proposed for the instability in a dynamical system with growing degrees of freedom. It is suggested that studies based on interacting chaotic elements can replace both top-down and bottom-up approaches.

  20. Fractional Chaos Based Communication Systems-An Introduction

    Institute of Scientific and Technical Information of China (English)

    Juebang Yu

    2008-01-01

    As one of secure communication means, chaotic communication systems has been well-developed during the past three decades. Technical papers, both for theoretical and practical investigations, have reached a huge amount in number. On the other hand, fractional chaos, as a parallel ongoing research topic, also attracts many researchers to investigate. As far as the IT field is concerned, the research on control systems by using fractional chaos known as FOC (fractional order control) has been a hot issue for quite a long time. As a comparison, interesting enough, up to now we have not found any research result related to Fractional Chaos Communi cation (FCC) system, Le., a system based on fractional chaos. The motivation of the present article is to reveal the feasibility of realizing communication systems based upon FCC and their superiority over the conventional integer chaotic communication systems. Principles of FCC and its advantages over integer chaotic communication systems are also discussed.

  1. Biological conditions for oscillations and chaos generated by multispecies competition

    NARCIS (Netherlands)

    Huisman, J; Weissing, FJ

    2001-01-01

    We investigate biological mechanisms that generate oscillations and chaos in multispecies competition models. For this purpose, we use a competition model concerned with competition for abiotic essential resources. Because phytoplankton and plants consume quite a number of abiotic essential resource

  2. 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...

  3. 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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2014-12-15

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

  5. Secular Chaos and the Production of Hot Jupiters

    CERN Document Server

    Wu, Yanqin

    2010-01-01

    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 towards 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 (Lithwick & Wu, 2010). After an extended period of eccentricity diffusion, the inner planet's pericentre can approach the star to within a few stellar radii. Strong tidal interactions and ensuing tidal dissipation extracts orbital energy from the planet and pulls it inward, creating a hot Jupiter. In contrast to other proposed channels for the production of hot Jupiters, such a scenario (which we term...

  6. Controlling chaos using an exponential control

    CERN Document Server

    Gadre, S D; Gadre, Sangeeta D; Varma, V S

    1995-01-01

    We demonstrate that chaos can be controlled using a multiplicative exponential feedback control. All three types of unstable orbits - unstable fixed points, limit cycles and chaotic trajectories can be stabilized using this control. The control is effective both for maps and flows. The control is significant, particularly for systems with several degrees of freedom, as knowledge of only one variable on the desired unstable orbit is sufficient to settle the system on to that orbit. We find, that in all the cases studied, the transient time is a decreasing function of the stiffness of control. But increasing the stiffness beyond an optimum value can increase the transient time. The control can also be used to create suitable new stable attractors in a map, which did not exist in the original system.

  7. Digital Communications Using Chaos and Nonlinear Dynamics

    CERN Document Server

    Larson, Lawrence E; Liu, Jia-Ming

    2006-01-01

    This book introduces readers to a new and exciting cross-disciplinary field of digital communications with chaos. This field was born around 15 years ago, when it was first demonstrated that nonlinear systems which produce complex non-periodic noise-like chaotic signals, can be synchronized and modulated to carry useful information. Thus, chaotic signals can be used instead of pseudo-random digital sequences for spread-spectrum and private communication applications. This deceptively simple idea spun hundreds of research papers, and many novel communication schemes based on chaotic signals have been proposed. However, only very recently researchers have begun to make a transition from academic studies toward practical implementation issues, and many "promising" schemes had to be discarded or re-formulated. This book describes the state of the art (both theoretical and experimental) of this novel field. The book is written by leading experts in the fields of Nonlinear Dynamics and Electrical Engineering who pa...

  8. Theory of Secular Chaos and Mercury's Orbit

    CERN Document Server

    Lithwick, Yoram

    2010-01-01

    We study the chaotic orbital evolution of planetary systems, focusing on secular (i.e., orbit-averaged) interactions, because these often dominate on long timescales. We first focus on the evolution of a test particle that is forced by multiple massive planets. To linear order in eccentricity and inclination, its orbit precesses with constant frequencies. But nonlinearities can shift the frequencies into and out of secular resonance with the planets' eigenfrequencies, or with linear combinations of those frequencies. The overlap of these nonlinear secular resonances drive secular chaos in planetary systems. We quantify the resulting dynamics for the first time by calculating the locations and widths of nonlinear secular resonances. When results from both analytical calculations and numerical integrations are displayed together in a newly developed "map of the mean momenta" (MMM), the agreement is excellent. This map is particularly revealing for non-coplanar planetary systems and demonstrates graphically that...

  9. Chaos in body-vortex interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby; Aref, Hassan

    2010-01-01

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

  10. Spatial chaos-based image encryption design

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    In recent years, the chaos based cryptographic algorithms have suggested some new and efficient ways to develop secure image encryption techniques, but the drawbacks of small key space and weak security in one-dimensional chaotic cryptosystems are obvious. In this paper, permutation and sub- stitution methods are incorporated to present a stronger image encryption algorithm. Spatial chaotic maps are used to realize the position permutation, and to confuse the relationship between the ci- pher-image and the plain-image. The experimental results demonstrate that the suggested encryption scheme of image has the advantages of large key space and high security; moreover, the distribution of grey values of the encrypted image has a random-like behavior.

  11. Spatial chaos-based image encryption design

    Institute of Scientific and Technical Information of China (English)

    LIU ShuTang; SUN FuYan

    2009-01-01

    In recent years, the chaos based cryptographic algorithms have suggested some new and efficient ways to develop secure image encryption techniques, but the drawbacks of small key space and weak security in one-dimensional chaotic cryptosystems are obvious. In this paper, permutation and sub-stitution methods are incorporated to present a stronger image encryption algorithm. Spatial chaotic maps are used to realize the position permutation, and to confuse the relationship between the ci-pher-image and the plain-image. The experimental results demonstrate that the suggested encryption scheme of image has the advantages of large key space and high security; moreover, the distribution of grey values of the encrypted image has a random-like behavior.

  12. Time reversibility, computer simulation, algorithms, chaos

    CERN Document Server

    Hoover, William Graham

    2012-01-01

    A small army of physicists, chemists, mathematicians, and engineers has joined forces to attack a classic problem, the "reversibility paradox", with modern tools. This book describes their work from the perspective of computer simulation, emphasizing the author's approach to the problem of understanding the compatibility, and even inevitability, of the irreversible second law of thermodynamics with an underlying time-reversible mechanics. Computer simulation has made it possible to probe reversibility from a variety of directions and "chaos theory" or "nonlinear dynamics" has supplied a useful vocabulary and a set of concepts, which allow a fuller explanation of irreversibility than that available to Boltzmann or to Green, Kubo and Onsager. Clear illustration of concepts is emphasized throughout, and reinforced with a glossary of technical terms from the specialized fields which have been combined here to focus on a common theme. The book begins with a discussion, contrasting the idealized reversibility of ba...

  13. Chaos synchronization based on intermittent state observer

    Institute of Scientific and Technical Information of China (English)

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

    2004-01-01

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

  14. Mechanics From Newton's Laws to Deterministic Chaos

    CERN Document Server

    Scheck, Florian

    2010-01-01

    This book covers all topics in mechanics from elementary Newtonian mechanics, the principles of canonical mechanics and rigid body mechanics to relativistic mechanics and nonlinear dynamics. It was among the first textbooks to include dynamical systems and deterministic chaos in due detail. As compared to the previous editions the present fifth edition is updated and revised with more explanations, additional examples and sections on Noether's theorem. Symmetries and invariance principles, the basic geometric aspects of mechanics as well as elements of continuum mechanics also play an important role. The book will enable the reader to develop general principles from which equations of motion follow, to understand the importance of canonical mechanics and of symmetries as a basis for quantum mechanics, and to get practice in using general theoretical concepts and tools that are essential for all branches of physics. The book contains more than 120 problems with complete solutions, as well as some practical exa...

  15. Stochastic chaos in a turbulent swirling flow

    CERN Document Server

    Faranda, Davide; Saint-Michel, Brice; Wiertel, Cecile; Padilla, Vincent; Dubrulle, Berengere; Daviaud, Francois

    2016-01-01

    We report the experimental evidence of the existence of a random attractor in a fully developed turbulent swirling flow. By defining a global observable which tracks the asymmetry in the flux of angular momentum imparted to the flow, we can first reconstruct the associated turbulent attractor and then follow its route towards chaos. We further show that the experimental attractor can be modeled by stochastic Duffing equations, that match the quantitative properties of the experimental flow, namely the number of quasi-stationary states and transition rates among them, the effective dimensions, and the continuity of the first Lyapunov exponents. Such properties can neither be recovered using deterministic models nor using stochastic differential equations based on effective potentials obtained by inverting the probability distributions of the experimental global observables. Our findings open the way to low dimensional modeling of systems featuring a large number of degrees of freedom and multiple quasi-station...

  16. Chaos suppression in gas-solid fluidization.

    Science.gov (United States)

    Pence, Deborah V.; Beasley, Donald E.

    1998-06-01

    Fluidization in granular materials occurs primarily as a result of a dynamic balance between gravitational forces and forces resulting from the flow of a fluid through a bed of discrete particles. For systems where the fluidizing medium and the particles have significantly different densities, density wave instabilities create local pockets of very high void fraction termed bubbles. The fluidization regime is termed the bubbling regime. Such a system is appropriately termed a self-excited nonlinear system. The present study examines chaos suppression resulting from an opposing oscillatory flow in gas-solid fluidization. Time series data representing local, instantaneous pressure were acquired at the surface of a horizontal cylinder submerged in a bubbling fluidized bed. The particles had a weight mean diameter of 345 &mgr;m and a narrow size distribution. The state of fluidization corresponded to the bubbling regime and total air flow rates employed in the present study ranged from 10% to 40% greater than that required for minimum fluidization. The behavior of time-varying local pressure in fluidized beds in the absence of a secondary flow is consistent with deterministic chaos. Kolmogorov entropy estimates from local, instantaneous pressure suggest that the degree of chaotic behavior can be substantially suppressed by the presence of an opposing, oscillatory secondary flow. Pressure signals clearly show a "phase-locking" phenomenon coincident with the imposed frequency. In the present study, the greatest degree of suppression occurred for operating conditions with low primary and secondary flow rates, and a secondary flow oscillation frequency of 15 Hz. (c) 1998 American Institute of Physics.

  17. 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.

  18. Controlling of Beam Halo-chaos by Adaptation Method

    Institute of Scientific and Technical Information of China (English)

    FANGJin-qing; GAOYuan; LUOXiao-shu

    2003-01-01

    In this paper, the parametric adaptation method for controlling the beam halo-chaos in the periodic focusing channels of high-current proton linacs is proposed. The study of proton beam halo-chaos based on controlled beam envelope equation and the Particles-in-Cell simulations for proton beam dynamics show that the proton beam chaotic envelope as well as the beam rsm radius can be controlled to the matched radius using this method.

  19. Chaos and Nonlinear Dynamics in a Quantum Artificial Economy

    CERN Document Server

    Gonçalves, Carlos Pedro

    2012-01-01

    Chaos and nonlinear economic dynamics are addressed for a quantum coupled map lattice model of an artificial economy, with quantized supply and demand equilibrium conditions. The measure theoretic properties and the patterns that emerge in both the economic business volume dynamics' diagrams as well as in the quantum mean field averages are addressed and conclusions are drawn in regards to the application of quantum chaos theory to address signatures of chaotic dynamics in relevant discrete economic state variables.

  20. Secure Communication System Based on Chaos in Optical Fibre

    Institute of Scientific and Technical Information of China (English)

    Pak; L; Chu; Fan; Zhang; William; Mak; Robust; Lai

    2003-01-01

    1 IntroductionRecently, there have been intense research activities on the study of synchronized chaos generated by fibre lasers and its application to secure communication systems. So far, all studies concentrate on two aspects: (1) the effect of the transmission channel between the transmitter and the receiver has been neglected, and (2) the chaos and the signal are carried by one wavelength. Both theoretical and experimental investigations make